Starting phenix.real_space_refine on Sun May 25 01:39:24 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8pbd_17585/05_2025/8pbd_17585.cif Found real_map, /net/cci-nas-00/data/ceres_data/8pbd_17585/05_2025/8pbd_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_17585/05_2025/8pbd_17585.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8pbd_17585/05_2025/8pbd_17585.map" model { file = "/net/cci-nas-00/data/ceres_data/8pbd_17585/05_2025/8pbd_17585.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8pbd_17585/05_2025/8pbd_17585.cif" } resolution = 2.83 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } 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): 0.06s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/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: 8.84, per 1000 atoms: 0.34 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: 6.24 Conformation dependent library (CDL) restraints added in 3.0 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: 8.70 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: 9.18 Time building geometry restraints manager: 7.33 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 339 or resid 401 through 402)) selection = (chain 'B' and (resid 21 through 339 or resid 400 through 401)) selection = (chain 'C' and (resid 21 through 339 or resid 400 through 401)) selection = (chain 'D' and (resid 21 through 339 or resid 400 through 401)) selection = (chain 'E' and (resid 21 through 339 or resid 400 through 401)) selection = (chain 'F' and (resid 21 through 339 or resid 400 through 401)) selection = (chain 'G' and (resid 21 through 339 or resid 400 through 401)) selection = (chain 'H' and (resid 21 through 339 or resid 400 through 401)) selection = (chain 'I' and (resid 21 through 339 or resid 400 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: 0.010 Construct map_model_manager: 0.020 Extract box with map and model: 0.880 Check model and map are aligned: 0.180 Set scattering table: 0.250 Process input model: 54.510 Find NCS groups from input model: 1.640 Set up NCS constraints: 0.100 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:10.570 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 68.660 ------------------------------------------------------------------------------- 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. 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 HIS 0.004 0.002 HIS C 294 PHE 0.009 0.001 PHE G 126 TYR 0.009 0.001 TYR B 301 ARG 0.004 0.001 ARG I 229 Details of bonding type rmsd hydrogen bonds : bond 0.25628 ( 1159) hydrogen bonds : angle 9.18582 ( 3100) covalent geometry : bond 0.00738 (26875) covalent geometry : angle 0.52157 (36550) *********************** 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 : 2.444 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: 0.6575 (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: 0.8427 (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: 1.5513 time to fit residues: 1588.9879 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 : 2.689 ------------------------------------------------------------------------------- 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 272 optimal weight: 3.9990 chunk 244 optimal weight: 1.9990 chunk 135 optimal weight: 0.5980 chunk 83 optimal weight: 3.9990 chunk 165 optimal weight: 0.7980 chunk 130 optimal weight: 5.9990 chunk 253 optimal weight: 9.9990 chunk 97 optimal weight: 2.9990 chunk 153 optimal weight: 1.9990 chunk 188 optimal weight: 0.8980 chunk 293 optimal weight: 0.9990 overall best weight: 1.0584 ------------------------------------------------------------------------------- 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 ** H 145 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 34 ASN J 135 GLN Total number of N/Q/H flips: 20 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3660 r_free = 0.3660 target = 0.146249 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3265 r_free = 0.3265 target = 0.111972 restraints weight = 31988.781| |-----------------------------------------------------------------------------| r_work (start): 0.3213 rms_B_bonded: 1.98 r_work: 0.3093 rms_B_bonded: 2.63 restraints_weight: 0.5000 r_work: 0.2965 rms_B_bonded: 4.31 restraints_weight: 0.2500 r_work (final): 0.2965 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7984 moved from start: 0.2382 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 26875 Z= 0.139 Angle : 0.508 6.578 36550 Z= 0.271 Chirality : 0.040 0.155 4139 Planarity : 0.004 0.035 4521 Dihedral : 14.047 148.169 4476 Min Nonbonded Distance : 2.223 Molprobity Statistics. All-atom Clashscore : 6.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.44 % Favored : 98.56 % Rotamer: Outliers : 3.34 % Allowed : 17.53 % Favored : 79.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.32 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.11 (0.13), residues: 3196 helix: -0.74 (0.12), residues: 1400 sheet: -1.37 (0.23), residues: 490 loop : -2.04 (0.14), residues: 1306 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS I 244 PHE 0.011 0.001 PHE I 126 TYR 0.008 0.001 TYR I 301 ARG 0.008 0.001 ARG F 215 Details of bonding type rmsd hydrogen bonds : bond 0.04100 ( 1159) hydrogen bonds : angle 4.93965 ( 3100) covalent geometry : bond 0.00301 (26875) covalent geometry : angle 0.50815 (36550) *********************** 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 822 residues out of total 2607 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 87 poor density : 735 time to evaluate : 2.658 Fit side-chains revert: symmetry clash REVERT: A 33 ILE cc_start: 0.7616 (mm) cc_final: 0.7250 (mp) REVERT: A 37 ASP cc_start: 0.7141 (m-30) cc_final: 0.6885 (m-30) REVERT: A 40 LYS cc_start: 0.6863 (mtpp) cc_final: 0.6143 (mtpt) REVERT: A 42 GLU cc_start: 0.6638 (pt0) cc_final: 0.6427 (pt0) REVERT: A 68 GLU cc_start: 0.6665 (mt-10) cc_final: 0.6036 (tm-30) REVERT: A 77 GLU cc_start: 0.7674 (OUTLIER) cc_final: 0.7268 (mp0) REVERT: A 84 MET cc_start: 0.8867 (mtp) cc_final: 0.8658 (mtp) REVERT: A 107 LYS cc_start: 0.7141 (mmtm) cc_final: 0.6687 (mttm) REVERT: A 130 ARG cc_start: 0.7214 (OUTLIER) cc_final: 0.5606 (ptp90) REVERT: A 145 GLN cc_start: 0.8470 (mt0) cc_final: 0.8175 (mt0) REVERT: A 186 LEU cc_start: 0.8357 (mm) cc_final: 0.8145 (mm) REVERT: A 202 GLN cc_start: 0.8253 (mm-40) cc_final: 0.7885 (tt0) REVERT: A 210 MET cc_start: 0.7971 (mtp) cc_final: 0.7393 (mtp) REVERT: A 247 ARG cc_start: 0.7295 (mtp-110) cc_final: 0.6817 (mmm-85) REVERT: A 254 ARG cc_start: 0.7521 (ttp80) cc_final: 0.7156 (tmt90) REVERT: A 303 ARG cc_start: 0.7424 (mtp180) cc_final: 0.6744 (mtm180) REVERT: A 308 GLU cc_start: 0.7163 (pt0) cc_final: 0.6758 (tt0) REVERT: A 329 ILE cc_start: 0.8626 (mt) cc_final: 0.8190 (mt) REVERT: B 30 GLN cc_start: 0.6788 (mp10) cc_final: 0.6488 (mp10) REVERT: B 42 GLU cc_start: 0.7438 (mt-10) cc_final: 0.6954 (mt-10) REVERT: B 43 GLU cc_start: 0.7597 (mt-10) cc_final: 0.7233 (mt-10) REVERT: B 59 GLU cc_start: 0.8089 (mt-10) cc_final: 0.7691 (tt0) REVERT: B 95 ARG cc_start: 0.7849 (ttp80) cc_final: 0.7279 (ttt-90) REVERT: B 107 LYS cc_start: 0.7741 (mmtm) cc_final: 0.6871 (ptpt) REVERT: B 206 GLN cc_start: 0.7541 (mt0) cc_final: 0.7050 (mt0) REVERT: B 306 ARG cc_start: 0.7567 (tpp80) cc_final: 0.6939 (ptm-80) REVERT: B 324 GLU cc_start: 0.8307 (mt-10) cc_final: 0.8079 (mt-10) REVERT: B 332 ASP cc_start: 0.8817 (p0) cc_final: 0.8576 (p0) REVERT: C 80 LYS cc_start: 0.7944 (mtmm) cc_final: 0.7558 (ttpp) REVERT: C 82 VAL cc_start: 0.8910 (OUTLIER) cc_final: 0.8651 (p) REVERT: C 94 GLN cc_start: 0.7773 (mm-40) cc_final: 0.6995 (tp40) REVERT: C 95 ARG cc_start: 0.8202 (ttp80) cc_final: 0.7774 (ttm170) REVERT: C 107 LYS cc_start: 0.7880 (mmtm) cc_final: 0.7128 (ptpp) REVERT: C 154 GLU cc_start: 0.7748 (mt-10) cc_final: 0.6951 (mt-10) REVERT: C 181 SER cc_start: 0.8643 (t) cc_final: 0.8186 (p) REVERT: C 202 GLN cc_start: 0.7977 (mm-40) cc_final: 0.7434 (mt0) REVERT: C 216 TYR cc_start: 0.8985 (m-80) cc_final: 0.8623 (m-80) REVERT: C 222 ASP cc_start: 0.8787 (OUTLIER) cc_final: 0.8481 (t70) REVERT: C 251 MET cc_start: 0.8172 (ttm) cc_final: 0.7677 (mtt) REVERT: C 308 GLU cc_start: 0.8561 (pm20) cc_final: 0.8062 (pm20) REVERT: D 27 ARG cc_start: 0.8459 (OUTLIER) cc_final: 0.7423 (mtp180) REVERT: D 37 ASP cc_start: 0.7113 (m-30) cc_final: 0.6757 (m-30) REVERT: D 57 LYS cc_start: 0.7902 (tttp) cc_final: 0.7675 (ttpt) REVERT: D 68 GLU cc_start: 0.8041 (mt-10) cc_final: 0.7706 (tp30) REVERT: D 94 GLN cc_start: 0.7612 (mm-40) cc_final: 0.6874 (tm-30) REVERT: D 107 LYS cc_start: 0.8319 (mmtm) cc_final: 0.7960 (mtmt) REVERT: D 181 SER cc_start: 0.9024 (t) cc_final: 0.8493 (p) REVERT: D 187 ASP cc_start: 0.8967 (OUTLIER) cc_final: 0.8554 (t70) REVERT: D 334 VAL cc_start: 0.9190 (t) cc_final: 0.8890 (p) REVERT: E 68 GLU cc_start: 0.7840 (mp0) cc_final: 0.7337 (tp30) REVERT: E 98 GLU cc_start: 0.8433 (tp30) cc_final: 0.8179 (mm-30) REVERT: E 107 LYS cc_start: 0.8027 (mmtm) cc_final: 0.7579 (mtmt) REVERT: E 176 GLU cc_start: 0.8515 (mm-30) cc_final: 0.7997 (tt0) REVERT: E 202 GLN cc_start: 0.7926 (mm-40) cc_final: 0.7682 (mt0) REVERT: E 211 MET cc_start: 0.9098 (mtt) cc_final: 0.8806 (mtt) REVERT: F 39 LYS cc_start: 0.7376 (mttt) cc_final: 0.6599 (mtmt) REVERT: F 43 GLU cc_start: 0.7887 (mt-10) cc_final: 0.7361 (mp0) REVERT: F 68 GLU cc_start: 0.7885 (mt-10) cc_final: 0.7669 (mp0) REVERT: F 95 ARG cc_start: 0.8217 (ttp80) cc_final: 0.7898 (ttp-110) REVERT: F 187 ASP cc_start: 0.8748 (m-30) cc_final: 0.8515 (m-30) REVERT: F 202 GLN cc_start: 0.8115 (mm-40) cc_final: 0.7719 (mt0) REVERT: G 39 LYS cc_start: 0.7773 (mttt) cc_final: 0.7448 (mtpp) REVERT: G 94 GLN cc_start: 0.7818 (OUTLIER) cc_final: 0.7524 (tp-100) REVERT: G 98 GLU cc_start: 0.8251 (mm-30) cc_final: 0.8018 (mm-30) REVERT: G 107 LYS cc_start: 0.7129 (mmtm) cc_final: 0.6598 (ttmm) REVERT: G 176 GLU cc_start: 0.8219 (mm-30) cc_final: 0.7882 (mm-30) REVERT: G 187 ASP cc_start: 0.8785 (m-30) cc_final: 0.8457 (m-30) REVERT: G 202 GLN cc_start: 0.8037 (mm-40) cc_final: 0.7760 (mt0) REVERT: G 247 ARG cc_start: 0.8205 (mtp-110) cc_final: 0.7856 (mtp85) REVERT: G 300 LEU cc_start: 0.8447 (OUTLIER) cc_final: 0.8152 (mt) REVERT: G 308 GLU cc_start: 0.8319 (pm20) cc_final: 0.7983 (pm20) REVERT: H 27 ARG cc_start: 0.7733 (mtp-110) cc_final: 0.7290 (tmt170) REVERT: H 39 LYS cc_start: 0.7724 (mttt) cc_final: 0.7429 (mtpm) REVERT: H 66 ILE cc_start: 0.8376 (mm) cc_final: 0.8078 (mp) REVERT: H 94 GLN cc_start: 0.8493 (mm-40) cc_final: 0.8226 (tp40) REVERT: H 96 ARG cc_start: 0.7824 (ttt90) cc_final: 0.7564 (ttt180) REVERT: H 187 ASP cc_start: 0.8563 (m-30) cc_final: 0.8340 (m-30) REVERT: H 205 TYR cc_start: 0.8647 (m-80) cc_final: 0.8372 (m-10) REVERT: H 210 MET cc_start: 0.8733 (mtp) cc_final: 0.8468 (mtm) REVERT: H 247 ARG cc_start: 0.7971 (mtp-110) cc_final: 0.7396 (mmm160) REVERT: H 254 ARG cc_start: 0.8098 (ttt-90) cc_final: 0.7833 (tmm-80) REVERT: H 258 GLU cc_start: 0.8159 (mt-10) cc_final: 0.7954 (mt-10) REVERT: I 27 ARG cc_start: 0.8159 (mtp-110) cc_final: 0.7874 (mtp-110) REVERT: I 39 LYS cc_start: 0.8165 (mttt) cc_final: 0.7814 (mmmm) REVERT: I 40 LYS cc_start: 0.7695 (mtpp) cc_final: 0.7235 (mtmm) REVERT: I 50 GLU cc_start: 0.8643 (mp0) cc_final: 0.7773 (mp0) REVERT: I 90 THR cc_start: 0.8271 (OUTLIER) cc_final: 0.8044 (p) REVERT: I 110 ASP cc_start: 0.8642 (m-30) cc_final: 0.8346 (m-30) REVERT: I 154 GLU cc_start: 0.8027 (mt-10) cc_final: 0.7817 (mt-10) REVERT: I 176 GLU cc_start: 0.7339 (mm-30) cc_final: 0.7031 (tm-30) REVERT: I 215 ARG cc_start: 0.7979 (tmm160) cc_final: 0.7762 (tmm160) REVERT: I 223 SER cc_start: 0.9347 (t) cc_final: 0.9132 (t) REVERT: I 247 ARG cc_start: 0.7869 (mtp-110) cc_final: 0.7434 (mtp85) REVERT: I 322 GLU cc_start: 0.8153 (tt0) cc_final: 0.7820 (tt0) REVERT: J 39 LYS cc_start: 0.7161 (mttt) cc_final: 0.6263 (mmmt) REVERT: J 40 LYS cc_start: 0.7014 (mtpp) cc_final: 0.6558 (mtpt) REVERT: J 42 GLU cc_start: 0.7076 (mt-10) cc_final: 0.6722 (tp30) REVERT: J 50 GLU cc_start: 0.7918 (mp0) cc_final: 0.7305 (mp0) REVERT: J 68 GLU cc_start: 0.7584 (mt-10) cc_final: 0.7118 (tm-30) REVERT: J 73 LYS cc_start: 0.6827 (mttt) cc_final: 0.5970 (tptt) REVERT: J 77 GLU cc_start: 0.7179 (mp0) cc_final: 0.5990 (mp0) REVERT: J 95 ARG cc_start: 0.8077 (ttp-170) cc_final: 0.7678 (ttm110) REVERT: J 110 ASP cc_start: 0.8092 (m-30) cc_final: 0.7881 (m-30) REVERT: J 124 GLU cc_start: 0.9097 (tt0) cc_final: 0.8803 (tt0) REVERT: J 154 GLU cc_start: 0.7991 (mt-10) cc_final: 0.7455 (mm-30) REVERT: J 183 SER cc_start: 0.8483 (m) cc_final: 0.8247 (m) REVERT: J 184 ASP cc_start: 0.8472 (m-30) cc_final: 0.8135 (m-30) REVERT: J 231 ASP cc_start: 0.8540 (m-30) cc_final: 0.8330 (m-30) REVERT: J 243 MET cc_start: 0.8716 (mtm) cc_final: 0.8510 (mtp) REVERT: J 247 ARG cc_start: 0.7382 (mtp-110) cc_final: 0.6703 (ttm-80) REVERT: J 258 GLU cc_start: 0.7734 (mt-10) cc_final: 0.7137 (tp30) REVERT: J 308 GLU cc_start: 0.7865 (pm20) cc_final: 0.7063 (mt-10) REVERT: J 332 ASP cc_start: 0.8198 (p0) cc_final: 0.7842 (p0) outliers start: 87 outliers final: 29 residues processed: 778 average time/residue: 1.4984 time to fit residues: 1331.7537 Evaluate side-chains 680 residues out of total 2607 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 642 time to evaluate : 2.930 ------------------------------------------------------------------------------- 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 C residue 222 ASP Chi-restraints excluded: chain D residue 27 ARG Chi-restraints excluded: chain D residue 97 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 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 38 VAL 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 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 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 233 optimal weight: 7.9990 chunk 50 optimal weight: 4.9990 chunk 255 optimal weight: 5.9990 chunk 241 optimal weight: 5.9990 chunk 38 optimal weight: 5.9990 chunk 3 optimal weight: 2.9990 chunk 180 optimal weight: 0.0770 chunk 196 optimal weight: 5.9990 chunk 292 optimal weight: 6.9990 chunk 248 optimal weight: 10.0000 chunk 61 optimal weight: 4.9990 overall best weight: 3.8146 ------------------------------------------------------------------------------- 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** E 330 ASN G 244 HIS H 244 HIS I 23 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3606 r_free = 0.3606 target = 0.141515 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3205 r_free = 0.3205 target = 0.107536 restraints weight = 32548.580| |-----------------------------------------------------------------------------| r_work (start): 0.3132 rms_B_bonded: 1.96 r_work: 0.3011 rms_B_bonded: 2.59 restraints_weight: 0.5000 r_work: 0.2883 rms_B_bonded: 4.23 restraints_weight: 0.2500 r_work (final): 0.2883 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8057 moved from start: 0.2756 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.051 26875 Z= 0.314 Angle : 0.607 9.396 36550 Z= 0.319 Chirality : 0.044 0.167 4139 Planarity : 0.005 0.051 4521 Dihedral : 14.374 145.379 4459 Min Nonbonded Distance : 2.138 Molprobity Statistics. All-atom Clashscore : 7.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.88 % Favored : 97.12 % Rotamer: Outliers : 4.95 % Allowed : 19.41 % Favored : 75.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.32 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.46 (0.13), residues: 3196 helix: -0.09 (0.13), residues: 1380 sheet: -0.52 (0.27), residues: 380 loop : -1.96 (0.13), residues: 1436 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.008 0.002 HIS E 294 PHE 0.015 0.002 PHE F 126 TYR 0.016 0.002 TYR I 315 ARG 0.009 0.001 ARG D 215 Details of bonding type rmsd hydrogen bonds : bond 0.04983 ( 1159) hydrogen bonds : angle 4.85316 ( 3100) covalent geometry : bond 0.00726 (26875) covalent geometry : angle 0.60746 (36550) *********************** 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 774 residues out of total 2607 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 129 poor density : 645 time to evaluate : 2.856 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 27 ARG cc_start: 0.7494 (mmm160) cc_final: 0.7275 (mmm160) REVERT: A 33 ILE cc_start: 0.7840 (mm) cc_final: 0.7191 (mp) REVERT: A 37 ASP cc_start: 0.7417 (m-30) cc_final: 0.7183 (m-30) REVERT: A 40 LYS cc_start: 0.6934 (mtpp) cc_final: 0.6163 (mtpt) REVERT: A 42 GLU cc_start: 0.6768 (pt0) cc_final: 0.6549 (pt0) REVERT: A 66 ILE cc_start: 0.6847 (OUTLIER) cc_final: 0.6485 (tt) REVERT: A 68 GLU cc_start: 0.6650 (mt-10) cc_final: 0.5973 (tm-30) REVERT: A 70 LYS cc_start: 0.6466 (ttpt) cc_final: 0.6164 (ttpt) REVERT: A 84 MET cc_start: 0.8882 (mtp) cc_final: 0.8590 (mtp) REVERT: A 98 GLU cc_start: 0.7748 (mt-10) cc_final: 0.7547 (mm-30) REVERT: A 107 LYS cc_start: 0.7259 (mmtm) cc_final: 0.6855 (mttm) REVERT: A 130 ARG cc_start: 0.7374 (OUTLIER) cc_final: 0.7121 (ttp80) REVERT: A 145 GLN cc_start: 0.8653 (mt0) cc_final: 0.8342 (mt0) REVERT: A 202 GLN cc_start: 0.8184 (mm-40) cc_final: 0.7717 (tt0) REVERT: A 210 MET cc_start: 0.8151 (mtp) cc_final: 0.7503 (mtp) REVERT: A 247 ARG cc_start: 0.7429 (mtp-110) cc_final: 0.6889 (mmm-85) REVERT: A 303 ARG cc_start: 0.7436 (mtp180) cc_final: 0.6861 (mtm180) REVERT: A 308 GLU cc_start: 0.7520 (pt0) cc_final: 0.6883 (tt0) REVERT: A 329 ILE cc_start: 0.8657 (mt) cc_final: 0.7877 (mt) REVERT: B 40 LYS cc_start: 0.7180 (mtpp) cc_final: 0.5712 (mtpt) REVERT: B 42 GLU cc_start: 0.7400 (mt-10) cc_final: 0.6938 (mt-10) REVERT: B 43 GLU cc_start: 0.7663 (mt-10) cc_final: 0.6910 (pp20) REVERT: B 95 ARG cc_start: 0.7960 (ttp80) cc_final: 0.7540 (ttt-90) REVERT: B 107 LYS cc_start: 0.7776 (mmtm) cc_final: 0.6848 (ptpt) REVERT: B 215 ARG cc_start: 0.8261 (OUTLIER) cc_final: 0.7688 (ttt90) REVERT: B 332 ASP cc_start: 0.8815 (p0) cc_final: 0.8426 (p0) REVERT: C 94 GLN cc_start: 0.7863 (mm-40) cc_final: 0.7188 (tm-30) REVERT: C 95 ARG cc_start: 0.8207 (ttp80) cc_final: 0.7556 (ttp-170) REVERT: C 107 LYS cc_start: 0.8218 (mmtm) cc_final: 0.7576 (ptmt) REVERT: C 154 GLU cc_start: 0.7655 (mt-10) cc_final: 0.6736 (mt-10) REVERT: C 181 SER cc_start: 0.8662 (t) cc_final: 0.8208 (p) REVERT: C 187 ASP cc_start: 0.8708 (OUTLIER) cc_final: 0.8441 (m-30) REVERT: C 202 GLN cc_start: 0.7970 (mm-40) cc_final: 0.7445 (mt0) REVERT: C 216 TYR cc_start: 0.9048 (m-80) cc_final: 0.8775 (m-80) REVERT: C 243 MET cc_start: 0.8368 (mtm) cc_final: 0.8031 (mtt) REVERT: C 308 GLU cc_start: 0.8534 (pm20) cc_final: 0.8052 (pm20) REVERT: D 37 ASP cc_start: 0.7315 (m-30) cc_final: 0.6808 (m-30) REVERT: D 57 LYS cc_start: 0.7996 (tttp) cc_final: 0.7742 (ttpt) REVERT: D 68 GLU cc_start: 0.8209 (mt-10) cc_final: 0.7565 (tp30) REVERT: D 94 GLN cc_start: 0.7741 (mm-40) cc_final: 0.6913 (tm-30) REVERT: D 107 LYS cc_start: 0.8348 (mmtm) cc_final: 0.7941 (mtmt) REVERT: D 181 SER cc_start: 0.8965 (t) cc_final: 0.8753 (t) REVERT: D 187 ASP cc_start: 0.9053 (OUTLIER) cc_final: 0.8637 (t70) REVERT: D 247 ARG cc_start: 0.8085 (mtp-110) cc_final: 0.7003 (mtm110) REVERT: E 27 ARG cc_start: 0.8471 (OUTLIER) cc_final: 0.7313 (mtp180) REVERT: E 107 LYS cc_start: 0.8076 (mmtm) cc_final: 0.7648 (mtmt) REVERT: E 176 GLU cc_start: 0.8484 (mm-30) cc_final: 0.7980 (tt0) REVERT: E 211 MET cc_start: 0.9119 (mtt) cc_final: 0.8772 (mtt) REVERT: F 39 LYS cc_start: 0.7501 (mttt) cc_final: 0.6770 (mtmt) REVERT: F 43 GLU cc_start: 0.8060 (mt-10) cc_final: 0.7528 (mp0) REVERT: F 68 GLU cc_start: 0.8101 (mt-10) cc_final: 0.7645 (mp0) REVERT: F 95 ARG cc_start: 0.8171 (ttp80) cc_final: 0.7808 (ttp-110) REVERT: F 187 ASP cc_start: 0.8647 (m-30) cc_final: 0.8405 (m-30) REVERT: F 202 GLN cc_start: 0.8231 (mm-40) cc_final: 0.7806 (mt0) REVERT: F 222 ASP cc_start: 0.9133 (OUTLIER) cc_final: 0.8683 (t70) REVERT: F 223 SER cc_start: 0.9257 (t) cc_final: 0.8969 (p) REVERT: F 257 ASP cc_start: 0.8459 (m-30) cc_final: 0.8253 (m-30) REVERT: G 39 LYS cc_start: 0.7718 (mttt) cc_final: 0.7325 (mtpp) REVERT: G 91 GLU cc_start: 0.8272 (OUTLIER) cc_final: 0.7869 (tt0) REVERT: G 94 GLN cc_start: 0.7881 (OUTLIER) cc_final: 0.7475 (tp-100) REVERT: G 107 LYS cc_start: 0.7670 (mmtm) cc_final: 0.6790 (ttmm) REVERT: G 176 GLU cc_start: 0.8264 (mm-30) cc_final: 0.7895 (mm-30) REVERT: G 187 ASP cc_start: 0.8672 (m-30) cc_final: 0.8416 (m-30) REVERT: G 202 GLN cc_start: 0.8257 (mm-40) cc_final: 0.7925 (mt0) REVERT: G 247 ARG cc_start: 0.8278 (mtp-110) cc_final: 0.8017 (mtp85) REVERT: G 308 GLU cc_start: 0.8343 (pm20) cc_final: 0.7915 (pm20) REVERT: H 27 ARG cc_start: 0.7836 (mtp-110) cc_final: 0.7361 (tmt170) REVERT: H 39 LYS cc_start: 0.7762 (mttt) cc_final: 0.7473 (mtpm) REVERT: H 64 LYS cc_start: 0.7132 (OUTLIER) cc_final: 0.6758 (ttmm) REVERT: H 66 ILE cc_start: 0.8342 (mm) cc_final: 0.8044 (mp) REVERT: H 94 GLN cc_start: 0.8505 (mm-40) cc_final: 0.8167 (tp40) REVERT: H 205 TYR cc_start: 0.8851 (m-80) cc_final: 0.8534 (m-10) REVERT: H 210 MET cc_start: 0.8795 (mtp) cc_final: 0.8517 (mtm) REVERT: H 247 ARG cc_start: 0.8042 (mtp-110) cc_final: 0.7477 (mmm160) REVERT: H 254 ARG cc_start: 0.8197 (ttt-90) cc_final: 0.7829 (tmm-80) REVERT: I 23 GLN cc_start: 0.7193 (mt0) cc_final: 0.6912 (mt0) REVERT: I 27 ARG cc_start: 0.8148 (mtp-110) cc_final: 0.7883 (mtp85) REVERT: I 39 LYS cc_start: 0.7996 (mttt) cc_final: 0.7658 (mmmm) REVERT: I 40 LYS cc_start: 0.7809 (mtpp) cc_final: 0.7348 (mttp) REVERT: I 43 GLU cc_start: 0.7727 (mt-10) cc_final: 0.7317 (tp30) REVERT: I 50 GLU cc_start: 0.8710 (mp0) cc_final: 0.7734 (mp0) REVERT: I 110 ASP cc_start: 0.8672 (m-30) cc_final: 0.8428 (m-30) REVERT: I 176 GLU cc_start: 0.7295 (mm-30) cc_final: 0.7026 (tm-30) REVERT: I 223 SER cc_start: 0.9367 (t) cc_final: 0.9097 (t) REVERT: I 247 ARG cc_start: 0.7927 (mtp-110) cc_final: 0.7706 (mtp85) REVERT: I 322 GLU cc_start: 0.8262 (tt0) cc_final: 0.8055 (tt0) REVERT: I 332 ASP cc_start: 0.8257 (p0) cc_final: 0.7988 (p0) REVERT: J 39 LYS cc_start: 0.7150 (mttt) cc_final: 0.6505 (mmmt) REVERT: J 40 LYS cc_start: 0.7542 (mtpp) cc_final: 0.6455 (mtpt) REVERT: J 50 GLU cc_start: 0.8044 (mp0) cc_final: 0.7194 (mp0) REVERT: J 68 GLU cc_start: 0.7607 (mt-10) cc_final: 0.7346 (tm-30) REVERT: J 73 LYS cc_start: 0.6756 (mttt) cc_final: 0.6339 (tptt) REVERT: J 77 GLU cc_start: 0.7306 (mp0) cc_final: 0.6862 (mp0) REVERT: J 109 LEU cc_start: 0.8578 (OUTLIER) cc_final: 0.8278 (mp) REVERT: J 110 ASP cc_start: 0.8189 (m-30) cc_final: 0.7813 (m-30) REVERT: J 184 ASP cc_start: 0.8421 (m-30) cc_final: 0.7898 (m-30) REVERT: J 187 ASP cc_start: 0.8513 (OUTLIER) cc_final: 0.8167 (m-30) REVERT: J 213 GLU cc_start: 0.8117 (mt-10) cc_final: 0.7647 (mp0) REVERT: J 222 ASP cc_start: 0.8827 (OUTLIER) cc_final: 0.8578 (t0) REVERT: J 247 ARG cc_start: 0.7657 (mtp-110) cc_final: 0.7327 (mtp85) REVERT: J 250 ARG cc_start: 0.8370 (tpt170) cc_final: 0.6261 (ttm170) REVERT: J 308 GLU cc_start: 0.7872 (pm20) cc_final: 0.6934 (mt-10) outliers start: 129 outliers final: 67 residues processed: 711 average time/residue: 1.5351 time to fit residues: 1243.4836 Evaluate side-chains 671 residues out of total 2607 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 80 poor density : 591 time to evaluate : 2.566 ------------------------------------------------------------------------------- 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 87 THR Chi-restraints excluded: chain A residue 106 SER Chi-restraints excluded: chain A residue 130 ARG Chi-restraints excluded: chain A residue 223 SER Chi-restraints excluded: chain A residue 230 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 99 ILE 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 99 ILE Chi-restraints excluded: chain C residue 104 THR 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 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 D residue 273 VAL 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 230 THR Chi-restraints excluded: chain E residue 273 VAL 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 130 ARG Chi-restraints excluded: chain F residue 145 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 161 ASP Chi-restraints excluded: chain G residue 272 GLN Chi-restraints excluded: chain H residue 64 LYS Chi-restraints excluded: chain H residue 82 VAL Chi-restraints excluded: chain H residue 90 THR Chi-restraints excluded: chain H residue 142 VAL Chi-restraints excluded: chain H residue 261 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 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 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 222 ASP Chi-restraints excluded: chain J residue 239 SER Chi-restraints excluded: chain J residue 255 LEU Chi-restraints excluded: chain J residue 272 GLN 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 277 optimal weight: 0.8980 chunk 212 optimal weight: 0.9980 chunk 197 optimal weight: 0.7980 chunk 177 optimal weight: 0.8980 chunk 272 optimal weight: 2.9990 chunk 317 optimal weight: 30.0000 chunk 32 optimal weight: 0.0030 chunk 151 optimal weight: 0.9990 chunk 47 optimal weight: 6.9990 chunk 75 optimal weight: 1.9990 chunk 273 optimal weight: 0.0980 overall best weight: 0.5390 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 272 GLN B 202 GLN B 242 GLN ** C 145 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 272 GLN D 145 GLN ** E 145 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 23 GLN H 290 ASN J 94 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3679 r_free = 0.3679 target = 0.148177 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3289 r_free = 0.3289 target = 0.113949 restraints weight = 32187.633| |-----------------------------------------------------------------------------| r_work (start): 0.3178 rms_B_bonded: 2.02 r_work: 0.3055 rms_B_bonded: 2.67 restraints_weight: 0.5000 r_work: 0.2927 rms_B_bonded: 4.37 restraints_weight: 0.2500 r_work (final): 0.2927 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7954 moved from start: 0.3164 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 26875 Z= 0.106 Angle : 0.462 7.498 36550 Z= 0.245 Chirality : 0.039 0.136 4139 Planarity : 0.003 0.034 4521 Dihedral : 13.788 144.394 4457 Min Nonbonded Distance : 2.260 Molprobity Statistics. All-atom Clashscore : 6.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.44 % Favored : 98.56 % Rotamer: Outliers : 2.45 % Allowed : 23.13 % Favored : 74.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.32 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.83 (0.14), residues: 3196 helix: 0.33 (0.13), residues: 1450 sheet: -0.24 (0.27), residues: 380 loop : -1.58 (0.14), residues: 1366 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.007 0.001 HIS A 138 PHE 0.012 0.001 PHE J 259 TYR 0.009 0.001 TYR B 301 ARG 0.010 0.000 ARG E 215 Details of bonding type rmsd hydrogen bonds : bond 0.03066 ( 1159) hydrogen bonds : angle 4.34829 ( 3100) covalent geometry : bond 0.00228 (26875) covalent geometry : angle 0.46152 (36550) *********************** 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 720 residues out of total 2607 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 656 time to evaluate : 2.642 Fit side-chains revert: symmetry clash REVERT: A 37 ASP cc_start: 0.7488 (m-30) cc_final: 0.7205 (m-30) REVERT: A 40 LYS cc_start: 0.7358 (mtpp) cc_final: 0.6251 (mtpt) REVERT: A 42 GLU cc_start: 0.6746 (pt0) cc_final: 0.6521 (pt0) REVERT: A 66 ILE cc_start: 0.7025 (mm) cc_final: 0.6661 (tt) REVERT: A 68 GLU cc_start: 0.6612 (mt-10) cc_final: 0.5950 (tm-30) REVERT: A 70 LYS cc_start: 0.6743 (ttpt) cc_final: 0.6515 (ttpt) REVERT: A 77 GLU cc_start: 0.7540 (OUTLIER) cc_final: 0.7263 (mp0) REVERT: A 84 MET cc_start: 0.8829 (mtp) cc_final: 0.8489 (mtp) REVERT: A 98 GLU cc_start: 0.7781 (mt-10) cc_final: 0.7501 (mm-30) REVERT: A 107 LYS cc_start: 0.7201 (mmtm) cc_final: 0.6820 (mttm) REVERT: A 210 MET cc_start: 0.8096 (mtp) cc_final: 0.7449 (mtp) REVERT: A 254 ARG cc_start: 0.7291 (ttp80) cc_final: 0.7003 (tmt90) REVERT: A 303 ARG cc_start: 0.7481 (mtp180) cc_final: 0.7249 (mtm110) REVERT: A 308 GLU cc_start: 0.7357 (pt0) cc_final: 0.6697 (tt0) REVERT: A 329 ILE cc_start: 0.8599 (mt) cc_final: 0.7980 (mt) REVERT: B 42 GLU cc_start: 0.7302 (mt-10) cc_final: 0.6826 (mt-10) REVERT: B 43 GLU cc_start: 0.7623 (mt-10) cc_final: 0.7267 (mt-10) REVERT: B 95 ARG cc_start: 0.7916 (ttp80) cc_final: 0.7505 (ttt-90) REVERT: B 107 LYS cc_start: 0.7776 (mmtm) cc_final: 0.6864 (ptpt) REVERT: B 145 GLN cc_start: 0.8238 (mt0) cc_final: 0.7965 (mp10) REVERT: B 158 MET cc_start: 0.8454 (mtp) cc_final: 0.8149 (mtm) REVERT: B 215 ARG cc_start: 0.8004 (OUTLIER) cc_final: 0.7600 (tpt-90) REVERT: B 235 ARG cc_start: 0.8840 (ttp-170) cc_final: 0.8577 (ttp80) REVERT: B 306 ARG cc_start: 0.7737 (tpp80) cc_final: 0.6886 (ptm-80) REVERT: B 332 ASP cc_start: 0.8743 (p0) cc_final: 0.8490 (p0) REVERT: C 33 ILE cc_start: 0.8478 (mm) cc_final: 0.8259 (mm) REVERT: C 94 GLN cc_start: 0.7793 (mm-40) cc_final: 0.6946 (tp40) REVERT: C 95 ARG cc_start: 0.8266 (ttp80) cc_final: 0.7727 (ttp-170) REVERT: C 107 LYS cc_start: 0.8200 (mmtm) cc_final: 0.7518 (ptpp) REVERT: C 154 GLU cc_start: 0.7638 (mt-10) cc_final: 0.6770 (mt-10) REVERT: C 181 SER cc_start: 0.8853 (t) cc_final: 0.8609 (p) REVERT: C 202 GLN cc_start: 0.7827 (mm-40) cc_final: 0.7404 (mt0) REVERT: C 216 TYR cc_start: 0.9082 (m-80) cc_final: 0.8770 (m-80) REVERT: C 222 ASP cc_start: 0.8891 (t70) cc_final: 0.8554 (t70) REVERT: C 308 GLU cc_start: 0.8621 (pm20) cc_final: 0.8399 (pm20) REVERT: D 27 ARG cc_start: 0.8284 (OUTLIER) cc_final: 0.7389 (mtp180) REVERT: D 29 GLU cc_start: 0.7144 (mm-30) cc_final: 0.6878 (mm-30) REVERT: D 30 GLN cc_start: 0.7551 (mt0) cc_final: 0.7316 (mp10) REVERT: D 37 ASP cc_start: 0.7259 (m-30) cc_final: 0.6966 (m-30) REVERT: D 57 LYS cc_start: 0.7936 (tttp) cc_final: 0.7636 (ttpt) REVERT: D 94 GLN cc_start: 0.7633 (mm-40) cc_final: 0.6781 (tm-30) REVERT: D 107 LYS cc_start: 0.8303 (mmtm) cc_final: 0.7886 (mtmt) REVERT: D 187 ASP cc_start: 0.9014 (OUTLIER) cc_final: 0.8715 (t70) REVERT: D 247 ARG cc_start: 0.8015 (mtp-110) cc_final: 0.7798 (ttt-90) REVERT: D 334 VAL cc_start: 0.9196 (t) cc_final: 0.8862 (p) REVERT: E 68 GLU cc_start: 0.8022 (mp0) cc_final: 0.7553 (tp30) REVERT: E 107 LYS cc_start: 0.8008 (mmtm) cc_final: 0.7584 (mtmt) REVERT: E 176 GLU cc_start: 0.8482 (mm-30) cc_final: 0.7889 (tt0) REVERT: E 211 MET cc_start: 0.9107 (mtt) cc_final: 0.8795 (mtt) REVERT: F 27 ARG cc_start: 0.8530 (mtp180) cc_final: 0.8244 (mmm160) REVERT: F 39 LYS cc_start: 0.7251 (mttt) cc_final: 0.6499 (mtmt) REVERT: F 43 GLU cc_start: 0.7908 (mt-10) cc_final: 0.7357 (mp0) REVERT: F 68 GLU cc_start: 0.7944 (mt-10) cc_final: 0.7680 (mp0) REVERT: F 95 ARG cc_start: 0.8181 (ttp80) cc_final: 0.7821 (ttp-110) REVERT: F 187 ASP cc_start: 0.8652 (m-30) cc_final: 0.8210 (m-30) REVERT: F 202 GLN cc_start: 0.8126 (mm-40) cc_final: 0.7759 (mt0) REVERT: F 206 GLN cc_start: 0.8622 (OUTLIER) cc_final: 0.7788 (mt0) REVERT: G 39 LYS cc_start: 0.7680 (mttt) cc_final: 0.7355 (mtpp) REVERT: G 94 GLN cc_start: 0.7825 (OUTLIER) cc_final: 0.7514 (tp-100) REVERT: G 107 LYS cc_start: 0.7656 (mmtm) cc_final: 0.6767 (ttmt) REVERT: G 176 GLU cc_start: 0.8145 (mm-30) cc_final: 0.7823 (mm-30) REVERT: G 187 ASP cc_start: 0.8382 (m-30) cc_final: 0.7999 (m-30) REVERT: G 202 GLN cc_start: 0.7978 (mm-40) cc_final: 0.7770 (mt0) REVERT: G 247 ARG cc_start: 0.8204 (mtp-110) cc_final: 0.7906 (mtp85) REVERT: G 306 ARG cc_start: 0.7670 (ttm110) cc_final: 0.6969 (ttp80) REVERT: G 308 GLU cc_start: 0.8215 (pm20) cc_final: 0.7839 (pm20) REVERT: H 27 ARG cc_start: 0.7655 (mtp-110) cc_final: 0.7210 (tmt170) REVERT: H 39 LYS cc_start: 0.7582 (mttt) cc_final: 0.7291 (mtpm) REVERT: H 43 GLU cc_start: 0.8208 (mt-10) cc_final: 0.7983 (mt-10) REVERT: H 94 GLN cc_start: 0.8354 (mm-40) cc_final: 0.8009 (tp40) REVERT: H 206 GLN cc_start: 0.8670 (mt0) cc_final: 0.8379 (mt0) REVERT: H 247 ARG cc_start: 0.7964 (mtp-110) cc_final: 0.7307 (mmm160) REVERT: H 254 ARG cc_start: 0.8083 (ttt-90) cc_final: 0.7832 (tmm-80) REVERT: I 37 ASP cc_start: 0.7799 (m-30) cc_final: 0.7504 (m-30) REVERT: I 39 LYS cc_start: 0.7852 (mttt) cc_final: 0.7584 (mmmm) REVERT: I 40 LYS cc_start: 0.7588 (mtpp) cc_final: 0.7169 (mttp) REVERT: I 43 GLU cc_start: 0.7638 (mt-10) cc_final: 0.7222 (tp30) REVERT: I 109 LEU cc_start: 0.8681 (OUTLIER) cc_final: 0.8319 (mp) REVERT: I 110 ASP cc_start: 0.8669 (m-30) cc_final: 0.8400 (m-30) REVERT: I 176 GLU cc_start: 0.7225 (mm-30) cc_final: 0.6933 (tm-30) REVERT: I 247 ARG cc_start: 0.7814 (mtp-110) cc_final: 0.7380 (mtp85) REVERT: I 332 ASP cc_start: 0.8296 (p0) cc_final: 0.7995 (p0) REVERT: J 39 LYS cc_start: 0.6611 (mttt) cc_final: 0.5917 (mmmt) REVERT: J 40 LYS cc_start: 0.6889 (mtpp) cc_final: 0.6447 (mtpt) REVERT: J 42 GLU cc_start: 0.7132 (tp30) cc_final: 0.6456 (tt0) REVERT: J 50 GLU cc_start: 0.7866 (mp0) cc_final: 0.6900 (mp0) REVERT: J 68 GLU cc_start: 0.7336 (mt-10) cc_final: 0.7112 (tm-30) REVERT: J 73 LYS cc_start: 0.6664 (mttt) cc_final: 0.6268 (tptt) REVERT: J 77 GLU cc_start: 0.7109 (OUTLIER) cc_final: 0.6662 (mp0) REVERT: J 95 ARG cc_start: 0.7965 (ttp-170) cc_final: 0.7690 (ttm110) REVERT: J 110 ASP cc_start: 0.7957 (m-30) cc_final: 0.7499 (m-30) REVERT: J 124 GLU cc_start: 0.9193 (tt0) cc_final: 0.8790 (tt0) REVERT: J 135 GLN cc_start: 0.8522 (mm-40) cc_final: 0.6666 (mp-120) REVERT: J 154 GLU cc_start: 0.8047 (mt-10) cc_final: 0.7548 (mm-30) REVERT: J 169 GLU cc_start: 0.8315 (pm20) cc_final: 0.8063 (pm20) REVERT: J 184 ASP cc_start: 0.8561 (m-30) cc_final: 0.8204 (m-30) REVERT: J 187 ASP cc_start: 0.8307 (OUTLIER) cc_final: 0.7630 (m-30) REVERT: J 247 ARG cc_start: 0.7417 (mtp-110) cc_final: 0.7160 (mtp85) REVERT: J 299 ARG cc_start: 0.8632 (mtm180) cc_final: 0.8138 (mmm-85) REVERT: J 308 GLU cc_start: 0.7892 (pm20) cc_final: 0.6937 (mt-10) REVERT: J 332 ASP cc_start: 0.8639 (p0) cc_final: 0.8292 (p0) outliers start: 64 outliers final: 31 residues processed: 681 average time/residue: 1.5051 time to fit residues: 1167.2157 Evaluate side-chains 656 residues out of total 2607 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 616 time to evaluate : 2.943 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 77 GLU Chi-restraints excluded: chain A residue 88 THR 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 82 VAL Chi-restraints excluded: chain B residue 113 LEU Chi-restraints excluded: chain B residue 215 ARG Chi-restraints excluded: chain B residue 272 GLN Chi-restraints excluded: chain D residue 27 ARG Chi-restraints excluded: chain D residue 125 MET Chi-restraints excluded: chain D residue 161 ASP 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 E residue 296 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 297 THR Chi-restraints excluded: chain G residue 26 SER 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 H residue 28 LEU Chi-restraints excluded: chain H residue 308 GLU Chi-restraints excluded: chain I residue 99 ILE Chi-restraints excluded: chain I residue 109 LEU 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 130 ARG Chi-restraints excluded: chain J residue 187 ASP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 323 random chunks: chunk 143 optimal weight: 3.9990 chunk 180 optimal weight: 0.0870 chunk 308 optimal weight: 8.9990 chunk 87 optimal weight: 0.8980 chunk 204 optimal weight: 0.8980 chunk 117 optimal weight: 3.9990 chunk 63 optimal weight: 2.9990 chunk 305 optimal weight: 6.9990 chunk 149 optimal weight: 2.9990 chunk 4 optimal weight: 0.8980 chunk 266 optimal weight: 0.9990 overall best weight: 0.7560 ------------------------------------------------------------------------------- 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** F 200 GLN H 34 ASN I 135 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3678 r_free = 0.3678 target = 0.148192 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3298 r_free = 0.3298 target = 0.114526 restraints weight = 32203.286| |-----------------------------------------------------------------------------| r_work (start): 0.3289 rms_B_bonded: 1.98 r_work: 0.3170 rms_B_bonded: 2.65 restraints_weight: 0.5000 r_work: 0.3041 rms_B_bonded: 4.35 restraints_weight: 0.2500 r_work (final): 0.3041 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7952 moved from start: 0.3345 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 26875 Z= 0.112 Angle : 0.459 7.394 36550 Z= 0.242 Chirality : 0.038 0.134 4139 Planarity : 0.003 0.041 4521 Dihedral : 13.592 143.312 4454 Min Nonbonded Distance : 2.239 Molprobity Statistics. All-atom Clashscore : 6.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.00 % Favored : 98.00 % Rotamer: Outliers : 3.22 % Allowed : 23.05 % Favored : 73.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.32 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.24 (0.14), residues: 3196 helix: 0.81 (0.14), residues: 1390 sheet: -0.04 (0.27), residues: 380 loop : -1.14 (0.15), residues: 1426 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.005 0.001 HIS A 138 PHE 0.011 0.001 PHE F 126 TYR 0.008 0.001 TYR G 315 ARG 0.009 0.001 ARG C 215 Details of bonding type rmsd hydrogen bonds : bond 0.03003 ( 1159) hydrogen bonds : angle 4.16144 ( 3100) covalent geometry : bond 0.00247 (26875) covalent geometry : angle 0.45911 (36550) *********************** 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 716 residues out of total 2607 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 84 poor density : 632 time to evaluate : 2.729 Fit side-chains revert: symmetry clash REVERT: A 37 ASP cc_start: 0.7473 (m-30) cc_final: 0.7164 (m-30) REVERT: A 40 LYS cc_start: 0.7383 (mtpp) cc_final: 0.6270 (mtpt) REVERT: A 42 GLU cc_start: 0.6770 (pt0) cc_final: 0.6530 (pt0) REVERT: A 68 GLU cc_start: 0.6672 (mt-10) cc_final: 0.6006 (tm-30) REVERT: A 70 LYS cc_start: 0.6707 (ttpt) cc_final: 0.6500 (ttpt) REVERT: A 77 GLU cc_start: 0.7668 (OUTLIER) cc_final: 0.7371 (mp0) REVERT: A 84 MET cc_start: 0.8800 (mtp) cc_final: 0.8483 (mtp) REVERT: A 98 GLU cc_start: 0.7780 (mt-10) cc_final: 0.7518 (mm-30) REVERT: A 107 LYS cc_start: 0.7181 (mmtm) cc_final: 0.6734 (mttm) REVERT: A 186 LEU cc_start: 0.8160 (mm) cc_final: 0.7924 (mm) REVERT: A 206 GLN cc_start: 0.7405 (OUTLIER) cc_final: 0.6865 (mt0) REVERT: A 210 MET cc_start: 0.8106 (mtp) cc_final: 0.7433 (mtp) REVERT: A 251 MET cc_start: 0.7772 (mtp) cc_final: 0.7475 (mtp) REVERT: A 254 ARG cc_start: 0.7348 (ttp80) cc_final: 0.7050 (tmt90) REVERT: A 303 ARG cc_start: 0.7470 (mtp180) cc_final: 0.7002 (mtm180) REVERT: A 308 GLU cc_start: 0.7308 (pt0) cc_final: 0.6667 (tt0) REVERT: A 329 ILE cc_start: 0.8669 (mt) cc_final: 0.8039 (mt) REVERT: B 42 GLU cc_start: 0.7243 (mt-10) cc_final: 0.6718 (mt-10) REVERT: B 43 GLU cc_start: 0.7491 (mt-10) cc_final: 0.7119 (mt-10) REVERT: B 95 ARG cc_start: 0.7917 (ttp80) cc_final: 0.7497 (ttt-90) REVERT: B 107 LYS cc_start: 0.7781 (mmtm) cc_final: 0.6857 (ptpt) REVERT: B 215 ARG cc_start: 0.8100 (OUTLIER) cc_final: 0.7701 (tpt-90) REVERT: B 332 ASP cc_start: 0.8747 (p0) cc_final: 0.8458 (p0) REVERT: C 88 THR cc_start: 0.9172 (p) cc_final: 0.8960 (p) REVERT: C 94 GLN cc_start: 0.7794 (mm-40) cc_final: 0.6945 (tp40) REVERT: C 95 ARG cc_start: 0.8175 (ttp80) cc_final: 0.7671 (ttp-170) REVERT: C 107 LYS cc_start: 0.8183 (mmtm) cc_final: 0.7507 (ptpp) REVERT: C 145 GLN cc_start: 0.8434 (mp10) cc_final: 0.7796 (mp10) REVERT: C 154 GLU cc_start: 0.7601 (mt-10) cc_final: 0.6779 (mt-10) REVERT: C 181 SER cc_start: 0.8848 (t) cc_final: 0.8607 (p) REVERT: C 202 GLN cc_start: 0.7785 (mm-40) cc_final: 0.7518 (mt0) REVERT: C 206 GLN cc_start: 0.7526 (mt0) cc_final: 0.7040 (mt0) REVERT: C 215 ARG cc_start: 0.8206 (ttt90) cc_final: 0.7850 (tpt-90) REVERT: C 222 ASP cc_start: 0.8773 (t70) cc_final: 0.8337 (t70) REVERT: C 251 MET cc_start: 0.8005 (OUTLIER) cc_final: 0.7418 (mpt) REVERT: C 308 GLU cc_start: 0.8619 (pm20) cc_final: 0.8395 (pm20) REVERT: D 27 ARG cc_start: 0.8232 (OUTLIER) cc_final: 0.7357 (mtp180) REVERT: D 29 GLU cc_start: 0.7272 (mm-30) cc_final: 0.7010 (mm-30) REVERT: D 37 ASP cc_start: 0.7202 (m-30) cc_final: 0.6919 (m-30) REVERT: D 42 GLU cc_start: 0.7995 (mt-10) cc_final: 0.7674 (mm-30) REVERT: D 94 GLN cc_start: 0.7663 (mm-40) cc_final: 0.6829 (tm-30) REVERT: D 107 LYS cc_start: 0.8294 (mmtm) cc_final: 0.7870 (mtmt) REVERT: D 187 ASP cc_start: 0.9021 (OUTLIER) cc_final: 0.8712 (t70) REVERT: D 247 ARG cc_start: 0.7956 (mtp-110) cc_final: 0.7742 (ttt-90) REVERT: E 27 ARG cc_start: 0.8333 (mtp180) cc_final: 0.8081 (ttt-90) REVERT: E 68 GLU cc_start: 0.8129 (mp0) cc_final: 0.7578 (tp30) REVERT: E 107 LYS cc_start: 0.8016 (mmtm) cc_final: 0.7550 (mtmt) REVERT: E 211 MET cc_start: 0.9124 (mtt) cc_final: 0.8768 (mtt) REVERT: E 243 MET cc_start: 0.8713 (OUTLIER) cc_final: 0.8454 (mtt) REVERT: E 338 LYS cc_start: 0.7866 (tppp) cc_final: 0.6563 (mptt) REVERT: F 27 ARG cc_start: 0.8380 (mtp180) cc_final: 0.8097 (mmm160) REVERT: F 39 LYS cc_start: 0.7280 (mttt) cc_final: 0.6530 (mtmt) REVERT: F 43 GLU cc_start: 0.7926 (mt-10) cc_final: 0.7373 (mp0) REVERT: F 68 GLU cc_start: 0.7987 (mt-10) cc_final: 0.7633 (mp0) REVERT: F 80 LYS cc_start: 0.8264 (mtpt) cc_final: 0.7965 (mtmm) REVERT: F 95 ARG cc_start: 0.8142 (ttp80) cc_final: 0.7808 (ttp-110) REVERT: F 176 GLU cc_start: 0.8376 (mm-30) cc_final: 0.8170 (mm-30) REVERT: F 187 ASP cc_start: 0.8652 (m-30) cc_final: 0.8179 (m-30) REVERT: F 202 GLN cc_start: 0.8117 (mm-40) cc_final: 0.7749 (mt0) REVERT: G 39 LYS cc_start: 0.7704 (mttt) cc_final: 0.7378 (mtpp) REVERT: G 94 GLN cc_start: 0.7833 (OUTLIER) cc_final: 0.7528 (tp-100) REVERT: G 107 LYS cc_start: 0.7650 (mmtm) cc_final: 0.6713 (ttmt) REVERT: G 111 LYS cc_start: 0.8220 (ttpp) cc_final: 0.7839 (mtpp) REVERT: G 125 MET cc_start: 0.8980 (OUTLIER) cc_final: 0.8381 (mtm) REVERT: G 176 GLU cc_start: 0.8128 (mm-30) cc_final: 0.7799 (mm-30) REVERT: G 187 ASP cc_start: 0.8383 (m-30) cc_final: 0.8121 (m-30) REVERT: G 202 GLN cc_start: 0.8070 (mm-40) cc_final: 0.7836 (mt0) REVERT: G 247 ARG cc_start: 0.8169 (mtp-110) cc_final: 0.7924 (mtp85) REVERT: G 306 ARG cc_start: 0.7705 (ttm110) cc_final: 0.6983 (ttp80) REVERT: G 308 GLU cc_start: 0.8216 (pm20) cc_final: 0.7841 (pm20) REVERT: H 27 ARG cc_start: 0.7614 (mtp-110) cc_final: 0.7208 (tmt170) REVERT: H 39 LYS cc_start: 0.7607 (mttt) cc_final: 0.7303 (mtpm) REVERT: H 43 GLU cc_start: 0.8184 (mt-10) cc_final: 0.7958 (mt-10) REVERT: H 94 GLN cc_start: 0.8373 (mm-40) cc_final: 0.8047 (tp40) REVERT: H 206 GLN cc_start: 0.8648 (OUTLIER) cc_final: 0.8338 (mt0) REVERT: H 247 ARG cc_start: 0.7930 (mtp-110) cc_final: 0.7258 (mmm160) REVERT: H 254 ARG cc_start: 0.8065 (ttt-90) cc_final: 0.7709 (tmm-80) REVERT: I 37 ASP cc_start: 0.7871 (m-30) cc_final: 0.7554 (m-30) REVERT: I 39 LYS cc_start: 0.7833 (mttt) cc_final: 0.7494 (mmmm) REVERT: I 40 LYS cc_start: 0.7629 (mtpp) cc_final: 0.7222 (mttp) REVERT: I 43 GLU cc_start: 0.7636 (mt-10) cc_final: 0.7229 (tp30) REVERT: I 109 LEU cc_start: 0.8726 (OUTLIER) cc_final: 0.8352 (mp) REVERT: I 110 ASP cc_start: 0.8678 (m-30) cc_final: 0.8360 (m-30) REVERT: I 176 GLU cc_start: 0.7235 (mm-30) cc_final: 0.6961 (tm-30) REVERT: I 177 ARG cc_start: 0.8117 (OUTLIER) cc_final: 0.7372 (ttt90) REVERT: I 247 ARG cc_start: 0.7807 (mtp-110) cc_final: 0.7338 (mtp85) REVERT: J 39 LYS cc_start: 0.6668 (mttt) cc_final: 0.5922 (mmmt) REVERT: J 40 LYS cc_start: 0.6938 (mtpp) cc_final: 0.6073 (mttt) REVERT: J 42 GLU cc_start: 0.7056 (tp30) cc_final: 0.6443 (tt0) REVERT: J 43 GLU cc_start: 0.6863 (OUTLIER) cc_final: 0.6330 (pp20) REVERT: J 50 GLU cc_start: 0.7732 (mp0) cc_final: 0.7121 (mp0) REVERT: J 73 LYS cc_start: 0.6675 (mttt) cc_final: 0.6083 (tptt) REVERT: J 77 GLU cc_start: 0.7376 (OUTLIER) cc_final: 0.6817 (mp0) REVERT: J 95 ARG cc_start: 0.7951 (ttp-170) cc_final: 0.7678 (ttm110) REVERT: J 110 ASP cc_start: 0.7948 (m-30) cc_final: 0.7476 (m-30) REVERT: J 154 GLU cc_start: 0.8055 (mt-10) cc_final: 0.7596 (mm-30) REVERT: J 177 ARG cc_start: 0.8306 (OUTLIER) cc_final: 0.7573 (ttt180) REVERT: J 184 ASP cc_start: 0.8567 (m-30) cc_final: 0.8222 (m-30) REVERT: J 187 ASP cc_start: 0.8145 (OUTLIER) cc_final: 0.7422 (m-30) REVERT: J 299 ARG cc_start: 0.8578 (mtm180) cc_final: 0.8155 (mtt-85) REVERT: J 308 GLU cc_start: 0.7924 (pm20) cc_final: 0.6985 (mt-10) REVERT: J 332 ASP cc_start: 0.8561 (p0) cc_final: 0.8206 (p0) outliers start: 84 outliers final: 40 residues processed: 669 average time/residue: 1.4799 time to fit residues: 1129.2745 Evaluate side-chains 650 residues out of total 2607 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 594 time to evaluate : 2.851 ------------------------------------------------------------------------------- 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 128 GLU Chi-restraints excluded: chain A residue 206 GLN 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 113 LEU Chi-restraints excluded: chain B residue 215 ARG Chi-restraints excluded: chain B residue 272 GLN Chi-restraints excluded: chain C residue 251 MET Chi-restraints excluded: chain C residue 330 ASN Chi-restraints excluded: chain D residue 27 ARG Chi-restraints excluded: chain D residue 128 GLU Chi-restraints excluded: chain D residue 161 ASP 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 125 MET Chi-restraints excluded: chain E residue 161 ASP Chi-restraints excluded: chain E residue 243 MET 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 272 GLN Chi-restraints excluded: chain F residue 297 THR Chi-restraints excluded: chain G residue 26 SER 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 272 GLN Chi-restraints excluded: chain H residue 25 ILE Chi-restraints excluded: chain H residue 28 LEU Chi-restraints excluded: chain H residue 206 GLN 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 109 LEU Chi-restraints excluded: chain I residue 177 ARG 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 43 GLU Chi-restraints excluded: chain J residue 77 GLU Chi-restraints excluded: chain J residue 88 THR 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 300 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 323 random chunks: chunk 14 optimal weight: 5.9990 chunk 32 optimal weight: 8.9990 chunk 147 optimal weight: 4.9990 chunk 250 optimal weight: 2.9990 chunk 303 optimal weight: 1.9990 chunk 254 optimal weight: 0.8980 chunk 311 optimal weight: 4.9990 chunk 177 optimal weight: 2.9990 chunk 187 optimal weight: 9.9990 chunk 195 optimal weight: 0.6980 chunk 28 optimal weight: 5.9990 overall best weight: 1.9186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 272 GLN B 135 GLN ** D 145 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 145 GLN F 200 GLN H 34 ASN I 135 GLN J 135 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3647 r_free = 0.3647 target = 0.145308 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3249 r_free = 0.3249 target = 0.111059 restraints weight = 32169.547| |-----------------------------------------------------------------------------| r_work (start): 0.3201 rms_B_bonded: 2.00 r_work: 0.3080 rms_B_bonded: 2.65 restraints_weight: 0.5000 r_work: 0.2951 rms_B_bonded: 4.34 restraints_weight: 0.2500 r_work (final): 0.2951 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7999 moved from start: 0.3322 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 26875 Z= 0.180 Angle : 0.505 8.151 36550 Z= 0.266 Chirality : 0.040 0.142 4139 Planarity : 0.003 0.039 4521 Dihedral : 13.609 143.195 4454 Min Nonbonded Distance : 2.216 Molprobity Statistics. All-atom Clashscore : 6.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.03 % Favored : 97.97 % Rotamer: Outliers : 3.99 % Allowed : 23.21 % Favored : 72.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.32 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.12 (0.14), residues: 3196 helix: 0.95 (0.14), residues: 1380 sheet: 0.02 (0.27), residues: 380 loop : -1.12 (0.15), residues: 1436 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.006 0.001 HIS E 294 PHE 0.012 0.001 PHE F 126 TYR 0.013 0.001 TYR G 315 ARG 0.010 0.001 ARG D 215 Details of bonding type rmsd hydrogen bonds : bond 0.03617 ( 1159) hydrogen bonds : angle 4.25921 ( 3100) covalent geometry : bond 0.00412 (26875) covalent geometry : angle 0.50530 (36550) *********************** 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 713 residues out of total 2607 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 104 poor density : 609 time to evaluate : 2.757 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 37 ASP cc_start: 0.7725 (m-30) cc_final: 0.7357 (m-30) REVERT: A 40 LYS cc_start: 0.7286 (mtpp) cc_final: 0.6194 (mtpt) REVERT: A 42 GLU cc_start: 0.6735 (pt0) cc_final: 0.6521 (pt0) REVERT: A 66 ILE cc_start: 0.7117 (OUTLIER) cc_final: 0.6755 (tt) REVERT: A 68 GLU cc_start: 0.6773 (mt-10) cc_final: 0.6165 (tm-30) REVERT: A 98 GLU cc_start: 0.7684 (mt-10) cc_final: 0.7458 (mm-30) REVERT: A 107 LYS cc_start: 0.7190 (mmtm) cc_final: 0.6956 (tptt) REVERT: A 186 LEU cc_start: 0.8245 (mm) cc_final: 0.7989 (mm) REVERT: A 206 GLN cc_start: 0.7414 (OUTLIER) cc_final: 0.6827 (mt0) REVERT: A 210 MET cc_start: 0.8147 (mtp) cc_final: 0.7453 (mtp) REVERT: A 251 MET cc_start: 0.7783 (mtp) cc_final: 0.7468 (mtp) REVERT: A 254 ARG cc_start: 0.7376 (ttp80) cc_final: 0.7021 (tmt90) REVERT: A 303 ARG cc_start: 0.7442 (mtp180) cc_final: 0.6962 (mtm180) REVERT: A 308 GLU cc_start: 0.7312 (pt0) cc_final: 0.6562 (tt0) REVERT: A 329 ILE cc_start: 0.8678 (mt) cc_final: 0.8247 (mt) REVERT: B 42 GLU cc_start: 0.7282 (mt-10) cc_final: 0.6756 (mt-10) REVERT: B 43 GLU cc_start: 0.7540 (mt-10) cc_final: 0.7183 (mt-10) REVERT: B 50 GLU cc_start: 0.8321 (OUTLIER) cc_final: 0.7359 (mp0) REVERT: B 72 ASP cc_start: 0.7594 (m-30) cc_final: 0.7336 (m-30) REVERT: B 95 ARG cc_start: 0.7931 (ttp80) cc_final: 0.7505 (ttt-90) REVERT: B 107 LYS cc_start: 0.7755 (mmtm) cc_final: 0.6866 (ptpt) REVERT: B 145 GLN cc_start: 0.8300 (mt0) cc_final: 0.8091 (mp10) REVERT: B 215 ARG cc_start: 0.8160 (OUTLIER) cc_final: 0.7922 (tpt-90) REVERT: B 332 ASP cc_start: 0.8785 (p0) cc_final: 0.8381 (p0) REVERT: C 33 ILE cc_start: 0.8579 (mm) cc_final: 0.8344 (mm) REVERT: C 94 GLN cc_start: 0.7798 (mm-40) cc_final: 0.7025 (tm-30) REVERT: C 95 ARG cc_start: 0.8208 (ttp80) cc_final: 0.7610 (ttp-170) REVERT: C 107 LYS cc_start: 0.8197 (mmtm) cc_final: 0.7516 (ptpp) REVERT: C 145 GLN cc_start: 0.8603 (mp10) cc_final: 0.7821 (mp10) REVERT: C 154 GLU cc_start: 0.7506 (mt-10) cc_final: 0.6730 (mt-10) REVERT: C 181 SER cc_start: 0.8683 (t) cc_final: 0.8227 (p) REVERT: C 187 ASP cc_start: 0.8676 (OUTLIER) cc_final: 0.8474 (m-30) REVERT: C 202 GLN cc_start: 0.7755 (mm-40) cc_final: 0.7440 (mt0) REVERT: C 216 TYR cc_start: 0.9015 (m-80) cc_final: 0.8804 (m-80) REVERT: C 222 ASP cc_start: 0.8949 (t70) cc_final: 0.8605 (t70) REVERT: D 27 ARG cc_start: 0.8382 (OUTLIER) cc_final: 0.7698 (mtp180) REVERT: D 29 GLU cc_start: 0.7333 (mm-30) cc_final: 0.7031 (mm-30) REVERT: D 37 ASP cc_start: 0.7290 (m-30) cc_final: 0.6984 (m-30) REVERT: D 94 GLN cc_start: 0.7716 (mm-40) cc_final: 0.6886 (tm-30) REVERT: D 107 LYS cc_start: 0.8321 (mmtm) cc_final: 0.7884 (mtmt) REVERT: D 187 ASP cc_start: 0.9024 (OUTLIER) cc_final: 0.8635 (t70) REVERT: D 215 ARG cc_start: 0.8201 (ttt90) cc_final: 0.7961 (tpt-90) REVERT: D 247 ARG cc_start: 0.7997 (mtp-110) cc_final: 0.7759 (ttt-90) REVERT: E 68 GLU cc_start: 0.8148 (mp0) cc_final: 0.7619 (tp30) REVERT: E 107 LYS cc_start: 0.8030 (mmtm) cc_final: 0.7595 (mtmt) REVERT: E 145 GLN cc_start: 0.8979 (OUTLIER) cc_final: 0.8562 (mp10) REVERT: E 176 GLU cc_start: 0.8351 (mm-30) cc_final: 0.7787 (tt0) REVERT: E 211 MET cc_start: 0.9158 (mtt) cc_final: 0.8879 (mtt) REVERT: E 215 ARG cc_start: 0.8136 (tpt-90) cc_final: 0.7898 (tmt90) REVERT: E 243 MET cc_start: 0.8742 (OUTLIER) cc_final: 0.8510 (mtt) REVERT: F 39 LYS cc_start: 0.7316 (mttt) cc_final: 0.6595 (mtmt) REVERT: F 43 GLU cc_start: 0.7974 (mt-10) cc_final: 0.7379 (mp0) REVERT: F 68 GLU cc_start: 0.8163 (mt-10) cc_final: 0.7655 (mp0) REVERT: F 95 ARG cc_start: 0.8164 (ttp80) cc_final: 0.7828 (ttp-110) REVERT: F 158 MET cc_start: 0.8796 (ttm) cc_final: 0.8513 (ttm) REVERT: F 202 GLN cc_start: 0.8182 (mm-40) cc_final: 0.7727 (mt0) REVERT: F 206 GLN cc_start: 0.8671 (OUTLIER) cc_final: 0.7865 (mt0) REVERT: G 39 LYS cc_start: 0.7689 (mttt) cc_final: 0.7330 (mtpp) REVERT: G 94 GLN cc_start: 0.7861 (OUTLIER) cc_final: 0.7552 (tp-100) REVERT: G 107 LYS cc_start: 0.7683 (mmtm) cc_final: 0.6758 (ttmt) REVERT: G 111 LYS cc_start: 0.8293 (ttpp) cc_final: 0.8008 (mtpp) REVERT: G 176 GLU cc_start: 0.8159 (mm-30) cc_final: 0.7794 (mm-30) REVERT: G 187 ASP cc_start: 0.8343 (m-30) cc_final: 0.8101 (m-30) REVERT: G 202 GLN cc_start: 0.8047 (mm-40) cc_final: 0.7806 (mt0) REVERT: G 247 ARG cc_start: 0.8235 (mtp-110) cc_final: 0.8001 (mtp85) REVERT: G 306 ARG cc_start: 0.7721 (ttm110) cc_final: 0.6990 (ttp80) REVERT: G 308 GLU cc_start: 0.8198 (pm20) cc_final: 0.7833 (pm20) REVERT: H 27 ARG cc_start: 0.7669 (mtp-110) cc_final: 0.7119 (tmt170) REVERT: H 39 LYS cc_start: 0.7681 (mttt) cc_final: 0.7285 (mtmm) REVERT: H 43 GLU cc_start: 0.8196 (mt-10) cc_final: 0.7977 (mt-10) REVERT: H 94 GLN cc_start: 0.8393 (mm-40) cc_final: 0.8035 (tp40) REVERT: H 206 GLN cc_start: 0.8613 (OUTLIER) cc_final: 0.8149 (mt0) REVERT: H 247 ARG cc_start: 0.7971 (mtp-110) cc_final: 0.7313 (mmm160) REVERT: H 254 ARG cc_start: 0.8073 (ttt-90) cc_final: 0.7654 (tmm-80) REVERT: H 257 ASP cc_start: 0.8559 (m-30) cc_final: 0.8195 (m-30) REVERT: I 27 ARG cc_start: 0.7651 (OUTLIER) cc_final: 0.7281 (tmt-80) REVERT: I 39 LYS cc_start: 0.7930 (mttt) cc_final: 0.7601 (mmmm) REVERT: I 40 LYS cc_start: 0.7676 (mtpp) cc_final: 0.7289 (mttp) REVERT: I 43 GLU cc_start: 0.7624 (mt-10) cc_final: 0.7248 (tp30) REVERT: I 75 LEU cc_start: 0.8223 (OUTLIER) cc_final: 0.7808 (mt) REVERT: I 109 LEU cc_start: 0.8682 (OUTLIER) cc_final: 0.8287 (mp) REVERT: I 176 GLU cc_start: 0.7271 (mm-30) cc_final: 0.7003 (tm-30) REVERT: J 39 LYS cc_start: 0.6707 (mttt) cc_final: 0.5961 (mmmt) REVERT: J 40 LYS cc_start: 0.6972 (mtpp) cc_final: 0.6130 (mttt) REVERT: J 42 GLU cc_start: 0.7131 (tp30) cc_final: 0.6516 (tt0) REVERT: J 43 GLU cc_start: 0.6893 (OUTLIER) cc_final: 0.6287 (pp20) REVERT: J 50 GLU cc_start: 0.7890 (mp0) cc_final: 0.7036 (mp0) REVERT: J 73 LYS cc_start: 0.6598 (mttt) cc_final: 0.5998 (tptt) REVERT: J 77 GLU cc_start: 0.7407 (OUTLIER) cc_final: 0.6679 (mp0) REVERT: J 80 LYS cc_start: 0.7755 (OUTLIER) cc_final: 0.7490 (ttmm) REVERT: J 95 ARG cc_start: 0.7957 (ttp-170) cc_final: 0.7691 (ttm110) REVERT: J 110 ASP cc_start: 0.8216 (m-30) cc_final: 0.7882 (m-30) REVERT: J 177 ARG cc_start: 0.8288 (OUTLIER) cc_final: 0.7554 (ttt180) REVERT: J 184 ASP cc_start: 0.8532 (m-30) cc_final: 0.8124 (m-30) REVERT: J 187 ASP cc_start: 0.8300 (OUTLIER) cc_final: 0.7619 (m-30) REVERT: J 299 ARG cc_start: 0.8633 (mtm180) cc_final: 0.8142 (mtt-85) REVERT: J 308 GLU cc_start: 0.7903 (pm20) cc_final: 0.6931 (mt-10) REVERT: J 332 ASP cc_start: 0.8592 (p0) cc_final: 0.8111 (p0) outliers start: 104 outliers final: 55 residues processed: 659 average time/residue: 1.5328 time to fit residues: 1154.7511 Evaluate side-chains 652 residues out of total 2607 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 75 poor density : 577 time to evaluate : 3.093 ------------------------------------------------------------------------------- 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 87 THR Chi-restraints excluded: chain A residue 88 THR Chi-restraints excluded: chain A residue 99 ILE Chi-restraints excluded: chain A residue 206 GLN Chi-restraints excluded: chain A residue 208 SER Chi-restraints excluded: chain B residue 31 CYS Chi-restraints excluded: chain B residue 50 GLU Chi-restraints excluded: chain B residue 82 VAL Chi-restraints excluded: chain B residue 113 LEU Chi-restraints excluded: chain B residue 215 ARG Chi-restraints excluded: chain C residue 31 CYS Chi-restraints excluded: chain C residue 81 LEU 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 121 SER Chi-restraints excluded: chain D residue 161 ASP Chi-restraints excluded: chain D residue 187 ASP Chi-restraints excluded: chain D residue 231 ASP Chi-restraints excluded: chain D residue 330 ASN Chi-restraints excluded: chain D residue 334 VAL 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 161 ASP 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 26 SER 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 161 ASP Chi-restraints excluded: chain G residue 272 GLN Chi-restraints excluded: chain H residue 25 ILE Chi-restraints excluded: chain H residue 28 LEU 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 75 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 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 80 LYS Chi-restraints excluded: chain J residue 88 THR 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 239 SER Chi-restraints excluded: chain J residue 300 LEU Chi-restraints excluded: chain J residue 322 GLU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 323 random chunks: chunk 292 optimal weight: 4.9990 chunk 190 optimal weight: 0.0970 chunk 187 optimal weight: 8.9990 chunk 75 optimal weight: 4.9990 chunk 297 optimal weight: 1.9990 chunk 208 optimal weight: 0.5980 chunk 243 optimal weight: 2.9990 chunk 138 optimal weight: 4.9990 chunk 257 optimal weight: 3.9990 chunk 181 optimal weight: 3.9990 chunk 179 optimal weight: 7.9990 overall best weight: 1.9384 ------------------------------------------------------------------------------- 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** F 200 GLN H 34 ASN H 290 ASN J 135 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3647 r_free = 0.3647 target = 0.145241 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3251 r_free = 0.3251 target = 0.111072 restraints weight = 32185.835| |-----------------------------------------------------------------------------| r_work (start): 0.3202 rms_B_bonded: 1.99 r_work: 0.3080 rms_B_bonded: 2.65 restraints_weight: 0.5000 r_work: 0.2952 rms_B_bonded: 4.34 restraints_weight: 0.2500 r_work (final): 0.2952 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8034 moved from start: 0.3391 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 26875 Z= 0.180 Angle : 0.505 8.336 36550 Z= 0.266 Chirality : 0.040 0.145 4139 Planarity : 0.003 0.040 4521 Dihedral : 13.641 143.370 4454 Min Nonbonded Distance : 2.216 Molprobity Statistics. All-atom Clashscore : 6.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.19 % Favored : 97.81 % Rotamer: Outliers : 4.45 % Allowed : 23.09 % Favored : 72.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.32 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.02 (0.14), residues: 3196 helix: 1.01 (0.14), residues: 1380 sheet: 0.13 (0.27), residues: 380 loop : -1.05 (0.15), residues: 1436 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.006 0.001 HIS E 294 PHE 0.013 0.001 PHE F 126 TYR 0.013 0.001 TYR G 315 ARG 0.009 0.001 ARG D 215 Details of bonding type rmsd hydrogen bonds : bond 0.03585 ( 1159) hydrogen bonds : angle 4.28357 ( 3100) covalent geometry : bond 0.00413 (26875) covalent geometry : angle 0.50517 (36550) *********************** 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 711 residues out of total 2607 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 116 poor density : 595 time to evaluate : 2.918 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 33 ILE cc_start: 0.7860 (mm) cc_final: 0.7235 (mp) REVERT: A 37 ASP cc_start: 0.7518 (m-30) cc_final: 0.7260 (m-30) REVERT: A 40 LYS cc_start: 0.7343 (mtpp) cc_final: 0.6282 (mtpt) REVERT: A 42 GLU cc_start: 0.6775 (pt0) cc_final: 0.6554 (pt0) REVERT: A 68 GLU cc_start: 0.6778 (mt-10) cc_final: 0.6197 (tm-30) REVERT: A 70 LYS cc_start: 0.7109 (ttpt) cc_final: 0.6805 (ttpt) REVERT: A 107 LYS cc_start: 0.7166 (mmtm) cc_final: 0.6933 (tptt) REVERT: A 186 LEU cc_start: 0.8300 (OUTLIER) cc_final: 0.8038 (mm) REVERT: A 210 MET cc_start: 0.8176 (mtp) cc_final: 0.7307 (mtp) REVERT: A 251 MET cc_start: 0.7763 (mtp) cc_final: 0.7402 (mtp) REVERT: A 254 ARG cc_start: 0.7422 (ttp80) cc_final: 0.7051 (tmt90) REVERT: A 303 ARG cc_start: 0.7423 (mtp180) cc_final: 0.6916 (mtm180) REVERT: A 308 GLU cc_start: 0.7317 (pt0) cc_final: 0.6555 (tt0) REVERT: A 329 ILE cc_start: 0.8691 (mt) cc_final: 0.8202 (mt) REVERT: B 40 LYS cc_start: 0.7009 (mtpp) cc_final: 0.5804 (mtpt) REVERT: B 42 GLU cc_start: 0.7168 (mt-10) cc_final: 0.6659 (mt-10) REVERT: B 43 GLU cc_start: 0.7562 (mt-10) cc_final: 0.7203 (mt-10) REVERT: B 50 GLU cc_start: 0.8335 (OUTLIER) cc_final: 0.7403 (mp0) REVERT: B 72 ASP cc_start: 0.7608 (m-30) cc_final: 0.7322 (m-30) REVERT: B 88 THR cc_start: 0.9097 (OUTLIER) cc_final: 0.8797 (p) REVERT: B 95 ARG cc_start: 0.7929 (ttp80) cc_final: 0.7501 (ttt-90) REVERT: B 107 LYS cc_start: 0.7763 (mmtm) cc_final: 0.6869 (ptpt) REVERT: B 206 GLN cc_start: 0.7694 (mt0) cc_final: 0.7375 (mt0) REVERT: B 215 ARG cc_start: 0.8274 (OUTLIER) cc_final: 0.8033 (tpt-90) REVERT: B 332 ASP cc_start: 0.8813 (p0) cc_final: 0.8390 (p0) REVERT: C 33 ILE cc_start: 0.8610 (mm) cc_final: 0.8370 (mm) REVERT: C 94 GLN cc_start: 0.7826 (mm-40) cc_final: 0.7106 (tm-30) REVERT: C 95 ARG cc_start: 0.8235 (ttp80) cc_final: 0.7571 (ttp-170) REVERT: C 107 LYS cc_start: 0.8270 (mmtm) cc_final: 0.7609 (ptmt) REVERT: C 145 GLN cc_start: 0.8701 (mp10) cc_final: 0.8162 (mp10) REVERT: C 154 GLU cc_start: 0.7589 (mt-10) cc_final: 0.6784 (mt-10) REVERT: C 181 SER cc_start: 0.8686 (t) cc_final: 0.8222 (p) REVERT: C 187 ASP cc_start: 0.8677 (OUTLIER) cc_final: 0.8472 (m-30) REVERT: C 202 GLN cc_start: 0.7762 (mm-40) cc_final: 0.7456 (mt0) REVERT: C 215 ARG cc_start: 0.8501 (tpt-90) cc_final: 0.8278 (tpt-90) REVERT: C 222 ASP cc_start: 0.8958 (OUTLIER) cc_final: 0.8603 (t70) REVERT: D 27 ARG cc_start: 0.8398 (OUTLIER) cc_final: 0.7753 (mtp180) REVERT: D 37 ASP cc_start: 0.7353 (m-30) cc_final: 0.7044 (m-30) REVERT: D 42 GLU cc_start: 0.7887 (mm-30) cc_final: 0.7661 (mm-30) REVERT: D 94 GLN cc_start: 0.7712 (mm-40) cc_final: 0.6883 (tm-30) REVERT: D 107 LYS cc_start: 0.8329 (mmtm) cc_final: 0.7934 (mtmt) REVERT: D 187 ASP cc_start: 0.9056 (OUTLIER) cc_final: 0.8680 (t70) REVERT: D 215 ARG cc_start: 0.8162 (ttt90) cc_final: 0.7954 (tpt-90) REVERT: E 27 ARG cc_start: 0.8428 (mtp180) cc_final: 0.8095 (ttt-90) REVERT: E 68 GLU cc_start: 0.8123 (mp0) cc_final: 0.7666 (tp30) REVERT: E 107 LYS cc_start: 0.8003 (mmtm) cc_final: 0.7598 (mtmt) REVERT: E 176 GLU cc_start: 0.8367 (mm-30) cc_final: 0.7828 (tt0) REVERT: E 211 MET cc_start: 0.9155 (mtt) cc_final: 0.8888 (mtt) REVERT: E 215 ARG cc_start: 0.8178 (tpt-90) cc_final: 0.7918 (tmt90) REVERT: E 243 MET cc_start: 0.8771 (OUTLIER) cc_final: 0.8546 (mtt) REVERT: E 338 LYS cc_start: 0.7900 (tppp) cc_final: 0.6525 (mptt) REVERT: F 39 LYS cc_start: 0.7404 (mttt) cc_final: 0.6628 (mtmt) REVERT: F 43 GLU cc_start: 0.7980 (mt-10) cc_final: 0.7422 (mp0) REVERT: F 68 GLU cc_start: 0.8232 (mt-10) cc_final: 0.7679 (mp0) REVERT: F 95 ARG cc_start: 0.8187 (ttp80) cc_final: 0.7854 (ttp-110) REVERT: F 158 MET cc_start: 0.8839 (ttm) cc_final: 0.8355 (ttp) REVERT: F 202 GLN cc_start: 0.8209 (mm-40) cc_final: 0.7757 (mt0) REVERT: F 206 GLN cc_start: 0.8676 (OUTLIER) cc_final: 0.7846 (mt0) REVERT: G 39 LYS cc_start: 0.7660 (mttt) cc_final: 0.7271 (mtpp) REVERT: G 91 GLU cc_start: 0.8083 (OUTLIER) cc_final: 0.7618 (tt0) REVERT: G 94 GLN cc_start: 0.7879 (OUTLIER) cc_final: 0.7571 (tp-100) REVERT: G 107 LYS cc_start: 0.7930 (mmtm) cc_final: 0.6947 (ttmt) REVERT: G 111 LYS cc_start: 0.8308 (ttpp) cc_final: 0.8059 (mtpp) REVERT: G 150 ARG cc_start: 0.8006 (mtp85) cc_final: 0.7768 (mtp180) REVERT: G 176 GLU cc_start: 0.8240 (mm-30) cc_final: 0.7909 (mm-30) REVERT: G 187 ASP cc_start: 0.8323 (m-30) cc_final: 0.8105 (m-30) REVERT: G 202 GLN cc_start: 0.8074 (mm-40) cc_final: 0.7835 (mt0) REVERT: G 247 ARG cc_start: 0.8235 (mtp-110) cc_final: 0.8005 (mtp85) REVERT: G 306 ARG cc_start: 0.7732 (ttm110) cc_final: 0.6993 (ttp80) REVERT: G 308 GLU cc_start: 0.8199 (pm20) cc_final: 0.7862 (pm20) REVERT: H 27 ARG cc_start: 0.7617 (mtp-110) cc_final: 0.7301 (tmt170) REVERT: H 39 LYS cc_start: 0.7717 (mttt) cc_final: 0.7316 (mtmm) REVERT: H 247 ARG cc_start: 0.8008 (mtp-110) cc_final: 0.7357 (mmm160) REVERT: H 254 ARG cc_start: 0.8115 (ttt-90) cc_final: 0.7741 (tmm-80) REVERT: H 257 ASP cc_start: 0.8568 (m-30) cc_final: 0.8150 (m-30) REVERT: I 27 ARG cc_start: 0.7976 (OUTLIER) cc_final: 0.7592 (tmt-80) REVERT: I 39 LYS cc_start: 0.7933 (mttt) cc_final: 0.7609 (mmmm) REVERT: I 40 LYS cc_start: 0.7709 (mtpp) cc_final: 0.7286 (mttp) REVERT: I 43 GLU cc_start: 0.7642 (mt-10) cc_final: 0.7263 (tp30) REVERT: I 80 LYS cc_start: 0.8002 (ttmp) cc_final: 0.7721 (mtmt) REVERT: I 176 GLU cc_start: 0.7277 (mm-30) cc_final: 0.7023 (tm-30) REVERT: J 39 LYS cc_start: 0.6901 (mttt) cc_final: 0.6215 (mmmt) REVERT: J 40 LYS cc_start: 0.7032 (mtpp) cc_final: 0.6154 (mttt) REVERT: J 42 GLU cc_start: 0.7155 (tp30) cc_final: 0.6535 (tt0) REVERT: J 43 GLU cc_start: 0.6949 (OUTLIER) cc_final: 0.6344 (pp20) REVERT: J 50 GLU cc_start: 0.7918 (mp0) cc_final: 0.7130 (mp0) REVERT: J 73 LYS cc_start: 0.6597 (mttt) cc_final: 0.6178 (tptt) REVERT: J 77 GLU cc_start: 0.7411 (OUTLIER) cc_final: 0.6938 (mp0) REVERT: J 80 LYS cc_start: 0.7776 (OUTLIER) cc_final: 0.7503 (ttmm) REVERT: J 95 ARG cc_start: 0.7984 (ttp-170) cc_final: 0.7705 (ttm110) REVERT: J 110 ASP cc_start: 0.8231 (m-30) cc_final: 0.7904 (m-30) REVERT: J 177 ARG cc_start: 0.8285 (OUTLIER) cc_final: 0.7560 (ttt180) REVERT: J 184 ASP cc_start: 0.8519 (m-30) cc_final: 0.8011 (m-30) REVERT: J 187 ASP cc_start: 0.8342 (OUTLIER) cc_final: 0.7669 (m-30) REVERT: J 222 ASP cc_start: 0.8671 (OUTLIER) cc_final: 0.8376 (t0) REVERT: J 299 ARG cc_start: 0.8677 (mtm180) cc_final: 0.8465 (mtp180) REVERT: J 308 GLU cc_start: 0.7956 (pm20) cc_final: 0.6957 (mt-10) REVERT: J 332 ASP cc_start: 0.8578 (p0) cc_final: 0.8063 (p0) outliers start: 116 outliers final: 67 residues processed: 654 average time/residue: 1.5359 time to fit residues: 1146.1985 Evaluate side-chains 668 residues out of total 2607 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 86 poor density : 582 time to evaluate : 2.894 ------------------------------------------------------------------------------- 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 87 THR Chi-restraints excluded: chain A residue 88 THR Chi-restraints excluded: chain A residue 99 ILE Chi-restraints excluded: chain A residue 128 GLU Chi-restraints excluded: chain A residue 186 LEU Chi-restraints excluded: chain B residue 23 GLN Chi-restraints excluded: chain B residue 31 CYS Chi-restraints excluded: chain B residue 50 GLU 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 215 ARG Chi-restraints excluded: chain B residue 223 SER Chi-restraints excluded: chain C residue 31 CYS Chi-restraints excluded: chain C residue 104 THR Chi-restraints excluded: chain C residue 128 GLU Chi-restraints excluded: chain C residue 187 ASP Chi-restraints excluded: chain C residue 222 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 121 SER Chi-restraints excluded: chain D residue 158 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 231 ASP Chi-restraints excluded: chain D residue 274 ASP Chi-restraints excluded: chain D residue 330 ASN Chi-restraints excluded: chain D residue 334 VAL 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 149 ASP 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 F residue 319 CYS Chi-restraints excluded: chain G residue 26 SER 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 272 GLN Chi-restraints excluded: chain H residue 25 ILE Chi-restraints excluded: chain H residue 28 LEU Chi-restraints excluded: chain H residue 68 GLU Chi-restraints excluded: chain H residue 142 VAL 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 81 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 121 SER Chi-restraints excluded: chain I residue 201 THR Chi-restraints excluded: chain I residue 212 VAL Chi-restraints excluded: chain I residue 322 GLU 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 80 LYS 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 300 LEU Chi-restraints excluded: chain J residue 322 GLU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 323 random chunks: chunk 291 optimal weight: 4.9990 chunk 308 optimal weight: 5.9990 chunk 189 optimal weight: 2.9990 chunk 141 optimal weight: 0.9990 chunk 86 optimal weight: 2.9990 chunk 57 optimal weight: 0.6980 chunk 157 optimal weight: 3.9990 chunk 242 optimal weight: 0.2980 chunk 3 optimal weight: 2.9990 chunk 162 optimal weight: 6.9990 chunk 102 optimal weight: 0.9980 overall best weight: 1.1984 ------------------------------------------------------------------------------- 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 ** both conformations clash, **PLEASE CHECK MANUALLY** F 200 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: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3666 r_free = 0.3666 target = 0.147029 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3276 r_free = 0.3276 target = 0.113008 restraints weight = 32085.477| |-----------------------------------------------------------------------------| r_work (start): 0.3270 rms_B_bonded: 2.00 r_work: 0.3151 rms_B_bonded: 2.66 restraints_weight: 0.5000 r_work: 0.3022 rms_B_bonded: 4.37 restraints_weight: 0.2500 r_work (final): 0.3022 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8027 moved from start: 0.3523 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 26875 Z= 0.135 Angle : 0.480 7.827 36550 Z= 0.253 Chirality : 0.039 0.142 4139 Planarity : 0.003 0.039 4521 Dihedral : 13.612 143.216 4454 Min Nonbonded Distance : 2.238 Molprobity Statistics. All-atom Clashscore : 6.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.97 % Favored : 98.03 % Rotamer: Outliers : 3.84 % Allowed : 24.17 % Favored : 72.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.32 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.17 (0.15), residues: 3196 helix: 1.11 (0.14), residues: 1390 sheet: 0.22 (0.27), residues: 380 loop : -0.88 (0.15), residues: 1426 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.005 0.001 HIS E 294 PHE 0.021 0.001 PHE J 259 TYR 0.012 0.001 TYR G 315 ARG 0.010 0.001 ARG B 130 Details of bonding type rmsd hydrogen bonds : bond 0.03201 ( 1159) hydrogen bonds : angle 4.18028 ( 3100) covalent geometry : bond 0.00304 (26875) covalent geometry : angle 0.47974 (36550) *********************** 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 708 residues out of total 2607 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 100 poor density : 608 time to evaluate : 2.915 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 37 ASP cc_start: 0.7259 (m-30) cc_final: 0.6755 (m-30) REVERT: A 40 LYS cc_start: 0.7427 (mtpp) cc_final: 0.6109 (mppt) REVERT: A 42 GLU cc_start: 0.6778 (pt0) cc_final: 0.6564 (pt0) REVERT: A 68 GLU cc_start: 0.6784 (mt-10) cc_final: 0.6090 (tm-30) REVERT: A 70 LYS cc_start: 0.7022 (ttpt) cc_final: 0.6653 (ttpt) REVERT: A 107 LYS cc_start: 0.7264 (mmtm) cc_final: 0.6946 (tptt) REVERT: A 186 LEU cc_start: 0.8278 (OUTLIER) cc_final: 0.8009 (mm) REVERT: A 210 MET cc_start: 0.8208 (mtp) cc_final: 0.7371 (mtp) REVERT: A 251 MET cc_start: 0.7781 (mtp) cc_final: 0.7403 (mtp) REVERT: A 254 ARG cc_start: 0.7416 (ttp80) cc_final: 0.7115 (tmt90) REVERT: A 303 ARG cc_start: 0.7421 (mtp180) cc_final: 0.6901 (mtm180) REVERT: A 308 GLU cc_start: 0.7281 (pt0) cc_final: 0.6545 (tt0) REVERT: A 329 ILE cc_start: 0.8600 (mt) cc_final: 0.8190 (mt) REVERT: B 40 LYS cc_start: 0.6985 (mtpp) cc_final: 0.5789 (mtpt) REVERT: B 42 GLU cc_start: 0.7108 (mt-10) cc_final: 0.6542 (mt-10) REVERT: B 43 GLU cc_start: 0.7605 (mt-10) cc_final: 0.7251 (mt-10) REVERT: B 72 ASP cc_start: 0.7584 (m-30) cc_final: 0.7364 (m-30) REVERT: B 88 THR cc_start: 0.9102 (OUTLIER) cc_final: 0.8815 (p) REVERT: B 95 ARG cc_start: 0.7936 (ttp80) cc_final: 0.7557 (ttt-90) REVERT: B 100 ILE cc_start: 0.9162 (mp) cc_final: 0.8906 (pp) REVERT: B 107 LYS cc_start: 0.7808 (mmtm) cc_final: 0.6909 (ptpt) REVERT: B 145 GLN cc_start: 0.8225 (mp10) cc_final: 0.7972 (mp10) REVERT: B 206 GLN cc_start: 0.7652 (mt0) cc_final: 0.7389 (mt0) REVERT: B 215 ARG cc_start: 0.8255 (OUTLIER) cc_final: 0.8018 (tpt-90) REVERT: B 332 ASP cc_start: 0.8848 (p0) cc_final: 0.8484 (p0) REVERT: C 33 ILE cc_start: 0.8573 (mm) cc_final: 0.8350 (mm) REVERT: C 88 THR cc_start: 0.9121 (p) cc_final: 0.8912 (p) REVERT: C 94 GLN cc_start: 0.7799 (mm-40) cc_final: 0.7010 (tm-30) REVERT: C 95 ARG cc_start: 0.8121 (ttp80) cc_final: 0.7446 (ttp-170) REVERT: C 107 LYS cc_start: 0.8320 (mmtm) cc_final: 0.7643 (ptmt) REVERT: C 145 GLN cc_start: 0.8646 (mp10) cc_final: 0.8097 (mp10) REVERT: C 154 GLU cc_start: 0.7606 (mt-10) cc_final: 0.6886 (mt-10) REVERT: C 181 SER cc_start: 0.8681 (t) cc_final: 0.8216 (p) REVERT: C 202 GLN cc_start: 0.7714 (mm-40) cc_final: 0.7432 (mt0) REVERT: C 222 ASP cc_start: 0.8945 (OUTLIER) cc_final: 0.8528 (t70) REVERT: C 251 MET cc_start: 0.7878 (OUTLIER) cc_final: 0.7349 (mpt) REVERT: D 27 ARG cc_start: 0.8379 (OUTLIER) cc_final: 0.7613 (mtp180) REVERT: D 37 ASP cc_start: 0.7287 (m-30) cc_final: 0.6993 (m-30) REVERT: D 42 GLU cc_start: 0.7914 (mm-30) cc_final: 0.7683 (mm-30) REVERT: D 94 GLN cc_start: 0.7715 (mm-40) cc_final: 0.6900 (tm-30) REVERT: D 107 LYS cc_start: 0.8330 (mmtm) cc_final: 0.7936 (mtmt) REVERT: D 187 ASP cc_start: 0.9054 (OUTLIER) cc_final: 0.8701 (t70) REVERT: E 27 ARG cc_start: 0.8424 (mtp180) cc_final: 0.8129 (ttt-90) REVERT: E 57 LYS cc_start: 0.8290 (tttp) cc_final: 0.7813 (tttt) REVERT: E 68 GLU cc_start: 0.7996 (mp0) cc_final: 0.7552 (tp30) REVERT: E 107 LYS cc_start: 0.8000 (mmtm) cc_final: 0.7598 (mtmt) REVERT: E 176 GLU cc_start: 0.8333 (mm-30) cc_final: 0.7805 (tt0) REVERT: E 211 MET cc_start: 0.9122 (mtt) cc_final: 0.8855 (mtt) REVERT: E 215 ARG cc_start: 0.8098 (tpt-90) cc_final: 0.7838 (tmt90) REVERT: E 306 ARG cc_start: 0.7728 (ttp-110) cc_final: 0.7395 (tmm160) REVERT: E 338 LYS cc_start: 0.7903 (tppp) cc_final: 0.6521 (mptt) REVERT: F 39 LYS cc_start: 0.7389 (mttt) cc_final: 0.6628 (mtmt) REVERT: F 43 GLU cc_start: 0.7927 (mt-10) cc_final: 0.7395 (mp0) REVERT: F 68 GLU cc_start: 0.8208 (mt-10) cc_final: 0.7629 (mp0) REVERT: F 158 MET cc_start: 0.8795 (ttm) cc_final: 0.8327 (ttp) REVERT: F 176 GLU cc_start: 0.8401 (mm-30) cc_final: 0.8186 (mm-30) REVERT: F 202 GLN cc_start: 0.8185 (mm-40) cc_final: 0.7740 (mt0) REVERT: F 206 GLN cc_start: 0.8693 (OUTLIER) cc_final: 0.7912 (mt0) REVERT: G 39 LYS cc_start: 0.7685 (mttt) cc_final: 0.7298 (mtpp) REVERT: G 94 GLN cc_start: 0.7883 (OUTLIER) cc_final: 0.7575 (tp-100) REVERT: G 107 LYS cc_start: 0.7920 (mmtm) cc_final: 0.6952 (ttmm) REVERT: G 111 LYS cc_start: 0.8274 (ttpp) cc_final: 0.8024 (mtpp) REVERT: G 125 MET cc_start: 0.9005 (mtm) cc_final: 0.8652 (ptp) REVERT: G 150 ARG cc_start: 0.7979 (mtp85) cc_final: 0.7758 (mtp180) REVERT: G 176 GLU cc_start: 0.8212 (mm-30) cc_final: 0.7895 (mm-30) REVERT: G 187 ASP cc_start: 0.8329 (m-30) cc_final: 0.8109 (m-30) REVERT: G 202 GLN cc_start: 0.8133 (mm-40) cc_final: 0.7899 (mt0) REVERT: G 247 ARG cc_start: 0.8206 (mtp-110) cc_final: 0.7977 (mtp85) REVERT: G 306 ARG cc_start: 0.7801 (ttm110) cc_final: 0.7021 (ttp80) REVERT: G 308 GLU cc_start: 0.8207 (pm20) cc_final: 0.7894 (pm20) REVERT: H 27 ARG cc_start: 0.7545 (mtp-110) cc_final: 0.7282 (tmt170) REVERT: H 30 GLN cc_start: 0.7935 (mt0) cc_final: 0.7428 (mm-40) REVERT: H 39 LYS cc_start: 0.7678 (mttt) cc_final: 0.7280 (mtmm) REVERT: H 40 LYS cc_start: 0.7646 (mtpp) cc_final: 0.7364 (mtpt) REVERT: H 96 ARG cc_start: 0.7834 (OUTLIER) cc_final: 0.7528 (ttt90) REVERT: H 206 GLN cc_start: 0.8736 (OUTLIER) cc_final: 0.8293 (mt0) REVERT: H 247 ARG cc_start: 0.8004 (mtp-110) cc_final: 0.7330 (mmm160) REVERT: H 257 ASP cc_start: 0.8522 (m-30) cc_final: 0.8086 (m-30) REVERT: H 306 ARG cc_start: 0.7373 (OUTLIER) cc_final: 0.7100 (ttt-90) REVERT: I 27 ARG cc_start: 0.7504 (OUTLIER) cc_final: 0.7008 (tmt-80) REVERT: I 39 LYS cc_start: 0.7929 (mttt) cc_final: 0.7607 (mmmm) REVERT: I 40 LYS cc_start: 0.7695 (mtpp) cc_final: 0.7301 (mttp) REVERT: I 43 GLU cc_start: 0.7624 (mt-10) cc_final: 0.7247 (tp30) REVERT: I 75 LEU cc_start: 0.8442 (OUTLIER) cc_final: 0.8014 (mt) REVERT: I 80 LYS cc_start: 0.7981 (ttmp) cc_final: 0.7730 (mtmt) REVERT: I 108 GLU cc_start: 0.8594 (tp30) cc_final: 0.8098 (mm-30) REVERT: I 176 GLU cc_start: 0.7258 (mm-30) cc_final: 0.7024 (tm-30) REVERT: I 247 ARG cc_start: 0.7839 (mtp85) cc_final: 0.7301 (mtp85) REVERT: J 39 LYS cc_start: 0.6901 (mttt) cc_final: 0.6250 (mmmt) REVERT: J 40 LYS cc_start: 0.7058 (mtpp) cc_final: 0.6465 (mttt) REVERT: J 42 GLU cc_start: 0.7251 (tp30) cc_final: 0.6488 (tt0) REVERT: J 50 GLU cc_start: 0.7861 (mp0) cc_final: 0.7098 (mp0) REVERT: J 73 LYS cc_start: 0.6567 (mttt) cc_final: 0.5944 (tptt) REVERT: J 77 GLU cc_start: 0.7469 (OUTLIER) cc_final: 0.6743 (mp0) REVERT: J 80 LYS cc_start: 0.7772 (OUTLIER) cc_final: 0.7500 (ttmm) REVERT: J 95 ARG cc_start: 0.7998 (ttp-170) cc_final: 0.7719 (ttm110) REVERT: J 154 GLU cc_start: 0.8026 (mt-10) cc_final: 0.7555 (mm-30) REVERT: J 184 ASP cc_start: 0.8538 (m-30) cc_final: 0.8197 (m-30) REVERT: J 187 ASP cc_start: 0.8215 (OUTLIER) cc_final: 0.7512 (m-30) REVERT: J 222 ASP cc_start: 0.8590 (OUTLIER) cc_final: 0.8299 (t0) REVERT: J 231 ASP cc_start: 0.8321 (m-30) cc_final: 0.8072 (m-30) REVERT: J 299 ARG cc_start: 0.8655 (mtm180) cc_final: 0.8218 (mtt-85) REVERT: J 308 GLU cc_start: 0.7939 (pm20) cc_final: 0.6911 (mt-10) REVERT: J 332 ASP cc_start: 0.8512 (p0) cc_final: 0.7993 (p0) outliers start: 100 outliers final: 63 residues processed: 652 average time/residue: 1.5225 time to fit residues: 1137.9108 Evaluate side-chains 675 residues out of total 2607 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 81 poor density : 594 time to evaluate : 2.588 ------------------------------------------------------------------------------- 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 99 ILE Chi-restraints excluded: chain A residue 186 LEU Chi-restraints excluded: chain A residue 208 SER 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 215 ARG Chi-restraints excluded: chain B residue 223 SER Chi-restraints excluded: chain C residue 31 CYS Chi-restraints excluded: chain C residue 81 LEU Chi-restraints excluded: chain C residue 128 GLU Chi-restraints excluded: chain C residue 222 ASP Chi-restraints excluded: chain C residue 251 MET 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 181 SER Chi-restraints excluded: chain D residue 187 ASP Chi-restraints excluded: chain D residue 231 ASP Chi-restraints excluded: chain D residue 272 GLN 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 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 161 ASP Chi-restraints excluded: chain F residue 206 GLN Chi-restraints excluded: chain F residue 223 SER 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 26 SER 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 272 GLN Chi-restraints excluded: chain H residue 25 ILE Chi-restraints excluded: chain H residue 28 LEU Chi-restraints excluded: chain H residue 96 ARG 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 75 LEU Chi-restraints excluded: chain I residue 81 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 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 322 GLU Chi-restraints excluded: chain J residue 27 ARG Chi-restraints excluded: chain J residue 77 GLU Chi-restraints excluded: chain J residue 80 LYS Chi-restraints excluded: chain J residue 130 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 300 LEU Chi-restraints excluded: chain J residue 322 GLU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 323 random chunks: chunk 117 optimal weight: 0.9980 chunk 98 optimal weight: 9.9990 chunk 187 optimal weight: 0.7980 chunk 132 optimal weight: 0.0970 chunk 255 optimal weight: 6.9990 chunk 319 optimal weight: 3.9990 chunk 134 optimal weight: 5.9990 chunk 243 optimal weight: 2.9990 chunk 60 optimal weight: 0.9990 chunk 240 optimal weight: 3.9990 chunk 216 optimal weight: 8.9990 overall best weight: 1.1782 ------------------------------------------------------------------------------- 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 ** both conformations clash, **PLEASE CHECK MANUALLY** F 200 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** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3669 r_free = 0.3669 target = 0.147250 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3286 r_free = 0.3286 target = 0.113669 restraints weight = 32353.375| |-----------------------------------------------------------------------------| r_work (start): 0.3231 rms_B_bonded: 1.98 r_work: 0.3110 rms_B_bonded: 2.65 restraints_weight: 0.5000 r_work: 0.2981 rms_B_bonded: 4.35 restraints_weight: 0.2500 r_work (final): 0.2981 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7986 moved from start: 0.3587 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 26875 Z= 0.134 Angle : 0.481 7.614 36550 Z= 0.254 Chirality : 0.039 0.142 4139 Planarity : 0.003 0.039 4521 Dihedral : 13.607 142.527 4454 Min Nonbonded Distance : 2.243 Molprobity Statistics. All-atom Clashscore : 6.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.07 % Favored : 97.93 % Rotamer: Outliers : 3.76 % Allowed : 24.59 % Favored : 71.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.32 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.28 (0.15), residues: 3196 helix: 1.19 (0.14), residues: 1390 sheet: 0.25 (0.27), residues: 380 loop : -0.81 (0.15), residues: 1426 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.005 0.001 HIS E 294 PHE 0.013 0.001 PHE F 126 TYR 0.014 0.001 TYR G 315 ARG 0.010 0.001 ARG B 130 Details of bonding type rmsd hydrogen bonds : bond 0.03175 ( 1159) hydrogen bonds : angle 4.14429 ( 3100) covalent geometry : bond 0.00304 (26875) covalent geometry : angle 0.48134 (36550) *********************** 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 699 residues out of total 2607 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 98 poor density : 601 time to evaluate : 2.844 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 37 ASP cc_start: 0.7235 (m-30) cc_final: 0.6751 (m-30) REVERT: A 40 LYS cc_start: 0.7433 (mtpp) cc_final: 0.6158 (mppt) REVERT: A 68 GLU cc_start: 0.6770 (mt-10) cc_final: 0.6032 (tm-30) REVERT: A 70 LYS cc_start: 0.6986 (ttpt) cc_final: 0.6631 (ttpt) REVERT: A 107 LYS cc_start: 0.7244 (mmtm) cc_final: 0.6931 (tptt) REVERT: A 186 LEU cc_start: 0.8235 (OUTLIER) cc_final: 0.7964 (mm) REVERT: A 210 MET cc_start: 0.8149 (mtp) cc_final: 0.7323 (mtp) REVERT: A 251 MET cc_start: 0.7823 (mtp) cc_final: 0.7446 (mtp) REVERT: A 254 ARG cc_start: 0.7362 (ttp80) cc_final: 0.7090 (tmt90) REVERT: A 303 ARG cc_start: 0.7357 (mtp180) cc_final: 0.6830 (mtm180) REVERT: A 308 GLU cc_start: 0.7240 (pt0) cc_final: 0.6489 (tt0) REVERT: A 329 ILE cc_start: 0.8569 (mt) cc_final: 0.8142 (mt) REVERT: B 42 GLU cc_start: 0.7070 (mt-10) cc_final: 0.6511 (mt-10) REVERT: B 43 GLU cc_start: 0.7531 (mt-10) cc_final: 0.7177 (mt-10) REVERT: B 88 THR cc_start: 0.9051 (OUTLIER) cc_final: 0.8768 (p) REVERT: B 95 ARG cc_start: 0.7904 (ttp80) cc_final: 0.7515 (ttt-90) REVERT: B 100 ILE cc_start: 0.9160 (mp) cc_final: 0.8916 (pp) REVERT: B 107 LYS cc_start: 0.7800 (mmtm) cc_final: 0.6910 (ptpt) REVERT: B 206 GLN cc_start: 0.7578 (mt0) cc_final: 0.7357 (mt0) REVERT: B 215 ARG cc_start: 0.8221 (OUTLIER) cc_final: 0.8020 (tpt-90) REVERT: B 272 GLN cc_start: 0.7729 (pt0) cc_final: 0.7442 (mt0) REVERT: B 332 ASP cc_start: 0.8787 (p0) cc_final: 0.8420 (p0) REVERT: C 88 THR cc_start: 0.9099 (OUTLIER) cc_final: 0.8887 (p) REVERT: C 94 GLN cc_start: 0.7831 (mm-40) cc_final: 0.7094 (tm-30) REVERT: C 95 ARG cc_start: 0.8106 (ttp80) cc_final: 0.7434 (ttp-170) REVERT: C 107 LYS cc_start: 0.8294 (mmtm) cc_final: 0.7576 (ptpp) REVERT: C 145 GLN cc_start: 0.8619 (mp10) cc_final: 0.7982 (mp10) REVERT: C 154 GLU cc_start: 0.7621 (mt-10) cc_final: 0.6906 (mt-10) REVERT: C 181 SER cc_start: 0.8629 (t) cc_final: 0.8124 (p) REVERT: C 206 GLN cc_start: 0.7523 (mt0) cc_final: 0.7071 (mt0) REVERT: C 222 ASP cc_start: 0.8857 (OUTLIER) cc_final: 0.8402 (t70) REVERT: C 251 MET cc_start: 0.7879 (OUTLIER) cc_final: 0.7314 (mpt) REVERT: D 27 ARG cc_start: 0.8325 (OUTLIER) cc_final: 0.7587 (mtp180) REVERT: D 42 GLU cc_start: 0.7890 (mm-30) cc_final: 0.7648 (mm-30) REVERT: D 94 GLN cc_start: 0.7700 (mm-40) cc_final: 0.6877 (tm-30) REVERT: D 107 LYS cc_start: 0.8299 (mmtm) cc_final: 0.7899 (mtmt) REVERT: D 187 ASP cc_start: 0.9031 (OUTLIER) cc_final: 0.8661 (t70) REVERT: D 215 ARG cc_start: 0.8193 (tpt-90) cc_final: 0.7926 (tpt-90) REVERT: D 306 ARG cc_start: 0.7539 (ttp-110) cc_final: 0.7054 (ttm110) REVERT: E 27 ARG cc_start: 0.8395 (mtp180) cc_final: 0.8110 (ttt-90) REVERT: E 68 GLU cc_start: 0.8003 (mp0) cc_final: 0.7519 (tp30) REVERT: E 107 LYS cc_start: 0.7976 (mmtm) cc_final: 0.7562 (mtmt) REVERT: E 176 GLU cc_start: 0.8319 (mm-30) cc_final: 0.7756 (tt0) REVERT: E 187 ASP cc_start: 0.8718 (OUTLIER) cc_final: 0.7870 (m-30) REVERT: E 211 MET cc_start: 0.9105 (mtt) cc_final: 0.8837 (mtt) REVERT: E 215 ARG cc_start: 0.8064 (tpt-90) cc_final: 0.7779 (tmt90) REVERT: E 306 ARG cc_start: 0.7670 (ttp-110) cc_final: 0.7332 (tmm160) REVERT: E 338 LYS cc_start: 0.7843 (tppp) cc_final: 0.6427 (mptt) REVERT: F 27 ARG cc_start: 0.8419 (mtp180) cc_final: 0.8003 (ttt-90) REVERT: F 39 LYS cc_start: 0.7333 (mttt) cc_final: 0.6582 (mtmt) REVERT: F 43 GLU cc_start: 0.7893 (mt-10) cc_final: 0.7349 (mp0) REVERT: F 68 GLU cc_start: 0.8161 (mt-10) cc_final: 0.7611 (mp0) REVERT: F 158 MET cc_start: 0.8721 (ttm) cc_final: 0.8418 (ttm) REVERT: F 176 GLU cc_start: 0.8388 (mm-30) cc_final: 0.8175 (mm-30) REVERT: F 202 GLN cc_start: 0.8164 (mm-40) cc_final: 0.7707 (mt0) REVERT: F 206 GLN cc_start: 0.8663 (OUTLIER) cc_final: 0.7881 (mt0) REVERT: G 39 LYS cc_start: 0.7652 (mttt) cc_final: 0.7262 (mtpp) REVERT: G 91 GLU cc_start: 0.8068 (OUTLIER) cc_final: 0.7592 (tt0) REVERT: G 94 GLN cc_start: 0.7858 (mm-40) cc_final: 0.7548 (tp-100) REVERT: G 107 LYS cc_start: 0.7902 (mmtm) cc_final: 0.6924 (ttmm) REVERT: G 111 LYS cc_start: 0.8254 (ttpp) cc_final: 0.8007 (mtpp) REVERT: G 125 MET cc_start: 0.9040 (mtm) cc_final: 0.8627 (ptp) REVERT: G 150 ARG cc_start: 0.7899 (mtp85) cc_final: 0.7625 (mtp180) REVERT: G 176 GLU cc_start: 0.8212 (mm-30) cc_final: 0.7904 (mm-30) REVERT: G 187 ASP cc_start: 0.8284 (m-30) cc_final: 0.8062 (m-30) REVERT: G 202 GLN cc_start: 0.8092 (mm-40) cc_final: 0.7859 (mt0) REVERT: G 247 ARG cc_start: 0.8196 (mtp-110) cc_final: 0.7963 (mtp85) REVERT: G 306 ARG cc_start: 0.7786 (ttm110) cc_final: 0.7004 (ttp80) REVERT: G 308 GLU cc_start: 0.8209 (pm20) cc_final: 0.7865 (pm20) REVERT: H 27 ARG cc_start: 0.7510 (mtp-110) cc_final: 0.7181 (tmt170) REVERT: H 30 GLN cc_start: 0.7913 (mt0) cc_final: 0.7403 (mm-40) REVERT: H 39 LYS cc_start: 0.7653 (mttt) cc_final: 0.7266 (mtmm) REVERT: H 40 LYS cc_start: 0.7662 (mtpp) cc_final: 0.7388 (mtpt) REVERT: H 96 ARG cc_start: 0.7799 (OUTLIER) cc_final: 0.7524 (ttt90) REVERT: H 247 ARG cc_start: 0.7962 (mtp-110) cc_final: 0.7274 (mmm160) REVERT: H 254 ARG cc_start: 0.8098 (ttp-170) cc_final: 0.7711 (tmm-80) REVERT: H 306 ARG cc_start: 0.7356 (OUTLIER) cc_final: 0.7095 (ttt-90) REVERT: I 27 ARG cc_start: 0.7633 (OUTLIER) cc_final: 0.7178 (tmt-80) REVERT: I 39 LYS cc_start: 0.7890 (mttt) cc_final: 0.7574 (mmmm) REVERT: I 40 LYS cc_start: 0.7697 (mtpp) cc_final: 0.7262 (mttp) REVERT: I 43 GLU cc_start: 0.7624 (mt-10) cc_final: 0.7254 (tp30) REVERT: I 75 LEU cc_start: 0.8405 (OUTLIER) cc_final: 0.7980 (mt) REVERT: I 80 LYS cc_start: 0.7972 (ttmp) cc_final: 0.7718 (mtmt) REVERT: I 110 ASP cc_start: 0.8684 (m-30) cc_final: 0.8369 (m-30) REVERT: I 176 GLU cc_start: 0.7249 (mm-30) cc_final: 0.6997 (tm-30) REVERT: I 247 ARG cc_start: 0.7889 (mtp85) cc_final: 0.7314 (mtp85) REVERT: J 39 LYS cc_start: 0.6882 (mttt) cc_final: 0.6181 (mmmt) REVERT: J 40 LYS cc_start: 0.7024 (mtpp) cc_final: 0.6091 (mttt) REVERT: J 42 GLU cc_start: 0.7231 (tp30) cc_final: 0.6489 (tt0) REVERT: J 43 GLU cc_start: 0.6953 (OUTLIER) cc_final: 0.6387 (pp20) REVERT: J 50 GLU cc_start: 0.7820 (mp0) cc_final: 0.7062 (mp0) REVERT: J 73 LYS cc_start: 0.6522 (mttt) cc_final: 0.5886 (tptt) REVERT: J 77 GLU cc_start: 0.7355 (OUTLIER) cc_final: 0.6691 (mp0) REVERT: J 95 ARG cc_start: 0.7935 (ttp-170) cc_final: 0.7653 (ttm110) REVERT: J 154 GLU cc_start: 0.7972 (mt-10) cc_final: 0.7495 (mm-30) REVERT: J 177 ARG cc_start: 0.8239 (OUTLIER) cc_final: 0.7681 (ttt180) REVERT: J 184 ASP cc_start: 0.8522 (m-30) cc_final: 0.8197 (m-30) REVERT: J 187 ASP cc_start: 0.8182 (OUTLIER) cc_final: 0.7477 (m-30) REVERT: J 222 ASP cc_start: 0.8552 (OUTLIER) cc_final: 0.8232 (t0) REVERT: J 231 ASP cc_start: 0.8262 (m-30) cc_final: 0.7987 (m-30) REVERT: J 254 ARG cc_start: 0.7142 (mtm110) cc_final: 0.6765 (tmm160) REVERT: J 299 ARG cc_start: 0.8616 (mtm180) cc_final: 0.8303 (mtt-85) REVERT: J 308 GLU cc_start: 0.7955 (pm20) cc_final: 0.6939 (mt-10) outliers start: 98 outliers final: 67 residues processed: 647 average time/residue: 1.5018 time to fit residues: 1109.0244 Evaluate side-chains 672 residues out of total 2607 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 87 poor density : 585 time to evaluate : 2.954 ------------------------------------------------------------------------------- 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 87 THR Chi-restraints excluded: chain A residue 99 ILE Chi-restraints excluded: chain A residue 128 GLU Chi-restraints excluded: chain A residue 186 LEU 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 31 CYS Chi-restraints excluded: chain C residue 88 THR Chi-restraints excluded: chain C residue 104 THR Chi-restraints excluded: chain C residue 128 GLU Chi-restraints excluded: chain C residue 222 ASP Chi-restraints excluded: chain C residue 233 SER Chi-restraints excluded: chain C residue 251 MET 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 181 SER Chi-restraints excluded: chain D residue 187 ASP Chi-restraints excluded: chain D residue 231 ASP 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 161 ASP Chi-restraints excluded: chain E residue 187 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 161 ASP Chi-restraints excluded: chain F residue 206 GLN Chi-restraints excluded: chain F residue 223 SER 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 26 SER Chi-restraints excluded: chain G residue 38 VAL Chi-restraints excluded: chain G residue 91 GLU Chi-restraints excluded: chain G residue 97 SER Chi-restraints excluded: chain G residue 161 ASP Chi-restraints excluded: chain G residue 272 GLN Chi-restraints excluded: chain H residue 25 ILE Chi-restraints excluded: chain H residue 28 LEU Chi-restraints excluded: chain H residue 96 ARG Chi-restraints excluded: chain H residue 142 VAL 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 75 LEU Chi-restraints excluded: chain I residue 88 THR 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 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 322 GLU 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 128 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 300 LEU Chi-restraints excluded: chain J residue 322 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 323 random chunks: chunk 136 optimal weight: 1.9990 chunk 274 optimal weight: 6.9990 chunk 294 optimal weight: 0.0050 chunk 20 optimal weight: 0.9990 chunk 204 optimal weight: 2.9990 chunk 227 optimal weight: 5.9990 chunk 224 optimal weight: 0.1980 chunk 278 optimal weight: 4.9990 chunk 306 optimal weight: 2.9990 chunk 105 optimal weight: 0.6980 chunk 107 optimal weight: 0.9980 overall best weight: 0.5796 ------------------------------------------------------------------------------- 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** D 242 GLN ** E 145 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 200 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** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3703 r_free = 0.3703 target = 0.150339 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3327 r_free = 0.3327 target = 0.116860 restraints weight = 32092.046| |-----------------------------------------------------------------------------| r_work (start): 0.3318 rms_B_bonded: 1.98 r_work: 0.3201 rms_B_bonded: 2.65 restraints_weight: 0.5000 r_work: 0.3072 rms_B_bonded: 4.37 restraints_weight: 0.2500 r_work (final): 0.3072 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7927 moved from start: 0.3772 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.046 26875 Z= 0.104 Angle : 0.461 8.174 36550 Z= 0.243 Chirality : 0.039 0.140 4139 Planarity : 0.003 0.043 4521 Dihedral : 13.522 142.261 4454 Min Nonbonded Distance : 2.264 Molprobity Statistics. All-atom Clashscore : 6.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.47 % Favored : 98.53 % Rotamer: Outliers : 2.76 % Allowed : 25.70 % Favored : 71.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.32 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.48 (0.15), residues: 3196 helix: 1.35 (0.14), residues: 1390 sheet: 0.35 (0.27), residues: 380 loop : -0.70 (0.16), residues: 1426 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.005 0.001 HIS A 138 PHE 0.012 0.001 PHE F 126 TYR 0.010 0.001 TYR G 315 ARG 0.009 0.000 ARG B 130 Details of bonding type rmsd hydrogen bonds : bond 0.02752 ( 1159) hydrogen bonds : angle 4.01699 ( 3100) covalent geometry : bond 0.00231 (26875) covalent geometry : angle 0.46055 (36550) ********************** 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 690 residues out of total 2607 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 72 poor density : 618 time to evaluate : 2.704 Fit side-chains revert: symmetry clash REVERT: A 40 LYS cc_start: 0.7432 (mtpp) cc_final: 0.6123 (mppt) REVERT: A 68 GLU cc_start: 0.6691 (mt-10) cc_final: 0.5878 (tm-30) REVERT: A 72 ASP cc_start: 0.6971 (m-30) cc_final: 0.6482 (m-30) REVERT: A 107 LYS cc_start: 0.7254 (mmtm) cc_final: 0.6948 (tptt) REVERT: A 186 LEU cc_start: 0.8255 (OUTLIER) cc_final: 0.8003 (mm) REVERT: A 210 MET cc_start: 0.8175 (mtp) cc_final: 0.7322 (mtp) REVERT: A 251 MET cc_start: 0.7805 (mtp) cc_final: 0.7477 (mtp) REVERT: A 254 ARG cc_start: 0.7313 (ttp80) cc_final: 0.7087 (tmt90) REVERT: A 303 ARG cc_start: 0.7462 (mtp180) cc_final: 0.6909 (mtm180) REVERT: A 308 GLU cc_start: 0.7202 (pt0) cc_final: 0.6470 (tt0) REVERT: A 324 GLU cc_start: 0.8274 (mt-10) cc_final: 0.7720 (mt-10) REVERT: A 329 ILE cc_start: 0.8536 (mt) cc_final: 0.8064 (mt) REVERT: B 42 GLU cc_start: 0.6997 (mt-10) cc_final: 0.6447 (mt-10) REVERT: B 43 GLU cc_start: 0.7526 (mt-10) cc_final: 0.7138 (mt-10) REVERT: B 88 THR cc_start: 0.9042 (OUTLIER) cc_final: 0.8771 (p) REVERT: B 95 ARG cc_start: 0.7874 (ttp80) cc_final: 0.7505 (ttt-90) REVERT: B 107 LYS cc_start: 0.7766 (mmtm) cc_final: 0.6869 (ptpt) REVERT: B 272 GLN cc_start: 0.7799 (pt0) cc_final: 0.7446 (mt0) REVERT: B 274 ASP cc_start: 0.5606 (t0) cc_final: 0.4638 (p0) REVERT: B 306 ARG cc_start: 0.7833 (mmm-85) cc_final: 0.7240 (ptm-80) REVERT: B 332 ASP cc_start: 0.8789 (p0) cc_final: 0.8495 (p0) REVERT: C 88 THR cc_start: 0.9089 (OUTLIER) cc_final: 0.8880 (p) REVERT: C 94 GLN cc_start: 0.7779 (mm-40) cc_final: 0.6924 (tm-30) REVERT: C 95 ARG cc_start: 0.8008 (ttp80) cc_final: 0.7384 (ttp-170) REVERT: C 107 LYS cc_start: 0.8254 (mmtm) cc_final: 0.7527 (ptpp) REVERT: C 145 GLN cc_start: 0.8472 (mp10) cc_final: 0.7703 (mp10) REVERT: C 181 SER cc_start: 0.8620 (t) cc_final: 0.8116 (p) REVERT: C 206 GLN cc_start: 0.7507 (mt0) cc_final: 0.7103 (mm-40) REVERT: C 222 ASP cc_start: 0.8846 (t70) cc_final: 0.8123 (t70) REVERT: C 243 MET cc_start: 0.8566 (mtt) cc_final: 0.8197 (mtm) REVERT: D 27 ARG cc_start: 0.8243 (OUTLIER) cc_final: 0.7316 (mtp180) REVERT: D 42 GLU cc_start: 0.7877 (mm-30) cc_final: 0.7644 (mm-30) REVERT: D 94 GLN cc_start: 0.7645 (mm-40) cc_final: 0.6816 (tm-30) REVERT: D 107 LYS cc_start: 0.8279 (mmtm) cc_final: 0.7877 (mtmt) REVERT: D 187 ASP cc_start: 0.8993 (OUTLIER) cc_final: 0.8639 (t70) REVERT: D 306 ARG cc_start: 0.7481 (ttp-110) cc_final: 0.6999 (ttm110) REVERT: E 68 GLU cc_start: 0.8002 (mp0) cc_final: 0.7485 (tp30) REVERT: E 107 LYS cc_start: 0.8012 (mmtm) cc_final: 0.7542 (mtmt) REVERT: E 176 GLU cc_start: 0.8165 (mm-30) cc_final: 0.7575 (tt0) REVERT: E 211 MET cc_start: 0.9056 (mtt) cc_final: 0.8780 (mtt) REVERT: E 306 ARG cc_start: 0.7595 (ttp-110) cc_final: 0.7252 (tmm160) REVERT: E 338 LYS cc_start: 0.7778 (tppp) cc_final: 0.6324 (mptt) REVERT: F 27 ARG cc_start: 0.8205 (mtp180) cc_final: 0.7875 (ttt-90) REVERT: F 39 LYS cc_start: 0.7213 (mttt) cc_final: 0.6362 (mtpp) REVERT: F 43 GLU cc_start: 0.7990 (mt-10) cc_final: 0.7373 (mp0) REVERT: F 68 GLU cc_start: 0.8113 (mt-10) cc_final: 0.7757 (mp0) REVERT: F 158 MET cc_start: 0.8666 (ttm) cc_final: 0.8207 (ttp) REVERT: F 176 GLU cc_start: 0.8183 (mm-30) cc_final: 0.7968 (mm-30) REVERT: F 202 GLN cc_start: 0.8137 (mm-40) cc_final: 0.7728 (mt0) REVERT: F 206 GLN cc_start: 0.8566 (OUTLIER) cc_final: 0.8000 (mt0) REVERT: G 27 ARG cc_start: 0.7966 (mmm160) cc_final: 0.7667 (mmm160) REVERT: G 39 LYS cc_start: 0.7652 (mttt) cc_final: 0.7275 (mtpp) REVERT: G 64 LYS cc_start: 0.7114 (ttmm) cc_final: 0.6851 (tppp) REVERT: G 94 GLN cc_start: 0.7829 (OUTLIER) cc_final: 0.7412 (tp-100) REVERT: G 107 LYS cc_start: 0.7876 (mmtm) cc_final: 0.6902 (ttmm) REVERT: G 111 LYS cc_start: 0.8219 (ttpp) cc_final: 0.7963 (mtpp) REVERT: G 125 MET cc_start: 0.9011 (mtm) cc_final: 0.8640 (ptp) REVERT: G 176 GLU cc_start: 0.8154 (mm-30) cc_final: 0.7860 (mm-30) REVERT: G 187 ASP cc_start: 0.8295 (m-30) cc_final: 0.8077 (m-30) REVERT: G 247 ARG cc_start: 0.8158 (mtp-110) cc_final: 0.7922 (mtp85) REVERT: G 306 ARG cc_start: 0.7781 (ttm110) cc_final: 0.6968 (ttp80) REVERT: G 308 GLU cc_start: 0.8182 (pm20) cc_final: 0.7800 (pm20) REVERT: H 27 ARG cc_start: 0.7395 (mtp-110) cc_final: 0.7172 (tmt170) REVERT: H 30 GLN cc_start: 0.7994 (mt0) cc_final: 0.7477 (mm-40) REVERT: H 39 LYS cc_start: 0.7659 (mttt) cc_final: 0.7233 (mtmm) REVERT: H 40 LYS cc_start: 0.7615 (mtpp) cc_final: 0.7351 (mtpt) REVERT: H 96 ARG cc_start: 0.7738 (OUTLIER) cc_final: 0.7525 (ttt90) REVERT: H 247 ARG cc_start: 0.7904 (mtp-110) cc_final: 0.7367 (mmm160) REVERT: H 254 ARG cc_start: 0.8018 (ttp-170) cc_final: 0.7630 (tmm-80) REVERT: H 257 ASP cc_start: 0.8511 (m-30) cc_final: 0.8231 (m-30) REVERT: I 27 ARG cc_start: 0.7267 (OUTLIER) cc_final: 0.7002 (tmt-80) REVERT: I 39 LYS cc_start: 0.7862 (mttt) cc_final: 0.7549 (mmmm) REVERT: I 40 LYS cc_start: 0.7667 (mtpp) cc_final: 0.7229 (mttp) REVERT: I 43 GLU cc_start: 0.7666 (mt-10) cc_final: 0.7276 (tp30) REVERT: I 75 LEU cc_start: 0.8370 (OUTLIER) cc_final: 0.7932 (mt) REVERT: I 176 GLU cc_start: 0.7260 (mm-30) cc_final: 0.6977 (tm-30) REVERT: I 247 ARG cc_start: 0.7918 (mtp85) cc_final: 0.7374 (mtp85) REVERT: J 39 LYS cc_start: 0.6838 (mttt) cc_final: 0.6143 (mmmt) REVERT: J 40 LYS cc_start: 0.6985 (mtpp) cc_final: 0.6024 (mttt) REVERT: J 42 GLU cc_start: 0.7222 (tp30) cc_final: 0.6507 (tt0) REVERT: J 43 GLU cc_start: 0.6904 (OUTLIER) cc_final: 0.6305 (pp20) REVERT: J 50 GLU cc_start: 0.7737 (mp0) cc_final: 0.6980 (mp0) REVERT: J 73 LYS cc_start: 0.6532 (mttt) cc_final: 0.5828 (tptm) REVERT: J 77 GLU cc_start: 0.7390 (OUTLIER) cc_final: 0.6707 (mp0) REVERT: J 95 ARG cc_start: 0.7907 (ttp-170) cc_final: 0.7644 (ttm110) REVERT: J 110 ASP cc_start: 0.8193 (m-30) cc_final: 0.7840 (m-30) REVERT: J 124 GLU cc_start: 0.9172 (tt0) cc_final: 0.8736 (tt0) REVERT: J 154 GLU cc_start: 0.7903 (mt-10) cc_final: 0.7492 (mm-30) REVERT: J 184 ASP cc_start: 0.8555 (m-30) cc_final: 0.8168 (m-30) REVERT: J 187 ASP cc_start: 0.8124 (OUTLIER) cc_final: 0.7420 (m-30) REVERT: J 214 SER cc_start: 0.7169 (t) cc_final: 0.6737 (t) REVERT: J 222 ASP cc_start: 0.8422 (OUTLIER) cc_final: 0.8137 (t0) REVERT: J 254 ARG cc_start: 0.7008 (mtm110) cc_final: 0.6721 (tmm160) REVERT: J 299 ARG cc_start: 0.8585 (mtm180) cc_final: 0.8187 (mtt-85) REVERT: J 308 GLU cc_start: 0.7938 (pm20) cc_final: 0.6912 (mt-10) outliers start: 72 outliers final: 45 residues processed: 653 average time/residue: 1.4608 time to fit residues: 1090.8987 Evaluate side-chains 644 residues out of total 2607 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 585 time to evaluate : 2.570 ------------------------------------------------------------------------------- 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 99 ILE Chi-restraints excluded: chain A residue 186 LEU Chi-restraints excluded: chain A residue 266 THR Chi-restraints excluded: chain B residue 31 CYS 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 88 THR Chi-restraints excluded: chain C residue 128 GLU 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 161 ASP Chi-restraints excluded: chain D residue 181 SER Chi-restraints excluded: chain D residue 187 ASP Chi-restraints excluded: chain D residue 231 ASP Chi-restraints excluded: chain D residue 330 ASN Chi-restraints excluded: chain E residue 48 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 273 VAL Chi-restraints excluded: chain E residue 296 SER Chi-restraints excluded: chain F residue 112 LEU 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 223 SER Chi-restraints excluded: chain F residue 272 GLN Chi-restraints excluded: chain F residue 297 THR Chi-restraints excluded: chain G residue 26 SER 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 H residue 25 ILE Chi-restraints excluded: chain H residue 28 LEU Chi-restraints excluded: chain H residue 96 ARG Chi-restraints excluded: chain H residue 142 VAL 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 75 LEU Chi-restraints excluded: chain I residue 90 THR 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 I residue 311 ILE Chi-restraints excluded: chain I residue 322 GLU 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 130 ARG Chi-restraints excluded: chain J residue 187 ASP Chi-restraints excluded: chain J residue 222 ASP 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 68 optimal weight: 7.9990 chunk 60 optimal weight: 0.9980 chunk 39 optimal weight: 6.9990 chunk 53 optimal weight: 2.9990 chunk 233 optimal weight: 8.9990 chunk 242 optimal weight: 5.9990 chunk 133 optimal weight: 4.9990 chunk 167 optimal weight: 0.8980 chunk 84 optimal weight: 0.9980 chunk 310 optimal weight: 0.0020 chunk 229 optimal weight: 4.9990 overall best weight: 1.1790 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 272 GLN B 330 ASN C 30 GLN C 101 GLN C 145 GLN C 272 GLN ** D 145 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 145 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 202 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: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3679 r_free = 0.3679 target = 0.148119 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3299 r_free = 0.3299 target = 0.114578 restraints weight = 32391.050| |-----------------------------------------------------------------------------| r_work (start): 0.3290 rms_B_bonded: 1.98 r_work: 0.3170 rms_B_bonded: 2.65 restraints_weight: 0.5000 r_work: 0.3042 rms_B_bonded: 4.36 restraints_weight: 0.2500 r_work (final): 0.3042 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7958 moved from start: 0.3739 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 26875 Z= 0.135 Angle : 0.487 8.374 36550 Z= 0.257 Chirality : 0.039 0.143 4139 Planarity : 0.003 0.041 4521 Dihedral : 13.536 140.925 4454 Min Nonbonded Distance : 2.246 Molprobity Statistics. All-atom Clashscore : 6.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.94 % Favored : 98.06 % Rotamer: Outliers : 2.72 % Allowed : 26.28 % Favored : 71.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.32 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.49 (0.15), residues: 3196 helix: 1.35 (0.14), residues: 1390 sheet: 0.37 (0.27), residues: 380 loop : -0.68 (0.16), residues: 1426 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.005 0.001 HIS A 138 PHE 0.013 0.001 PHE F 126 TYR 0.015 0.001 TYR G 315 ARG 0.010 0.001 ARG C 27 Details of bonding type rmsd hydrogen bonds : bond 0.03096 ( 1159) hydrogen bonds : angle 4.05425 ( 3100) covalent geometry : bond 0.00307 (26875) covalent geometry : angle 0.48728 (36550) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 24969.89 seconds wall clock time: 428 minutes 23.26 seconds (25703.26 seconds total)