Starting phenix.real_space_refine on Thu Jan 15 13:03:22 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8pbd_17585/01_2026/8pbd_17585.cif Found real_map, /net/cci-nas-00/data/ceres_data/8pbd_17585/01_2026/8pbd_17585.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.83 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8pbd_17585/01_2026/8pbd_17585.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8pbd_17585/01_2026/8pbd_17585.map" model { file = "/net/cci-nas-00/data/ceres_data/8pbd_17585/01_2026/8pbd_17585.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8pbd_17585/01_2026/8pbd_17585.cif" } resolution = 2.83 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= 0.072 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians Ca 20 9.91 5 P 84 5.49 5 S 139 5.16 5 C 16254 2.51 5 N 4665 2.21 5 O 5204 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 20 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5927/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 26366 Number of models: 1 Model: "" Number of chains: 13 Chain: "A" Number of atoms: 2384 Number of conformers: 1 Conformer: "" Number of residues, atoms: 311, 2384 Classifications: {'peptide': 311} Modifications used: {'COO': 1} Link IDs: {'CIS': 1, 'PTRANS': 10, 'TRANS': 299} Chain breaks: 1 Chain: "K" Number of atoms: 121 Number of conformers: 1 Conformer: "" Number of residues, atoms: 16, 121 Classifications: {'peptide': 16} Link IDs: {'PTRANS': 3, 'TRANS': 12} Chain: "T" Number of atoms: 585 Number of conformers: 1 Conformer: "" Number of residues, atoms: 27, 585 Classifications: {'DNA': 27} Link IDs: {'rna3p': 26} Chain: "U" Number of atoms: 522 Number of conformers: 1 Conformer: "" Number of residues, atoms: 27, 522 Classifications: {'DNA': 27} Link IDs: {'rna3p': 26} Chain: "A" Number of atoms: 34 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 34 Unusual residues: {' CA': 3, 'ATP': 1} Classifications: {'undetermined': 4} Link IDs: {None: 3} Chain: "B" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' CA': 1} Classifications: {'undetermined': 1} Chain: "C" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' CA': 1} Classifications: {'undetermined': 1} Chain: "D" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' CA': 1} Classifications: {'undetermined': 1} Chain: "E" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' CA': 1} Classifications: {'undetermined': 1} Chain: "F" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' CA': 1} Classifications: {'undetermined': 1} Chain: "G" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' CA': 1} Classifications: {'undetermined': 1} Chain: "H" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' CA': 1} Classifications: {'undetermined': 1} Chain: "I" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' CA': 1} Classifications: {'undetermined': 1} Restraints were copied for chains: B, C, D, E, F, G, H, I, J, L, M, N, O, P, Q, R, S Time building chain proxies: 4.45, per 1000 atoms: 0.17 Number of scatterers: 26366 At special positions: 0 Unit cell: (123.88, 121.272, 220.376, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) Ca 20 19.99 S 139 16.00 P 84 15.00 O 5204 8.00 N 4665 7.00 C 16254 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 2.64 Conformation dependent library (CDL) restraints added in 1.2 seconds 6392 Ramachandran restraints generated. 3196 Oldfield, 0 Emsley, 3196 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5968 Finding SS restraints... Secondary structure from input PDB file: 170 helices and 30 sheets defined 51.4% alpha, 16.3% beta 20 base pairs and 36 stacking pairs defined. Time for finding SS restraints: 3.74 Creating SS restraints... Processing helix chain 'A' and resid 24 through 32 removed outlier: 3.796A pdb=" N GLN A 30 " --> pdb=" O ARG A 27 " (cutoff:3.500A) Processing helix chain 'A' and resid 34 through 43 Processing helix chain 'A' and resid 48 through 54 Processing helix chain 'A' and resid 56 through 62 removed outlier: 3.688A pdb=" N LEU A 60 " --> pdb=" O PRO A 56 " (cutoff:3.500A) Processing helix chain 'A' and resid 67 through 82 removed outlier: 3.789A pdb=" N LEU A 81 " --> pdb=" O GLU A 77 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N VAL A 82 " --> pdb=" O ALA A 78 " (cutoff:3.500A) Processing helix chain 'A' and resid 89 through 98 removed outlier: 3.775A pdb=" N GLU A 98 " --> pdb=" O GLN A 94 " (cutoff:3.500A) Processing helix chain 'A' and resid 106 through 114 removed outlier: 3.589A pdb=" N LEU A 112 " --> pdb=" O GLU A 108 " (cutoff:3.500A) Processing helix chain 'A' and resid 132 through 144 Processing helix chain 'A' and resid 145 through 146 No H-bonds generated for 'chain 'A' and resid 145 through 146' Processing helix chain 'A' and resid 147 through 151 Processing helix chain 'A' and resid 167 through 179 removed outlier: 3.789A pdb=" N LEU A 171 " --> pdb=" O ARG A 167 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N VAL A 174 " --> pdb=" O ARG A 170 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N ARG A 177 " --> pdb=" O ALA A 173 " (cutoff:3.500A) Processing helix chain 'A' and resid 181 through 186 Processing helix chain 'A' and resid 196 through 214 removed outlier: 3.935A pdb=" N LEU A 204 " --> pdb=" O GLN A 200 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N TYR A 205 " --> pdb=" O THR A 201 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N ALA A 209 " --> pdb=" O TYR A 205 " (cutoff:3.500A) removed outlier: 3.795A pdb=" N VAL A 212 " --> pdb=" O SER A 208 " (cutoff:3.500A) removed outlier: 3.744A pdb=" N GLU A 213 " --> pdb=" O ALA A 209 " (cutoff:3.500A) Processing helix chain 'A' and resid 227 through 232 removed outlier: 3.817A pdb=" N TYR A 232 " --> pdb=" O TYR A 228 " (cutoff:3.500A) Processing helix chain 'A' and resid 234 through 236 No H-bonds generated for 'chain 'A' and resid 234 through 236' Processing helix chain 'A' and resid 237 through 259 Processing helix chain 'A' and resid 288 through 296 removed outlier: 3.740A pdb=" N ILE A 292 " --> pdb=" O GLY A 288 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N ALA A 295 " --> pdb=" O ILE A 291 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N SER A 296 " --> pdb=" O ILE A 292 " (cutoff:3.500A) Processing helix chain 'B' and resid 24 through 32 removed outlier: 3.795A pdb=" N GLN B 30 " --> pdb=" O ARG B 27 " (cutoff:3.500A) Processing helix chain 'B' and resid 34 through 43 Processing helix chain 'B' and resid 48 through 54 Processing helix chain 'B' and resid 56 through 62 removed outlier: 3.688A pdb=" N LEU B 60 " --> pdb=" O PRO B 56 " (cutoff:3.500A) Processing helix chain 'B' and resid 67 through 82 removed outlier: 3.789A pdb=" N LEU B 81 " --> pdb=" O GLU B 77 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N VAL B 82 " --> pdb=" O ALA B 78 " (cutoff:3.500A) Processing helix chain 'B' and resid 89 through 98 removed outlier: 3.775A pdb=" N GLU B 98 " --> pdb=" O GLN B 94 " (cutoff:3.500A) Processing helix chain 'B' and resid 106 through 114 removed outlier: 3.590A pdb=" N LEU B 112 " --> pdb=" O GLU B 108 " (cutoff:3.500A) Processing helix chain 'B' and resid 132 through 144 Processing helix chain 'B' and resid 145 through 146 No H-bonds generated for 'chain 'B' and resid 145 through 146' Processing helix chain 'B' and resid 147 through 151 Processing helix chain 'B' and resid 167 through 179 removed outlier: 3.789A pdb=" N LEU B 171 " --> pdb=" O ARG B 167 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N VAL B 174 " --> pdb=" O ARG B 170 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N ARG B 177 " --> pdb=" O ALA B 173 " (cutoff:3.500A) Processing helix chain 'B' and resid 181 through 186 Processing helix chain 'B' and resid 196 through 214 removed outlier: 3.935A pdb=" N LEU B 204 " --> pdb=" O GLN B 200 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N TYR B 205 " --> pdb=" O THR B 201 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N ALA B 209 " --> pdb=" O TYR B 205 " (cutoff:3.500A) removed outlier: 3.794A pdb=" N VAL B 212 " --> pdb=" O SER B 208 " (cutoff:3.500A) removed outlier: 3.744A pdb=" N GLU B 213 " --> pdb=" O ALA B 209 " (cutoff:3.500A) Processing helix chain 'B' and resid 227 through 232 removed outlier: 3.816A pdb=" N TYR B 232 " --> pdb=" O TYR B 228 " (cutoff:3.500A) Processing helix chain 'B' and resid 234 through 236 No H-bonds generated for 'chain 'B' and resid 234 through 236' Processing helix chain 'B' and resid 237 through 259 Processing helix chain 'B' and resid 288 through 296 removed outlier: 3.740A pdb=" N ILE B 292 " --> pdb=" O GLY B 288 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N ALA B 295 " --> pdb=" O ILE B 291 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N SER B 296 " --> pdb=" O ILE B 292 " (cutoff:3.500A) Processing helix chain 'C' and resid 24 through 32 removed outlier: 3.796A pdb=" N GLN C 30 " --> pdb=" O ARG C 27 " (cutoff:3.500A) Processing helix chain 'C' and resid 34 through 43 Processing helix chain 'C' and resid 48 through 54 Processing helix chain 'C' and resid 56 through 62 removed outlier: 3.688A pdb=" N LEU C 60 " --> pdb=" O PRO C 56 " (cutoff:3.500A) Processing helix chain 'C' and resid 67 through 82 removed outlier: 3.789A pdb=" N LEU C 81 " --> pdb=" O GLU C 77 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N VAL C 82 " --> pdb=" O ALA C 78 " (cutoff:3.500A) Processing helix chain 'C' and resid 89 through 98 removed outlier: 3.776A pdb=" N GLU C 98 " --> pdb=" O GLN C 94 " (cutoff:3.500A) Processing helix chain 'C' and resid 106 through 114 removed outlier: 3.590A pdb=" N LEU C 112 " --> pdb=" O GLU C 108 " (cutoff:3.500A) Processing helix chain 'C' and resid 132 through 144 Processing helix chain 'C' and resid 145 through 146 No H-bonds generated for 'chain 'C' and resid 145 through 146' Processing helix chain 'C' and resid 147 through 151 Processing helix chain 'C' and resid 167 through 179 removed outlier: 3.789A pdb=" N LEU C 171 " --> pdb=" O ARG C 167 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N VAL C 174 " --> pdb=" O ARG C 170 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N ARG C 177 " --> pdb=" O ALA C 173 " (cutoff:3.500A) Processing helix chain 'C' and resid 181 through 186 Processing helix chain 'C' and resid 196 through 214 removed outlier: 3.935A pdb=" N LEU C 204 " --> pdb=" O GLN C 200 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N TYR C 205 " --> pdb=" O THR C 201 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N ALA C 209 " --> pdb=" O TYR C 205 " (cutoff:3.500A) removed outlier: 3.795A pdb=" N VAL C 212 " --> pdb=" O SER C 208 " (cutoff:3.500A) removed outlier: 3.743A pdb=" N GLU C 213 " --> pdb=" O ALA C 209 " (cutoff:3.500A) Processing helix chain 'C' and resid 227 through 232 removed outlier: 3.817A pdb=" N TYR C 232 " --> pdb=" O TYR C 228 " (cutoff:3.500A) Processing helix chain 'C' and resid 234 through 236 No H-bonds generated for 'chain 'C' and resid 234 through 236' Processing helix chain 'C' and resid 237 through 259 Processing helix chain 'C' and resid 288 through 296 removed outlier: 3.740A pdb=" N ILE C 292 " --> pdb=" O GLY C 288 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N ALA C 295 " --> pdb=" O ILE C 291 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N SER C 296 " --> pdb=" O ILE C 292 " (cutoff:3.500A) Processing helix chain 'D' and resid 24 through 32 removed outlier: 3.795A pdb=" N GLN D 30 " --> pdb=" O ARG D 27 " (cutoff:3.500A) Processing helix chain 'D' and resid 34 through 43 Processing helix chain 'D' and resid 48 through 54 Processing helix chain 'D' and resid 56 through 62 removed outlier: 3.688A pdb=" N LEU D 60 " --> pdb=" O PRO D 56 " (cutoff:3.500A) Processing helix chain 'D' and resid 67 through 82 removed outlier: 3.789A pdb=" N LEU D 81 " --> pdb=" O GLU D 77 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N VAL D 82 " --> pdb=" O ALA D 78 " (cutoff:3.500A) Processing helix chain 'D' and resid 89 through 98 removed outlier: 3.776A pdb=" N GLU D 98 " --> pdb=" O GLN D 94 " (cutoff:3.500A) Processing helix chain 'D' and resid 106 through 114 removed outlier: 3.590A pdb=" N LEU D 112 " --> pdb=" O GLU D 108 " (cutoff:3.500A) Processing helix chain 'D' and resid 132 through 144 Processing helix chain 'D' and resid 145 through 146 No H-bonds generated for 'chain 'D' and resid 145 through 146' Processing helix chain 'D' and resid 147 through 151 Processing helix chain 'D' and resid 167 through 179 removed outlier: 3.790A pdb=" N LEU D 171 " --> pdb=" O ARG D 167 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N VAL D 174 " --> pdb=" O ARG D 170 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N ARG D 177 " --> pdb=" O ALA D 173 " (cutoff:3.500A) Processing helix chain 'D' and resid 181 through 186 Processing helix chain 'D' and resid 196 through 214 removed outlier: 3.935A pdb=" N LEU D 204 " --> pdb=" O GLN D 200 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N TYR D 205 " --> pdb=" O THR D 201 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N ALA D 209 " --> pdb=" O TYR D 205 " (cutoff:3.500A) removed outlier: 3.794A pdb=" N VAL D 212 " --> pdb=" O SER D 208 " (cutoff:3.500A) removed outlier: 3.743A pdb=" N GLU D 213 " --> pdb=" O ALA D 209 " (cutoff:3.500A) Processing helix chain 'D' and resid 227 through 232 removed outlier: 3.818A pdb=" N TYR D 232 " --> pdb=" O TYR D 228 " (cutoff:3.500A) Processing helix chain 'D' and resid 234 through 236 No H-bonds generated for 'chain 'D' and resid 234 through 236' Processing helix chain 'D' and resid 237 through 259 Processing helix chain 'D' and resid 288 through 296 removed outlier: 3.740A pdb=" N ILE D 292 " --> pdb=" O GLY D 288 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N ALA D 295 " --> pdb=" O ILE D 291 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N SER D 296 " --> pdb=" O ILE D 292 " (cutoff:3.500A) Processing helix chain 'E' and resid 24 through 32 removed outlier: 3.796A pdb=" N GLN E 30 " --> pdb=" O ARG E 27 " (cutoff:3.500A) Processing helix chain 'E' and resid 34 through 43 Processing helix chain 'E' and resid 48 through 54 Processing helix chain 'E' and resid 56 through 62 removed outlier: 3.688A pdb=" N LEU E 60 " --> pdb=" O PRO E 56 " (cutoff:3.500A) Processing helix chain 'E' and resid 67 through 82 removed outlier: 3.788A pdb=" N LEU E 81 " --> pdb=" O GLU E 77 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N VAL E 82 " --> pdb=" O ALA E 78 " (cutoff:3.500A) Processing helix chain 'E' and resid 89 through 98 removed outlier: 3.775A pdb=" N GLU E 98 " --> pdb=" O GLN E 94 " (cutoff:3.500A) Processing helix chain 'E' and resid 106 through 114 removed outlier: 3.589A pdb=" N LEU E 112 " --> pdb=" O GLU E 108 " (cutoff:3.500A) Processing helix chain 'E' and resid 132 through 144 Processing helix chain 'E' and resid 145 through 146 No H-bonds generated for 'chain 'E' and resid 145 through 146' Processing helix chain 'E' and resid 147 through 151 Processing helix chain 'E' and resid 167 through 179 removed outlier: 3.789A pdb=" N LEU E 171 " --> pdb=" O ARG E 167 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N VAL E 174 " --> pdb=" O ARG E 170 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N ARG E 177 " --> pdb=" O ALA E 173 " (cutoff:3.500A) Processing helix chain 'E' and resid 181 through 186 Processing helix chain 'E' and resid 196 through 214 removed outlier: 3.935A pdb=" N LEU E 204 " --> pdb=" O GLN E 200 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N TYR E 205 " --> pdb=" O THR E 201 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N ALA E 209 " --> pdb=" O TYR E 205 " (cutoff:3.500A) removed outlier: 3.795A pdb=" N VAL E 212 " --> pdb=" O SER E 208 " (cutoff:3.500A) removed outlier: 3.744A pdb=" N GLU E 213 " --> pdb=" O ALA E 209 " (cutoff:3.500A) Processing helix chain 'E' and resid 227 through 232 removed outlier: 3.816A pdb=" N TYR E 232 " --> pdb=" O TYR E 228 " (cutoff:3.500A) Processing helix chain 'E' and resid 234 through 236 No H-bonds generated for 'chain 'E' and resid 234 through 236' Processing helix chain 'E' and resid 237 through 259 Processing helix chain 'E' and resid 288 through 296 removed outlier: 3.740A pdb=" N ILE E 292 " --> pdb=" O GLY E 288 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N ALA E 295 " --> pdb=" O ILE E 291 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N SER E 296 " --> pdb=" O ILE E 292 " (cutoff:3.500A) Processing helix chain 'F' and resid 24 through 32 removed outlier: 3.795A pdb=" N GLN F 30 " --> pdb=" O ARG F 27 " (cutoff:3.500A) Processing helix chain 'F' and resid 34 through 43 Processing helix chain 'F' and resid 48 through 54 Processing helix chain 'F' and resid 56 through 62 removed outlier: 3.688A pdb=" N LEU F 60 " --> pdb=" O PRO F 56 " (cutoff:3.500A) Processing helix chain 'F' and resid 67 through 82 removed outlier: 3.789A pdb=" N LEU F 81 " --> pdb=" O GLU F 77 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N VAL F 82 " --> pdb=" O ALA F 78 " (cutoff:3.500A) Processing helix chain 'F' and resid 89 through 98 removed outlier: 3.777A pdb=" N GLU F 98 " --> pdb=" O GLN F 94 " (cutoff:3.500A) Processing helix chain 'F' and resid 106 through 114 removed outlier: 3.589A pdb=" N LEU F 112 " --> pdb=" O GLU F 108 " (cutoff:3.500A) Processing helix chain 'F' and resid 132 through 144 Processing helix chain 'F' and resid 145 through 146 No H-bonds generated for 'chain 'F' and resid 145 through 146' Processing helix chain 'F' and resid 147 through 151 Processing helix chain 'F' and resid 167 through 179 removed outlier: 3.789A pdb=" N LEU F 171 " --> pdb=" O ARG F 167 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N VAL F 174 " --> pdb=" O ARG F 170 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N ARG F 177 " --> pdb=" O ALA F 173 " (cutoff:3.500A) Processing helix chain 'F' and resid 181 through 186 Processing helix chain 'F' and resid 196 through 214 removed outlier: 3.936A pdb=" N LEU F 204 " --> pdb=" O GLN F 200 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N TYR F 205 " --> pdb=" O THR F 201 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N ALA F 209 " --> pdb=" O TYR F 205 " (cutoff:3.500A) removed outlier: 3.794A pdb=" N VAL F 212 " --> pdb=" O SER F 208 " (cutoff:3.500A) removed outlier: 3.744A pdb=" N GLU F 213 " --> pdb=" O ALA F 209 " (cutoff:3.500A) Processing helix chain 'F' and resid 227 through 232 removed outlier: 3.817A pdb=" N TYR F 232 " --> pdb=" O TYR F 228 " (cutoff:3.500A) Processing helix chain 'F' and resid 234 through 236 No H-bonds generated for 'chain 'F' and resid 234 through 236' Processing helix chain 'F' and resid 237 through 259 Processing helix chain 'F' and resid 288 through 296 removed outlier: 3.740A pdb=" N ILE F 292 " --> pdb=" O GLY F 288 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N ALA F 295 " --> pdb=" O ILE F 291 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N SER F 296 " --> pdb=" O ILE F 292 " (cutoff:3.500A) Processing helix chain 'G' and resid 24 through 32 removed outlier: 3.795A pdb=" N GLN G 30 " --> pdb=" O ARG G 27 " (cutoff:3.500A) Processing helix chain 'G' and resid 34 through 43 Processing helix chain 'G' and resid 48 through 54 Processing helix chain 'G' and resid 56 through 62 removed outlier: 3.688A pdb=" N LEU G 60 " --> pdb=" O PRO G 56 " (cutoff:3.500A) Processing helix chain 'G' and resid 67 through 82 removed outlier: 3.789A pdb=" N LEU G 81 " --> pdb=" O GLU G 77 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N VAL G 82 " --> pdb=" O ALA G 78 " (cutoff:3.500A) Processing helix chain 'G' and resid 89 through 98 removed outlier: 3.775A pdb=" N GLU G 98 " --> pdb=" O GLN G 94 " (cutoff:3.500A) Processing helix chain 'G' and resid 106 through 114 removed outlier: 3.590A pdb=" N LEU G 112 " --> pdb=" O GLU G 108 " (cutoff:3.500A) Processing helix chain 'G' and resid 132 through 144 Processing helix chain 'G' and resid 145 through 146 No H-bonds generated for 'chain 'G' and resid 145 through 146' Processing helix chain 'G' and resid 147 through 151 Processing helix chain 'G' and resid 167 through 179 removed outlier: 3.790A pdb=" N LEU G 171 " --> pdb=" O ARG G 167 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N VAL G 174 " --> pdb=" O ARG G 170 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N ARG G 177 " --> pdb=" O ALA G 173 " (cutoff:3.500A) Processing helix chain 'G' and resid 181 through 186 Processing helix chain 'G' and resid 196 through 214 removed outlier: 3.936A pdb=" N LEU G 204 " --> pdb=" O GLN G 200 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N TYR G 205 " --> pdb=" O THR G 201 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N ALA G 209 " --> pdb=" O TYR G 205 " (cutoff:3.500A) removed outlier: 3.794A pdb=" N VAL G 212 " --> pdb=" O SER G 208 " (cutoff:3.500A) removed outlier: 3.743A pdb=" N GLU G 213 " --> pdb=" O ALA G 209 " (cutoff:3.500A) Processing helix chain 'G' and resid 227 through 232 removed outlier: 3.817A pdb=" N TYR G 232 " --> pdb=" O TYR G 228 " (cutoff:3.500A) Processing helix chain 'G' and resid 234 through 236 No H-bonds generated for 'chain 'G' and resid 234 through 236' Processing helix chain 'G' and resid 237 through 259 Processing helix chain 'G' and resid 288 through 296 removed outlier: 3.740A pdb=" N ILE G 292 " --> pdb=" O GLY G 288 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N ALA G 295 " --> pdb=" O ILE G 291 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N SER G 296 " --> pdb=" O ILE G 292 " (cutoff:3.500A) Processing helix chain 'H' and resid 24 through 32 removed outlier: 3.796A pdb=" N GLN H 30 " --> pdb=" O ARG H 27 " (cutoff:3.500A) Processing helix chain 'H' and resid 34 through 43 Processing helix chain 'H' and resid 48 through 54 Processing helix chain 'H' and resid 56 through 62 removed outlier: 3.688A pdb=" N LEU H 60 " --> pdb=" O PRO H 56 " (cutoff:3.500A) Processing helix chain 'H' and resid 67 through 82 removed outlier: 3.789A pdb=" N LEU H 81 " --> pdb=" O GLU H 77 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N VAL H 82 " --> pdb=" O ALA H 78 " (cutoff:3.500A) Processing helix chain 'H' and resid 89 through 98 removed outlier: 3.775A pdb=" N GLU H 98 " --> pdb=" O GLN H 94 " (cutoff:3.500A) Processing helix chain 'H' and resid 106 through 114 removed outlier: 3.590A pdb=" N LEU H 112 " --> pdb=" O GLU H 108 " (cutoff:3.500A) Processing helix chain 'H' and resid 132 through 144 Processing helix chain 'H' and resid 145 through 146 No H-bonds generated for 'chain 'H' and resid 145 through 146' Processing helix chain 'H' and resid 147 through 151 Processing helix chain 'H' and resid 167 through 179 removed outlier: 3.789A pdb=" N LEU H 171 " --> pdb=" O ARG H 167 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N VAL H 174 " --> pdb=" O ARG H 170 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N ARG H 177 " --> pdb=" O ALA H 173 " (cutoff:3.500A) Processing helix chain 'H' and resid 181 through 186 Processing helix chain 'H' and resid 196 through 214 removed outlier: 3.935A pdb=" N LEU H 204 " --> pdb=" O GLN H 200 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N TYR H 205 " --> pdb=" O THR H 201 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N ALA H 209 " --> pdb=" O TYR H 205 " (cutoff:3.500A) removed outlier: 3.794A pdb=" N VAL H 212 " --> pdb=" O SER H 208 " (cutoff:3.500A) removed outlier: 3.743A pdb=" N GLU H 213 " --> pdb=" O ALA H 209 " (cutoff:3.500A) Processing helix chain 'H' and resid 227 through 232 removed outlier: 3.817A pdb=" N TYR H 232 " --> pdb=" O TYR H 228 " (cutoff:3.500A) Processing helix chain 'H' and resid 234 through 236 No H-bonds generated for 'chain 'H' and resid 234 through 236' Processing helix chain 'H' and resid 237 through 259 Processing helix chain 'H' and resid 288 through 296 removed outlier: 3.740A pdb=" N ILE H 292 " --> pdb=" O GLY H 288 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N ALA H 295 " --> pdb=" O ILE H 291 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N SER H 296 " --> pdb=" O ILE H 292 " (cutoff:3.500A) Processing helix chain 'I' and resid 24 through 32 removed outlier: 3.796A pdb=" N GLN I 30 " --> pdb=" O ARG I 27 " (cutoff:3.500A) Processing helix chain 'I' and resid 34 through 43 Processing helix chain 'I' and resid 48 through 54 Processing helix chain 'I' and resid 56 through 62 removed outlier: 3.688A pdb=" N LEU I 60 " --> pdb=" O PRO I 56 " (cutoff:3.500A) Processing helix chain 'I' and resid 67 through 82 removed outlier: 3.789A pdb=" N LEU I 81 " --> pdb=" O GLU I 77 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N VAL I 82 " --> pdb=" O ALA I 78 " (cutoff:3.500A) Processing helix chain 'I' and resid 89 through 98 removed outlier: 3.776A pdb=" N GLU I 98 " --> pdb=" O GLN I 94 " (cutoff:3.500A) Processing helix chain 'I' and resid 106 through 114 removed outlier: 3.590A pdb=" N LEU I 112 " --> pdb=" O GLU I 108 " (cutoff:3.500A) Processing helix chain 'I' and resid 132 through 144 Processing helix chain 'I' and resid 145 through 146 No H-bonds generated for 'chain 'I' and resid 145 through 146' Processing helix chain 'I' and resid 147 through 151 Processing helix chain 'I' and resid 167 through 179 removed outlier: 3.789A pdb=" N LEU I 171 " --> pdb=" O ARG I 167 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N VAL I 174 " --> pdb=" O ARG I 170 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N ARG I 177 " --> pdb=" O ALA I 173 " (cutoff:3.500A) Processing helix chain 'I' and resid 181 through 186 Processing helix chain 'I' and resid 196 through 214 removed outlier: 3.935A pdb=" N LEU I 204 " --> pdb=" O GLN I 200 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N TYR I 205 " --> pdb=" O THR I 201 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N ALA I 209 " --> pdb=" O TYR I 205 " (cutoff:3.500A) removed outlier: 3.794A pdb=" N VAL I 212 " --> pdb=" O SER I 208 " (cutoff:3.500A) removed outlier: 3.743A pdb=" N GLU I 213 " --> pdb=" O ALA I 209 " (cutoff:3.500A) Processing helix chain 'I' and resid 227 through 232 removed outlier: 3.817A pdb=" N TYR I 232 " --> pdb=" O TYR I 228 " (cutoff:3.500A) Processing helix chain 'I' and resid 234 through 236 No H-bonds generated for 'chain 'I' and resid 234 through 236' Processing helix chain 'I' and resid 237 through 259 Processing helix chain 'I' and resid 288 through 296 removed outlier: 3.739A pdb=" N ILE I 292 " --> pdb=" O GLY I 288 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N ALA I 295 " --> pdb=" O ILE I 291 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N SER I 296 " --> pdb=" O ILE I 292 " (cutoff:3.500A) Processing helix chain 'J' and resid 24 through 32 removed outlier: 3.797A pdb=" N GLN J 30 " --> pdb=" O ARG J 27 " (cutoff:3.500A) Processing helix chain 'J' and resid 34 through 43 Processing helix chain 'J' and resid 48 through 54 Processing helix chain 'J' and resid 56 through 62 removed outlier: 3.688A pdb=" N LEU J 60 " --> pdb=" O PRO J 56 " (cutoff:3.500A) Processing helix chain 'J' and resid 67 through 82 removed outlier: 3.789A pdb=" N LEU J 81 " --> pdb=" O GLU J 77 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N VAL J 82 " --> pdb=" O ALA J 78 " (cutoff:3.500A) Processing helix chain 'J' and resid 88 through 98 removed outlier: 3.775A pdb=" N GLU J 98 " --> pdb=" O GLN J 94 " (cutoff:3.500A) Processing helix chain 'J' and resid 106 through 114 removed outlier: 3.589A pdb=" N LEU J 112 " --> pdb=" O GLU J 108 " (cutoff:3.500A) Processing helix chain 'J' and resid 132 through 144 Processing helix chain 'J' and resid 145 through 146 No H-bonds generated for 'chain 'J' and resid 145 through 146' Processing helix chain 'J' and resid 147 through 151 Processing helix chain 'J' and resid 167 through 179 removed outlier: 3.789A pdb=" N LEU J 171 " --> pdb=" O ARG J 167 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N VAL J 174 " --> pdb=" O ARG J 170 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N ARG J 177 " --> pdb=" O ALA J 173 " (cutoff:3.500A) Processing helix chain 'J' and resid 181 through 186 Processing helix chain 'J' and resid 196 through 214 removed outlier: 3.935A pdb=" N LEU J 204 " --> pdb=" O GLN J 200 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N TYR J 205 " --> pdb=" O THR J 201 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N ALA J 209 " --> pdb=" O TYR J 205 " (cutoff:3.500A) removed outlier: 3.794A pdb=" N VAL J 212 " --> pdb=" O SER J 208 " (cutoff:3.500A) removed outlier: 3.743A pdb=" N GLU J 213 " --> pdb=" O ALA J 209 " (cutoff:3.500A) Processing helix chain 'J' and resid 227 through 232 removed outlier: 3.817A pdb=" N TYR J 232 " --> pdb=" O TYR J 228 " (cutoff:3.500A) Processing helix chain 'J' and resid 234 through 236 No H-bonds generated for 'chain 'J' and resid 234 through 236' Processing helix chain 'J' and resid 237 through 259 Processing helix chain 'J' and resid 288 through 296 removed outlier: 3.740A pdb=" N ILE J 292 " --> pdb=" O GLY J 288 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N ALA J 295 " --> pdb=" O ILE J 291 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N SER J 296 " --> pdb=" O ILE J 292 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 87 through 88 removed outlier: 6.902A pdb=" N ALA B 157 " --> pdb=" O ALA B 190 " (cutoff:3.500A) removed outlier: 8.145A pdb=" N ALA B 192 " --> pdb=" O ALA B 157 " (cutoff:3.500A) removed outlier: 6.419A pdb=" N TYR B 159 " --> pdb=" O ALA B 192 " (cutoff:3.500A) removed outlier: 6.920A pdb=" N LYS B 156 " --> pdb=" O LEU B 218 " (cutoff:3.500A) removed outlier: 8.466A pdb=" N ILE B 220 " --> pdb=" O LYS B 156 " (cutoff:3.500A) removed outlier: 6.448A pdb=" N MET B 158 " --> pdb=" O ILE B 220 " (cutoff:3.500A) removed outlier: 7.573A pdb=" N ASP B 222 " --> pdb=" O MET B 158 " (cutoff:3.500A) removed outlier: 6.560A pdb=" N ILE B 160 " --> pdb=" O ASP B 222 " (cutoff:3.500A) removed outlier: 8.285A pdb=" N VAL B 264 " --> pdb=" O ALA B 217 " (cutoff:3.500A) removed outlier: 6.719A pdb=" N LEU B 219 " --> pdb=" O VAL B 264 " (cutoff:3.500A) removed outlier: 7.998A pdb=" N THR B 266 " --> pdb=" O LEU B 219 " (cutoff:3.500A) removed outlier: 7.172A pdb=" N VAL B 221 " --> pdb=" O THR B 266 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N GLY B 127 " --> pdb=" O ASN B 267 " (cutoff:3.500A) removed outlier: 6.561A pdb=" N TYR B 301 " --> pdb=" O ILE B 314 " (cutoff:3.500A) removed outlier: 5.758A pdb=" N ILE B 314 " --> pdb=" O TYR B 301 " (cutoff:3.500A) removed outlier: 6.607A pdb=" N ARG B 303 " --> pdb=" O CYS B 312 " (cutoff:3.500A) removed outlier: 5.705A pdb=" N CYS B 312 " --> pdb=" O ARG B 303 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 101 through 102 Processing sheet with id=AA3, first strand: chain 'A' and resid 189 through 193 removed outlier: 6.901A pdb=" N ALA A 157 " --> pdb=" O ALA A 190 " (cutoff:3.500A) removed outlier: 8.145A pdb=" N ALA A 192 " --> pdb=" O ALA A 157 " (cutoff:3.500A) removed outlier: 6.419A pdb=" N TYR A 159 " --> pdb=" O ALA A 192 " (cutoff:3.500A) removed outlier: 6.921A pdb=" N LYS A 156 " --> pdb=" O LEU A 218 " (cutoff:3.500A) removed outlier: 8.465A pdb=" N ILE A 220 " --> pdb=" O LYS A 156 " (cutoff:3.500A) removed outlier: 6.448A pdb=" N MET A 158 " --> pdb=" O ILE A 220 " (cutoff:3.500A) removed outlier: 7.573A pdb=" N ASP A 222 " --> pdb=" O MET A 158 " (cutoff:3.500A) removed outlier: 6.561A pdb=" N ILE A 160 " --> pdb=" O ASP A 222 " (cutoff:3.500A) removed outlier: 8.284A pdb=" N VAL A 264 " --> pdb=" O ALA A 217 " (cutoff:3.500A) removed outlier: 6.718A pdb=" N LEU A 219 " --> pdb=" O VAL A 264 " (cutoff:3.500A) removed outlier: 7.998A pdb=" N THR A 266 " --> pdb=" O LEU A 219 " (cutoff:3.500A) removed outlier: 7.172A pdb=" N VAL A 221 " --> pdb=" O THR A 266 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N GLY A 127 " --> pdb=" O ASN A 267 " (cutoff:3.500A) removed outlier: 6.561A pdb=" N TYR A 301 " --> pdb=" O ILE A 314 " (cutoff:3.500A) removed outlier: 5.758A pdb=" N ILE A 314 " --> pdb=" O TYR A 301 " (cutoff:3.500A) removed outlier: 6.607A pdb=" N ARG A 303 " --> pdb=" O CYS A 312 " (cutoff:3.500A) removed outlier: 5.705A pdb=" N CYS A 312 " --> pdb=" O ARG A 303 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 269 through 271 Processing sheet with id=AA5, first strand: chain 'B' and resid 87 through 88 removed outlier: 6.901A pdb=" N ALA C 157 " --> pdb=" O ALA C 190 " (cutoff:3.500A) removed outlier: 8.146A pdb=" N ALA C 192 " --> pdb=" O ALA C 157 " (cutoff:3.500A) removed outlier: 6.419A pdb=" N TYR C 159 " --> pdb=" O ALA C 192 " (cutoff:3.500A) removed outlier: 6.920A pdb=" N LYS C 156 " --> pdb=" O LEU C 218 " (cutoff:3.500A) removed outlier: 8.466A pdb=" N ILE C 220 " --> pdb=" O LYS C 156 " (cutoff:3.500A) removed outlier: 6.448A pdb=" N MET C 158 " --> pdb=" O ILE C 220 " (cutoff:3.500A) removed outlier: 7.573A pdb=" N ASP C 222 " --> pdb=" O MET C 158 " (cutoff:3.500A) removed outlier: 6.560A pdb=" N ILE C 160 " --> pdb=" O ASP C 222 " (cutoff:3.500A) removed outlier: 8.285A pdb=" N VAL C 264 " --> pdb=" O ALA C 217 " (cutoff:3.500A) removed outlier: 6.718A pdb=" N LEU C 219 " --> pdb=" O VAL C 264 " (cutoff:3.500A) removed outlier: 7.998A pdb=" N THR C 266 " --> pdb=" O LEU C 219 " (cutoff:3.500A) removed outlier: 7.172A pdb=" N VAL C 221 " --> pdb=" O THR C 266 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N GLY C 127 " --> pdb=" O ASN C 267 " (cutoff:3.500A) removed outlier: 6.561A pdb=" N TYR C 301 " --> pdb=" O ILE C 314 " (cutoff:3.500A) removed outlier: 5.759A pdb=" N ILE C 314 " --> pdb=" O TYR C 301 " (cutoff:3.500A) removed outlier: 6.607A pdb=" N ARG C 303 " --> pdb=" O CYS C 312 " (cutoff:3.500A) removed outlier: 5.704A pdb=" N CYS C 312 " --> pdb=" O ARG C 303 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 101 through 102 Processing sheet with id=AA7, first strand: chain 'B' and resid 269 through 271 Processing sheet with id=AA8, first strand: chain 'C' and resid 87 through 88 removed outlier: 6.900A pdb=" N ALA D 157 " --> pdb=" O ALA D 190 " (cutoff:3.500A) removed outlier: 8.145A pdb=" N ALA D 192 " --> pdb=" O ALA D 157 " (cutoff:3.500A) removed outlier: 6.420A pdb=" N TYR D 159 " --> pdb=" O ALA D 192 " (cutoff:3.500A) removed outlier: 6.921A pdb=" N LYS D 156 " --> pdb=" O LEU D 218 " (cutoff:3.500A) removed outlier: 8.465A pdb=" N ILE D 220 " --> pdb=" O LYS D 156 " (cutoff:3.500A) removed outlier: 6.447A pdb=" N MET D 158 " --> pdb=" O ILE D 220 " (cutoff:3.500A) removed outlier: 7.573A pdb=" N ASP D 222 " --> pdb=" O MET D 158 " (cutoff:3.500A) removed outlier: 6.560A pdb=" N ILE D 160 " --> pdb=" O ASP D 222 " (cutoff:3.500A) removed outlier: 8.284A pdb=" N VAL D 264 " --> pdb=" O ALA D 217 " (cutoff:3.500A) removed outlier: 6.719A pdb=" N LEU D 219 " --> pdb=" O VAL D 264 " (cutoff:3.500A) removed outlier: 7.999A pdb=" N THR D 266 " --> pdb=" O LEU D 219 " (cutoff:3.500A) removed outlier: 7.173A pdb=" N VAL D 221 " --> pdb=" O THR D 266 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N GLY D 127 " --> pdb=" O ASN D 267 " (cutoff:3.500A) removed outlier: 6.561A pdb=" N TYR D 301 " --> pdb=" O ILE D 314 " (cutoff:3.500A) removed outlier: 5.758A pdb=" N ILE D 314 " --> pdb=" O TYR D 301 " (cutoff:3.500A) removed outlier: 6.607A pdb=" N ARG D 303 " --> pdb=" O CYS D 312 " (cutoff:3.500A) removed outlier: 5.705A pdb=" N CYS D 312 " --> pdb=" O ARG D 303 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'C' and resid 101 through 102 Processing sheet with id=AB1, first strand: chain 'C' and resid 269 through 271 Processing sheet with id=AB2, first strand: chain 'D' and resid 87 through 88 removed outlier: 6.901A pdb=" N ALA E 157 " --> pdb=" O ALA E 190 " (cutoff:3.500A) removed outlier: 8.145A pdb=" N ALA E 192 " --> pdb=" O ALA E 157 " (cutoff:3.500A) removed outlier: 6.420A pdb=" N TYR E 159 " --> pdb=" O ALA E 192 " (cutoff:3.500A) removed outlier: 6.921A pdb=" N LYS E 156 " --> pdb=" O LEU E 218 " (cutoff:3.500A) removed outlier: 8.466A pdb=" N ILE E 220 " --> pdb=" O LYS E 156 " (cutoff:3.500A) removed outlier: 6.447A pdb=" N MET E 158 " --> pdb=" O ILE E 220 " (cutoff:3.500A) removed outlier: 7.573A pdb=" N ASP E 222 " --> pdb=" O MET E 158 " (cutoff:3.500A) removed outlier: 6.559A pdb=" N ILE E 160 " --> pdb=" O ASP E 222 " (cutoff:3.500A) removed outlier: 8.285A pdb=" N VAL E 264 " --> pdb=" O ALA E 217 " (cutoff:3.500A) removed outlier: 6.718A pdb=" N LEU E 219 " --> pdb=" O VAL E 264 " (cutoff:3.500A) removed outlier: 7.999A pdb=" N THR E 266 " --> pdb=" O LEU E 219 " (cutoff:3.500A) removed outlier: 7.173A pdb=" N VAL E 221 " --> pdb=" O THR E 266 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N GLY E 127 " --> pdb=" O ASN E 267 " (cutoff:3.500A) removed outlier: 6.561A pdb=" N TYR E 301 " --> pdb=" O ILE E 314 " (cutoff:3.500A) removed outlier: 5.758A pdb=" N ILE E 314 " --> pdb=" O TYR E 301 " (cutoff:3.500A) removed outlier: 6.607A pdb=" N ARG E 303 " --> pdb=" O CYS E 312 " (cutoff:3.500A) removed outlier: 5.705A pdb=" N CYS E 312 " --> pdb=" O ARG E 303 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'D' and resid 101 through 102 Processing sheet with id=AB4, first strand: chain 'D' and resid 269 through 271 Processing sheet with id=AB5, first strand: chain 'E' and resid 87 through 88 removed outlier: 6.901A pdb=" N ALA F 157 " --> pdb=" O ALA F 190 " (cutoff:3.500A) removed outlier: 8.146A pdb=" N ALA F 192 " --> pdb=" O ALA F 157 " (cutoff:3.500A) removed outlier: 6.420A pdb=" N TYR F 159 " --> pdb=" O ALA F 192 " (cutoff:3.500A) removed outlier: 6.920A pdb=" N LYS F 156 " --> pdb=" O LEU F 218 " (cutoff:3.500A) removed outlier: 8.465A pdb=" N ILE F 220 " --> pdb=" O LYS F 156 " (cutoff:3.500A) removed outlier: 6.447A pdb=" N MET F 158 " --> pdb=" O ILE F 220 " (cutoff:3.500A) removed outlier: 7.573A pdb=" N ASP F 222 " --> pdb=" O MET F 158 " (cutoff:3.500A) removed outlier: 6.560A pdb=" N ILE F 160 " --> pdb=" O ASP F 222 " (cutoff:3.500A) removed outlier: 8.285A pdb=" N VAL F 264 " --> pdb=" O ALA F 217 " (cutoff:3.500A) removed outlier: 6.718A pdb=" N LEU F 219 " --> pdb=" O VAL F 264 " (cutoff:3.500A) removed outlier: 7.999A pdb=" N THR F 266 " --> pdb=" O LEU F 219 " (cutoff:3.500A) removed outlier: 7.173A pdb=" N VAL F 221 " --> pdb=" O THR F 266 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N GLY F 127 " --> pdb=" O ASN F 267 " (cutoff:3.500A) removed outlier: 6.561A pdb=" N TYR F 301 " --> pdb=" O ILE F 314 " (cutoff:3.500A) removed outlier: 5.758A pdb=" N ILE F 314 " --> pdb=" O TYR F 301 " (cutoff:3.500A) removed outlier: 6.607A pdb=" N ARG F 303 " --> pdb=" O CYS F 312 " (cutoff:3.500A) removed outlier: 5.705A pdb=" N CYS F 312 " --> pdb=" O ARG F 303 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'E' and resid 101 through 102 Processing sheet with id=AB7, first strand: chain 'E' and resid 269 through 271 Processing sheet with id=AB8, first strand: chain 'F' and resid 87 through 88 removed outlier: 6.902A pdb=" N ALA G 157 " --> pdb=" O ALA G 190 " (cutoff:3.500A) removed outlier: 8.146A pdb=" N ALA G 192 " --> pdb=" O ALA G 157 " (cutoff:3.500A) removed outlier: 6.420A pdb=" N TYR G 159 " --> pdb=" O ALA G 192 " (cutoff:3.500A) removed outlier: 6.921A pdb=" N LYS G 156 " --> pdb=" O LEU G 218 " (cutoff:3.500A) removed outlier: 8.465A pdb=" N ILE G 220 " --> pdb=" O LYS G 156 " (cutoff:3.500A) removed outlier: 6.448A pdb=" N MET G 158 " --> pdb=" O ILE G 220 " (cutoff:3.500A) removed outlier: 7.573A pdb=" N ASP G 222 " --> pdb=" O MET G 158 " (cutoff:3.500A) removed outlier: 6.560A pdb=" N ILE G 160 " --> pdb=" O ASP G 222 " (cutoff:3.500A) removed outlier: 8.285A pdb=" N VAL G 264 " --> pdb=" O ALA G 217 " (cutoff:3.500A) removed outlier: 6.718A pdb=" N LEU G 219 " --> pdb=" O VAL G 264 " (cutoff:3.500A) removed outlier: 7.999A pdb=" N THR G 266 " --> pdb=" O LEU G 219 " (cutoff:3.500A) removed outlier: 7.172A pdb=" N VAL G 221 " --> pdb=" O THR G 266 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N GLY G 127 " --> pdb=" O ASN G 267 " (cutoff:3.500A) removed outlier: 6.561A pdb=" N TYR G 301 " --> pdb=" O ILE G 314 " (cutoff:3.500A) removed outlier: 5.758A pdb=" N ILE G 314 " --> pdb=" O TYR G 301 " (cutoff:3.500A) removed outlier: 6.607A pdb=" N ARG G 303 " --> pdb=" O CYS G 312 " (cutoff:3.500A) removed outlier: 5.705A pdb=" N CYS G 312 " --> pdb=" O ARG G 303 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'F' and resid 101 through 102 Processing sheet with id=AC1, first strand: chain 'F' and resid 269 through 271 Processing sheet with id=AC2, first strand: chain 'G' and resid 87 through 88 removed outlier: 6.902A pdb=" N ALA H 157 " --> pdb=" O ALA H 190 " (cutoff:3.500A) removed outlier: 8.145A pdb=" N ALA H 192 " --> pdb=" O ALA H 157 " (cutoff:3.500A) removed outlier: 6.420A pdb=" N TYR H 159 " --> pdb=" O ALA H 192 " (cutoff:3.500A) removed outlier: 6.920A pdb=" N LYS H 156 " --> pdb=" O LEU H 218 " (cutoff:3.500A) removed outlier: 8.465A pdb=" N ILE H 220 " --> pdb=" O LYS H 156 " (cutoff:3.500A) removed outlier: 6.447A pdb=" N MET H 158 " --> pdb=" O ILE H 220 " (cutoff:3.500A) removed outlier: 7.573A pdb=" N ASP H 222 " --> pdb=" O MET H 158 " (cutoff:3.500A) removed outlier: 6.560A pdb=" N ILE H 160 " --> pdb=" O ASP H 222 " (cutoff:3.500A) removed outlier: 8.284A pdb=" N VAL H 264 " --> pdb=" O ALA H 217 " (cutoff:3.500A) removed outlier: 6.719A pdb=" N LEU H 219 " --> pdb=" O VAL H 264 " (cutoff:3.500A) removed outlier: 7.998A pdb=" N THR H 266 " --> pdb=" O LEU H 219 " (cutoff:3.500A) removed outlier: 7.173A pdb=" N VAL H 221 " --> pdb=" O THR H 266 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N GLY H 127 " --> pdb=" O ASN H 267 " (cutoff:3.500A) removed outlier: 6.561A pdb=" N TYR H 301 " --> pdb=" O ILE H 314 " (cutoff:3.500A) removed outlier: 5.758A pdb=" N ILE H 314 " --> pdb=" O TYR H 301 " (cutoff:3.500A) removed outlier: 6.607A pdb=" N ARG H 303 " --> pdb=" O CYS H 312 " (cutoff:3.500A) removed outlier: 5.705A pdb=" N CYS H 312 " --> pdb=" O ARG H 303 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'G' and resid 101 through 102 Processing sheet with id=AC4, first strand: chain 'G' and resid 269 through 271 Processing sheet with id=AC5, first strand: chain 'H' and resid 87 through 88 removed outlier: 6.901A pdb=" N ALA I 157 " --> pdb=" O ALA I 190 " (cutoff:3.500A) removed outlier: 8.145A pdb=" N ALA I 192 " --> pdb=" O ALA I 157 " (cutoff:3.500A) removed outlier: 6.419A pdb=" N TYR I 159 " --> pdb=" O ALA I 192 " (cutoff:3.500A) removed outlier: 6.920A pdb=" N LYS I 156 " --> pdb=" O LEU I 218 " (cutoff:3.500A) removed outlier: 8.465A pdb=" N ILE I 220 " --> pdb=" O LYS I 156 " (cutoff:3.500A) removed outlier: 6.448A pdb=" N MET I 158 " --> pdb=" O ILE I 220 " (cutoff:3.500A) removed outlier: 7.573A pdb=" N ASP I 222 " --> pdb=" O MET I 158 " (cutoff:3.500A) removed outlier: 6.559A pdb=" N ILE I 160 " --> pdb=" O ASP I 222 " (cutoff:3.500A) removed outlier: 8.284A pdb=" N VAL I 264 " --> pdb=" O ALA I 217 " (cutoff:3.500A) removed outlier: 6.719A pdb=" N LEU I 219 " --> pdb=" O VAL I 264 " (cutoff:3.500A) removed outlier: 7.998A pdb=" N THR I 266 " --> pdb=" O LEU I 219 " (cutoff:3.500A) removed outlier: 7.172A pdb=" N VAL I 221 " --> pdb=" O THR I 266 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N GLY I 127 " --> pdb=" O ASN I 267 " (cutoff:3.500A) removed outlier: 6.561A pdb=" N TYR I 301 " --> pdb=" O ILE I 314 " (cutoff:3.500A) removed outlier: 5.758A pdb=" N ILE I 314 " --> pdb=" O TYR I 301 " (cutoff:3.500A) removed outlier: 6.607A pdb=" N ARG I 303 " --> pdb=" O CYS I 312 " (cutoff:3.500A) removed outlier: 5.705A pdb=" N CYS I 312 " --> pdb=" O ARG I 303 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'H' and resid 101 through 102 Processing sheet with id=AC7, first strand: chain 'H' and resid 269 through 271 Processing sheet with id=AC8, first strand: chain 'I' and resid 87 through 88 removed outlier: 6.901A pdb=" N ALA J 157 " --> pdb=" O ALA J 190 " (cutoff:3.500A) removed outlier: 8.146A pdb=" N ALA J 192 " --> pdb=" O ALA J 157 " (cutoff:3.500A) removed outlier: 6.420A pdb=" N TYR J 159 " --> pdb=" O ALA J 192 " (cutoff:3.500A) removed outlier: 6.921A pdb=" N LYS J 156 " --> pdb=" O LEU J 218 " (cutoff:3.500A) removed outlier: 8.466A pdb=" N ILE J 220 " --> pdb=" O LYS J 156 " (cutoff:3.500A) removed outlier: 6.447A pdb=" N MET J 158 " --> pdb=" O ILE J 220 " (cutoff:3.500A) removed outlier: 7.572A pdb=" N ASP J 222 " --> pdb=" O MET J 158 " (cutoff:3.500A) removed outlier: 6.560A pdb=" N ILE J 160 " --> pdb=" O ASP J 222 " (cutoff:3.500A) removed outlier: 8.284A pdb=" N VAL J 264 " --> pdb=" O ALA J 217 " (cutoff:3.500A) removed outlier: 6.718A pdb=" N LEU J 219 " --> pdb=" O VAL J 264 " (cutoff:3.500A) removed outlier: 7.999A pdb=" N THR J 266 " --> pdb=" O LEU J 219 " (cutoff:3.500A) removed outlier: 7.172A pdb=" N VAL J 221 " --> pdb=" O THR J 266 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N GLY J 127 " --> pdb=" O ASN J 267 " (cutoff:3.500A) removed outlier: 6.560A pdb=" N TYR J 301 " --> pdb=" O ILE J 314 " (cutoff:3.500A) removed outlier: 5.758A pdb=" N ILE J 314 " --> pdb=" O TYR J 301 " (cutoff:3.500A) removed outlier: 6.607A pdb=" N ARG J 303 " --> pdb=" O CYS J 312 " (cutoff:3.500A) removed outlier: 5.704A pdb=" N CYS J 312 " --> pdb=" O ARG J 303 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'I' and resid 101 through 102 Processing sheet with id=AD1, first strand: chain 'I' and resid 269 through 271 Processing sheet with id=AD2, first strand: chain 'J' and resid 101 through 102 Processing sheet with id=AD3, first strand: chain 'J' and resid 269 through 271 1109 hydrogen bonds defined for protein. 3000 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 50 hydrogen bonds 100 hydrogen bond angles 0 basepair planarities 20 basepair parallelities 36 stacking parallelities Total time for adding SS restraints: 5.12 Time building geometry restraints manager: 3.45 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 6155 1.33 - 1.45: 5382 1.45 - 1.57: 14983 1.57 - 1.69: 136 1.69 - 1.81: 219 Bond restraints: 26875 Sorted by residual: bond pdb=" CA TYR G 232 " pdb=" CB TYR G 232 " ideal model delta sigma weight residual 1.528 1.502 0.026 1.51e-02 4.39e+03 3.04e+00 bond pdb=" CA TYR F 232 " pdb=" CB TYR F 232 " ideal model delta sigma weight residual 1.528 1.502 0.026 1.51e-02 4.39e+03 3.00e+00 bond pdb=" CA TYR H 232 " pdb=" CB TYR H 232 " ideal model delta sigma weight residual 1.528 1.503 0.026 1.51e-02 4.39e+03 2.93e+00 bond pdb=" CA TYR D 232 " pdb=" CB TYR D 232 " ideal model delta sigma weight residual 1.528 1.503 0.026 1.51e-02 4.39e+03 2.92e+00 bond pdb=" CA TYR B 232 " pdb=" CB TYR B 232 " ideal model delta sigma weight residual 1.528 1.503 0.026 1.51e-02 4.39e+03 2.89e+00 ... (remaining 26870 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.21: 35357 1.21 - 2.41: 972 2.41 - 3.62: 181 3.62 - 4.82: 30 4.82 - 6.03: 10 Bond angle restraints: 36550 Sorted by residual: angle pdb=" C PHE A 129 " pdb=" N ARG A 130 " pdb=" CA ARG A 130 " ideal model delta sigma weight residual 121.54 127.57 -6.03 1.91e+00 2.74e-01 9.97e+00 angle pdb=" C PHE J 129 " pdb=" N ARG J 130 " pdb=" CA ARG J 130 " ideal model delta sigma weight residual 121.54 127.57 -6.03 1.91e+00 2.74e-01 9.97e+00 angle pdb=" C PHE C 129 " pdb=" N ARG C 130 " pdb=" CA ARG C 130 " ideal model delta sigma weight residual 121.54 127.56 -6.02 1.91e+00 2.74e-01 9.95e+00 angle pdb=" C PHE I 129 " pdb=" N ARG I 130 " pdb=" CA ARG I 130 " ideal model delta sigma weight residual 121.54 127.53 -5.99 1.91e+00 2.74e-01 9.84e+00 angle pdb=" C PHE D 129 " pdb=" N ARG D 130 " pdb=" CA ARG D 130 " ideal model delta sigma weight residual 121.54 127.52 -5.98 1.91e+00 2.74e-01 9.81e+00 ... (remaining 36545 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 30.81: 15674 30.81 - 61.62: 665 61.62 - 92.43: 41 92.43 - 123.24: 0 123.24 - 154.05: 1 Dihedral angle restraints: 16381 sinusoidal: 7088 harmonic: 9293 Sorted by residual: dihedral pdb=" C4' DT U 1 " pdb=" C3' DT U 1 " pdb=" O3' DT U 1 " pdb=" P DC U 2 " ideal model delta sinusoidal sigma weight residual 220.00 65.95 154.05 1 3.50e+01 8.16e-04 1.49e+01 dihedral pdb=" CA ASP H 316 " pdb=" CB ASP H 316 " pdb=" CG ASP H 316 " pdb=" OD1 ASP H 316 " ideal model delta sinusoidal sigma weight residual -30.00 -83.00 53.00 1 2.00e+01 2.50e-03 9.56e+00 dihedral pdb=" CA ASP A 316 " pdb=" CB ASP A 316 " pdb=" CG ASP A 316 " pdb=" OD1 ASP A 316 " ideal model delta sinusoidal sigma weight residual -30.00 -82.98 52.98 1 2.00e+01 2.50e-03 9.55e+00 ... (remaining 16378 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.028: 2289 0.028 - 0.057: 1210 0.057 - 0.085: 413 0.085 - 0.113: 214 0.113 - 0.141: 13 Chirality restraints: 4139 Sorted by residual: chirality pdb=" C3' DG T 2 " pdb=" C4' DG T 2 " pdb=" O3' DG T 2 " pdb=" C2' DG T 2 " both_signs ideal model delta sigma weight residual False -2.66 -2.52 -0.14 2.00e-01 2.50e+01 5.01e-01 chirality pdb=" CA VAL L3290 " pdb=" N VAL L3290 " pdb=" C VAL L3290 " pdb=" CB VAL L3290 " both_signs ideal model delta sigma weight residual False 2.44 2.56 -0.12 2.00e-01 2.50e+01 3.75e-01 chirality pdb=" CA VAL M3290 " pdb=" N VAL M3290 " pdb=" C VAL M3290 " pdb=" CB VAL M3290 " both_signs ideal model delta sigma weight residual False 2.44 2.56 -0.12 2.00e-01 2.50e+01 3.73e-01 ... (remaining 4136 not shown) Planarity restraints: 4521 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1' DA T 18 " 0.015 2.00e-02 2.50e+03 6.92e-03 1.32e+00 pdb=" N9 DA T 18 " -0.016 2.00e-02 2.50e+03 pdb=" C8 DA T 18 " -0.002 2.00e-02 2.50e+03 pdb=" N7 DA T 18 " 0.001 2.00e-02 2.50e+03 pdb=" C5 DA T 18 " 0.000 2.00e-02 2.50e+03 pdb=" C6 DA T 18 " 0.002 2.00e-02 2.50e+03 pdb=" N6 DA T 18 " 0.004 2.00e-02 2.50e+03 pdb=" N1 DA T 18 " 0.001 2.00e-02 2.50e+03 pdb=" C2 DA T 18 " -0.001 2.00e-02 2.50e+03 pdb=" N3 DA T 18 " -0.002 2.00e-02 2.50e+03 pdb=" C4 DA T 18 " -0.002 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' DA T 15 " 0.014 2.00e-02 2.50e+03 6.32e-03 1.10e+00 pdb=" N9 DA T 15 " -0.014 2.00e-02 2.50e+03 pdb=" C8 DA T 15 " -0.002 2.00e-02 2.50e+03 pdb=" N7 DA T 15 " 0.001 2.00e-02 2.50e+03 pdb=" C5 DA T 15 " -0.001 2.00e-02 2.50e+03 pdb=" C6 DA T 15 " 0.001 2.00e-02 2.50e+03 pdb=" N6 DA T 15 " 0.005 2.00e-02 2.50e+03 pdb=" N1 DA T 15 " -0.000 2.00e-02 2.50e+03 pdb=" C2 DA T 15 " -0.000 2.00e-02 2.50e+03 pdb=" N3 DA T 15 " -0.002 2.00e-02 2.50e+03 pdb=" C4 DA T 15 " -0.002 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ARG E 167 " -0.017 5.00e-02 4.00e+02 2.51e-02 1.01e+00 pdb=" N PRO E 168 " 0.043 5.00e-02 4.00e+02 pdb=" CA PRO E 168 " -0.013 5.00e-02 4.00e+02 pdb=" CD PRO E 168 " -0.014 5.00e-02 4.00e+02 ... (remaining 4518 not shown) Histogram of nonbonded interaction distances: 2.15 - 2.70: 932 2.70 - 3.25: 26667 3.25 - 3.80: 41632 3.80 - 4.35: 59171 4.35 - 4.90: 95745 Nonbonded interactions: 224147 Sorted by model distance: nonbonded pdb=" OG1 THR G 134 " pdb="CA CA G 401 " model vdw 2.152 2.510 nonbonded pdb=" OG1 THR I 134 " pdb="CA CA I 401 " model vdw 2.152 2.510 nonbonded pdb=" OG1 THR H 134 " pdb="CA CA H 401 " model vdw 2.152 2.510 nonbonded pdb=" OG1 THR D 134 " pdb="CA CA D 401 " model vdw 2.152 2.510 nonbonded pdb=" OG1 THR C 134 " pdb="CA CA C 401 " model vdw 2.152 2.510 ... (remaining 224142 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and resid 21 through 402) selection = (chain 'B' and resid 21 through 401) selection = (chain 'C' and resid 21 through 401) selection = (chain 'D' and resid 21 through 401) selection = (chain 'E' and resid 21 through 401) selection = (chain 'F' and resid 21 through 401) selection = (chain 'G' and resid 21 through 401) selection = (chain 'H' and resid 21 through 401) selection = (chain 'I' and resid 21 through 401) selection = chain 'J' } ncs_group { reference = chain 'K' selection = chain 'L' selection = chain 'M' selection = chain 'N' selection = chain 'O' selection = chain 'P' selection = chain 'Q' selection = chain 'R' selection = chain 'S' } 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: 0.490 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.030 Extract box with map and model: 0.380 Check model and map are aligned: 0.080 Set scattering table: 0.090 Process input model: 26.570 Find NCS groups from input model: 0.840 Set up NCS constraints: 0.050 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:7.800 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 36.340 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7966 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 : 0.007 0.041 26875 Z= 0.327 Angle : 0.522 6.030 36550 Z= 0.283 Chirality : 0.041 0.141 4139 Planarity : 0.003 0.025 4521 Dihedral : 15.391 154.054 10413 Min Nonbonded Distance : 2.152 Molprobity Statistics. All-atom Clashscore : 5.21 Ramachandran Plot: Outliers : 0.31 % Allowed : 6.23 % Favored : 93.46 % Rotamer: Outliers : 1.92 % Allowed : 6.14 % Favored : 91.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.32 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -4.28 (0.11), residues: 3196 helix: -2.99 (0.09), residues: 1360 sheet: -2.18 (0.23), residues: 480 loop : -2.77 (0.12), residues: 1356 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG I 229 TYR 0.009 0.001 TYR B 301 PHE 0.009 0.001 PHE G 126 HIS 0.004 0.002 HIS C 294 Details of bonding type rmsd covalent geometry : bond 0.00738 (26875) covalent geometry : angle 0.52157 (36550) hydrogen bonds : bond 0.25628 ( 1159) hydrogen bonds : angle 9.18582 ( 3100) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6392 Ramachandran restraints generated. 3196 Oldfield, 0 Emsley, 3196 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6392 Ramachandran restraints generated. 3196 Oldfield, 0 Emsley, 3196 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 924 residues out of total 2607 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 874 time to evaluate : 0.699 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 40 LYS cc_start: 0.7490 (mtpp) cc_final: 0.6507 (mtpt) REVERT: A 68 GLU cc_start: 0.7149 (mt-10) cc_final: 0.6568 (tm-30) REVERT: A 94 GLN cc_start: 0.8543 (mm-40) cc_final: 0.8224 (mt0) REVERT: A 176 GLU cc_start: 0.7254 (mm-30) cc_final: 0.6973 (mm-30) REVERT: A 202 GLN cc_start: 0.8343 (mm-40) cc_final: 0.8085 (tt0) REVERT: A 247 ARG cc_start: 0.8231 (mtp-110) cc_final: 0.7992 (mmm-85) REVERT: A 303 ARG cc_start: 0.7845 (mtp180) cc_final: 0.7607 (mtm180) REVERT: A 329 ILE cc_start: 0.8060 (mt) cc_final: 0.7774 (mt) REVERT: B 26 SER cc_start: 0.7862 (p) cc_final: 0.7366 (p) REVERT: B 33 ILE cc_start: 0.8471 (mm) cc_final: 0.8228 (mm) REVERT: B 42 GLU cc_start: 0.7648 (mt-10) cc_final: 0.7296 (mt-10) REVERT: B 43 GLU cc_start: 0.7706 (mt-10) cc_final: 0.7352 (pp20) REVERT: B 94 GLN cc_start: 0.8369 (mm-40) cc_final: 0.8078 (mm-40) REVERT: B 95 ARG cc_start: 0.8061 (ttp80) cc_final: 0.7741 (ttt-90) REVERT: B 206 GLN cc_start: 0.8094 (mt0) cc_final: 0.7863 (mt0) REVERT: B 232 TYR cc_start: 0.9070 (m-80) cc_final: 0.8851 (m-80) REVERT: C 82 VAL cc_start: 0.9006 (OUTLIER) cc_final: 0.8796 (p) REVERT: C 94 GLN cc_start: 0.8010 (mm-40) cc_final: 0.7421 (tp40) REVERT: C 95 ARG cc_start: 0.8339 (ttp80) cc_final: 0.7782 (ttp-170) REVERT: C 107 LYS cc_start: 0.8249 (mmtm) cc_final: 0.7905 (ptpp) REVERT: C 154 GLU cc_start: 0.7672 (mt-10) cc_final: 0.7230 (mt-10) REVERT: C 202 GLN cc_start: 0.8214 (mm-40) cc_final: 0.7717 (mt0) REVERT: C 216 TYR cc_start: 0.8968 (m-80) cc_final: 0.8728 (m-80) REVERT: C 232 TYR cc_start: 0.9196 (m-80) cc_final: 0.8853 (m-80) REVERT: C 251 MET cc_start: 0.8319 (ttm) cc_final: 0.8069 (tpt) REVERT: D 34 ASN cc_start: 0.6981 (OUTLIER) cc_final: 0.6510 (t0) REVERT: D 37 ASP cc_start: 0.6792 (m-30) cc_final: 0.6461 (m-30) REVERT: D 57 LYS cc_start: 0.8277 (tttp) cc_final: 0.8071 (ttpt) REVERT: D 68 GLU cc_start: 0.7845 (mt-10) cc_final: 0.7624 (tp30) REVERT: D 94 GLN cc_start: 0.7989 (mm-40) cc_final: 0.7377 (tm-30) REVERT: D 107 LYS cc_start: 0.8382 (mmtm) cc_final: 0.8164 (mtmt) REVERT: D 181 SER cc_start: 0.8642 (t) cc_final: 0.8438 (t) REVERT: D 330 ASN cc_start: 0.9052 (m-40) cc_final: 0.8818 (m110) REVERT: E 34 ASN cc_start: 0.7170 (OUTLIER) cc_final: 0.6862 (t160) REVERT: E 81 LEU cc_start: 0.8800 (mt) cc_final: 0.8511 (mt) REVERT: E 107 LYS cc_start: 0.8218 (mmtm) cc_final: 0.7751 (ttmt) REVERT: E 196 ASN cc_start: 0.8771 (p0) cc_final: 0.8426 (p0) REVERT: E 202 GLN cc_start: 0.8224 (mm-40) cc_final: 0.7673 (mt0) REVERT: E 211 MET cc_start: 0.9097 (mtt) cc_final: 0.8816 (mtt) REVERT: E 243 MET cc_start: 0.9050 (mtm) cc_final: 0.8715 (mtt) REVERT: E 251 MET cc_start: 0.8280 (ttm) cc_final: 0.8079 (ttm) REVERT: E 272 GLN cc_start: 0.8518 (pt0) cc_final: 0.8250 (mt0) REVERT: E 296 SER cc_start: 0.8815 (p) cc_final: 0.8537 (m) REVERT: F 26 SER cc_start: 0.9037 (p) cc_final: 0.8799 (m) REVERT: F 39 LYS cc_start: 0.7952 (mttt) cc_final: 0.7403 (mtpp) REVERT: F 68 GLU cc_start: 0.8396 (mt-10) cc_final: 0.8158 (mp0) REVERT: F 95 ARG cc_start: 0.8440 (ttp80) cc_final: 0.8073 (ttp-110) REVERT: F 158 MET cc_start: 0.9055 (ttm) cc_final: 0.8816 (ttp) REVERT: F 202 GLN cc_start: 0.8594 (mm-40) cc_final: 0.8028 (mt0) REVERT: F 206 GLN cc_start: 0.8854 (mt0) cc_final: 0.8503 (mt0) REVERT: F 253 LEU cc_start: 0.8913 (tp) cc_final: 0.8673 (tp) REVERT: G 39 LYS cc_start: 0.8363 (mttt) cc_final: 0.7928 (mtpp) REVERT: G 107 LYS cc_start: 0.7294 (mmtm) cc_final: 0.7081 (ttmm) REVERT: G 187 ASP cc_start: 0.8754 (m-30) cc_final: 0.8523 (m-30) REVERT: G 202 GLN cc_start: 0.8542 (mm-40) cc_final: 0.8186 (mt0) REVERT: G 285 LYS cc_start: 0.8833 (OUTLIER) cc_final: 0.8542 (ptmt) REVERT: G 308 GLU cc_start: 0.8295 (pm20) cc_final: 0.8087 (pm20) REVERT: H 27 ARG cc_start: 0.8046 (mtp-110) cc_final: 0.7366 (tmt170) REVERT: H 39 LYS cc_start: 0.8642 (mttt) cc_final: 0.8285 (mtpm) REVERT: H 94 GLN cc_start: 0.8632 (mm-40) cc_final: 0.8390 (tp40) REVERT: H 125 MET cc_start: 0.8665 (mtp) cc_final: 0.8388 (mtm) REVERT: H 158 MET cc_start: 0.8720 (ttm) cc_final: 0.8329 (ttm) REVERT: H 187 ASP cc_start: 0.8631 (m-30) cc_final: 0.8408 (m-30) REVERT: H 254 ARG cc_start: 0.8386 (ttt-90) cc_final: 0.8103 (tmm-80) REVERT: I 27 ARG cc_start: 0.8444 (mtp-110) cc_final: 0.8224 (mtp-110) REVERT: I 33 ILE cc_start: 0.8221 (mm) cc_final: 0.7936 (mm) REVERT: I 39 LYS cc_start: 0.8739 (mttt) cc_final: 0.8394 (mmmm) REVERT: I 40 LYS cc_start: 0.8562 (mtpp) cc_final: 0.8065 (mtmm) REVERT: I 50 GLU cc_start: 0.8810 (mp0) cc_final: 0.8574 (mp0) REVERT: I 94 GLN cc_start: 0.8826 (mm-40) cc_final: 0.8549 (tp40) REVERT: I 125 MET cc_start: 0.8812 (mtp) cc_final: 0.8498 (mtp) REVERT: I 223 SER cc_start: 0.9124 (t) cc_final: 0.8903 (t) REVERT: I 247 ARG cc_start: 0.8240 (mtp-110) cc_final: 0.8033 (mtp85) REVERT: I 285 LYS cc_start: 0.8887 (OUTLIER) cc_final: 0.8684 (ptpt) REVERT: I 322 GLU cc_start: 0.7731 (tt0) cc_final: 0.7496 (tt0) REVERT: J 38 VAL cc_start: 0.8027 (t) cc_final: 0.7799 (m) REVERT: J 39 LYS cc_start: 0.8539 (mttt) cc_final: 0.7774 (mmmt) REVERT: J 40 LYS cc_start: 0.8232 (mtpp) cc_final: 0.7632 (mtpt) REVERT: J 50 GLU cc_start: 0.8500 (mp0) cc_final: 0.8120 (mp0) REVERT: J 73 LYS cc_start: 0.6797 (mttt) cc_final: 0.6358 (tptt) REVERT: J 101 GLN cc_start: 0.8832 (mt0) cc_final: 0.8478 (mt0) REVERT: J 112 LEU cc_start: 0.8659 (tp) cc_final: 0.8446 (tp) REVERT: J 184 ASP cc_start: 0.7989 (m-30) cc_final: 0.7787 (m-30) REVERT: J 231 ASP cc_start: 0.8638 (m-30) cc_final: 0.8397 (m-30) REVERT: J 249 LEU cc_start: 0.9057 (mt) cc_final: 0.8793 (mp) REVERT: J 308 GLU cc_start: 0.7778 (pm20) cc_final: 0.7514 (mt-10) REVERT: J 332 ASP cc_start: 0.8251 (p0) cc_final: 0.8019 (p0) outliers start: 50 outliers final: 5 residues processed: 900 average time/residue: 0.7941 time to fit residues: 808.2827 Evaluate side-chains 623 residues out of total 2607 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 613 time to evaluate : 0.828 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 82 VAL Chi-restraints excluded: chain A residue 125 MET Chi-restraints excluded: chain B residue 99 ILE Chi-restraints excluded: chain C residue 82 VAL Chi-restraints excluded: chain D residue 34 ASN Chi-restraints excluded: chain E residue 34 ASN Chi-restraints excluded: chain G residue 285 LYS Chi-restraints excluded: chain H residue 82 VAL Chi-restraints excluded: chain H residue 149 ASP Chi-restraints excluded: chain I residue 285 LYS Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 323 random chunks: chunk 197 optimal weight: 1.9990 chunk 215 optimal weight: 0.9990 chunk 20 optimal weight: 0.9980 chunk 132 optimal weight: 0.8980 chunk 261 optimal weight: 0.6980 chunk 248 optimal weight: 10.0000 chunk 207 optimal weight: 2.9990 chunk 155 optimal weight: 7.9990 chunk 244 optimal weight: 1.9990 chunk 183 optimal weight: 3.9990 chunk 298 optimal weight: 0.6980 overall best weight: 0.8582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 135 GLN A 244 HIS A 330 ASN B 145 GLN B 202 GLN B 244 HIS C 23 GLN C 30 GLN C 145 GLN C 244 HIS D 30 GLN D 135 GLN D 202 GLN D 244 HIS D 330 ASN ** E 145 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 244 HIS F 244 HIS G 242 GLN G 244 HIS ** H 145 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 244 HIS J 34 ASN J 135 GLN Total number of N/Q/H flips: 22 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3667 r_free = 0.3667 target = 0.146826 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3270 r_free = 0.3270 target = 0.112412 restraints weight = 32161.285| |-----------------------------------------------------------------------------| r_work (start): 0.3218 rms_B_bonded: 2.00 r_work: 0.3097 rms_B_bonded: 2.66 restraints_weight: 0.5000 r_work: 0.2969 rms_B_bonded: 4.34 restraints_weight: 0.2500 r_work (final): 0.2969 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7971 moved from start: 0.2389 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 26875 Z= 0.131 Angle : 0.502 6.565 36550 Z= 0.268 Chirality : 0.039 0.153 4139 Planarity : 0.004 0.036 4521 Dihedral : 14.003 148.016 4476 Min Nonbonded Distance : 2.232 Molprobity Statistics. All-atom Clashscore : 6.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.44 % Favored : 98.56 % Rotamer: Outliers : 3.15 % Allowed : 17.68 % Favored : 79.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.32 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.14 (0.13), residues: 3196 helix: -0.80 (0.12), residues: 1410 sheet: -1.37 (0.23), residues: 490 loop : -2.03 (0.14), residues: 1296 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG F 215 TYR 0.007 0.001 TYR I 301 PHE 0.010 0.001 PHE E 248 HIS 0.003 0.001 HIS G 244 Details of bonding type rmsd covalent geometry : bond 0.00280 (26875) covalent geometry : angle 0.50207 (36550) hydrogen bonds : bond 0.04123 ( 1159) hydrogen bonds : angle 4.93848 ( 3100) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6392 Ramachandran restraints generated. 3196 Oldfield, 0 Emsley, 3196 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6392 Ramachandran restraints generated. 3196 Oldfield, 0 Emsley, 3196 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 826 residues out of total 2607 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 82 poor density : 744 time to evaluate : 0.957 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 37 ASP cc_start: 0.7037 (m-30) cc_final: 0.6766 (m-30) REVERT: A 40 LYS cc_start: 0.6855 (mtpp) cc_final: 0.6137 (mtpt) REVERT: A 42 GLU cc_start: 0.6629 (pt0) cc_final: 0.6418 (pt0) REVERT: A 68 GLU cc_start: 0.6759 (mt-10) cc_final: 0.6111 (tm-30) REVERT: A 77 GLU cc_start: 0.7662 (OUTLIER) cc_final: 0.7267 (mp0) REVERT: A 84 MET cc_start: 0.8867 (mtp) cc_final: 0.8661 (mtp) REVERT: A 107 LYS cc_start: 0.7142 (mmtm) cc_final: 0.6684 (mttm) REVERT: A 130 ARG cc_start: 0.7186 (OUTLIER) cc_final: 0.5584 (ptp90) REVERT: A 145 GLN cc_start: 0.8465 (mt0) cc_final: 0.8198 (mt0) REVERT: A 186 LEU cc_start: 0.8344 (mm) cc_final: 0.8129 (mm) REVERT: A 202 GLN cc_start: 0.8251 (mm-40) cc_final: 0.7887 (tt0) REVERT: A 210 MET cc_start: 0.7952 (mtp) cc_final: 0.7376 (mtp) REVERT: A 247 ARG cc_start: 0.7277 (mtp-110) cc_final: 0.6807 (mmm-85) REVERT: A 254 ARG cc_start: 0.7431 (ttp80) cc_final: 0.7063 (tmt90) REVERT: A 303 ARG cc_start: 0.7427 (mtp180) cc_final: 0.6685 (mtm180) REVERT: A 308 GLU cc_start: 0.7142 (pt0) cc_final: 0.6781 (tt0) REVERT: A 324 GLU cc_start: 0.8207 (mt-10) cc_final: 0.7832 (mt-10) REVERT: A 329 ILE cc_start: 0.8612 (mt) cc_final: 0.8189 (mt) REVERT: B 30 GLN cc_start: 0.6772 (mp10) cc_final: 0.6483 (mp10) REVERT: B 42 GLU cc_start: 0.7426 (mt-10) cc_final: 0.6946 (mt-10) REVERT: B 43 GLU cc_start: 0.7592 (mt-10) cc_final: 0.7227 (mt-10) REVERT: B 95 ARG cc_start: 0.7838 (ttp80) cc_final: 0.7260 (ttt-90) REVERT: B 107 LYS cc_start: 0.7742 (mmtm) cc_final: 0.6870 (ptpt) REVERT: B 206 GLN cc_start: 0.7544 (mt0) cc_final: 0.7049 (mt0) REVERT: B 235 ARG cc_start: 0.8968 (ttp-170) cc_final: 0.8635 (ttp80) REVERT: B 306 ARG cc_start: 0.7613 (tpp80) cc_final: 0.6970 (ptm-80) REVERT: B 324 GLU cc_start: 0.8311 (mt-10) cc_final: 0.8066 (mt-10) REVERT: B 332 ASP cc_start: 0.8812 (p0) cc_final: 0.8569 (p0) REVERT: C 80 LYS cc_start: 0.7967 (mtmm) cc_final: 0.7583 (ttpp) REVERT: C 82 VAL cc_start: 0.8902 (OUTLIER) cc_final: 0.8636 (p) REVERT: C 94 GLN cc_start: 0.7740 (mm-40) cc_final: 0.6954 (tp40) REVERT: C 95 ARG cc_start: 0.8190 (ttp80) cc_final: 0.7764 (ttm170) REVERT: C 107 LYS cc_start: 0.7874 (mmtm) cc_final: 0.7202 (ptpp) REVERT: C 154 GLU cc_start: 0.7751 (mt-10) cc_final: 0.6952 (mt-10) REVERT: C 181 SER cc_start: 0.8637 (t) cc_final: 0.8176 (p) REVERT: C 202 GLN cc_start: 0.7972 (mm-40) cc_final: 0.7424 (mt0) REVERT: C 216 TYR cc_start: 0.8980 (m-80) cc_final: 0.8614 (m-80) REVERT: C 222 ASP cc_start: 0.8786 (t70) cc_final: 0.8474 (t70) REVERT: C 251 MET cc_start: 0.8197 (ttm) cc_final: 0.7716 (mtt) REVERT: C 308 GLU cc_start: 0.8498 (pm20) cc_final: 0.8010 (pm20) REVERT: C 334 VAL cc_start: 0.9246 (t) cc_final: 0.8933 (p) REVERT: D 27 ARG cc_start: 0.8447 (OUTLIER) cc_final: 0.7369 (mtp180) REVERT: D 37 ASP cc_start: 0.7105 (m-30) cc_final: 0.6765 (m-30) REVERT: D 57 LYS cc_start: 0.7968 (tttp) cc_final: 0.7667 (ttpt) REVERT: D 68 GLU cc_start: 0.8031 (mt-10) cc_final: 0.7695 (tp30) REVERT: D 94 GLN cc_start: 0.7601 (mm-40) cc_final: 0.6998 (tm-30) REVERT: D 107 LYS cc_start: 0.8308 (mmtm) cc_final: 0.7937 (mtmt) REVERT: D 181 SER cc_start: 0.9019 (t) cc_final: 0.8481 (p) REVERT: D 187 ASP cc_start: 0.8974 (OUTLIER) cc_final: 0.8615 (t70) REVERT: D 334 VAL cc_start: 0.9191 (t) cc_final: 0.8889 (p) REVERT: E 68 GLU cc_start: 0.7863 (mp0) cc_final: 0.7359 (tp30) REVERT: E 98 GLU cc_start: 0.8430 (tp30) cc_final: 0.8178 (mm-30) REVERT: E 107 LYS cc_start: 0.8022 (mmtm) cc_final: 0.7555 (mtmt) REVERT: E 176 GLU cc_start: 0.8507 (mm-30) cc_final: 0.7985 (tt0) REVERT: E 202 GLN cc_start: 0.7913 (mm-40) cc_final: 0.7664 (mt0) REVERT: F 39 LYS cc_start: 0.7357 (mttt) cc_final: 0.6493 (mtpp) REVERT: F 43 GLU cc_start: 0.7877 (mt-10) cc_final: 0.7336 (mp0) REVERT: F 68 GLU cc_start: 0.7868 (mt-10) cc_final: 0.7651 (mp0) REVERT: F 95 ARG cc_start: 0.8211 (ttp80) cc_final: 0.7898 (ttp-110) REVERT: F 187 ASP cc_start: 0.8786 (m-30) cc_final: 0.8557 (m-30) REVERT: F 202 GLN cc_start: 0.8106 (mm-40) cc_final: 0.7740 (mt0) REVERT: G 29 GLU cc_start: 0.8664 (mt-10) cc_final: 0.8461 (mt-10) REVERT: G 39 LYS cc_start: 0.7765 (mttt) cc_final: 0.7331 (mtpp) REVERT: G 94 GLN cc_start: 0.7812 (OUTLIER) cc_final: 0.7520 (tp-100) REVERT: G 98 GLU cc_start: 0.8240 (mm-30) cc_final: 0.8008 (mm-30) REVERT: G 107 LYS cc_start: 0.7109 (mmtm) cc_final: 0.6585 (ttmm) REVERT: G 176 GLU cc_start: 0.8203 (mm-30) cc_final: 0.7858 (mm-30) REVERT: G 177 ARG cc_start: 0.8702 (tmm-80) cc_final: 0.8489 (ttt-90) REVERT: G 187 ASP cc_start: 0.8788 (m-30) cc_final: 0.8443 (m-30) REVERT: G 202 GLN cc_start: 0.8027 (mm-40) cc_final: 0.7751 (mt0) REVERT: G 247 ARG cc_start: 0.8210 (mtp-110) cc_final: 0.7862 (mtp85) REVERT: G 300 LEU cc_start: 0.8432 (OUTLIER) cc_final: 0.8147 (mt) REVERT: G 308 GLU cc_start: 0.8317 (pm20) cc_final: 0.7940 (pm20) REVERT: H 27 ARG cc_start: 0.7733 (mtp-110) cc_final: 0.7288 (tmt170) REVERT: H 39 LYS cc_start: 0.7706 (mttt) cc_final: 0.7417 (mtpm) REVERT: H 66 ILE cc_start: 0.8368 (mm) cc_final: 0.8068 (mp) REVERT: H 94 GLN cc_start: 0.8469 (mm-40) cc_final: 0.8217 (tp40) REVERT: H 96 ARG cc_start: 0.7811 (ttt90) cc_final: 0.7577 (ttt180) REVERT: H 187 ASP cc_start: 0.8560 (m-30) cc_final: 0.8318 (m-30) REVERT: H 205 TYR cc_start: 0.8633 (m-80) cc_final: 0.8340 (m-10) REVERT: H 210 MET cc_start: 0.8724 (mtp) cc_final: 0.8458 (mtm) REVERT: H 247 ARG cc_start: 0.7959 (mtp-110) cc_final: 0.7381 (mmm160) REVERT: H 254 ARG cc_start: 0.8091 (ttt-90) cc_final: 0.7826 (tmm-80) REVERT: H 258 GLU cc_start: 0.8145 (mt-10) cc_final: 0.7939 (mt-10) REVERT: I 27 ARG cc_start: 0.8147 (mtp-110) cc_final: 0.7874 (mtp-110) REVERT: I 39 LYS cc_start: 0.8153 (mttt) cc_final: 0.7802 (mmmm) REVERT: I 40 LYS cc_start: 0.7710 (mtpp) cc_final: 0.7230 (mtmm) REVERT: I 50 GLU cc_start: 0.8634 (mp0) cc_final: 0.7781 (mp0) REVERT: I 110 ASP cc_start: 0.8647 (m-30) cc_final: 0.8342 (m-30) REVERT: I 154 GLU cc_start: 0.8022 (mt-10) cc_final: 0.7812 (mt-10) REVERT: I 176 GLU cc_start: 0.7326 (mm-30) cc_final: 0.7020 (tm-30) REVERT: I 215 ARG cc_start: 0.7967 (tmm160) cc_final: 0.7750 (tmm160) REVERT: I 223 SER cc_start: 0.9337 (t) cc_final: 0.9132 (t) REVERT: I 247 ARG cc_start: 0.7847 (mtp-110) cc_final: 0.7415 (mtp85) REVERT: I 322 GLU cc_start: 0.8156 (tt0) cc_final: 0.7808 (tt0) REVERT: J 39 LYS cc_start: 0.7149 (mttt) cc_final: 0.6394 (mmmt) REVERT: J 40 LYS cc_start: 0.6985 (mtpp) cc_final: 0.6524 (mtpt) REVERT: J 42 GLU cc_start: 0.7066 (mt-10) cc_final: 0.6722 (tp30) REVERT: J 50 GLU cc_start: 0.7912 (mp0) cc_final: 0.7305 (mp0) REVERT: J 68 GLU cc_start: 0.7510 (mt-10) cc_final: 0.7143 (tm-30) REVERT: J 73 LYS cc_start: 0.6821 (mttt) cc_final: 0.5972 (tptt) REVERT: J 77 GLU cc_start: 0.7176 (mp0) cc_final: 0.5997 (mp0) REVERT: J 95 ARG cc_start: 0.8065 (ttp-170) cc_final: 0.7662 (ttm110) REVERT: J 110 ASP cc_start: 0.8079 (m-30) cc_final: 0.7870 (m-30) REVERT: J 124 GLU cc_start: 0.9091 (tt0) cc_final: 0.8806 (tt0) REVERT: J 154 GLU cc_start: 0.7982 (mt-10) cc_final: 0.7450 (mm-30) REVERT: J 183 SER cc_start: 0.8468 (m) cc_final: 0.8235 (m) REVERT: J 184 ASP cc_start: 0.8462 (m-30) cc_final: 0.8132 (m-30) REVERT: J 231 ASP cc_start: 0.8541 (m-30) cc_final: 0.8324 (m-30) REVERT: J 243 MET cc_start: 0.8674 (mtm) cc_final: 0.8463 (mtp) REVERT: J 247 ARG cc_start: 0.7370 (mtp-110) cc_final: 0.6718 (ttm-80) REVERT: J 258 GLU cc_start: 0.7713 (mt-10) cc_final: 0.7084 (tp30) REVERT: J 308 GLU cc_start: 0.7877 (pm20) cc_final: 0.7100 (mt-10) REVERT: J 332 ASP cc_start: 0.8186 (p0) cc_final: 0.7853 (p0) outliers start: 82 outliers final: 27 residues processed: 787 average time/residue: 0.7472 time to fit residues: 669.7875 Evaluate side-chains 677 residues out of total 2607 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 643 time to evaluate : 0.926 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 77 GLU Chi-restraints excluded: chain A residue 82 VAL Chi-restraints excluded: chain A residue 130 ARG Chi-restraints excluded: chain B residue 31 CYS Chi-restraints excluded: chain B residue 82 VAL Chi-restraints excluded: chain B residue 99 ILE Chi-restraints excluded: chain B residue 272 GLN Chi-restraints excluded: chain C residue 43 GLU Chi-restraints excluded: chain C residue 82 VAL Chi-restraints excluded: chain C residue 99 ILE Chi-restraints excluded: chain D residue 27 ARG Chi-restraints excluded: chain D residue 125 MET Chi-restraints excluded: chain D residue 187 ASP Chi-restraints excluded: chain D residue 272 GLN Chi-restraints excluded: chain E residue 87 THR Chi-restraints excluded: chain E residue 125 MET Chi-restraints excluded: chain E residue 161 ASP Chi-restraints excluded: chain F residue 97 SER Chi-restraints excluded: chain F residue 112 LEU Chi-restraints excluded: chain F residue 125 MET Chi-restraints excluded: chain F residue 272 GLN Chi-restraints excluded: chain G residue 94 GLN Chi-restraints excluded: chain G residue 161 ASP Chi-restraints excluded: chain G residue 272 GLN Chi-restraints excluded: chain G residue 300 LEU Chi-restraints excluded: chain H residue 82 VAL Chi-restraints excluded: chain H residue 90 THR Chi-restraints excluded: chain H residue 109 LEU Chi-restraints excluded: chain H residue 308 GLU Chi-restraints excluded: chain I residue 97 SER Chi-restraints excluded: chain I residue 99 ILE Chi-restraints excluded: chain I residue 183 SER Chi-restraints excluded: chain I residue 201 THR Chi-restraints excluded: chain J residue 100 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 323 random chunks: chunk 242 optimal weight: 2.9990 chunk 9 optimal weight: 0.7980 chunk 196 optimal weight: 3.9990 chunk 226 optimal weight: 4.9990 chunk 259 optimal weight: 4.9990 chunk 269 optimal weight: 7.9990 chunk 109 optimal weight: 3.9990 chunk 11 optimal weight: 0.4980 chunk 218 optimal weight: 9.9990 chunk 19 optimal weight: 3.9990 chunk 251 optimal weight: 5.9990 overall best weight: 2.4586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 135 GLN B 145 GLN B 202 GLN C 272 GLN ** D 145 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 93 HIS ** E 145 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 23 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3630 r_free = 0.3630 target = 0.143586 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3226 r_free = 0.3226 target = 0.109135 restraints weight = 32369.916| |-----------------------------------------------------------------------------| r_work (start): 0.3196 rms_B_bonded: 2.00 r_work: 0.3075 rms_B_bonded: 2.65 restraints_weight: 0.5000 r_work: 0.2946 rms_B_bonded: 4.33 restraints_weight: 0.2500 r_work (final): 0.2946 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8074 moved from start: 0.2744 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.036 26875 Z= 0.218 Angle : 0.535 8.399 36550 Z= 0.282 Chirality : 0.041 0.136 4139 Planarity : 0.004 0.043 4521 Dihedral : 14.026 144.866 4459 Min Nonbonded Distance : 2.186 Molprobity Statistics. All-atom Clashscore : 6.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.41 % Favored : 97.59 % Rotamer: Outliers : 3.99 % Allowed : 19.91 % Favored : 76.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.32 % 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: -1.32 (0.14), residues: 3196 helix: 0.09 (0.14), residues: 1380 sheet: -1.15 (0.22), residues: 490 loop : -1.75 (0.14), residues: 1326 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG D 215 TYR 0.012 0.001 TYR C 228 PHE 0.012 0.002 PHE F 126 HIS 0.005 0.001 HIS H 294 Details of bonding type rmsd covalent geometry : bond 0.00501 (26875) covalent geometry : angle 0.53517 (36550) hydrogen bonds : bond 0.04317 ( 1159) hydrogen bonds : angle 4.65843 ( 3100) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6392 Ramachandran restraints generated. 3196 Oldfield, 0 Emsley, 3196 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6392 Ramachandran restraints generated. 3196 Oldfield, 0 Emsley, 3196 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 758 residues out of total 2607 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 104 poor density : 654 time to evaluate : 0.973 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 40 LYS cc_start: 0.6956 (mtpp) cc_final: 0.6273 (mtpt) REVERT: A 42 GLU cc_start: 0.6757 (pt0) cc_final: 0.6549 (pt0) REVERT: A 66 ILE cc_start: 0.7155 (OUTLIER) cc_final: 0.6744 (tt) REVERT: A 68 GLU cc_start: 0.6600 (mt-10) cc_final: 0.6072 (tm-30) REVERT: A 70 LYS cc_start: 0.6548 (ttpt) cc_final: 0.6304 (ttpt) REVERT: A 77 GLU cc_start: 0.7974 (OUTLIER) cc_final: 0.7616 (mp0) REVERT: A 98 GLU cc_start: 0.7743 (mt-10) cc_final: 0.7535 (mm-30) REVERT: A 107 LYS cc_start: 0.7198 (mmtm) cc_final: 0.6799 (mttm) REVERT: A 130 ARG cc_start: 0.7430 (OUTLIER) cc_final: 0.7211 (ttp80) REVERT: A 145 GLN cc_start: 0.8650 (mt0) cc_final: 0.8320 (mt0) REVERT: A 202 GLN cc_start: 0.8125 (mm-40) cc_final: 0.7715 (tt0) REVERT: A 210 MET cc_start: 0.8197 (mtp) cc_final: 0.7569 (mtp) REVERT: A 247 ARG cc_start: 0.7398 (mtp-110) cc_final: 0.6923 (mmm-85) REVERT: A 254 ARG cc_start: 0.7546 (ttp80) cc_final: 0.7186 (tmt90) REVERT: A 303 ARG cc_start: 0.7564 (mtp180) cc_final: 0.6917 (mtm180) REVERT: A 308 GLU cc_start: 0.7348 (pt0) cc_final: 0.6809 (tt0) REVERT: A 329 ILE cc_start: 0.8651 (mt) cc_final: 0.8052 (mt) REVERT: B 42 GLU cc_start: 0.7422 (mt-10) cc_final: 0.6970 (mt-10) REVERT: B 43 GLU cc_start: 0.7650 (mt-10) cc_final: 0.6922 (pp20) REVERT: B 77 GLU cc_start: 0.7777 (mp0) cc_final: 0.7263 (mm-30) REVERT: B 95 ARG cc_start: 0.7989 (ttp80) cc_final: 0.7565 (ttt-90) REVERT: B 107 LYS cc_start: 0.7752 (mmtm) cc_final: 0.6841 (ptpt) REVERT: B 324 GLU cc_start: 0.8463 (mt-10) cc_final: 0.8243 (mt-10) REVERT: B 332 ASP cc_start: 0.8820 (p0) cc_final: 0.8525 (p0) REVERT: C 80 LYS cc_start: 0.7798 (mtmm) cc_final: 0.7459 (ttpp) REVERT: C 94 GLN cc_start: 0.7830 (mm-40) cc_final: 0.7062 (tm-30) REVERT: C 95 ARG cc_start: 0.8238 (ttp80) cc_final: 0.7603 (ttp-170) REVERT: C 107 LYS cc_start: 0.8217 (mmtm) cc_final: 0.7552 (ptmt) REVERT: C 145 GLN cc_start: 0.8970 (mt0) cc_final: 0.8768 (mp10) REVERT: C 154 GLU cc_start: 0.7765 (mt-10) cc_final: 0.6932 (mt-10) REVERT: C 181 SER cc_start: 0.8801 (t) cc_final: 0.8538 (p) REVERT: C 187 ASP cc_start: 0.8707 (OUTLIER) cc_final: 0.8469 (m-30) REVERT: C 202 GLN cc_start: 0.7972 (mm-40) cc_final: 0.7508 (mt0) REVERT: C 216 TYR cc_start: 0.9085 (m-80) cc_final: 0.8820 (m-80) REVERT: C 243 MET cc_start: 0.8404 (mtm) cc_final: 0.8045 (mtt) REVERT: C 308 GLU cc_start: 0.8593 (pm20) cc_final: 0.8113 (pm20) REVERT: D 37 ASP cc_start: 0.7137 (m-30) cc_final: 0.6648 (m-30) REVERT: D 57 LYS cc_start: 0.7986 (tttp) cc_final: 0.7699 (ttpt) REVERT: D 68 GLU cc_start: 0.8174 (mt-10) cc_final: 0.7592 (tp30) REVERT: D 72 ASP cc_start: 0.7850 (m-30) cc_final: 0.7373 (m-30) REVERT: D 94 GLN cc_start: 0.7740 (mm-40) cc_final: 0.6972 (tm-30) REVERT: D 107 LYS cc_start: 0.8262 (mmtm) cc_final: 0.7900 (mtmt) REVERT: D 187 ASP cc_start: 0.9056 (OUTLIER) cc_final: 0.8664 (t70) REVERT: D 247 ARG cc_start: 0.8095 (mtp-110) cc_final: 0.7799 (ttt-90) REVERT: D 334 VAL cc_start: 0.9181 (t) cc_final: 0.8934 (p) REVERT: E 27 ARG cc_start: 0.8491 (OUTLIER) cc_final: 0.6917 (mtp180) REVERT: E 68 GLU cc_start: 0.7892 (mp0) cc_final: 0.7437 (tp30) REVERT: E 107 LYS cc_start: 0.8079 (mmtm) cc_final: 0.7665 (mtmt) REVERT: E 176 GLU cc_start: 0.8488 (mm-30) cc_final: 0.7958 (tt0) REVERT: F 39 LYS cc_start: 0.7424 (mttt) cc_final: 0.6664 (mtmt) REVERT: F 43 GLU cc_start: 0.7942 (mt-10) cc_final: 0.7414 (mp0) REVERT: F 68 GLU cc_start: 0.7951 (mt-10) cc_final: 0.7639 (mp0) REVERT: F 95 ARG cc_start: 0.8224 (ttp80) cc_final: 0.7844 (ttp-110) REVERT: F 187 ASP cc_start: 0.8702 (m-30) cc_final: 0.8425 (m-30) REVERT: F 202 GLN cc_start: 0.8246 (mm-40) cc_final: 0.7831 (mt0) REVERT: F 223 SER cc_start: 0.9214 (t) cc_final: 0.8932 (p) REVERT: G 39 LYS cc_start: 0.7773 (mttt) cc_final: 0.7412 (mtpp) REVERT: G 91 GLU cc_start: 0.8264 (OUTLIER) cc_final: 0.7877 (tt0) REVERT: G 94 GLN cc_start: 0.7892 (OUTLIER) cc_final: 0.7615 (tp-100) REVERT: G 107 LYS cc_start: 0.7261 (mmtm) cc_final: 0.6662 (ttmm) REVERT: G 142 VAL cc_start: 0.9176 (t) cc_final: 0.8947 (p) REVERT: G 176 GLU cc_start: 0.8254 (mm-30) cc_final: 0.7921 (mm-30) REVERT: G 187 ASP cc_start: 0.8604 (m-30) cc_final: 0.8247 (m-30) REVERT: G 202 GLN cc_start: 0.8132 (mm-40) cc_final: 0.7850 (mt0) REVERT: G 247 ARG cc_start: 0.8257 (mtp-110) cc_final: 0.7981 (mtp85) REVERT: G 308 GLU cc_start: 0.8289 (pm20) cc_final: 0.7902 (pm20) REVERT: H 27 ARG cc_start: 0.7843 (mtp-110) cc_final: 0.7232 (tmt170) REVERT: H 39 LYS cc_start: 0.7735 (mttt) cc_final: 0.7462 (mtpm) REVERT: H 66 ILE cc_start: 0.8335 (mm) cc_final: 0.8007 (mp) REVERT: H 94 GLN cc_start: 0.8447 (mm-40) cc_final: 0.8145 (tp40) REVERT: H 118 GLU cc_start: 0.8629 (tt0) cc_final: 0.8343 (tt0) REVERT: H 125 MET cc_start: 0.9068 (mtp) cc_final: 0.8750 (mtp) REVERT: H 205 TYR cc_start: 0.8768 (m-80) cc_final: 0.8403 (m-80) REVERT: H 210 MET cc_start: 0.8763 (mtp) cc_final: 0.8516 (mtm) REVERT: H 247 ARG cc_start: 0.8056 (mtp-110) cc_final: 0.7476 (mmm160) REVERT: H 254 ARG cc_start: 0.8217 (ttt-90) cc_final: 0.7836 (tmm-80) REVERT: I 27 ARG cc_start: 0.8160 (mtp-110) cc_final: 0.7809 (mtp-110) REVERT: I 39 LYS cc_start: 0.8004 (mttt) cc_final: 0.7721 (mmmm) REVERT: I 40 LYS cc_start: 0.7729 (mtpp) cc_final: 0.7306 (mttp) REVERT: I 43 GLU cc_start: 0.7726 (mt-10) cc_final: 0.7305 (tp30) REVERT: I 50 GLU cc_start: 0.8630 (mp0) cc_final: 0.7700 (mp0) REVERT: I 91 GLU cc_start: 0.8152 (mt-10) cc_final: 0.7257 (tm-30) REVERT: I 176 GLU cc_start: 0.7268 (mm-30) cc_final: 0.7015 (tm-30) REVERT: I 223 SER cc_start: 0.9331 (t) cc_final: 0.9061 (t) REVERT: I 247 ARG cc_start: 0.7949 (mtp-110) cc_final: 0.7436 (mtp85) REVERT: I 322 GLU cc_start: 0.8127 (tt0) cc_final: 0.7883 (tt0) REVERT: I 332 ASP cc_start: 0.8283 (p0) cc_final: 0.8055 (p0) REVERT: J 39 LYS cc_start: 0.7162 (mttt) cc_final: 0.6484 (mmmt) REVERT: J 40 LYS cc_start: 0.7216 (mtpp) cc_final: 0.6740 (mtpt) REVERT: J 42 GLU cc_start: 0.7083 (mt-10) cc_final: 0.6823 (tp30) REVERT: J 50 GLU cc_start: 0.8039 (mp0) cc_final: 0.7265 (mp0) REVERT: J 68 GLU cc_start: 0.7573 (mt-10) cc_final: 0.7330 (tm-30) REVERT: J 73 LYS cc_start: 0.6775 (mttt) cc_final: 0.6140 (tptt) REVERT: J 77 GLU cc_start: 0.7352 (mp0) cc_final: 0.6703 (mp0) REVERT: J 95 ARG cc_start: 0.8023 (ttp-170) cc_final: 0.7660 (ttm110) REVERT: J 109 LEU cc_start: 0.8635 (OUTLIER) cc_final: 0.8371 (mp) REVERT: J 110 ASP cc_start: 0.8214 (m-30) cc_final: 0.7837 (m-30) REVERT: J 184 ASP cc_start: 0.8518 (m-30) cc_final: 0.8051 (m-30) REVERT: J 187 ASP cc_start: 0.8416 (OUTLIER) cc_final: 0.8095 (m-30) REVERT: J 247 ARG cc_start: 0.7651 (mtp-110) cc_final: 0.7436 (mtp85) REVERT: J 308 GLU cc_start: 0.7919 (pm20) cc_final: 0.7044 (mt-10) REVERT: J 332 ASP cc_start: 0.8267 (p0) cc_final: 0.7899 (p0) outliers start: 104 outliers final: 50 residues processed: 706 average time/residue: 0.7955 time to fit residues: 636.3594 Evaluate side-chains 676 residues out of total 2607 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 616 time to evaluate : 1.114 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 66 ILE Chi-restraints excluded: chain A residue 77 GLU Chi-restraints excluded: chain A residue 82 VAL Chi-restraints excluded: chain A residue 87 THR Chi-restraints excluded: chain A residue 106 SER Chi-restraints excluded: chain A residue 130 ARG Chi-restraints excluded: chain B residue 31 CYS Chi-restraints excluded: chain B residue 82 VAL Chi-restraints excluded: chain B residue 223 SER Chi-restraints excluded: chain B residue 272 GLN Chi-restraints excluded: chain C residue 43 GLU Chi-restraints excluded: chain C residue 99 ILE Chi-restraints excluded: chain C residue 104 THR Chi-restraints excluded: chain C residue 187 ASP Chi-restraints excluded: chain C residue 274 ASP Chi-restraints excluded: chain D residue 97 SER Chi-restraints excluded: chain D residue 121 SER Chi-restraints excluded: chain D residue 125 MET Chi-restraints excluded: chain D residue 187 ASP Chi-restraints excluded: chain D residue 222 ASP Chi-restraints excluded: chain D residue 272 GLN Chi-restraints excluded: chain E residue 27 ARG Chi-restraints excluded: chain E residue 87 THR Chi-restraints excluded: chain E residue 125 MET Chi-restraints excluded: chain E residue 161 ASP Chi-restraints excluded: chain E residue 334 VAL Chi-restraints excluded: chain F residue 26 SER Chi-restraints excluded: chain F residue 97 SER Chi-restraints excluded: chain F residue 112 LEU Chi-restraints excluded: chain F residue 145 GLN Chi-restraints excluded: chain F residue 272 GLN Chi-restraints excluded: chain F residue 297 THR Chi-restraints excluded: chain G residue 38 VAL Chi-restraints excluded: chain G residue 91 GLU Chi-restraints excluded: chain G residue 94 GLN Chi-restraints excluded: chain G residue 97 SER Chi-restraints excluded: chain G residue 125 MET Chi-restraints excluded: chain G residue 161 ASP Chi-restraints excluded: chain G residue 272 GLN Chi-restraints excluded: chain H residue 82 VAL Chi-restraints excluded: chain H residue 90 THR Chi-restraints excluded: chain H residue 308 GLU Chi-restraints excluded: chain I residue 90 THR Chi-restraints excluded: chain I residue 97 SER Chi-restraints excluded: chain I residue 99 ILE Chi-restraints excluded: chain I residue 109 LEU Chi-restraints excluded: chain I residue 121 SER Chi-restraints excluded: chain I residue 149 ASP Chi-restraints excluded: chain I residue 183 SER Chi-restraints excluded: chain I residue 201 THR Chi-restraints excluded: chain I residue 212 VAL Chi-restraints excluded: chain I residue 214 SER Chi-restraints excluded: chain I residue 261 VAL Chi-restraints excluded: chain J residue 88 THR Chi-restraints excluded: chain J residue 97 SER Chi-restraints excluded: chain J residue 109 LEU Chi-restraints excluded: chain J residue 187 ASP Chi-restraints excluded: chain J residue 214 SER Chi-restraints excluded: chain J residue 255 LEU Chi-restraints excluded: chain J residue 322 GLU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 323 random chunks: chunk 93 optimal weight: 10.0000 chunk 17 optimal weight: 6.9990 chunk 296 optimal weight: 6.9990 chunk 232 optimal weight: 0.8980 chunk 161 optimal weight: 4.9990 chunk 61 optimal weight: 10.0000 chunk 133 optimal weight: 3.9990 chunk 9 optimal weight: 3.9990 chunk 136 optimal weight: 1.9990 chunk 69 optimal weight: 1.9990 chunk 155 optimal weight: 7.9990 overall best weight: 2.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 272 GLN ** D 145 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 145 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 145 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3627 r_free = 0.3627 target = 0.143463 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3232 r_free = 0.3232 target = 0.109608 restraints weight = 32378.001| |-----------------------------------------------------------------------------| r_work (start): 0.3176 rms_B_bonded: 1.97 r_work: 0.3055 rms_B_bonded: 2.62 restraints_weight: 0.5000 r_work: 0.2925 rms_B_bonded: 4.29 restraints_weight: 0.2500 r_work (final): 0.2925 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8031 moved from start: 0.2999 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.037 26875 Z= 0.224 Angle : 0.534 8.843 36550 Z= 0.282 Chirality : 0.042 0.135 4139 Planarity : 0.004 0.046 4521 Dihedral : 13.997 144.283 4456 Min Nonbonded Distance : 2.182 Molprobity Statistics. All-atom Clashscore : 6.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.10 % Favored : 97.90 % Rotamer: Outliers : 4.76 % Allowed : 20.68 % Favored : 74.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.32 % 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: -0.88 (0.14), residues: 3196 helix: 0.41 (0.14), residues: 1380 sheet: -0.32 (0.27), residues: 380 loop : -1.63 (0.14), residues: 1436 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG D 215 TYR 0.016 0.001 TYR G 315 PHE 0.014 0.002 PHE F 126 HIS 0.009 0.001 HIS E 294 Details of bonding type rmsd covalent geometry : bond 0.00514 (26875) covalent geometry : angle 0.53389 (36550) hydrogen bonds : bond 0.04069 ( 1159) hydrogen bonds : angle 4.54350 ( 3100) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6392 Ramachandran restraints generated. 3196 Oldfield, 0 Emsley, 3196 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6392 Ramachandran restraints generated. 3196 Oldfield, 0 Emsley, 3196 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 748 residues out of total 2607 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 124 poor density : 624 time to evaluate : 1.019 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 29 GLU cc_start: 0.7128 (mt-10) cc_final: 0.6870 (mm-30) REVERT: A 33 ILE cc_start: 0.7600 (mm) cc_final: 0.6942 (mp) REVERT: A 40 LYS cc_start: 0.7125 (mtpp) cc_final: 0.6443 (mtpt) REVERT: A 42 GLU cc_start: 0.6812 (pt0) cc_final: 0.6573 (pt0) REVERT: A 66 ILE cc_start: 0.6847 (mm) cc_final: 0.6542 (tt) REVERT: A 68 GLU cc_start: 0.6695 (mt-10) cc_final: 0.5976 (tm-30) REVERT: A 70 LYS cc_start: 0.6647 (ttpt) cc_final: 0.6374 (ttpt) REVERT: A 84 MET cc_start: 0.8860 (mtp) cc_final: 0.8580 (mtp) REVERT: A 98 GLU cc_start: 0.7687 (mt-10) cc_final: 0.7470 (mm-30) REVERT: A 107 LYS cc_start: 0.7233 (mmtm) cc_final: 0.6831 (mttm) REVERT: A 130 ARG cc_start: 0.7346 (OUTLIER) cc_final: 0.6923 (tmm160) REVERT: A 145 GLN cc_start: 0.8636 (mt0) cc_final: 0.8262 (mt0) REVERT: A 202 GLN cc_start: 0.8139 (mm-40) cc_final: 0.7690 (tt0) REVERT: A 210 MET cc_start: 0.8182 (mtp) cc_final: 0.7499 (mtp) REVERT: A 247 ARG cc_start: 0.7355 (mtp-110) cc_final: 0.6876 (mmm-85) REVERT: A 254 ARG cc_start: 0.7517 (ttp80) cc_final: 0.7134 (tmt90) REVERT: A 303 ARG cc_start: 0.7633 (mtp180) cc_final: 0.7026 (mtm180) REVERT: A 308 GLU cc_start: 0.7354 (pt0) cc_final: 0.6579 (tt0) REVERT: A 329 ILE cc_start: 0.8708 (mt) cc_final: 0.8077 (mt) REVERT: B 40 LYS cc_start: 0.7176 (mtpp) cc_final: 0.5968 (mtmt) REVERT: B 42 GLU cc_start: 0.7400 (mt-10) cc_final: 0.6915 (mt-10) REVERT: B 43 GLU cc_start: 0.7609 (mt-10) cc_final: 0.7260 (mt-10) REVERT: B 50 GLU cc_start: 0.8389 (OUTLIER) cc_final: 0.7515 (mp0) REVERT: B 95 ARG cc_start: 0.7974 (ttp80) cc_final: 0.7567 (ttt-90) REVERT: B 107 LYS cc_start: 0.7604 (mmtm) cc_final: 0.6734 (ptpt) REVERT: B 215 ARG cc_start: 0.8134 (tmm160) cc_final: 0.7768 (tpt-90) REVERT: B 332 ASP cc_start: 0.8820 (p0) cc_final: 0.8368 (p0) REVERT: C 33 ILE cc_start: 0.8630 (mm) cc_final: 0.8372 (mm) REVERT: C 50 GLU cc_start: 0.8471 (OUTLIER) cc_final: 0.7452 (mp0) REVERT: C 94 GLN cc_start: 0.7806 (mm-40) cc_final: 0.7041 (tm-30) REVERT: C 95 ARG cc_start: 0.8123 (ttp80) cc_final: 0.7485 (ttp-170) REVERT: C 107 LYS cc_start: 0.8209 (mmtm) cc_final: 0.7565 (ptmt) REVERT: C 154 GLU cc_start: 0.7650 (mt-10) cc_final: 0.6754 (mt-10) REVERT: C 181 SER cc_start: 0.8859 (t) cc_final: 0.8594 (p) REVERT: C 187 ASP cc_start: 0.8688 (OUTLIER) cc_final: 0.8408 (m-30) REVERT: C 202 GLN cc_start: 0.7911 (mm-40) cc_final: 0.7478 (mt0) REVERT: C 216 TYR cc_start: 0.9046 (m-80) cc_final: 0.8772 (m-80) REVERT: C 243 MET cc_start: 0.8362 (mtm) cc_final: 0.8000 (mtt) REVERT: C 308 GLU cc_start: 0.8562 (pm20) cc_final: 0.8348 (pm20) REVERT: D 27 ARG cc_start: 0.8300 (OUTLIER) cc_final: 0.7445 (mtp180) REVERT: D 29 GLU cc_start: 0.7320 (mm-30) cc_final: 0.7088 (mm-30) REVERT: D 30 GLN cc_start: 0.7504 (mt0) cc_final: 0.7254 (mp10) REVERT: D 37 ASP cc_start: 0.7337 (m-30) cc_final: 0.7005 (m-30) REVERT: D 57 LYS cc_start: 0.7950 (tttp) cc_final: 0.7684 (ttpt) REVERT: D 94 GLN cc_start: 0.7767 (mm-40) cc_final: 0.6933 (tm-30) REVERT: D 107 LYS cc_start: 0.8328 (mmtm) cc_final: 0.7914 (mtmt) REVERT: D 111 LYS cc_start: 0.8544 (OUTLIER) cc_final: 0.8095 (ttmt) REVERT: D 187 ASP cc_start: 0.9034 (OUTLIER) cc_final: 0.8661 (t70) REVERT: D 200 GLN cc_start: 0.9130 (tt0) cc_final: 0.8881 (tt0) REVERT: D 247 ARG cc_start: 0.8027 (mtp-110) cc_final: 0.7719 (ttt-90) REVERT: D 334 VAL cc_start: 0.9205 (t) cc_final: 0.8994 (p) REVERT: E 27 ARG cc_start: 0.8505 (OUTLIER) cc_final: 0.7322 (mtp180) REVERT: E 68 GLU cc_start: 0.8046 (mp0) cc_final: 0.7620 (tp30) REVERT: E 107 LYS cc_start: 0.8054 (mmtm) cc_final: 0.7638 (mtmt) REVERT: E 176 GLU cc_start: 0.8454 (mm-30) cc_final: 0.7943 (tt0) REVERT: E 243 MET cc_start: 0.8800 (OUTLIER) cc_final: 0.8563 (mtt) REVERT: E 334 VAL cc_start: 0.8851 (OUTLIER) cc_final: 0.8650 (p) REVERT: F 39 LYS cc_start: 0.7423 (mttt) cc_final: 0.6699 (mtmt) REVERT: F 43 GLU cc_start: 0.8025 (mt-10) cc_final: 0.7461 (mp0) REVERT: F 68 GLU cc_start: 0.8145 (mt-10) cc_final: 0.7647 (mp0) REVERT: F 95 ARG cc_start: 0.8163 (ttp80) cc_final: 0.7827 (ttp-110) REVERT: F 202 GLN cc_start: 0.8209 (mm-40) cc_final: 0.7827 (mt0) REVERT: F 206 GLN cc_start: 0.8692 (OUTLIER) cc_final: 0.7831 (mt0) REVERT: F 222 ASP cc_start: 0.9120 (OUTLIER) cc_final: 0.8672 (t70) REVERT: F 223 SER cc_start: 0.9175 (t) cc_final: 0.8922 (p) REVERT: G 39 LYS cc_start: 0.7760 (mttt) cc_final: 0.7372 (mtpp) REVERT: G 91 GLU cc_start: 0.8224 (OUTLIER) cc_final: 0.7826 (tt0) REVERT: G 94 GLN cc_start: 0.7868 (OUTLIER) cc_final: 0.7542 (tp-100) REVERT: G 107 LYS cc_start: 0.7718 (mmtm) cc_final: 0.6844 (ttmt) REVERT: G 176 GLU cc_start: 0.8173 (mm-30) cc_final: 0.7803 (mm-30) REVERT: G 187 ASP cc_start: 0.8285 (m-30) cc_final: 0.8058 (m-30) REVERT: G 202 GLN cc_start: 0.8113 (mm-40) cc_final: 0.7806 (mt0) REVERT: G 247 ARG cc_start: 0.8263 (mtp-110) cc_final: 0.7988 (mtp85) REVERT: G 306 ARG cc_start: 0.7765 (ttm110) cc_final: 0.6864 (ttp80) REVERT: G 308 GLU cc_start: 0.8183 (pm20) cc_final: 0.7805 (pm20) REVERT: H 27 ARG cc_start: 0.7879 (mtp-110) cc_final: 0.7472 (tmt170) REVERT: H 39 LYS cc_start: 0.7713 (mttt) cc_final: 0.7412 (mtpm) REVERT: H 64 LYS cc_start: 0.7093 (OUTLIER) cc_final: 0.6772 (ttmm) REVERT: H 94 GLN cc_start: 0.8422 (mm-40) cc_final: 0.8079 (tp40) REVERT: H 210 MET cc_start: 0.8704 (mtp) cc_final: 0.8447 (mtm) REVERT: H 247 ARG cc_start: 0.8014 (mtp-110) cc_final: 0.7415 (mmm160) REVERT: H 254 ARG cc_start: 0.8174 (ttt-90) cc_final: 0.7839 (tmm-80) REVERT: I 39 LYS cc_start: 0.7818 (mttt) cc_final: 0.7489 (mmmm) REVERT: I 40 LYS cc_start: 0.7673 (mtpp) cc_final: 0.7228 (mttp) REVERT: I 43 GLU cc_start: 0.7682 (mt-10) cc_final: 0.7286 (tp30) REVERT: I 50 GLU cc_start: 0.8629 (mp0) cc_final: 0.7528 (mp0) REVERT: I 110 ASP cc_start: 0.8680 (m-30) cc_final: 0.8416 (m-30) REVERT: I 176 GLU cc_start: 0.7245 (mm-30) cc_final: 0.6974 (tm-30) REVERT: I 223 SER cc_start: 0.9301 (t) cc_final: 0.9001 (t) REVERT: J 39 LYS cc_start: 0.7175 (mttt) cc_final: 0.6482 (mmmt) REVERT: J 40 LYS cc_start: 0.7318 (mtpp) cc_final: 0.6772 (mtpt) REVERT: J 50 GLU cc_start: 0.7961 (mp0) cc_final: 0.7135 (mp0) REVERT: J 73 LYS cc_start: 0.6676 (mttt) cc_final: 0.6065 (tptt) REVERT: J 77 GLU cc_start: 0.7148 (OUTLIER) cc_final: 0.6522 (mp0) REVERT: J 110 ASP cc_start: 0.8086 (m-30) cc_final: 0.7637 (m-30) REVERT: J 184 ASP cc_start: 0.8517 (m-30) cc_final: 0.8026 (m-30) REVERT: J 187 ASP cc_start: 0.8409 (OUTLIER) cc_final: 0.8108 (m-30) REVERT: J 222 ASP cc_start: 0.8763 (OUTLIER) cc_final: 0.8491 (t0) REVERT: J 247 ARG cc_start: 0.7594 (mtp-110) cc_final: 0.7266 (mtp85) REVERT: J 299 ARG cc_start: 0.8751 (mtm180) cc_final: 0.8318 (mmm-85) REVERT: J 308 GLU cc_start: 0.7913 (pm20) cc_final: 0.6965 (mt-10) REVERT: J 332 ASP cc_start: 0.8545 (p0) cc_final: 0.8304 (p0) outliers start: 124 outliers final: 71 residues processed: 687 average time/residue: 0.7668 time to fit residues: 595.5004 Evaluate side-chains 690 residues out of total 2607 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 89 poor density : 601 time to evaluate : 1.010 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 77 GLU Chi-restraints excluded: chain A residue 87 THR Chi-restraints excluded: chain A residue 88 THR Chi-restraints excluded: chain A residue 106 SER Chi-restraints excluded: chain A residue 128 GLU Chi-restraints excluded: chain A residue 130 ARG Chi-restraints excluded: chain A residue 208 SER Chi-restraints excluded: chain B residue 31 CYS Chi-restraints excluded: chain B residue 49 VAL Chi-restraints excluded: chain B residue 50 GLU Chi-restraints excluded: chain B residue 82 VAL Chi-restraints excluded: chain B residue 99 ILE Chi-restraints excluded: chain B residue 223 SER Chi-restraints excluded: chain C residue 43 GLU Chi-restraints excluded: chain C residue 50 GLU Chi-restraints excluded: chain C residue 81 LEU Chi-restraints excluded: chain C residue 99 ILE Chi-restraints excluded: chain C residue 104 THR Chi-restraints excluded: chain C residue 128 GLU Chi-restraints excluded: chain C residue 176 GLU Chi-restraints excluded: chain C residue 187 ASP Chi-restraints excluded: chain C residue 274 ASP Chi-restraints excluded: chain D residue 27 ARG Chi-restraints excluded: chain D residue 97 SER Chi-restraints excluded: chain D residue 111 LYS Chi-restraints excluded: chain D residue 121 SER Chi-restraints excluded: chain D residue 125 MET Chi-restraints excluded: chain D residue 128 GLU Chi-restraints excluded: chain D residue 187 ASP Chi-restraints excluded: chain D residue 222 ASP Chi-restraints excluded: chain D residue 272 GLN Chi-restraints excluded: chain D residue 273 VAL Chi-restraints excluded: chain D residue 274 ASP Chi-restraints excluded: chain D residue 330 ASN Chi-restraints excluded: chain E residue 27 ARG Chi-restraints excluded: chain E residue 48 THR Chi-restraints excluded: chain E residue 87 THR Chi-restraints excluded: chain E residue 112 LEU Chi-restraints excluded: chain E residue 125 MET Chi-restraints excluded: chain E residue 161 ASP Chi-restraints excluded: chain E residue 243 MET Chi-restraints excluded: chain E residue 255 LEU Chi-restraints excluded: chain E residue 273 VAL Chi-restraints excluded: chain E residue 296 SER Chi-restraints excluded: chain E residue 334 VAL Chi-restraints excluded: chain F residue 26 SER Chi-restraints excluded: chain F residue 94 GLN Chi-restraints excluded: chain F residue 97 SER Chi-restraints excluded: chain F residue 112 LEU Chi-restraints excluded: chain F residue 125 MET Chi-restraints excluded: chain F residue 145 GLN Chi-restraints excluded: chain F residue 206 GLN Chi-restraints excluded: chain F residue 222 ASP Chi-restraints excluded: chain F residue 272 GLN Chi-restraints excluded: chain F residue 273 VAL Chi-restraints excluded: chain F residue 297 THR Chi-restraints excluded: chain G residue 38 VAL Chi-restraints excluded: chain G residue 43 GLU Chi-restraints excluded: chain G residue 91 GLU Chi-restraints excluded: chain G residue 94 GLN Chi-restraints excluded: chain G residue 97 SER Chi-restraints excluded: chain G residue 125 MET Chi-restraints excluded: chain G residue 161 ASP Chi-restraints excluded: chain G residue 272 GLN Chi-restraints excluded: chain H residue 64 LYS Chi-restraints excluded: chain H residue 142 VAL Chi-restraints excluded: chain H residue 308 GLU Chi-restraints excluded: chain I residue 90 THR Chi-restraints excluded: chain I residue 97 SER Chi-restraints excluded: chain I residue 99 ILE Chi-restraints excluded: chain I residue 109 LEU Chi-restraints excluded: chain I residue 121 SER Chi-restraints excluded: chain I residue 130 ARG Chi-restraints excluded: chain I residue 149 ASP Chi-restraints excluded: chain I residue 183 SER Chi-restraints excluded: chain I residue 185 VAL Chi-restraints excluded: chain I residue 201 THR Chi-restraints excluded: chain I residue 212 VAL Chi-restraints excluded: chain I residue 214 SER Chi-restraints excluded: chain J residue 77 GLU Chi-restraints excluded: chain J residue 88 THR Chi-restraints excluded: chain J residue 97 SER Chi-restraints excluded: chain J residue 130 ARG Chi-restraints excluded: chain J residue 187 ASP Chi-restraints excluded: chain J residue 214 SER Chi-restraints excluded: chain J residue 222 ASP Chi-restraints excluded: chain J residue 239 SER Chi-restraints excluded: chain J residue 255 LEU Chi-restraints excluded: chain J residue 300 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 323 random chunks: chunk 286 optimal weight: 10.0000 chunk 264 optimal weight: 7.9990 chunk 284 optimal weight: 9.9990 chunk 43 optimal weight: 3.9990 chunk 33 optimal weight: 5.9990 chunk 105 optimal weight: 2.9990 chunk 163 optimal weight: 4.9990 chunk 121 optimal weight: 4.9990 chunk 185 optimal weight: 6.9990 chunk 157 optimal weight: 0.9980 chunk 39 optimal weight: 1.9990 overall best weight: 2.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 145 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 145 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 145 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 34 ASN H 290 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3618 r_free = 0.3618 target = 0.142719 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3217 r_free = 0.3217 target = 0.108567 restraints weight = 32208.101| |-----------------------------------------------------------------------------| r_work (start): 0.3167 rms_B_bonded: 1.99 r_work: 0.3045 rms_B_bonded: 2.64 restraints_weight: 0.5000 r_work: 0.2917 rms_B_bonded: 4.29 restraints_weight: 0.2500 r_work (final): 0.2917 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8072 moved from start: 0.3144 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.044 26875 Z= 0.254 Angle : 0.559 9.432 36550 Z= 0.294 Chirality : 0.042 0.148 4139 Planarity : 0.004 0.044 4521 Dihedral : 14.030 144.074 4454 Min Nonbonded Distance : 2.171 Molprobity Statistics. All-atom Clashscore : 6.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.60 % Favored : 97.40 % Rotamer: Outliers : 4.87 % Allowed : 21.33 % Favored : 73.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.32 % 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: -0.71 (0.14), residues: 3196 helix: 0.50 (0.14), residues: 1380 sheet: -0.19 (0.27), residues: 380 loop : -1.51 (0.14), residues: 1436 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG D 215 TYR 0.016 0.002 TYR G 315 PHE 0.022 0.002 PHE J 259 HIS 0.009 0.001 HIS E 294 Details of bonding type rmsd covalent geometry : bond 0.00587 (26875) covalent geometry : angle 0.55858 (36550) hydrogen bonds : bond 0.04249 ( 1159) hydrogen bonds : angle 4.55522 ( 3100) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6392 Ramachandran restraints generated. 3196 Oldfield, 0 Emsley, 3196 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6392 Ramachandran restraints generated. 3196 Oldfield, 0 Emsley, 3196 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 743 residues out of total 2607 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 127 poor density : 616 time to evaluate : 0.896 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 37 ASP cc_start: 0.7680 (m-30) cc_final: 0.7342 (m-30) REVERT: A 40 LYS cc_start: 0.7040 (mtpp) cc_final: 0.6381 (mtpt) REVERT: A 42 GLU cc_start: 0.6994 (pt0) cc_final: 0.6698 (pt0) REVERT: A 66 ILE cc_start: 0.6856 (mm) cc_final: 0.6542 (tt) REVERT: A 68 GLU cc_start: 0.6877 (mt-10) cc_final: 0.6247 (tm-30) REVERT: A 70 LYS cc_start: 0.6521 (ttpt) cc_final: 0.6216 (ttpt) REVERT: A 72 ASP cc_start: 0.7171 (m-30) cc_final: 0.6956 (m-30) REVERT: A 107 LYS cc_start: 0.7207 (mmtm) cc_final: 0.6804 (mttm) REVERT: A 145 GLN cc_start: 0.8660 (mt0) cc_final: 0.8349 (mt0) REVERT: A 202 GLN cc_start: 0.8168 (mm-40) cc_final: 0.7479 (mt0) REVERT: A 210 MET cc_start: 0.8214 (mtp) cc_final: 0.7524 (mtp) REVERT: A 247 ARG cc_start: 0.7270 (mtp-110) cc_final: 0.6748 (mmm-85) REVERT: A 254 ARG cc_start: 0.7455 (ttp80) cc_final: 0.7058 (tmt90) REVERT: A 303 ARG cc_start: 0.7557 (mtp180) cc_final: 0.7032 (mtm180) REVERT: A 308 GLU cc_start: 0.7379 (pt0) cc_final: 0.6565 (tt0) REVERT: A 329 ILE cc_start: 0.8628 (mt) cc_final: 0.7923 (mt) REVERT: B 40 LYS cc_start: 0.7079 (mtpp) cc_final: 0.5806 (mtpt) REVERT: B 42 GLU cc_start: 0.7420 (mt-10) cc_final: 0.6933 (mt-10) REVERT: B 43 GLU cc_start: 0.7472 (mt-10) cc_final: 0.7147 (mt-10) REVERT: B 50 GLU cc_start: 0.8421 (OUTLIER) cc_final: 0.7512 (mp0) REVERT: B 95 ARG cc_start: 0.8017 (ttp80) cc_final: 0.7479 (ttt-90) REVERT: B 107 LYS cc_start: 0.7644 (mmtm) cc_final: 0.6772 (ptpt) REVERT: B 145 GLN cc_start: 0.8429 (mt0) cc_final: 0.8183 (mp10) REVERT: B 215 ARG cc_start: 0.8246 (tmm160) cc_final: 0.7963 (tpt-90) REVERT: B 332 ASP cc_start: 0.8816 (p0) cc_final: 0.8344 (p0) REVERT: C 94 GLN cc_start: 0.7853 (mm-40) cc_final: 0.7172 (tm-30) REVERT: C 95 ARG cc_start: 0.8147 (ttp80) cc_final: 0.7483 (ttp-170) REVERT: C 107 LYS cc_start: 0.8327 (mmtm) cc_final: 0.7644 (ptmt) REVERT: C 145 GLN cc_start: 0.8925 (mp10) cc_final: 0.8297 (mp10) REVERT: C 154 GLU cc_start: 0.7586 (mt-10) cc_final: 0.6727 (mt-10) REVERT: C 181 SER cc_start: 0.8838 (t) cc_final: 0.8556 (p) REVERT: C 202 GLN cc_start: 0.7941 (mm-40) cc_final: 0.7521 (mt0) REVERT: C 243 MET cc_start: 0.8415 (mtm) cc_final: 0.8047 (mtt) REVERT: D 27 ARG cc_start: 0.8312 (OUTLIER) cc_final: 0.7750 (mtp180) REVERT: D 37 ASP cc_start: 0.7352 (m-30) cc_final: 0.7031 (m-30) REVERT: D 39 LYS cc_start: 0.7737 (mmmm) cc_final: 0.7395 (mmmm) REVERT: D 57 LYS cc_start: 0.8000 (tttp) cc_final: 0.7704 (ttpt) REVERT: D 94 GLN cc_start: 0.7806 (mm-40) cc_final: 0.6941 (tm-30) REVERT: D 107 LYS cc_start: 0.8340 (mmtm) cc_final: 0.7962 (mtmt) REVERT: D 187 ASP cc_start: 0.9060 (OUTLIER) cc_final: 0.8688 (t70) REVERT: D 247 ARG cc_start: 0.7989 (mtp-110) cc_final: 0.7710 (ttt-90) REVERT: D 334 VAL cc_start: 0.9229 (t) cc_final: 0.9028 (p) REVERT: E 27 ARG cc_start: 0.8542 (OUTLIER) cc_final: 0.7341 (mtp180) REVERT: E 57 LYS cc_start: 0.8460 (tptm) cc_final: 0.8057 (tttt) REVERT: E 68 GLU cc_start: 0.7976 (mp0) cc_final: 0.7622 (tp30) REVERT: E 107 LYS cc_start: 0.8073 (mmtm) cc_final: 0.7672 (mtmt) REVERT: E 176 GLU cc_start: 0.8446 (mm-30) cc_final: 0.7951 (tt0) REVERT: E 215 ARG cc_start: 0.8258 (tpt-90) cc_final: 0.8042 (tmt90) REVERT: E 243 MET cc_start: 0.8885 (OUTLIER) cc_final: 0.8646 (mtt) REVERT: F 39 LYS cc_start: 0.7767 (mttt) cc_final: 0.6935 (mtmt) REVERT: F 43 GLU cc_start: 0.8176 (mt-10) cc_final: 0.7516 (mp0) REVERT: F 68 GLU cc_start: 0.8204 (mt-10) cc_final: 0.7710 (mp0) REVERT: F 80 LYS cc_start: 0.8317 (mtpt) cc_final: 0.8049 (mtmm) REVERT: F 95 ARG cc_start: 0.8175 (ttp80) cc_final: 0.7897 (ttp-110) REVERT: F 202 GLN cc_start: 0.8217 (mm-40) cc_final: 0.7808 (mt0) REVERT: F 206 GLN cc_start: 0.8719 (OUTLIER) cc_final: 0.7870 (mt0) REVERT: F 222 ASP cc_start: 0.9107 (OUTLIER) cc_final: 0.8627 (t70) REVERT: F 223 SER cc_start: 0.9165 (t) cc_final: 0.8927 (p) REVERT: G 39 LYS cc_start: 0.7706 (mttt) cc_final: 0.7311 (mtpp) REVERT: G 91 GLU cc_start: 0.8152 (OUTLIER) cc_final: 0.7729 (tt0) REVERT: G 94 GLN cc_start: 0.7899 (OUTLIER) cc_final: 0.7601 (tp-100) REVERT: G 107 LYS cc_start: 0.7959 (mmtm) cc_final: 0.7010 (ttmt) REVERT: G 176 GLU cc_start: 0.8249 (mm-30) cc_final: 0.7851 (mm-30) REVERT: G 202 GLN cc_start: 0.8264 (mm-40) cc_final: 0.7923 (mt0) REVERT: G 206 GLN cc_start: 0.8892 (OUTLIER) cc_final: 0.8338 (mt0) REVERT: G 247 ARG cc_start: 0.8259 (mtp-110) cc_final: 0.7995 (mtp85) REVERT: G 306 ARG cc_start: 0.7803 (ttm110) cc_final: 0.6962 (ttp80) REVERT: G 308 GLU cc_start: 0.8190 (pm20) cc_final: 0.7823 (pm20) REVERT: H 27 ARG cc_start: 0.7885 (mtp-110) cc_final: 0.7456 (tmt170) REVERT: H 39 LYS cc_start: 0.7760 (mttt) cc_final: 0.7356 (mtmm) REVERT: H 64 LYS cc_start: 0.7113 (OUTLIER) cc_final: 0.6770 (ttmm) REVERT: H 210 MET cc_start: 0.8759 (mtp) cc_final: 0.8485 (mtm) REVERT: H 247 ARG cc_start: 0.8062 (mtp-110) cc_final: 0.7421 (mmm160) REVERT: H 254 ARG cc_start: 0.8161 (ttt-90) cc_final: 0.7728 (tmm-80) REVERT: H 257 ASP cc_start: 0.8548 (m-30) cc_final: 0.8110 (m-30) REVERT: H 306 ARG cc_start: 0.7759 (OUTLIER) cc_final: 0.7287 (ttt-90) REVERT: I 39 LYS cc_start: 0.7988 (mttt) cc_final: 0.7653 (mmmm) REVERT: I 40 LYS cc_start: 0.7761 (mtpp) cc_final: 0.7291 (mttp) REVERT: I 43 GLU cc_start: 0.7680 (mt-10) cc_final: 0.7302 (tp30) REVERT: I 223 SER cc_start: 0.9336 (t) cc_final: 0.9035 (t) REVERT: I 332 ASP cc_start: 0.8311 (p0) cc_final: 0.8014 (p0) REVERT: J 39 LYS cc_start: 0.6914 (mttt) cc_final: 0.6249 (mmmt) REVERT: J 40 LYS cc_start: 0.7611 (mtpp) cc_final: 0.6847 (mtpp) REVERT: J 42 GLU cc_start: 0.7188 (tp30) cc_final: 0.6538 (tt0) REVERT: J 50 GLU cc_start: 0.7951 (mp0) cc_final: 0.7133 (mp0) REVERT: J 73 LYS cc_start: 0.6657 (mttt) cc_final: 0.6062 (tptt) REVERT: J 77 GLU cc_start: 0.7115 (OUTLIER) cc_final: 0.6502 (mp0) REVERT: J 110 ASP cc_start: 0.8026 (m-30) cc_final: 0.7572 (m-30) REVERT: J 184 ASP cc_start: 0.8575 (m-30) cc_final: 0.8138 (m-30) REVERT: J 187 ASP cc_start: 0.8381 (OUTLIER) cc_final: 0.7818 (m-30) REVERT: J 222 ASP cc_start: 0.8789 (OUTLIER) cc_final: 0.8532 (t0) REVERT: J 247 ARG cc_start: 0.7709 (mtp-110) cc_final: 0.7385 (mtp85) REVERT: J 299 ARG cc_start: 0.8738 (mtm180) cc_final: 0.8323 (mmm-85) REVERT: J 308 GLU cc_start: 0.7971 (pm20) cc_final: 0.6970 (mt-10) outliers start: 127 outliers final: 84 residues processed: 683 average time/residue: 0.7752 time to fit residues: 598.2711 Evaluate side-chains 688 residues out of total 2607 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 99 poor density : 589 time to evaluate : 1.026 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 77 GLU Chi-restraints excluded: chain A residue 87 THR Chi-restraints excluded: chain A residue 88 THR Chi-restraints excluded: chain A residue 106 SER Chi-restraints excluded: chain A residue 208 SER Chi-restraints excluded: chain B residue 23 GLN Chi-restraints excluded: chain B residue 31 CYS Chi-restraints excluded: chain B residue 49 VAL Chi-restraints excluded: chain B residue 50 GLU Chi-restraints excluded: chain B residue 60 LEU Chi-restraints excluded: chain B residue 81 LEU Chi-restraints excluded: chain B residue 82 VAL Chi-restraints excluded: chain B residue 99 ILE Chi-restraints excluded: chain B residue 113 LEU Chi-restraints excluded: chain B residue 223 SER Chi-restraints excluded: chain C residue 43 GLU Chi-restraints excluded: chain C residue 81 LEU Chi-restraints excluded: chain C residue 99 ILE Chi-restraints excluded: chain C residue 104 THR Chi-restraints excluded: chain C residue 128 GLU Chi-restraints excluded: chain C residue 176 GLU Chi-restraints excluded: chain C residue 187 ASP Chi-restraints excluded: chain D residue 27 ARG Chi-restraints excluded: chain D residue 97 SER Chi-restraints excluded: chain D residue 121 SER Chi-restraints excluded: chain D residue 125 MET Chi-restraints excluded: chain D residue 161 ASP Chi-restraints excluded: chain D residue 181 SER Chi-restraints excluded: chain D residue 187 ASP Chi-restraints excluded: chain D residue 222 ASP Chi-restraints excluded: chain D residue 272 GLN Chi-restraints excluded: chain D residue 273 VAL Chi-restraints excluded: chain D residue 274 ASP Chi-restraints excluded: chain D residue 314 ILE Chi-restraints excluded: chain D residue 330 ASN Chi-restraints excluded: chain E residue 27 ARG Chi-restraints excluded: chain E residue 48 THR Chi-restraints excluded: chain E residue 87 THR Chi-restraints excluded: chain E residue 125 MET Chi-restraints excluded: chain E residue 161 ASP Chi-restraints excluded: chain E residue 243 MET Chi-restraints excluded: chain E residue 255 LEU Chi-restraints excluded: chain E residue 273 VAL Chi-restraints excluded: chain E residue 296 SER Chi-restraints excluded: chain E residue 334 VAL Chi-restraints excluded: chain F residue 26 SER Chi-restraints excluded: chain F residue 94 GLN Chi-restraints excluded: chain F residue 97 SER Chi-restraints excluded: chain F residue 112 LEU Chi-restraints excluded: chain F residue 125 MET Chi-restraints excluded: chain F residue 145 GLN Chi-restraints excluded: chain F residue 149 ASP Chi-restraints excluded: chain F residue 161 ASP Chi-restraints excluded: chain F residue 206 GLN Chi-restraints excluded: chain F residue 222 ASP Chi-restraints excluded: chain F residue 272 GLN Chi-restraints excluded: chain F residue 273 VAL Chi-restraints excluded: chain F residue 297 THR Chi-restraints excluded: chain F residue 319 CYS Chi-restraints excluded: chain G residue 38 VAL Chi-restraints excluded: chain G residue 43 GLU Chi-restraints excluded: chain G residue 91 GLU Chi-restraints excluded: chain G residue 94 GLN Chi-restraints excluded: chain G residue 97 SER Chi-restraints excluded: chain G residue 125 MET Chi-restraints excluded: chain G residue 161 ASP Chi-restraints excluded: chain G residue 206 GLN Chi-restraints excluded: chain G residue 272 GLN Chi-restraints excluded: chain H residue 64 LYS Chi-restraints excluded: chain H residue 142 VAL Chi-restraints excluded: chain H residue 306 ARG Chi-restraints excluded: chain H residue 308 GLU Chi-restraints excluded: chain I residue 28 LEU Chi-restraints excluded: chain I residue 90 THR Chi-restraints excluded: chain I residue 97 SER Chi-restraints excluded: chain I residue 99 ILE Chi-restraints excluded: chain I residue 109 LEU Chi-restraints excluded: chain I residue 121 SER Chi-restraints excluded: chain I residue 130 ARG Chi-restraints excluded: chain I residue 149 ASP Chi-restraints excluded: chain I residue 183 SER Chi-restraints excluded: chain I residue 201 THR Chi-restraints excluded: chain I residue 212 VAL Chi-restraints excluded: chain I residue 214 SER Chi-restraints excluded: chain I residue 261 VAL Chi-restraints excluded: chain J residue 58 LYS Chi-restraints excluded: chain J residue 77 GLU Chi-restraints excluded: chain J residue 88 THR Chi-restraints excluded: chain J residue 97 SER Chi-restraints excluded: chain J residue 130 ARG Chi-restraints excluded: chain J residue 187 ASP Chi-restraints excluded: chain J residue 214 SER Chi-restraints excluded: chain J residue 222 ASP Chi-restraints excluded: chain J residue 239 SER Chi-restraints excluded: chain J residue 255 LEU Chi-restraints excluded: chain J residue 261 VAL Chi-restraints excluded: chain J residue 272 GLN Chi-restraints excluded: chain J residue 300 LEU Chi-restraints excluded: chain J residue 322 GLU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 323 random chunks: chunk 32 optimal weight: 10.0000 chunk 150 optimal weight: 0.5980 chunk 115 optimal weight: 0.9980 chunk 225 optimal weight: 5.9990 chunk 288 optimal weight: 1.9990 chunk 157 optimal weight: 0.7980 chunk 314 optimal weight: 2.9990 chunk 236 optimal weight: 0.9980 chunk 121 optimal weight: 2.9990 chunk 114 optimal weight: 2.9990 chunk 320 optimal weight: 2.9990 overall best weight: 1.0782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 242 GLN ** C 145 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 272 GLN ** D 145 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 145 GLN H 290 ASN ** I 145 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3667 r_free = 0.3667 target = 0.147148 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3276 r_free = 0.3276 target = 0.112959 restraints weight = 32029.431| |-----------------------------------------------------------------------------| r_work (start): 0.3269 rms_B_bonded: 2.01 r_work: 0.3149 rms_B_bonded: 2.67 restraints_weight: 0.5000 r_work: 0.3019 rms_B_bonded: 4.39 restraints_weight: 0.2500 r_work (final): 0.3019 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8035 moved from start: 0.3377 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 26875 Z= 0.129 Angle : 0.477 8.251 36550 Z= 0.253 Chirality : 0.039 0.143 4139 Planarity : 0.003 0.039 4521 Dihedral : 13.742 143.757 4454 Min Nonbonded Distance : 2.236 Molprobity Statistics. All-atom Clashscore : 6.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.81 % Favored : 98.19 % Rotamer: Outliers : 3.72 % Allowed : 23.17 % Favored : 73.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.32 % 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: -0.23 (0.14), residues: 3196 helix: 0.84 (0.14), residues: 1390 sheet: 0.02 (0.27), residues: 380 loop : -1.18 (0.15), residues: 1426 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG B 130 TYR 0.008 0.001 TYR G 315 PHE 0.015 0.001 PHE F 126 HIS 0.006 0.001 HIS A 138 Details of bonding type rmsd covalent geometry : bond 0.00290 (26875) covalent geometry : angle 0.47726 (36550) hydrogen bonds : bond 0.03202 ( 1159) hydrogen bonds : angle 4.26599 ( 3100) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6392 Ramachandran restraints generated. 3196 Oldfield, 0 Emsley, 3196 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6392 Ramachandran restraints generated. 3196 Oldfield, 0 Emsley, 3196 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 715 residues out of total 2607 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 97 poor density : 618 time to evaluate : 1.035 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 40 LYS cc_start: 0.7336 (mtpp) cc_final: 0.6308 (mtpt) REVERT: A 42 GLU cc_start: 0.6849 (pt0) cc_final: 0.6604 (pt0) REVERT: A 66 ILE cc_start: 0.6842 (mm) cc_final: 0.6629 (tp) REVERT: A 68 GLU cc_start: 0.6806 (mt-10) cc_final: 0.6235 (tm-30) REVERT: A 70 LYS cc_start: 0.6788 (ttpt) cc_final: 0.6425 (ttpt) REVERT: A 77 GLU cc_start: 0.7564 (OUTLIER) cc_final: 0.7350 (mp0) REVERT: A 84 MET cc_start: 0.8861 (mtp) cc_final: 0.8601 (mtp) REVERT: A 107 LYS cc_start: 0.7165 (mmtm) cc_final: 0.6767 (mttm) REVERT: A 210 MET cc_start: 0.8133 (mtp) cc_final: 0.7406 (mtp) REVERT: A 247 ARG cc_start: 0.7204 (mtp-110) cc_final: 0.6559 (mmm-85) REVERT: A 254 ARG cc_start: 0.7446 (ttp80) cc_final: 0.7124 (tmt90) REVERT: A 303 ARG cc_start: 0.7542 (mtp180) cc_final: 0.7003 (mtm180) REVERT: A 308 GLU cc_start: 0.7258 (pt0) cc_final: 0.6736 (tt0) REVERT: A 329 ILE cc_start: 0.8579 (mt) cc_final: 0.7976 (mt) REVERT: B 37 ASP cc_start: 0.6311 (m-30) cc_final: 0.5915 (m-30) REVERT: B 40 LYS cc_start: 0.6978 (mtpp) cc_final: 0.5819 (mtmt) REVERT: B 42 GLU cc_start: 0.7169 (mt-10) cc_final: 0.6605 (mt-10) REVERT: B 43 GLU cc_start: 0.7470 (mt-10) cc_final: 0.7121 (mt-10) REVERT: B 72 ASP cc_start: 0.7547 (m-30) cc_final: 0.7197 (m-30) REVERT: B 77 GLU cc_start: 0.7723 (mp0) cc_final: 0.7207 (mm-30) REVERT: B 95 ARG cc_start: 0.8011 (ttp80) cc_final: 0.7508 (ttt-90) REVERT: B 107 LYS cc_start: 0.7791 (mmtm) cc_final: 0.6851 (ptpt) REVERT: B 145 GLN cc_start: 0.8313 (mt0) cc_final: 0.8099 (mp10) REVERT: B 206 GLN cc_start: 0.7518 (mt0) cc_final: 0.7227 (mt0) REVERT: B 215 ARG cc_start: 0.8214 (tmm160) cc_final: 0.7971 (tpt-90) REVERT: B 332 ASP cc_start: 0.8773 (p0) cc_final: 0.8397 (p0) REVERT: C 94 GLN cc_start: 0.7792 (mm-40) cc_final: 0.7012 (tm-30) REVERT: C 95 ARG cc_start: 0.8275 (ttp80) cc_final: 0.7583 (ttp-170) REVERT: C 107 LYS cc_start: 0.8283 (mmtm) cc_final: 0.7646 (ptmt) REVERT: C 145 GLN cc_start: 0.8759 (mp10) cc_final: 0.8125 (mp10) REVERT: C 154 GLU cc_start: 0.7542 (mt-10) cc_final: 0.6807 (mt-10) REVERT: C 181 SER cc_start: 0.8771 (t) cc_final: 0.8489 (p) REVERT: C 202 GLN cc_start: 0.7856 (mm-40) cc_final: 0.7471 (mt0) REVERT: C 243 MET cc_start: 0.8175 (mtm) cc_final: 0.7973 (mtt) REVERT: D 27 ARG cc_start: 0.8318 (OUTLIER) cc_final: 0.7225 (mtp180) REVERT: D 30 GLN cc_start: 0.7567 (mt0) cc_final: 0.7319 (mp10) REVERT: D 57 LYS cc_start: 0.7949 (tttp) cc_final: 0.7652 (ttpt) REVERT: D 94 GLN cc_start: 0.7759 (mm-40) cc_final: 0.6954 (tm-30) REVERT: D 107 LYS cc_start: 0.8322 (mmtm) cc_final: 0.7943 (mtmt) REVERT: D 187 ASP cc_start: 0.9059 (OUTLIER) cc_final: 0.8709 (t70) REVERT: D 334 VAL cc_start: 0.9229 (t) cc_final: 0.8917 (p) REVERT: E 57 LYS cc_start: 0.8407 (tptm) cc_final: 0.8020 (tttt) REVERT: E 68 GLU cc_start: 0.7988 (mp0) cc_final: 0.7746 (tp30) REVERT: E 107 LYS cc_start: 0.8013 (mmtm) cc_final: 0.7619 (mtmt) REVERT: E 145 GLN cc_start: 0.8998 (OUTLIER) cc_final: 0.8633 (mp10) REVERT: E 149 ASP cc_start: 0.8344 (t70) cc_final: 0.7942 (t70) REVERT: E 176 GLU cc_start: 0.8384 (mm-30) cc_final: 0.7850 (tt0) REVERT: E 215 ARG cc_start: 0.8194 (tpt-90) cc_final: 0.7950 (tmt90) REVERT: F 27 ARG cc_start: 0.8418 (mtp180) cc_final: 0.8094 (mmm160) REVERT: F 39 LYS cc_start: 0.7433 (mttt) cc_final: 0.6608 (mtmt) REVERT: F 43 GLU cc_start: 0.7991 (mt-10) cc_final: 0.7430 (mp0) REVERT: F 68 GLU cc_start: 0.8198 (mt-10) cc_final: 0.7687 (mp0) REVERT: F 202 GLN cc_start: 0.8208 (mm-40) cc_final: 0.7831 (mt0) REVERT: F 206 GLN cc_start: 0.8662 (OUTLIER) cc_final: 0.7829 (mt0) REVERT: G 39 LYS cc_start: 0.7606 (mttt) cc_final: 0.7224 (mtpp) REVERT: G 94 GLN cc_start: 0.7872 (OUTLIER) cc_final: 0.7566 (tp-100) REVERT: G 107 LYS cc_start: 0.7939 (mmtm) cc_final: 0.6969 (ttmt) REVERT: G 111 LYS cc_start: 0.8328 (ttpp) cc_final: 0.8071 (mtpp) REVERT: G 125 MET cc_start: 0.9017 (OUTLIER) cc_final: 0.8531 (mtm) REVERT: G 130 ARG cc_start: 0.8409 (ptp90) cc_final: 0.8132 (ptt-90) REVERT: G 176 GLU cc_start: 0.8161 (mm-30) cc_final: 0.7810 (mm-30) REVERT: G 187 ASP cc_start: 0.8249 (m-30) cc_final: 0.7916 (m-30) REVERT: G 191 TYR cc_start: 0.9494 (t80) cc_final: 0.9260 (t80) REVERT: G 202 GLN cc_start: 0.8071 (mm-40) cc_final: 0.7842 (mt0) REVERT: G 206 GLN cc_start: 0.8902 (OUTLIER) cc_final: 0.8363 (mt0) REVERT: G 247 ARG cc_start: 0.8222 (mtp-110) cc_final: 0.7941 (mtp85) REVERT: G 290 ASN cc_start: 0.9085 (m-40) cc_final: 0.8870 (m110) REVERT: G 306 ARG cc_start: 0.7861 (ttm110) cc_final: 0.7020 (tmm160) REVERT: G 308 GLU cc_start: 0.8235 (pm20) cc_final: 0.7903 (pm20) REVERT: H 27 ARG cc_start: 0.7705 (mtp-110) cc_final: 0.7416 (tmt170) REVERT: H 39 LYS cc_start: 0.7650 (mttt) cc_final: 0.7215 (mtmm) REVERT: H 94 GLN cc_start: 0.8447 (mm-40) cc_final: 0.8108 (tp40) REVERT: H 135 GLN cc_start: 0.9080 (mm-40) cc_final: 0.8806 (mp10) REVERT: H 206 GLN cc_start: 0.8751 (OUTLIER) cc_final: 0.8372 (mt0) REVERT: H 210 MET cc_start: 0.8541 (mtp) cc_final: 0.8340 (mtm) REVERT: H 247 ARG cc_start: 0.7989 (mtp-110) cc_final: 0.7466 (mmm160) REVERT: H 254 ARG cc_start: 0.8053 (ttt-90) cc_final: 0.7622 (tmm-80) REVERT: H 257 ASP cc_start: 0.8537 (m-30) cc_final: 0.8020 (m-30) REVERT: I 27 ARG cc_start: 0.8132 (OUTLIER) cc_final: 0.7821 (tmt-80) REVERT: I 39 LYS cc_start: 0.7853 (mttt) cc_final: 0.7519 (mmmm) REVERT: I 40 LYS cc_start: 0.7662 (mtpp) cc_final: 0.7273 (mttp) REVERT: I 43 GLU cc_start: 0.7609 (mt-10) cc_final: 0.7243 (tp30) REVERT: I 80 LYS cc_start: 0.8090 (mtmt) cc_final: 0.7861 (mtmm) REVERT: I 109 LEU cc_start: 0.8726 (OUTLIER) cc_final: 0.8345 (mp) REVERT: I 110 ASP cc_start: 0.8675 (m-30) cc_final: 0.8397 (m-30) REVERT: I 332 ASP cc_start: 0.8350 (p0) cc_final: 0.7992 (p0) REVERT: J 39 LYS cc_start: 0.6763 (mttt) cc_final: 0.6067 (mmmt) REVERT: J 40 LYS cc_start: 0.7001 (mtpp) cc_final: 0.6415 (mttt) REVERT: J 42 GLU cc_start: 0.7168 (tp30) cc_final: 0.6532 (tt0) REVERT: J 50 GLU cc_start: 0.7800 (mp0) cc_final: 0.6794 (mp0) REVERT: J 73 LYS cc_start: 0.6559 (mttt) cc_final: 0.5969 (tptt) REVERT: J 77 GLU cc_start: 0.7461 (OUTLIER) cc_final: 0.6821 (mp0) REVERT: J 110 ASP cc_start: 0.8216 (m-30) cc_final: 0.7908 (m-30) REVERT: J 154 GLU cc_start: 0.8124 (mt-10) cc_final: 0.7653 (mm-30) REVERT: J 177 ARG cc_start: 0.8369 (OUTLIER) cc_final: 0.7712 (ttt180) REVERT: J 184 ASP cc_start: 0.8639 (m-30) cc_final: 0.8296 (m-30) REVERT: J 187 ASP cc_start: 0.8149 (OUTLIER) cc_final: 0.7407 (m-30) REVERT: J 222 ASP cc_start: 0.8639 (OUTLIER) cc_final: 0.8358 (t0) REVERT: J 299 ARG cc_start: 0.8675 (mtm180) cc_final: 0.8291 (mtt-85) REVERT: J 308 GLU cc_start: 0.7946 (pm20) cc_final: 0.6930 (mt-10) REVERT: J 332 ASP cc_start: 0.8572 (p0) cc_final: 0.8184 (p0) outliers start: 97 outliers final: 54 residues processed: 668 average time/residue: 0.7846 time to fit residues: 592.8638 Evaluate side-chains 668 residues out of total 2607 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 599 time to evaluate : 0.867 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 77 GLU Chi-restraints excluded: chain A residue 87 THR Chi-restraints excluded: chain A residue 88 THR Chi-restraints excluded: chain B residue 31 CYS Chi-restraints excluded: chain B residue 49 VAL Chi-restraints excluded: chain B residue 60 LEU Chi-restraints excluded: chain B residue 82 VAL Chi-restraints excluded: chain B residue 113 LEU Chi-restraints excluded: chain B residue 272 GLN Chi-restraints excluded: chain C residue 43 GLU Chi-restraints excluded: chain C residue 128 GLU Chi-restraints excluded: chain C residue 187 ASP Chi-restraints excluded: chain C residue 330 ASN Chi-restraints excluded: chain D residue 27 ARG Chi-restraints excluded: chain D residue 97 SER Chi-restraints excluded: chain D residue 161 ASP Chi-restraints excluded: chain D residue 187 ASP Chi-restraints excluded: chain D residue 237 GLU Chi-restraints excluded: chain D residue 272 GLN Chi-restraints excluded: chain D residue 274 ASP Chi-restraints excluded: chain D residue 330 ASN Chi-restraints excluded: chain E residue 48 THR Chi-restraints excluded: chain E residue 87 THR Chi-restraints excluded: chain E residue 112 LEU Chi-restraints excluded: chain E residue 125 MET Chi-restraints excluded: chain E residue 145 GLN Chi-restraints excluded: chain E residue 161 ASP Chi-restraints excluded: chain E residue 273 VAL Chi-restraints excluded: chain E residue 296 SER Chi-restraints excluded: chain F residue 97 SER Chi-restraints excluded: chain F residue 112 LEU Chi-restraints excluded: chain F residue 125 MET Chi-restraints excluded: chain F residue 145 GLN Chi-restraints excluded: chain F residue 149 ASP Chi-restraints excluded: chain F residue 206 GLN Chi-restraints excluded: chain F residue 272 GLN Chi-restraints excluded: chain F residue 273 VAL Chi-restraints excluded: chain F residue 297 THR Chi-restraints excluded: chain G residue 38 VAL Chi-restraints excluded: chain G residue 94 GLN Chi-restraints excluded: chain G residue 125 MET Chi-restraints excluded: chain G residue 161 ASP Chi-restraints excluded: chain G residue 206 GLN Chi-restraints excluded: chain G residue 272 GLN Chi-restraints excluded: chain H residue 26 SER Chi-restraints excluded: chain H residue 68 GLU Chi-restraints excluded: chain H residue 82 VAL Chi-restraints excluded: chain H residue 142 VAL Chi-restraints excluded: chain H residue 206 GLN Chi-restraints excluded: chain H residue 272 GLN Chi-restraints excluded: chain H residue 308 GLU Chi-restraints excluded: chain I residue 27 ARG Chi-restraints excluded: chain I residue 28 LEU Chi-restraints excluded: chain I residue 90 THR Chi-restraints excluded: chain I residue 99 ILE Chi-restraints excluded: chain I residue 109 LEU Chi-restraints excluded: chain I residue 121 SER Chi-restraints excluded: chain I residue 183 SER Chi-restraints excluded: chain I residue 201 THR Chi-restraints excluded: chain I residue 212 VAL Chi-restraints excluded: chain I residue 214 SER Chi-restraints excluded: chain J residue 77 GLU Chi-restraints excluded: chain J residue 130 ARG Chi-restraints excluded: chain J residue 177 ARG Chi-restraints excluded: chain J residue 187 ASP Chi-restraints excluded: chain J residue 222 ASP Chi-restraints excluded: chain J residue 239 SER Chi-restraints excluded: chain J residue 272 GLN Chi-restraints excluded: chain J residue 300 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 323 random chunks: chunk 36 optimal weight: 0.9990 chunk 40 optimal weight: 2.9990 chunk 153 optimal weight: 1.9990 chunk 77 optimal weight: 0.9980 chunk 309 optimal weight: 6.9990 chunk 67 optimal weight: 3.9990 chunk 279 optimal weight: 20.0000 chunk 272 optimal weight: 0.9990 chunk 213 optimal weight: 3.9990 chunk 298 optimal weight: 20.0000 chunk 132 optimal weight: 0.9990 overall best weight: 1.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 272 GLN C 145 GLN ** D 145 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 145 GLN F 23 GLN H 34 ASN ** H 145 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 145 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 135 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3665 r_free = 0.3665 target = 0.147011 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3273 r_free = 0.3273 target = 0.112796 restraints weight = 32000.601| |-----------------------------------------------------------------------------| r_work (start): 0.3267 rms_B_bonded: 2.00 r_work: 0.3147 rms_B_bonded: 2.66 restraints_weight: 0.5000 r_work: 0.3017 rms_B_bonded: 4.37 restraints_weight: 0.2500 r_work (final): 0.3017 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8032 moved from start: 0.3462 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 26875 Z= 0.136 Angle : 0.483 8.166 36550 Z= 0.255 Chirality : 0.039 0.140 4139 Planarity : 0.003 0.039 4521 Dihedral : 13.662 142.871 4454 Min Nonbonded Distance : 2.239 Molprobity Statistics. All-atom Clashscore : 6.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.22 % Favored : 97.78 % Rotamer: Outliers : 3.87 % Allowed : 23.40 % Favored : 72.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.32 % 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: 0.03 (0.14), residues: 3196 helix: 1.02 (0.14), residues: 1390 sheet: 0.14 (0.27), residues: 380 loop : -1.00 (0.15), residues: 1426 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG D 215 TYR 0.010 0.001 TYR G 315 PHE 0.014 0.001 PHE F 126 HIS 0.006 0.001 HIS A 138 Details of bonding type rmsd covalent geometry : bond 0.00307 (26875) covalent geometry : angle 0.48346 (36550) hydrogen bonds : bond 0.03261 ( 1159) hydrogen bonds : angle 4.21472 ( 3100) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6392 Ramachandran restraints generated. 3196 Oldfield, 0 Emsley, 3196 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6392 Ramachandran restraints generated. 3196 Oldfield, 0 Emsley, 3196 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 710 residues out of total 2607 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 101 poor density : 609 time to evaluate : 1.058 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 40 LYS cc_start: 0.7327 (mtpp) cc_final: 0.6311 (mtpt) REVERT: A 42 GLU cc_start: 0.6924 (pt0) cc_final: 0.6677 (pt0) REVERT: A 66 ILE cc_start: 0.6818 (mm) cc_final: 0.6606 (tp) REVERT: A 68 GLU cc_start: 0.6808 (mt-10) cc_final: 0.6230 (tm-30) REVERT: A 70 LYS cc_start: 0.6769 (ttpt) cc_final: 0.6400 (ttpt) REVERT: A 107 LYS cc_start: 0.7158 (mmtm) cc_final: 0.6761 (mttm) REVERT: A 210 MET cc_start: 0.8178 (mtp) cc_final: 0.7214 (mtp) REVERT: A 247 ARG cc_start: 0.7079 (mtp-110) cc_final: 0.6447 (mmm-85) REVERT: A 254 ARG cc_start: 0.7416 (ttp80) cc_final: 0.7105 (tmt90) REVERT: A 303 ARG cc_start: 0.7586 (mtp180) cc_final: 0.6970 (mtm180) REVERT: A 308 GLU cc_start: 0.7373 (pt0) cc_final: 0.6719 (tt0) REVERT: A 329 ILE cc_start: 0.8597 (mt) cc_final: 0.7978 (mt) REVERT: B 42 GLU cc_start: 0.7133 (mt-10) cc_final: 0.6639 (mt-10) REVERT: B 43 GLU cc_start: 0.7483 (mt-10) cc_final: 0.7135 (mt-10) REVERT: B 72 ASP cc_start: 0.7531 (m-30) cc_final: 0.7219 (m-30) REVERT: B 77 GLU cc_start: 0.7893 (mp0) cc_final: 0.7236 (mm-30) REVERT: B 88 THR cc_start: 0.9119 (OUTLIER) cc_final: 0.8861 (p) REVERT: B 95 ARG cc_start: 0.7936 (ttp80) cc_final: 0.7518 (ttt-90) REVERT: B 107 LYS cc_start: 0.7810 (mmtm) cc_final: 0.6922 (ptpt) REVERT: B 206 GLN cc_start: 0.7490 (mt0) cc_final: 0.7249 (mt0) REVERT: B 215 ARG cc_start: 0.8205 (OUTLIER) cc_final: 0.7988 (tpt-90) REVERT: B 306 ARG cc_start: 0.7916 (mmm-85) cc_final: 0.7261 (ptm-80) REVERT: B 332 ASP cc_start: 0.8776 (p0) cc_final: 0.8379 (p0) REVERT: C 94 GLN cc_start: 0.7789 (mm-40) cc_final: 0.7004 (tm-30) REVERT: C 95 ARG cc_start: 0.8164 (ttp80) cc_final: 0.7471 (ttp-170) REVERT: C 107 LYS cc_start: 0.8309 (mmtm) cc_final: 0.7640 (ptmt) REVERT: C 145 GLN cc_start: 0.8892 (OUTLIER) cc_final: 0.8298 (mp10) REVERT: C 154 GLU cc_start: 0.7543 (mt-10) cc_final: 0.6832 (mt-10) REVERT: C 181 SER cc_start: 0.8676 (t) cc_final: 0.8209 (p) REVERT: C 187 ASP cc_start: 0.8664 (OUTLIER) cc_final: 0.8457 (m-30) REVERT: C 202 GLN cc_start: 0.7844 (mm-40) cc_final: 0.7448 (mt0) REVERT: C 243 MET cc_start: 0.8181 (mtm) cc_final: 0.7981 (mtt) REVERT: D 27 ARG cc_start: 0.8316 (OUTLIER) cc_final: 0.7305 (mtp180) REVERT: D 30 GLN cc_start: 0.7545 (mt0) cc_final: 0.7319 (mp10) REVERT: D 42 GLU cc_start: 0.7865 (mt-10) cc_final: 0.7553 (mm-30) REVERT: D 94 GLN cc_start: 0.7774 (mm-40) cc_final: 0.6977 (tm-30) REVERT: D 107 LYS cc_start: 0.8320 (mmtm) cc_final: 0.7933 (mtmt) REVERT: D 111 LYS cc_start: 0.8470 (OUTLIER) cc_final: 0.8140 (ttmt) REVERT: D 187 ASP cc_start: 0.9084 (OUTLIER) cc_final: 0.8718 (t70) REVERT: D 215 ARG cc_start: 0.8053 (ttt90) cc_final: 0.7847 (tpt-90) REVERT: D 334 VAL cc_start: 0.9205 (t) cc_final: 0.8979 (p) REVERT: E 57 LYS cc_start: 0.8401 (tptm) cc_final: 0.8011 (tttt) REVERT: E 68 GLU cc_start: 0.8099 (mp0) cc_final: 0.7736 (tp30) REVERT: E 107 LYS cc_start: 0.8018 (mmtm) cc_final: 0.7616 (mtmt) REVERT: E 145 GLN cc_start: 0.8965 (OUTLIER) cc_final: 0.8501 (mp10) REVERT: E 176 GLU cc_start: 0.8364 (mm-30) cc_final: 0.7825 (tt0) REVERT: E 243 MET cc_start: 0.8808 (OUTLIER) cc_final: 0.8554 (mtt) REVERT: F 27 ARG cc_start: 0.8400 (mtp180) cc_final: 0.8170 (ttt-90) REVERT: F 39 LYS cc_start: 0.7416 (mttt) cc_final: 0.6626 (mtmt) REVERT: F 43 GLU cc_start: 0.7892 (mt-10) cc_final: 0.7374 (mp0) REVERT: F 68 GLU cc_start: 0.8189 (mt-10) cc_final: 0.7661 (mp0) REVERT: F 95 ARG cc_start: 0.8210 (ttp80) cc_final: 0.7917 (ttp-110) REVERT: F 202 GLN cc_start: 0.8193 (mm-40) cc_final: 0.7824 (mt0) REVERT: F 206 GLN cc_start: 0.8686 (OUTLIER) cc_final: 0.7872 (mt0) REVERT: G 39 LYS cc_start: 0.7688 (mttt) cc_final: 0.7303 (mtpp) REVERT: G 94 GLN cc_start: 0.7873 (OUTLIER) cc_final: 0.7472 (tp-100) REVERT: G 107 LYS cc_start: 0.7938 (mmtm) cc_final: 0.6947 (ttmm) REVERT: G 111 LYS cc_start: 0.8325 (ttpp) cc_final: 0.8077 (mtpp) REVERT: G 125 MET cc_start: 0.8996 (OUTLIER) cc_final: 0.8472 (mtm) REVERT: G 130 ARG cc_start: 0.8425 (OUTLIER) cc_final: 0.8201 (ptp90) REVERT: G 176 GLU cc_start: 0.8152 (mm-30) cc_final: 0.7798 (mm-30) REVERT: G 187 ASP cc_start: 0.8279 (m-30) cc_final: 0.7917 (m-30) REVERT: G 202 GLN cc_start: 0.8140 (mm-40) cc_final: 0.7869 (mt0) REVERT: G 206 GLN cc_start: 0.8949 (OUTLIER) cc_final: 0.8398 (mt0) REVERT: G 247 ARG cc_start: 0.8209 (mtp-110) cc_final: 0.7989 (mtp85) REVERT: G 306 ARG cc_start: 0.7848 (ttm110) cc_final: 0.6988 (tmm160) REVERT: G 308 GLU cc_start: 0.8231 (pm20) cc_final: 0.7902 (pm20) REVERT: H 39 LYS cc_start: 0.7648 (mttt) cc_final: 0.7209 (mtmm) REVERT: H 40 LYS cc_start: 0.7622 (mtpp) cc_final: 0.7331 (mtpt) REVERT: H 206 GLN cc_start: 0.8675 (OUTLIER) cc_final: 0.8293 (mt0) REVERT: H 247 ARG cc_start: 0.7985 (mtp-110) cc_final: 0.7316 (mmm160) REVERT: H 254 ARG cc_start: 0.8109 (ttt-90) cc_final: 0.7762 (tmm-80) REVERT: I 27 ARG cc_start: 0.7674 (OUTLIER) cc_final: 0.7356 (tmt-80) REVERT: I 39 LYS cc_start: 0.7810 (mttt) cc_final: 0.7492 (mmmm) REVERT: I 40 LYS cc_start: 0.7696 (mtpp) cc_final: 0.7304 (mttp) REVERT: I 43 GLU cc_start: 0.7612 (mt-10) cc_final: 0.7269 (tp30) REVERT: I 74 ILE cc_start: 0.8265 (mt) cc_final: 0.8015 (mp) REVERT: I 109 LEU cc_start: 0.8714 (OUTLIER) cc_final: 0.8344 (mp) REVERT: I 187 ASP cc_start: 0.8205 (m-30) cc_final: 0.7970 (m-30) REVERT: I 332 ASP cc_start: 0.8403 (p0) cc_final: 0.8132 (p0) REVERT: J 39 LYS cc_start: 0.6904 (mttt) cc_final: 0.6253 (mmmt) REVERT: J 40 LYS cc_start: 0.6982 (mtpp) cc_final: 0.6474 (mttt) REVERT: J 42 GLU cc_start: 0.7222 (tp30) cc_final: 0.6484 (tt0) REVERT: J 50 GLU cc_start: 0.7778 (mp0) cc_final: 0.7048 (mp0) REVERT: J 73 LYS cc_start: 0.6549 (mttt) cc_final: 0.5955 (tptt) REVERT: J 77 GLU cc_start: 0.7429 (OUTLIER) cc_final: 0.6783 (mp0) REVERT: J 135 GLN cc_start: 0.8555 (mm-40) cc_final: 0.6650 (mp-120) REVERT: J 177 ARG cc_start: 0.8368 (OUTLIER) cc_final: 0.7806 (ttt180) REVERT: J 184 ASP cc_start: 0.8630 (m-30) cc_final: 0.8296 (m-30) REVERT: J 187 ASP cc_start: 0.8120 (OUTLIER) cc_final: 0.7354 (m-30) REVERT: J 222 ASP cc_start: 0.8596 (OUTLIER) cc_final: 0.8291 (t0) REVERT: J 299 ARG cc_start: 0.8650 (mtm180) cc_final: 0.8227 (mtt-85) REVERT: J 308 GLU cc_start: 0.7963 (pm20) cc_final: 0.6937 (mt-10) outliers start: 101 outliers final: 59 residues processed: 661 average time/residue: 0.7527 time to fit residues: 564.7125 Evaluate side-chains 675 residues out of total 2607 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 80 poor density : 595 time to evaluate : 0.910 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 87 THR Chi-restraints excluded: chain A residue 88 THR Chi-restraints excluded: chain A residue 128 GLU Chi-restraints excluded: chain B residue 23 GLN Chi-restraints excluded: chain B residue 31 CYS Chi-restraints excluded: chain B residue 60 LEU Chi-restraints excluded: chain B residue 82 VAL Chi-restraints excluded: chain B residue 88 THR Chi-restraints excluded: chain B residue 113 LEU Chi-restraints excluded: chain B residue 187 ASP Chi-restraints excluded: chain B residue 215 ARG Chi-restraints excluded: chain B residue 223 SER Chi-restraints excluded: chain C residue 43 GLU Chi-restraints excluded: chain C residue 81 LEU Chi-restraints excluded: chain C residue 128 GLU Chi-restraints excluded: chain C residue 145 GLN Chi-restraints excluded: chain C residue 187 ASP Chi-restraints excluded: chain C residue 330 ASN Chi-restraints excluded: chain D residue 27 ARG Chi-restraints excluded: chain D residue 97 SER Chi-restraints excluded: chain D residue 111 LYS Chi-restraints excluded: chain D residue 128 GLU Chi-restraints excluded: chain D residue 161 ASP Chi-restraints excluded: chain D residue 181 SER Chi-restraints excluded: chain D residue 187 ASP Chi-restraints excluded: chain D residue 274 ASP Chi-restraints excluded: chain D residue 330 ASN Chi-restraints excluded: chain E residue 48 THR Chi-restraints excluded: chain E residue 87 THR Chi-restraints excluded: chain E residue 112 LEU Chi-restraints excluded: chain E residue 125 MET Chi-restraints excluded: chain E residue 145 GLN Chi-restraints excluded: chain E residue 161 ASP Chi-restraints excluded: chain E residue 243 MET Chi-restraints excluded: chain E residue 273 VAL Chi-restraints excluded: chain E residue 296 SER Chi-restraints excluded: chain F residue 97 SER Chi-restraints excluded: chain F residue 112 LEU Chi-restraints excluded: chain F residue 125 MET Chi-restraints excluded: chain F residue 158 MET Chi-restraints excluded: chain F residue 161 ASP Chi-restraints excluded: chain F residue 206 GLN Chi-restraints excluded: chain F residue 272 GLN Chi-restraints excluded: chain F residue 273 VAL Chi-restraints excluded: chain F residue 297 THR Chi-restraints excluded: chain G residue 38 VAL Chi-restraints excluded: chain G residue 94 GLN Chi-restraints excluded: chain G residue 97 SER Chi-restraints excluded: chain G residue 125 MET Chi-restraints excluded: chain G residue 130 ARG Chi-restraints excluded: chain G residue 161 ASP Chi-restraints excluded: chain G residue 206 GLN Chi-restraints excluded: chain G residue 272 GLN Chi-restraints excluded: chain G residue 319 CYS Chi-restraints excluded: chain H residue 26 SER Chi-restraints excluded: chain H residue 68 GLU Chi-restraints excluded: chain H residue 82 VAL Chi-restraints excluded: chain H residue 142 VAL Chi-restraints excluded: chain H residue 206 GLN Chi-restraints excluded: chain H residue 272 GLN Chi-restraints excluded: chain H residue 308 GLU Chi-restraints excluded: chain I residue 27 ARG Chi-restraints excluded: chain I residue 28 LEU Chi-restraints excluded: chain I residue 90 THR Chi-restraints excluded: chain I residue 99 ILE Chi-restraints excluded: chain I residue 109 LEU Chi-restraints excluded: chain I residue 121 SER Chi-restraints excluded: chain I residue 183 SER Chi-restraints excluded: chain I residue 201 THR Chi-restraints excluded: chain I residue 212 VAL Chi-restraints excluded: chain I residue 214 SER Chi-restraints excluded: chain J residue 77 GLU Chi-restraints excluded: chain J residue 109 LEU Chi-restraints excluded: chain J residue 130 ARG Chi-restraints excluded: chain J residue 177 ARG Chi-restraints excluded: chain J residue 187 ASP Chi-restraints excluded: chain J residue 222 ASP Chi-restraints excluded: chain J residue 239 SER Chi-restraints excluded: chain J residue 272 GLN Chi-restraints excluded: chain J residue 300 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 323 random chunks: chunk 21 optimal weight: 1.9990 chunk 48 optimal weight: 5.9990 chunk 165 optimal weight: 2.9990 chunk 218 optimal weight: 3.9990 chunk 200 optimal weight: 0.9980 chunk 164 optimal weight: 3.9990 chunk 234 optimal weight: 1.9990 chunk 129 optimal weight: 1.9990 chunk 126 optimal weight: 0.9990 chunk 160 optimal weight: 0.9990 chunk 288 optimal weight: 1.9990 overall best weight: 1.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 272 GLN ** C 145 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 145 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 145 GLN H 23 GLN H 34 ASN ** H 145 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 145 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3663 r_free = 0.3663 target = 0.146710 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3275 r_free = 0.3275 target = 0.112808 restraints weight = 32374.491| |-----------------------------------------------------------------------------| r_work (start): 0.3267 rms_B_bonded: 1.99 r_work: 0.3147 rms_B_bonded: 2.64 restraints_weight: 0.5000 r_work: 0.3017 rms_B_bonded: 4.34 restraints_weight: 0.2500 r_work (final): 0.3017 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7980 moved from start: 0.3503 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 26875 Z= 0.148 Angle : 0.494 8.060 36550 Z= 0.260 Chirality : 0.040 0.143 4139 Planarity : 0.003 0.042 4521 Dihedral : 13.633 142.647 4454 Min Nonbonded Distance : 2.237 Molprobity Statistics. All-atom Clashscore : 6.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.00 % Favored : 98.00 % Rotamer: Outliers : 3.64 % Allowed : 24.05 % Favored : 72.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.32 % 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: 0.16 (0.14), residues: 3196 helix: 1.11 (0.14), residues: 1390 sheet: 0.22 (0.27), residues: 380 loop : -0.92 (0.15), residues: 1426 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG D 215 TYR 0.012 0.001 TYR G 315 PHE 0.014 0.001 PHE F 126 HIS 0.006 0.001 HIS A 138 Details of bonding type rmsd covalent geometry : bond 0.00336 (26875) covalent geometry : angle 0.49421 (36550) hydrogen bonds : bond 0.03318 ( 1159) hydrogen bonds : angle 4.20582 ( 3100) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6392 Ramachandran restraints generated. 3196 Oldfield, 0 Emsley, 3196 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6392 Ramachandran restraints generated. 3196 Oldfield, 0 Emsley, 3196 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 699 residues out of total 2607 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 95 poor density : 604 time to evaluate : 0.940 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 29 GLU cc_start: 0.7151 (mt-10) cc_final: 0.6930 (mm-30) REVERT: A 33 ILE cc_start: 0.8004 (mp) cc_final: 0.7335 (mm) REVERT: A 40 LYS cc_start: 0.7295 (mtpp) cc_final: 0.6286 (mtpt) REVERT: A 42 GLU cc_start: 0.6865 (pt0) cc_final: 0.6616 (pt0) REVERT: A 66 ILE cc_start: 0.6852 (mm) cc_final: 0.6649 (tp) REVERT: A 68 GLU cc_start: 0.6810 (mt-10) cc_final: 0.6247 (tm-30) REVERT: A 70 LYS cc_start: 0.6740 (ttpt) cc_final: 0.6375 (ttpt) REVERT: A 107 LYS cc_start: 0.7141 (mmtm) cc_final: 0.6736 (mttm) REVERT: A 210 MET cc_start: 0.8035 (mtp) cc_final: 0.7230 (mtp) REVERT: A 247 ARG cc_start: 0.7045 (mtp-110) cc_final: 0.6478 (mmm-85) REVERT: A 251 MET cc_start: 0.7964 (mtp) cc_final: 0.7612 (mtp) REVERT: A 254 ARG cc_start: 0.7342 (ttp80) cc_final: 0.7011 (tmt90) REVERT: A 303 ARG cc_start: 0.7462 (mtp180) cc_final: 0.6847 (mtm180) REVERT: A 308 GLU cc_start: 0.7294 (pt0) cc_final: 0.6421 (tt0) REVERT: A 329 ILE cc_start: 0.8566 (mt) cc_final: 0.7886 (mt) REVERT: B 42 GLU cc_start: 0.7093 (mt-10) cc_final: 0.6569 (mt-10) REVERT: B 43 GLU cc_start: 0.7502 (mt-10) cc_final: 0.7127 (mt-10) REVERT: B 72 ASP cc_start: 0.7561 (m-30) cc_final: 0.7293 (m-30) REVERT: B 88 THR cc_start: 0.9068 (OUTLIER) cc_final: 0.8761 (p) REVERT: B 95 ARG cc_start: 0.7911 (ttp80) cc_final: 0.7482 (ttt-90) REVERT: B 107 LYS cc_start: 0.7762 (mmtm) cc_final: 0.6875 (ptpt) REVERT: B 145 GLN cc_start: 0.8362 (mp10) cc_final: 0.8157 (mp10) REVERT: B 206 GLN cc_start: 0.7456 (mt0) cc_final: 0.7177 (mt0) REVERT: B 215 ARG cc_start: 0.8244 (OUTLIER) cc_final: 0.8010 (tpt-90) REVERT: B 332 ASP cc_start: 0.8759 (p0) cc_final: 0.8340 (p0) REVERT: C 33 ILE cc_start: 0.8650 (mm) cc_final: 0.8403 (mm) REVERT: C 94 GLN cc_start: 0.7769 (mm-40) cc_final: 0.6980 (tm-30) REVERT: C 95 ARG cc_start: 0.8141 (ttp80) cc_final: 0.7443 (ttp-170) REVERT: C 107 LYS cc_start: 0.8279 (mmtm) cc_final: 0.7591 (ptmt) REVERT: C 145 GLN cc_start: 0.8727 (mp10) cc_final: 0.8121 (mp10) REVERT: C 154 GLU cc_start: 0.7522 (mt-10) cc_final: 0.6891 (mt-10) REVERT: C 181 SER cc_start: 0.8843 (t) cc_final: 0.8542 (p) REVERT: C 187 ASP cc_start: 0.8652 (OUTLIER) cc_final: 0.8451 (m-30) REVERT: C 202 GLN cc_start: 0.7708 (mm-40) cc_final: 0.7427 (mt0) REVERT: C 243 MET cc_start: 0.8138 (mtm) cc_final: 0.7920 (mtt) REVERT: D 27 ARG cc_start: 0.8293 (OUTLIER) cc_final: 0.7437 (mtp180) REVERT: D 30 GLN cc_start: 0.7621 (mt0) cc_final: 0.7321 (mp10) REVERT: D 37 ASP cc_start: 0.7268 (m-30) cc_final: 0.6972 (m-30) REVERT: D 42 GLU cc_start: 0.7896 (mt-10) cc_final: 0.7594 (mm-30) REVERT: D 94 GLN cc_start: 0.7735 (mm-40) cc_final: 0.6906 (tm-30) REVERT: D 107 LYS cc_start: 0.8286 (mmtm) cc_final: 0.7890 (mtmt) REVERT: D 111 LYS cc_start: 0.8431 (OUTLIER) cc_final: 0.8100 (ttmt) REVERT: D 187 ASP cc_start: 0.9042 (OUTLIER) cc_final: 0.8677 (t70) REVERT: D 215 ARG cc_start: 0.7982 (ttt90) cc_final: 0.7780 (tpt-90) REVERT: D 334 VAL cc_start: 0.9197 (t) cc_final: 0.8962 (p) REVERT: E 27 ARG cc_start: 0.8397 (mtp180) cc_final: 0.8163 (ttt-90) REVERT: E 57 LYS cc_start: 0.8426 (tptm) cc_final: 0.8047 (tttt) REVERT: E 68 GLU cc_start: 0.8039 (mp0) cc_final: 0.7669 (tp30) REVERT: E 107 LYS cc_start: 0.7961 (mmtm) cc_final: 0.7546 (mtmt) REVERT: E 145 GLN cc_start: 0.8986 (OUTLIER) cc_final: 0.8568 (mp10) REVERT: E 176 GLU cc_start: 0.8336 (mm-30) cc_final: 0.7777 (tt0) REVERT: E 243 MET cc_start: 0.8768 (OUTLIER) cc_final: 0.8524 (mtt) REVERT: F 39 LYS cc_start: 0.7460 (mttt) cc_final: 0.6674 (mtmt) REVERT: F 43 GLU cc_start: 0.7876 (mt-10) cc_final: 0.7338 (mp0) REVERT: F 68 GLU cc_start: 0.8212 (mt-10) cc_final: 0.7627 (mp0) REVERT: F 95 ARG cc_start: 0.8184 (ttp80) cc_final: 0.7890 (ttp-110) REVERT: F 202 GLN cc_start: 0.8156 (mm-40) cc_final: 0.7685 (mt0) REVERT: F 206 GLN cc_start: 0.8654 (OUTLIER) cc_final: 0.7832 (mt0) REVERT: G 39 LYS cc_start: 0.7650 (mttt) cc_final: 0.7266 (mtpp) REVERT: G 94 GLN cc_start: 0.7837 (OUTLIER) cc_final: 0.7433 (tp-100) REVERT: G 107 LYS cc_start: 0.7936 (mmtm) cc_final: 0.6974 (ttmm) REVERT: G 111 LYS cc_start: 0.8259 (ttpp) cc_final: 0.8017 (mtpp) REVERT: G 176 GLU cc_start: 0.8139 (mm-30) cc_final: 0.7778 (mm-30) REVERT: G 187 ASP cc_start: 0.8223 (m-30) cc_final: 0.7854 (m-30) REVERT: G 202 GLN cc_start: 0.8093 (mm-40) cc_final: 0.7801 (mt0) REVERT: G 206 GLN cc_start: 0.8962 (OUTLIER) cc_final: 0.8406 (mt0) REVERT: G 247 ARG cc_start: 0.8175 (mtp-110) cc_final: 0.7944 (mtp85) REVERT: G 306 ARG cc_start: 0.7823 (ttm110) cc_final: 0.6940 (tmm160) REVERT: G 308 GLU cc_start: 0.8200 (pm20) cc_final: 0.7858 (pm20) REVERT: H 27 ARG cc_start: 0.7667 (mtp-110) cc_final: 0.7352 (tmt170) REVERT: H 39 LYS cc_start: 0.7611 (mttt) cc_final: 0.7177 (mtmm) REVERT: H 40 LYS cc_start: 0.7627 (mtpp) cc_final: 0.7352 (mtpt) REVERT: H 206 GLN cc_start: 0.8703 (OUTLIER) cc_final: 0.8335 (mt0) REVERT: H 247 ARG cc_start: 0.7939 (mtp-110) cc_final: 0.7249 (mmm160) REVERT: H 254 ARG cc_start: 0.8019 (ttt-90) cc_final: 0.7657 (tmm-80) REVERT: H 306 ARG cc_start: 0.7367 (OUTLIER) cc_final: 0.7109 (ttt-90) REVERT: I 23 GLN cc_start: 0.7248 (mt0) cc_final: 0.6927 (mt0) REVERT: I 27 ARG cc_start: 0.7988 (OUTLIER) cc_final: 0.7384 (tmt-80) REVERT: I 39 LYS cc_start: 0.7930 (mttt) cc_final: 0.7608 (mmmm) REVERT: I 40 LYS cc_start: 0.7654 (mtpp) cc_final: 0.7274 (mttp) REVERT: I 43 GLU cc_start: 0.7659 (mt-10) cc_final: 0.7281 (tp30) REVERT: I 109 LEU cc_start: 0.8717 (OUTLIER) cc_final: 0.8354 (mp) REVERT: I 247 ARG cc_start: 0.7801 (mtp85) cc_final: 0.7284 (ttt180) REVERT: I 332 ASP cc_start: 0.8383 (p0) cc_final: 0.8114 (p0) REVERT: J 39 LYS cc_start: 0.6884 (mttt) cc_final: 0.6208 (mmmt) REVERT: J 40 LYS cc_start: 0.6978 (mtpp) cc_final: 0.6107 (mttt) REVERT: J 42 GLU cc_start: 0.7162 (tp30) cc_final: 0.6443 (tt0) REVERT: J 43 GLU cc_start: 0.6957 (OUTLIER) cc_final: 0.6401 (pp20) REVERT: J 50 GLU cc_start: 0.7803 (mp0) cc_final: 0.7043 (mp0) REVERT: J 73 LYS cc_start: 0.6546 (mttt) cc_final: 0.5953 (tptt) REVERT: J 77 GLU cc_start: 0.7463 (OUTLIER) cc_final: 0.6832 (mp0) REVERT: J 177 ARG cc_start: 0.8256 (OUTLIER) cc_final: 0.7489 (ttt180) REVERT: J 184 ASP cc_start: 0.8604 (m-30) cc_final: 0.8267 (m-30) REVERT: J 187 ASP cc_start: 0.7997 (OUTLIER) cc_final: 0.7180 (m-30) REVERT: J 222 ASP cc_start: 0.8598 (OUTLIER) cc_final: 0.8254 (t0) REVERT: J 299 ARG cc_start: 0.8613 (mtm180) cc_final: 0.8178 (mtt-85) REVERT: J 308 GLU cc_start: 0.7929 (pm20) cc_final: 0.6871 (mt-10) REVERT: J 332 ASP cc_start: 0.8475 (p0) cc_final: 0.7980 (p0) outliers start: 95 outliers final: 55 residues processed: 648 average time/residue: 0.7503 time to fit residues: 551.6791 Evaluate side-chains 662 residues out of total 2607 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 75 poor density : 587 time to evaluate : 0.964 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 87 THR Chi-restraints excluded: chain A residue 128 GLU Chi-restraints excluded: chain B residue 23 GLN Chi-restraints excluded: chain B residue 31 CYS Chi-restraints excluded: chain B residue 60 LEU Chi-restraints excluded: chain B residue 82 VAL Chi-restraints excluded: chain B residue 88 THR Chi-restraints excluded: chain B residue 113 LEU Chi-restraints excluded: chain B residue 187 ASP Chi-restraints excluded: chain B residue 215 ARG Chi-restraints excluded: chain B residue 223 SER Chi-restraints excluded: chain C residue 43 GLU Chi-restraints excluded: chain C residue 81 LEU Chi-restraints excluded: chain C residue 128 GLU Chi-restraints excluded: chain C residue 187 ASP Chi-restraints excluded: chain C residue 330 ASN Chi-restraints excluded: chain D residue 27 ARG Chi-restraints excluded: chain D residue 97 SER Chi-restraints excluded: chain D residue 111 LYS Chi-restraints excluded: chain D residue 161 ASP Chi-restraints excluded: chain D residue 187 ASP Chi-restraints excluded: chain D residue 273 VAL Chi-restraints excluded: chain D residue 274 ASP Chi-restraints excluded: chain D residue 330 ASN Chi-restraints excluded: chain E residue 48 THR Chi-restraints excluded: chain E residue 87 THR Chi-restraints excluded: chain E residue 112 LEU Chi-restraints excluded: chain E residue 125 MET Chi-restraints excluded: chain E residue 145 GLN Chi-restraints excluded: chain E residue 161 ASP Chi-restraints excluded: chain E residue 243 MET Chi-restraints excluded: chain E residue 273 VAL Chi-restraints excluded: chain E residue 296 SER Chi-restraints excluded: chain F residue 97 SER Chi-restraints excluded: chain F residue 112 LEU Chi-restraints excluded: chain F residue 125 MET Chi-restraints excluded: chain F residue 145 GLN Chi-restraints excluded: chain F residue 158 MET Chi-restraints excluded: chain F residue 161 ASP Chi-restraints excluded: chain F residue 206 GLN Chi-restraints excluded: chain F residue 272 GLN Chi-restraints excluded: chain F residue 273 VAL Chi-restraints excluded: chain F residue 297 THR Chi-restraints excluded: chain G residue 38 VAL Chi-restraints excluded: chain G residue 94 GLN Chi-restraints excluded: chain G residue 97 SER Chi-restraints excluded: chain G residue 161 ASP Chi-restraints excluded: chain G residue 206 GLN Chi-restraints excluded: chain G residue 272 GLN Chi-restraints excluded: chain G residue 319 CYS Chi-restraints excluded: chain H residue 26 SER Chi-restraints excluded: chain H residue 82 VAL Chi-restraints excluded: chain H residue 142 VAL Chi-restraints excluded: chain H residue 206 GLN Chi-restraints excluded: chain H residue 272 GLN Chi-restraints excluded: chain H residue 306 ARG Chi-restraints excluded: chain H residue 308 GLU Chi-restraints excluded: chain I residue 27 ARG Chi-restraints excluded: chain I residue 28 LEU Chi-restraints excluded: chain I residue 90 THR Chi-restraints excluded: chain I residue 99 ILE Chi-restraints excluded: chain I residue 109 LEU Chi-restraints excluded: chain I residue 121 SER Chi-restraints excluded: chain I residue 183 SER Chi-restraints excluded: chain I residue 201 THR Chi-restraints excluded: chain I residue 212 VAL Chi-restraints excluded: chain J residue 43 GLU Chi-restraints excluded: chain J residue 77 GLU Chi-restraints excluded: chain J residue 109 LEU Chi-restraints excluded: chain J residue 177 ARG Chi-restraints excluded: chain J residue 187 ASP Chi-restraints excluded: chain J residue 222 ASP Chi-restraints excluded: chain J residue 239 SER Chi-restraints excluded: chain J residue 272 GLN Chi-restraints excluded: chain J residue 300 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 323 random chunks: chunk 133 optimal weight: 4.9990 chunk 103 optimal weight: 0.9990 chunk 144 optimal weight: 0.9980 chunk 171 optimal weight: 2.9990 chunk 295 optimal weight: 2.9990 chunk 79 optimal weight: 6.9990 chunk 127 optimal weight: 5.9990 chunk 251 optimal weight: 9.9990 chunk 186 optimal weight: 10.0000 chunk 202 optimal weight: 1.9990 chunk 111 optimal weight: 0.7980 overall best weight: 1.5586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 272 GLN ** C 145 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 145 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 145 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 23 GLN H 34 ASN ** H 145 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 290 ASN ** I 145 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 135 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3660 r_free = 0.3660 target = 0.146385 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3271 r_free = 0.3271 target = 0.112574 restraints weight = 32370.963| |-----------------------------------------------------------------------------| r_work (start): 0.3264 rms_B_bonded: 1.99 r_work: 0.3145 rms_B_bonded: 2.63 restraints_weight: 0.5000 r_work: 0.3016 rms_B_bonded: 4.32 restraints_weight: 0.2500 r_work (final): 0.3016 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7987 moved from start: 0.3526 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.054 26875 Z= 0.158 Angle : 0.504 8.169 36550 Z= 0.266 Chirality : 0.040 0.151 4139 Planarity : 0.003 0.042 4521 Dihedral : 13.622 142.414 4454 Min Nonbonded Distance : 2.232 Molprobity Statistics. All-atom Clashscore : 6.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.25 % Favored : 97.75 % Rotamer: Outliers : 3.64 % Allowed : 24.24 % Favored : 72.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.32 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.19 (0.14), residues: 3196 helix: 1.21 (0.14), residues: 1370 sheet: 0.23 (0.27), residues: 380 loop : -0.96 (0.15), residues: 1446 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG B 130 TYR 0.013 0.001 TYR G 315 PHE 0.020 0.001 PHE J 259 HIS 0.006 0.001 HIS A 138 Details of bonding type rmsd covalent geometry : bond 0.00361 (26875) covalent geometry : angle 0.50352 (36550) hydrogen bonds : bond 0.03395 ( 1159) hydrogen bonds : angle 4.23295 ( 3100) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6392 Ramachandran restraints generated. 3196 Oldfield, 0 Emsley, 3196 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6392 Ramachandran restraints generated. 3196 Oldfield, 0 Emsley, 3196 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 689 residues out of total 2607 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 95 poor density : 594 time to evaluate : 0.983 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 29 GLU cc_start: 0.7153 (mt-10) cc_final: 0.6925 (mm-30) REVERT: A 33 ILE cc_start: 0.8043 (mp) cc_final: 0.7406 (mm) REVERT: A 37 ASP cc_start: 0.7806 (m-30) cc_final: 0.7418 (m-30) REVERT: A 40 LYS cc_start: 0.7307 (mtpp) cc_final: 0.6294 (mtpt) REVERT: A 42 GLU cc_start: 0.6889 (pt0) cc_final: 0.6639 (pt0) REVERT: A 66 ILE cc_start: 0.6873 (mm) cc_final: 0.6672 (tp) REVERT: A 68 GLU cc_start: 0.6783 (mt-10) cc_final: 0.6223 (tm-30) REVERT: A 70 LYS cc_start: 0.6834 (ttpt) cc_final: 0.6432 (ttpt) REVERT: A 107 LYS cc_start: 0.7133 (mmtm) cc_final: 0.6899 (tptt) REVERT: A 135 GLN cc_start: 0.7964 (OUTLIER) cc_final: 0.7709 (mp10) REVERT: A 247 ARG cc_start: 0.7154 (mtp-110) cc_final: 0.6470 (mmm-85) REVERT: A 254 ARG cc_start: 0.7344 (ttp80) cc_final: 0.7022 (tmt90) REVERT: A 303 ARG cc_start: 0.7429 (mtp180) cc_final: 0.6837 (mtm180) REVERT: A 308 GLU cc_start: 0.7316 (pt0) cc_final: 0.6628 (tt0) REVERT: A 329 ILE cc_start: 0.8507 (mt) cc_final: 0.7885 (mt) REVERT: B 40 LYS cc_start: 0.6917 (mtpp) cc_final: 0.5711 (mtpt) REVERT: B 42 GLU cc_start: 0.7101 (mt-10) cc_final: 0.6611 (mt-10) REVERT: B 43 GLU cc_start: 0.7478 (mt-10) cc_final: 0.7129 (mt-10) REVERT: B 72 ASP cc_start: 0.7520 (m-30) cc_final: 0.7207 (m-30) REVERT: B 88 THR cc_start: 0.9061 (OUTLIER) cc_final: 0.8754 (p) REVERT: B 95 ARG cc_start: 0.7842 (ttp80) cc_final: 0.7378 (ttt-90) REVERT: B 107 LYS cc_start: 0.7739 (mmtm) cc_final: 0.6901 (ptpt) REVERT: B 206 GLN cc_start: 0.7484 (mt0) cc_final: 0.7227 (mt0) REVERT: B 215 ARG cc_start: 0.8250 (OUTLIER) cc_final: 0.8013 (tpt-90) REVERT: B 332 ASP cc_start: 0.8773 (p0) cc_final: 0.8361 (p0) REVERT: C 33 ILE cc_start: 0.8669 (mm) cc_final: 0.8428 (mm) REVERT: C 94 GLN cc_start: 0.7835 (mm-40) cc_final: 0.7123 (tm-30) REVERT: C 95 ARG cc_start: 0.8103 (ttp80) cc_final: 0.7403 (ttp-170) REVERT: C 107 LYS cc_start: 0.8295 (mmtm) cc_final: 0.7612 (ptmt) REVERT: C 145 GLN cc_start: 0.8746 (mp10) cc_final: 0.7985 (mp10) REVERT: C 154 GLU cc_start: 0.7519 (mt-10) cc_final: 0.6883 (mt-10) REVERT: C 181 SER cc_start: 0.8624 (t) cc_final: 0.8126 (p) REVERT: C 187 ASP cc_start: 0.8658 (OUTLIER) cc_final: 0.8446 (m-30) REVERT: C 202 GLN cc_start: 0.7687 (mm-40) cc_final: 0.7409 (mt0) REVERT: C 243 MET cc_start: 0.8138 (mtm) cc_final: 0.7916 (mtt) REVERT: D 27 ARG cc_start: 0.8349 (OUTLIER) cc_final: 0.7548 (mtp180) REVERT: D 30 GLN cc_start: 0.7582 (mt0) cc_final: 0.7257 (mp10) REVERT: D 37 ASP cc_start: 0.7271 (m-30) cc_final: 0.6974 (m-30) REVERT: D 42 GLU cc_start: 0.7865 (mt-10) cc_final: 0.7523 (mm-30) REVERT: D 94 GLN cc_start: 0.7745 (mm-40) cc_final: 0.6918 (tm-30) REVERT: D 107 LYS cc_start: 0.8291 (mmtm) cc_final: 0.7896 (mtmt) REVERT: D 111 LYS cc_start: 0.8434 (OUTLIER) cc_final: 0.8100 (ttmt) REVERT: D 187 ASP cc_start: 0.9043 (OUTLIER) cc_final: 0.8685 (t70) REVERT: D 334 VAL cc_start: 0.9208 (t) cc_final: 0.8965 (p) REVERT: E 27 ARG cc_start: 0.8420 (mtp180) cc_final: 0.8198 (ttt-90) REVERT: E 57 LYS cc_start: 0.8434 (tptm) cc_final: 0.8070 (tttt) REVERT: E 68 GLU cc_start: 0.8028 (mp0) cc_final: 0.7657 (tp30) REVERT: E 107 LYS cc_start: 0.7962 (mmtm) cc_final: 0.7540 (mtmt) REVERT: E 243 MET cc_start: 0.8791 (OUTLIER) cc_final: 0.8554 (mtt) REVERT: F 27 ARG cc_start: 0.8465 (mtp180) cc_final: 0.8122 (ttt90) REVERT: F 39 LYS cc_start: 0.7473 (mttt) cc_final: 0.6692 (mtmt) REVERT: F 43 GLU cc_start: 0.7873 (mt-10) cc_final: 0.7274 (mp0) REVERT: F 68 GLU cc_start: 0.8194 (mt-10) cc_final: 0.7620 (mp0) REVERT: F 95 ARG cc_start: 0.8175 (ttp80) cc_final: 0.7874 (ttp-110) REVERT: F 202 GLN cc_start: 0.8165 (mm-40) cc_final: 0.7675 (mt0) REVERT: F 206 GLN cc_start: 0.8660 (OUTLIER) cc_final: 0.7839 (mt0) REVERT: G 39 LYS cc_start: 0.7667 (mttt) cc_final: 0.7268 (mtpp) REVERT: G 91 GLU cc_start: 0.8230 (OUTLIER) cc_final: 0.7833 (tt0) REVERT: G 94 GLN cc_start: 0.7843 (OUTLIER) cc_final: 0.7441 (tp-100) REVERT: G 107 LYS cc_start: 0.7940 (mmtm) cc_final: 0.6973 (ttmm) REVERT: G 111 LYS cc_start: 0.8258 (ttpp) cc_final: 0.8014 (mtpp) REVERT: G 125 MET cc_start: 0.9040 (mtm) cc_final: 0.8642 (ptp) REVERT: G 130 ARG cc_start: 0.8460 (ptp90) cc_final: 0.8221 (ptt-90) REVERT: G 176 GLU cc_start: 0.8136 (mm-30) cc_final: 0.7770 (mm-30) REVERT: G 187 ASP cc_start: 0.8242 (m-30) cc_final: 0.7872 (m-30) REVERT: G 202 GLN cc_start: 0.8007 (mm-40) cc_final: 0.7749 (mt0) REVERT: G 206 GLN cc_start: 0.8942 (OUTLIER) cc_final: 0.8372 (mt0) REVERT: G 247 ARG cc_start: 0.8186 (mtp-110) cc_final: 0.7957 (mtp85) REVERT: G 306 ARG cc_start: 0.7753 (ttm110) cc_final: 0.6882 (tmm160) REVERT: G 308 GLU cc_start: 0.8189 (pm20) cc_final: 0.7848 (pm20) REVERT: H 27 ARG cc_start: 0.7672 (OUTLIER) cc_final: 0.7339 (tmt170) REVERT: H 30 GLN cc_start: 0.8191 (mt0) cc_final: 0.7653 (mm-40) REVERT: H 39 LYS cc_start: 0.7643 (mttt) cc_final: 0.7181 (mtmm) REVERT: H 206 GLN cc_start: 0.8730 (OUTLIER) cc_final: 0.8358 (mt0) REVERT: H 247 ARG cc_start: 0.7950 (mtp-110) cc_final: 0.7256 (mmm160) REVERT: H 254 ARG cc_start: 0.8068 (ttt-90) cc_final: 0.7703 (tmm-80) REVERT: H 306 ARG cc_start: 0.7357 (OUTLIER) cc_final: 0.7101 (ttt-90) REVERT: I 27 ARG cc_start: 0.7574 (OUTLIER) cc_final: 0.7033 (tmt-80) REVERT: I 39 LYS cc_start: 0.7899 (mttt) cc_final: 0.7572 (mmmm) REVERT: I 40 LYS cc_start: 0.7741 (mtpp) cc_final: 0.7330 (mttp) REVERT: I 43 GLU cc_start: 0.7678 (mt-10) cc_final: 0.7297 (tp30) REVERT: I 109 LEU cc_start: 0.8712 (OUTLIER) cc_final: 0.8347 (mp) REVERT: I 332 ASP cc_start: 0.8380 (p0) cc_final: 0.8101 (p0) REVERT: J 39 LYS cc_start: 0.6884 (mttt) cc_final: 0.6186 (mmmt) REVERT: J 40 LYS cc_start: 0.6997 (mtpp) cc_final: 0.6128 (mttt) REVERT: J 42 GLU cc_start: 0.7173 (tp30) cc_final: 0.6436 (tt0) REVERT: J 43 GLU cc_start: 0.6845 (OUTLIER) cc_final: 0.6281 (pp20) REVERT: J 50 GLU cc_start: 0.7772 (mp0) cc_final: 0.7054 (mp0) REVERT: J 73 LYS cc_start: 0.6555 (mttt) cc_final: 0.5943 (tptt) REVERT: J 77 GLU cc_start: 0.7445 (OUTLIER) cc_final: 0.6783 (mp0) REVERT: J 177 ARG cc_start: 0.8247 (OUTLIER) cc_final: 0.7482 (ttt180) REVERT: J 184 ASP cc_start: 0.8595 (m-30) cc_final: 0.8223 (m-30) REVERT: J 187 ASP cc_start: 0.8054 (OUTLIER) cc_final: 0.7256 (m-30) REVERT: J 222 ASP cc_start: 0.8597 (OUTLIER) cc_final: 0.8243 (t0) REVERT: J 299 ARG cc_start: 0.8640 (mtm180) cc_final: 0.8208 (mtt-85) REVERT: J 308 GLU cc_start: 0.7927 (pm20) cc_final: 0.6875 (mt-10) REVERT: J 332 ASP cc_start: 0.8440 (p0) cc_final: 0.8008 (p0) outliers start: 95 outliers final: 60 residues processed: 639 average time/residue: 0.7746 time to fit residues: 561.2465 Evaluate side-chains 676 residues out of total 2607 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 82 poor density : 594 time to evaluate : 0.963 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 87 THR Chi-restraints excluded: chain A residue 128 GLU Chi-restraints excluded: chain A residue 135 GLN Chi-restraints excluded: chain A residue 266 THR Chi-restraints excluded: chain B residue 23 GLN Chi-restraints excluded: chain B residue 31 CYS Chi-restraints excluded: chain B residue 60 LEU Chi-restraints excluded: chain B residue 82 VAL Chi-restraints excluded: chain B residue 88 THR Chi-restraints excluded: chain B residue 113 LEU Chi-restraints excluded: chain B residue 187 ASP Chi-restraints excluded: chain B residue 215 ARG Chi-restraints excluded: chain B residue 223 SER Chi-restraints excluded: chain C residue 43 GLU Chi-restraints excluded: chain C residue 81 LEU Chi-restraints excluded: chain C residue 128 GLU Chi-restraints excluded: chain C residue 187 ASP Chi-restraints excluded: chain C residue 233 SER Chi-restraints excluded: chain C residue 330 ASN Chi-restraints excluded: chain D residue 27 ARG Chi-restraints excluded: chain D residue 97 SER Chi-restraints excluded: chain D residue 111 LYS Chi-restraints excluded: chain D residue 161 ASP Chi-restraints excluded: chain D residue 181 SER Chi-restraints excluded: chain D residue 187 ASP Chi-restraints excluded: chain D residue 273 VAL Chi-restraints excluded: chain D residue 274 ASP Chi-restraints excluded: chain D residue 330 ASN Chi-restraints excluded: chain E residue 48 THR Chi-restraints excluded: chain E residue 87 THR Chi-restraints excluded: chain E residue 112 LEU Chi-restraints excluded: chain E residue 125 MET Chi-restraints excluded: chain E residue 161 ASP Chi-restraints excluded: chain E residue 243 MET Chi-restraints excluded: chain E residue 273 VAL Chi-restraints excluded: chain E residue 296 SER Chi-restraints excluded: chain F residue 97 SER Chi-restraints excluded: chain F residue 112 LEU Chi-restraints excluded: chain F residue 125 MET Chi-restraints excluded: chain F residue 145 GLN Chi-restraints excluded: chain F residue 161 ASP Chi-restraints excluded: chain F residue 206 GLN Chi-restraints excluded: chain F residue 272 GLN Chi-restraints excluded: chain F residue 273 VAL Chi-restraints excluded: chain F residue 297 THR Chi-restraints excluded: chain G residue 38 VAL Chi-restraints excluded: chain G residue 91 GLU Chi-restraints excluded: chain G residue 94 GLN Chi-restraints excluded: chain G residue 97 SER Chi-restraints excluded: chain G residue 161 ASP Chi-restraints excluded: chain G residue 206 GLN Chi-restraints excluded: chain G residue 272 GLN Chi-restraints excluded: chain G residue 319 CYS Chi-restraints excluded: chain H residue 26 SER Chi-restraints excluded: chain H residue 27 ARG Chi-restraints excluded: chain H residue 68 GLU Chi-restraints excluded: chain H residue 82 VAL Chi-restraints excluded: chain H residue 142 VAL Chi-restraints excluded: chain H residue 206 GLN Chi-restraints excluded: chain H residue 272 GLN Chi-restraints excluded: chain H residue 306 ARG Chi-restraints excluded: chain H residue 308 GLU Chi-restraints excluded: chain I residue 27 ARG Chi-restraints excluded: chain I residue 28 LEU Chi-restraints excluded: chain I residue 90 THR Chi-restraints excluded: chain I residue 97 SER Chi-restraints excluded: chain I residue 99 ILE Chi-restraints excluded: chain I residue 109 LEU Chi-restraints excluded: chain I residue 121 SER Chi-restraints excluded: chain I residue 149 ASP Chi-restraints excluded: chain I residue 183 SER Chi-restraints excluded: chain I residue 201 THR Chi-restraints excluded: chain I residue 212 VAL Chi-restraints excluded: chain J residue 43 GLU Chi-restraints excluded: chain J residue 77 GLU Chi-restraints excluded: chain J residue 109 LEU Chi-restraints excluded: chain J residue 177 ARG Chi-restraints excluded: chain J residue 187 ASP Chi-restraints excluded: chain J residue 222 ASP Chi-restraints excluded: chain J residue 239 SER Chi-restraints excluded: chain J residue 272 GLN Chi-restraints excluded: chain J residue 300 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 323 random chunks: chunk 313 optimal weight: 20.0000 chunk 56 optimal weight: 4.9990 chunk 27 optimal weight: 5.9990 chunk 234 optimal weight: 1.9990 chunk 262 optimal weight: 0.1980 chunk 203 optimal weight: 2.9990 chunk 200 optimal weight: 0.0980 chunk 167 optimal weight: 0.9980 chunk 60 optimal weight: 1.9990 chunk 111 optimal weight: 0.8980 chunk 39 optimal weight: 2.9990 overall best weight: 0.8382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 135 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 272 GLN B 272 GLN ** C 145 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 145 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 145 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 34 ASN ** H 145 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 290 ASN ** I 145 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 135 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3684 r_free = 0.3684 target = 0.148594 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3296 r_free = 0.3296 target = 0.114503 restraints weight = 31876.385| |-----------------------------------------------------------------------------| r_work (start): 0.3291 rms_B_bonded: 2.00 r_work: 0.3172 rms_B_bonded: 2.67 restraints_weight: 0.5000 r_work: 0.3042 rms_B_bonded: 4.39 restraints_weight: 0.2500 r_work (final): 0.3042 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8010 moved from start: 0.3645 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.061 26875 Z= 0.119 Angle : 0.486 8.426 36550 Z= 0.256 Chirality : 0.039 0.188 4139 Planarity : 0.003 0.041 4521 Dihedral : 13.587 142.488 4454 Min Nonbonded Distance : 2.239 Molprobity Statistics. All-atom Clashscore : 6.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.91 % Favored : 98.09 % Rotamer: Outliers : 3.03 % Allowed : 24.93 % Favored : 72.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.32 % 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: 0.32 (0.15), residues: 3196 helix: 1.31 (0.14), residues: 1370 sheet: 0.30 (0.27), residues: 380 loop : -0.87 (0.15), residues: 1446 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG B 130 TYR 0.012 0.001 TYR G 315 PHE 0.014 0.001 PHE F 126 HIS 0.006 0.001 HIS A 138 Details of bonding type rmsd covalent geometry : bond 0.00266 (26875) covalent geometry : angle 0.48630 (36550) hydrogen bonds : bond 0.03056 ( 1159) hydrogen bonds : angle 4.14765 ( 3100) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6392 Ramachandran restraints generated. 3196 Oldfield, 0 Emsley, 3196 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6392 Ramachandran restraints generated. 3196 Oldfield, 0 Emsley, 3196 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 698 residues out of total 2607 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 79 poor density : 619 time to evaluate : 0.835 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 40 LYS cc_start: 0.7315 (mtpp) cc_final: 0.6391 (mtpt) REVERT: A 42 GLU cc_start: 0.6889 (pt0) cc_final: 0.6642 (pt0) REVERT: A 66 ILE cc_start: 0.6946 (mm) cc_final: 0.6725 (tp) REVERT: A 68 GLU cc_start: 0.6747 (mt-10) cc_final: 0.6190 (tm-30) REVERT: A 70 LYS cc_start: 0.6863 (ttpt) cc_final: 0.6458 (ttpt) REVERT: A 107 LYS cc_start: 0.7132 (mmtm) cc_final: 0.6901 (tptt) REVERT: A 210 MET cc_start: 0.8193 (mtm) cc_final: 0.7515 (mtp) REVERT: A 247 ARG cc_start: 0.7087 (mtp-110) cc_final: 0.6520 (mmm-85) REVERT: A 251 MET cc_start: 0.7956 (mtp) cc_final: 0.7756 (mtp) REVERT: A 254 ARG cc_start: 0.7394 (ttp80) cc_final: 0.7113 (tmt90) REVERT: A 303 ARG cc_start: 0.7585 (mtp180) cc_final: 0.7002 (mtm180) REVERT: A 308 GLU cc_start: 0.7285 (pt0) cc_final: 0.6557 (tt0) REVERT: A 309 THR cc_start: 0.8066 (p) cc_final: 0.7665 (t) REVERT: A 329 ILE cc_start: 0.8476 (mt) cc_final: 0.7835 (mt) REVERT: B 40 LYS cc_start: 0.6890 (mtpp) cc_final: 0.5773 (mtmt) REVERT: B 42 GLU cc_start: 0.7089 (mt-10) cc_final: 0.6603 (mt-10) REVERT: B 43 GLU cc_start: 0.7462 (mt-10) cc_final: 0.7083 (mt-10) REVERT: B 72 ASP cc_start: 0.7406 (m-30) cc_final: 0.7114 (m-30) REVERT: B 88 THR cc_start: 0.9079 (OUTLIER) cc_final: 0.8835 (p) REVERT: B 95 ARG cc_start: 0.7925 (ttp80) cc_final: 0.7508 (ttt-90) REVERT: B 107 LYS cc_start: 0.7789 (mmtm) cc_final: 0.6956 (ptpt) REVERT: B 204 LEU cc_start: 0.9123 (mt) cc_final: 0.8823 (mt) REVERT: B 206 GLN cc_start: 0.7508 (mt0) cc_final: 0.7289 (mt0) REVERT: B 332 ASP cc_start: 0.8784 (p0) cc_final: 0.8372 (p0) REVERT: C 33 ILE cc_start: 0.8638 (mm) cc_final: 0.8390 (mm) REVERT: C 94 GLN cc_start: 0.7802 (mm-40) cc_final: 0.6981 (tm-30) REVERT: C 95 ARG cc_start: 0.8106 (ttp80) cc_final: 0.7432 (ttp-170) REVERT: C 107 LYS cc_start: 0.8323 (mmtm) cc_final: 0.7651 (ptmt) REVERT: C 145 GLN cc_start: 0.8749 (mp10) cc_final: 0.8047 (mp10) REVERT: C 154 GLU cc_start: 0.7519 (mt-10) cc_final: 0.6849 (mt-10) REVERT: C 181 SER cc_start: 0.8637 (t) cc_final: 0.8147 (p) REVERT: C 187 ASP cc_start: 0.8654 (OUTLIER) cc_final: 0.8433 (m-30) REVERT: C 202 GLN cc_start: 0.7665 (mm-40) cc_final: 0.7423 (mt0) REVERT: C 222 ASP cc_start: 0.8843 (t70) cc_final: 0.8414 (t70) REVERT: C 231 ASP cc_start: 0.9025 (m-30) cc_final: 0.8501 (m-30) REVERT: C 251 MET cc_start: 0.8140 (ttm) cc_final: 0.7601 (mpt) REVERT: D 27 ARG cc_start: 0.8298 (OUTLIER) cc_final: 0.7305 (mtp180) REVERT: D 42 GLU cc_start: 0.7878 (mt-10) cc_final: 0.7566 (mm-30) REVERT: D 94 GLN cc_start: 0.7761 (mm-40) cc_final: 0.6962 (tm-30) REVERT: D 107 LYS cc_start: 0.8311 (mmtm) cc_final: 0.7926 (mtmt) REVERT: D 187 ASP cc_start: 0.9058 (OUTLIER) cc_final: 0.8683 (t70) REVERT: D 215 ARG cc_start: 0.8155 (tpt-90) cc_final: 0.7929 (tpt-90) REVERT: D 306 ARG cc_start: 0.7542 (ttp-110) cc_final: 0.7081 (ttm110) REVERT: D 334 VAL cc_start: 0.9206 (t) cc_final: 0.8989 (p) REVERT: E 27 ARG cc_start: 0.8356 (mtp180) cc_final: 0.7704 (tpt-90) REVERT: E 57 LYS cc_start: 0.8461 (tptm) cc_final: 0.8103 (tttt) REVERT: E 68 GLU cc_start: 0.7943 (mp0) cc_final: 0.7557 (tp30) REVERT: E 107 LYS cc_start: 0.8003 (mmtm) cc_final: 0.7597 (mtmt) REVERT: E 176 GLU cc_start: 0.8341 (mm-30) cc_final: 0.7793 (tt0) REVERT: E 243 MET cc_start: 0.8855 (OUTLIER) cc_final: 0.8554 (mtt) REVERT: E 306 ARG cc_start: 0.7690 (ttp-110) cc_final: 0.7356 (tmm160) REVERT: F 27 ARG cc_start: 0.8429 (mtp180) cc_final: 0.8016 (ttt-90) REVERT: F 39 LYS cc_start: 0.7502 (mttt) cc_final: 0.6722 (mtmt) REVERT: F 43 GLU cc_start: 0.7898 (mt-10) cc_final: 0.7304 (mp0) REVERT: F 68 GLU cc_start: 0.8274 (mt-10) cc_final: 0.7825 (mp0) REVERT: F 202 GLN cc_start: 0.8165 (mm-40) cc_final: 0.7655 (mt0) REVERT: F 206 GLN cc_start: 0.8657 (OUTLIER) cc_final: 0.7830 (mt0) REVERT: G 39 LYS cc_start: 0.7706 (mttt) cc_final: 0.7306 (mtpp) REVERT: G 94 GLN cc_start: 0.7858 (OUTLIER) cc_final: 0.7557 (tp-100) REVERT: G 107 LYS cc_start: 0.7972 (mmtm) cc_final: 0.7011 (ttmm) REVERT: G 111 LYS cc_start: 0.8289 (ttpp) cc_final: 0.8040 (mtpp) REVERT: G 125 MET cc_start: 0.9033 (mtm) cc_final: 0.8649 (ptp) REVERT: G 176 GLU cc_start: 0.8151 (mm-30) cc_final: 0.7781 (mm-30) REVERT: G 187 ASP cc_start: 0.8259 (m-30) cc_final: 0.7873 (m-30) REVERT: G 202 GLN cc_start: 0.8081 (mm-40) cc_final: 0.7841 (mt0) REVERT: G 206 GLN cc_start: 0.8984 (OUTLIER) cc_final: 0.8416 (mt0) REVERT: G 247 ARG cc_start: 0.8184 (mtp-110) cc_final: 0.7960 (mtp85) REVERT: G 290 ASN cc_start: 0.9092 (m-40) cc_final: 0.8876 (m110) REVERT: G 306 ARG cc_start: 0.7774 (ttm110) cc_final: 0.6916 (tmm160) REVERT: G 308 GLU cc_start: 0.8200 (pm20) cc_final: 0.7881 (pm20) REVERT: H 27 ARG cc_start: 0.7667 (mtp-110) cc_final: 0.7392 (tmt170) REVERT: H 30 GLN cc_start: 0.8199 (mt0) cc_final: 0.7672 (mm-40) REVERT: H 39 LYS cc_start: 0.7642 (mttt) cc_final: 0.7197 (mtmm) REVERT: H 40 LYS cc_start: 0.7730 (mtpp) cc_final: 0.7461 (mtpt) REVERT: H 206 GLN cc_start: 0.8745 (OUTLIER) cc_final: 0.8393 (mt0) REVERT: H 247 ARG cc_start: 0.7960 (mtp-110) cc_final: 0.7434 (mmm160) REVERT: H 254 ARG cc_start: 0.8062 (ttt-90) cc_final: 0.7683 (tmm-80) REVERT: H 306 ARG cc_start: 0.7386 (OUTLIER) cc_final: 0.7137 (ttt-90) REVERT: I 27 ARG cc_start: 0.7529 (OUTLIER) cc_final: 0.7172 (tmt-80) REVERT: I 39 LYS cc_start: 0.7910 (mttt) cc_final: 0.7583 (mmmm) REVERT: I 40 LYS cc_start: 0.7749 (mtpp) cc_final: 0.7318 (mttp) REVERT: I 43 GLU cc_start: 0.7656 (mt-10) cc_final: 0.7295 (tp30) REVERT: I 109 LEU cc_start: 0.8760 (OUTLIER) cc_final: 0.8403 (mp) REVERT: I 215 ARG cc_start: 0.8193 (tmm160) cc_final: 0.7989 (tmm160) REVERT: I 247 ARG cc_start: 0.7856 (mtp85) cc_final: 0.7222 (mtp85) REVERT: I 332 ASP cc_start: 0.8295 (p0) cc_final: 0.8042 (p0) REVERT: J 39 LYS cc_start: 0.6885 (mttt) cc_final: 0.6190 (mmmt) REVERT: J 40 LYS cc_start: 0.7019 (mtpp) cc_final: 0.6155 (mttt) REVERT: J 42 GLU cc_start: 0.7191 (tp30) cc_final: 0.6447 (tt0) REVERT: J 43 GLU cc_start: 0.6884 (OUTLIER) cc_final: 0.6348 (pp20) REVERT: J 50 GLU cc_start: 0.7781 (mp0) cc_final: 0.7062 (mp0) REVERT: J 73 LYS cc_start: 0.6529 (mttt) cc_final: 0.5923 (tptt) REVERT: J 77 GLU cc_start: 0.7359 (OUTLIER) cc_final: 0.6712 (mp0) REVERT: J 154 GLU cc_start: 0.7970 (mt-10) cc_final: 0.7536 (mm-30) REVERT: J 177 ARG cc_start: 0.8248 (OUTLIER) cc_final: 0.7640 (ttt180) REVERT: J 184 ASP cc_start: 0.8622 (m-30) cc_final: 0.8305 (m-30) REVERT: J 187 ASP cc_start: 0.7990 (OUTLIER) cc_final: 0.7181 (m-30) REVERT: J 211 MET cc_start: 0.8595 (mtt) cc_final: 0.8336 (mtt) REVERT: J 222 ASP cc_start: 0.8529 (OUTLIER) cc_final: 0.8177 (t0) REVERT: J 254 ARG cc_start: 0.7095 (mtm110) cc_final: 0.6731 (tmm160) REVERT: J 299 ARG cc_start: 0.8656 (mtm180) cc_final: 0.8212 (mtt-85) REVERT: J 308 GLU cc_start: 0.7955 (pm20) cc_final: 0.6917 (mt-10) outliers start: 79 outliers final: 52 residues processed: 653 average time/residue: 0.7464 time to fit residues: 554.6253 Evaluate side-chains 666 residues out of total 2607 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 597 time to evaluate : 0.963 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 87 THR Chi-restraints excluded: chain A residue 99 ILE Chi-restraints excluded: chain A residue 128 GLU Chi-restraints excluded: chain A residue 266 THR Chi-restraints excluded: chain B residue 31 CYS Chi-restraints excluded: chain B residue 60 LEU Chi-restraints excluded: chain B residue 82 VAL Chi-restraints excluded: chain B residue 88 THR Chi-restraints excluded: chain B residue 113 LEU Chi-restraints excluded: chain B residue 223 SER Chi-restraints excluded: chain C residue 43 GLU Chi-restraints excluded: chain C residue 128 GLU Chi-restraints excluded: chain C residue 187 ASP Chi-restraints excluded: chain C residue 330 ASN Chi-restraints excluded: chain D residue 27 ARG Chi-restraints excluded: chain D residue 97 SER Chi-restraints excluded: chain D residue 161 ASP Chi-restraints excluded: chain D residue 187 ASP Chi-restraints excluded: chain D residue 273 VAL Chi-restraints excluded: chain D residue 274 ASP Chi-restraints excluded: chain D residue 330 ASN Chi-restraints excluded: chain E residue 43 GLU Chi-restraints excluded: chain E residue 48 THR Chi-restraints excluded: chain E residue 87 THR Chi-restraints excluded: chain E residue 125 MET Chi-restraints excluded: chain E residue 161 ASP Chi-restraints excluded: chain E residue 243 MET Chi-restraints excluded: chain E residue 273 VAL Chi-restraints excluded: chain E residue 296 SER Chi-restraints excluded: chain F residue 97 SER Chi-restraints excluded: chain F residue 112 LEU Chi-restraints excluded: chain F residue 125 MET Chi-restraints excluded: chain F residue 145 GLN Chi-restraints excluded: chain F residue 206 GLN Chi-restraints excluded: chain F residue 272 GLN Chi-restraints excluded: chain F residue 297 THR Chi-restraints excluded: chain G residue 38 VAL Chi-restraints excluded: chain G residue 94 GLN Chi-restraints excluded: chain G residue 97 SER Chi-restraints excluded: chain G residue 161 ASP Chi-restraints excluded: chain G residue 206 GLN Chi-restraints excluded: chain G residue 272 GLN Chi-restraints excluded: chain H residue 26 SER Chi-restraints excluded: chain H residue 82 VAL Chi-restraints excluded: chain H residue 142 VAL Chi-restraints excluded: chain H residue 206 GLN Chi-restraints excluded: chain H residue 213 GLU Chi-restraints excluded: chain H residue 272 GLN Chi-restraints excluded: chain H residue 306 ARG Chi-restraints excluded: chain H residue 308 GLU Chi-restraints excluded: chain I residue 27 ARG Chi-restraints excluded: chain I residue 28 LEU Chi-restraints excluded: chain I residue 90 THR Chi-restraints excluded: chain I residue 99 ILE Chi-restraints excluded: chain I residue 109 LEU Chi-restraints excluded: chain I residue 121 SER Chi-restraints excluded: chain I residue 183 SER Chi-restraints excluded: chain I residue 201 THR Chi-restraints excluded: chain I residue 212 VAL Chi-restraints excluded: chain J residue 27 ARG Chi-restraints excluded: chain J residue 43 GLU Chi-restraints excluded: chain J residue 77 GLU Chi-restraints excluded: chain J residue 109 LEU Chi-restraints excluded: chain J residue 177 ARG Chi-restraints excluded: chain J residue 187 ASP Chi-restraints excluded: chain J residue 222 ASP Chi-restraints excluded: chain J residue 239 SER Chi-restraints excluded: chain J residue 272 GLN Chi-restraints excluded: chain J residue 300 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 323 random chunks: chunk 236 optimal weight: 0.3980 chunk 165 optimal weight: 2.9990 chunk 50 optimal weight: 4.9990 chunk 162 optimal weight: 4.9990 chunk 183 optimal weight: 2.9990 chunk 320 optimal weight: 3.9990 chunk 244 optimal weight: 3.9990 chunk 108 optimal weight: 3.9990 chunk 300 optimal weight: 6.9990 chunk 151 optimal weight: 0.9990 chunk 43 optimal weight: 0.6980 overall best weight: 1.6186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 272 GLN B 272 GLN ** C 145 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 145 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 145 GLN H 23 GLN H 34 ASN H 290 ASN ** I 145 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 135 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3663 r_free = 0.3663 target = 0.146635 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3269 r_free = 0.3269 target = 0.112429 restraints weight = 32000.140| |-----------------------------------------------------------------------------| r_work (start): 0.3240 rms_B_bonded: 2.00 r_work: 0.3117 rms_B_bonded: 2.67 restraints_weight: 0.5000 r_work: 0.2987 rms_B_bonded: 4.38 restraints_weight: 0.2500 r_work (final): 0.2987 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8034 moved from start: 0.3593 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.060 26875 Z= 0.162 Angle : 0.506 8.251 36550 Z= 0.268 Chirality : 0.040 0.150 4139 Planarity : 0.003 0.041 4521 Dihedral : 13.624 141.343 4454 Min Nonbonded Distance : 2.228 Molprobity Statistics. All-atom Clashscore : 6.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.38 % Favored : 97.62 % Rotamer: Outliers : 3.53 % Allowed : 24.59 % Favored : 71.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.32 % 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: 0.30 (0.15), residues: 3196 helix: 1.30 (0.14), residues: 1370 sheet: 0.28 (0.27), residues: 380 loop : -0.88 (0.15), residues: 1446 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG G 130 TYR 0.018 0.001 TYR G 315 PHE 0.021 0.001 PHE J 259 HIS 0.006 0.001 HIS A 138 Details of bonding type rmsd covalent geometry : bond 0.00373 (26875) covalent geometry : angle 0.50648 (36550) hydrogen bonds : bond 0.03441 ( 1159) hydrogen bonds : angle 4.21053 ( 3100) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 13035.65 seconds wall clock time: 221 minutes 39.76 seconds (13299.76 seconds total)