Starting phenix.real_space_refine on Sun Feb 8 09:05:34 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9i07_52553/02_2026/9i07_52553.cif Found real_map, /net/cci-nas-00/data/ceres_data/9i07_52553/02_2026/9i07_52553.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9i07_52553/02_2026/9i07_52553.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9i07_52553/02_2026/9i07_52553.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9i07_52553/02_2026/9i07_52553.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9i07_52553/02_2026/9i07_52553.map" } resolution = 3.1 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= 0.065 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: 5 Type Number sf(0) Gaussians P 32 5.49 5 S 176 5.16 5 C 27120 2.51 5 N 7480 2.21 5 O 8376 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 122 residue(s): 0.03s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 43184 Number of models: 1 Model: "" Number of chains: 32 Chain: "O" Number of atoms: 2766 Number of conformers: 1 Conformer: "" Number of residues, atoms: 368, 2766 Classifications: {'peptide': 368} Link IDs: {'PTRANS': 17, 'TRANS': 350} Chain: "P" Number of atoms: 2544 Number of conformers: 1 Conformer: "" Number of residues, atoms: 337, 2544 Classifications: {'peptide': 337} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 11, 'TRANS': 325} Chain: "Q" Number of atoms: 2766 Number of conformers: 1 Conformer: "" Number of residues, atoms: 368, 2766 Classifications: {'peptide': 368} Link IDs: {'PTRANS': 17, 'TRANS': 350} Chain: "R" Number of atoms: 2544 Number of conformers: 1 Conformer: "" Number of residues, atoms: 337, 2544 Classifications: {'peptide': 337} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 11, 'TRANS': 325} Chain: "A" Number of atoms: 2766 Number of conformers: 1 Conformer: "" Number of residues, atoms: 368, 2766 Classifications: {'peptide': 368} Link IDs: {'PTRANS': 17, 'TRANS': 350} Chain: "B" Number of atoms: 2544 Number of conformers: 1 Conformer: "" Number of residues, atoms: 337, 2544 Classifications: {'peptide': 337} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 11, 'TRANS': 325} Chain: "C" Number of atoms: 2766 Number of conformers: 1 Conformer: "" Number of residues, atoms: 368, 2766 Classifications: {'peptide': 368} Link IDs: {'PTRANS': 17, 'TRANS': 350} Chain: "D" Number of atoms: 2544 Number of conformers: 1 Conformer: "" Number of residues, atoms: 337, 2544 Classifications: {'peptide': 337} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 11, 'TRANS': 325} Chain: "E" Number of atoms: 2766 Number of conformers: 1 Conformer: "" Number of residues, atoms: 368, 2766 Classifications: {'peptide': 368} Link IDs: {'PTRANS': 17, 'TRANS': 350} Chain: "F" Number of atoms: 2544 Number of conformers: 1 Conformer: "" Number of residues, atoms: 337, 2544 Classifications: {'peptide': 337} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 11, 'TRANS': 325} Chain: "G" Number of atoms: 2766 Number of conformers: 1 Conformer: "" Number of residues, atoms: 368, 2766 Classifications: {'peptide': 368} Link IDs: {'PTRANS': 17, 'TRANS': 350} Chain: "H" Number of atoms: 2544 Number of conformers: 1 Conformer: "" Number of residues, atoms: 337, 2544 Classifications: {'peptide': 337} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 11, 'TRANS': 325} Chain: "I" Number of atoms: 2766 Number of conformers: 1 Conformer: "" Number of residues, atoms: 368, 2766 Classifications: {'peptide': 368} Link IDs: {'PTRANS': 17, 'TRANS': 350} Chain: "J" Number of atoms: 2544 Number of conformers: 1 Conformer: "" Number of residues, atoms: 337, 2544 Classifications: {'peptide': 337} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 11, 'TRANS': 325} Chain: "K" Number of atoms: 2766 Number of conformers: 1 Conformer: "" Number of residues, atoms: 368, 2766 Classifications: {'peptide': 368} Link IDs: {'PTRANS': 17, 'TRANS': 350} Chain: "L" Number of atoms: 2544 Number of conformers: 1 Conformer: "" Number of residues, atoms: 337, 2544 Classifications: {'peptide': 337} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 11, 'TRANS': 325} Chain: "O" Number of atoms: 44 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 44 Unusual residues: {'NAD': 1} Classifications: {'undetermined': 1} Chain: "P" Number of atoms: 44 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 44 Unusual residues: {'NAD': 1} Classifications: {'undetermined': 1} Chain: "Q" Number of atoms: 44 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 44 Unusual residues: {'NAD': 1} Classifications: {'undetermined': 1} Chain: "R" Number of atoms: 44 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 44 Unusual residues: {'NAD': 1} Classifications: {'undetermined': 1} Chain: "A" Number of atoms: 44 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 44 Unusual residues: {'NAD': 1} Classifications: {'undetermined': 1} Chain: "B" Number of atoms: 44 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 44 Unusual residues: {'NAD': 1} Classifications: {'undetermined': 1} Chain: "C" Number of atoms: 44 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 44 Unusual residues: {'NAD': 1} Classifications: {'undetermined': 1} Chain: "D" Number of atoms: 44 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 44 Unusual residues: {'NAD': 1} Classifications: {'undetermined': 1} Chain: "E" Number of atoms: 44 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 44 Unusual residues: {'NAD': 1} Classifications: {'undetermined': 1} Chain: "F" Number of atoms: 44 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 44 Unusual residues: {'NAD': 1} Classifications: {'undetermined': 1} Chain: "G" Number of atoms: 44 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 44 Unusual residues: {'NAD': 1} Classifications: {'undetermined': 1} Chain: "H" Number of atoms: 44 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 44 Unusual residues: {'NAD': 1} Classifications: {'undetermined': 1} Chain: "I" Number of atoms: 44 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 44 Unusual residues: {'NAD': 1} Classifications: {'undetermined': 1} Chain: "J" Number of atoms: 44 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 44 Unusual residues: {'NAD': 1} Classifications: {'undetermined': 1} Chain: "K" Number of atoms: 44 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 44 Unusual residues: {'NAD': 1} Classifications: {'undetermined': 1} Chain: "L" Number of atoms: 44 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 44 Unusual residues: {'NAD': 1} Classifications: {'undetermined': 1} Time building chain proxies: 9.83, per 1000 atoms: 0.23 Number of scatterers: 43184 At special positions: 0 Unit cell: (177.633, 173.247, 107.457, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 176 16.00 P 32 15.00 O 8376 8.00 N 7480 7.00 C 27120 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=8, symmetry=0 Simple disulfide: pdb=" SG CYS O 349 " - pdb=" SG CYS O 358 " distance=2.04 Simple disulfide: pdb=" SG CYS Q 349 " - pdb=" SG CYS Q 358 " distance=2.03 Simple disulfide: pdb=" SG CYS A 349 " - pdb=" SG CYS A 358 " distance=2.03 Simple disulfide: pdb=" SG CYS C 349 " - pdb=" SG CYS C 358 " distance=2.03 Simple disulfide: pdb=" SG CYS E 349 " - pdb=" SG CYS E 358 " distance=2.03 Simple disulfide: pdb=" SG CYS G 349 " - pdb=" SG CYS G 358 " distance=2.03 Simple disulfide: pdb=" SG CYS I 349 " - pdb=" SG CYS I 358 " distance=2.03 Simple disulfide: pdb=" SG CYS K 349 " - pdb=" SG CYS K 358 " distance=2.02 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 3.47 Conformation dependent library (CDL) restraints added in 1.7 seconds 11216 Ramachandran restraints generated. 5608 Oldfield, 0 Emsley, 5608 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 10288 Finding SS restraints... Secondary structure from input PDB file: 224 helices and 50 sheets defined 36.8% alpha, 29.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.99 Creating SS restraints... Processing helix chain 'O' and resid 10 through 19 Processing helix chain 'O' and resid 34 through 46 removed outlier: 4.111A pdb=" N SER O 39 " --> pdb=" O GLY O 34 " (cutoff:3.500A) Processing helix chain 'O' and resid 78 through 82 Processing helix chain 'O' and resid 83 through 88 Processing helix chain 'O' and resid 101 through 106 Processing helix chain 'O' and resid 106 through 112 Processing helix chain 'O' and resid 133 through 137 Processing helix chain 'O' and resid 148 through 165 Proline residue: O 156 - end of helix Processing helix chain 'O' and resid 198 through 202 removed outlier: 3.509A pdb=" N LEU O 201 " --> pdb=" O ALA O 198 " (cutoff:3.500A) removed outlier: 3.826A pdb=" N ASN O 202 " --> pdb=" O ALA O 199 " (cutoff:3.500A) No H-bonds generated for 'chain 'O' and resid 198 through 202' Processing helix chain 'O' and resid 211 through 217 removed outlier: 3.717A pdb=" N SER O 215 " --> pdb=" O LYS O 212 " (cutoff:3.500A) Processing helix chain 'O' and resid 218 through 222 Processing helix chain 'O' and resid 251 through 265 Processing helix chain 'O' and resid 279 through 284 Processing helix chain 'O' and resid 295 through 297 No H-bonds generated for 'chain 'O' and resid 295 through 297' Processing helix chain 'O' and resid 314 through 330 Processing helix chain 'O' and resid 343 through 351 Processing helix chain 'P' and resid 9 through 20 Processing helix chain 'P' and resid 36 through 46 Processing helix chain 'P' and resid 78 through 82 Processing helix chain 'P' and resid 83 through 88 Processing helix chain 'P' and resid 101 through 112 removed outlier: 4.098A pdb=" N HIS P 108 " --> pdb=" O GLY P 104 " (cutoff:3.500A) removed outlier: 3.839A pdb=" N LEU P 109 " --> pdb=" O ALA P 105 " (cutoff:3.500A) Processing helix chain 'P' and resid 133 through 137 Processing helix chain 'P' and resid 148 through 165 Proline residue: P 156 - end of helix removed outlier: 3.533A pdb=" N VAL P 160 " --> pdb=" O PRO P 156 " (cutoff:3.500A) Processing helix chain 'P' and resid 209 through 218 removed outlier: 5.382A pdb=" N ALA P 215 " --> pdb=" O ALA P 211 " (cutoff:3.500A) Processing helix chain 'P' and resid 219 through 222 Processing helix chain 'P' and resid 251 through 266 Processing helix chain 'P' and resid 279 through 284 Processing helix chain 'P' and resid 314 through 330 Processing helix chain 'Q' and resid 10 through 19 Processing helix chain 'Q' and resid 34 through 46 removed outlier: 4.190A pdb=" N SER Q 39 " --> pdb=" O GLY Q 34 " (cutoff:3.500A) Processing helix chain 'Q' and resid 78 through 82 Processing helix chain 'Q' and resid 101 through 106 Processing helix chain 'Q' and resid 106 through 112 Processing helix chain 'Q' and resid 133 through 137 Processing helix chain 'Q' and resid 148 through 165 Proline residue: Q 156 - end of helix Processing helix chain 'Q' and resid 211 through 217 Processing helix chain 'Q' and resid 218 through 222 Processing helix chain 'Q' and resid 251 through 265 Processing helix chain 'Q' and resid 279 through 284 Processing helix chain 'Q' and resid 295 through 297 No H-bonds generated for 'chain 'Q' and resid 295 through 297' Processing helix chain 'Q' and resid 314 through 331 Processing helix chain 'Q' and resid 343 through 352 removed outlier: 3.849A pdb=" N ASP Q 351 " --> pdb=" O ASP Q 347 " (cutoff:3.500A) Processing helix chain 'R' and resid 9 through 20 Processing helix chain 'R' and resid 36 through 46 Processing helix chain 'R' and resid 78 through 82 Processing helix chain 'R' and resid 83 through 88 Processing helix chain 'R' and resid 101 through 112 removed outlier: 4.467A pdb=" N HIS R 108 " --> pdb=" O GLY R 104 " (cutoff:3.500A) removed outlier: 4.310A pdb=" N LEU R 109 " --> pdb=" O ALA R 105 " (cutoff:3.500A) Processing helix chain 'R' and resid 133 through 137 Processing helix chain 'R' and resid 148 through 165 Proline residue: R 156 - end of helix removed outlier: 3.787A pdb=" N VAL R 160 " --> pdb=" O PRO R 156 " (cutoff:3.500A) Processing helix chain 'R' and resid 209 through 218 removed outlier: 5.697A pdb=" N ALA R 215 " --> pdb=" O ALA R 211 " (cutoff:3.500A) Processing helix chain 'R' and resid 219 through 222 Processing helix chain 'R' and resid 251 through 266 Processing helix chain 'R' and resid 279 through 284 Processing helix chain 'R' and resid 295 through 297 No H-bonds generated for 'chain 'R' and resid 295 through 297' Processing helix chain 'R' and resid 314 through 330 Processing helix chain 'A' and resid 10 through 19 Processing helix chain 'A' and resid 34 through 45 removed outlier: 3.787A pdb=" N SER A 39 " --> pdb=" O GLY A 34 " (cutoff:3.500A) Processing helix chain 'A' and resid 78 through 82 Processing helix chain 'A' and resid 83 through 88 Processing helix chain 'A' and resid 101 through 112 removed outlier: 4.096A pdb=" N LYS A 107 " --> pdb=" O PRO A 103 " (cutoff:3.500A) removed outlier: 4.624A pdb=" N HIS A 108 " --> pdb=" O GLY A 104 " (cutoff:3.500A) removed outlier: 4.242A pdb=" N ILE A 109 " --> pdb=" O ALA A 105 " (cutoff:3.500A) Processing helix chain 'A' and resid 133 through 137 Processing helix chain 'A' and resid 148 through 165 Proline residue: A 156 - end of helix removed outlier: 3.606A pdb=" N VAL A 160 " --> pdb=" O PRO A 156 " (cutoff:3.500A) Processing helix chain 'A' and resid 198 through 202 removed outlier: 3.743A pdb=" N ASN A 202 " --> pdb=" O ALA A 199 " (cutoff:3.500A) Processing helix chain 'A' and resid 213 through 217 Processing helix chain 'A' and resid 218 through 222 Processing helix chain 'A' and resid 251 through 265 Processing helix chain 'A' and resid 279 through 284 Processing helix chain 'A' and resid 295 through 297 No H-bonds generated for 'chain 'A' and resid 295 through 297' Processing helix chain 'A' and resid 314 through 331 removed outlier: 3.501A pdb=" N ARG A 320 " --> pdb=" O GLY A 316 " (cutoff:3.500A) Processing helix chain 'A' and resid 343 through 352 removed outlier: 3.899A pdb=" N ASP A 351 " --> pdb=" O ASP A 347 " (cutoff:3.500A) Processing helix chain 'B' and resid 9 through 19 Processing helix chain 'B' and resid 36 through 46 Processing helix chain 'B' and resid 78 through 82 Processing helix chain 'B' and resid 83 through 88 Processing helix chain 'B' and resid 101 through 110 removed outlier: 3.893A pdb=" N HIS B 108 " --> pdb=" O GLY B 104 " (cutoff:3.500A) removed outlier: 3.798A pdb=" N LEU B 109 " --> pdb=" O ALA B 105 " (cutoff:3.500A) Processing helix chain 'B' and resid 133 through 137 Processing helix chain 'B' and resid 148 through 165 Proline residue: B 156 - end of helix Processing helix chain 'B' and resid 209 through 214 removed outlier: 3.691A pdb=" N VAL B 214 " --> pdb=" O ALA B 210 " (cutoff:3.500A) Processing helix chain 'B' and resid 218 through 222 Processing helix chain 'B' and resid 251 through 266 Processing helix chain 'B' and resid 279 through 284 Processing helix chain 'B' and resid 295 through 297 No H-bonds generated for 'chain 'B' and resid 295 through 297' Processing helix chain 'B' and resid 314 through 330 Processing helix chain 'C' and resid 10 through 19 Processing helix chain 'C' and resid 34 through 46 removed outlier: 4.202A pdb=" N SER C 39 " --> pdb=" O GLY C 34 " (cutoff:3.500A) Processing helix chain 'C' and resid 78 through 82 Processing helix chain 'C' and resid 101 through 106 Processing helix chain 'C' and resid 106 through 112 Processing helix chain 'C' and resid 133 through 137 Processing helix chain 'C' and resid 148 through 165 Proline residue: C 156 - end of helix Processing helix chain 'C' and resid 198 through 202 removed outlier: 3.789A pdb=" N ASN C 202 " --> pdb=" O ALA C 199 " (cutoff:3.500A) Processing helix chain 'C' and resid 209 through 214 Processing helix chain 'C' and resid 215 through 217 No H-bonds generated for 'chain 'C' and resid 215 through 217' Processing helix chain 'C' and resid 218 through 222 Processing helix chain 'C' and resid 251 through 265 Processing helix chain 'C' and resid 279 through 284 Processing helix chain 'C' and resid 295 through 297 No H-bonds generated for 'chain 'C' and resid 295 through 297' Processing helix chain 'C' and resid 314 through 331 Processing helix chain 'C' and resid 343 through 350 Processing helix chain 'C' and resid 355 through 359 removed outlier: 4.136A pdb=" N LYS C 359 " --> pdb=" O GLU C 356 " (cutoff:3.500A) Processing helix chain 'D' and resid 9 through 19 Processing helix chain 'D' and resid 36 through 46 Processing helix chain 'D' and resid 78 through 82 Processing helix chain 'D' and resid 83 through 88 Processing helix chain 'D' and resid 101 through 111 removed outlier: 3.797A pdb=" N LYS D 107 " --> pdb=" O ASP D 103 " (cutoff:3.500A) removed outlier: 4.738A pdb=" N HIS D 108 " --> pdb=" O GLY D 104 " (cutoff:3.500A) removed outlier: 4.397A pdb=" N LEU D 109 " --> pdb=" O ALA D 105 " (cutoff:3.500A) Processing helix chain 'D' and resid 133 through 137 Processing helix chain 'D' and resid 148 through 165 Proline residue: D 156 - end of helix Processing helix chain 'D' and resid 209 through 218 removed outlier: 3.623A pdb=" N VAL D 214 " --> pdb=" O ALA D 210 " (cutoff:3.500A) removed outlier: 5.373A pdb=" N ALA D 215 " --> pdb=" O ALA D 211 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N LEU D 216 " --> pdb=" O LYS D 212 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N VAL D 217 " --> pdb=" O ALA D 213 " (cutoff:3.500A) Processing helix chain 'D' and resid 219 through 222 Processing helix chain 'D' and resid 251 through 266 Processing helix chain 'D' and resid 279 through 284 Processing helix chain 'D' and resid 295 through 297 No H-bonds generated for 'chain 'D' and resid 295 through 297' Processing helix chain 'D' and resid 314 through 330 Processing helix chain 'E' and resid 10 through 19 Processing helix chain 'E' and resid 34 through 46 removed outlier: 3.893A pdb=" N SER E 39 " --> pdb=" O GLY E 34 " (cutoff:3.500A) Processing helix chain 'E' and resid 78 through 82 Processing helix chain 'E' and resid 83 through 88 Processing helix chain 'E' and resid 101 through 106 Processing helix chain 'E' and resid 106 through 112 Processing helix chain 'E' and resid 133 through 137 Processing helix chain 'E' and resid 148 through 165 Proline residue: E 156 - end of helix removed outlier: 3.772A pdb=" N VAL E 160 " --> pdb=" O PRO E 156 " (cutoff:3.500A) Processing helix chain 'E' and resid 198 through 202 removed outlier: 3.508A pdb=" N LEU E 201 " --> pdb=" O ALA E 198 " (cutoff:3.500A) removed outlier: 3.827A pdb=" N ASN E 202 " --> pdb=" O ALA E 199 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 198 through 202' Processing helix chain 'E' and resid 211 through 217 removed outlier: 3.737A pdb=" N SER E 215 " --> pdb=" O LYS E 212 " (cutoff:3.500A) Processing helix chain 'E' and resid 218 through 222 Processing helix chain 'E' and resid 251 through 265 Processing helix chain 'E' and resid 279 through 284 Processing helix chain 'E' and resid 295 through 297 No H-bonds generated for 'chain 'E' and resid 295 through 297' Processing helix chain 'E' and resid 314 through 330 Processing helix chain 'E' and resid 343 through 351 Processing helix chain 'F' and resid 9 through 20 Processing helix chain 'F' and resid 36 through 46 Processing helix chain 'F' and resid 83 through 88 Processing helix chain 'F' and resid 101 through 112 removed outlier: 4.123A pdb=" N HIS F 108 " --> pdb=" O GLY F 104 " (cutoff:3.500A) removed outlier: 3.862A pdb=" N LEU F 109 " --> pdb=" O ALA F 105 " (cutoff:3.500A) Processing helix chain 'F' and resid 133 through 137 Processing helix chain 'F' and resid 148 through 165 Proline residue: F 156 - end of helix Processing helix chain 'F' and resid 209 through 218 removed outlier: 5.689A pdb=" N ALA F 215 " --> pdb=" O ALA F 211 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N LEU F 216 " --> pdb=" O LYS F 212 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N VAL F 217 " --> pdb=" O ALA F 213 " (cutoff:3.500A) Processing helix chain 'F' and resid 219 through 222 Processing helix chain 'F' and resid 251 through 266 Processing helix chain 'F' and resid 279 through 284 Processing helix chain 'F' and resid 314 through 330 Processing helix chain 'G' and resid 10 through 19 Processing helix chain 'G' and resid 34 through 46 removed outlier: 4.035A pdb=" N SER G 39 " --> pdb=" O GLY G 34 " (cutoff:3.500A) Processing helix chain 'G' and resid 78 through 82 Processing helix chain 'G' and resid 101 through 106 Processing helix chain 'G' and resid 106 through 112 Processing helix chain 'G' and resid 133 through 137 Processing helix chain 'G' and resid 148 through 165 Proline residue: G 156 - end of helix Processing helix chain 'G' and resid 198 through 202 removed outlier: 3.522A pdb=" N LEU G 201 " --> pdb=" O ALA G 198 " (cutoff:3.500A) removed outlier: 4.035A pdb=" N ASN G 202 " --> pdb=" O ALA G 199 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 198 through 202' Processing helix chain 'G' and resid 209 through 214 removed outlier: 3.567A pdb=" N VAL G 214 " --> pdb=" O ALA G 210 " (cutoff:3.500A) Processing helix chain 'G' and resid 215 through 217 No H-bonds generated for 'chain 'G' and resid 215 through 217' Processing helix chain 'G' and resid 218 through 222 Processing helix chain 'G' and resid 251 through 265 removed outlier: 3.505A pdb=" N VAL G 255 " --> pdb=" O THR G 251 " (cutoff:3.500A) Processing helix chain 'G' and resid 280 through 284 Processing helix chain 'G' and resid 295 through 297 No H-bonds generated for 'chain 'G' and resid 295 through 297' Processing helix chain 'G' and resid 314 through 331 Processing helix chain 'G' and resid 343 through 352 removed outlier: 3.741A pdb=" N ASP G 351 " --> pdb=" O ASP G 347 " (cutoff:3.500A) Processing helix chain 'H' and resid 9 through 20 Processing helix chain 'H' and resid 36 through 46 removed outlier: 3.556A pdb=" N LYS H 45 " --> pdb=" O SER H 41 " (cutoff:3.500A) Processing helix chain 'H' and resid 78 through 82 removed outlier: 3.551A pdb=" N ASN H 81 " --> pdb=" O ASN H 78 " (cutoff:3.500A) Processing helix chain 'H' and resid 83 through 88 Processing helix chain 'H' and resid 101 through 111 removed outlier: 4.480A pdb=" N HIS H 108 " --> pdb=" O GLY H 104 " (cutoff:3.500A) removed outlier: 4.407A pdb=" N LEU H 109 " --> pdb=" O ALA H 105 " (cutoff:3.500A) removed outlier: 3.740A pdb=" N ALA H 111 " --> pdb=" O LYS H 107 " (cutoff:3.500A) Processing helix chain 'H' and resid 133 through 137 Processing helix chain 'H' and resid 148 through 165 Proline residue: H 156 - end of helix removed outlier: 3.785A pdb=" N VAL H 160 " --> pdb=" O PRO H 156 " (cutoff:3.500A) Processing helix chain 'H' and resid 209 through 218 removed outlier: 5.906A pdb=" N ALA H 215 " --> pdb=" O ALA H 211 " (cutoff:3.500A) Processing helix chain 'H' and resid 219 through 222 Processing helix chain 'H' and resid 251 through 266 Processing helix chain 'H' and resid 279 through 284 Processing helix chain 'H' and resid 314 through 330 Processing helix chain 'I' and resid 10 through 19 Processing helix chain 'I' and resid 34 through 45 removed outlier: 3.733A pdb=" N SER I 39 " --> pdb=" O GLY I 34 " (cutoff:3.500A) Processing helix chain 'I' and resid 78 through 82 Processing helix chain 'I' and resid 83 through 88 Processing helix chain 'I' and resid 101 through 112 removed outlier: 4.075A pdb=" N LYS I 107 " --> pdb=" O PRO I 103 " (cutoff:3.500A) removed outlier: 4.587A pdb=" N HIS I 108 " --> pdb=" O GLY I 104 " (cutoff:3.500A) removed outlier: 4.221A pdb=" N ILE I 109 " --> pdb=" O ALA I 105 " (cutoff:3.500A) Processing helix chain 'I' and resid 133 through 137 Processing helix chain 'I' and resid 148 through 165 Proline residue: I 156 - end of helix Processing helix chain 'I' and resid 198 through 202 removed outlier: 3.691A pdb=" N ASN I 202 " --> pdb=" O ALA I 199 " (cutoff:3.500A) Processing helix chain 'I' and resid 213 through 217 Processing helix chain 'I' and resid 218 through 222 Processing helix chain 'I' and resid 251 through 265 removed outlier: 3.517A pdb=" N VAL I 255 " --> pdb=" O THR I 251 " (cutoff:3.500A) Processing helix chain 'I' and resid 279 through 284 Processing helix chain 'I' and resid 295 through 297 No H-bonds generated for 'chain 'I' and resid 295 through 297' Processing helix chain 'I' and resid 314 through 331 Processing helix chain 'I' and resid 343 through 352 removed outlier: 3.772A pdb=" N ASP I 351 " --> pdb=" O ASP I 347 " (cutoff:3.500A) Processing helix chain 'J' and resid 9 through 19 Processing helix chain 'J' and resid 36 through 46 Processing helix chain 'J' and resid 78 through 82 Processing helix chain 'J' and resid 83 through 88 Processing helix chain 'J' and resid 101 through 112 removed outlier: 3.982A pdb=" N HIS J 108 " --> pdb=" O GLY J 104 " (cutoff:3.500A) removed outlier: 3.913A pdb=" N LEU J 109 " --> pdb=" O ALA J 105 " (cutoff:3.500A) Processing helix chain 'J' and resid 133 through 137 Processing helix chain 'J' and resid 148 through 165 Proline residue: J 156 - end of helix Processing helix chain 'J' and resid 209 through 214 removed outlier: 3.692A pdb=" N VAL J 214 " --> pdb=" O ALA J 210 " (cutoff:3.500A) Processing helix chain 'J' and resid 218 through 222 Processing helix chain 'J' and resid 251 through 266 Processing helix chain 'J' and resid 279 through 284 Processing helix chain 'J' and resid 295 through 297 No H-bonds generated for 'chain 'J' and resid 295 through 297' Processing helix chain 'J' and resid 314 through 330 Processing helix chain 'K' and resid 10 through 19 Processing helix chain 'K' and resid 34 through 46 removed outlier: 4.175A pdb=" N SER K 39 " --> pdb=" O GLY K 34 " (cutoff:3.500A) Processing helix chain 'K' and resid 78 through 82 Processing helix chain 'K' and resid 101 through 112 removed outlier: 3.978A pdb=" N LYS K 107 " --> pdb=" O PRO K 103 " (cutoff:3.500A) removed outlier: 4.564A pdb=" N HIS K 108 " --> pdb=" O GLY K 104 " (cutoff:3.500A) removed outlier: 4.120A pdb=" N ILE K 109 " --> pdb=" O ALA K 105 " (cutoff:3.500A) Processing helix chain 'K' and resid 133 through 137 Processing helix chain 'K' and resid 148 through 165 Proline residue: K 156 - end of helix Processing helix chain 'K' and resid 198 through 202 removed outlier: 3.751A pdb=" N ASN K 202 " --> pdb=" O ALA K 199 " (cutoff:3.500A) Processing helix chain 'K' and resid 209 through 214 Processing helix chain 'K' and resid 215 through 217 No H-bonds generated for 'chain 'K' and resid 215 through 217' Processing helix chain 'K' and resid 218 through 222 Processing helix chain 'K' and resid 251 through 265 Processing helix chain 'K' and resid 279 through 284 removed outlier: 3.508A pdb=" N ARG K 284 " --> pdb=" O VAL K 281 " (cutoff:3.500A) Processing helix chain 'K' and resid 295 through 297 No H-bonds generated for 'chain 'K' and resid 295 through 297' Processing helix chain 'K' and resid 314 through 331 Processing helix chain 'K' and resid 343 through 352 removed outlier: 3.504A pdb=" N ASP K 351 " --> pdb=" O ASP K 347 " (cutoff:3.500A) Processing helix chain 'L' and resid 9 through 19 Processing helix chain 'L' and resid 36 through 46 Processing helix chain 'L' and resid 78 through 82 Processing helix chain 'L' and resid 83 through 88 Processing helix chain 'L' and resid 101 through 111 removed outlier: 3.826A pdb=" N LYS L 107 " --> pdb=" O ASP L 103 " (cutoff:3.500A) removed outlier: 4.759A pdb=" N HIS L 108 " --> pdb=" O GLY L 104 " (cutoff:3.500A) removed outlier: 4.405A pdb=" N LEU L 109 " --> pdb=" O ALA L 105 " (cutoff:3.500A) Processing helix chain 'L' and resid 133 through 137 Processing helix chain 'L' and resid 148 through 165 Proline residue: L 156 - end of helix Processing helix chain 'L' and resid 209 through 218 removed outlier: 3.679A pdb=" N VAL L 214 " --> pdb=" O ALA L 210 " (cutoff:3.500A) removed outlier: 5.386A pdb=" N ALA L 215 " --> pdb=" O ALA L 211 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N LEU L 216 " --> pdb=" O LYS L 212 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N VAL L 217 " --> pdb=" O ALA L 213 " (cutoff:3.500A) Processing helix chain 'L' and resid 219 through 222 Processing helix chain 'L' and resid 251 through 266 Processing helix chain 'L' and resid 279 through 284 Processing helix chain 'L' and resid 295 through 297 No H-bonds generated for 'chain 'L' and resid 295 through 297' Processing helix chain 'L' and resid 314 through 330 Processing sheet with id=AA1, first strand: chain 'O' and resid 57 through 60 removed outlier: 9.521A pdb=" N ASP O 26 " --> pdb=" O PRO O 70 " (cutoff:3.500A) removed outlier: 9.182A pdb=" N LYS O 72 " --> pdb=" O ASP O 26 " (cutoff:3.500A) removed outlier: 6.907A pdb=" N VAL O 28 " --> pdb=" O LYS O 72 " (cutoff:3.500A) removed outlier: 8.023A pdb=" N VAL O 74 " --> pdb=" O VAL O 28 " (cutoff:3.500A) removed outlier: 6.176A pdb=" N VAL O 30 " --> pdb=" O VAL O 74 " (cutoff:3.500A) removed outlier: 9.619A pdb=" N LEU O 1 " --> pdb=" O VAL O 27 " (cutoff:3.500A) removed outlier: 8.911A pdb=" N VAL O 29 " --> pdb=" O LEU O 1 " (cutoff:3.500A) removed outlier: 6.705A pdb=" N VAL O 3 " --> pdb=" O VAL O 29 " (cutoff:3.500A) removed outlier: 8.257A pdb=" N ASN O 31 " --> pdb=" O VAL O 3 " (cutoff:3.500A) removed outlier: 6.987A pdb=" N ILE O 5 " --> pdb=" O ASN O 31 " (cutoff:3.500A) removed outlier: 6.512A pdb=" N LYS O 2 " --> pdb=" O ILE O 91 " (cutoff:3.500A) removed outlier: 7.763A pdb=" N ILE O 93 " --> pdb=" O LYS O 2 " (cutoff:3.500A) removed outlier: 6.753A pdb=" N ALA O 4 " --> pdb=" O ILE O 93 " (cutoff:3.500A) removed outlier: 6.450A pdb=" N VAL O 92 " --> pdb=" O ILE O 117 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'O' and resid 204 through 207 removed outlier: 9.424A pdb=" N ASN O 226 " --> pdb=" O VAL O 168 " (cutoff:3.500A) removed outlier: 6.616A pdb=" N GLY O 170 " --> pdb=" O ASN O 226 " (cutoff:3.500A) removed outlier: 8.840A pdb=" N ILE O 228 " --> pdb=" O GLY O 170 " (cutoff:3.500A) removed outlier: 6.470A pdb=" N MET O 172 " --> pdb=" O ILE O 228 " (cutoff:3.500A) removed outlier: 8.005A pdb=" N LEU O 230 " --> pdb=" O MET O 172 " (cutoff:3.500A) removed outlier: 6.425A pdb=" N THR O 174 " --> pdb=" O LEU O 230 " (cutoff:3.500A) removed outlier: 7.102A pdb=" N VAL O 232 " --> pdb=" O THR O 174 " (cutoff:3.500A) removed outlier: 6.289A pdb=" N HIS O 176 " --> pdb=" O VAL O 232 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N LYS O 169 " --> pdb=" O ASN O 245 " (cutoff:3.500A) removed outlier: 4.933A pdb=" N VAL O 308 " --> pdb=" O ASP O 293 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'O' and resid 204 through 207 removed outlier: 9.424A pdb=" N ASN O 226 " --> pdb=" O VAL O 168 " (cutoff:3.500A) removed outlier: 6.616A pdb=" N GLY O 170 " --> pdb=" O ASN O 226 " (cutoff:3.500A) removed outlier: 8.840A pdb=" N ILE O 228 " --> pdb=" O GLY O 170 " (cutoff:3.500A) removed outlier: 6.470A pdb=" N MET O 172 " --> pdb=" O ILE O 228 " (cutoff:3.500A) removed outlier: 8.005A pdb=" N LEU O 230 " --> pdb=" O MET O 172 " (cutoff:3.500A) removed outlier: 6.425A pdb=" N THR O 174 " --> pdb=" O LEU O 230 " (cutoff:3.500A) removed outlier: 7.102A pdb=" N VAL O 232 " --> pdb=" O THR O 174 " (cutoff:3.500A) removed outlier: 6.289A pdb=" N HIS O 176 " --> pdb=" O VAL O 232 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N LYS O 169 " --> pdb=" O ASN O 245 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'P' and resid 57 through 58 removed outlier: 10.214A pdb=" N VAL P 70 " --> pdb=" O ASP P 26 " (cutoff:3.500A) removed outlier: 5.981A pdb=" N VAL P 28 " --> pdb=" O VAL P 70 " (cutoff:3.500A) removed outlier: 5.853A pdb=" N LEU P 1 " --> pdb=" O ASP P 26 " (cutoff:3.500A) removed outlier: 6.786A pdb=" N VAL P 28 " --> pdb=" O LEU P 1 " (cutoff:3.500A) removed outlier: 7.569A pdb=" N VAL P 3 " --> pdb=" O VAL P 28 " (cutoff:3.500A) removed outlier: 6.163A pdb=" N ILE P 30 " --> pdb=" O VAL P 3 " (cutoff:3.500A) removed outlier: 6.577A pdb=" N ILE P 5 " --> pdb=" O ILE P 30 " (cutoff:3.500A) removed outlier: 6.288A pdb=" N LYS P 2 " --> pdb=" O LEU P 91 " (cutoff:3.500A) removed outlier: 7.481A pdb=" N ILE P 93 " --> pdb=" O LYS P 2 " (cutoff:3.500A) removed outlier: 6.621A pdb=" N ALA P 4 " --> pdb=" O ILE P 93 " (cutoff:3.500A) removed outlier: 6.481A pdb=" N VAL P 92 " --> pdb=" O LEU P 117 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'P' and resid 204 through 206 removed outlier: 9.400A pdb=" N ASN P 226 " --> pdb=" O ILE P 168 " (cutoff:3.500A) removed outlier: 6.903A pdb=" N GLY P 170 " --> pdb=" O ASN P 226 " (cutoff:3.500A) removed outlier: 8.802A pdb=" N ILE P 228 " --> pdb=" O GLY P 170 " (cutoff:3.500A) removed outlier: 6.145A pdb=" N MET P 172 " --> pdb=" O ILE P 228 " (cutoff:3.500A) removed outlier: 7.754A pdb=" N LEU P 230 " --> pdb=" O MET P 172 " (cutoff:3.500A) removed outlier: 6.463A pdb=" N THR P 174 " --> pdb=" O LEU P 230 " (cutoff:3.500A) removed outlier: 7.131A pdb=" N VAL P 232 " --> pdb=" O THR P 174 " (cutoff:3.500A) removed outlier: 6.685A pdb=" N HIS P 176 " --> pdb=" O VAL P 232 " (cutoff:3.500A) removed outlier: 3.858A pdb=" N LYS P 169 " --> pdb=" O GLN P 245 " (cutoff:3.500A) removed outlier: 5.156A pdb=" N ILE P 308 " --> pdb=" O ASP P 293 " (cutoff:3.500A) removed outlier: 6.811A pdb=" N SER P 272 " --> pdb=" O ILE P 292 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'P' and resid 204 through 206 removed outlier: 9.400A pdb=" N ASN P 226 " --> pdb=" O ILE P 168 " (cutoff:3.500A) removed outlier: 6.903A pdb=" N GLY P 170 " --> pdb=" O ASN P 226 " (cutoff:3.500A) removed outlier: 8.802A pdb=" N ILE P 228 " --> pdb=" O GLY P 170 " (cutoff:3.500A) removed outlier: 6.145A pdb=" N MET P 172 " --> pdb=" O ILE P 228 " (cutoff:3.500A) removed outlier: 7.754A pdb=" N LEU P 230 " --> pdb=" O MET P 172 " (cutoff:3.500A) removed outlier: 6.463A pdb=" N THR P 174 " --> pdb=" O LEU P 230 " (cutoff:3.500A) removed outlier: 7.131A pdb=" N VAL P 232 " --> pdb=" O THR P 174 " (cutoff:3.500A) removed outlier: 6.685A pdb=" N HIS P 176 " --> pdb=" O VAL P 232 " (cutoff:3.500A) removed outlier: 3.858A pdb=" N LYS P 169 " --> pdb=" O GLN P 245 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'Q' and resid 57 through 60 removed outlier: 5.634A pdb=" N VAL Q 28 " --> pdb=" O PRO Q 70 " (cutoff:3.500A) removed outlier: 9.529A pdb=" N LEU Q 1 " --> pdb=" O VAL Q 27 " (cutoff:3.500A) removed outlier: 9.116A pdb=" N VAL Q 29 " --> pdb=" O LEU Q 1 " (cutoff:3.500A) removed outlier: 6.840A pdb=" N VAL Q 3 " --> pdb=" O VAL Q 29 " (cutoff:3.500A) removed outlier: 8.380A pdb=" N ASN Q 31 " --> pdb=" O VAL Q 3 " (cutoff:3.500A) removed outlier: 7.002A pdb=" N ILE Q 5 " --> pdb=" O ASN Q 31 " (cutoff:3.500A) removed outlier: 6.530A pdb=" N LYS Q 2 " --> pdb=" O ILE Q 91 " (cutoff:3.500A) removed outlier: 7.762A pdb=" N ILE Q 93 " --> pdb=" O LYS Q 2 " (cutoff:3.500A) removed outlier: 6.624A pdb=" N ALA Q 4 " --> pdb=" O ILE Q 93 " (cutoff:3.500A) removed outlier: 6.502A pdb=" N VAL Q 92 " --> pdb=" O ILE Q 117 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'Q' and resid 204 through 207 removed outlier: 9.328A pdb=" N ASN Q 226 " --> pdb=" O VAL Q 168 " (cutoff:3.500A) removed outlier: 6.510A pdb=" N GLY Q 170 " --> pdb=" O ASN Q 226 " (cutoff:3.500A) removed outlier: 8.704A pdb=" N ILE Q 228 " --> pdb=" O GLY Q 170 " (cutoff:3.500A) removed outlier: 6.437A pdb=" N MET Q 172 " --> pdb=" O ILE Q 228 " (cutoff:3.500A) removed outlier: 8.042A pdb=" N LEU Q 230 " --> pdb=" O MET Q 172 " (cutoff:3.500A) removed outlier: 6.663A pdb=" N THR Q 174 " --> pdb=" O LEU Q 230 " (cutoff:3.500A) removed outlier: 3.965A pdb=" N LYS Q 169 " --> pdb=" O ASN Q 245 " (cutoff:3.500A) removed outlier: 5.050A pdb=" N VAL Q 308 " --> pdb=" O ASP Q 293 " (cutoff:3.500A) removed outlier: 6.836A pdb=" N ASP Q 272 " --> pdb=" O ILE Q 292 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'Q' and resid 204 through 207 removed outlier: 9.328A pdb=" N ASN Q 226 " --> pdb=" O VAL Q 168 " (cutoff:3.500A) removed outlier: 6.510A pdb=" N GLY Q 170 " --> pdb=" O ASN Q 226 " (cutoff:3.500A) removed outlier: 8.704A pdb=" N ILE Q 228 " --> pdb=" O GLY Q 170 " (cutoff:3.500A) removed outlier: 6.437A pdb=" N MET Q 172 " --> pdb=" O ILE Q 228 " (cutoff:3.500A) removed outlier: 8.042A pdb=" N LEU Q 230 " --> pdb=" O MET Q 172 " (cutoff:3.500A) removed outlier: 6.663A pdb=" N THR Q 174 " --> pdb=" O LEU Q 230 " (cutoff:3.500A) removed outlier: 3.965A pdb=" N LYS Q 169 " --> pdb=" O ASN Q 245 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'R' and resid 57 through 58 removed outlier: 10.398A pdb=" N VAL R 70 " --> pdb=" O ASP R 26 " (cutoff:3.500A) removed outlier: 6.025A pdb=" N VAL R 28 " --> pdb=" O VAL R 70 " (cutoff:3.500A) removed outlier: 9.722A pdb=" N LEU R 1 " --> pdb=" O VAL R 27 " (cutoff:3.500A) removed outlier: 9.200A pdb=" N VAL R 29 " --> pdb=" O LEU R 1 " (cutoff:3.500A) removed outlier: 6.818A pdb=" N VAL R 3 " --> pdb=" O VAL R 29 " (cutoff:3.500A) removed outlier: 8.169A pdb=" N ASN R 31 " --> pdb=" O VAL R 3 " (cutoff:3.500A) removed outlier: 6.138A pdb=" N ILE R 5 " --> pdb=" O ASN R 31 " (cutoff:3.500A) removed outlier: 6.304A pdb=" N VAL R 92 " --> pdb=" O LEU R 117 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'R' and resid 204 through 207 removed outlier: 3.842A pdb=" N LYS R 169 " --> pdb=" O GLN R 245 " (cutoff:3.500A) removed outlier: 5.091A pdb=" N ILE R 308 " --> pdb=" O ASP R 293 " (cutoff:3.500A) removed outlier: 6.864A pdb=" N SER R 272 " --> pdb=" O ILE R 292 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'R' and resid 204 through 207 removed outlier: 3.842A pdb=" N LYS R 169 " --> pdb=" O GLN R 245 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 58 through 60 removed outlier: 3.646A pdb=" N THR A 63 " --> pdb=" O ILE A 60 " (cutoff:3.500A) removed outlier: 9.446A pdb=" N ASP A 26 " --> pdb=" O PRO A 70 " (cutoff:3.500A) removed outlier: 9.378A pdb=" N LYS A 72 " --> pdb=" O ASP A 26 " (cutoff:3.500A) removed outlier: 6.767A pdb=" N VAL A 28 " --> pdb=" O LYS A 72 " (cutoff:3.500A) removed outlier: 7.750A pdb=" N VAL A 74 " --> pdb=" O VAL A 28 " (cutoff:3.500A) removed outlier: 5.918A pdb=" N VAL A 30 " --> pdb=" O VAL A 74 " (cutoff:3.500A) removed outlier: 9.407A pdb=" N LEU A 1 " --> pdb=" O VAL A 27 " (cutoff:3.500A) removed outlier: 9.145A pdb=" N VAL A 29 " --> pdb=" O LEU A 1 " (cutoff:3.500A) removed outlier: 6.902A pdb=" N VAL A 3 " --> pdb=" O VAL A 29 " (cutoff:3.500A) removed outlier: 8.512A pdb=" N ASN A 31 " --> pdb=" O VAL A 3 " (cutoff:3.500A) removed outlier: 7.052A pdb=" N ILE A 5 " --> pdb=" O ASN A 31 " (cutoff:3.500A) removed outlier: 6.582A pdb=" N LYS A 2 " --> pdb=" O ILE A 91 " (cutoff:3.500A) removed outlier: 7.757A pdb=" N ILE A 93 " --> pdb=" O LYS A 2 " (cutoff:3.500A) removed outlier: 6.636A pdb=" N ALA A 4 " --> pdb=" O ILE A 93 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'A' and resid 46 through 47 removed outlier: 3.537A pdb=" N ASP A 47 " --> pdb=" O GLY A 51 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'A' and resid 204 through 207 removed outlier: 9.485A pdb=" N ASN A 226 " --> pdb=" O VAL A 168 " (cutoff:3.500A) removed outlier: 6.628A pdb=" N GLY A 170 " --> pdb=" O ASN A 226 " (cutoff:3.500A) removed outlier: 8.816A pdb=" N ILE A 228 " --> pdb=" O GLY A 170 " (cutoff:3.500A) removed outlier: 6.442A pdb=" N MET A 172 " --> pdb=" O ILE A 228 " (cutoff:3.500A) removed outlier: 8.007A pdb=" N LEU A 230 " --> pdb=" O MET A 172 " (cutoff:3.500A) removed outlier: 6.428A pdb=" N THR A 174 " --> pdb=" O LEU A 230 " (cutoff:3.500A) removed outlier: 3.849A pdb=" N LYS A 169 " --> pdb=" O ASN A 245 " (cutoff:3.500A) removed outlier: 5.038A pdb=" N VAL A 308 " --> pdb=" O ASP A 293 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'A' and resid 204 through 207 removed outlier: 9.485A pdb=" N ASN A 226 " --> pdb=" O VAL A 168 " (cutoff:3.500A) removed outlier: 6.628A pdb=" N GLY A 170 " --> pdb=" O ASN A 226 " (cutoff:3.500A) removed outlier: 8.816A pdb=" N ILE A 228 " --> pdb=" O GLY A 170 " (cutoff:3.500A) removed outlier: 6.442A pdb=" N MET A 172 " --> pdb=" O ILE A 228 " (cutoff:3.500A) removed outlier: 8.007A pdb=" N LEU A 230 " --> pdb=" O MET A 172 " (cutoff:3.500A) removed outlier: 6.428A pdb=" N THR A 174 " --> pdb=" O LEU A 230 " (cutoff:3.500A) removed outlier: 3.849A pdb=" N LYS A 169 " --> pdb=" O ASN A 245 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'B' and resid 57 through 58 removed outlier: 9.831A pdb=" N ASP B 26 " --> pdb=" O VAL B 70 " (cutoff:3.500A) removed outlier: 9.268A pdb=" N LYS B 72 " --> pdb=" O ASP B 26 " (cutoff:3.500A) removed outlier: 6.807A pdb=" N VAL B 28 " --> pdb=" O LYS B 72 " (cutoff:3.500A) removed outlier: 8.223A pdb=" N VAL B 74 " --> pdb=" O VAL B 28 " (cutoff:3.500A) removed outlier: 6.241A pdb=" N ILE B 30 " --> pdb=" O VAL B 74 " (cutoff:3.500A) removed outlier: 9.619A pdb=" N LEU B 1 " --> pdb=" O VAL B 27 " (cutoff:3.500A) removed outlier: 8.912A pdb=" N VAL B 29 " --> pdb=" O LEU B 1 " (cutoff:3.500A) removed outlier: 6.886A pdb=" N VAL B 3 " --> pdb=" O VAL B 29 " (cutoff:3.500A) removed outlier: 8.429A pdb=" N ASN B 31 " --> pdb=" O VAL B 3 " (cutoff:3.500A) removed outlier: 6.367A pdb=" N ILE B 5 " --> pdb=" O ASN B 31 " (cutoff:3.500A) removed outlier: 6.461A pdb=" N LYS B 2 " --> pdb=" O LEU B 91 " (cutoff:3.500A) removed outlier: 7.746A pdb=" N ILE B 93 " --> pdb=" O LYS B 2 " (cutoff:3.500A) removed outlier: 6.764A pdb=" N ALA B 4 " --> pdb=" O ILE B 93 " (cutoff:3.500A) removed outlier: 6.497A pdb=" N VAL B 92 " --> pdb=" O LEU B 117 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'B' and resid 204 through 207 removed outlier: 9.812A pdb=" N ASN B 226 " --> pdb=" O ILE B 168 " (cutoff:3.500A) removed outlier: 7.134A pdb=" N GLY B 170 " --> pdb=" O ASN B 226 " (cutoff:3.500A) removed outlier: 9.070A pdb=" N ILE B 228 " --> pdb=" O GLY B 170 " (cutoff:3.500A) removed outlier: 6.484A pdb=" N MET B 172 " --> pdb=" O ILE B 228 " (cutoff:3.500A) removed outlier: 8.088A pdb=" N LEU B 230 " --> pdb=" O MET B 172 " (cutoff:3.500A) removed outlier: 6.322A pdb=" N THR B 174 " --> pdb=" O LEU B 230 " (cutoff:3.500A) removed outlier: 7.359A pdb=" N VAL B 232 " --> pdb=" O THR B 174 " (cutoff:3.500A) removed outlier: 6.503A pdb=" N HIS B 176 " --> pdb=" O VAL B 232 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N LYS B 169 " --> pdb=" O GLN B 245 " (cutoff:3.500A) removed outlier: 5.127A pdb=" N ILE B 308 " --> pdb=" O ASP B 293 " (cutoff:3.500A) removed outlier: 6.855A pdb=" N SER B 272 " --> pdb=" O ILE B 292 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'B' and resid 204 through 207 removed outlier: 9.812A pdb=" N ASN B 226 " --> pdb=" O ILE B 168 " (cutoff:3.500A) removed outlier: 7.134A pdb=" N GLY B 170 " --> pdb=" O ASN B 226 " (cutoff:3.500A) removed outlier: 9.070A pdb=" N ILE B 228 " --> pdb=" O GLY B 170 " (cutoff:3.500A) removed outlier: 6.484A pdb=" N MET B 172 " --> pdb=" O ILE B 228 " (cutoff:3.500A) removed outlier: 8.088A pdb=" N LEU B 230 " --> pdb=" O MET B 172 " (cutoff:3.500A) removed outlier: 6.322A pdb=" N THR B 174 " --> pdb=" O LEU B 230 " (cutoff:3.500A) removed outlier: 7.359A pdb=" N VAL B 232 " --> pdb=" O THR B 174 " (cutoff:3.500A) removed outlier: 6.503A pdb=" N HIS B 176 " --> pdb=" O VAL B 232 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N LYS B 169 " --> pdb=" O GLN B 245 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'C' and resid 57 through 60 removed outlier: 9.629A pdb=" N ASP C 26 " --> pdb=" O PRO C 70 " (cutoff:3.500A) removed outlier: 9.547A pdb=" N LYS C 72 " --> pdb=" O ASP C 26 " (cutoff:3.500A) removed outlier: 6.982A pdb=" N VAL C 28 " --> pdb=" O LYS C 72 " (cutoff:3.500A) removed outlier: 8.073A pdb=" N VAL C 74 " --> pdb=" O VAL C 28 " (cutoff:3.500A) removed outlier: 6.465A pdb=" N VAL C 30 " --> pdb=" O VAL C 74 " (cutoff:3.500A) removed outlier: 9.378A pdb=" N LEU C 1 " --> pdb=" O VAL C 27 " (cutoff:3.500A) removed outlier: 9.094A pdb=" N VAL C 29 " --> pdb=" O LEU C 1 " (cutoff:3.500A) removed outlier: 6.752A pdb=" N VAL C 3 " --> pdb=" O VAL C 29 " (cutoff:3.500A) removed outlier: 8.275A pdb=" N ASN C 31 " --> pdb=" O VAL C 3 " (cutoff:3.500A) removed outlier: 6.925A pdb=" N ILE C 5 " --> pdb=" O ASN C 31 " (cutoff:3.500A) removed outlier: 6.554A pdb=" N VAL C 92 " --> pdb=" O ILE C 117 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'C' and resid 204 through 207 removed outlier: 9.534A pdb=" N ASN C 226 " --> pdb=" O VAL C 168 " (cutoff:3.500A) removed outlier: 6.651A pdb=" N GLY C 170 " --> pdb=" O ASN C 226 " (cutoff:3.500A) removed outlier: 8.924A pdb=" N ILE C 228 " --> pdb=" O GLY C 170 " (cutoff:3.500A) removed outlier: 6.469A pdb=" N MET C 172 " --> pdb=" O ILE C 228 " (cutoff:3.500A) removed outlier: 7.944A pdb=" N LEU C 230 " --> pdb=" O MET C 172 " (cutoff:3.500A) removed outlier: 6.326A pdb=" N THR C 174 " --> pdb=" O LEU C 230 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N LYS C 169 " --> pdb=" O ASN C 245 " (cutoff:3.500A) removed outlier: 5.012A pdb=" N VAL C 308 " --> pdb=" O ASP C 293 " (cutoff:3.500A) removed outlier: 6.871A pdb=" N ASP C 272 " --> pdb=" O ILE C 292 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'C' and resid 204 through 207 removed outlier: 9.534A pdb=" N ASN C 226 " --> pdb=" O VAL C 168 " (cutoff:3.500A) removed outlier: 6.651A pdb=" N GLY C 170 " --> pdb=" O ASN C 226 " (cutoff:3.500A) removed outlier: 8.924A pdb=" N ILE C 228 " --> pdb=" O GLY C 170 " (cutoff:3.500A) removed outlier: 6.469A pdb=" N MET C 172 " --> pdb=" O ILE C 228 " (cutoff:3.500A) removed outlier: 7.944A pdb=" N LEU C 230 " --> pdb=" O MET C 172 " (cutoff:3.500A) removed outlier: 6.326A pdb=" N THR C 174 " --> pdb=" O LEU C 230 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N LYS C 169 " --> pdb=" O ASN C 245 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'D' and resid 57 through 59 removed outlier: 10.048A pdb=" N VAL D 70 " --> pdb=" O ASP D 26 " (cutoff:3.500A) removed outlier: 5.948A pdb=" N VAL D 28 " --> pdb=" O VAL D 70 " (cutoff:3.500A) removed outlier: 9.699A pdb=" N LEU D 1 " --> pdb=" O VAL D 27 " (cutoff:3.500A) removed outlier: 9.255A pdb=" N VAL D 29 " --> pdb=" O LEU D 1 " (cutoff:3.500A) removed outlier: 7.066A pdb=" N VAL D 3 " --> pdb=" O VAL D 29 " (cutoff:3.500A) removed outlier: 8.391A pdb=" N ASN D 31 " --> pdb=" O VAL D 3 " (cutoff:3.500A) removed outlier: 6.360A pdb=" N ILE D 5 " --> pdb=" O ASN D 31 " (cutoff:3.500A) removed outlier: 6.543A pdb=" N VAL D 92 " --> pdb=" O LEU D 117 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'D' and resid 204 through 207 removed outlier: 8.675A pdb=" N ILE D 228 " --> pdb=" O GLY D 170 " (cutoff:3.500A) removed outlier: 6.260A pdb=" N MET D 172 " --> pdb=" O ILE D 228 " (cutoff:3.500A) removed outlier: 7.752A pdb=" N LEU D 230 " --> pdb=" O MET D 172 " (cutoff:3.500A) removed outlier: 6.270A pdb=" N THR D 174 " --> pdb=" O LEU D 230 " (cutoff:3.500A) removed outlier: 7.277A pdb=" N VAL D 232 " --> pdb=" O THR D 174 " (cutoff:3.500A) removed outlier: 6.492A pdb=" N HIS D 176 " --> pdb=" O VAL D 232 " (cutoff:3.500A) removed outlier: 3.869A pdb=" N LYS D 169 " --> pdb=" O GLN D 245 " (cutoff:3.500A) removed outlier: 5.087A pdb=" N ILE D 308 " --> pdb=" O ASP D 293 " (cutoff:3.500A) removed outlier: 6.916A pdb=" N SER D 272 " --> pdb=" O ILE D 292 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'D' and resid 204 through 207 removed outlier: 8.675A pdb=" N ILE D 228 " --> pdb=" O GLY D 170 " (cutoff:3.500A) removed outlier: 6.260A pdb=" N MET D 172 " --> pdb=" O ILE D 228 " (cutoff:3.500A) removed outlier: 7.752A pdb=" N LEU D 230 " --> pdb=" O MET D 172 " (cutoff:3.500A) removed outlier: 6.270A pdb=" N THR D 174 " --> pdb=" O LEU D 230 " (cutoff:3.500A) removed outlier: 7.277A pdb=" N VAL D 232 " --> pdb=" O THR D 174 " (cutoff:3.500A) removed outlier: 6.492A pdb=" N HIS D 176 " --> pdb=" O VAL D 232 " (cutoff:3.500A) removed outlier: 3.869A pdb=" N LYS D 169 " --> pdb=" O GLN D 245 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'E' and resid 57 through 60 removed outlier: 9.597A pdb=" N ASP E 26 " --> pdb=" O PRO E 70 " (cutoff:3.500A) removed outlier: 9.214A pdb=" N LYS E 72 " --> pdb=" O ASP E 26 " (cutoff:3.500A) removed outlier: 6.885A pdb=" N VAL E 28 " --> pdb=" O LYS E 72 " (cutoff:3.500A) removed outlier: 7.983A pdb=" N VAL E 74 " --> pdb=" O VAL E 28 " (cutoff:3.500A) removed outlier: 6.163A pdb=" N VAL E 30 " --> pdb=" O VAL E 74 " (cutoff:3.500A) removed outlier: 9.604A pdb=" N LEU E 1 " --> pdb=" O VAL E 27 " (cutoff:3.500A) removed outlier: 8.946A pdb=" N VAL E 29 " --> pdb=" O LEU E 1 " (cutoff:3.500A) removed outlier: 6.739A pdb=" N VAL E 3 " --> pdb=" O VAL E 29 " (cutoff:3.500A) removed outlier: 8.281A pdb=" N ASN E 31 " --> pdb=" O VAL E 3 " (cutoff:3.500A) removed outlier: 7.070A pdb=" N ILE E 5 " --> pdb=" O ASN E 31 " (cutoff:3.500A) removed outlier: 6.525A pdb=" N LYS E 2 " --> pdb=" O ILE E 91 " (cutoff:3.500A) removed outlier: 7.778A pdb=" N ILE E 93 " --> pdb=" O LYS E 2 " (cutoff:3.500A) removed outlier: 6.763A pdb=" N ALA E 4 " --> pdb=" O ILE E 93 " (cutoff:3.500A) removed outlier: 6.442A pdb=" N VAL E 92 " --> pdb=" O ILE E 117 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'E' and resid 204 through 207 removed outlier: 3.767A pdb=" N LYS E 169 " --> pdb=" O ASN E 245 " (cutoff:3.500A) removed outlier: 4.946A pdb=" N VAL E 308 " --> pdb=" O ASP E 293 " (cutoff:3.500A) removed outlier: 6.797A pdb=" N ASP E 272 " --> pdb=" O ILE E 292 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'E' and resid 204 through 207 removed outlier: 3.767A pdb=" N LYS E 169 " --> pdb=" O ASN E 245 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'F' and resid 57 through 58 removed outlier: 10.282A pdb=" N VAL F 70 " --> pdb=" O ASP F 26 " (cutoff:3.500A) removed outlier: 5.964A pdb=" N VAL F 28 " --> pdb=" O VAL F 70 " (cutoff:3.500A) removed outlier: 5.798A pdb=" N LEU F 1 " --> pdb=" O ASP F 26 " (cutoff:3.500A) removed outlier: 6.819A pdb=" N VAL F 28 " --> pdb=" O LEU F 1 " (cutoff:3.500A) removed outlier: 7.533A pdb=" N VAL F 3 " --> pdb=" O VAL F 28 " (cutoff:3.500A) removed outlier: 6.110A pdb=" N ILE F 30 " --> pdb=" O VAL F 3 " (cutoff:3.500A) removed outlier: 6.571A pdb=" N ILE F 5 " --> pdb=" O ILE F 30 " (cutoff:3.500A) removed outlier: 6.295A pdb=" N LYS F 2 " --> pdb=" O LEU F 91 " (cutoff:3.500A) removed outlier: 7.455A pdb=" N ILE F 93 " --> pdb=" O LYS F 2 " (cutoff:3.500A) removed outlier: 6.657A pdb=" N ALA F 4 " --> pdb=" O ILE F 93 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'F' and resid 204 through 206 removed outlier: 9.564A pdb=" N ASN F 226 " --> pdb=" O ILE F 168 " (cutoff:3.500A) removed outlier: 6.901A pdb=" N GLY F 170 " --> pdb=" O ASN F 226 " (cutoff:3.500A) removed outlier: 8.974A pdb=" N ILE F 228 " --> pdb=" O GLY F 170 " (cutoff:3.500A) removed outlier: 6.342A pdb=" N MET F 172 " --> pdb=" O ILE F 228 " (cutoff:3.500A) removed outlier: 7.915A pdb=" N LEU F 230 " --> pdb=" O MET F 172 " (cutoff:3.500A) removed outlier: 6.343A pdb=" N THR F 174 " --> pdb=" O LEU F 230 " (cutoff:3.500A) removed outlier: 7.094A pdb=" N VAL F 232 " --> pdb=" O THR F 174 " (cutoff:3.500A) removed outlier: 6.609A pdb=" N HIS F 176 " --> pdb=" O VAL F 232 " (cutoff:3.500A) removed outlier: 3.822A pdb=" N LYS F 169 " --> pdb=" O GLN F 245 " (cutoff:3.500A) removed outlier: 5.189A pdb=" N ILE F 308 " --> pdb=" O ASP F 293 " (cutoff:3.500A) removed outlier: 6.792A pdb=" N SER F 272 " --> pdb=" O ILE F 292 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'F' and resid 204 through 206 removed outlier: 9.564A pdb=" N ASN F 226 " --> pdb=" O ILE F 168 " (cutoff:3.500A) removed outlier: 6.901A pdb=" N GLY F 170 " --> pdb=" O ASN F 226 " (cutoff:3.500A) removed outlier: 8.974A pdb=" N ILE F 228 " --> pdb=" O GLY F 170 " (cutoff:3.500A) removed outlier: 6.342A pdb=" N MET F 172 " --> pdb=" O ILE F 228 " (cutoff:3.500A) removed outlier: 7.915A pdb=" N LEU F 230 " --> pdb=" O MET F 172 " (cutoff:3.500A) removed outlier: 6.343A pdb=" N THR F 174 " --> pdb=" O LEU F 230 " (cutoff:3.500A) removed outlier: 7.094A pdb=" N VAL F 232 " --> pdb=" O THR F 174 " (cutoff:3.500A) removed outlier: 6.609A pdb=" N HIS F 176 " --> pdb=" O VAL F 232 " (cutoff:3.500A) removed outlier: 3.822A pdb=" N LYS F 169 " --> pdb=" O GLN F 245 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'G' and resid 57 through 60 removed outlier: 5.698A pdb=" N VAL G 28 " --> pdb=" O PRO G 70 " (cutoff:3.500A) removed outlier: 5.949A pdb=" N LEU G 1 " --> pdb=" O ASP G 26 " (cutoff:3.500A) removed outlier: 6.775A pdb=" N VAL G 28 " --> pdb=" O LEU G 1 " (cutoff:3.500A) removed outlier: 7.329A pdb=" N VAL G 3 " --> pdb=" O VAL G 28 " (cutoff:3.500A) removed outlier: 6.174A pdb=" N VAL G 30 " --> pdb=" O VAL G 3 " (cutoff:3.500A) removed outlier: 6.523A pdb=" N ILE G 5 " --> pdb=" O VAL G 30 " (cutoff:3.500A) removed outlier: 6.528A pdb=" N LYS G 2 " --> pdb=" O ILE G 91 " (cutoff:3.500A) removed outlier: 7.783A pdb=" N ILE G 93 " --> pdb=" O LYS G 2 " (cutoff:3.500A) removed outlier: 6.592A pdb=" N ALA G 4 " --> pdb=" O ILE G 93 " (cutoff:3.500A) removed outlier: 6.485A pdb=" N VAL G 92 " --> pdb=" O ILE G 117 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'G' and resid 204 through 207 removed outlier: 9.349A pdb=" N ASN G 226 " --> pdb=" O VAL G 168 " (cutoff:3.500A) removed outlier: 6.529A pdb=" N GLY G 170 " --> pdb=" O ASN G 226 " (cutoff:3.500A) removed outlier: 8.723A pdb=" N ILE G 228 " --> pdb=" O GLY G 170 " (cutoff:3.500A) removed outlier: 6.434A pdb=" N MET G 172 " --> pdb=" O ILE G 228 " (cutoff:3.500A) removed outlier: 8.032A pdb=" N LEU G 230 " --> pdb=" O MET G 172 " (cutoff:3.500A) removed outlier: 6.657A pdb=" N THR G 174 " --> pdb=" O LEU G 230 " (cutoff:3.500A) removed outlier: 3.988A pdb=" N LYS G 169 " --> pdb=" O ASN G 245 " (cutoff:3.500A) removed outlier: 5.051A pdb=" N VAL G 308 " --> pdb=" O ASP G 293 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'G' and resid 204 through 207 removed outlier: 9.349A pdb=" N ASN G 226 " --> pdb=" O VAL G 168 " (cutoff:3.500A) removed outlier: 6.529A pdb=" N GLY G 170 " --> pdb=" O ASN G 226 " (cutoff:3.500A) removed outlier: 8.723A pdb=" N ILE G 228 " --> pdb=" O GLY G 170 " (cutoff:3.500A) removed outlier: 6.434A pdb=" N MET G 172 " --> pdb=" O ILE G 228 " (cutoff:3.500A) removed outlier: 8.032A pdb=" N LEU G 230 " --> pdb=" O MET G 172 " (cutoff:3.500A) removed outlier: 6.657A pdb=" N THR G 174 " --> pdb=" O LEU G 230 " (cutoff:3.500A) removed outlier: 3.988A pdb=" N LYS G 169 " --> pdb=" O ASN G 245 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'H' and resid 57 through 58 removed outlier: 10.241A pdb=" N VAL H 70 " --> pdb=" O ASP H 26 " (cutoff:3.500A) removed outlier: 5.932A pdb=" N VAL H 28 " --> pdb=" O VAL H 70 " (cutoff:3.500A) removed outlier: 9.835A pdb=" N LEU H 1 " --> pdb=" O VAL H 27 " (cutoff:3.500A) removed outlier: 9.068A pdb=" N VAL H 29 " --> pdb=" O LEU H 1 " (cutoff:3.500A) removed outlier: 6.785A pdb=" N VAL H 3 " --> pdb=" O VAL H 29 " (cutoff:3.500A) removed outlier: 8.089A pdb=" N ASN H 31 " --> pdb=" O VAL H 3 " (cutoff:3.500A) removed outlier: 6.133A pdb=" N ILE H 5 " --> pdb=" O ASN H 31 " (cutoff:3.500A) removed outlier: 6.293A pdb=" N VAL H 92 " --> pdb=" O LEU H 117 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'H' and resid 204 through 207 removed outlier: 3.724A pdb=" N ASN H 226 " --> pdb=" O GLY H 170 " (cutoff:3.500A) removed outlier: 3.853A pdb=" N LYS H 169 " --> pdb=" O GLN H 245 " (cutoff:3.500A) removed outlier: 5.124A pdb=" N ILE H 308 " --> pdb=" O ASP H 293 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'H' and resid 204 through 207 removed outlier: 3.724A pdb=" N ASN H 226 " --> pdb=" O GLY H 170 " (cutoff:3.500A) removed outlier: 3.853A pdb=" N LYS H 169 " --> pdb=" O GLN H 245 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'I' and resid 58 through 60 removed outlier: 3.644A pdb=" N THR I 63 " --> pdb=" O ILE I 60 " (cutoff:3.500A) removed outlier: 9.448A pdb=" N ASP I 26 " --> pdb=" O PRO I 70 " (cutoff:3.500A) removed outlier: 9.423A pdb=" N LYS I 72 " --> pdb=" O ASP I 26 " (cutoff:3.500A) removed outlier: 6.657A pdb=" N VAL I 28 " --> pdb=" O LYS I 72 " (cutoff:3.500A) removed outlier: 7.752A pdb=" N VAL I 74 " --> pdb=" O VAL I 28 " (cutoff:3.500A) removed outlier: 5.959A pdb=" N VAL I 30 " --> pdb=" O VAL I 74 " (cutoff:3.500A) removed outlier: 9.402A pdb=" N LEU I 1 " --> pdb=" O VAL I 27 " (cutoff:3.500A) removed outlier: 9.133A pdb=" N VAL I 29 " --> pdb=" O LEU I 1 " (cutoff:3.500A) removed outlier: 6.897A pdb=" N VAL I 3 " --> pdb=" O VAL I 29 " (cutoff:3.500A) removed outlier: 8.514A pdb=" N ASN I 31 " --> pdb=" O VAL I 3 " (cutoff:3.500A) removed outlier: 7.039A pdb=" N ILE I 5 " --> pdb=" O ASN I 31 " (cutoff:3.500A) removed outlier: 6.587A pdb=" N LYS I 2 " --> pdb=" O ILE I 91 " (cutoff:3.500A) removed outlier: 7.767A pdb=" N ILE I 93 " --> pdb=" O LYS I 2 " (cutoff:3.500A) removed outlier: 6.627A pdb=" N ALA I 4 " --> pdb=" O ILE I 93 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'I' and resid 46 through 47 removed outlier: 3.544A pdb=" N ASP I 47 " --> pdb=" O GLY I 51 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'I' and resid 204 through 207 removed outlier: 9.492A pdb=" N ASN I 226 " --> pdb=" O VAL I 168 " (cutoff:3.500A) removed outlier: 6.654A pdb=" N GLY I 170 " --> pdb=" O ASN I 226 " (cutoff:3.500A) removed outlier: 8.810A pdb=" N ILE I 228 " --> pdb=" O GLY I 170 " (cutoff:3.500A) removed outlier: 6.451A pdb=" N MET I 172 " --> pdb=" O ILE I 228 " (cutoff:3.500A) removed outlier: 7.976A pdb=" N LEU I 230 " --> pdb=" O MET I 172 " (cutoff:3.500A) removed outlier: 6.376A pdb=" N THR I 174 " --> pdb=" O LEU I 230 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N LYS I 169 " --> pdb=" O ASN I 245 " (cutoff:3.500A) removed outlier: 5.041A pdb=" N VAL I 308 " --> pdb=" O ASP I 293 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'I' and resid 204 through 207 removed outlier: 9.492A pdb=" N ASN I 226 " --> pdb=" O VAL I 168 " (cutoff:3.500A) removed outlier: 6.654A pdb=" N GLY I 170 " --> pdb=" O ASN I 226 " (cutoff:3.500A) removed outlier: 8.810A pdb=" N ILE I 228 " --> pdb=" O GLY I 170 " (cutoff:3.500A) removed outlier: 6.451A pdb=" N MET I 172 " --> pdb=" O ILE I 228 " (cutoff:3.500A) removed outlier: 7.976A pdb=" N LEU I 230 " --> pdb=" O MET I 172 " (cutoff:3.500A) removed outlier: 6.376A pdb=" N THR I 174 " --> pdb=" O LEU I 230 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N LYS I 169 " --> pdb=" O ASN I 245 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'J' and resid 57 through 58 removed outlier: 9.772A pdb=" N VAL J 70 " --> pdb=" O ASP J 26 " (cutoff:3.500A) removed outlier: 5.750A pdb=" N VAL J 28 " --> pdb=" O VAL J 70 " (cutoff:3.500A) removed outlier: 9.719A pdb=" N LEU J 1 " --> pdb=" O VAL J 27 " (cutoff:3.500A) removed outlier: 8.930A pdb=" N VAL J 29 " --> pdb=" O LEU J 1 " (cutoff:3.500A) removed outlier: 6.966A pdb=" N VAL J 3 " --> pdb=" O VAL J 29 " (cutoff:3.500A) removed outlier: 8.552A pdb=" N ASN J 31 " --> pdb=" O VAL J 3 " (cutoff:3.500A) removed outlier: 6.363A pdb=" N ILE J 5 " --> pdb=" O ASN J 31 " (cutoff:3.500A) removed outlier: 6.534A pdb=" N LYS J 2 " --> pdb=" O LEU J 91 " (cutoff:3.500A) removed outlier: 7.827A pdb=" N ILE J 93 " --> pdb=" O LYS J 2 " (cutoff:3.500A) removed outlier: 6.774A pdb=" N ALA J 4 " --> pdb=" O ILE J 93 " (cutoff:3.500A) removed outlier: 6.500A pdb=" N VAL J 92 " --> pdb=" O LEU J 117 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'J' and resid 204 through 207 removed outlier: 9.726A pdb=" N ASN J 226 " --> pdb=" O ILE J 168 " (cutoff:3.500A) removed outlier: 6.961A pdb=" N GLY J 170 " --> pdb=" O ASN J 226 " (cutoff:3.500A) removed outlier: 8.987A pdb=" N ILE J 228 " --> pdb=" O GLY J 170 " (cutoff:3.500A) removed outlier: 6.351A pdb=" N MET J 172 " --> pdb=" O ILE J 228 " (cutoff:3.500A) removed outlier: 8.022A pdb=" N LEU J 230 " --> pdb=" O MET J 172 " (cutoff:3.500A) removed outlier: 6.326A pdb=" N THR J 174 " --> pdb=" O LEU J 230 " (cutoff:3.500A) removed outlier: 7.350A pdb=" N VAL J 232 " --> pdb=" O THR J 174 " (cutoff:3.500A) removed outlier: 6.497A pdb=" N HIS J 176 " --> pdb=" O VAL J 232 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N LYS J 169 " --> pdb=" O GLN J 245 " (cutoff:3.500A) removed outlier: 5.029A pdb=" N ILE J 308 " --> pdb=" O ASP J 293 " (cutoff:3.500A) removed outlier: 6.842A pdb=" N SER J 272 " --> pdb=" O ILE J 292 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'J' and resid 204 through 207 removed outlier: 9.726A pdb=" N ASN J 226 " --> pdb=" O ILE J 168 " (cutoff:3.500A) removed outlier: 6.961A pdb=" N GLY J 170 " --> pdb=" O ASN J 226 " (cutoff:3.500A) removed outlier: 8.987A pdb=" N ILE J 228 " --> pdb=" O GLY J 170 " (cutoff:3.500A) removed outlier: 6.351A pdb=" N MET J 172 " --> pdb=" O ILE J 228 " (cutoff:3.500A) removed outlier: 8.022A pdb=" N LEU J 230 " --> pdb=" O MET J 172 " (cutoff:3.500A) removed outlier: 6.326A pdb=" N THR J 174 " --> pdb=" O LEU J 230 " (cutoff:3.500A) removed outlier: 7.350A pdb=" N VAL J 232 " --> pdb=" O THR J 174 " (cutoff:3.500A) removed outlier: 6.497A pdb=" N HIS J 176 " --> pdb=" O VAL J 232 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N LYS J 169 " --> pdb=" O GLN J 245 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'K' and resid 57 through 60 removed outlier: 9.604A pdb=" N ASP K 26 " --> pdb=" O PRO K 70 " (cutoff:3.500A) removed outlier: 9.491A pdb=" N LYS K 72 " --> pdb=" O ASP K 26 " (cutoff:3.500A) removed outlier: 6.973A pdb=" N VAL K 28 " --> pdb=" O LYS K 72 " (cutoff:3.500A) removed outlier: 8.124A pdb=" N VAL K 74 " --> pdb=" O VAL K 28 " (cutoff:3.500A) removed outlier: 6.372A pdb=" N VAL K 30 " --> pdb=" O VAL K 74 " (cutoff:3.500A) removed outlier: 9.392A pdb=" N LEU K 1 " --> pdb=" O VAL K 27 " (cutoff:3.500A) removed outlier: 9.069A pdb=" N VAL K 29 " --> pdb=" O LEU K 1 " (cutoff:3.500A) removed outlier: 6.814A pdb=" N VAL K 3 " --> pdb=" O VAL K 29 " (cutoff:3.500A) removed outlier: 8.250A pdb=" N ASN K 31 " --> pdb=" O VAL K 3 " (cutoff:3.500A) removed outlier: 6.921A pdb=" N ILE K 5 " --> pdb=" O ASN K 31 " (cutoff:3.500A) removed outlier: 6.560A pdb=" N VAL K 92 " --> pdb=" O ILE K 117 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'K' and resid 204 through 207 removed outlier: 9.523A pdb=" N ASN K 226 " --> pdb=" O VAL K 168 " (cutoff:3.500A) removed outlier: 6.635A pdb=" N GLY K 170 " --> pdb=" O ASN K 226 " (cutoff:3.500A) removed outlier: 8.907A pdb=" N ILE K 228 " --> pdb=" O GLY K 170 " (cutoff:3.500A) removed outlier: 6.458A pdb=" N MET K 172 " --> pdb=" O ILE K 228 " (cutoff:3.500A) removed outlier: 7.935A pdb=" N LEU K 230 " --> pdb=" O MET K 172 " (cutoff:3.500A) removed outlier: 6.326A pdb=" N THR K 174 " --> pdb=" O LEU K 230 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N LYS K 169 " --> pdb=" O ASN K 245 " (cutoff:3.500A) removed outlier: 5.029A pdb=" N VAL K 308 " --> pdb=" O ASP K 293 " (cutoff:3.500A) removed outlier: 6.868A pdb=" N ASP K 272 " --> pdb=" O ILE K 292 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'K' and resid 204 through 207 removed outlier: 9.523A pdb=" N ASN K 226 " --> pdb=" O VAL K 168 " (cutoff:3.500A) removed outlier: 6.635A pdb=" N GLY K 170 " --> pdb=" O ASN K 226 " (cutoff:3.500A) removed outlier: 8.907A pdb=" N ILE K 228 " --> pdb=" O GLY K 170 " (cutoff:3.500A) removed outlier: 6.458A pdb=" N MET K 172 " --> pdb=" O ILE K 228 " (cutoff:3.500A) removed outlier: 7.935A pdb=" N LEU K 230 " --> pdb=" O MET K 172 " (cutoff:3.500A) removed outlier: 6.326A pdb=" N THR K 174 " --> pdb=" O LEU K 230 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N LYS K 169 " --> pdb=" O ASN K 245 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'L' and resid 57 through 59 removed outlier: 10.365A pdb=" N ASP L 26 " --> pdb=" O VAL L 70 " (cutoff:3.500A) removed outlier: 9.560A pdb=" N LYS L 72 " --> pdb=" O ASP L 26 " (cutoff:3.500A) removed outlier: 6.815A pdb=" N VAL L 28 " --> pdb=" O LYS L 72 " (cutoff:3.500A) removed outlier: 8.159A pdb=" N VAL L 74 " --> pdb=" O VAL L 28 " (cutoff:3.500A) removed outlier: 6.214A pdb=" N ILE L 30 " --> pdb=" O VAL L 74 " (cutoff:3.500A) removed outlier: 5.923A pdb=" N LEU L 1 " --> pdb=" O ASP L 26 " (cutoff:3.500A) removed outlier: 6.670A pdb=" N VAL L 28 " --> pdb=" O LEU L 1 " (cutoff:3.500A) removed outlier: 7.409A pdb=" N VAL L 3 " --> pdb=" O VAL L 28 " (cutoff:3.500A) removed outlier: 6.390A pdb=" N ILE L 30 " --> pdb=" O VAL L 3 " (cutoff:3.500A) removed outlier: 6.553A pdb=" N ILE L 5 " --> pdb=" O ILE L 30 " (cutoff:3.500A) removed outlier: 6.506A pdb=" N VAL L 92 " --> pdb=" O LEU L 117 " (cutoff:3.500A) Processing sheet with id=AF4, first strand: chain 'L' and resid 204 through 207 removed outlier: 9.014A pdb=" N ILE L 228 " --> pdb=" O GLY L 170 " (cutoff:3.500A) removed outlier: 6.309A pdb=" N MET L 172 " --> pdb=" O ILE L 228 " (cutoff:3.500A) removed outlier: 7.779A pdb=" N LEU L 230 " --> pdb=" O MET L 172 " (cutoff:3.500A) removed outlier: 6.315A pdb=" N THR L 174 " --> pdb=" O LEU L 230 " (cutoff:3.500A) removed outlier: 7.280A pdb=" N VAL L 232 " --> pdb=" O THR L 174 " (cutoff:3.500A) removed outlier: 6.537A pdb=" N HIS L 176 " --> pdb=" O VAL L 232 " (cutoff:3.500A) removed outlier: 3.796A pdb=" N LYS L 169 " --> pdb=" O GLN L 245 " (cutoff:3.500A) removed outlier: 5.088A pdb=" N ILE L 308 " --> pdb=" O ASP L 293 " (cutoff:3.500A) removed outlier: 6.905A pdb=" N SER L 272 " --> pdb=" O ILE L 292 " (cutoff:3.500A) Processing sheet with id=AF5, first strand: chain 'L' and resid 204 through 207 removed outlier: 9.014A pdb=" N ILE L 228 " --> pdb=" O GLY L 170 " (cutoff:3.500A) removed outlier: 6.309A pdb=" N MET L 172 " --> pdb=" O ILE L 228 " (cutoff:3.500A) removed outlier: 7.779A pdb=" N LEU L 230 " --> pdb=" O MET L 172 " (cutoff:3.500A) removed outlier: 6.315A pdb=" N THR L 174 " --> pdb=" O LEU L 230 " (cutoff:3.500A) removed outlier: 7.280A pdb=" N VAL L 232 " --> pdb=" O THR L 174 " (cutoff:3.500A) removed outlier: 6.537A pdb=" N HIS L 176 " --> pdb=" O VAL L 232 " (cutoff:3.500A) removed outlier: 3.796A pdb=" N LYS L 169 " --> pdb=" O GLN L 245 " (cutoff:3.500A) 2091 hydrogen bonds defined for protein. 5445 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: 11.04 Time building geometry restraints manager: 4.41 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.32: 8212 1.32 - 1.45: 10088 1.45 - 1.57: 25356 1.57 - 1.69: 64 1.69 - 1.81: 248 Bond restraints: 43968 Sorted by residual: bond pdb=" C PRO F 79 " pdb=" O PRO F 79 " ideal model delta sigma weight residual 1.238 1.202 0.037 1.22e-02 6.72e+03 9.05e+00 bond pdb=" O3 NAD F 400 " pdb=" PA NAD F 400 " ideal model delta sigma weight residual 1.653 1.599 0.054 2.00e-02 2.50e+03 7.20e+00 bond pdb=" O3 NAD O 400 " pdb=" PA NAD O 400 " ideal model delta sigma weight residual 1.653 1.600 0.053 2.00e-02 2.50e+03 7.01e+00 bond pdb=" O3 NAD R 400 " pdb=" PA NAD R 400 " ideal model delta sigma weight residual 1.653 1.600 0.053 2.00e-02 2.50e+03 6.98e+00 bond pdb=" O3 NAD G 400 " pdb=" PA NAD G 400 " ideal model delta sigma weight residual 1.653 1.600 0.053 2.00e-02 2.50e+03 6.93e+00 ... (remaining 43963 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.85: 58436 1.85 - 3.70: 1172 3.70 - 5.55: 227 5.55 - 7.41: 15 7.41 - 9.26: 14 Bond angle restraints: 59864 Sorted by residual: angle pdb=" N ARG F 77 " pdb=" CA ARG F 77 " pdb=" C ARG F 77 " ideal model delta sigma weight residual 111.28 106.37 4.91 1.09e+00 8.42e-01 2.03e+01 angle pdb=" CA SER D 62 " pdb=" C SER D 62 " pdb=" O SER D 62 " ideal model delta sigma weight residual 121.20 117.17 4.03 1.04e+00 9.25e-01 1.50e+01 angle pdb=" N ALA P 199 " pdb=" CA ALA P 199 " pdb=" CB ALA P 199 " ideal model delta sigma weight residual 114.17 110.57 3.60 1.14e+00 7.69e-01 9.96e+00 angle pdb=" CA ASN F 78 " pdb=" C ASN F 78 " pdb=" O ASN F 78 " ideal model delta sigma weight residual 119.75 116.80 2.95 9.40e-01 1.13e+00 9.86e+00 angle pdb=" CA ASN F 78 " pdb=" C ASN F 78 " pdb=" N PRO F 79 " ideal model delta sigma weight residual 118.87 121.69 -2.82 9.00e-01 1.23e+00 9.80e+00 ... (remaining 59859 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.81: 24037 17.81 - 35.62: 2087 35.62 - 53.44: 564 53.44 - 71.25: 139 71.25 - 89.06: 37 Dihedral angle restraints: 26864 sinusoidal: 10848 harmonic: 16016 Sorted by residual: dihedral pdb=" CA ASN B 202 " pdb=" C ASN B 202 " pdb=" N ILE B 203 " pdb=" CA ILE B 203 " ideal model delta harmonic sigma weight residual 180.00 155.96 24.04 0 5.00e+00 4.00e-02 2.31e+01 dihedral pdb=" CA ASN Q 245 " pdb=" C ASN Q 245 " pdb=" N ILE Q 246 " pdb=" CA ILE Q 246 " ideal model delta harmonic sigma weight residual 180.00 -156.23 -23.77 0 5.00e+00 4.00e-02 2.26e+01 dihedral pdb=" CA LYS C 248 " pdb=" C LYS C 248 " pdb=" N VAL C 248A" pdb=" CA VAL C 248A" ideal model delta harmonic sigma weight residual -180.00 -158.06 -21.94 0 5.00e+00 4.00e-02 1.93e+01 ... (remaining 26861 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.037: 4370 0.037 - 0.074: 1801 0.074 - 0.112: 574 0.112 - 0.149: 320 0.149 - 0.186: 15 Chirality restraints: 7080 Sorted by residual: chirality pdb=" C2D NAD K 400 " pdb=" C1D NAD K 400 " pdb=" C3D NAD K 400 " pdb=" O2D NAD K 400 " both_signs ideal model delta sigma weight residual False -2.56 -2.75 0.19 2.00e-01 2.50e+01 8.66e-01 chirality pdb=" CA ILE F 143 " pdb=" N ILE F 143 " pdb=" C ILE F 143 " pdb=" CB ILE F 143 " both_signs ideal model delta sigma weight residual False 2.43 2.62 -0.18 2.00e-01 2.50e+01 8.54e-01 chirality pdb=" C2D NAD C 400 " pdb=" C1D NAD C 400 " pdb=" C3D NAD C 400 " pdb=" O2D NAD C 400 " both_signs ideal model delta sigma weight residual False -2.56 -2.74 0.18 2.00e-01 2.50e+01 8.38e-01 ... (remaining 7077 not shown) Planarity restraints: 7608 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG D 77 " 0.233 9.50e-02 1.11e+02 1.05e-01 6.73e+00 pdb=" NE ARG D 77 " -0.013 2.00e-02 2.50e+03 pdb=" CZ ARG D 77 " -0.004 2.00e-02 2.50e+03 pdb=" NH1 ARG D 77 " -0.002 2.00e-02 2.50e+03 pdb=" NH2 ARG D 77 " 0.009 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE Q 348 " 0.020 2.00e-02 2.50e+03 1.92e-02 6.46e+00 pdb=" CG PHE Q 348 " -0.044 2.00e-02 2.50e+03 pdb=" CD1 PHE Q 348 " 0.007 2.00e-02 2.50e+03 pdb=" CD2 PHE Q 348 " 0.012 2.00e-02 2.50e+03 pdb=" CE1 PHE Q 348 " 0.003 2.00e-02 2.50e+03 pdb=" CE2 PHE Q 348 " -0.002 2.00e-02 2.50e+03 pdb=" CZ PHE Q 348 " 0.005 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ILE R 125 " -0.037 5.00e-02 4.00e+02 5.61e-02 5.04e+00 pdb=" N PRO R 126 " 0.097 5.00e-02 4.00e+02 pdb=" CA PRO R 126 " -0.029 5.00e-02 4.00e+02 pdb=" CD PRO R 126 " -0.031 5.00e-02 4.00e+02 ... (remaining 7605 not shown) Histogram of nonbonded interaction distances: 1.80 - 2.42: 221 2.42 - 3.04: 28687 3.04 - 3.66: 65649 3.66 - 4.28: 108636 4.28 - 4.90: 179052 Nonbonded interactions: 382245 Sorted by model distance: nonbonded pdb=" OH TYR O 361 " pdb=" OG1 THR C 208 " model vdw 1.804 3.040 nonbonded pdb=" OH TYR Q 361 " pdb=" OG1 THR I 208 " model vdw 1.809 3.040 nonbonded pdb=" OG1 THR A 208 " pdb=" OH TYR G 361 " model vdw 1.819 3.040 nonbonded pdb=" OG1 THR Q 208 " pdb=" OH TYR I 361 " model vdw 1.881 3.040 nonbonded pdb=" O VAL O 37 " pdb=" OG1 THR O 41 " model vdw 1.915 3.040 ... (remaining 382240 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: 0.01 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 'O' selection = chain 'Q' } ncs_group { reference = chain 'B' selection = chain 'D' selection = chain 'F' selection = chain 'H' selection = chain 'J' selection = chain 'L' selection = chain 'P' selection = chain 'R' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 4.260 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: 0.020 Extract box with map and model: 0.520 Check model and map are aligned: 0.080 Set scattering table: 0.110 Process input model: 40.820 Find NCS groups from input model: 1.170 Set up NCS constraints: 0.150 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:1.230 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 48.370 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8570 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.054 43976 Z= 0.281 Angle : 0.678 9.258 59880 Z= 0.351 Chirality : 0.049 0.186 7080 Planarity : 0.005 0.105 7608 Dihedral : 15.246 89.062 16552 Min Nonbonded Distance : 1.804 Molprobity Statistics. All-atom Clashscore : 7.71 Ramachandran Plot: Outliers : 0.66 % Allowed : 6.33 % Favored : 93.01 % Rotamer: Outliers : 1.69 % Allowed : 19.34 % Favored : 78.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: -1.01 (0.11), residues: 5608 helix: -0.01 (0.13), residues: 1538 sheet: -0.52 (0.14), residues: 1240 loop : -1.06 (0.12), residues: 2830 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG L 77 TYR 0.019 0.003 TYR C 178 PHE 0.044 0.002 PHE Q 348 TRP 0.009 0.001 TRP R 315 HIS 0.004 0.001 HIS A 190 Details of bonding type rmsd covalent geometry : bond 0.00626 (43968) covalent geometry : angle 0.67845 (59864) SS BOND : bond 0.00412 ( 8) SS BOND : angle 0.72418 ( 16) hydrogen bonds : bond 0.15509 ( 1769) hydrogen bonds : angle 6.98799 ( 5445) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11216 Ramachandran restraints generated. 5608 Oldfield, 0 Emsley, 5608 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11216 Ramachandran restraints generated. 5608 Oldfield, 0 Emsley, 5608 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 728 residues out of total 4664 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 79 poor density : 649 time to evaluate : 1.589 Fit side-chains revert: symmetry clash REVERT: P 300 MET cc_start: 0.5775 (ttm) cc_final: 0.5510 (ttm) REVERT: K 164 GLU cc_start: 0.7442 (OUTLIER) cc_final: 0.7092 (mt-10) outliers start: 79 outliers final: 62 residues processed: 709 average time/residue: 0.2395 time to fit residues: 284.1623 Evaluate side-chains 692 residues out of total 4664 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 629 time to evaluate : 1.649 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain O residue 28 VAL Chi-restraints excluded: chain O residue 30 VAL Chi-restraints excluded: chain O residue 41 THR Chi-restraints excluded: chain O residue 201 LEU Chi-restraints excluded: chain O residue 240 VAL Chi-restraints excluded: chain P residue 84 TRP Chi-restraints excluded: chain P residue 286 THR Chi-restraints excluded: chain Q residue 84 TRP Chi-restraints excluded: chain Q residue 335 LEU Chi-restraints excluded: chain R residue 3 VAL Chi-restraints excluded: chain R residue 84 TRP Chi-restraints excluded: chain R residue 125 ILE Chi-restraints excluded: chain R residue 129 VAL Chi-restraints excluded: chain R residue 281 ILE Chi-restraints excluded: chain A residue 84 TRP Chi-restraints excluded: chain A residue 201 LEU Chi-restraints excluded: chain A residue 293 ASP Chi-restraints excluded: chain B residue 11 ILE Chi-restraints excluded: chain B residue 250 THR Chi-restraints excluded: chain B residue 302 ASP Chi-restraints excluded: chain B residue 305 VAL Chi-restraints excluded: chain B residue 327 ILE Chi-restraints excluded: chain C residue 41 THR Chi-restraints excluded: chain C residue 84 TRP Chi-restraints excluded: chain C residue 246 ILE Chi-restraints excluded: chain D residue 161 LEU Chi-restraints excluded: chain D residue 164 LYS Chi-restraints excluded: chain D residue 202 ASN Chi-restraints excluded: chain D residue 295 SER Chi-restraints excluded: chain E residue 30 VAL Chi-restraints excluded: chain E residue 41 THR Chi-restraints excluded: chain E residue 201 LEU Chi-restraints excluded: chain E residue 240 VAL Chi-restraints excluded: chain F residue 84 TRP Chi-restraints excluded: chain F residue 280 SER Chi-restraints excluded: chain F residue 287 ASP Chi-restraints excluded: chain F residue 290 SER Chi-restraints excluded: chain G residue 37 VAL Chi-restraints excluded: chain G residue 84 TRP Chi-restraints excluded: chain H residue 62 SER Chi-restraints excluded: chain H residue 84 TRP Chi-restraints excluded: chain H residue 129 VAL Chi-restraints excluded: chain H residue 281 ILE Chi-restraints excluded: chain I residue 73 VAL Chi-restraints excluded: chain I residue 84 TRP Chi-restraints excluded: chain I residue 335 LEU Chi-restraints excluded: chain I residue 361 TYR Chi-restraints excluded: chain J residue 116 VAL Chi-restraints excluded: chain J residue 250 THR Chi-restraints excluded: chain J residue 305 VAL Chi-restraints excluded: chain J residue 327 ILE Chi-restraints excluded: chain K residue 30 VAL Chi-restraints excluded: chain K residue 41 THR Chi-restraints excluded: chain K residue 84 TRP Chi-restraints excluded: chain K residue 164 GLU Chi-restraints excluded: chain K residue 207 SER Chi-restraints excluded: chain K residue 246 ILE Chi-restraints excluded: chain K residue 352 ASN Chi-restraints excluded: chain L residue 74 VAL Chi-restraints excluded: chain L residue 161 LEU Chi-restraints excluded: chain L residue 202 ASN Chi-restraints excluded: chain L residue 294 SER Chi-restraints excluded: chain L residue 295 SER Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 552 random chunks: chunk 394 optimal weight: 6.9990 chunk 430 optimal weight: 0.7980 chunk 41 optimal weight: 6.9990 chunk 265 optimal weight: 8.9990 chunk 523 optimal weight: 3.9990 chunk 497 optimal weight: 0.9980 chunk 414 optimal weight: 7.9990 chunk 310 optimal weight: 0.0570 chunk 488 optimal weight: 2.9990 chunk 366 optimal weight: 0.8980 chunk 223 optimal weight: 0.8980 overall best weight: 0.7298 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: O 146 ASN ** O 245 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P 146 ASN P 245 GLN P 319 GLN Q 176 HIS R 146 ASN R 152 ASN A 18BHIS A 61 ASN A 139 HIS A 176 HIS B 18BHIS B 202 ASN C 133 ASN C 176 HIS C 245 ASN C 319 GLN D 226 ASN E 146 ASN E 152 ASN ** E 245 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 139 HIS F 146 ASN F 256 ASN F 319 GLN G 176 HIS G 330 ASN H 139 HIS H 319 GLN I 18BHIS I 61 ASN I 176 HIS I 245 ASN K 61 ASN K 133 ASN K 176 HIS K 245 ASN K 319 GLN Total number of N/Q/H flips: 37 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3411 r_free = 0.3411 target = 0.141802 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3075 r_free = 0.3075 target = 0.114583 restraints weight = 47318.675| |-----------------------------------------------------------------------------| r_work (start): 0.3068 rms_B_bonded: 1.28 r_work: 0.2877 rms_B_bonded: 2.25 restraints_weight: 0.5000 r_work: 0.2769 rms_B_bonded: 3.73 restraints_weight: 0.2500 r_work (final): 0.2769 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8632 moved from start: 0.1083 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 43976 Z= 0.130 Angle : 0.562 9.275 59880 Z= 0.304 Chirality : 0.047 0.188 7080 Planarity : 0.005 0.052 7608 Dihedral : 9.273 89.434 6948 Min Nonbonded Distance : 2.365 Molprobity Statistics. All-atom Clashscore : 4.85 Ramachandran Plot: Outliers : 0.66 % Allowed : 5.22 % Favored : 94.12 % Rotamer: Outliers : 3.41 % Allowed : 16.23 % Favored : 80.36 % 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: -0.50 (0.11), residues: 5608 helix: 0.60 (0.14), residues: 1556 sheet: -0.48 (0.15), residues: 1182 loop : -0.73 (0.12), residues: 2870 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG F 77 TYR 0.011 0.002 TYR C 178 PHE 0.017 0.002 PHE J 157 TRP 0.009 0.001 TRP L 332 HIS 0.004 0.001 HIS E 176 Details of bonding type rmsd covalent geometry : bond 0.00296 (43968) covalent geometry : angle 0.56211 (59864) SS BOND : bond 0.00629 ( 8) SS BOND : angle 1.40449 ( 16) hydrogen bonds : bond 0.03704 ( 1769) hydrogen bonds : angle 5.21552 ( 5445) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11216 Ramachandran restraints generated. 5608 Oldfield, 0 Emsley, 5608 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11216 Ramachandran restraints generated. 5608 Oldfield, 0 Emsley, 5608 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 846 residues out of total 4664 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 159 poor density : 687 time to evaluate : 1.269 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: O 2 LYS cc_start: 0.8472 (mttm) cc_final: 0.8210 (mttp) REVERT: O 45 LYS cc_start: 0.8671 (tptt) cc_final: 0.8436 (tptt) REVERT: Q 350 LYS cc_start: 0.7767 (mmmm) cc_final: 0.7428 (mttp) REVERT: R 115 LYS cc_start: 0.7827 (ttmt) cc_final: 0.7591 (ttmt) REVERT: R 158 VAL cc_start: 0.8138 (t) cc_final: 0.7832 (t) REVERT: R 172 MET cc_start: 0.7320 (OUTLIER) cc_final: 0.7091 (tmt) REVERT: A 62 GLU cc_start: 0.8076 (OUTLIER) cc_final: 0.7758 (pm20) REVERT: A 87 LEU cc_start: 0.8627 (OUTLIER) cc_final: 0.8304 (mp) REVERT: A 122 LYS cc_start: 0.8216 (OUTLIER) cc_final: 0.7750 (tmtp) REVERT: C 81 LYS cc_start: 0.8661 (OUTLIER) cc_final: 0.8363 (mttt) REVERT: C 248 LYS cc_start: 0.7691 (OUTLIER) cc_final: 0.7394 (tptt) REVERT: C 284 ARG cc_start: 0.8491 (OUTLIER) cc_final: 0.8022 (mtp85) REVERT: C 361 TYR cc_start: 0.8011 (OUTLIER) cc_final: 0.7767 (m-80) REVERT: D 61 ASP cc_start: 0.7894 (t0) cc_final: 0.7660 (t0) REVERT: D 266 GLU cc_start: 0.6588 (OUTLIER) cc_final: 0.6251 (pt0) REVERT: D 331 LYS cc_start: 0.7511 (ttmm) cc_final: 0.7227 (mtpt) REVERT: E 62 GLU cc_start: 0.8051 (OUTLIER) cc_final: 0.7690 (pm20) REVERT: E 94 GLU cc_start: 0.8861 (OUTLIER) cc_final: 0.7867 (tm-30) REVERT: E 191 ARG cc_start: 0.9015 (OUTLIER) cc_final: 0.7432 (ptp90) REVERT: F 2 LYS cc_start: 0.6458 (mttt) cc_final: 0.5910 (mttm) REVERT: G 330 ASN cc_start: 0.7696 (m-40) cc_final: 0.7407 (m110) REVERT: H 84 TRP cc_start: 0.7308 (OUTLIER) cc_final: 0.6693 (m100) REVERT: H 158 VAL cc_start: 0.8077 (t) cc_final: 0.7764 (t) REVERT: I 60 ILE cc_start: 0.7674 (OUTLIER) cc_final: 0.7387 (pt) REVERT: I 62 GLU cc_start: 0.7961 (OUTLIER) cc_final: 0.7618 (pm20) REVERT: I 87 LEU cc_start: 0.8649 (OUTLIER) cc_final: 0.8341 (mp) REVERT: I 122 LYS cc_start: 0.8146 (OUTLIER) cc_final: 0.7723 (tmtp) REVERT: J 323 ASP cc_start: 0.8086 (OUTLIER) cc_final: 0.7777 (m-30) REVERT: K 61 ASN cc_start: 0.7728 (OUTLIER) cc_final: 0.7312 (t0) REVERT: K 248 LYS cc_start: 0.7830 (OUTLIER) cc_final: 0.7390 (tttt) REVERT: K 261 LYS cc_start: 0.7790 (tttt) cc_final: 0.7391 (ttmm) REVERT: K 361 TYR cc_start: 0.8014 (OUTLIER) cc_final: 0.7805 (m-80) REVERT: L 266 GLU cc_start: 0.6518 (OUTLIER) cc_final: 0.6180 (pt0) outliers start: 159 outliers final: 73 residues processed: 783 average time/residue: 0.2440 time to fit residues: 318.9666 Evaluate side-chains 695 residues out of total 4664 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 95 poor density : 600 time to evaluate : 1.299 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain O residue 41 THR Chi-restraints excluded: chain O residue 164 GLU Chi-restraints excluded: chain O residue 281 VAL Chi-restraints excluded: chain O residue 361 TYR Chi-restraints excluded: chain P residue 84 TRP Chi-restraints excluded: chain P residue 161 LEU Chi-restraints excluded: chain P residue 171 THR Chi-restraints excluded: chain P residue 191 ARG Chi-restraints excluded: chain P residue 241 ASP Chi-restraints excluded: chain Q residue 65 SER Chi-restraints excluded: chain Q residue 84 TRP Chi-restraints excluded: chain Q residue 289 SER Chi-restraints excluded: chain Q residue 335 LEU Chi-restraints excluded: chain R residue 3 VAL Chi-restraints excluded: chain R residue 37 VAL Chi-restraints excluded: chain R residue 62 SER Chi-restraints excluded: chain R residue 84 TRP Chi-restraints excluded: chain R residue 103 ASP Chi-restraints excluded: chain R residue 129 VAL Chi-restraints excluded: chain R residue 161 LEU Chi-restraints excluded: chain R residue 172 MET Chi-restraints excluded: chain R residue 241 ASP Chi-restraints excluded: chain R residue 324 LEU Chi-restraints excluded: chain A residue 23 SER Chi-restraints excluded: chain A residue 28 VAL Chi-restraints excluded: chain A residue 62 GLU Chi-restraints excluded: chain A residue 84 TRP Chi-restraints excluded: chain A residue 87 LEU Chi-restraints excluded: chain A residue 122 LYS Chi-restraints excluded: chain A residue 201 LEU Chi-restraints excluded: chain A residue 295 SER Chi-restraints excluded: chain B residue 241 ASP Chi-restraints excluded: chain B residue 305 VAL Chi-restraints excluded: chain B residue 327 ILE Chi-restraints excluded: chain C residue 25 LEU Chi-restraints excluded: chain C residue 62 GLU Chi-restraints excluded: chain C residue 63 THR Chi-restraints excluded: chain C residue 81 LYS Chi-restraints excluded: chain C residue 84 TRP Chi-restraints excluded: chain C residue 246 ILE Chi-restraints excluded: chain C residue 248 LYS Chi-restraints excluded: chain C residue 284 ARG Chi-restraints excluded: chain C residue 361 TYR Chi-restraints excluded: chain D residue 226 ASN Chi-restraints excluded: chain D residue 241 ASP Chi-restraints excluded: chain D residue 266 GLU Chi-restraints excluded: chain D residue 281 ILE Chi-restraints excluded: chain E residue 28 VAL Chi-restraints excluded: chain E residue 62 GLU Chi-restraints excluded: chain E residue 94 GLU Chi-restraints excluded: chain E residue 191 ARG Chi-restraints excluded: chain E residue 201 LEU Chi-restraints excluded: chain F residue 37 VAL Chi-restraints excluded: chain F residue 75 SER Chi-restraints excluded: chain F residue 84 TRP Chi-restraints excluded: chain F residue 151 THR Chi-restraints excluded: chain F residue 161 LEU Chi-restraints excluded: chain F residue 171 THR Chi-restraints excluded: chain F residue 191 ARG Chi-restraints excluded: chain F residue 281 ILE Chi-restraints excluded: chain G residue 84 TRP Chi-restraints excluded: chain G residue 289 SER Chi-restraints excluded: chain H residue 84 TRP Chi-restraints excluded: chain H residue 103 ASP Chi-restraints excluded: chain H residue 129 VAL Chi-restraints excluded: chain H residue 218 LEU Chi-restraints excluded: chain H residue 241 ASP Chi-restraints excluded: chain H residue 295 SER Chi-restraints excluded: chain I residue 23 SER Chi-restraints excluded: chain I residue 28 VAL Chi-restraints excluded: chain I residue 60 ILE Chi-restraints excluded: chain I residue 62 GLU Chi-restraints excluded: chain I residue 73 VAL Chi-restraints excluded: chain I residue 84 TRP Chi-restraints excluded: chain I residue 87 LEU Chi-restraints excluded: chain I residue 122 LYS Chi-restraints excluded: chain I residue 295 SER Chi-restraints excluded: chain I residue 335 LEU Chi-restraints excluded: chain J residue 116 VAL Chi-restraints excluded: chain J residue 125 ILE Chi-restraints excluded: chain J residue 241 ASP Chi-restraints excluded: chain J residue 305 VAL Chi-restraints excluded: chain J residue 323 ASP Chi-restraints excluded: chain J residue 327 ILE Chi-restraints excluded: chain K residue 61 ASN Chi-restraints excluded: chain K residue 63 THR Chi-restraints excluded: chain K residue 65 SER Chi-restraints excluded: chain K residue 84 TRP Chi-restraints excluded: chain K residue 246 ILE Chi-restraints excluded: chain K residue 248 LYS Chi-restraints excluded: chain K residue 361 TYR Chi-restraints excluded: chain L residue 62 SER Chi-restraints excluded: chain L residue 241 ASP Chi-restraints excluded: chain L residue 266 GLU Chi-restraints excluded: chain L residue 295 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 552 random chunks: chunk 119 optimal weight: 0.9990 chunk 244 optimal weight: 4.9990 chunk 130 optimal weight: 9.9990 chunk 23 optimal weight: 1.9990 chunk 548 optimal weight: 3.9990 chunk 549 optimal weight: 6.9990 chunk 501 optimal weight: 5.9990 chunk 249 optimal weight: 10.0000 chunk 349 optimal weight: 0.9980 chunk 493 optimal weight: 1.9990 chunk 357 optimal weight: 0.7980 overall best weight: 1.3586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: O 176 HIS P 152 ASN P 226 ASN Q 202 ASN A 61 ASN A 152 ASN B 152 ASN C 245 ASN D 81 ASN E 146 ASN E 176 HIS ** E 245 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 220 ASN I 61 ASN I 245 ASN K 245 ASN L 81 ASN Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3393 r_free = 0.3393 target = 0.140371 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.2984 r_free = 0.2984 target = 0.107876 restraints weight = 47204.083| |-----------------------------------------------------------------------------| r_work (start): 0.2977 rms_B_bonded: 1.51 r_work: 0.2796 rms_B_bonded: 2.71 restraints_weight: 0.5000 r_work: 0.2675 rms_B_bonded: 4.49 restraints_weight: 0.2500 r_work (final): 0.2675 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8674 moved from start: 0.1304 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 43976 Z= 0.152 Angle : 0.545 8.742 59880 Z= 0.294 Chirality : 0.047 0.185 7080 Planarity : 0.004 0.042 7608 Dihedral : 8.943 89.465 6893 Min Nonbonded Distance : 2.493 Molprobity Statistics. All-atom Clashscore : 5.12 Ramachandran Plot: Outliers : 0.66 % Allowed : 5.39 % Favored : 93.96 % Rotamer: Outliers : 4.01 % Allowed : 16.49 % Favored : 79.50 % 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 (0.11), residues: 5608 helix: 0.73 (0.14), residues: 1556 sheet: -0.56 (0.15), residues: 1136 loop : -0.64 (0.12), residues: 2916 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG F 77 TYR 0.016 0.002 TYR C 178 PHE 0.019 0.002 PHE J 157 TRP 0.008 0.001 TRP I 310 HIS 0.004 0.001 HIS C 176 Details of bonding type rmsd covalent geometry : bond 0.00357 (43968) covalent geometry : angle 0.54452 (59864) SS BOND : bond 0.00616 ( 8) SS BOND : angle 1.22919 ( 16) hydrogen bonds : bond 0.03612 ( 1769) hydrogen bonds : angle 4.95639 ( 5445) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11216 Ramachandran restraints generated. 5608 Oldfield, 0 Emsley, 5608 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11216 Ramachandran restraints generated. 5608 Oldfield, 0 Emsley, 5608 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 831 residues out of total 4664 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 187 poor density : 644 time to evaluate : 1.647 Fit side-chains revert: symmetry clash REVERT: O 2 LYS cc_start: 0.8441 (mttm) cc_final: 0.8154 (mttp) REVERT: O 45 LYS cc_start: 0.8715 (tptt) cc_final: 0.8499 (tptt) REVERT: O 94 GLU cc_start: 0.8869 (OUTLIER) cc_final: 0.7801 (tm-30) REVERT: O 268 LYS cc_start: 0.8948 (OUTLIER) cc_final: 0.8337 (tttt) REVERT: P 90 ASP cc_start: 0.7018 (m-30) cc_final: 0.6688 (m-30) REVERT: R 115 LYS cc_start: 0.7794 (ttmt) cc_final: 0.7520 (ttmt) REVERT: R 158 VAL cc_start: 0.8065 (OUTLIER) cc_final: 0.7726 (t) REVERT: R 172 MET cc_start: 0.7462 (OUTLIER) cc_final: 0.7204 (tmt) REVERT: A 60 ILE cc_start: 0.7694 (OUTLIER) cc_final: 0.7407 (pt) REVERT: A 62 GLU cc_start: 0.8220 (OUTLIER) cc_final: 0.7974 (pm20) REVERT: A 87 LEU cc_start: 0.8621 (OUTLIER) cc_final: 0.8233 (mp) REVERT: A 122 LYS cc_start: 0.8212 (OUTLIER) cc_final: 0.7749 (tmtp) REVERT: B 90 ASP cc_start: 0.6815 (m-30) cc_final: 0.6607 (m-30) REVERT: C 248 LYS cc_start: 0.7686 (OUTLIER) cc_final: 0.7356 (tptt) REVERT: C 284 ARG cc_start: 0.8568 (OUTLIER) cc_final: 0.8124 (mtp85) REVERT: C 361 TYR cc_start: 0.8152 (OUTLIER) cc_final: 0.7868 (m-80) REVERT: D 61 ASP cc_start: 0.8066 (t0) cc_final: 0.7846 (t0) REVERT: D 87 MET cc_start: 0.7833 (mtm) cc_final: 0.7525 (mtp) REVERT: D 266 GLU cc_start: 0.6665 (OUTLIER) cc_final: 0.6335 (pt0) REVERT: D 331 LYS cc_start: 0.7364 (ttmm) cc_final: 0.7133 (mtpt) REVERT: E 62 GLU cc_start: 0.8246 (OUTLIER) cc_final: 0.7791 (pm20) REVERT: E 94 GLU cc_start: 0.8847 (OUTLIER) cc_final: 0.7834 (tm-30) REVERT: E 134 GLU cc_start: 0.8576 (OUTLIER) cc_final: 0.8335 (pt0) REVERT: E 191 ARG cc_start: 0.9079 (OUTLIER) cc_final: 0.8091 (ptp-170) REVERT: E 268 LYS cc_start: 0.8967 (OUTLIER) cc_final: 0.8351 (tttt) REVERT: F 2 LYS cc_start: 0.6466 (mttt) cc_final: 0.6154 (mttm) REVERT: G 165 LEU cc_start: 0.8493 (OUTLIER) cc_final: 0.8208 (tp) REVERT: G 319 GLN cc_start: 0.9136 (tp40) cc_final: 0.8670 (mm110) REVERT: G 362 GLU cc_start: 0.8091 (OUTLIER) cc_final: 0.7763 (tm-30) REVERT: H 84 TRP cc_start: 0.7362 (OUTLIER) cc_final: 0.6874 (m100) REVERT: H 158 VAL cc_start: 0.8019 (t) cc_final: 0.7715 (t) REVERT: H 172 MET cc_start: 0.7341 (OUTLIER) cc_final: 0.7127 (tmt) REVERT: I 60 ILE cc_start: 0.7623 (OUTLIER) cc_final: 0.7315 (pt) REVERT: I 62 GLU cc_start: 0.8077 (OUTLIER) cc_final: 0.7701 (pm20) REVERT: I 73 VAL cc_start: 0.9122 (OUTLIER) cc_final: 0.8889 (t) REVERT: I 122 LYS cc_start: 0.8126 (OUTLIER) cc_final: 0.7663 (tmtp) REVERT: J 300 MET cc_start: 0.7324 (mmm) cc_final: 0.7079 (mtp) REVERT: J 323 ASP cc_start: 0.8090 (OUTLIER) cc_final: 0.7763 (m-30) REVERT: K 261 LYS cc_start: 0.7862 (tttt) cc_final: 0.7431 (ttmm) REVERT: K 361 TYR cc_start: 0.8242 (OUTLIER) cc_final: 0.7949 (m-80) REVERT: L 169 LYS cc_start: 0.8479 (OUTLIER) cc_final: 0.8230 (ptmm) REVERT: L 266 GLU cc_start: 0.6589 (OUTLIER) cc_final: 0.6318 (pt0) outliers start: 187 outliers final: 103 residues processed: 766 average time/residue: 0.2543 time to fit residues: 324.6336 Evaluate side-chains 738 residues out of total 4664 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 132 poor density : 606 time to evaluate : 1.717 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain O residue 30 VAL Chi-restraints excluded: chain O residue 94 GLU Chi-restraints excluded: chain O residue 164 GLU Chi-restraints excluded: chain O residue 201 LEU Chi-restraints excluded: chain O residue 268 LYS Chi-restraints excluded: chain O residue 281 VAL Chi-restraints excluded: chain O residue 357 GLU Chi-restraints excluded: chain O residue 361 TYR Chi-restraints excluded: chain P residue 84 TRP Chi-restraints excluded: chain P residue 161 LEU Chi-restraints excluded: chain P residue 171 THR Chi-restraints excluded: chain P residue 172 MET Chi-restraints excluded: chain P residue 191 ARG Chi-restraints excluded: chain P residue 241 ASP Chi-restraints excluded: chain P residue 286 THR Chi-restraints excluded: chain P residue 290 SER Chi-restraints excluded: chain Q residue 30 VAL Chi-restraints excluded: chain Q residue 65 SER Chi-restraints excluded: chain Q residue 84 TRP Chi-restraints excluded: chain Q residue 202 ASN Chi-restraints excluded: chain Q residue 248 LYS Chi-restraints excluded: chain Q residue 289 SER Chi-restraints excluded: chain Q residue 335 LEU Chi-restraints excluded: chain Q residue 361 TYR Chi-restraints excluded: chain R residue 3 VAL Chi-restraints excluded: chain R residue 37 VAL Chi-restraints excluded: chain R residue 62 SER Chi-restraints excluded: chain R residue 84 TRP Chi-restraints excluded: chain R residue 129 VAL Chi-restraints excluded: chain R residue 158 VAL Chi-restraints excluded: chain R residue 161 LEU Chi-restraints excluded: chain R residue 172 MET Chi-restraints excluded: chain R residue 241 ASP Chi-restraints excluded: chain R residue 295 SER Chi-restraints excluded: chain R residue 324 LEU Chi-restraints excluded: chain A residue 23 SER Chi-restraints excluded: chain A residue 60 ILE Chi-restraints excluded: chain A residue 62 GLU Chi-restraints excluded: chain A residue 84 TRP Chi-restraints excluded: chain A residue 87 LEU Chi-restraints excluded: chain A residue 122 LYS Chi-restraints excluded: chain A residue 123 SER Chi-restraints excluded: chain A residue 201 LEU Chi-restraints excluded: chain A residue 261 LYS Chi-restraints excluded: chain A residue 295 SER Chi-restraints excluded: chain B residue 52 THR Chi-restraints excluded: chain B residue 80 VAL Chi-restraints excluded: chain B residue 172 MET Chi-restraints excluded: chain B residue 281 ILE Chi-restraints excluded: chain B residue 305 VAL Chi-restraints excluded: chain B residue 327 ILE Chi-restraints excluded: chain C residue 1 LEU Chi-restraints excluded: chain C residue 21 LYS Chi-restraints excluded: chain C residue 62 GLU Chi-restraints excluded: chain C residue 63 THR Chi-restraints excluded: chain C residue 84 TRP Chi-restraints excluded: chain C residue 245 ASN Chi-restraints excluded: chain C residue 246 ILE Chi-restraints excluded: chain C residue 248 LYS Chi-restraints excluded: chain C residue 284 ARG Chi-restraints excluded: chain C residue 361 TYR Chi-restraints excluded: chain D residue 54 ASP Chi-restraints excluded: chain D residue 164 LYS Chi-restraints excluded: chain D residue 241 ASP Chi-restraints excluded: chain D residue 266 GLU Chi-restraints excluded: chain D residue 281 ILE Chi-restraints excluded: chain D residue 295 SER Chi-restraints excluded: chain E residue 28 VAL Chi-restraints excluded: chain E residue 30 VAL Chi-restraints excluded: chain E residue 62 GLU Chi-restraints excluded: chain E residue 94 GLU Chi-restraints excluded: chain E residue 134 GLU Chi-restraints excluded: chain E residue 146 ASN Chi-restraints excluded: chain E residue 191 ARG Chi-restraints excluded: chain E residue 201 LEU Chi-restraints excluded: chain E residue 268 LYS Chi-restraints excluded: chain E residue 357 GLU Chi-restraints excluded: chain F residue 37 VAL Chi-restraints excluded: chain F residue 75 SER Chi-restraints excluded: chain F residue 84 TRP Chi-restraints excluded: chain F residue 151 THR Chi-restraints excluded: chain F residue 161 LEU Chi-restraints excluded: chain F residue 191 ARG Chi-restraints excluded: chain F residue 220 ASN Chi-restraints excluded: chain F residue 241 ASP Chi-restraints excluded: chain G residue 84 TRP Chi-restraints excluded: chain G residue 165 LEU Chi-restraints excluded: chain G residue 289 SER Chi-restraints excluded: chain G residue 362 GLU Chi-restraints excluded: chain H residue 84 TRP Chi-restraints excluded: chain H residue 87 MET Chi-restraints excluded: chain H residue 103 ASP Chi-restraints excluded: chain H residue 129 VAL Chi-restraints excluded: chain H residue 135 GLU Chi-restraints excluded: chain H residue 161 LEU Chi-restraints excluded: chain H residue 172 MET Chi-restraints excluded: chain H residue 218 LEU Chi-restraints excluded: chain H residue 241 ASP Chi-restraints excluded: chain H residue 295 SER Chi-restraints excluded: chain I residue 23 SER Chi-restraints excluded: chain I residue 37 VAL Chi-restraints excluded: chain I residue 52 THR Chi-restraints excluded: chain I residue 60 ILE Chi-restraints excluded: chain I residue 62 GLU Chi-restraints excluded: chain I residue 73 VAL Chi-restraints excluded: chain I residue 84 TRP Chi-restraints excluded: chain I residue 122 LYS Chi-restraints excluded: chain I residue 261 LYS Chi-restraints excluded: chain I residue 295 SER Chi-restraints excluded: chain I residue 335 LEU Chi-restraints excluded: chain J residue 37 VAL Chi-restraints excluded: chain J residue 80 VAL Chi-restraints excluded: chain J residue 116 VAL Chi-restraints excluded: chain J residue 125 ILE Chi-restraints excluded: chain J residue 145 SER Chi-restraints excluded: chain J residue 281 ILE Chi-restraints excluded: chain J residue 305 VAL Chi-restraints excluded: chain J residue 323 ASP Chi-restraints excluded: chain J residue 327 ILE Chi-restraints excluded: chain K residue 1 LEU Chi-restraints excluded: chain K residue 63 THR Chi-restraints excluded: chain K residue 65 SER Chi-restraints excluded: chain K residue 84 TRP Chi-restraints excluded: chain K residue 246 ILE Chi-restraints excluded: chain K residue 250 VAL Chi-restraints excluded: chain K residue 361 TYR Chi-restraints excluded: chain L residue 54 ASP Chi-restraints excluded: chain L residue 169 LYS Chi-restraints excluded: chain L residue 241 ASP Chi-restraints excluded: chain L residue 266 GLU Chi-restraints excluded: chain L residue 281 ILE Chi-restraints excluded: chain L residue 295 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 552 random chunks: chunk 15 optimal weight: 4.9990 chunk 307 optimal weight: 0.7980 chunk 418 optimal weight: 7.9990 chunk 441 optimal weight: 1.9990 chunk 44 optimal weight: 0.7980 chunk 487 optimal weight: 0.9980 chunk 335 optimal weight: 0.9980 chunk 281 optimal weight: 2.9990 chunk 505 optimal weight: 2.9990 chunk 74 optimal weight: 6.9990 chunk 133 optimal weight: 2.9990 overall best weight: 1.1182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: P 220 ASN Q 202 ASN B 220 ASN C 245 ASN E 146 ASN ** E 245 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 220 ASN ** G 139 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 330 ASN I 152 ASN J 220 ASN L 81 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3403 r_free = 0.3403 target = 0.141209 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2993 r_free = 0.2993 target = 0.108553 restraints weight = 47174.886| |-----------------------------------------------------------------------------| r_work (start): 0.2985 rms_B_bonded: 1.56 r_work: 0.2801 rms_B_bonded: 2.80 restraints_weight: 0.5000 r_work: 0.2679 rms_B_bonded: 4.65 restraints_weight: 0.2500 r_work (final): 0.2679 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8667 moved from start: 0.1484 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 43976 Z= 0.134 Angle : 0.521 8.555 59880 Z= 0.281 Chirality : 0.046 0.195 7080 Planarity : 0.004 0.041 7608 Dihedral : 8.762 88.701 6892 Min Nonbonded Distance : 2.435 Molprobity Statistics. All-atom Clashscore : 5.38 Ramachandran Plot: Outliers : 0.66 % Allowed : 5.21 % Favored : 94.13 % Rotamer: Outliers : 3.90 % Allowed : 16.87 % Favored : 79.22 % 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: -0.35 (0.11), residues: 5608 helix: 0.85 (0.14), residues: 1556 sheet: -0.58 (0.15), residues: 1132 loop : -0.62 (0.12), residues: 2920 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG F 77 TYR 0.015 0.002 TYR C 178 PHE 0.019 0.002 PHE J 157 TRP 0.007 0.001 TRP L 332 HIS 0.004 0.001 HIS K 176 Details of bonding type rmsd covalent geometry : bond 0.00314 (43968) covalent geometry : angle 0.52114 (59864) SS BOND : bond 0.00588 ( 8) SS BOND : angle 1.26462 ( 16) hydrogen bonds : bond 0.03309 ( 1769) hydrogen bonds : angle 4.80871 ( 5445) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11216 Ramachandran restraints generated. 5608 Oldfield, 0 Emsley, 5608 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11216 Ramachandran restraints generated. 5608 Oldfield, 0 Emsley, 5608 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 812 residues out of total 4664 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 182 poor density : 630 time to evaluate : 1.635 Fit side-chains revert: symmetry clash REVERT: O 2 LYS cc_start: 0.8459 (mttm) cc_final: 0.8226 (mttp) REVERT: O 94 GLU cc_start: 0.8857 (OUTLIER) cc_final: 0.7783 (tm-30) REVERT: O 191 ARG cc_start: 0.9040 (OUTLIER) cc_final: 0.8672 (ptt180) REVERT: O 268 LYS cc_start: 0.8973 (OUTLIER) cc_final: 0.8349 (tttt) REVERT: P 90 ASP cc_start: 0.7073 (m-30) cc_final: 0.6717 (m-30) REVERT: Q 47 ASP cc_start: 0.8910 (t0) cc_final: 0.8686 (t0) REVERT: Q 319 GLN cc_start: 0.9122 (tp40) cc_final: 0.8674 (mm110) REVERT: R 115 LYS cc_start: 0.7767 (ttmt) cc_final: 0.7473 (ttmt) REVERT: R 158 VAL cc_start: 0.8070 (OUTLIER) cc_final: 0.7735 (t) REVERT: R 172 MET cc_start: 0.7444 (OUTLIER) cc_final: 0.7211 (tmt) REVERT: A 60 ILE cc_start: 0.7650 (OUTLIER) cc_final: 0.7366 (pt) REVERT: A 87 LEU cc_start: 0.8617 (OUTLIER) cc_final: 0.8225 (mp) REVERT: A 122 LYS cc_start: 0.8193 (OUTLIER) cc_final: 0.7718 (tmtp) REVERT: B 265 ASN cc_start: 0.7265 (m-40) cc_final: 0.7024 (m-40) REVERT: C 248 LYS cc_start: 0.7616 (OUTLIER) cc_final: 0.7286 (tptt) REVERT: C 284 ARG cc_start: 0.8553 (OUTLIER) cc_final: 0.8069 (mtp85) REVERT: C 361 TYR cc_start: 0.8177 (OUTLIER) cc_final: 0.7882 (m-80) REVERT: D 61 ASP cc_start: 0.8049 (t0) cc_final: 0.7829 (t0) REVERT: D 87 MET cc_start: 0.7820 (mtm) cc_final: 0.7485 (mtp) REVERT: D 266 GLU cc_start: 0.6662 (OUTLIER) cc_final: 0.6331 (pt0) REVERT: E 62 GLU cc_start: 0.8288 (OUTLIER) cc_final: 0.7937 (pm20) REVERT: E 94 GLU cc_start: 0.8838 (OUTLIER) cc_final: 0.7825 (tm-30) REVERT: E 134 GLU cc_start: 0.8572 (OUTLIER) cc_final: 0.8337 (pt0) REVERT: E 268 LYS cc_start: 0.8951 (OUTLIER) cc_final: 0.8349 (tttt) REVERT: F 2 LYS cc_start: 0.6388 (mttt) cc_final: 0.6069 (mttm) REVERT: F 300 MET cc_start: 0.6186 (tpp) cc_final: 0.5813 (ttm) REVERT: F 304 MET cc_start: 0.6712 (mtm) cc_final: 0.6327 (mtp) REVERT: G 165 LEU cc_start: 0.8489 (OUTLIER) cc_final: 0.8176 (tp) REVERT: G 319 GLN cc_start: 0.9121 (tp40) cc_final: 0.8691 (mm110) REVERT: G 362 GLU cc_start: 0.8084 (OUTLIER) cc_final: 0.7743 (tm-30) REVERT: H 84 TRP cc_start: 0.7356 (OUTLIER) cc_final: 0.6657 (m100) REVERT: H 169 LYS cc_start: 0.7280 (ptpp) cc_final: 0.6947 (pttm) REVERT: H 172 MET cc_start: 0.7449 (OUTLIER) cc_final: 0.7176 (tmt) REVERT: I 60 ILE cc_start: 0.7562 (OUTLIER) cc_final: 0.7318 (pt) REVERT: I 62 GLU cc_start: 0.8069 (OUTLIER) cc_final: 0.7745 (pm20) REVERT: I 73 VAL cc_start: 0.9111 (OUTLIER) cc_final: 0.8897 (t) REVERT: I 87 LEU cc_start: 0.8625 (OUTLIER) cc_final: 0.8319 (mp) REVERT: I 122 LYS cc_start: 0.8098 (OUTLIER) cc_final: 0.7637 (tmtp) REVERT: I 350 LYS cc_start: 0.8028 (mppt) cc_final: 0.7555 (mmmm) REVERT: J 56 ASP cc_start: 0.8108 (OUTLIER) cc_final: 0.7753 (t70) REVERT: J 61 ASP cc_start: 0.8599 (t0) cc_final: 0.8372 (t0) REVERT: J 300 MET cc_start: 0.7320 (mmm) cc_final: 0.7086 (mtp) REVERT: J 323 ASP cc_start: 0.8107 (OUTLIER) cc_final: 0.7742 (m-30) REVERT: K 248 LYS cc_start: 0.7765 (OUTLIER) cc_final: 0.7250 (tttt) REVERT: K 261 LYS cc_start: 0.7848 (tttt) cc_final: 0.7588 (ttmm) REVERT: K 361 TYR cc_start: 0.8275 (OUTLIER) cc_final: 0.7947 (m-80) REVERT: L 61 ASP cc_start: 0.7956 (t0) cc_final: 0.7675 (t0) REVERT: L 169 LYS cc_start: 0.8443 (OUTLIER) cc_final: 0.8187 (ptmm) REVERT: L 266 GLU cc_start: 0.6623 (OUTLIER) cc_final: 0.6318 (pt0) outliers start: 182 outliers final: 109 residues processed: 744 average time/residue: 0.2469 time to fit residues: 306.1861 Evaluate side-chains 738 residues out of total 4664 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 140 poor density : 598 time to evaluate : 1.456 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain O residue 30 VAL Chi-restraints excluded: chain O residue 94 GLU Chi-restraints excluded: chain O residue 191 ARG Chi-restraints excluded: chain O residue 201 LEU Chi-restraints excluded: chain O residue 268 LYS Chi-restraints excluded: chain O residue 281 VAL Chi-restraints excluded: chain O residue 289 SER Chi-restraints excluded: chain O residue 357 GLU Chi-restraints excluded: chain O residue 361 TYR Chi-restraints excluded: chain P residue 33 THR Chi-restraints excluded: chain P residue 84 TRP Chi-restraints excluded: chain P residue 154 LEU Chi-restraints excluded: chain P residue 161 LEU Chi-restraints excluded: chain P residue 171 THR Chi-restraints excluded: chain P residue 191 ARG Chi-restraints excluded: chain P residue 220 ASN Chi-restraints excluded: chain P residue 290 SER Chi-restraints excluded: chain P residue 292 ILE Chi-restraints excluded: chain P residue 298 MET Chi-restraints excluded: chain Q residue 30 VAL Chi-restraints excluded: chain Q residue 65 SER Chi-restraints excluded: chain Q residue 84 TRP Chi-restraints excluded: chain Q residue 165 LEU Chi-restraints excluded: chain Q residue 202 ASN Chi-restraints excluded: chain Q residue 248 LYS Chi-restraints excluded: chain Q residue 289 SER Chi-restraints excluded: chain Q residue 335 LEU Chi-restraints excluded: chain Q residue 361 TYR Chi-restraints excluded: chain R residue 3 VAL Chi-restraints excluded: chain R residue 37 VAL Chi-restraints excluded: chain R residue 62 SER Chi-restraints excluded: chain R residue 84 TRP Chi-restraints excluded: chain R residue 129 VAL Chi-restraints excluded: chain R residue 158 VAL Chi-restraints excluded: chain R residue 161 LEU Chi-restraints excluded: chain R residue 172 MET Chi-restraints excluded: chain R residue 241 ASP Chi-restraints excluded: chain R residue 324 LEU Chi-restraints excluded: chain A residue 23 SER Chi-restraints excluded: chain A residue 60 ILE Chi-restraints excluded: chain A residue 84 TRP Chi-restraints excluded: chain A residue 87 LEU Chi-restraints excluded: chain A residue 122 LYS Chi-restraints excluded: chain A residue 123 SER Chi-restraints excluded: chain A residue 201 LEU Chi-restraints excluded: chain A residue 261 LYS Chi-restraints excluded: chain A residue 295 SER Chi-restraints excluded: chain B residue 52 THR Chi-restraints excluded: chain B residue 80 VAL Chi-restraints excluded: chain B residue 172 MET Chi-restraints excluded: chain B residue 281 ILE Chi-restraints excluded: chain B residue 305 VAL Chi-restraints excluded: chain B residue 327 ILE Chi-restraints excluded: chain C residue 1 LEU Chi-restraints excluded: chain C residue 62 GLU Chi-restraints excluded: chain C residue 63 THR Chi-restraints excluded: chain C residue 65 SER Chi-restraints excluded: chain C residue 84 TRP Chi-restraints excluded: chain C residue 246 ILE Chi-restraints excluded: chain C residue 248 LYS Chi-restraints excluded: chain C residue 284 ARG Chi-restraints excluded: chain C residue 361 TYR Chi-restraints excluded: chain D residue 54 ASP Chi-restraints excluded: chain D residue 164 LYS Chi-restraints excluded: chain D residue 226 ASN Chi-restraints excluded: chain D residue 241 ASP Chi-restraints excluded: chain D residue 266 GLU Chi-restraints excluded: chain D residue 281 ILE Chi-restraints excluded: chain D residue 295 SER Chi-restraints excluded: chain E residue 22 ASP Chi-restraints excluded: chain E residue 28 VAL Chi-restraints excluded: chain E residue 30 VAL Chi-restraints excluded: chain E residue 62 GLU Chi-restraints excluded: chain E residue 94 GLU Chi-restraints excluded: chain E residue 134 GLU Chi-restraints excluded: chain E residue 191 ARG Chi-restraints excluded: chain E residue 201 LEU Chi-restraints excluded: chain E residue 268 LYS Chi-restraints excluded: chain E residue 357 GLU Chi-restraints excluded: chain F residue 37 VAL Chi-restraints excluded: chain F residue 75 SER Chi-restraints excluded: chain F residue 84 TRP Chi-restraints excluded: chain F residue 151 THR Chi-restraints excluded: chain F residue 161 LEU Chi-restraints excluded: chain F residue 174 THR Chi-restraints excluded: chain F residue 191 ARG Chi-restraints excluded: chain G residue 30 VAL Chi-restraints excluded: chain G residue 84 TRP Chi-restraints excluded: chain G residue 165 LEU Chi-restraints excluded: chain G residue 289 SER Chi-restraints excluded: chain G residue 362 GLU Chi-restraints excluded: chain H residue 25 LEU Chi-restraints excluded: chain H residue 62 SER Chi-restraints excluded: chain H residue 84 TRP Chi-restraints excluded: chain H residue 87 MET Chi-restraints excluded: chain H residue 103 ASP Chi-restraints excluded: chain H residue 129 VAL Chi-restraints excluded: chain H residue 135 GLU Chi-restraints excluded: chain H residue 161 LEU Chi-restraints excluded: chain H residue 172 MET Chi-restraints excluded: chain H residue 218 LEU Chi-restraints excluded: chain H residue 241 ASP Chi-restraints excluded: chain H residue 295 SER Chi-restraints excluded: chain H residue 300 MET Chi-restraints excluded: chain I residue 1 LEU Chi-restraints excluded: chain I residue 23 SER Chi-restraints excluded: chain I residue 28 VAL Chi-restraints excluded: chain I residue 37 VAL Chi-restraints excluded: chain I residue 60 ILE Chi-restraints excluded: chain I residue 62 GLU Chi-restraints excluded: chain I residue 73 VAL Chi-restraints excluded: chain I residue 84 TRP Chi-restraints excluded: chain I residue 87 LEU Chi-restraints excluded: chain I residue 122 LYS Chi-restraints excluded: chain I residue 261 LYS Chi-restraints excluded: chain I residue 295 SER Chi-restraints excluded: chain I residue 335 LEU Chi-restraints excluded: chain J residue 56 ASP Chi-restraints excluded: chain J residue 98 VAL Chi-restraints excluded: chain J residue 116 VAL Chi-restraints excluded: chain J residue 125 ILE Chi-restraints excluded: chain J residue 145 SER Chi-restraints excluded: chain J residue 281 ILE Chi-restraints excluded: chain J residue 305 VAL Chi-restraints excluded: chain J residue 323 ASP Chi-restraints excluded: chain J residue 327 ILE Chi-restraints excluded: chain K residue 1 LEU Chi-restraints excluded: chain K residue 63 THR Chi-restraints excluded: chain K residue 65 SER Chi-restraints excluded: chain K residue 84 TRP Chi-restraints excluded: chain K residue 246 ILE Chi-restraints excluded: chain K residue 248 LYS Chi-restraints excluded: chain K residue 250 VAL Chi-restraints excluded: chain K residue 292 ILE Chi-restraints excluded: chain K residue 361 TYR Chi-restraints excluded: chain L residue 54 ASP Chi-restraints excluded: chain L residue 169 LYS Chi-restraints excluded: chain L residue 241 ASP Chi-restraints excluded: chain L residue 266 GLU Chi-restraints excluded: chain L residue 281 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 552 random chunks: chunk 507 optimal weight: 4.9990 chunk 270 optimal weight: 3.9990 chunk 107 optimal weight: 5.9990 chunk 127 optimal weight: 10.0000 chunk 540 optimal weight: 0.9980 chunk 83 optimal weight: 4.9990 chunk 191 optimal weight: 1.9990 chunk 448 optimal weight: 20.0000 chunk 419 optimal weight: 0.0770 chunk 543 optimal weight: 8.9990 chunk 198 optimal weight: 2.9990 overall best weight: 2.0144 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: O 61 ASN ** O 245 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P 220 ASN P 333 GLN Q 202 ASN A 152 ASN B 220 ASN B 333 GLN C 245 ASN D 81 ASN E 146 ASN ** E 245 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 313 ASN ** G 139 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 152 ASN J 18BHIS J 220 ASN L 81 ASN Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3379 r_free = 0.3379 target = 0.139191 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2966 r_free = 0.2966 target = 0.106565 restraints weight = 47118.559| |-----------------------------------------------------------------------------| r_work (start): 0.2955 rms_B_bonded: 1.52 r_work: 0.2774 rms_B_bonded: 2.69 restraints_weight: 0.5000 r_work: 0.2651 rms_B_bonded: 4.52 restraints_weight: 0.2500 r_work (final): 0.2651 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8696 moved from start: 0.1446 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.038 43976 Z= 0.191 Angle : 0.562 8.559 59880 Z= 0.301 Chirality : 0.048 0.210 7080 Planarity : 0.005 0.043 7608 Dihedral : 9.054 87.427 6891 Min Nonbonded Distance : 2.407 Molprobity Statistics. All-atom Clashscore : 5.49 Ramachandran Plot: Outliers : 0.66 % Allowed : 5.72 % Favored : 93.62 % Rotamer: Outliers : 4.14 % Allowed : 16.98 % Favored : 78.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.40 (0.11), residues: 5608 helix: 0.75 (0.13), residues: 1572 sheet: -0.52 (0.15), residues: 1120 loop : -0.66 (0.12), residues: 2916 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG F 77 TYR 0.020 0.003 TYR C 178 PHE 0.022 0.002 PHE J 157 TRP 0.008 0.001 TRP I 310 HIS 0.005 0.001 HIS R 176 Details of bonding type rmsd covalent geometry : bond 0.00451 (43968) covalent geometry : angle 0.56151 (59864) SS BOND : bond 0.00621 ( 8) SS BOND : angle 1.20517 ( 16) hydrogen bonds : bond 0.03650 ( 1769) hydrogen bonds : angle 4.86564 ( 5445) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11216 Ramachandran restraints generated. 5608 Oldfield, 0 Emsley, 5608 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11216 Ramachandran restraints generated. 5608 Oldfield, 0 Emsley, 5608 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 821 residues out of total 4664 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 193 poor density : 628 time to evaluate : 1.726 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: O 2 LYS cc_start: 0.8495 (mttm) cc_final: 0.8208 (mttp) REVERT: O 94 GLU cc_start: 0.8903 (OUTLIER) cc_final: 0.7823 (tm-30) REVERT: O 191 ARG cc_start: 0.9056 (OUTLIER) cc_final: 0.8716 (ptt180) REVERT: O 268 LYS cc_start: 0.8966 (OUTLIER) cc_final: 0.8335 (tttt) REVERT: R 158 VAL cc_start: 0.8116 (OUTLIER) cc_final: 0.7762 (t) REVERT: R 172 MET cc_start: 0.7477 (OUTLIER) cc_final: 0.7225 (tmt) REVERT: A 60 ILE cc_start: 0.7636 (OUTLIER) cc_final: 0.7335 (pt) REVERT: A 87 LEU cc_start: 0.8630 (OUTLIER) cc_final: 0.8280 (mp) REVERT: A 122 LYS cc_start: 0.8222 (OUTLIER) cc_final: 0.7742 (tmtp) REVERT: A 350 LYS cc_start: 0.8041 (mppt) cc_final: 0.7553 (mmmm) REVERT: B 90 ASP cc_start: 0.6931 (m-30) cc_final: 0.6719 (m-30) REVERT: B 126 PRO cc_start: 0.8241 (Cg_exo) cc_final: 0.7959 (Cg_endo) REVERT: B 265 ASN cc_start: 0.7264 (m-40) cc_final: 0.7001 (m-40) REVERT: C 134 GLU cc_start: 0.8258 (pm20) cc_final: 0.8026 (pm20) REVERT: C 284 ARG cc_start: 0.8593 (OUTLIER) cc_final: 0.8243 (mtp85) REVERT: C 361 TYR cc_start: 0.8173 (OUTLIER) cc_final: 0.7864 (m-80) REVERT: D 61 ASP cc_start: 0.8046 (t0) cc_final: 0.7831 (t0) REVERT: D 87 MET cc_start: 0.7852 (mtm) cc_final: 0.7543 (mtp) REVERT: D 191 ARG cc_start: 0.7884 (ttp-110) cc_final: 0.7680 (ttp80) REVERT: D 266 GLU cc_start: 0.6674 (OUTLIER) cc_final: 0.6414 (pt0) REVERT: E 62 GLU cc_start: 0.8332 (pt0) cc_final: 0.7941 (pm20) REVERT: E 94 GLU cc_start: 0.8894 (OUTLIER) cc_final: 0.7818 (tm-30) REVERT: E 191 ARG cc_start: 0.9131 (OUTLIER) cc_final: 0.7555 (ptp90) REVERT: E 245 ASN cc_start: 0.8108 (p0) cc_final: 0.7908 (p0) REVERT: E 268 LYS cc_start: 0.8920 (OUTLIER) cc_final: 0.8335 (tttt) REVERT: F 2 LYS cc_start: 0.6309 (mttt) cc_final: 0.5721 (mttm) REVERT: G 165 LEU cc_start: 0.8521 (OUTLIER) cc_final: 0.8226 (tp) REVERT: G 362 GLU cc_start: 0.8182 (OUTLIER) cc_final: 0.7872 (tm-30) REVERT: H 84 TRP cc_start: 0.7374 (OUTLIER) cc_final: 0.6859 (m100) REVERT: H 172 MET cc_start: 0.7370 (OUTLIER) cc_final: 0.7124 (tmt) REVERT: I 60 ILE cc_start: 0.7598 (OUTLIER) cc_final: 0.7314 (pt) REVERT: I 62 GLU cc_start: 0.8113 (OUTLIER) cc_final: 0.7823 (pm20) REVERT: I 73 VAL cc_start: 0.9157 (OUTLIER) cc_final: 0.8950 (t) REVERT: I 87 LEU cc_start: 0.8654 (OUTLIER) cc_final: 0.8342 (mp) REVERT: I 122 LYS cc_start: 0.8137 (OUTLIER) cc_final: 0.7681 (tmtp) REVERT: I 191 ARG cc_start: 0.8952 (OUTLIER) cc_final: 0.8472 (mtp180) REVERT: J 56 ASP cc_start: 0.8119 (OUTLIER) cc_final: 0.7751 (t70) REVERT: J 61 ASP cc_start: 0.8650 (t0) cc_final: 0.8405 (t0) REVERT: J 77 ARG cc_start: 0.7700 (mmm160) cc_final: 0.7468 (mmm160) REVERT: J 300 MET cc_start: 0.7338 (mmm) cc_final: 0.7075 (mtp) REVERT: J 323 ASP cc_start: 0.8120 (OUTLIER) cc_final: 0.7801 (m-30) REVERT: K 134 GLU cc_start: 0.8251 (pm20) cc_final: 0.8031 (pm20) REVERT: K 164 GLU cc_start: 0.7768 (OUTLIER) cc_final: 0.7317 (mt-10) REVERT: K 248 LYS cc_start: 0.7799 (OUTLIER) cc_final: 0.7283 (tttt) REVERT: K 261 LYS cc_start: 0.7921 (tttt) cc_final: 0.7492 (ttmm) REVERT: K 361 TYR cc_start: 0.8228 (OUTLIER) cc_final: 0.7903 (m-80) REVERT: L 61 ASP cc_start: 0.7905 (t0) cc_final: 0.7643 (t0) REVERT: L 169 LYS cc_start: 0.8488 (OUTLIER) cc_final: 0.8233 (ptmm) REVERT: L 191 ARG cc_start: 0.7918 (ttp-110) cc_final: 0.7547 (ttp80) outliers start: 193 outliers final: 125 residues processed: 751 average time/residue: 0.2599 time to fit residues: 325.4537 Evaluate side-chains 749 residues out of total 4664 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 155 poor density : 594 time to evaluate : 1.618 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain O residue 30 VAL Chi-restraints excluded: chain O residue 94 GLU Chi-restraints excluded: chain O residue 146 ASN Chi-restraints excluded: chain O residue 191 ARG Chi-restraints excluded: chain O residue 201 LEU Chi-restraints excluded: chain O residue 268 LYS Chi-restraints excluded: chain O residue 281 VAL Chi-restraints excluded: chain O residue 289 SER Chi-restraints excluded: chain O residue 357 GLU Chi-restraints excluded: chain O residue 361 TYR Chi-restraints excluded: chain P residue 33 THR Chi-restraints excluded: chain P residue 84 TRP Chi-restraints excluded: chain P residue 154 LEU Chi-restraints excluded: chain P residue 161 LEU Chi-restraints excluded: chain P residue 171 THR Chi-restraints excluded: chain P residue 191 ARG Chi-restraints excluded: chain P residue 241 ASP Chi-restraints excluded: chain P residue 286 THR Chi-restraints excluded: chain P residue 290 SER Chi-restraints excluded: chain P residue 292 ILE Chi-restraints excluded: chain Q residue 1 LEU Chi-restraints excluded: chain Q residue 30 VAL Chi-restraints excluded: chain Q residue 65 SER Chi-restraints excluded: chain Q residue 84 TRP Chi-restraints excluded: chain Q residue 202 ASN Chi-restraints excluded: chain Q residue 248 LYS Chi-restraints excluded: chain Q residue 289 SER Chi-restraints excluded: chain Q residue 335 LEU Chi-restraints excluded: chain Q residue 361 TYR Chi-restraints excluded: chain R residue 3 VAL Chi-restraints excluded: chain R residue 37 VAL Chi-restraints excluded: chain R residue 62 SER Chi-restraints excluded: chain R residue 84 TRP Chi-restraints excluded: chain R residue 129 VAL Chi-restraints excluded: chain R residue 158 VAL Chi-restraints excluded: chain R residue 161 LEU Chi-restraints excluded: chain R residue 172 MET Chi-restraints excluded: chain R residue 241 ASP Chi-restraints excluded: chain R residue 244 VAL Chi-restraints excluded: chain R residue 281 ILE Chi-restraints excluded: chain R residue 295 SER Chi-restraints excluded: chain R residue 324 LEU Chi-restraints excluded: chain A residue 23 SER Chi-restraints excluded: chain A residue 52 THR Chi-restraints excluded: chain A residue 60 ILE Chi-restraints excluded: chain A residue 84 TRP Chi-restraints excluded: chain A residue 87 LEU Chi-restraints excluded: chain A residue 122 LYS Chi-restraints excluded: chain A residue 123 SER Chi-restraints excluded: chain A residue 201 LEU Chi-restraints excluded: chain A residue 208 THR Chi-restraints excluded: chain A residue 261 LYS Chi-restraints excluded: chain A residue 295 SER Chi-restraints excluded: chain B residue 52 THR Chi-restraints excluded: chain B residue 75 SER Chi-restraints excluded: chain B residue 80 VAL Chi-restraints excluded: chain B residue 98 VAL Chi-restraints excluded: chain B residue 172 MET Chi-restraints excluded: chain B residue 281 ILE Chi-restraints excluded: chain B residue 305 VAL Chi-restraints excluded: chain B residue 327 ILE Chi-restraints excluded: chain C residue 1 LEU Chi-restraints excluded: chain C residue 62 GLU Chi-restraints excluded: chain C residue 65 SER Chi-restraints excluded: chain C residue 84 TRP Chi-restraints excluded: chain C residue 246 ILE Chi-restraints excluded: chain C residue 284 ARG Chi-restraints excluded: chain C residue 361 TYR Chi-restraints excluded: chain D residue 54 ASP Chi-restraints excluded: chain D residue 127 THR Chi-restraints excluded: chain D residue 164 LYS Chi-restraints excluded: chain D residue 241 ASP Chi-restraints excluded: chain D residue 266 GLU Chi-restraints excluded: chain D residue 281 ILE Chi-restraints excluded: chain D residue 295 SER Chi-restraints excluded: chain E residue 22 ASP Chi-restraints excluded: chain E residue 28 VAL Chi-restraints excluded: chain E residue 30 VAL Chi-restraints excluded: chain E residue 94 GLU Chi-restraints excluded: chain E residue 146 ASN Chi-restraints excluded: chain E residue 191 ARG Chi-restraints excluded: chain E residue 201 LEU Chi-restraints excluded: chain E residue 268 LYS Chi-restraints excluded: chain F residue 3 VAL Chi-restraints excluded: chain F residue 37 VAL Chi-restraints excluded: chain F residue 75 SER Chi-restraints excluded: chain F residue 84 TRP Chi-restraints excluded: chain F residue 151 THR Chi-restraints excluded: chain F residue 161 LEU Chi-restraints excluded: chain F residue 174 THR Chi-restraints excluded: chain F residue 191 ARG Chi-restraints excluded: chain F residue 241 ASP Chi-restraints excluded: chain G residue 30 VAL Chi-restraints excluded: chain G residue 84 TRP Chi-restraints excluded: chain G residue 165 LEU Chi-restraints excluded: chain G residue 289 SER Chi-restraints excluded: chain G residue 339 VAL Chi-restraints excluded: chain G residue 362 GLU Chi-restraints excluded: chain H residue 25 LEU Chi-restraints excluded: chain H residue 62 SER Chi-restraints excluded: chain H residue 74 VAL Chi-restraints excluded: chain H residue 84 TRP Chi-restraints excluded: chain H residue 103 ASP Chi-restraints excluded: chain H residue 129 VAL Chi-restraints excluded: chain H residue 135 GLU Chi-restraints excluded: chain H residue 161 LEU Chi-restraints excluded: chain H residue 172 MET Chi-restraints excluded: chain H residue 218 LEU Chi-restraints excluded: chain H residue 241 ASP Chi-restraints excluded: chain H residue 295 SER Chi-restraints excluded: chain H residue 300 MET Chi-restraints excluded: chain I residue 23 SER Chi-restraints excluded: chain I residue 28 VAL Chi-restraints excluded: chain I residue 37 VAL Chi-restraints excluded: chain I residue 52 THR Chi-restraints excluded: chain I residue 60 ILE Chi-restraints excluded: chain I residue 62 GLU Chi-restraints excluded: chain I residue 73 VAL Chi-restraints excluded: chain I residue 84 TRP Chi-restraints excluded: chain I residue 87 LEU Chi-restraints excluded: chain I residue 122 LYS Chi-restraints excluded: chain I residue 191 ARG Chi-restraints excluded: chain I residue 201 LEU Chi-restraints excluded: chain I residue 261 LYS Chi-restraints excluded: chain I residue 268 LYS Chi-restraints excluded: chain I residue 295 SER Chi-restraints excluded: chain I residue 335 LEU Chi-restraints excluded: chain J residue 37 VAL Chi-restraints excluded: chain J residue 56 ASP Chi-restraints excluded: chain J residue 80 VAL Chi-restraints excluded: chain J residue 98 VAL Chi-restraints excluded: chain J residue 116 VAL Chi-restraints excluded: chain J residue 125 ILE Chi-restraints excluded: chain J residue 145 SER Chi-restraints excluded: chain J residue 241 ASP Chi-restraints excluded: chain J residue 281 ILE Chi-restraints excluded: chain J residue 305 VAL Chi-restraints excluded: chain J residue 323 ASP Chi-restraints excluded: chain J residue 327 ILE Chi-restraints excluded: chain K residue 1 LEU Chi-restraints excluded: chain K residue 30 VAL Chi-restraints excluded: chain K residue 65 SER Chi-restraints excluded: chain K residue 84 TRP Chi-restraints excluded: chain K residue 164 GLU Chi-restraints excluded: chain K residue 201 LEU Chi-restraints excluded: chain K residue 246 ILE Chi-restraints excluded: chain K residue 248 LYS Chi-restraints excluded: chain K residue 250 VAL Chi-restraints excluded: chain K residue 361 TYR Chi-restraints excluded: chain L residue 54 ASP Chi-restraints excluded: chain L residue 138 THR Chi-restraints excluded: chain L residue 161 LEU Chi-restraints excluded: chain L residue 169 LYS Chi-restraints excluded: chain L residue 241 ASP Chi-restraints excluded: chain L residue 281 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 552 random chunks: chunk 53 optimal weight: 8.9990 chunk 405 optimal weight: 7.9990 chunk 505 optimal weight: 6.9990 chunk 32 optimal weight: 2.9990 chunk 52 optimal weight: 0.5980 chunk 272 optimal weight: 6.9990 chunk 501 optimal weight: 0.7980 chunk 112 optimal weight: 0.3980 chunk 205 optimal weight: 4.9990 chunk 371 optimal weight: 2.9990 chunk 482 optimal weight: 0.7980 overall best weight: 1.1182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: O 61 ASN ** O 245 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 202 ASN B 220 ASN E 146 ASN ** G 139 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 319 GLN J 220 ASN L 81 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3401 r_free = 0.3401 target = 0.141063 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2997 r_free = 0.2997 target = 0.108848 restraints weight = 47134.185| |-----------------------------------------------------------------------------| r_work (start): 0.2990 rms_B_bonded: 1.52 r_work: 0.2801 rms_B_bonded: 2.76 restraints_weight: 0.5000 r_work: 0.2678 rms_B_bonded: 4.60 restraints_weight: 0.2500 r_work (final): 0.2678 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8669 moved from start: 0.1617 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 43976 Z= 0.133 Angle : 0.518 8.630 59880 Z= 0.279 Chirality : 0.046 0.216 7080 Planarity : 0.004 0.041 7608 Dihedral : 8.799 87.190 6891 Min Nonbonded Distance : 2.458 Molprobity Statistics. All-atom Clashscore : 5.90 Ramachandran Plot: Outliers : 0.66 % Allowed : 5.14 % Favored : 94.20 % Rotamer: Outliers : 3.73 % Allowed : 17.47 % Favored : 78.80 % 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: -0.31 (0.12), residues: 5608 helix: 0.88 (0.14), residues: 1572 sheet: -0.49 (0.15), residues: 1148 loop : -0.63 (0.12), residues: 2888 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG F 77 TYR 0.015 0.002 TYR C 178 PHE 0.019 0.002 PHE J 157 TRP 0.007 0.001 TRP D 332 HIS 0.004 0.001 HIS K 176 Details of bonding type rmsd covalent geometry : bond 0.00311 (43968) covalent geometry : angle 0.51725 (59864) SS BOND : bond 0.00564 ( 8) SS BOND : angle 1.22311 ( 16) hydrogen bonds : bond 0.03235 ( 1769) hydrogen bonds : angle 4.71203 ( 5445) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11216 Ramachandran restraints generated. 5608 Oldfield, 0 Emsley, 5608 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11216 Ramachandran restraints generated. 5608 Oldfield, 0 Emsley, 5608 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 792 residues out of total 4664 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 174 poor density : 618 time to evaluate : 1.670 Fit side-chains revert: symmetry clash REVERT: O 2 LYS cc_start: 0.8505 (mttm) cc_final: 0.8205 (mttp) REVERT: O 94 GLU cc_start: 0.8883 (OUTLIER) cc_final: 0.7822 (tm-30) REVERT: O 191 ARG cc_start: 0.9051 (OUTLIER) cc_final: 0.8701 (ptt180) REVERT: O 268 LYS cc_start: 0.8955 (OUTLIER) cc_final: 0.8319 (tttt) REVERT: P 20 ARG cc_start: 0.8223 (OUTLIER) cc_final: 0.5268 (mpt-90) REVERT: R 158 VAL cc_start: 0.8092 (OUTLIER) cc_final: 0.7751 (t) REVERT: R 172 MET cc_start: 0.7462 (OUTLIER) cc_final: 0.7232 (tmt) REVERT: R 306 LYS cc_start: 0.8045 (OUTLIER) cc_final: 0.7741 (tptm) REVERT: A 60 ILE cc_start: 0.7549 (OUTLIER) cc_final: 0.7303 (pt) REVERT: A 87 LEU cc_start: 0.8622 (OUTLIER) cc_final: 0.8231 (mp) REVERT: A 122 LYS cc_start: 0.8165 (OUTLIER) cc_final: 0.7678 (tmtp) REVERT: B 126 PRO cc_start: 0.8238 (Cg_exo) cc_final: 0.7966 (Cg_endo) REVERT: B 265 ASN cc_start: 0.7223 (m-40) cc_final: 0.6960 (m-40) REVERT: C 284 ARG cc_start: 0.8569 (OUTLIER) cc_final: 0.8197 (mtp85) REVERT: C 361 TYR cc_start: 0.8181 (OUTLIER) cc_final: 0.7882 (m-80) REVERT: D 54 ASP cc_start: 0.8204 (OUTLIER) cc_final: 0.7787 (m-30) REVERT: D 61 ASP cc_start: 0.8071 (t0) cc_final: 0.7857 (t0) REVERT: D 87 MET cc_start: 0.7832 (mtm) cc_final: 0.7531 (mtp) REVERT: D 191 ARG cc_start: 0.7874 (ttp-110) cc_final: 0.7670 (ttp80) REVERT: D 266 GLU cc_start: 0.6651 (OUTLIER) cc_final: 0.6325 (pt0) REVERT: E 62 GLU cc_start: 0.8382 (pt0) cc_final: 0.7896 (pm20) REVERT: E 94 GLU cc_start: 0.8865 (OUTLIER) cc_final: 0.7801 (tm-30) REVERT: E 191 ARG cc_start: 0.9095 (OUTLIER) cc_final: 0.8090 (ptp-170) REVERT: E 268 LYS cc_start: 0.8926 (OUTLIER) cc_final: 0.8323 (tttt) REVERT: F 2 LYS cc_start: 0.6375 (mttt) cc_final: 0.5863 (mtpp) REVERT: F 20 ARG cc_start: 0.8227 (OUTLIER) cc_final: 0.4612 (mpt-90) REVERT: G 165 LEU cc_start: 0.8533 (OUTLIER) cc_final: 0.8198 (tp) REVERT: G 362 GLU cc_start: 0.8131 (OUTLIER) cc_final: 0.7808 (tm-30) REVERT: H 84 TRP cc_start: 0.7347 (OUTLIER) cc_final: 0.6564 (m100) REVERT: H 169 LYS cc_start: 0.7241 (ptpp) cc_final: 0.6808 (pttm) REVERT: H 172 MET cc_start: 0.7471 (OUTLIER) cc_final: 0.7196 (tmt) REVERT: I 60 ILE cc_start: 0.7433 (OUTLIER) cc_final: 0.7214 (pt) REVERT: I 62 GLU cc_start: 0.8070 (OUTLIER) cc_final: 0.7817 (pm20) REVERT: I 73 VAL cc_start: 0.9148 (OUTLIER) cc_final: 0.8945 (t) REVERT: I 87 LEU cc_start: 0.8637 (OUTLIER) cc_final: 0.8324 (mp) REVERT: I 122 LYS cc_start: 0.8095 (OUTLIER) cc_final: 0.7634 (tmtp) REVERT: I 350 LYS cc_start: 0.8106 (mptt) cc_final: 0.7622 (mmmm) REVERT: J 56 ASP cc_start: 0.8100 (OUTLIER) cc_final: 0.7725 (t70) REVERT: J 61 ASP cc_start: 0.8639 (t0) cc_final: 0.8385 (t0) REVERT: J 77 ARG cc_start: 0.7714 (mmm160) cc_final: 0.7496 (mmm160) REVERT: J 300 MET cc_start: 0.7337 (mmm) cc_final: 0.7076 (mtp) REVERT: J 323 ASP cc_start: 0.8112 (OUTLIER) cc_final: 0.7754 (m-30) REVERT: K 134 GLU cc_start: 0.8211 (pm20) cc_final: 0.7981 (pm20) REVERT: K 261 LYS cc_start: 0.7845 (tttt) cc_final: 0.7585 (ttmm) REVERT: K 361 TYR cc_start: 0.8223 (OUTLIER) cc_final: 0.7887 (m-80) REVERT: L 1 LEU cc_start: 0.7897 (tp) cc_final: 0.7671 (tp) REVERT: L 61 ASP cc_start: 0.7883 (t0) cc_final: 0.7651 (t0) REVERT: L 169 LYS cc_start: 0.8447 (OUTLIER) cc_final: 0.8196 (ptmm) REVERT: L 268 LYS cc_start: 0.8114 (OUTLIER) cc_final: 0.7895 (mtpp) outliers start: 174 outliers final: 117 residues processed: 732 average time/residue: 0.2625 time to fit residues: 319.3349 Evaluate side-chains 742 residues out of total 4664 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 149 poor density : 593 time to evaluate : 1.320 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain O residue 30 VAL Chi-restraints excluded: chain O residue 61 ASN Chi-restraints excluded: chain O residue 94 GLU Chi-restraints excluded: chain O residue 146 ASN Chi-restraints excluded: chain O residue 191 ARG Chi-restraints excluded: chain O residue 201 LEU Chi-restraints excluded: chain O residue 268 LYS Chi-restraints excluded: chain O residue 281 VAL Chi-restraints excluded: chain O residue 289 SER Chi-restraints excluded: chain O residue 357 GLU Chi-restraints excluded: chain O residue 361 TYR Chi-restraints excluded: chain P residue 20 ARG Chi-restraints excluded: chain P residue 84 TRP Chi-restraints excluded: chain P residue 154 LEU Chi-restraints excluded: chain P residue 161 LEU Chi-restraints excluded: chain P residue 191 ARG Chi-restraints excluded: chain P residue 241 ASP Chi-restraints excluded: chain P residue 286 THR Chi-restraints excluded: chain P residue 290 SER Chi-restraints excluded: chain P residue 292 ILE Chi-restraints excluded: chain Q residue 1 LEU Chi-restraints excluded: chain Q residue 30 VAL Chi-restraints excluded: chain Q residue 65 SER Chi-restraints excluded: chain Q residue 84 TRP Chi-restraints excluded: chain Q residue 202 ASN Chi-restraints excluded: chain Q residue 248 LYS Chi-restraints excluded: chain Q residue 289 SER Chi-restraints excluded: chain Q residue 335 LEU Chi-restraints excluded: chain Q residue 361 TYR Chi-restraints excluded: chain R residue 3 VAL Chi-restraints excluded: chain R residue 37 VAL Chi-restraints excluded: chain R residue 62 SER Chi-restraints excluded: chain R residue 84 TRP Chi-restraints excluded: chain R residue 129 VAL Chi-restraints excluded: chain R residue 158 VAL Chi-restraints excluded: chain R residue 161 LEU Chi-restraints excluded: chain R residue 172 MET Chi-restraints excluded: chain R residue 241 ASP Chi-restraints excluded: chain R residue 306 LYS Chi-restraints excluded: chain R residue 324 LEU Chi-restraints excluded: chain A residue 1 LEU Chi-restraints excluded: chain A residue 23 SER Chi-restraints excluded: chain A residue 60 ILE Chi-restraints excluded: chain A residue 62 GLU Chi-restraints excluded: chain A residue 84 TRP Chi-restraints excluded: chain A residue 87 LEU Chi-restraints excluded: chain A residue 122 LYS Chi-restraints excluded: chain A residue 123 SER Chi-restraints excluded: chain A residue 201 LEU Chi-restraints excluded: chain A residue 208 THR Chi-restraints excluded: chain A residue 261 LYS Chi-restraints excluded: chain A residue 295 SER Chi-restraints excluded: chain B residue 52 THR Chi-restraints excluded: chain B residue 172 MET Chi-restraints excluded: chain B residue 241 ASP Chi-restraints excluded: chain B residue 281 ILE Chi-restraints excluded: chain B residue 305 VAL Chi-restraints excluded: chain B residue 327 ILE Chi-restraints excluded: chain C residue 1 LEU Chi-restraints excluded: chain C residue 62 GLU Chi-restraints excluded: chain C residue 63 THR Chi-restraints excluded: chain C residue 65 SER Chi-restraints excluded: chain C residue 84 TRP Chi-restraints excluded: chain C residue 246 ILE Chi-restraints excluded: chain C residue 284 ARG Chi-restraints excluded: chain C residue 292 ILE Chi-restraints excluded: chain C residue 361 TYR Chi-restraints excluded: chain D residue 54 ASP Chi-restraints excluded: chain D residue 226 ASN Chi-restraints excluded: chain D residue 241 ASP Chi-restraints excluded: chain D residue 266 GLU Chi-restraints excluded: chain D residue 281 ILE Chi-restraints excluded: chain D residue 295 SER Chi-restraints excluded: chain E residue 22 ASP Chi-restraints excluded: chain E residue 28 VAL Chi-restraints excluded: chain E residue 30 VAL Chi-restraints excluded: chain E residue 94 GLU Chi-restraints excluded: chain E residue 146 ASN Chi-restraints excluded: chain E residue 191 ARG Chi-restraints excluded: chain E residue 201 LEU Chi-restraints excluded: chain E residue 268 LYS Chi-restraints excluded: chain E residue 357 GLU Chi-restraints excluded: chain F residue 3 VAL Chi-restraints excluded: chain F residue 20 ARG Chi-restraints excluded: chain F residue 37 VAL Chi-restraints excluded: chain F residue 75 SER Chi-restraints excluded: chain F residue 84 TRP Chi-restraints excluded: chain F residue 151 THR Chi-restraints excluded: chain F residue 161 LEU Chi-restraints excluded: chain F residue 174 THR Chi-restraints excluded: chain F residue 191 ARG Chi-restraints excluded: chain F residue 292 ILE Chi-restraints excluded: chain G residue 30 VAL Chi-restraints excluded: chain G residue 84 TRP Chi-restraints excluded: chain G residue 165 LEU Chi-restraints excluded: chain G residue 289 SER Chi-restraints excluded: chain G residue 331 LYS Chi-restraints excluded: chain G residue 339 VAL Chi-restraints excluded: chain G residue 362 GLU Chi-restraints excluded: chain H residue 25 LEU Chi-restraints excluded: chain H residue 62 SER Chi-restraints excluded: chain H residue 84 TRP Chi-restraints excluded: chain H residue 103 ASP Chi-restraints excluded: chain H residue 129 VAL Chi-restraints excluded: chain H residue 161 LEU Chi-restraints excluded: chain H residue 172 MET Chi-restraints excluded: chain H residue 218 LEU Chi-restraints excluded: chain H residue 241 ASP Chi-restraints excluded: chain I residue 23 SER Chi-restraints excluded: chain I residue 28 VAL Chi-restraints excluded: chain I residue 37 VAL Chi-restraints excluded: chain I residue 52 THR Chi-restraints excluded: chain I residue 60 ILE Chi-restraints excluded: chain I residue 62 GLU Chi-restraints excluded: chain I residue 73 VAL Chi-restraints excluded: chain I residue 84 TRP Chi-restraints excluded: chain I residue 87 LEU Chi-restraints excluded: chain I residue 122 LYS Chi-restraints excluded: chain I residue 159 LYS Chi-restraints excluded: chain I residue 201 LEU Chi-restraints excluded: chain I residue 208 THR Chi-restraints excluded: chain I residue 295 SER Chi-restraints excluded: chain I residue 335 LEU Chi-restraints excluded: chain J residue 25 LEU Chi-restraints excluded: chain J residue 37 VAL Chi-restraints excluded: chain J residue 56 ASP Chi-restraints excluded: chain J residue 80 VAL Chi-restraints excluded: chain J residue 98 VAL Chi-restraints excluded: chain J residue 116 VAL Chi-restraints excluded: chain J residue 125 ILE Chi-restraints excluded: chain J residue 145 SER Chi-restraints excluded: chain J residue 281 ILE Chi-restraints excluded: chain J residue 305 VAL Chi-restraints excluded: chain J residue 323 ASP Chi-restraints excluded: chain J residue 327 ILE Chi-restraints excluded: chain K residue 1 LEU Chi-restraints excluded: chain K residue 30 VAL Chi-restraints excluded: chain K residue 63 THR Chi-restraints excluded: chain K residue 65 SER Chi-restraints excluded: chain K residue 84 TRP Chi-restraints excluded: chain K residue 246 ILE Chi-restraints excluded: chain K residue 250 VAL Chi-restraints excluded: chain K residue 361 TYR Chi-restraints excluded: chain L residue 54 ASP Chi-restraints excluded: chain L residue 138 THR Chi-restraints excluded: chain L residue 169 LYS Chi-restraints excluded: chain L residue 241 ASP Chi-restraints excluded: chain L residue 268 LYS Chi-restraints excluded: chain L residue 281 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 552 random chunks: chunk 69 optimal weight: 8.9990 chunk 211 optimal weight: 0.9990 chunk 479 optimal weight: 7.9990 chunk 210 optimal weight: 0.9990 chunk 217 optimal weight: 1.9990 chunk 414 optimal weight: 8.9990 chunk 445 optimal weight: 3.9990 chunk 538 optimal weight: 0.9990 chunk 428 optimal weight: 2.9990 chunk 36 optimal weight: 10.0000 chunk 443 optimal weight: 0.4980 overall best weight: 1.0988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: O 61 ASN ** O 245 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 202 ASN B 220 ASN E 146 ASN ** E 245 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 139 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 330 ASN I 152 ASN J 220 ASN L 81 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3405 r_free = 0.3405 target = 0.141389 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3004 r_free = 0.3004 target = 0.109383 restraints weight = 46926.915| |-----------------------------------------------------------------------------| r_work (start): 0.2999 rms_B_bonded: 1.52 r_work: 0.2810 rms_B_bonded: 2.73 restraints_weight: 0.5000 r_work: 0.2689 rms_B_bonded: 4.55 restraints_weight: 0.2500 r_work (final): 0.2689 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8663 moved from start: 0.1705 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 43976 Z= 0.131 Angle : 0.512 8.637 59880 Z= 0.276 Chirality : 0.046 0.226 7080 Planarity : 0.004 0.042 7608 Dihedral : 8.731 86.788 6891 Min Nonbonded Distance : 2.313 Molprobity Statistics. All-atom Clashscore : 5.85 Ramachandran Plot: Outliers : 0.66 % Allowed : 5.24 % Favored : 94.10 % Rotamer: Outliers : 3.90 % Allowed : 17.69 % Favored : 78.41 % 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: -0.27 (0.12), residues: 5608 helix: 0.95 (0.14), residues: 1572 sheet: -0.49 (0.15), residues: 1152 loop : -0.62 (0.12), residues: 2884 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG L 191 TYR 0.015 0.002 TYR K 178 PHE 0.021 0.002 PHE Q 348 TRP 0.007 0.001 TRP I 310 HIS 0.004 0.001 HIS K 176 Details of bonding type rmsd covalent geometry : bond 0.00306 (43968) covalent geometry : angle 0.51171 (59864) SS BOND : bond 0.00547 ( 8) SS BOND : angle 1.18870 ( 16) hydrogen bonds : bond 0.03164 ( 1769) hydrogen bonds : angle 4.64860 ( 5445) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11216 Ramachandran restraints generated. 5608 Oldfield, 0 Emsley, 5608 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11216 Ramachandran restraints generated. 5608 Oldfield, 0 Emsley, 5608 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 790 residues out of total 4664 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 182 poor density : 608 time to evaluate : 1.861 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: O 2 LYS cc_start: 0.8520 (mttm) cc_final: 0.8209 (mttp) REVERT: O 94 GLU cc_start: 0.8858 (OUTLIER) cc_final: 0.7800 (tm-30) REVERT: O 191 ARG cc_start: 0.9053 (OUTLIER) cc_final: 0.8712 (ptt180) REVERT: O 268 LYS cc_start: 0.8955 (OUTLIER) cc_final: 0.8320 (tttt) REVERT: P 20 ARG cc_start: 0.8237 (OUTLIER) cc_final: 0.5352 (mpt-90) REVERT: R 158 VAL cc_start: 0.8088 (OUTLIER) cc_final: 0.7755 (t) REVERT: R 172 MET cc_start: 0.7444 (OUTLIER) cc_final: 0.7237 (tmt) REVERT: R 306 LYS cc_start: 0.8136 (OUTLIER) cc_final: 0.7734 (tptm) REVERT: A 60 ILE cc_start: 0.7488 (OUTLIER) cc_final: 0.7257 (pt) REVERT: A 87 LEU cc_start: 0.8619 (OUTLIER) cc_final: 0.8219 (mp) REVERT: A 122 LYS cc_start: 0.8155 (OUTLIER) cc_final: 0.7710 (tmtp) REVERT: B 126 PRO cc_start: 0.8248 (Cg_exo) cc_final: 0.7982 (Cg_endo) REVERT: C 164 GLU cc_start: 0.7680 (OUTLIER) cc_final: 0.7193 (mt-10) REVERT: C 284 ARG cc_start: 0.8558 (OUTLIER) cc_final: 0.8184 (mtp85) REVERT: C 361 TYR cc_start: 0.8184 (OUTLIER) cc_final: 0.7854 (m-80) REVERT: D 54 ASP cc_start: 0.8177 (OUTLIER) cc_final: 0.7760 (m-30) REVERT: D 61 ASP cc_start: 0.8040 (t0) cc_final: 0.7832 (t0) REVERT: D 87 MET cc_start: 0.7831 (mtm) cc_final: 0.7527 (mtp) REVERT: D 266 GLU cc_start: 0.6654 (OUTLIER) cc_final: 0.6318 (pt0) REVERT: E 62 GLU cc_start: 0.8380 (OUTLIER) cc_final: 0.8055 (pm20) REVERT: E 94 GLU cc_start: 0.8850 (OUTLIER) cc_final: 0.7784 (tm-30) REVERT: E 191 ARG cc_start: 0.9095 (OUTLIER) cc_final: 0.8108 (ptp-170) REVERT: E 268 LYS cc_start: 0.8897 (OUTLIER) cc_final: 0.8299 (tttt) REVERT: F 2 LYS cc_start: 0.6429 (mttt) cc_final: 0.5894 (mtpp) REVERT: F 20 ARG cc_start: 0.8224 (OUTLIER) cc_final: 0.4575 (mpt-90) REVERT: F 304 MET cc_start: 0.6731 (mtp) cc_final: 0.6003 (mtp) REVERT: G 165 LEU cc_start: 0.8527 (OUTLIER) cc_final: 0.8175 (tp) REVERT: G 362 GLU cc_start: 0.8148 (OUTLIER) cc_final: 0.7780 (tm-30) REVERT: H 84 TRP cc_start: 0.7340 (OUTLIER) cc_final: 0.6566 (m100) REVERT: H 172 MET cc_start: 0.7495 (OUTLIER) cc_final: 0.7190 (tmt) REVERT: I 60 ILE cc_start: 0.7353 (OUTLIER) cc_final: 0.7143 (pt) REVERT: I 62 GLU cc_start: 0.8079 (OUTLIER) cc_final: 0.7861 (pm20) REVERT: I 73 VAL cc_start: 0.9152 (OUTLIER) cc_final: 0.8949 (t) REVERT: I 87 LEU cc_start: 0.8638 (OUTLIER) cc_final: 0.8319 (mp) REVERT: I 122 LYS cc_start: 0.8096 (OUTLIER) cc_final: 0.7630 (tmtp) REVERT: I 191 ARG cc_start: 0.8913 (OUTLIER) cc_final: 0.8465 (mtp180) REVERT: I 350 LYS cc_start: 0.8103 (mptt) cc_final: 0.7619 (mmmm) REVERT: J 56 ASP cc_start: 0.8085 (OUTLIER) cc_final: 0.7719 (t70) REVERT: J 300 MET cc_start: 0.7321 (mmm) cc_final: 0.7059 (mtp) REVERT: J 323 ASP cc_start: 0.8134 (OUTLIER) cc_final: 0.7820 (m-30) REVERT: K 134 GLU cc_start: 0.8217 (pm20) cc_final: 0.7991 (pm20) REVERT: K 164 GLU cc_start: 0.7681 (OUTLIER) cc_final: 0.7173 (mt-10) REVERT: K 248 LYS cc_start: 0.7727 (OUTLIER) cc_final: 0.7177 (tttt) REVERT: K 261 LYS cc_start: 0.7844 (tttt) cc_final: 0.7577 (ttmm) REVERT: K 361 TYR cc_start: 0.8230 (OUTLIER) cc_final: 0.7870 (m-80) REVERT: L 1 LEU cc_start: 0.7910 (tp) cc_final: 0.7696 (tp) REVERT: L 54 ASP cc_start: 0.8168 (OUTLIER) cc_final: 0.7758 (m-30) REVERT: L 61 ASP cc_start: 0.7838 (t0) cc_final: 0.7619 (t0) REVERT: L 169 LYS cc_start: 0.8449 (OUTLIER) cc_final: 0.8207 (ptmm) REVERT: L 268 LYS cc_start: 0.8150 (OUTLIER) cc_final: 0.7932 (mtpp) outliers start: 182 outliers final: 118 residues processed: 728 average time/residue: 0.2569 time to fit residues: 309.4489 Evaluate side-chains 744 residues out of total 4664 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 156 poor density : 588 time to evaluate : 1.663 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain O residue 30 VAL Chi-restraints excluded: chain O residue 94 GLU Chi-restraints excluded: chain O residue 146 ASN Chi-restraints excluded: chain O residue 191 ARG Chi-restraints excluded: chain O residue 201 LEU Chi-restraints excluded: chain O residue 268 LYS Chi-restraints excluded: chain O residue 289 SER Chi-restraints excluded: chain O residue 357 GLU Chi-restraints excluded: chain O residue 361 TYR Chi-restraints excluded: chain P residue 20 ARG Chi-restraints excluded: chain P residue 33 THR Chi-restraints excluded: chain P residue 84 TRP Chi-restraints excluded: chain P residue 154 LEU Chi-restraints excluded: chain P residue 161 LEU Chi-restraints excluded: chain P residue 171 THR Chi-restraints excluded: chain P residue 191 ARG Chi-restraints excluded: chain P residue 241 ASP Chi-restraints excluded: chain P residue 286 THR Chi-restraints excluded: chain P residue 290 SER Chi-restraints excluded: chain P residue 292 ILE Chi-restraints excluded: chain Q residue 1 LEU Chi-restraints excluded: chain Q residue 30 VAL Chi-restraints excluded: chain Q residue 65 SER Chi-restraints excluded: chain Q residue 84 TRP Chi-restraints excluded: chain Q residue 248 LYS Chi-restraints excluded: chain Q residue 289 SER Chi-restraints excluded: chain Q residue 335 LEU Chi-restraints excluded: chain Q residue 361 TYR Chi-restraints excluded: chain R residue 3 VAL Chi-restraints excluded: chain R residue 62 SER Chi-restraints excluded: chain R residue 84 TRP Chi-restraints excluded: chain R residue 129 VAL Chi-restraints excluded: chain R residue 158 VAL Chi-restraints excluded: chain R residue 161 LEU Chi-restraints excluded: chain R residue 172 MET Chi-restraints excluded: chain R residue 241 ASP Chi-restraints excluded: chain R residue 306 LYS Chi-restraints excluded: chain R residue 324 LEU Chi-restraints excluded: chain A residue 23 SER Chi-restraints excluded: chain A residue 60 ILE Chi-restraints excluded: chain A residue 62 GLU Chi-restraints excluded: chain A residue 84 TRP Chi-restraints excluded: chain A residue 87 LEU Chi-restraints excluded: chain A residue 122 LYS Chi-restraints excluded: chain A residue 123 SER Chi-restraints excluded: chain A residue 201 LEU Chi-restraints excluded: chain A residue 208 THR Chi-restraints excluded: chain A residue 261 LYS Chi-restraints excluded: chain A residue 295 SER Chi-restraints excluded: chain B residue 52 THR Chi-restraints excluded: chain B residue 98 VAL Chi-restraints excluded: chain B residue 172 MET Chi-restraints excluded: chain B residue 241 ASP Chi-restraints excluded: chain B residue 281 ILE Chi-restraints excluded: chain B residue 305 VAL Chi-restraints excluded: chain B residue 327 ILE Chi-restraints excluded: chain C residue 1 LEU Chi-restraints excluded: chain C residue 21 LYS Chi-restraints excluded: chain C residue 62 GLU Chi-restraints excluded: chain C residue 63 THR Chi-restraints excluded: chain C residue 65 SER Chi-restraints excluded: chain C residue 84 TRP Chi-restraints excluded: chain C residue 164 GLU Chi-restraints excluded: chain C residue 246 ILE Chi-restraints excluded: chain C residue 284 ARG Chi-restraints excluded: chain C residue 292 ILE Chi-restraints excluded: chain C residue 361 TYR Chi-restraints excluded: chain D residue 54 ASP Chi-restraints excluded: chain D residue 164 LYS Chi-restraints excluded: chain D residue 241 ASP Chi-restraints excluded: chain D residue 266 GLU Chi-restraints excluded: chain D residue 281 ILE Chi-restraints excluded: chain D residue 295 SER Chi-restraints excluded: chain E residue 22 ASP Chi-restraints excluded: chain E residue 28 VAL Chi-restraints excluded: chain E residue 30 VAL Chi-restraints excluded: chain E residue 62 GLU Chi-restraints excluded: chain E residue 94 GLU Chi-restraints excluded: chain E residue 191 ARG Chi-restraints excluded: chain E residue 201 LEU Chi-restraints excluded: chain E residue 268 LYS Chi-restraints excluded: chain E residue 357 GLU Chi-restraints excluded: chain F residue 3 VAL Chi-restraints excluded: chain F residue 20 ARG Chi-restraints excluded: chain F residue 37 VAL Chi-restraints excluded: chain F residue 75 SER Chi-restraints excluded: chain F residue 84 TRP Chi-restraints excluded: chain F residue 151 THR Chi-restraints excluded: chain F residue 161 LEU Chi-restraints excluded: chain F residue 191 ARG Chi-restraints excluded: chain F residue 292 ILE Chi-restraints excluded: chain G residue 1 LEU Chi-restraints excluded: chain G residue 25 LEU Chi-restraints excluded: chain G residue 30 VAL Chi-restraints excluded: chain G residue 84 TRP Chi-restraints excluded: chain G residue 165 LEU Chi-restraints excluded: chain G residue 289 SER Chi-restraints excluded: chain G residue 339 VAL Chi-restraints excluded: chain G residue 362 GLU Chi-restraints excluded: chain H residue 25 LEU Chi-restraints excluded: chain H residue 62 SER Chi-restraints excluded: chain H residue 84 TRP Chi-restraints excluded: chain H residue 103 ASP Chi-restraints excluded: chain H residue 129 VAL Chi-restraints excluded: chain H residue 161 LEU Chi-restraints excluded: chain H residue 172 MET Chi-restraints excluded: chain H residue 218 LEU Chi-restraints excluded: chain H residue 241 ASP Chi-restraints excluded: chain I residue 1 LEU Chi-restraints excluded: chain I residue 23 SER Chi-restraints excluded: chain I residue 28 VAL Chi-restraints excluded: chain I residue 37 VAL Chi-restraints excluded: chain I residue 52 THR Chi-restraints excluded: chain I residue 60 ILE Chi-restraints excluded: chain I residue 62 GLU Chi-restraints excluded: chain I residue 73 VAL Chi-restraints excluded: chain I residue 84 TRP Chi-restraints excluded: chain I residue 87 LEU Chi-restraints excluded: chain I residue 122 LYS Chi-restraints excluded: chain I residue 159 LYS Chi-restraints excluded: chain I residue 191 ARG Chi-restraints excluded: chain I residue 201 LEU Chi-restraints excluded: chain I residue 208 THR Chi-restraints excluded: chain I residue 261 LYS Chi-restraints excluded: chain I residue 295 SER Chi-restraints excluded: chain I residue 335 LEU Chi-restraints excluded: chain J residue 25 LEU Chi-restraints excluded: chain J residue 37 VAL Chi-restraints excluded: chain J residue 56 ASP Chi-restraints excluded: chain J residue 98 VAL Chi-restraints excluded: chain J residue 116 VAL Chi-restraints excluded: chain J residue 125 ILE Chi-restraints excluded: chain J residue 145 SER Chi-restraints excluded: chain J residue 241 ASP Chi-restraints excluded: chain J residue 281 ILE Chi-restraints excluded: chain J residue 305 VAL Chi-restraints excluded: chain J residue 323 ASP Chi-restraints excluded: chain J residue 327 ILE Chi-restraints excluded: chain K residue 1 LEU Chi-restraints excluded: chain K residue 30 VAL Chi-restraints excluded: chain K residue 63 THR Chi-restraints excluded: chain K residue 65 SER Chi-restraints excluded: chain K residue 84 TRP Chi-restraints excluded: chain K residue 164 GLU Chi-restraints excluded: chain K residue 201 LEU Chi-restraints excluded: chain K residue 246 ILE Chi-restraints excluded: chain K residue 248 LYS Chi-restraints excluded: chain K residue 250 VAL Chi-restraints excluded: chain K residue 361 TYR Chi-restraints excluded: chain L residue 54 ASP Chi-restraints excluded: chain L residue 138 THR Chi-restraints excluded: chain L residue 169 LYS Chi-restraints excluded: chain L residue 241 ASP Chi-restraints excluded: chain L residue 268 LYS Chi-restraints excluded: chain L residue 281 ILE Chi-restraints excluded: chain L residue 295 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 552 random chunks: chunk 503 optimal weight: 0.9990 chunk 301 optimal weight: 7.9990 chunk 510 optimal weight: 0.9980 chunk 350 optimal weight: 8.9990 chunk 496 optimal weight: 0.9990 chunk 167 optimal weight: 4.9990 chunk 17 optimal weight: 2.9990 chunk 165 optimal weight: 0.8980 chunk 15 optimal weight: 1.9990 chunk 537 optimal weight: 0.8980 chunk 349 optimal weight: 0.6980 overall best weight: 0.8982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** O 245 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 319 GLN A 319 GLN B 220 ASN C 139 HIS C 146 ASN E 146 ASN ** E 245 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 139 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 319 GLN J 220 ASN L 81 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3418 r_free = 0.3418 target = 0.142453 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3017 r_free = 0.3017 target = 0.110298 restraints weight = 47306.457| |-----------------------------------------------------------------------------| r_work (start): 0.3010 rms_B_bonded: 1.56 r_work: 0.2818 rms_B_bonded: 2.83 restraints_weight: 0.5000 r_work: 0.2697 rms_B_bonded: 4.67 restraints_weight: 0.2500 r_work (final): 0.2697 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8653 moved from start: 0.1832 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 43976 Z= 0.119 Angle : 0.502 8.587 59880 Z= 0.271 Chirality : 0.046 0.244 7080 Planarity : 0.004 0.057 7608 Dihedral : 8.589 87.097 6891 Min Nonbonded Distance : 2.534 Molprobity Statistics. All-atom Clashscore : 6.06 Ramachandran Plot: Outliers : 0.62 % Allowed : 5.06 % Favored : 94.31 % Rotamer: Outliers : 3.56 % Allowed : 18.35 % Favored : 78.09 % 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: -0.20 (0.12), residues: 5608 helix: 1.05 (0.14), residues: 1572 sheet: -0.47 (0.15), residues: 1152 loop : -0.60 (0.12), residues: 2884 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG L 77 TYR 0.014 0.002 TYR K 178 PHE 0.022 0.001 PHE Q 348 TRP 0.007 0.001 TRP D 84 HIS 0.003 0.001 HIS K 176 Details of bonding type rmsd covalent geometry : bond 0.00278 (43968) covalent geometry : angle 0.50124 (59864) SS BOND : bond 0.00532 ( 8) SS BOND : angle 1.18822 ( 16) hydrogen bonds : bond 0.03025 ( 1769) hydrogen bonds : angle 4.56095 ( 5445) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11216 Ramachandran restraints generated. 5608 Oldfield, 0 Emsley, 5608 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11216 Ramachandran restraints generated. 5608 Oldfield, 0 Emsley, 5608 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 778 residues out of total 4664 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 166 poor density : 612 time to evaluate : 1.762 Fit side-chains REVERT: O 2 LYS cc_start: 0.8491 (mttm) cc_final: 0.8184 (mttp) REVERT: O 94 GLU cc_start: 0.8840 (OUTLIER) cc_final: 0.7778 (tm-30) REVERT: O 191 ARG cc_start: 0.9031 (OUTLIER) cc_final: 0.8673 (ptt180) REVERT: O 268 LYS cc_start: 0.8955 (OUTLIER) cc_final: 0.8323 (tttt) REVERT: P 20 ARG cc_start: 0.8240 (OUTLIER) cc_final: 0.5316 (mpt-90) REVERT: Q 350 LYS cc_start: 0.7795 (mmmm) cc_final: 0.7320 (mttp) REVERT: Q 361 TYR cc_start: 0.8022 (OUTLIER) cc_final: 0.7678 (t80) REVERT: R 115 LYS cc_start: 0.7633 (ttmt) cc_final: 0.7363 (tttt) REVERT: R 158 VAL cc_start: 0.8065 (OUTLIER) cc_final: 0.7759 (t) REVERT: R 172 MET cc_start: 0.7401 (OUTLIER) cc_final: 0.7182 (tmt) REVERT: R 212 LYS cc_start: 0.7317 (mttt) cc_final: 0.7028 (mtpt) REVERT: R 306 LYS cc_start: 0.8162 (OUTLIER) cc_final: 0.7816 (tptm) REVERT: A 87 LEU cc_start: 0.8641 (OUTLIER) cc_final: 0.8276 (mp) REVERT: A 122 LYS cc_start: 0.8202 (OUTLIER) cc_final: 0.7757 (tmtp) REVERT: B 114 LYS cc_start: 0.8012 (mttt) cc_final: 0.7791 (mttt) REVERT: B 126 PRO cc_start: 0.8212 (Cg_exo) cc_final: 0.7956 (Cg_endo) REVERT: B 323 ASP cc_start: 0.8059 (m-30) cc_final: 0.7726 (m-30) REVERT: C 164 GLU cc_start: 0.7655 (OUTLIER) cc_final: 0.7174 (mt-10) REVERT: C 284 ARG cc_start: 0.8556 (OUTLIER) cc_final: 0.8179 (mtp85) REVERT: C 361 TYR cc_start: 0.8203 (OUTLIER) cc_final: 0.7880 (m-80) REVERT: D 54 ASP cc_start: 0.8157 (OUTLIER) cc_final: 0.7740 (m-30) REVERT: D 61 ASP cc_start: 0.7977 (t0) cc_final: 0.7772 (t0) REVERT: D 87 MET cc_start: 0.7846 (mtm) cc_final: 0.7559 (mtp) REVERT: D 266 GLU cc_start: 0.6670 (OUTLIER) cc_final: 0.6350 (pt0) REVERT: E 62 GLU cc_start: 0.8342 (OUTLIER) cc_final: 0.7994 (pm20) REVERT: E 94 GLU cc_start: 0.8837 (OUTLIER) cc_final: 0.7756 (tm-30) REVERT: E 191 ARG cc_start: 0.9087 (OUTLIER) cc_final: 0.8060 (ptp-170) REVERT: E 268 LYS cc_start: 0.8904 (OUTLIER) cc_final: 0.8287 (tttt) REVERT: F 2 LYS cc_start: 0.6431 (mttt) cc_final: 0.5905 (mtpp) REVERT: F 20 ARG cc_start: 0.8225 (OUTLIER) cc_final: 0.5196 (mpt-90) REVERT: G 165 LEU cc_start: 0.8528 (OUTLIER) cc_final: 0.8197 (tp) REVERT: G 362 GLU cc_start: 0.8144 (OUTLIER) cc_final: 0.7718 (tm-30) REVERT: H 84 TRP cc_start: 0.7303 (OUTLIER) cc_final: 0.6539 (m100) REVERT: H 94 GLU cc_start: 0.7568 (OUTLIER) cc_final: 0.6464 (tm-30) REVERT: H 169 LYS cc_start: 0.7169 (ptpp) cc_final: 0.6656 (pttm) REVERT: H 172 MET cc_start: 0.7459 (OUTLIER) cc_final: 0.7180 (tmt) REVERT: I 73 VAL cc_start: 0.9147 (OUTLIER) cc_final: 0.8921 (t) REVERT: I 87 LEU cc_start: 0.8633 (OUTLIER) cc_final: 0.8341 (mp) REVERT: I 122 LYS cc_start: 0.8085 (OUTLIER) cc_final: 0.7630 (tmtp) REVERT: I 191 ARG cc_start: 0.8878 (OUTLIER) cc_final: 0.8426 (mtp180) REVERT: I 350 LYS cc_start: 0.8100 (mptt) cc_final: 0.7643 (mmmm) REVERT: J 56 ASP cc_start: 0.8116 (OUTLIER) cc_final: 0.7729 (t70) REVERT: J 169 LYS cc_start: 0.8104 (pttt) cc_final: 0.7786 (pttt) REVERT: J 300 MET cc_start: 0.7351 (mmm) cc_final: 0.7084 (mtp) REVERT: J 323 ASP cc_start: 0.8143 (OUTLIER) cc_final: 0.7837 (m-30) REVERT: K 164 GLU cc_start: 0.7670 (OUTLIER) cc_final: 0.7166 (mt-10) REVERT: K 248 LYS cc_start: 0.7651 (OUTLIER) cc_final: 0.7109 (tttt) REVERT: K 261 LYS cc_start: 0.7825 (tttt) cc_final: 0.7388 (ttmm) REVERT: K 361 TYR cc_start: 0.8241 (OUTLIER) cc_final: 0.7894 (m-80) REVERT: L 1 LEU cc_start: 0.7894 (tp) cc_final: 0.7691 (tp) REVERT: L 54 ASP cc_start: 0.8212 (OUTLIER) cc_final: 0.7813 (m-30) REVERT: L 61 ASP cc_start: 0.7845 (t0) cc_final: 0.7629 (t0) REVERT: L 169 LYS cc_start: 0.8466 (OUTLIER) cc_final: 0.8239 (ptmm) REVERT: L 220 ASN cc_start: 0.8049 (t0) cc_final: 0.7797 (t0) REVERT: L 268 LYS cc_start: 0.8149 (OUTLIER) cc_final: 0.7935 (mtpp) outliers start: 166 outliers final: 115 residues processed: 724 average time/residue: 0.2638 time to fit residues: 314.2860 Evaluate side-chains 736 residues out of total 4664 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 152 poor density : 584 time to evaluate : 2.096 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain O residue 30 VAL Chi-restraints excluded: chain O residue 94 GLU Chi-restraints excluded: chain O residue 191 ARG Chi-restraints excluded: chain O residue 201 LEU Chi-restraints excluded: chain O residue 268 LYS Chi-restraints excluded: chain O residue 281 VAL Chi-restraints excluded: chain O residue 289 SER Chi-restraints excluded: chain O residue 357 GLU Chi-restraints excluded: chain O residue 361 TYR Chi-restraints excluded: chain P residue 20 ARG Chi-restraints excluded: chain P residue 33 THR Chi-restraints excluded: chain P residue 84 TRP Chi-restraints excluded: chain P residue 154 LEU Chi-restraints excluded: chain P residue 161 LEU Chi-restraints excluded: chain P residue 171 THR Chi-restraints excluded: chain P residue 191 ARG Chi-restraints excluded: chain P residue 241 ASP Chi-restraints excluded: chain P residue 286 THR Chi-restraints excluded: chain P residue 290 SER Chi-restraints excluded: chain P residue 292 ILE Chi-restraints excluded: chain Q residue 1 LEU Chi-restraints excluded: chain Q residue 65 SER Chi-restraints excluded: chain Q residue 84 TRP Chi-restraints excluded: chain Q residue 248 LYS Chi-restraints excluded: chain Q residue 289 SER Chi-restraints excluded: chain Q residue 335 LEU Chi-restraints excluded: chain Q residue 361 TYR Chi-restraints excluded: chain R residue 3 VAL Chi-restraints excluded: chain R residue 62 SER Chi-restraints excluded: chain R residue 84 TRP Chi-restraints excluded: chain R residue 129 VAL Chi-restraints excluded: chain R residue 158 VAL Chi-restraints excluded: chain R residue 161 LEU Chi-restraints excluded: chain R residue 172 MET Chi-restraints excluded: chain R residue 241 ASP Chi-restraints excluded: chain R residue 306 LYS Chi-restraints excluded: chain A residue 1 LEU Chi-restraints excluded: chain A residue 23 SER Chi-restraints excluded: chain A residue 52 THR Chi-restraints excluded: chain A residue 62 GLU Chi-restraints excluded: chain A residue 84 TRP Chi-restraints excluded: chain A residue 87 LEU Chi-restraints excluded: chain A residue 122 LYS Chi-restraints excluded: chain A residue 123 SER Chi-restraints excluded: chain A residue 201 LEU Chi-restraints excluded: chain A residue 208 THR Chi-restraints excluded: chain A residue 261 LYS Chi-restraints excluded: chain A residue 295 SER Chi-restraints excluded: chain B residue 52 THR Chi-restraints excluded: chain B residue 98 VAL Chi-restraints excluded: chain B residue 172 MET Chi-restraints excluded: chain B residue 241 ASP Chi-restraints excluded: chain B residue 281 ILE Chi-restraints excluded: chain B residue 305 VAL Chi-restraints excluded: chain B residue 327 ILE Chi-restraints excluded: chain C residue 1 LEU Chi-restraints excluded: chain C residue 21 LYS Chi-restraints excluded: chain C residue 62 GLU Chi-restraints excluded: chain C residue 63 THR Chi-restraints excluded: chain C residue 65 SER Chi-restraints excluded: chain C residue 84 TRP Chi-restraints excluded: chain C residue 164 GLU Chi-restraints excluded: chain C residue 246 ILE Chi-restraints excluded: chain C residue 284 ARG Chi-restraints excluded: chain C residue 292 ILE Chi-restraints excluded: chain C residue 335 LEU Chi-restraints excluded: chain C residue 361 TYR Chi-restraints excluded: chain D residue 54 ASP Chi-restraints excluded: chain D residue 164 LYS Chi-restraints excluded: chain D residue 241 ASP Chi-restraints excluded: chain D residue 266 GLU Chi-restraints excluded: chain D residue 281 ILE Chi-restraints excluded: chain D residue 295 SER Chi-restraints excluded: chain E residue 22 ASP Chi-restraints excluded: chain E residue 28 VAL Chi-restraints excluded: chain E residue 30 VAL Chi-restraints excluded: chain E residue 62 GLU Chi-restraints excluded: chain E residue 94 GLU Chi-restraints excluded: chain E residue 146 ASN Chi-restraints excluded: chain E residue 191 ARG Chi-restraints excluded: chain E residue 201 LEU Chi-restraints excluded: chain E residue 268 LYS Chi-restraints excluded: chain E residue 357 GLU Chi-restraints excluded: chain F residue 3 VAL Chi-restraints excluded: chain F residue 20 ARG Chi-restraints excluded: chain F residue 37 VAL Chi-restraints excluded: chain F residue 75 SER Chi-restraints excluded: chain F residue 84 TRP Chi-restraints excluded: chain F residue 151 THR Chi-restraints excluded: chain F residue 161 LEU Chi-restraints excluded: chain F residue 191 ARG Chi-restraints excluded: chain F residue 292 ILE Chi-restraints excluded: chain F residue 300 MET Chi-restraints excluded: chain G residue 1 LEU Chi-restraints excluded: chain G residue 30 VAL Chi-restraints excluded: chain G residue 84 TRP Chi-restraints excluded: chain G residue 165 LEU Chi-restraints excluded: chain G residue 289 SER Chi-restraints excluded: chain G residue 331 LYS Chi-restraints excluded: chain G residue 339 VAL Chi-restraints excluded: chain G residue 362 GLU Chi-restraints excluded: chain H residue 62 SER Chi-restraints excluded: chain H residue 74 VAL Chi-restraints excluded: chain H residue 84 TRP Chi-restraints excluded: chain H residue 94 GLU Chi-restraints excluded: chain H residue 103 ASP Chi-restraints excluded: chain H residue 129 VAL Chi-restraints excluded: chain H residue 172 MET Chi-restraints excluded: chain H residue 218 LEU Chi-restraints excluded: chain H residue 241 ASP Chi-restraints excluded: chain I residue 1 LEU Chi-restraints excluded: chain I residue 23 SER Chi-restraints excluded: chain I residue 28 VAL Chi-restraints excluded: chain I residue 52 THR Chi-restraints excluded: chain I residue 73 VAL Chi-restraints excluded: chain I residue 84 TRP Chi-restraints excluded: chain I residue 87 LEU Chi-restraints excluded: chain I residue 122 LYS Chi-restraints excluded: chain I residue 159 LYS Chi-restraints excluded: chain I residue 191 ARG Chi-restraints excluded: chain I residue 201 LEU Chi-restraints excluded: chain I residue 208 THR Chi-restraints excluded: chain I residue 261 LYS Chi-restraints excluded: chain I residue 295 SER Chi-restraints excluded: chain I residue 335 LEU Chi-restraints excluded: chain J residue 37 VAL Chi-restraints excluded: chain J residue 56 ASP Chi-restraints excluded: chain J residue 98 VAL Chi-restraints excluded: chain J residue 116 VAL Chi-restraints excluded: chain J residue 125 ILE Chi-restraints excluded: chain J residue 145 SER Chi-restraints excluded: chain J residue 241 ASP Chi-restraints excluded: chain J residue 281 ILE Chi-restraints excluded: chain J residue 305 VAL Chi-restraints excluded: chain J residue 323 ASP Chi-restraints excluded: chain J residue 327 ILE Chi-restraints excluded: chain K residue 1 LEU Chi-restraints excluded: chain K residue 63 THR Chi-restraints excluded: chain K residue 65 SER Chi-restraints excluded: chain K residue 84 TRP Chi-restraints excluded: chain K residue 164 GLU Chi-restraints excluded: chain K residue 246 ILE Chi-restraints excluded: chain K residue 248 LYS Chi-restraints excluded: chain K residue 250 VAL Chi-restraints excluded: chain K residue 361 TYR Chi-restraints excluded: chain L residue 54 ASP Chi-restraints excluded: chain L residue 138 THR Chi-restraints excluded: chain L residue 169 LYS Chi-restraints excluded: chain L residue 241 ASP Chi-restraints excluded: chain L residue 268 LYS Chi-restraints excluded: chain L residue 281 ILE Chi-restraints excluded: chain L residue 295 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 552 random chunks: chunk 424 optimal weight: 2.9990 chunk 37 optimal weight: 6.9990 chunk 93 optimal weight: 4.9990 chunk 417 optimal weight: 0.0670 chunk 57 optimal weight: 10.0000 chunk 355 optimal weight: 2.9990 chunk 158 optimal weight: 4.9990 chunk 354 optimal weight: 3.9990 chunk 27 optimal weight: 5.9990 chunk 111 optimal weight: 0.2980 chunk 43 optimal weight: 0.0050 overall best weight: 1.2736 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: O 61 ASN O 146 ASN ** O 245 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 319 GLN B 220 ASN C 146 ASN E 146 ASN ** E 245 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 139 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 319 GLN J 220 ASN J 265 ASN L 81 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3406 r_free = 0.3406 target = 0.141506 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3006 r_free = 0.3006 target = 0.109497 restraints weight = 46996.846| |-----------------------------------------------------------------------------| r_work (start): 0.2999 rms_B_bonded: 1.54 r_work: 0.2807 rms_B_bonded: 2.76 restraints_weight: 0.5000 r_work: 0.2684 rms_B_bonded: 4.61 restraints_weight: 0.2500 r_work (final): 0.2684 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8665 moved from start: 0.1830 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 43976 Z= 0.141 Angle : 0.518 8.423 59880 Z= 0.279 Chirality : 0.047 0.243 7080 Planarity : 0.004 0.052 7608 Dihedral : 8.708 86.972 6891 Min Nonbonded Distance : 2.469 Molprobity Statistics. All-atom Clashscore : 5.96 Ramachandran Plot: Outliers : 0.61 % Allowed : 5.33 % Favored : 94.06 % Rotamer: Outliers : 3.60 % Allowed : 18.14 % Favored : 78.26 % 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: -0.22 (0.12), residues: 5608 helix: 1.01 (0.14), residues: 1572 sheet: -0.44 (0.15), residues: 1152 loop : -0.61 (0.12), residues: 2884 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG L 77 TYR 0.017 0.002 TYR K 178 PHE 0.024 0.002 PHE Q 348 TRP 0.007 0.001 TRP L 332 HIS 0.004 0.001 HIS C 176 Details of bonding type rmsd covalent geometry : bond 0.00331 (43968) covalent geometry : angle 0.51730 (59864) SS BOND : bond 0.00540 ( 8) SS BOND : angle 1.11448 ( 16) hydrogen bonds : bond 0.03187 ( 1769) hydrogen bonds : angle 4.59499 ( 5445) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11216 Ramachandran restraints generated. 5608 Oldfield, 0 Emsley, 5608 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11216 Ramachandran restraints generated. 5608 Oldfield, 0 Emsley, 5608 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 773 residues out of total 4664 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 168 poor density : 605 time to evaluate : 1.722 Fit side-chains REVERT: O 2 LYS cc_start: 0.8480 (mttm) cc_final: 0.8153 (mttp) REVERT: O 94 GLU cc_start: 0.8874 (OUTLIER) cc_final: 0.7804 (tm-30) REVERT: O 191 ARG cc_start: 0.9044 (OUTLIER) cc_final: 0.8703 (ptt180) REVERT: O 268 LYS cc_start: 0.8965 (OUTLIER) cc_final: 0.8314 (tttt) REVERT: P 20 ARG cc_start: 0.8229 (OUTLIER) cc_final: 0.5251 (mpt-90) REVERT: Q 361 TYR cc_start: 0.8026 (OUTLIER) cc_final: 0.7695 (t80) REVERT: Q 362 GLU cc_start: 0.8801 (tm-30) cc_final: 0.8273 (tm-30) REVERT: R 158 VAL cc_start: 0.7874 (OUTLIER) cc_final: 0.7564 (t) REVERT: R 172 MET cc_start: 0.7448 (OUTLIER) cc_final: 0.7248 (tmt) REVERT: R 212 LYS cc_start: 0.7309 (mttt) cc_final: 0.7019 (mtpt) REVERT: R 306 LYS cc_start: 0.8214 (OUTLIER) cc_final: 0.7826 (tptm) REVERT: A 87 LEU cc_start: 0.8630 (OUTLIER) cc_final: 0.8243 (mp) REVERT: A 122 LYS cc_start: 0.8210 (OUTLIER) cc_final: 0.7766 (tmtp) REVERT: B 126 PRO cc_start: 0.8203 (Cg_exo) cc_final: 0.7941 (Cg_endo) REVERT: B 323 ASP cc_start: 0.8051 (m-30) cc_final: 0.7741 (m-30) REVERT: C 164 GLU cc_start: 0.7677 (OUTLIER) cc_final: 0.7190 (mt-10) REVERT: C 284 ARG cc_start: 0.8566 (OUTLIER) cc_final: 0.8189 (mtp85) REVERT: C 361 TYR cc_start: 0.8195 (OUTLIER) cc_final: 0.7866 (m-80) REVERT: D 54 ASP cc_start: 0.8163 (OUTLIER) cc_final: 0.7749 (m-30) REVERT: D 61 ASP cc_start: 0.7991 (t0) cc_final: 0.7778 (t0) REVERT: D 87 MET cc_start: 0.7845 (mtm) cc_final: 0.7557 (mtp) REVERT: D 266 GLU cc_start: 0.6661 (OUTLIER) cc_final: 0.6346 (pt0) REVERT: E 62 GLU cc_start: 0.8342 (OUTLIER) cc_final: 0.7991 (pm20) REVERT: E 94 GLU cc_start: 0.8869 (OUTLIER) cc_final: 0.7777 (tm-30) REVERT: E 191 ARG cc_start: 0.9125 (OUTLIER) cc_final: 0.8127 (ptp-170) REVERT: E 268 LYS cc_start: 0.8898 (OUTLIER) cc_final: 0.8301 (tttt) REVERT: F 2 LYS cc_start: 0.6398 (mttt) cc_final: 0.5937 (mmmt) REVERT: F 20 ARG cc_start: 0.8223 (OUTLIER) cc_final: 0.5143 (mpt-90) REVERT: G 165 LEU cc_start: 0.8565 (OUTLIER) cc_final: 0.8235 (tp) REVERT: G 362 GLU cc_start: 0.8162 (OUTLIER) cc_final: 0.7737 (tm-30) REVERT: H 84 TRP cc_start: 0.7328 (OUTLIER) cc_final: 0.6538 (m100) REVERT: H 94 GLU cc_start: 0.7592 (OUTLIER) cc_final: 0.6443 (tm-30) REVERT: H 169 LYS cc_start: 0.7092 (ptpp) cc_final: 0.6522 (ptpp) REVERT: H 172 MET cc_start: 0.7377 (OUTLIER) cc_final: 0.7122 (tmt) REVERT: I 87 LEU cc_start: 0.8631 (OUTLIER) cc_final: 0.8312 (mp) REVERT: I 122 LYS cc_start: 0.8099 (OUTLIER) cc_final: 0.7634 (tmtp) REVERT: I 191 ARG cc_start: 0.8900 (OUTLIER) cc_final: 0.8435 (mtp180) REVERT: I 350 LYS cc_start: 0.8063 (mptt) cc_final: 0.7605 (mmmm) REVERT: J 56 ASP cc_start: 0.8094 (OUTLIER) cc_final: 0.7699 (t70) REVERT: J 169 LYS cc_start: 0.8140 (pttt) cc_final: 0.7777 (pttt) REVERT: J 300 MET cc_start: 0.7373 (mmm) cc_final: 0.7093 (mtp) REVERT: J 323 ASP cc_start: 0.8137 (OUTLIER) cc_final: 0.7856 (m-30) REVERT: K 134 GLU cc_start: 0.8217 (pm20) cc_final: 0.7987 (pm20) REVERT: K 164 GLU cc_start: 0.7687 (OUTLIER) cc_final: 0.7172 (mt-10) REVERT: K 248 LYS cc_start: 0.7650 (OUTLIER) cc_final: 0.7118 (tttt) REVERT: K 261 LYS cc_start: 0.7829 (tttt) cc_final: 0.7395 (ttmm) REVERT: K 361 TYR cc_start: 0.8219 (OUTLIER) cc_final: 0.7844 (m-80) REVERT: L 54 ASP cc_start: 0.8223 (OUTLIER) cc_final: 0.7823 (m-30) REVERT: L 61 ASP cc_start: 0.7793 (t0) cc_final: 0.7585 (t0) REVERT: L 169 LYS cc_start: 0.8487 (OUTLIER) cc_final: 0.8261 (ptmm) REVERT: L 220 ASN cc_start: 0.8021 (t0) cc_final: 0.7811 (t0) REVERT: L 268 LYS cc_start: 0.8170 (OUTLIER) cc_final: 0.7920 (mtpp) outliers start: 168 outliers final: 117 residues processed: 718 average time/residue: 0.2680 time to fit residues: 317.1416 Evaluate side-chains 741 residues out of total 4664 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 153 poor density : 588 time to evaluate : 1.696 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain O residue 30 VAL Chi-restraints excluded: chain O residue 61 ASN Chi-restraints excluded: chain O residue 94 GLU Chi-restraints excluded: chain O residue 146 ASN Chi-restraints excluded: chain O residue 191 ARG Chi-restraints excluded: chain O residue 201 LEU Chi-restraints excluded: chain O residue 268 LYS Chi-restraints excluded: chain O residue 281 VAL Chi-restraints excluded: chain O residue 289 SER Chi-restraints excluded: chain O residue 357 GLU Chi-restraints excluded: chain O residue 361 TYR Chi-restraints excluded: chain P residue 20 ARG Chi-restraints excluded: chain P residue 33 THR Chi-restraints excluded: chain P residue 84 TRP Chi-restraints excluded: chain P residue 154 LEU Chi-restraints excluded: chain P residue 161 LEU Chi-restraints excluded: chain P residue 171 THR Chi-restraints excluded: chain P residue 191 ARG Chi-restraints excluded: chain P residue 241 ASP Chi-restraints excluded: chain P residue 286 THR Chi-restraints excluded: chain P residue 290 SER Chi-restraints excluded: chain P residue 292 ILE Chi-restraints excluded: chain Q residue 1 LEU Chi-restraints excluded: chain Q residue 65 SER Chi-restraints excluded: chain Q residue 84 TRP Chi-restraints excluded: chain Q residue 248 LYS Chi-restraints excluded: chain Q residue 289 SER Chi-restraints excluded: chain Q residue 335 LEU Chi-restraints excluded: chain Q residue 361 TYR Chi-restraints excluded: chain R residue 3 VAL Chi-restraints excluded: chain R residue 37 VAL Chi-restraints excluded: chain R residue 62 SER Chi-restraints excluded: chain R residue 84 TRP Chi-restraints excluded: chain R residue 129 VAL Chi-restraints excluded: chain R residue 158 VAL Chi-restraints excluded: chain R residue 161 LEU Chi-restraints excluded: chain R residue 172 MET Chi-restraints excluded: chain R residue 241 ASP Chi-restraints excluded: chain R residue 306 LYS Chi-restraints excluded: chain A residue 1 LEU Chi-restraints excluded: chain A residue 23 SER Chi-restraints excluded: chain A residue 52 THR Chi-restraints excluded: chain A residue 62 GLU Chi-restraints excluded: chain A residue 84 TRP Chi-restraints excluded: chain A residue 87 LEU Chi-restraints excluded: chain A residue 122 LYS Chi-restraints excluded: chain A residue 123 SER Chi-restraints excluded: chain A residue 201 LEU Chi-restraints excluded: chain A residue 208 THR Chi-restraints excluded: chain A residue 261 LYS Chi-restraints excluded: chain A residue 295 SER Chi-restraints excluded: chain B residue 52 THR Chi-restraints excluded: chain B residue 98 VAL Chi-restraints excluded: chain B residue 172 MET Chi-restraints excluded: chain B residue 241 ASP Chi-restraints excluded: chain B residue 281 ILE Chi-restraints excluded: chain B residue 305 VAL Chi-restraints excluded: chain B residue 327 ILE Chi-restraints excluded: chain C residue 1 LEU Chi-restraints excluded: chain C residue 62 GLU Chi-restraints excluded: chain C residue 63 THR Chi-restraints excluded: chain C residue 65 SER Chi-restraints excluded: chain C residue 84 TRP Chi-restraints excluded: chain C residue 164 GLU Chi-restraints excluded: chain C residue 246 ILE Chi-restraints excluded: chain C residue 250 VAL Chi-restraints excluded: chain C residue 284 ARG Chi-restraints excluded: chain C residue 335 LEU Chi-restraints excluded: chain C residue 361 TYR Chi-restraints excluded: chain D residue 54 ASP Chi-restraints excluded: chain D residue 241 ASP Chi-restraints excluded: chain D residue 266 GLU Chi-restraints excluded: chain D residue 281 ILE Chi-restraints excluded: chain D residue 295 SER Chi-restraints excluded: chain E residue 22 ASP Chi-restraints excluded: chain E residue 28 VAL Chi-restraints excluded: chain E residue 30 VAL Chi-restraints excluded: chain E residue 62 GLU Chi-restraints excluded: chain E residue 94 GLU Chi-restraints excluded: chain E residue 191 ARG Chi-restraints excluded: chain E residue 201 LEU Chi-restraints excluded: chain E residue 268 LYS Chi-restraints excluded: chain E residue 357 GLU Chi-restraints excluded: chain F residue 20 ARG Chi-restraints excluded: chain F residue 37 VAL Chi-restraints excluded: chain F residue 75 SER Chi-restraints excluded: chain F residue 84 TRP Chi-restraints excluded: chain F residue 151 THR Chi-restraints excluded: chain F residue 161 LEU Chi-restraints excluded: chain F residue 191 ARG Chi-restraints excluded: chain F residue 292 ILE Chi-restraints excluded: chain F residue 300 MET Chi-restraints excluded: chain G residue 1 LEU Chi-restraints excluded: chain G residue 25 LEU Chi-restraints excluded: chain G residue 30 VAL Chi-restraints excluded: chain G residue 84 TRP Chi-restraints excluded: chain G residue 165 LEU Chi-restraints excluded: chain G residue 289 SER Chi-restraints excluded: chain G residue 331 LYS Chi-restraints excluded: chain G residue 339 VAL Chi-restraints excluded: chain G residue 362 GLU Chi-restraints excluded: chain H residue 25 LEU Chi-restraints excluded: chain H residue 62 SER Chi-restraints excluded: chain H residue 74 VAL Chi-restraints excluded: chain H residue 84 TRP Chi-restraints excluded: chain H residue 94 GLU Chi-restraints excluded: chain H residue 103 ASP Chi-restraints excluded: chain H residue 129 VAL Chi-restraints excluded: chain H residue 172 MET Chi-restraints excluded: chain H residue 218 LEU Chi-restraints excluded: chain H residue 241 ASP Chi-restraints excluded: chain I residue 1 LEU Chi-restraints excluded: chain I residue 23 SER Chi-restraints excluded: chain I residue 28 VAL Chi-restraints excluded: chain I residue 52 THR Chi-restraints excluded: chain I residue 84 TRP Chi-restraints excluded: chain I residue 87 LEU Chi-restraints excluded: chain I residue 122 LYS Chi-restraints excluded: chain I residue 159 LYS Chi-restraints excluded: chain I residue 191 ARG Chi-restraints excluded: chain I residue 201 LEU Chi-restraints excluded: chain I residue 208 THR Chi-restraints excluded: chain I residue 261 LYS Chi-restraints excluded: chain I residue 295 SER Chi-restraints excluded: chain I residue 335 LEU Chi-restraints excluded: chain J residue 37 VAL Chi-restraints excluded: chain J residue 56 ASP Chi-restraints excluded: chain J residue 98 VAL Chi-restraints excluded: chain J residue 116 VAL Chi-restraints excluded: chain J residue 125 ILE Chi-restraints excluded: chain J residue 145 SER Chi-restraints excluded: chain J residue 241 ASP Chi-restraints excluded: chain J residue 305 VAL Chi-restraints excluded: chain J residue 323 ASP Chi-restraints excluded: chain J residue 327 ILE Chi-restraints excluded: chain K residue 1 LEU Chi-restraints excluded: chain K residue 30 VAL Chi-restraints excluded: chain K residue 63 THR Chi-restraints excluded: chain K residue 65 SER Chi-restraints excluded: chain K residue 84 TRP Chi-restraints excluded: chain K residue 164 GLU Chi-restraints excluded: chain K residue 246 ILE Chi-restraints excluded: chain K residue 248 LYS Chi-restraints excluded: chain K residue 250 VAL Chi-restraints excluded: chain K residue 361 TYR Chi-restraints excluded: chain L residue 54 ASP Chi-restraints excluded: chain L residue 138 THR Chi-restraints excluded: chain L residue 161 LEU Chi-restraints excluded: chain L residue 169 LYS Chi-restraints excluded: chain L residue 241 ASP Chi-restraints excluded: chain L residue 268 LYS Chi-restraints excluded: chain L residue 281 ILE Chi-restraints excluded: chain L residue 295 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 552 random chunks: chunk 242 optimal weight: 0.8980 chunk 330 optimal weight: 5.9990 chunk 35 optimal weight: 3.9990 chunk 442 optimal weight: 0.0670 chunk 33 optimal weight: 0.2980 chunk 537 optimal weight: 0.9980 chunk 68 optimal weight: 7.9990 chunk 431 optimal weight: 1.9990 chunk 289 optimal weight: 1.9990 chunk 399 optimal weight: 5.9990 chunk 55 optimal weight: 6.9990 overall best weight: 0.8520 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: O 146 ASN ** O 245 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 220 ASN C 146 ASN E 146 ASN ** E 245 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 139 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 220 ASN ** L 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3428 r_free = 0.3428 target = 0.143384 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3028 r_free = 0.3028 target = 0.111113 restraints weight = 47090.740| |-----------------------------------------------------------------------------| r_work (start): 0.3010 rms_B_bonded: 1.58 r_work: 0.2822 rms_B_bonded: 2.85 restraints_weight: 0.5000 r_work: 0.2699 rms_B_bonded: 4.78 restraints_weight: 0.2500 r_work (final): 0.2699 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8651 moved from start: 0.1945 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 43976 Z= 0.117 Angle : 0.501 8.346 59880 Z= 0.270 Chirality : 0.046 0.259 7080 Planarity : 0.004 0.043 7608 Dihedral : 8.544 87.215 6890 Min Nonbonded Distance : 2.527 Molprobity Statistics. All-atom Clashscore : 6.02 Ramachandran Plot: Outliers : 0.61 % Allowed : 5.19 % Favored : 94.20 % Rotamer: Outliers : 3.34 % Allowed : 18.48 % Favored : 78.17 % 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: -0.17 (0.12), residues: 5608 helix: 1.09 (0.14), residues: 1572 sheet: -0.43 (0.15), residues: 1152 loop : -0.59 (0.12), residues: 2884 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG L 77 TYR 0.013 0.002 TYR K 178 PHE 0.021 0.001 PHE Q 348 TRP 0.008 0.001 TRP D 84 HIS 0.003 0.001 HIS C 176 Details of bonding type rmsd covalent geometry : bond 0.00273 (43968) covalent geometry : angle 0.50041 (59864) SS BOND : bond 0.00506 ( 8) SS BOND : angle 1.13749 ( 16) hydrogen bonds : bond 0.02976 ( 1769) hydrogen bonds : angle 4.51952 ( 5445) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11216 Ramachandran restraints generated. 5608 Oldfield, 0 Emsley, 5608 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11216 Ramachandran restraints generated. 5608 Oldfield, 0 Emsley, 5608 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 763 residues out of total 4664 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 156 poor density : 607 time to evaluate : 1.723 Fit side-chains REVERT: O 2 LYS cc_start: 0.8493 (mttm) cc_final: 0.8181 (mttp) REVERT: O 94 GLU cc_start: 0.8844 (OUTLIER) cc_final: 0.7811 (tm-30) REVERT: O 191 ARG cc_start: 0.9033 (OUTLIER) cc_final: 0.8678 (ptt180) REVERT: O 268 LYS cc_start: 0.8958 (OUTLIER) cc_final: 0.8314 (tttt) REVERT: P 20 ARG cc_start: 0.8211 (OUTLIER) cc_final: 0.5291 (mpt-90) REVERT: P 248 LYS cc_start: 0.7075 (tttt) cc_final: 0.6698 (tttt) REVERT: P 326 ASP cc_start: 0.7135 (OUTLIER) cc_final: 0.6547 (m-30) REVERT: Q 350 LYS cc_start: 0.7779 (mmmm) cc_final: 0.7202 (mmtp) REVERT: Q 361 TYR cc_start: 0.7979 (OUTLIER) cc_final: 0.7660 (t80) REVERT: R 84 TRP cc_start: 0.7332 (OUTLIER) cc_final: 0.6611 (m100) REVERT: R 158 VAL cc_start: 0.7836 (t) cc_final: 0.7536 (t) REVERT: R 172 MET cc_start: 0.7418 (OUTLIER) cc_final: 0.7190 (tmt) REVERT: R 212 LYS cc_start: 0.7307 (mttt) cc_final: 0.7003 (mtpt) REVERT: R 306 LYS cc_start: 0.8184 (OUTLIER) cc_final: 0.7826 (tptm) REVERT: A 87 LEU cc_start: 0.8633 (OUTLIER) cc_final: 0.8247 (mp) REVERT: A 122 LYS cc_start: 0.8196 (OUTLIER) cc_final: 0.7745 (tmtp) REVERT: B 114 LYS cc_start: 0.8008 (mttt) cc_final: 0.7720 (mttt) REVERT: B 126 PRO cc_start: 0.8197 (Cg_exo) cc_final: 0.7945 (Cg_endo) REVERT: B 323 ASP cc_start: 0.8063 (m-30) cc_final: 0.7736 (m-30) REVERT: C 50 LEU cc_start: 0.9237 (mt) cc_final: 0.8968 (mt) REVERT: C 164 GLU cc_start: 0.7635 (OUTLIER) cc_final: 0.7146 (mt-10) REVERT: C 284 ARG cc_start: 0.8559 (OUTLIER) cc_final: 0.8174 (mtp85) REVERT: C 361 TYR cc_start: 0.8180 (OUTLIER) cc_final: 0.7853 (m-80) REVERT: D 54 ASP cc_start: 0.8160 (OUTLIER) cc_final: 0.7746 (m-30) REVERT: D 61 ASP cc_start: 0.7972 (t0) cc_final: 0.7770 (t0) REVERT: D 87 MET cc_start: 0.7793 (mtm) cc_final: 0.7517 (mtp) REVERT: D 266 GLU cc_start: 0.6653 (OUTLIER) cc_final: 0.6336 (pt0) REVERT: E 62 GLU cc_start: 0.8324 (OUTLIER) cc_final: 0.7982 (pm20) REVERT: E 94 GLU cc_start: 0.8847 (OUTLIER) cc_final: 0.7771 (tm-30) REVERT: E 191 ARG cc_start: 0.9104 (OUTLIER) cc_final: 0.8066 (ptp-170) REVERT: E 253 GLU cc_start: 0.7592 (mp0) cc_final: 0.7279 (mp0) REVERT: E 268 LYS cc_start: 0.8883 (OUTLIER) cc_final: 0.8274 (tttt) REVERT: F 2 LYS cc_start: 0.6366 (mttt) cc_final: 0.5908 (mmmt) REVERT: F 20 ARG cc_start: 0.8225 (OUTLIER) cc_final: 0.5183 (mpt-90) REVERT: G 165 LEU cc_start: 0.8543 (OUTLIER) cc_final: 0.8213 (tp) REVERT: G 362 GLU cc_start: 0.8118 (OUTLIER) cc_final: 0.7655 (tm-30) REVERT: H 94 GLU cc_start: 0.7570 (OUTLIER) cc_final: 0.6455 (tm-30) REVERT: H 169 LYS cc_start: 0.7052 (ptpp) cc_final: 0.6501 (ptpp) REVERT: H 172 MET cc_start: 0.7437 (OUTLIER) cc_final: 0.7177 (tmt) REVERT: H 298 MET cc_start: 0.7728 (ptp) cc_final: 0.7519 (ptm) REVERT: I 87 LEU cc_start: 0.8612 (OUTLIER) cc_final: 0.8312 (mp) REVERT: I 122 LYS cc_start: 0.8056 (OUTLIER) cc_final: 0.7581 (tmtp) REVERT: I 191 ARG cc_start: 0.8884 (OUTLIER) cc_final: 0.8413 (mtp180) REVERT: I 350 LYS cc_start: 0.8077 (mptt) cc_final: 0.7629 (mmmm) REVERT: I 362 GLU cc_start: 0.8747 (tm-30) cc_final: 0.6258 (mt-10) REVERT: J 56 ASP cc_start: 0.8118 (OUTLIER) cc_final: 0.7712 (t70) REVERT: J 169 LYS cc_start: 0.8158 (pttt) cc_final: 0.7763 (pttt) REVERT: J 300 MET cc_start: 0.7344 (mmm) cc_final: 0.7070 (mtp) REVERT: J 323 ASP cc_start: 0.8131 (OUTLIER) cc_final: 0.7870 (m-30) REVERT: K 50 LEU cc_start: 0.9302 (mt) cc_final: 0.9084 (mt) REVERT: K 164 GLU cc_start: 0.7673 (OUTLIER) cc_final: 0.7166 (mt-10) REVERT: K 248 LYS cc_start: 0.7643 (OUTLIER) cc_final: 0.7106 (tttt) REVERT: K 261 LYS cc_start: 0.7805 (tttt) cc_final: 0.7373 (ttmm) REVERT: K 361 TYR cc_start: 0.8211 (OUTLIER) cc_final: 0.7846 (m-80) REVERT: L 54 ASP cc_start: 0.8210 (OUTLIER) cc_final: 0.7814 (m-30) REVERT: L 61 ASP cc_start: 0.7814 (t0) cc_final: 0.7596 (t0) REVERT: L 169 LYS cc_start: 0.8434 (OUTLIER) cc_final: 0.8209 (ptmm) REVERT: L 268 LYS cc_start: 0.8156 (OUTLIER) cc_final: 0.7914 (mtpp) outliers start: 156 outliers final: 112 residues processed: 716 average time/residue: 0.2528 time to fit residues: 300.1414 Evaluate side-chains 738 residues out of total 4664 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 148 poor density : 590 time to evaluate : 1.589 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain O residue 30 VAL Chi-restraints excluded: chain O residue 94 GLU Chi-restraints excluded: chain O residue 146 ASN Chi-restraints excluded: chain O residue 191 ARG Chi-restraints excluded: chain O residue 201 LEU Chi-restraints excluded: chain O residue 268 LYS Chi-restraints excluded: chain O residue 281 VAL Chi-restraints excluded: chain O residue 289 SER Chi-restraints excluded: chain O residue 357 GLU Chi-restraints excluded: chain P residue 20 ARG Chi-restraints excluded: chain P residue 84 TRP Chi-restraints excluded: chain P residue 154 LEU Chi-restraints excluded: chain P residue 161 LEU Chi-restraints excluded: chain P residue 171 THR Chi-restraints excluded: chain P residue 191 ARG Chi-restraints excluded: chain P residue 241 ASP Chi-restraints excluded: chain P residue 286 THR Chi-restraints excluded: chain P residue 290 SER Chi-restraints excluded: chain P residue 292 ILE Chi-restraints excluded: chain P residue 326 ASP Chi-restraints excluded: chain Q residue 1 LEU Chi-restraints excluded: chain Q residue 25 LEU Chi-restraints excluded: chain Q residue 30 VAL Chi-restraints excluded: chain Q residue 65 SER Chi-restraints excluded: chain Q residue 84 TRP Chi-restraints excluded: chain Q residue 248 LYS Chi-restraints excluded: chain Q residue 289 SER Chi-restraints excluded: chain Q residue 335 LEU Chi-restraints excluded: chain Q residue 361 TYR Chi-restraints excluded: chain R residue 3 VAL Chi-restraints excluded: chain R residue 84 TRP Chi-restraints excluded: chain R residue 129 VAL Chi-restraints excluded: chain R residue 161 LEU Chi-restraints excluded: chain R residue 172 MET Chi-restraints excluded: chain R residue 241 ASP Chi-restraints excluded: chain R residue 300 MET Chi-restraints excluded: chain R residue 306 LYS Chi-restraints excluded: chain A residue 1 LEU Chi-restraints excluded: chain A residue 23 SER Chi-restraints excluded: chain A residue 52 THR Chi-restraints excluded: chain A residue 62 GLU Chi-restraints excluded: chain A residue 84 TRP Chi-restraints excluded: chain A residue 87 LEU Chi-restraints excluded: chain A residue 122 LYS Chi-restraints excluded: chain A residue 123 SER Chi-restraints excluded: chain A residue 201 LEU Chi-restraints excluded: chain A residue 208 THR Chi-restraints excluded: chain A residue 261 LYS Chi-restraints excluded: chain A residue 295 SER Chi-restraints excluded: chain B residue 98 VAL Chi-restraints excluded: chain B residue 172 MET Chi-restraints excluded: chain B residue 241 ASP Chi-restraints excluded: chain B residue 281 ILE Chi-restraints excluded: chain B residue 305 VAL Chi-restraints excluded: chain B residue 327 ILE Chi-restraints excluded: chain C residue 1 LEU Chi-restraints excluded: chain C residue 21 LYS Chi-restraints excluded: chain C residue 62 GLU Chi-restraints excluded: chain C residue 63 THR Chi-restraints excluded: chain C residue 65 SER Chi-restraints excluded: chain C residue 84 TRP Chi-restraints excluded: chain C residue 164 GLU Chi-restraints excluded: chain C residue 246 ILE Chi-restraints excluded: chain C residue 250 VAL Chi-restraints excluded: chain C residue 284 ARG Chi-restraints excluded: chain C residue 335 LEU Chi-restraints excluded: chain C residue 361 TYR Chi-restraints excluded: chain D residue 54 ASP Chi-restraints excluded: chain D residue 164 LYS Chi-restraints excluded: chain D residue 241 ASP Chi-restraints excluded: chain D residue 266 GLU Chi-restraints excluded: chain D residue 281 ILE Chi-restraints excluded: chain D residue 295 SER Chi-restraints excluded: chain E residue 28 VAL Chi-restraints excluded: chain E residue 30 VAL Chi-restraints excluded: chain E residue 62 GLU Chi-restraints excluded: chain E residue 94 GLU Chi-restraints excluded: chain E residue 146 ASN Chi-restraints excluded: chain E residue 191 ARG Chi-restraints excluded: chain E residue 201 LEU Chi-restraints excluded: chain E residue 268 LYS Chi-restraints excluded: chain E residue 357 GLU Chi-restraints excluded: chain F residue 20 ARG Chi-restraints excluded: chain F residue 37 VAL Chi-restraints excluded: chain F residue 75 SER Chi-restraints excluded: chain F residue 84 TRP Chi-restraints excluded: chain F residue 151 THR Chi-restraints excluded: chain F residue 161 LEU Chi-restraints excluded: chain F residue 191 ARG Chi-restraints excluded: chain F residue 292 ILE Chi-restraints excluded: chain F residue 300 MET Chi-restraints excluded: chain G residue 1 LEU Chi-restraints excluded: chain G residue 25 LEU Chi-restraints excluded: chain G residue 30 VAL Chi-restraints excluded: chain G residue 84 TRP Chi-restraints excluded: chain G residue 165 LEU Chi-restraints excluded: chain G residue 289 SER Chi-restraints excluded: chain G residue 331 LYS Chi-restraints excluded: chain G residue 339 VAL Chi-restraints excluded: chain G residue 362 GLU Chi-restraints excluded: chain H residue 25 LEU Chi-restraints excluded: chain H residue 62 SER Chi-restraints excluded: chain H residue 74 VAL Chi-restraints excluded: chain H residue 94 GLU Chi-restraints excluded: chain H residue 103 ASP Chi-restraints excluded: chain H residue 129 VAL Chi-restraints excluded: chain H residue 172 MET Chi-restraints excluded: chain H residue 218 LEU Chi-restraints excluded: chain H residue 241 ASP Chi-restraints excluded: chain I residue 1 LEU Chi-restraints excluded: chain I residue 23 SER Chi-restraints excluded: chain I residue 28 VAL Chi-restraints excluded: chain I residue 52 THR Chi-restraints excluded: chain I residue 84 TRP Chi-restraints excluded: chain I residue 87 LEU Chi-restraints excluded: chain I residue 122 LYS Chi-restraints excluded: chain I residue 159 LYS Chi-restraints excluded: chain I residue 191 ARG Chi-restraints excluded: chain I residue 201 LEU Chi-restraints excluded: chain I residue 208 THR Chi-restraints excluded: chain I residue 261 LYS Chi-restraints excluded: chain I residue 295 SER Chi-restraints excluded: chain I residue 335 LEU Chi-restraints excluded: chain J residue 37 VAL Chi-restraints excluded: chain J residue 56 ASP Chi-restraints excluded: chain J residue 116 VAL Chi-restraints excluded: chain J residue 125 ILE Chi-restraints excluded: chain J residue 145 SER Chi-restraints excluded: chain J residue 241 ASP Chi-restraints excluded: chain J residue 305 VAL Chi-restraints excluded: chain J residue 323 ASP Chi-restraints excluded: chain J residue 327 ILE Chi-restraints excluded: chain K residue 1 LEU Chi-restraints excluded: chain K residue 30 VAL Chi-restraints excluded: chain K residue 63 THR Chi-restraints excluded: chain K residue 65 SER Chi-restraints excluded: chain K residue 84 TRP Chi-restraints excluded: chain K residue 164 GLU Chi-restraints excluded: chain K residue 246 ILE Chi-restraints excluded: chain K residue 248 LYS Chi-restraints excluded: chain K residue 250 VAL Chi-restraints excluded: chain K residue 361 TYR Chi-restraints excluded: chain L residue 54 ASP Chi-restraints excluded: chain L residue 169 LYS Chi-restraints excluded: chain L residue 241 ASP Chi-restraints excluded: chain L residue 268 LYS Chi-restraints excluded: chain L residue 281 ILE Chi-restraints excluded: chain L residue 295 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 552 random chunks: chunk 273 optimal weight: 0.9990 chunk 38 optimal weight: 0.0000 chunk 76 optimal weight: 0.0370 chunk 331 optimal weight: 6.9990 chunk 383 optimal weight: 5.9990 chunk 378 optimal weight: 0.9980 chunk 188 optimal weight: 10.0000 chunk 129 optimal weight: 2.9990 chunk 130 optimal weight: 10.0000 chunk 332 optimal weight: 0.3980 chunk 455 optimal weight: 4.9990 overall best weight: 0.4864 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: O 146 ASN ** O 245 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 226 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 220 ASN C 146 ASN E 146 ASN ** E 245 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 139 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 152 ASN I 319 GLN J 220 ASN K 146 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3447 r_free = 0.3447 target = 0.145093 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3053 r_free = 0.3053 target = 0.113060 restraints weight = 47190.099| |-----------------------------------------------------------------------------| r_work (start): 0.3047 rms_B_bonded: 1.58 r_work: 0.2859 rms_B_bonded: 2.83 restraints_weight: 0.5000 r_work: 0.2737 rms_B_bonded: 4.74 restraints_weight: 0.2500 r_work (final): 0.2737 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8615 moved from start: 0.2141 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.039 43976 Z= 0.100 Angle : 0.482 8.313 59880 Z= 0.260 Chirality : 0.045 0.238 7080 Planarity : 0.004 0.049 7608 Dihedral : 8.235 87.613 6888 Min Nonbonded Distance : 2.496 Molprobity Statistics. All-atom Clashscore : 6.31 Ramachandran Plot: Outliers : 0.61 % Allowed : 4.96 % Favored : 94.44 % Rotamer: Outliers : 2.96 % Allowed : 19.13 % Favored : 77.92 % 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: -0.10 (0.12), residues: 5608 helix: 1.22 (0.14), residues: 1572 sheet: -0.50 (0.15), residues: 1150 loop : -0.55 (0.12), residues: 2886 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG D 191 TYR 0.011 0.001 TYR K 178 PHE 0.020 0.001 PHE Q 348 TRP 0.010 0.001 TRP D 84 HIS 0.003 0.001 HIS R 139 Details of bonding type rmsd covalent geometry : bond 0.00230 (43968) covalent geometry : angle 0.48197 (59864) SS BOND : bond 0.00467 ( 8) SS BOND : angle 1.13797 ( 16) hydrogen bonds : bond 0.02731 ( 1769) hydrogen bonds : angle 4.41880 ( 5445) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 12684.33 seconds wall clock time: 218 minutes 12.18 seconds (13092.18 seconds total)