Starting phenix.real_space_refine on Fri Feb 6 15:04:04 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8pbd_17585/02_2026/8pbd_17585.cif Found real_map, /net/cci-nas-00/data/ceres_data/8pbd_17585/02_2026/8pbd_17585.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.83 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8pbd_17585/02_2026/8pbd_17585.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8pbd_17585/02_2026/8pbd_17585.map" model { file = "/net/cci-nas-00/data/ceres_data/8pbd_17585/02_2026/8pbd_17585.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8pbd_17585/02_2026/8pbd_17585.cif" } resolution = 2.83 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.072 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians Ca 20 9.91 5 P 84 5.49 5 S 139 5.16 5 C 16254 2.51 5 N 4665 2.21 5 O 5204 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 20 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 26366 Number of models: 1 Model: "" Number of chains: 31 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: "B" 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: "C" 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: "D" 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: "E" 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: "F" 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: "G" 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: "H" 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: "I" 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: "J" 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: "L" 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: "M" 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: "N" 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: "O" 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: "P" 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: "Q" 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: "R" 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: "S" 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: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 33 Unusual residues: {' CA': 2, 'ATP': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "C" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 33 Unusual residues: {' CA': 2, 'ATP': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "D" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 33 Unusual residues: {' CA': 2, 'ATP': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "E" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 33 Unusual residues: {' CA': 2, 'ATP': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "F" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 33 Unusual residues: {' CA': 2, 'ATP': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "G" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 33 Unusual residues: {' CA': 2, 'ATP': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "H" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 33 Unusual residues: {' CA': 2, 'ATP': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "I" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 33 Unusual residues: {' CA': 2, 'ATP': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "J" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' CA': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 6.84, per 1000 atoms: 0.26 Number of scatterers: 26366 At special positions: 0 Unit cell: (123.88, 121.272, 220.376, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) Ca 20 19.99 S 139 16.00 P 84 15.00 O 5204 8.00 N 4665 7.00 C 16254 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 2.56 Conformation dependent library (CDL) restraints added in 1.1 seconds 6392 Ramachandran restraints generated. 3196 Oldfield, 0 Emsley, 3196 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5968 Finding SS restraints... Secondary structure from input PDB file: 170 helices and 30 sheets defined 51.4% alpha, 16.3% beta 20 base pairs and 36 stacking pairs defined. Time for finding SS restraints: 3.38 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: 6.80 Time building geometry restraints manager: 3.32 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 6155 1.33 - 1.45: 5382 1.45 - 1.57: 14983 1.57 - 1.69: 136 1.69 - 1.81: 219 Bond restraints: 26875 Sorted by residual: bond pdb=" CA TYR G 232 " pdb=" CB TYR G 232 " ideal model delta sigma weight residual 1.528 1.502 0.026 1.51e-02 4.39e+03 3.04e+00 bond pdb=" CA TYR F 232 " pdb=" CB TYR F 232 " ideal model delta sigma weight residual 1.528 1.502 0.026 1.51e-02 4.39e+03 3.00e+00 bond pdb=" CA TYR H 232 " pdb=" CB TYR H 232 " ideal model delta sigma weight residual 1.528 1.503 0.026 1.51e-02 4.39e+03 2.93e+00 bond pdb=" CA TYR D 232 " pdb=" CB TYR D 232 " ideal model delta sigma weight residual 1.528 1.503 0.026 1.51e-02 4.39e+03 2.92e+00 bond pdb=" CA TYR B 232 " pdb=" CB TYR B 232 " ideal model delta sigma weight residual 1.528 1.503 0.026 1.51e-02 4.39e+03 2.89e+00 ... (remaining 26870 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.21: 35357 1.21 - 2.41: 972 2.41 - 3.62: 181 3.62 - 4.82: 30 4.82 - 6.03: 10 Bond angle restraints: 36550 Sorted by residual: angle pdb=" C PHE A 129 " pdb=" N ARG A 130 " pdb=" CA ARG A 130 " ideal model delta sigma weight residual 121.54 127.57 -6.03 1.91e+00 2.74e-01 9.97e+00 angle pdb=" C PHE J 129 " pdb=" N ARG J 130 " pdb=" CA ARG J 130 " ideal model delta sigma weight residual 121.54 127.57 -6.03 1.91e+00 2.74e-01 9.97e+00 angle pdb=" C PHE C 129 " pdb=" N ARG C 130 " pdb=" CA ARG C 130 " ideal model delta sigma weight residual 121.54 127.56 -6.02 1.91e+00 2.74e-01 9.95e+00 angle pdb=" C PHE I 129 " pdb=" N ARG I 130 " pdb=" CA ARG I 130 " ideal model delta sigma weight residual 121.54 127.53 -5.99 1.91e+00 2.74e-01 9.84e+00 angle pdb=" C PHE D 129 " pdb=" N ARG D 130 " pdb=" CA ARG D 130 " ideal model delta sigma weight residual 121.54 127.52 -5.98 1.91e+00 2.74e-01 9.81e+00 ... (remaining 36545 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 30.81: 15674 30.81 - 61.62: 665 61.62 - 92.43: 41 92.43 - 123.24: 0 123.24 - 154.05: 1 Dihedral angle restraints: 16381 sinusoidal: 7088 harmonic: 9293 Sorted by residual: dihedral pdb=" C4' DT U 1 " pdb=" C3' DT U 1 " pdb=" O3' DT U 1 " pdb=" P DC U 2 " ideal model delta sinusoidal sigma weight residual 220.00 65.95 154.05 1 3.50e+01 8.16e-04 1.49e+01 dihedral pdb=" CA ASP H 316 " pdb=" CB ASP H 316 " pdb=" CG ASP H 316 " pdb=" OD1 ASP H 316 " ideal model delta sinusoidal sigma weight residual -30.00 -83.00 53.00 1 2.00e+01 2.50e-03 9.56e+00 dihedral pdb=" CA ASP A 316 " pdb=" CB ASP A 316 " pdb=" CG ASP A 316 " pdb=" OD1 ASP A 316 " ideal model delta sinusoidal sigma weight residual -30.00 -82.98 52.98 1 2.00e+01 2.50e-03 9.55e+00 ... (remaining 16378 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.028: 2289 0.028 - 0.057: 1210 0.057 - 0.085: 413 0.085 - 0.113: 214 0.113 - 0.141: 13 Chirality restraints: 4139 Sorted by residual: chirality pdb=" C3' DG T 2 " pdb=" C4' DG T 2 " pdb=" O3' DG T 2 " pdb=" C2' DG T 2 " both_signs ideal model delta sigma weight residual False -2.66 -2.52 -0.14 2.00e-01 2.50e+01 5.01e-01 chirality pdb=" CA VAL L3290 " pdb=" N VAL L3290 " pdb=" C VAL L3290 " pdb=" CB VAL L3290 " both_signs ideal model delta sigma weight residual False 2.44 2.56 -0.12 2.00e-01 2.50e+01 3.75e-01 chirality pdb=" CA VAL M3290 " pdb=" N VAL M3290 " pdb=" C VAL M3290 " pdb=" CB VAL M3290 " both_signs ideal model delta sigma weight residual False 2.44 2.56 -0.12 2.00e-01 2.50e+01 3.73e-01 ... (remaining 4136 not shown) Planarity restraints: 4521 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1' DA T 18 " 0.015 2.00e-02 2.50e+03 6.92e-03 1.32e+00 pdb=" N9 DA T 18 " -0.016 2.00e-02 2.50e+03 pdb=" C8 DA T 18 " -0.002 2.00e-02 2.50e+03 pdb=" N7 DA T 18 " 0.001 2.00e-02 2.50e+03 pdb=" C5 DA T 18 " 0.000 2.00e-02 2.50e+03 pdb=" C6 DA T 18 " 0.002 2.00e-02 2.50e+03 pdb=" N6 DA T 18 " 0.004 2.00e-02 2.50e+03 pdb=" N1 DA T 18 " 0.001 2.00e-02 2.50e+03 pdb=" C2 DA T 18 " -0.001 2.00e-02 2.50e+03 pdb=" N3 DA T 18 " -0.002 2.00e-02 2.50e+03 pdb=" C4 DA T 18 " -0.002 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' DA T 15 " 0.014 2.00e-02 2.50e+03 6.32e-03 1.10e+00 pdb=" N9 DA T 15 " -0.014 2.00e-02 2.50e+03 pdb=" C8 DA T 15 " -0.002 2.00e-02 2.50e+03 pdb=" N7 DA T 15 " 0.001 2.00e-02 2.50e+03 pdb=" C5 DA T 15 " -0.001 2.00e-02 2.50e+03 pdb=" C6 DA T 15 " 0.001 2.00e-02 2.50e+03 pdb=" N6 DA T 15 " 0.005 2.00e-02 2.50e+03 pdb=" N1 DA T 15 " -0.000 2.00e-02 2.50e+03 pdb=" C2 DA T 15 " -0.000 2.00e-02 2.50e+03 pdb=" N3 DA T 15 " -0.002 2.00e-02 2.50e+03 pdb=" C4 DA T 15 " -0.002 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ARG E 167 " -0.017 5.00e-02 4.00e+02 2.51e-02 1.01e+00 pdb=" N PRO E 168 " 0.043 5.00e-02 4.00e+02 pdb=" CA PRO E 168 " -0.013 5.00e-02 4.00e+02 pdb=" CD PRO E 168 " -0.014 5.00e-02 4.00e+02 ... (remaining 4518 not shown) Histogram of nonbonded interaction distances: 2.15 - 2.70: 932 2.70 - 3.25: 26667 3.25 - 3.80: 41632 3.80 - 4.35: 59171 4.35 - 4.90: 95745 Nonbonded interactions: 224147 Sorted by model distance: nonbonded pdb=" OG1 THR G 134 " pdb="CA CA G 401 " model vdw 2.152 2.510 nonbonded pdb=" OG1 THR I 134 " pdb="CA CA I 401 " model vdw 2.152 2.510 nonbonded pdb=" OG1 THR H 134 " pdb="CA CA H 401 " model vdw 2.152 2.510 nonbonded pdb=" OG1 THR D 134 " pdb="CA CA D 401 " model vdw 2.152 2.510 nonbonded pdb=" OG1 THR C 134 " pdb="CA CA C 401 " model vdw 2.152 2.510 ... (remaining 224142 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and resid 21 through 402) selection = (chain 'B' and resid 21 through 401) selection = (chain 'C' and resid 21 through 401) selection = (chain 'D' and resid 21 through 401) selection = (chain 'E' and resid 21 through 401) selection = (chain 'F' and resid 21 through 401) selection = (chain 'G' and resid 21 through 401) selection = (chain 'H' and resid 21 through 401) selection = (chain 'I' and resid 21 through 401) selection = chain 'J' } ncs_group { reference = chain 'K' selection = chain 'L' selection = chain 'M' selection = chain 'N' selection = chain 'O' selection = chain 'P' selection = chain 'Q' selection = chain 'R' selection = chain 'S' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.750 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.380 Check model and map are aligned: 0.060 Set scattering table: 0.070 Process input model: 29.820 Find NCS groups from input model: 0.840 Set up NCS constraints: 0.070 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:8.940 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 40.960 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7966 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.041 26875 Z= 0.327 Angle : 0.522 6.030 36550 Z= 0.283 Chirality : 0.041 0.141 4139 Planarity : 0.003 0.025 4521 Dihedral : 15.391 154.054 10413 Min Nonbonded Distance : 2.152 Molprobity Statistics. All-atom Clashscore : 5.21 Ramachandran Plot: Outliers : 0.31 % Allowed : 6.23 % Favored : 93.46 % Rotamer: Outliers : 1.92 % Allowed : 6.14 % Favored : 91.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.32 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -4.28 (0.11), residues: 3196 helix: -2.99 (0.09), residues: 1360 sheet: -2.18 (0.23), residues: 480 loop : -2.77 (0.12), residues: 1356 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG I 229 TYR 0.009 0.001 TYR B 301 PHE 0.009 0.001 PHE G 126 HIS 0.004 0.002 HIS C 294 Details of bonding type rmsd covalent geometry : bond 0.00738 (26875) covalent geometry : angle 0.52157 (36550) hydrogen bonds : bond 0.25628 ( 1159) hydrogen bonds : angle 9.18582 ( 3100) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6392 Ramachandran restraints generated. 3196 Oldfield, 0 Emsley, 3196 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6392 Ramachandran restraints generated. 3196 Oldfield, 0 Emsley, 3196 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 924 residues out of total 2607 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 874 time to evaluate : 0.983 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 40 LYS cc_start: 0.7490 (mtpp) cc_final: 0.6507 (mtpt) REVERT: A 68 GLU cc_start: 0.7149 (mt-10) cc_final: 0.6568 (tm-30) REVERT: A 94 GLN cc_start: 0.8543 (mm-40) cc_final: 0.8224 (mt0) REVERT: A 176 GLU cc_start: 0.7254 (mm-30) cc_final: 0.6973 (mm-30) REVERT: A 202 GLN cc_start: 0.8343 (mm-40) cc_final: 0.8085 (tt0) REVERT: A 247 ARG cc_start: 0.8231 (mtp-110) cc_final: 0.7992 (mmm-85) REVERT: A 303 ARG cc_start: 0.7845 (mtp180) cc_final: 0.7607 (mtm180) REVERT: A 329 ILE cc_start: 0.8060 (mt) cc_final: 0.7774 (mt) REVERT: B 26 SER cc_start: 0.7862 (p) cc_final: 0.7366 (p) REVERT: B 33 ILE cc_start: 0.8471 (mm) cc_final: 0.8228 (mm) REVERT: B 42 GLU cc_start: 0.7648 (mt-10) cc_final: 0.7296 (mt-10) REVERT: B 43 GLU cc_start: 0.7706 (mt-10) cc_final: 0.7352 (pp20) REVERT: B 94 GLN cc_start: 0.8369 (mm-40) cc_final: 0.8078 (mm-40) REVERT: B 95 ARG cc_start: 0.8061 (ttp80) cc_final: 0.7741 (ttt-90) REVERT: B 206 GLN cc_start: 0.8094 (mt0) cc_final: 0.7863 (mt0) REVERT: B 232 TYR cc_start: 0.9070 (m-80) cc_final: 0.8851 (m-80) REVERT: C 82 VAL cc_start: 0.9006 (OUTLIER) cc_final: 0.8796 (p) REVERT: C 94 GLN cc_start: 0.8010 (mm-40) cc_final: 0.7421 (tp40) REVERT: C 95 ARG cc_start: 0.8339 (ttp80) cc_final: 0.7782 (ttp-170) REVERT: C 107 LYS cc_start: 0.8249 (mmtm) cc_final: 0.7905 (ptpp) REVERT: C 154 GLU cc_start: 0.7672 (mt-10) cc_final: 0.7230 (mt-10) REVERT: C 202 GLN cc_start: 0.8214 (mm-40) cc_final: 0.7717 (mt0) REVERT: C 216 TYR cc_start: 0.8968 (m-80) cc_final: 0.8728 (m-80) REVERT: C 232 TYR cc_start: 0.9196 (m-80) cc_final: 0.8853 (m-80) REVERT: C 251 MET cc_start: 0.8319 (ttm) cc_final: 0.8069 (tpt) REVERT: D 34 ASN cc_start: 0.6981 (OUTLIER) cc_final: 0.6510 (t0) REVERT: D 37 ASP cc_start: 0.6792 (m-30) cc_final: 0.6461 (m-30) REVERT: D 57 LYS cc_start: 0.8277 (tttp) cc_final: 0.8071 (ttpt) REVERT: D 68 GLU cc_start: 0.7845 (mt-10) cc_final: 0.7624 (tp30) REVERT: D 94 GLN cc_start: 0.7989 (mm-40) cc_final: 0.7377 (tm-30) REVERT: D 107 LYS cc_start: 0.8382 (mmtm) cc_final: 0.8164 (mtmt) REVERT: D 181 SER cc_start: 0.8642 (t) cc_final: 0.8438 (t) REVERT: D 330 ASN cc_start: 0.9052 (m-40) cc_final: 0.8818 (m110) REVERT: E 34 ASN cc_start: 0.7170 (OUTLIER) cc_final: 0.6862 (t160) REVERT: E 81 LEU cc_start: 0.8800 (mt) cc_final: 0.8511 (mt) REVERT: E 107 LYS cc_start: 0.8218 (mmtm) cc_final: 0.7751 (ttmt) REVERT: E 196 ASN cc_start: 0.8771 (p0) cc_final: 0.8427 (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: 0.8814 (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: 0.8157 (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: 0.7927 (mtpp) REVERT: G 107 LYS cc_start: 0.7294 (mmtm) cc_final: 0.7081 (ttmm) REVERT: G 187 ASP cc_start: 0.8754 (m-30) cc_final: 0.8523 (m-30) REVERT: G 202 GLN cc_start: 0.8542 (mm-40) cc_final: 0.8186 (mt0) REVERT: G 285 LYS cc_start: 0.8833 (OUTLIER) cc_final: 0.8542 (ptmt) REVERT: G 308 GLU cc_start: 0.8295 (pm20) cc_final: 0.8087 (pm20) REVERT: H 27 ARG cc_start: 0.8046 (mtp-110) cc_final: 0.7366 (tmt170) REVERT: H 39 LYS cc_start: 0.8642 (mttt) cc_final: 0.8285 (mtpm) REVERT: H 94 GLN cc_start: 0.8632 (mm-40) cc_final: 0.8390 (tp40) REVERT: H 125 MET cc_start: 0.8665 (mtp) cc_final: 0.8388 (mtm) REVERT: H 158 MET cc_start: 0.8720 (ttm) cc_final: 0.8329 (ttm) REVERT: H 187 ASP cc_start: 0.8631 (m-30) cc_final: 0.8408 (m-30) REVERT: H 254 ARG cc_start: 0.8386 (ttt-90) cc_final: 0.8103 (tmm-80) REVERT: I 27 ARG cc_start: 0.8444 (mtp-110) cc_final: 0.8224 (mtp-110) REVERT: I 33 ILE cc_start: 0.8221 (mm) cc_final: 0.7936 (mm) REVERT: I 39 LYS cc_start: 0.8739 (mttt) cc_final: 0.8394 (mmmm) REVERT: I 40 LYS cc_start: 0.8562 (mtpp) cc_final: 0.8065 (mtmm) REVERT: I 50 GLU cc_start: 0.8810 (mp0) cc_final: 0.8574 (mp0) REVERT: I 94 GLN cc_start: 0.8826 (mm-40) cc_final: 0.8549 (tp40) REVERT: I 125 MET cc_start: 0.8812 (mtp) cc_final: 0.8498 (mtp) REVERT: I 223 SER cc_start: 0.9124 (t) cc_final: 0.8903 (t) REVERT: I 247 ARG cc_start: 0.8240 (mtp-110) cc_final: 0.8033 (mtp85) REVERT: I 285 LYS cc_start: 0.8887 (OUTLIER) cc_final: 0.8684 (ptpt) REVERT: I 322 GLU cc_start: 0.7731 (tt0) cc_final: 0.7496 (tt0) REVERT: J 38 VAL cc_start: 0.8027 (t) cc_final: 0.7799 (m) REVERT: J 39 LYS cc_start: 0.8539 (mttt) cc_final: 0.7774 (mmmt) REVERT: J 40 LYS cc_start: 0.8232 (mtpp) cc_final: 0.7632 (mtpt) REVERT: J 50 GLU cc_start: 0.8500 (mp0) cc_final: 0.8120 (mp0) REVERT: J 73 LYS cc_start: 0.6797 (mttt) cc_final: 0.6358 (tptt) REVERT: J 101 GLN cc_start: 0.8832 (mt0) cc_final: 0.8478 (mt0) REVERT: J 112 LEU cc_start: 0.8659 (tp) cc_final: 0.8446 (tp) REVERT: J 184 ASP cc_start: 0.7989 (m-30) cc_final: 0.7787 (m-30) REVERT: J 231 ASP cc_start: 0.8638 (m-30) cc_final: 0.8397 (m-30) REVERT: J 249 LEU cc_start: 0.9057 (mt) cc_final: 0.8793 (mp) REVERT: J 308 GLU cc_start: 0.7778 (pm20) cc_final: 0.7514 (mt-10) REVERT: J 332 ASP cc_start: 0.8251 (p0) cc_final: 0.8019 (p0) outliers start: 50 outliers final: 5 residues processed: 900 average time/residue: 0.7864 time to fit residues: 799.2334 Evaluate side-chains 623 residues out of total 2607 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 613 time to evaluate : 0.928 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 82 VAL Chi-restraints excluded: chain A residue 125 MET Chi-restraints excluded: chain B residue 99 ILE Chi-restraints excluded: chain C residue 82 VAL Chi-restraints excluded: chain D residue 34 ASN Chi-restraints excluded: chain E residue 34 ASN Chi-restraints excluded: chain G residue 285 LYS Chi-restraints excluded: chain H residue 82 VAL Chi-restraints excluded: chain H residue 149 ASP Chi-restraints excluded: chain I residue 285 LYS Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 323 random chunks: chunk 197 optimal weight: 1.9990 chunk 215 optimal weight: 0.9990 chunk 20 optimal weight: 0.9980 chunk 132 optimal weight: 0.8980 chunk 261 optimal weight: 0.6980 chunk 248 optimal weight: 10.0000 chunk 207 optimal weight: 2.9990 chunk 155 optimal weight: 7.9990 chunk 244 optimal weight: 1.9990 chunk 183 optimal weight: 3.9990 chunk 298 optimal weight: 0.6980 overall best weight: 0.8582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 135 GLN A 244 HIS A 330 ASN B 145 GLN B 202 GLN B 244 HIS C 23 GLN C 30 GLN C 145 GLN C 244 HIS D 30 GLN D 135 GLN D 202 GLN D 244 HIS D 330 ASN ** E 145 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 244 HIS F 244 HIS G 242 GLN G 244 HIS ** H 145 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 244 HIS J 34 ASN J 135 GLN Total number of N/Q/H flips: 22 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3667 r_free = 0.3667 target = 0.146826 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3270 r_free = 0.3270 target = 0.112412 restraints weight = 32161.285| |-----------------------------------------------------------------------------| r_work (start): 0.3218 rms_B_bonded: 2.00 r_work: 0.3097 rms_B_bonded: 2.66 restraints_weight: 0.5000 r_work: 0.2968 rms_B_bonded: 4.35 restraints_weight: 0.2500 r_work (final): 0.2968 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7969 moved from start: 0.2389 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 26875 Z= 0.131 Angle : 0.502 6.565 36550 Z= 0.268 Chirality : 0.039 0.153 4139 Planarity : 0.004 0.036 4521 Dihedral : 14.003 148.016 4476 Min Nonbonded Distance : 2.232 Molprobity Statistics. All-atom Clashscore : 6.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.44 % Favored : 98.56 % Rotamer: Outliers : 3.15 % Allowed : 17.68 % Favored : 79.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.32 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.14 (0.13), residues: 3196 helix: -0.80 (0.12), residues: 1410 sheet: -1.37 (0.23), residues: 490 loop : -2.03 (0.14), residues: 1296 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG F 215 TYR 0.007 0.001 TYR I 301 PHE 0.010 0.001 PHE E 248 HIS 0.003 0.001 HIS G 244 Details of bonding type rmsd covalent geometry : bond 0.00280 (26875) covalent geometry : angle 0.50207 (36550) hydrogen bonds : bond 0.04123 ( 1159) hydrogen bonds : angle 4.93848 ( 3100) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6392 Ramachandran restraints generated. 3196 Oldfield, 0 Emsley, 3196 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6392 Ramachandran restraints generated. 3196 Oldfield, 0 Emsley, 3196 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 826 residues out of total 2607 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 82 poor density : 744 time to evaluate : 0.956 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 37 ASP cc_start: 0.7031 (m-30) cc_final: 0.6758 (m-30) REVERT: A 40 LYS cc_start: 0.6850 (mtpp) cc_final: 0.6129 (mtpt) REVERT: A 42 GLU cc_start: 0.6621 (pt0) cc_final: 0.6410 (pt0) REVERT: A 68 GLU cc_start: 0.6755 (mt-10) cc_final: 0.6108 (tm-30) REVERT: A 77 GLU cc_start: 0.7660 (OUTLIER) cc_final: 0.7265 (mp0) REVERT: A 84 MET cc_start: 0.8864 (mtp) cc_final: 0.8656 (mtp) REVERT: A 107 LYS cc_start: 0.7139 (mmtm) cc_final: 0.6680 (mttm) REVERT: A 130 ARG cc_start: 0.7175 (OUTLIER) cc_final: 0.5574 (ptp90) REVERT: A 145 GLN cc_start: 0.8458 (mt0) cc_final: 0.8190 (mt0) REVERT: A 186 LEU cc_start: 0.8339 (mm) cc_final: 0.8125 (mm) REVERT: A 202 GLN cc_start: 0.8250 (mm-40) cc_final: 0.7885 (tt0) REVERT: A 210 MET cc_start: 0.7946 (mtp) cc_final: 0.7370 (mtp) REVERT: A 247 ARG cc_start: 0.7275 (mtp-110) cc_final: 0.6802 (mmm-85) REVERT: A 254 ARG cc_start: 0.7420 (ttp80) cc_final: 0.7052 (tmt90) REVERT: A 303 ARG cc_start: 0.7420 (mtp180) cc_final: 0.6677 (mtm180) REVERT: A 308 GLU cc_start: 0.7135 (pt0) cc_final: 0.6772 (tt0) REVERT: A 324 GLU cc_start: 0.8205 (mt-10) cc_final: 0.7829 (mt-10) REVERT: A 329 ILE cc_start: 0.8609 (mt) cc_final: 0.8184 (mt) REVERT: B 30 GLN cc_start: 0.6761 (mp10) cc_final: 0.6473 (mp10) REVERT: B 42 GLU cc_start: 0.7420 (mt-10) cc_final: 0.6941 (mt-10) REVERT: B 43 GLU cc_start: 0.7587 (mt-10) cc_final: 0.7221 (mt-10) REVERT: B 95 ARG cc_start: 0.7837 (ttp80) cc_final: 0.7259 (ttt-90) REVERT: B 107 LYS cc_start: 0.7739 (mmtm) cc_final: 0.6866 (ptpt) REVERT: B 206 GLN cc_start: 0.7530 (mt0) cc_final: 0.7035 (mt0) REVERT: B 235 ARG cc_start: 0.8966 (ttp-170) cc_final: 0.8632 (ttp80) REVERT: B 306 ARG cc_start: 0.7607 (tpp80) cc_final: 0.6966 (ptm-80) REVERT: B 324 GLU cc_start: 0.8314 (mt-10) cc_final: 0.8067 (mt-10) REVERT: B 332 ASP cc_start: 0.8809 (p0) cc_final: 0.8566 (p0) REVERT: C 80 LYS cc_start: 0.7961 (mtmm) cc_final: 0.7578 (ttpp) REVERT: C 82 VAL cc_start: 0.8899 (OUTLIER) cc_final: 0.8634 (p) REVERT: C 94 GLN cc_start: 0.7739 (mm-40) cc_final: 0.6951 (tp40) REVERT: C 95 ARG cc_start: 0.8189 (ttp80) cc_final: 0.7763 (ttm170) REVERT: C 107 LYS cc_start: 0.7870 (mmtm) cc_final: 0.7198 (ptpp) REVERT: C 154 GLU cc_start: 0.7744 (mt-10) cc_final: 0.6942 (mt-10) REVERT: C 181 SER cc_start: 0.8634 (t) cc_final: 0.8172 (p) REVERT: C 202 GLN cc_start: 0.7971 (mm-40) cc_final: 0.7420 (mt0) REVERT: C 216 TYR cc_start: 0.8978 (m-80) cc_final: 0.8611 (m-80) REVERT: C 222 ASP cc_start: 0.8785 (t70) cc_final: 0.8473 (t70) REVERT: C 251 MET cc_start: 0.8197 (ttm) cc_final: 0.7715 (mtt) REVERT: C 308 GLU cc_start: 0.8497 (pm20) cc_final: 0.8009 (pm20) REVERT: C 334 VAL cc_start: 0.9246 (t) cc_final: 0.8930 (p) REVERT: D 27 ARG cc_start: 0.8443 (OUTLIER) cc_final: 0.7366 (mtp180) REVERT: D 37 ASP cc_start: 0.7107 (m-30) cc_final: 0.6766 (m-30) REVERT: D 57 LYS cc_start: 0.7968 (tttp) cc_final: 0.7667 (ttpt) REVERT: D 68 GLU cc_start: 0.8031 (mt-10) cc_final: 0.7692 (tp30) REVERT: D 94 GLN cc_start: 0.7601 (mm-40) cc_final: 0.6998 (tm-30) REVERT: D 107 LYS cc_start: 0.8309 (mmtm) cc_final: 0.7936 (mtmt) REVERT: D 181 SER cc_start: 0.9018 (t) cc_final: 0.8480 (p) REVERT: D 187 ASP cc_start: 0.8973 (OUTLIER) cc_final: 0.8614 (t70) REVERT: D 334 VAL cc_start: 0.9190 (t) cc_final: 0.8888 (p) REVERT: E 68 GLU cc_start: 0.7862 (mp0) cc_final: 0.7355 (tp30) REVERT: E 98 GLU cc_start: 0.8431 (tp30) cc_final: 0.8179 (mm-30) REVERT: E 107 LYS cc_start: 0.8021 (mmtm) cc_final: 0.7553 (mtmt) REVERT: E 176 GLU cc_start: 0.8513 (mm-30) cc_final: 0.7986 (tt0) REVERT: E 202 GLN cc_start: 0.7912 (mm-40) cc_final: 0.7660 (mt0) REVERT: F 39 LYS cc_start: 0.7354 (mttt) cc_final: 0.6491 (mtpp) REVERT: F 43 GLU cc_start: 0.7879 (mt-10) cc_final: 0.7334 (mp0) REVERT: F 68 GLU cc_start: 0.7872 (mt-10) cc_final: 0.7652 (mp0) REVERT: F 95 ARG cc_start: 0.8213 (ttp80) cc_final: 0.7900 (ttp-110) REVERT: F 187 ASP cc_start: 0.8786 (m-30) cc_final: 0.8557 (m-30) REVERT: F 202 GLN cc_start: 0.8106 (mm-40) cc_final: 0.7738 (mt0) REVERT: G 29 GLU cc_start: 0.8663 (mt-10) cc_final: 0.8461 (mt-10) REVERT: G 39 LYS cc_start: 0.7761 (mttt) cc_final: 0.7327 (mtpp) REVERT: G 94 GLN cc_start: 0.7810 (OUTLIER) cc_final: 0.7518 (tp-100) REVERT: G 98 GLU cc_start: 0.8239 (mm-30) cc_final: 0.8008 (mm-30) REVERT: G 107 LYS cc_start: 0.7109 (mmtm) cc_final: 0.6583 (ttmm) REVERT: G 176 GLU cc_start: 0.8205 (mm-30) cc_final: 0.7860 (mm-30) REVERT: G 177 ARG cc_start: 0.8700 (tmm-80) cc_final: 0.8488 (ttt-90) REVERT: G 187 ASP cc_start: 0.8787 (m-30) cc_final: 0.8441 (m-30) REVERT: G 202 GLN cc_start: 0.8029 (mm-40) cc_final: 0.7751 (mt0) REVERT: G 247 ARG cc_start: 0.8208 (mtp-110) cc_final: 0.7860 (mtp85) REVERT: G 300 LEU cc_start: 0.8430 (OUTLIER) cc_final: 0.8146 (mt) REVERT: G 308 GLU cc_start: 0.8317 (pm20) cc_final: 0.7941 (pm20) REVERT: H 27 ARG cc_start: 0.7732 (mtp-110) cc_final: 0.7284 (tmt170) REVERT: H 39 LYS cc_start: 0.7699 (mttt) cc_final: 0.7410 (mtpm) REVERT: H 66 ILE cc_start: 0.8366 (mm) cc_final: 0.8066 (mp) REVERT: H 94 GLN cc_start: 0.8468 (mm-40) cc_final: 0.8216 (tp40) REVERT: H 96 ARG cc_start: 0.7804 (ttt90) cc_final: 0.7572 (ttt180) REVERT: H 187 ASP cc_start: 0.8556 (m-30) cc_final: 0.8313 (m-30) REVERT: H 205 TYR cc_start: 0.8629 (m-80) cc_final: 0.8337 (m-10) REVERT: H 210 MET cc_start: 0.8720 (mtp) cc_final: 0.8454 (mtm) REVERT: H 247 ARG cc_start: 0.7959 (mtp-110) cc_final: 0.7380 (mmm160) REVERT: H 254 ARG cc_start: 0.8090 (ttt-90) cc_final: 0.7824 (tmm-80) REVERT: H 258 GLU cc_start: 0.8143 (mt-10) cc_final: 0.7936 (mt-10) REVERT: I 27 ARG cc_start: 0.8143 (mtp-110) cc_final: 0.7868 (mtp-110) REVERT: I 39 LYS cc_start: 0.8144 (mttt) cc_final: 0.7795 (mmmm) REVERT: I 40 LYS cc_start: 0.7701 (mtpp) cc_final: 0.7220 (mtmm) REVERT: I 50 GLU cc_start: 0.8627 (mp0) cc_final: 0.7770 (mp0) REVERT: I 110 ASP cc_start: 0.8644 (m-30) cc_final: 0.8340 (m-30) REVERT: I 154 GLU cc_start: 0.8013 (mt-10) cc_final: 0.7803 (mt-10) REVERT: I 176 GLU cc_start: 0.7331 (mm-30) cc_final: 0.7015 (tm-30) REVERT: I 215 ARG cc_start: 0.7963 (tmm160) cc_final: 0.7745 (tmm160) REVERT: I 223 SER cc_start: 0.9338 (t) cc_final: 0.9132 (t) REVERT: I 247 ARG cc_start: 0.7847 (mtp-110) cc_final: 0.7414 (mtp85) REVERT: I 322 GLU cc_start: 0.8160 (tt0) cc_final: 0.7810 (tt0) REVERT: J 39 LYS cc_start: 0.7137 (mttt) cc_final: 0.6385 (mmmt) REVERT: J 40 LYS cc_start: 0.6974 (mtpp) cc_final: 0.6516 (mtpt) REVERT: J 42 GLU cc_start: 0.7058 (mt-10) cc_final: 0.6716 (tp30) REVERT: J 50 GLU cc_start: 0.7903 (mp0) cc_final: 0.7295 (mp0) REVERT: J 68 GLU cc_start: 0.7519 (mt-10) cc_final: 0.7143 (tm-30) REVERT: J 73 LYS cc_start: 0.6818 (mttt) cc_final: 0.5971 (tptt) REVERT: J 77 GLU cc_start: 0.7166 (mp0) cc_final: 0.5990 (mp0) REVERT: J 95 ARG cc_start: 0.8063 (ttp-170) cc_final: 0.7660 (ttm110) REVERT: J 110 ASP cc_start: 0.8080 (m-30) cc_final: 0.7870 (m-30) REVERT: J 124 GLU cc_start: 0.9093 (tt0) cc_final: 0.8804 (tt0) REVERT: J 154 GLU cc_start: 0.7973 (mt-10) cc_final: 0.7439 (mm-30) REVERT: J 183 SER cc_start: 0.8459 (m) cc_final: 0.8228 (m) REVERT: J 184 ASP cc_start: 0.8454 (m-30) cc_final: 0.8122 (m-30) REVERT: J 231 ASP cc_start: 0.8539 (m-30) cc_final: 0.8321 (m-30) REVERT: J 243 MET cc_start: 0.8671 (mtm) cc_final: 0.8460 (mtp) REVERT: J 247 ARG cc_start: 0.7368 (mtp-110) cc_final: 0.6715 (ttm-80) REVERT: J 258 GLU cc_start: 0.7704 (mt-10) cc_final: 0.7074 (tp30) REVERT: J 308 GLU cc_start: 0.7876 (pm20) cc_final: 0.7098 (mt-10) REVERT: J 332 ASP cc_start: 0.8183 (p0) cc_final: 0.7847 (p0) outliers start: 82 outliers final: 27 residues processed: 787 average time/residue: 0.7124 time to fit residues: 637.5588 Evaluate side-chains 677 residues out of total 2607 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 643 time to evaluate : 0.865 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 77 GLU Chi-restraints excluded: chain A residue 82 VAL Chi-restraints excluded: chain A residue 130 ARG Chi-restraints excluded: chain B residue 31 CYS Chi-restraints excluded: chain B residue 82 VAL Chi-restraints excluded: chain B residue 99 ILE Chi-restraints excluded: chain B residue 272 GLN Chi-restraints excluded: chain C residue 43 GLU Chi-restraints excluded: chain C residue 82 VAL Chi-restraints excluded: chain C residue 99 ILE Chi-restraints excluded: chain D residue 27 ARG Chi-restraints excluded: chain D residue 125 MET Chi-restraints excluded: chain D residue 187 ASP Chi-restraints excluded: chain D residue 272 GLN Chi-restraints excluded: chain E residue 87 THR Chi-restraints excluded: chain E residue 125 MET Chi-restraints excluded: chain E residue 161 ASP Chi-restraints excluded: chain F residue 97 SER Chi-restraints excluded: chain F residue 112 LEU Chi-restraints excluded: chain F residue 125 MET Chi-restraints excluded: chain F residue 272 GLN Chi-restraints excluded: chain G residue 94 GLN Chi-restraints excluded: chain G residue 161 ASP Chi-restraints excluded: chain G residue 272 GLN Chi-restraints excluded: chain G residue 300 LEU Chi-restraints excluded: chain H residue 82 VAL Chi-restraints excluded: chain H residue 90 THR Chi-restraints excluded: chain H residue 109 LEU Chi-restraints excluded: chain H residue 308 GLU Chi-restraints excluded: chain I residue 97 SER Chi-restraints excluded: chain I residue 99 ILE Chi-restraints excluded: chain I residue 183 SER Chi-restraints excluded: chain I residue 201 THR Chi-restraints excluded: chain J residue 100 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 323 random chunks: chunk 242 optimal weight: 2.9990 chunk 9 optimal weight: 0.7980 chunk 196 optimal weight: 3.9990 chunk 226 optimal weight: 4.9990 chunk 259 optimal weight: 4.9990 chunk 269 optimal weight: 7.9990 chunk 109 optimal weight: 3.9990 chunk 11 optimal weight: 0.3980 chunk 218 optimal weight: 9.9990 chunk 19 optimal weight: 3.9990 chunk 251 optimal weight: 5.9990 overall best weight: 2.4386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 135 GLN B 145 GLN B 202 GLN C 272 GLN ** D 145 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 93 HIS ** E 145 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 23 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3631 r_free = 0.3631 target = 0.143592 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3226 r_free = 0.3226 target = 0.109173 restraints weight = 32377.103| |-----------------------------------------------------------------------------| r_work (start): 0.3199 rms_B_bonded: 1.98 r_work: 0.3080 rms_B_bonded: 2.62 restraints_weight: 0.5000 r_work: 0.2951 rms_B_bonded: 4.29 restraints_weight: 0.2500 r_work (final): 0.2951 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8016 moved from start: 0.2744 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.040 26875 Z= 0.216 Angle : 0.535 8.411 36550 Z= 0.282 Chirality : 0.041 0.146 4139 Planarity : 0.004 0.045 4521 Dihedral : 14.026 144.792 4459 Min Nonbonded Distance : 2.180 Molprobity Statistics. All-atom Clashscore : 6.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.38 % Favored : 97.62 % Rotamer: Outliers : 4.07 % Allowed : 19.91 % Favored : 76.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.32 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.28 (0.14), residues: 3196 helix: 0.09 (0.14), residues: 1380 sheet: -0.50 (0.27), residues: 380 loop : -1.89 (0.13), residues: 1436 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG D 215 TYR 0.013 0.001 TYR C 228 PHE 0.012 0.001 PHE F 126 HIS 0.005 0.001 HIS I 294 Details of bonding type rmsd covalent geometry : bond 0.00495 (26875) covalent geometry : angle 0.53545 (36550) hydrogen bonds : bond 0.04334 ( 1159) hydrogen bonds : angle 4.65521 ( 3100) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6392 Ramachandran restraints generated. 3196 Oldfield, 0 Emsley, 3196 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6392 Ramachandran restraints generated. 3196 Oldfield, 0 Emsley, 3196 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 758 residues out of total 2607 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 106 poor density : 652 time to evaluate : 1.080 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 40 LYS cc_start: 0.6930 (mtpp) cc_final: 0.6247 (mtpt) REVERT: A 42 GLU cc_start: 0.6720 (pt0) cc_final: 0.6514 (pt0) REVERT: A 66 ILE cc_start: 0.6985 (OUTLIER) cc_final: 0.6544 (tt) REVERT: A 68 GLU cc_start: 0.6595 (mt-10) cc_final: 0.6055 (tm-30) REVERT: A 70 LYS cc_start: 0.6566 (ttpt) cc_final: 0.6319 (ttpt) REVERT: A 77 GLU cc_start: 0.7971 (OUTLIER) cc_final: 0.7607 (mp0) REVERT: A 98 GLU cc_start: 0.7746 (mt-10) cc_final: 0.7509 (mm-30) REVERT: A 107 LYS cc_start: 0.7186 (mmtm) cc_final: 0.6779 (mttm) REVERT: A 130 ARG cc_start: 0.7408 (OUTLIER) cc_final: 0.7185 (ttp80) REVERT: A 145 GLN cc_start: 0.8618 (mt0) cc_final: 0.8290 (mt0) REVERT: A 202 GLN cc_start: 0.8100 (mm-40) cc_final: 0.7695 (tt0) REVERT: A 210 MET cc_start: 0.8132 (mtp) cc_final: 0.7495 (mtp) REVERT: A 247 ARG cc_start: 0.7343 (mtp-110) cc_final: 0.6860 (mmm-85) REVERT: A 254 ARG cc_start: 0.7484 (ttp80) cc_final: 0.7123 (tmt90) REVERT: A 303 ARG cc_start: 0.7514 (mtp180) cc_final: 0.6861 (mtm180) REVERT: A 308 GLU cc_start: 0.7314 (pt0) cc_final: 0.6761 (tt0) REVERT: A 329 ILE cc_start: 0.8638 (mt) cc_final: 0.8033 (mt) REVERT: B 42 GLU cc_start: 0.7380 (mt-10) cc_final: 0.6932 (mt-10) REVERT: B 43 GLU cc_start: 0.7629 (mt-10) cc_final: 0.6901 (pp20) REVERT: B 77 GLU cc_start: 0.7780 (mp0) cc_final: 0.7267 (mm-30) REVERT: B 95 ARG cc_start: 0.7954 (ttp80) cc_final: 0.7559 (ttt-90) REVERT: B 107 LYS cc_start: 0.7720 (mmtm) cc_final: 0.6804 (ptpt) REVERT: B 324 GLU cc_start: 0.8454 (mt-10) cc_final: 0.8223 (mt-10) REVERT: B 332 ASP cc_start: 0.8795 (p0) cc_final: 0.8496 (p0) REVERT: C 80 LYS cc_start: 0.7770 (mtmm) cc_final: 0.7434 (ttpp) REVERT: C 94 GLN cc_start: 0.7808 (mm-40) cc_final: 0.7023 (tm-30) REVERT: C 95 ARG cc_start: 0.8197 (ttp80) cc_final: 0.7559 (ttp-170) REVERT: C 107 LYS cc_start: 0.8183 (mmtm) cc_final: 0.7504 (ptmt) REVERT: C 145 GLN cc_start: 0.8949 (mt0) cc_final: 0.8398 (mp10) REVERT: C 154 GLU cc_start: 0.7725 (mt-10) cc_final: 0.6874 (mt-10) REVERT: C 181 SER cc_start: 0.8780 (t) cc_final: 0.8507 (p) REVERT: C 187 ASP cc_start: 0.8687 (OUTLIER) cc_final: 0.8449 (m-30) REVERT: C 202 GLN cc_start: 0.7925 (mm-40) cc_final: 0.7451 (mt0) REVERT: C 216 TYR cc_start: 0.9055 (m-80) cc_final: 0.8792 (m-80) REVERT: C 243 MET cc_start: 0.8363 (mtm) cc_final: 0.7986 (mtt) REVERT: C 308 GLU cc_start: 0.8588 (pm20) cc_final: 0.8097 (pm20) REVERT: D 37 ASP cc_start: 0.7245 (m-30) cc_final: 0.6766 (m-30) REVERT: D 57 LYS cc_start: 0.7957 (tttp) cc_final: 0.7673 (ttpt) REVERT: D 68 GLU cc_start: 0.8171 (mt-10) cc_final: 0.7564 (tp30) REVERT: D 72 ASP cc_start: 0.7816 (m-30) cc_final: 0.7336 (m-30) REVERT: D 94 GLN cc_start: 0.7719 (mm-40) cc_final: 0.6930 (tm-30) REVERT: D 107 LYS cc_start: 0.8326 (mmtm) cc_final: 0.7931 (mtmt) REVERT: D 181 SER cc_start: 0.8993 (t) cc_final: 0.8789 (t) REVERT: D 187 ASP cc_start: 0.9030 (OUTLIER) cc_final: 0.8640 (t70) REVERT: D 247 ARG cc_start: 0.8046 (mtp-110) cc_final: 0.7746 (ttt-90) REVERT: D 334 VAL cc_start: 0.9163 (t) cc_final: 0.8904 (p) REVERT: E 68 GLU cc_start: 0.7877 (mp0) cc_final: 0.7392 (tp30) REVERT: E 107 LYS cc_start: 0.8036 (mmtm) cc_final: 0.7605 (mtmt) REVERT: E 176 GLU cc_start: 0.8469 (mm-30) cc_final: 0.7925 (tt0) REVERT: F 39 LYS cc_start: 0.7365 (mttt) cc_final: 0.6600 (mtmt) REVERT: F 43 GLU cc_start: 0.7900 (mt-10) cc_final: 0.7361 (mp0) REVERT: F 68 GLU cc_start: 0.7928 (mt-10) cc_final: 0.7599 (mp0) REVERT: F 95 ARG cc_start: 0.8199 (ttp80) cc_final: 0.7821 (ttp-110) REVERT: F 187 ASP cc_start: 0.8676 (m-30) cc_final: 0.8360 (m-30) REVERT: F 202 GLN cc_start: 0.8210 (mm-40) cc_final: 0.7774 (mt0) REVERT: F 223 SER cc_start: 0.9240 (t) cc_final: 0.8943 (p) REVERT: G 39 LYS cc_start: 0.7729 (mttt) cc_final: 0.7369 (mtpp) REVERT: G 91 GLU cc_start: 0.8232 (OUTLIER) cc_final: 0.7840 (tt0) REVERT: G 94 GLN cc_start: 0.7854 (OUTLIER) cc_final: 0.7572 (tp-100) REVERT: G 107 LYS cc_start: 0.7228 (mmtm) cc_final: 0.6618 (ttmm) REVERT: G 142 VAL cc_start: 0.9170 (t) cc_final: 0.8933 (p) REVERT: G 176 GLU cc_start: 0.8239 (mm-30) cc_final: 0.7899 (mm-30) REVERT: G 187 ASP cc_start: 0.8568 (m-30) cc_final: 0.8207 (m-30) REVERT: G 202 GLN cc_start: 0.8083 (mm-40) cc_final: 0.7782 (mt0) REVERT: G 247 ARG cc_start: 0.8226 (mtp-110) cc_final: 0.7938 (mtp85) REVERT: G 300 LEU cc_start: 0.8471 (OUTLIER) cc_final: 0.8266 (mt) REVERT: G 308 GLU cc_start: 0.8265 (pm20) cc_final: 0.7864 (pm20) REVERT: H 27 ARG cc_start: 0.7816 (mtp-110) cc_final: 0.7186 (tmt170) REVERT: H 39 LYS cc_start: 0.7693 (mttt) cc_final: 0.7419 (mtpm) REVERT: H 66 ILE cc_start: 0.8313 (mm) cc_final: 0.7985 (mp) REVERT: H 94 GLN cc_start: 0.8435 (mm-40) cc_final: 0.8133 (tp40) REVERT: H 125 MET cc_start: 0.9060 (mtp) cc_final: 0.8736 (mtp) REVERT: H 205 TYR cc_start: 0.8727 (m-80) cc_final: 0.8363 (m-80) REVERT: H 210 MET cc_start: 0.8698 (mtp) cc_final: 0.8425 (mtm) REVERT: H 247 ARG cc_start: 0.7973 (mtp-110) cc_final: 0.7369 (mmm160) REVERT: H 254 ARG cc_start: 0.8171 (ttt-90) cc_final: 0.7779 (tmm-80) REVERT: I 27 ARG cc_start: 0.8135 (mtp-110) cc_final: 0.7782 (mtp-110) REVERT: I 37 ASP cc_start: 0.7642 (m-30) cc_final: 0.7428 (m-30) REVERT: I 39 LYS cc_start: 0.7971 (mttt) cc_final: 0.7692 (mmmm) REVERT: I 40 LYS cc_start: 0.7683 (mtpp) cc_final: 0.7261 (mttp) REVERT: I 43 GLU cc_start: 0.7714 (mt-10) cc_final: 0.7285 (tp30) REVERT: I 50 GLU cc_start: 0.8598 (mp0) cc_final: 0.7653 (mp0) REVERT: I 91 GLU cc_start: 0.8129 (mt-10) cc_final: 0.7221 (tm-30) REVERT: I 176 GLU cc_start: 0.7251 (mm-30) cc_final: 0.6976 (tm-30) REVERT: I 223 SER cc_start: 0.9337 (t) cc_final: 0.9074 (t) REVERT: I 247 ARG cc_start: 0.7893 (mtp-110) cc_final: 0.7360 (mtp85) REVERT: I 322 GLU cc_start: 0.8141 (tt0) cc_final: 0.7876 (tt0) REVERT: I 332 ASP cc_start: 0.8266 (p0) cc_final: 0.8041 (p0) REVERT: J 39 LYS cc_start: 0.7128 (mttt) cc_final: 0.6456 (mmmt) REVERT: J 40 LYS cc_start: 0.7177 (mtpp) cc_final: 0.6709 (mtpt) REVERT: J 42 GLU cc_start: 0.7056 (mt-10) cc_final: 0.6796 (tp30) REVERT: J 50 GLU cc_start: 0.7999 (mp0) cc_final: 0.7221 (mp0) REVERT: J 68 GLU cc_start: 0.7424 (mt-10) cc_final: 0.7224 (tm-30) REVERT: J 73 LYS cc_start: 0.6770 (mttt) cc_final: 0.6134 (tptt) REVERT: J 77 GLU cc_start: 0.7330 (mp0) cc_final: 0.6676 (mp0) REVERT: J 95 ARG cc_start: 0.7998 (ttp-170) cc_final: 0.7643 (ttm110) REVERT: J 109 LEU cc_start: 0.8589 (OUTLIER) cc_final: 0.8322 (mp) REVERT: J 110 ASP cc_start: 0.8184 (m-30) cc_final: 0.7799 (m-30) REVERT: J 184 ASP cc_start: 0.8486 (m-30) cc_final: 0.8015 (m-30) REVERT: J 187 ASP cc_start: 0.8391 (OUTLIER) cc_final: 0.8069 (m-30) REVERT: J 247 ARG cc_start: 0.7597 (mtp-110) cc_final: 0.7374 (mtp85) REVERT: J 308 GLU cc_start: 0.7896 (pm20) cc_final: 0.7001 (mt-10) REVERT: J 332 ASP cc_start: 0.8241 (p0) cc_final: 0.7873 (p0) outliers start: 106 outliers final: 50 residues processed: 704 average time/residue: 0.6996 time to fit residues: 559.1379 Evaluate side-chains 680 residues out of total 2607 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 620 time to evaluate : 0.978 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 66 ILE Chi-restraints excluded: chain A residue 77 GLU Chi-restraints excluded: chain A residue 82 VAL Chi-restraints excluded: chain A residue 87 THR Chi-restraints excluded: chain A residue 106 SER Chi-restraints excluded: chain A residue 130 ARG Chi-restraints excluded: chain B residue 31 CYS Chi-restraints excluded: chain B residue 82 VAL Chi-restraints excluded: chain B residue 223 SER Chi-restraints excluded: chain B residue 272 GLN Chi-restraints excluded: chain C residue 43 GLU Chi-restraints excluded: chain C residue 99 ILE Chi-restraints excluded: chain C residue 104 THR Chi-restraints excluded: chain C residue 187 ASP Chi-restraints excluded: chain C residue 274 ASP Chi-restraints excluded: chain D residue 97 SER Chi-restraints excluded: chain D residue 121 SER Chi-restraints excluded: chain D residue 125 MET Chi-restraints excluded: chain D residue 187 ASP Chi-restraints excluded: chain D residue 222 ASP Chi-restraints excluded: chain D residue 272 GLN Chi-restraints excluded: chain E residue 87 THR Chi-restraints excluded: chain E residue 125 MET Chi-restraints excluded: chain E residue 161 ASP Chi-restraints excluded: chain E residue 334 VAL Chi-restraints excluded: chain F residue 26 SER Chi-restraints excluded: chain F residue 94 GLN Chi-restraints excluded: chain F residue 97 SER Chi-restraints excluded: chain F residue 112 LEU Chi-restraints excluded: chain F residue 145 GLN Chi-restraints excluded: chain F residue 272 GLN Chi-restraints excluded: chain F residue 297 THR Chi-restraints excluded: chain G residue 38 VAL Chi-restraints excluded: chain G residue 91 GLU Chi-restraints excluded: chain G residue 94 GLN Chi-restraints excluded: chain G residue 97 SER Chi-restraints excluded: chain G residue 125 MET Chi-restraints excluded: chain G residue 161 ASP Chi-restraints excluded: chain G residue 272 GLN Chi-restraints excluded: chain G residue 300 LEU Chi-restraints excluded: chain H residue 82 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 88 THR Chi-restraints excluded: chain J residue 97 SER Chi-restraints excluded: chain J residue 109 LEU Chi-restraints excluded: chain J residue 187 ASP Chi-restraints excluded: chain J residue 214 SER Chi-restraints excluded: chain J residue 255 LEU Chi-restraints excluded: chain J residue 322 GLU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 323 random chunks: chunk 93 optimal weight: 10.0000 chunk 17 optimal weight: 8.9990 chunk 296 optimal weight: 10.0000 chunk 232 optimal weight: 0.9990 chunk 161 optimal weight: 2.9990 chunk 61 optimal weight: 10.0000 chunk 133 optimal weight: 5.9990 chunk 9 optimal weight: 3.9990 chunk 136 optimal weight: 1.9990 chunk 69 optimal weight: 2.9990 chunk 155 optimal weight: 7.9990 overall best weight: 2.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 272 GLN ** D 145 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 145 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3627 r_free = 0.3627 target = 0.143455 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3231 r_free = 0.3231 target = 0.109564 restraints weight = 32379.562| |-----------------------------------------------------------------------------| r_work (start): 0.3178 rms_B_bonded: 1.97 r_work: 0.3056 rms_B_bonded: 2.61 restraints_weight: 0.5000 r_work: 0.2929 rms_B_bonded: 4.25 restraints_weight: 0.2500 r_work (final): 0.2929 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8048 moved from start: 0.2986 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.036 26875 Z= 0.225 Angle : 0.535 8.839 36550 Z= 0.282 Chirality : 0.042 0.135 4139 Planarity : 0.004 0.046 4521 Dihedral : 13.999 144.276 4456 Min Nonbonded Distance : 2.179 Molprobity Statistics. All-atom Clashscore : 6.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.10 % Favored : 97.90 % Rotamer: Outliers : 4.64 % Allowed : 20.79 % Favored : 74.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.32 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.87 (0.14), residues: 3196 helix: 0.41 (0.14), residues: 1380 sheet: -0.31 (0.27), residues: 380 loop : -1.63 (0.14), residues: 1436 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG E 215 TYR 0.014 0.001 TYR G 315 PHE 0.014 0.002 PHE F 126 HIS 0.007 0.001 HIS E 294 Details of bonding type rmsd covalent geometry : bond 0.00517 (26875) covalent geometry : angle 0.53470 (36550) hydrogen bonds : bond 0.04082 ( 1159) hydrogen bonds : angle 4.55040 ( 3100) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6392 Ramachandran restraints generated. 3196 Oldfield, 0 Emsley, 3196 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6392 Ramachandran restraints generated. 3196 Oldfield, 0 Emsley, 3196 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 746 residues out of total 2607 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 121 poor density : 625 time to evaluate : 0.856 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 29 GLU cc_start: 0.7130 (mt-10) cc_final: 0.6879 (mm-30) REVERT: A 33 ILE cc_start: 0.7603 (mm) cc_final: 0.6954 (mp) REVERT: A 40 LYS cc_start: 0.7139 (mtpp) cc_final: 0.6459 (mtpt) REVERT: A 42 GLU cc_start: 0.6836 (pt0) cc_final: 0.6597 (pt0) REVERT: A 66 ILE cc_start: 0.6867 (mm) cc_final: 0.6558 (tt) REVERT: A 68 GLU cc_start: 0.6692 (mt-10) cc_final: 0.5982 (tm-30) REVERT: A 70 LYS cc_start: 0.6669 (ttpt) cc_final: 0.6395 (ttpt) REVERT: A 84 MET cc_start: 0.8871 (mtp) cc_final: 0.8591 (mtp) REVERT: A 98 GLU cc_start: 0.7689 (mt-10) cc_final: 0.7478 (mm-30) REVERT: A 107 LYS cc_start: 0.7242 (mmtm) cc_final: 0.6844 (mttm) REVERT: A 130 ARG cc_start: 0.7386 (OUTLIER) cc_final: 0.6956 (tmm160) REVERT: A 145 GLN cc_start: 0.8649 (mt0) cc_final: 0.8280 (mt0) REVERT: A 202 GLN cc_start: 0.8145 (mm-40) cc_final: 0.7700 (tt0) REVERT: A 210 MET cc_start: 0.8205 (mtp) cc_final: 0.7500 (mtp) REVERT: A 247 ARG cc_start: 0.7366 (mtp-110) cc_final: 0.6919 (mmm-85) REVERT: A 254 ARG cc_start: 0.7571 (ttp80) cc_final: 0.7198 (tmt90) REVERT: A 303 ARG cc_start: 0.7656 (mtp180) cc_final: 0.7053 (mtm180) REVERT: A 308 GLU cc_start: 0.7373 (pt0) cc_final: 0.6607 (tt0) REVERT: A 329 ILE cc_start: 0.8719 (mt) cc_final: 0.8086 (mt) REVERT: B 40 LYS cc_start: 0.7191 (mtpp) cc_final: 0.5982 (mtmt) REVERT: B 42 GLU cc_start: 0.7420 (mt-10) cc_final: 0.6932 (mt-10) REVERT: B 43 GLU cc_start: 0.7622 (mt-10) cc_final: 0.7274 (mt-10) REVERT: B 50 GLU cc_start: 0.8407 (OUTLIER) cc_final: 0.7535 (mp0) REVERT: B 95 ARG cc_start: 0.7980 (ttp80) cc_final: 0.7574 (ttt-90) REVERT: B 107 LYS cc_start: 0.7619 (mmtm) cc_final: 0.6771 (ptpt) REVERT: B 215 ARG cc_start: 0.8114 (tmm160) cc_final: 0.7754 (tpt-90) REVERT: B 332 ASP cc_start: 0.8824 (p0) cc_final: 0.8403 (p0) REVERT: C 33 ILE cc_start: 0.8637 (mm) cc_final: 0.8374 (mm) REVERT: C 50 GLU cc_start: 0.8482 (OUTLIER) cc_final: 0.7465 (mp0) REVERT: C 94 GLN cc_start: 0.7807 (mm-40) cc_final: 0.7051 (tm-30) REVERT: C 95 ARG cc_start: 0.8139 (ttp80) cc_final: 0.7502 (ttp-170) REVERT: C 107 LYS cc_start: 0.8220 (mmtm) cc_final: 0.7581 (ptmt) REVERT: C 154 GLU cc_start: 0.7669 (mt-10) cc_final: 0.6751 (mt-10) REVERT: C 181 SER cc_start: 0.8865 (t) cc_final: 0.8604 (p) REVERT: C 187 ASP cc_start: 0.8694 (OUTLIER) cc_final: 0.8415 (m-30) REVERT: C 202 GLN cc_start: 0.7916 (mm-40) cc_final: 0.7493 (mt0) REVERT: C 243 MET cc_start: 0.8369 (mtm) cc_final: 0.8015 (mtt) REVERT: C 308 GLU cc_start: 0.8608 (pm20) cc_final: 0.8399 (pm20) REVERT: D 27 ARG cc_start: 0.8324 (OUTLIER) cc_final: 0.7498 (mtp180) REVERT: D 29 GLU cc_start: 0.7328 (mm-30) cc_final: 0.7097 (mm-30) REVERT: D 30 GLN cc_start: 0.7523 (mt0) cc_final: 0.7273 (mp10) REVERT: D 37 ASP cc_start: 0.7342 (m-30) cc_final: 0.7009 (m-30) REVERT: D 57 LYS cc_start: 0.7959 (tttp) cc_final: 0.7693 (ttpt) REVERT: D 94 GLN cc_start: 0.7774 (mm-40) cc_final: 0.6948 (tm-30) REVERT: D 107 LYS cc_start: 0.8342 (mmtm) cc_final: 0.7932 (mtmt) REVERT: D 111 LYS cc_start: 0.8560 (OUTLIER) cc_final: 0.8105 (ttmt) REVERT: D 187 ASP cc_start: 0.9039 (OUTLIER) cc_final: 0.8667 (t70) REVERT: D 247 ARG cc_start: 0.8048 (mtp-110) cc_final: 0.7745 (ttt-90) REVERT: D 334 VAL cc_start: 0.9208 (t) cc_final: 0.9000 (p) REVERT: E 68 GLU cc_start: 0.8007 (mp0) cc_final: 0.7588 (tp30) REVERT: E 107 LYS cc_start: 0.8069 (mmtm) cc_final: 0.7660 (mtmt) REVERT: E 176 GLU cc_start: 0.8446 (mm-30) cc_final: 0.7950 (tt0) REVERT: F 39 LYS cc_start: 0.7451 (mttt) cc_final: 0.6735 (mtmt) REVERT: F 43 GLU cc_start: 0.8036 (mt-10) cc_final: 0.7484 (mp0) REVERT: F 68 GLU cc_start: 0.8149 (mt-10) cc_final: 0.7662 (mp0) REVERT: F 95 ARG cc_start: 0.8173 (ttp80) cc_final: 0.7838 (ttp-110) REVERT: F 187 ASP cc_start: 0.8641 (m-30) cc_final: 0.8342 (m-30) REVERT: F 202 GLN cc_start: 0.8196 (mm-40) cc_final: 0.7775 (mt0) REVERT: F 206 GLN cc_start: 0.8702 (OUTLIER) cc_final: 0.7846 (mt0) REVERT: F 222 ASP cc_start: 0.9114 (OUTLIER) cc_final: 0.8662 (t70) REVERT: F 223 SER cc_start: 0.9169 (t) cc_final: 0.8920 (p) REVERT: G 39 LYS cc_start: 0.7787 (mttt) cc_final: 0.7400 (mtpp) REVERT: G 91 GLU cc_start: 0.8223 (OUTLIER) cc_final: 0.7822 (tt0) REVERT: G 94 GLN cc_start: 0.7877 (OUTLIER) cc_final: 0.7552 (tp-100) REVERT: G 107 LYS cc_start: 0.7724 (mmtm) cc_final: 0.6859 (ttmt) REVERT: G 176 GLU cc_start: 0.8170 (mm-30) cc_final: 0.7799 (mm-30) REVERT: G 187 ASP cc_start: 0.8304 (m-30) cc_final: 0.8081 (m-30) REVERT: G 202 GLN cc_start: 0.8122 (mm-40) cc_final: 0.7824 (mt0) REVERT: G 247 ARG cc_start: 0.8268 (mtp-110) cc_final: 0.7998 (mtp85) REVERT: G 306 ARG cc_start: 0.7774 (ttm110) cc_final: 0.6910 (ttp80) REVERT: G 308 GLU cc_start: 0.8181 (pm20) cc_final: 0.7805 (pm20) REVERT: H 27 ARG cc_start: 0.7904 (mtp-110) cc_final: 0.7491 (tmt170) REVERT: H 39 LYS cc_start: 0.7707 (mttt) cc_final: 0.7394 (mtpm) REVERT: H 64 LYS cc_start: 0.7086 (OUTLIER) cc_final: 0.6763 (ttmm) REVERT: H 94 GLN cc_start: 0.8419 (mm-40) cc_final: 0.8078 (tp40) REVERT: H 210 MET cc_start: 0.8716 (mtp) cc_final: 0.8460 (mtm) REVERT: H 247 ARG cc_start: 0.8022 (mtp-110) cc_final: 0.7428 (mmm160) REVERT: H 254 ARG cc_start: 0.8189 (ttt-90) cc_final: 0.7855 (tmm-80) REVERT: I 39 LYS cc_start: 0.7991 (mttt) cc_final: 0.7643 (mmmm) REVERT: I 40 LYS cc_start: 0.7712 (mtpp) cc_final: 0.7261 (mttp) REVERT: I 43 GLU cc_start: 0.7692 (mt-10) cc_final: 0.7295 (tp30) REVERT: I 50 GLU cc_start: 0.8646 (mp0) cc_final: 0.7551 (mp0) REVERT: I 110 ASP cc_start: 0.8691 (m-30) cc_final: 0.8425 (m-30) REVERT: I 176 GLU cc_start: 0.7255 (mm-30) cc_final: 0.6996 (tm-30) REVERT: I 223 SER cc_start: 0.9301 (t) cc_final: 0.9007 (t) REVERT: I 332 ASP cc_start: 0.8344 (p0) cc_final: 0.8079 (p0) REVERT: J 39 LYS cc_start: 0.7206 (mttt) cc_final: 0.6504 (mmmt) REVERT: J 40 LYS cc_start: 0.7351 (mtpp) cc_final: 0.6851 (mtpt) REVERT: J 50 GLU cc_start: 0.7980 (mp0) cc_final: 0.7158 (mp0) REVERT: J 73 LYS cc_start: 0.6683 (mttt) cc_final: 0.6074 (tptt) REVERT: J 77 GLU cc_start: 0.7169 (OUTLIER) cc_final: 0.6549 (mp0) REVERT: J 110 ASP cc_start: 0.8097 (m-30) cc_final: 0.7648 (m-30) REVERT: J 184 ASP cc_start: 0.8532 (m-30) cc_final: 0.8041 (m-30) REVERT: J 187 ASP cc_start: 0.8402 (OUTLIER) cc_final: 0.8108 (m-30) REVERT: J 222 ASP cc_start: 0.8770 (OUTLIER) cc_final: 0.8493 (t0) REVERT: J 247 ARG cc_start: 0.7610 (mtp-110) cc_final: 0.7286 (mtp85) REVERT: J 308 GLU cc_start: 0.7920 (pm20) cc_final: 0.6987 (mt-10) REVERT: J 332 ASP cc_start: 0.8552 (p0) cc_final: 0.8310 (p0) outliers start: 121 outliers final: 73 residues processed: 687 average time/residue: 0.7267 time to fit residues: 565.7558 Evaluate side-chains 692 residues out of total 2607 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 88 poor density : 604 time to evaluate : 0.718 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 77 GLU Chi-restraints excluded: chain A residue 87 THR Chi-restraints excluded: chain A residue 88 THR Chi-restraints excluded: chain A residue 106 SER Chi-restraints excluded: chain A residue 128 GLU Chi-restraints excluded: chain A residue 130 ARG Chi-restraints excluded: chain A residue 208 SER Chi-restraints excluded: chain B residue 31 CYS Chi-restraints excluded: chain B residue 49 VAL Chi-restraints excluded: chain B residue 50 GLU Chi-restraints excluded: chain B residue 82 VAL Chi-restraints excluded: chain B residue 99 ILE Chi-restraints excluded: chain B residue 223 SER Chi-restraints excluded: chain C residue 43 GLU Chi-restraints excluded: chain C residue 50 GLU Chi-restraints excluded: chain C residue 81 LEU Chi-restraints excluded: chain C residue 99 ILE Chi-restraints excluded: chain C residue 104 THR Chi-restraints excluded: chain C residue 128 GLU Chi-restraints excluded: chain C residue 176 GLU Chi-restraints excluded: chain C residue 187 ASP Chi-restraints excluded: chain C residue 274 ASP Chi-restraints excluded: chain D residue 27 ARG Chi-restraints excluded: chain D residue 97 SER Chi-restraints excluded: chain D residue 111 LYS Chi-restraints excluded: chain D residue 121 SER Chi-restraints excluded: chain D residue 125 MET Chi-restraints excluded: chain D residue 187 ASP Chi-restraints excluded: chain D residue 222 ASP Chi-restraints excluded: chain D residue 272 GLN Chi-restraints excluded: chain D residue 273 VAL Chi-restraints excluded: chain D residue 274 ASP Chi-restraints excluded: chain D residue 330 ASN Chi-restraints excluded: chain E residue 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 255 LEU Chi-restraints excluded: chain E residue 273 VAL Chi-restraints excluded: chain E residue 296 SER Chi-restraints excluded: chain F residue 26 SER Chi-restraints excluded: chain F residue 94 GLN Chi-restraints excluded: chain F residue 97 SER Chi-restraints excluded: chain F residue 112 LEU Chi-restraints excluded: chain F residue 125 MET Chi-restraints excluded: chain F residue 145 GLN Chi-restraints excluded: chain F residue 158 MET Chi-restraints excluded: chain F residue 206 GLN Chi-restraints excluded: chain F residue 222 ASP Chi-restraints excluded: chain F residue 272 GLN Chi-restraints excluded: chain F residue 273 VAL Chi-restraints excluded: chain F residue 297 THR Chi-restraints excluded: chain G residue 38 VAL Chi-restraints excluded: chain G residue 43 GLU Chi-restraints excluded: chain G residue 91 GLU Chi-restraints excluded: chain G residue 94 GLN Chi-restraints excluded: chain G residue 97 SER Chi-restraints excluded: chain G residue 125 MET Chi-restraints excluded: chain G residue 161 ASP Chi-restraints excluded: chain G residue 272 GLN Chi-restraints excluded: chain H residue 64 LYS Chi-restraints excluded: chain H residue 90 THR Chi-restraints excluded: chain H residue 142 VAL Chi-restraints excluded: chain H residue 308 GLU Chi-restraints excluded: chain I residue 90 THR Chi-restraints excluded: chain I residue 97 SER Chi-restraints excluded: chain I residue 99 ILE Chi-restraints excluded: chain I residue 109 LEU Chi-restraints excluded: chain I residue 121 SER Chi-restraints excluded: chain I residue 130 ARG Chi-restraints excluded: chain I residue 149 ASP Chi-restraints excluded: chain I residue 183 SER Chi-restraints excluded: chain I residue 185 VAL Chi-restraints excluded: chain I residue 201 THR Chi-restraints excluded: chain I residue 212 VAL Chi-restraints excluded: chain I residue 214 SER Chi-restraints excluded: chain J residue 77 GLU Chi-restraints excluded: chain J residue 88 THR Chi-restraints excluded: chain J residue 97 SER Chi-restraints excluded: chain J residue 130 ARG Chi-restraints excluded: chain J residue 187 ASP Chi-restraints excluded: chain J residue 214 SER Chi-restraints excluded: chain J residue 222 ASP Chi-restraints excluded: chain J residue 239 SER Chi-restraints excluded: chain J residue 255 LEU Chi-restraints excluded: chain J residue 300 LEU Chi-restraints excluded: chain J residue 322 GLU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 323 random chunks: chunk 286 optimal weight: 5.9990 chunk 264 optimal weight: 7.9990 chunk 284 optimal weight: 7.9990 chunk 43 optimal weight: 2.9990 chunk 33 optimal weight: 5.9990 chunk 105 optimal weight: 3.9990 chunk 163 optimal weight: 2.9990 chunk 121 optimal weight: 1.9990 chunk 185 optimal weight: 7.9990 chunk 157 optimal weight: 5.9990 chunk 39 optimal weight: 0.9990 overall best weight: 2.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 145 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 145 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 145 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 34 ASN H 290 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3626 r_free = 0.3626 target = 0.143411 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3226 r_free = 0.3226 target = 0.109244 restraints weight = 32151.278| |-----------------------------------------------------------------------------| r_work (start): 0.3155 rms_B_bonded: 1.99 r_work: 0.3032 rms_B_bonded: 2.64 restraints_weight: 0.5000 r_work: 0.2905 rms_B_bonded: 4.30 restraints_weight: 0.2500 r_work (final): 0.2905 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8040 moved from start: 0.3158 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.042 26875 Z= 0.226 Angle : 0.537 9.155 36550 Z= 0.283 Chirality : 0.042 0.153 4139 Planarity : 0.004 0.040 4521 Dihedral : 13.963 144.101 4454 Min Nonbonded Distance : 2.182 Molprobity Statistics. All-atom Clashscore : 6.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.35 % Favored : 97.65 % Rotamer: Outliers : 4.76 % Allowed : 21.48 % Favored : 73.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.32 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.64 (0.14), residues: 3196 helix: 0.56 (0.14), residues: 1380 sheet: -0.17 (0.27), residues: 380 loop : -1.47 (0.14), residues: 1436 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG D 215 TYR 0.015 0.001 TYR G 315 PHE 0.022 0.002 PHE J 259 HIS 0.008 0.001 HIS E 294 Details of bonding type rmsd covalent geometry : bond 0.00520 (26875) covalent geometry : angle 0.53707 (36550) hydrogen bonds : bond 0.04047 ( 1159) hydrogen bonds : angle 4.50354 ( 3100) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6392 Ramachandran restraints generated. 3196 Oldfield, 0 Emsley, 3196 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6392 Ramachandran restraints generated. 3196 Oldfield, 0 Emsley, 3196 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 752 residues out of total 2607 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 124 poor density : 628 time to evaluate : 0.825 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 37 ASP cc_start: 0.7662 (m-30) cc_final: 0.7323 (m-30) REVERT: A 40 LYS cc_start: 0.7017 (mtpp) cc_final: 0.6361 (mtpt) REVERT: A 42 GLU cc_start: 0.6949 (pt0) cc_final: 0.6654 (pt0) REVERT: A 66 ILE cc_start: 0.6835 (mm) cc_final: 0.6512 (tt) REVERT: A 68 GLU cc_start: 0.6809 (mt-10) cc_final: 0.6173 (tm-30) REVERT: A 70 LYS cc_start: 0.6570 (ttpt) cc_final: 0.6253 (ttpt) REVERT: A 72 ASP cc_start: 0.7148 (m-30) cc_final: 0.6908 (m-30) REVERT: A 84 MET cc_start: 0.8867 (mtp) cc_final: 0.8599 (mtp) REVERT: A 98 GLU cc_start: 0.7703 (mt-10) cc_final: 0.7490 (mm-30) REVERT: A 107 LYS cc_start: 0.7194 (mmtm) cc_final: 0.6786 (mttm) REVERT: A 145 GLN cc_start: 0.8640 (mt0) cc_final: 0.8329 (mt0) REVERT: A 202 GLN cc_start: 0.8145 (mm-40) cc_final: 0.7415 (mt0) REVERT: A 206 GLN cc_start: 0.7512 (OUTLIER) cc_final: 0.7009 (mt0) REVERT: A 210 MET cc_start: 0.8211 (mtp) cc_final: 0.7538 (mtp) REVERT: A 247 ARG cc_start: 0.7220 (mtp-110) cc_final: 0.6691 (mmm-85) REVERT: A 254 ARG cc_start: 0.7463 (ttp80) cc_final: 0.7073 (tmt90) REVERT: A 303 ARG cc_start: 0.7556 (mtp180) cc_final: 0.7017 (mtm180) REVERT: A 308 GLU cc_start: 0.7325 (pt0) cc_final: 0.6521 (tt0) REVERT: A 329 ILE cc_start: 0.8654 (mt) cc_final: 0.7840 (mt) REVERT: B 40 LYS cc_start: 0.7093 (mtpp) cc_final: 0.5906 (mtmt) REVERT: B 42 GLU cc_start: 0.7400 (mt-10) cc_final: 0.6922 (mt-10) REVERT: B 43 GLU cc_start: 0.7432 (mt-10) cc_final: 0.7097 (mt-10) REVERT: B 50 GLU cc_start: 0.8381 (OUTLIER) cc_final: 0.7455 (mp0) REVERT: B 95 ARG cc_start: 0.8010 (ttp80) cc_final: 0.7467 (ttt-90) REVERT: B 107 LYS cc_start: 0.7598 (mmtm) cc_final: 0.6777 (ptpt) REVERT: B 145 GLN cc_start: 0.8384 (mt0) cc_final: 0.8157 (mp10) REVERT: B 206 GLN cc_start: 0.7559 (mt0) cc_final: 0.7136 (mt0) REVERT: B 215 ARG cc_start: 0.8225 (tmm160) cc_final: 0.7878 (tpt-90) REVERT: B 332 ASP cc_start: 0.8815 (p0) cc_final: 0.8378 (p0) REVERT: C 33 ILE cc_start: 0.8639 (mm) cc_final: 0.8345 (mm) REVERT: C 50 GLU cc_start: 0.8452 (OUTLIER) cc_final: 0.7476 (mp0) REVERT: C 94 GLN cc_start: 0.7848 (mm-40) cc_final: 0.7152 (tm-30) REVERT: C 95 ARG cc_start: 0.8129 (ttp80) cc_final: 0.7475 (ttp-170) REVERT: C 107 LYS cc_start: 0.8274 (mmtm) cc_final: 0.7614 (ptmt) REVERT: C 145 GLN cc_start: 0.8910 (mp10) cc_final: 0.8286 (mp10) REVERT: C 154 GLU cc_start: 0.7569 (mt-10) cc_final: 0.6926 (mt-10) REVERT: C 181 SER cc_start: 0.8829 (t) cc_final: 0.8543 (p) REVERT: C 202 GLN cc_start: 0.7914 (mm-40) cc_final: 0.7492 (mt0) REVERT: C 243 MET cc_start: 0.8385 (mtm) cc_final: 0.8019 (mtt) REVERT: D 27 ARG cc_start: 0.8341 (OUTLIER) cc_final: 0.7751 (mtp180) REVERT: D 37 ASP cc_start: 0.7348 (m-30) cc_final: 0.7034 (m-30) REVERT: D 39 LYS cc_start: 0.7688 (mmmm) cc_final: 0.7361 (mmmm) REVERT: D 57 LYS cc_start: 0.7976 (tttp) cc_final: 0.7686 (ttpt) REVERT: D 94 GLN cc_start: 0.7783 (mm-40) cc_final: 0.6905 (tm-30) REVERT: D 107 LYS cc_start: 0.8318 (mmtm) cc_final: 0.7934 (mtmt) REVERT: D 187 ASP cc_start: 0.9040 (OUTLIER) cc_final: 0.8678 (t70) REVERT: D 247 ARG cc_start: 0.7962 (mtp-110) cc_final: 0.7688 (ttt-90) REVERT: D 334 VAL cc_start: 0.9222 (t) cc_final: 0.9018 (p) REVERT: E 57 LYS cc_start: 0.8434 (tptm) cc_final: 0.8038 (tttt) REVERT: E 68 GLU cc_start: 0.7991 (mp0) cc_final: 0.7601 (tp30) REVERT: E 107 LYS cc_start: 0.8051 (mmtm) cc_final: 0.7639 (mtmt) REVERT: E 176 GLU cc_start: 0.8441 (mm-30) cc_final: 0.7934 (tt0) REVERT: E 215 ARG cc_start: 0.8250 (tpt-90) cc_final: 0.8029 (tmt90) REVERT: F 39 LYS cc_start: 0.7560 (mttt) cc_final: 0.6737 (mtmt) REVERT: F 43 GLU cc_start: 0.8061 (mt-10) cc_final: 0.7435 (mp0) REVERT: F 68 GLU cc_start: 0.8218 (mt-10) cc_final: 0.7721 (mp0) REVERT: F 95 ARG cc_start: 0.8157 (ttp80) cc_final: 0.7885 (ttp-110) REVERT: F 202 GLN cc_start: 0.8200 (mm-40) cc_final: 0.7743 (mt0) REVERT: F 206 GLN cc_start: 0.8697 (OUTLIER) cc_final: 0.7834 (mt0) REVERT: F 222 ASP cc_start: 0.9133 (OUTLIER) cc_final: 0.8697 (t70) REVERT: F 223 SER cc_start: 0.9170 (t) cc_final: 0.8917 (p) REVERT: G 39 LYS cc_start: 0.7667 (mttt) cc_final: 0.7277 (mtpp) REVERT: G 91 GLU cc_start: 0.8231 (OUTLIER) cc_final: 0.7825 (tt0) REVERT: G 94 GLN cc_start: 0.7868 (OUTLIER) cc_final: 0.7474 (tp-100) REVERT: G 107 LYS cc_start: 0.7884 (mmtm) cc_final: 0.6924 (ttmt) REVERT: G 176 GLU cc_start: 0.8238 (mm-30) cc_final: 0.7852 (mm-30) REVERT: G 187 ASP cc_start: 0.8251 (m-30) cc_final: 0.8043 (m-30) REVERT: G 202 GLN cc_start: 0.8132 (mm-40) cc_final: 0.7796 (mt0) REVERT: G 206 GLN cc_start: 0.8903 (OUTLIER) cc_final: 0.8332 (mt0) REVERT: G 247 ARG cc_start: 0.8254 (mtp-110) cc_final: 0.7981 (mtp85) REVERT: G 306 ARG cc_start: 0.7786 (ttm110) cc_final: 0.6920 (ttp80) REVERT: G 308 GLU cc_start: 0.8187 (pm20) cc_final: 0.7821 (pm20) REVERT: H 27 ARG cc_start: 0.7809 (mtp-110) cc_final: 0.7421 (tmt170) REVERT: H 39 LYS cc_start: 0.7724 (mttt) cc_final: 0.7327 (mtmm) REVERT: H 64 LYS cc_start: 0.7085 (OUTLIER) cc_final: 0.6780 (ttmm) REVERT: H 210 MET cc_start: 0.8695 (mtp) cc_final: 0.8435 (mtm) REVERT: H 247 ARG cc_start: 0.8045 (mtp-110) cc_final: 0.7395 (mmm160) REVERT: H 254 ARG cc_start: 0.8174 (ttt-90) cc_final: 0.7754 (tmm-80) REVERT: H 257 ASP cc_start: 0.8514 (m-30) cc_final: 0.8075 (m-30) REVERT: H 306 ARG cc_start: 0.7744 (OUTLIER) cc_final: 0.7282 (ttt-90) REVERT: I 39 LYS cc_start: 0.7964 (mttt) cc_final: 0.7636 (mmmm) REVERT: I 40 LYS cc_start: 0.7644 (mtpp) cc_final: 0.7195 (mttp) REVERT: I 43 GLU cc_start: 0.7663 (mt-10) cc_final: 0.7282 (tp30) REVERT: I 50 GLU cc_start: 0.8686 (mp0) cc_final: 0.7847 (mp0) REVERT: I 176 GLU cc_start: 0.7284 (mm-30) cc_final: 0.7010 (tm-30) REVERT: I 215 ARG cc_start: 0.8395 (tmm160) cc_final: 0.8187 (tmm160) REVERT: I 332 ASP cc_start: 0.8303 (p0) cc_final: 0.7977 (p0) REVERT: J 39 LYS cc_start: 0.6887 (mttt) cc_final: 0.6226 (mmmt) REVERT: J 40 LYS cc_start: 0.7397 (mtpp) cc_final: 0.6651 (mtpp) REVERT: J 42 GLU cc_start: 0.7054 (tp30) cc_final: 0.6488 (tt0) REVERT: J 50 GLU cc_start: 0.7952 (mp0) cc_final: 0.7105 (mp0) REVERT: J 73 LYS cc_start: 0.6643 (mttt) cc_final: 0.6051 (tptt) REVERT: J 77 GLU cc_start: 0.7107 (OUTLIER) cc_final: 0.6576 (mp0) REVERT: J 110 ASP cc_start: 0.8017 (m-30) cc_final: 0.7555 (m-30) REVERT: J 135 GLN cc_start: 0.8746 (mm-40) cc_final: 0.6932 (mp-120) REVERT: J 184 ASP cc_start: 0.8586 (m-30) cc_final: 0.8175 (m-30) REVERT: J 187 ASP cc_start: 0.8348 (OUTLIER) cc_final: 0.7754 (m-30) REVERT: J 215 ARG cc_start: 0.7116 (tpt-90) cc_final: 0.6904 (tpt-90) REVERT: J 222 ASP cc_start: 0.8768 (OUTLIER) cc_final: 0.8485 (t0) REVERT: J 247 ARG cc_start: 0.7639 (mtp-110) cc_final: 0.7303 (mtp85) REVERT: J 299 ARG cc_start: 0.8681 (mtm180) cc_final: 0.8238 (mmm-85) REVERT: J 308 GLU cc_start: 0.7961 (pm20) cc_final: 0.6955 (mt-10) outliers start: 124 outliers final: 79 residues processed: 690 average time/residue: 0.7649 time to fit residues: 597.5429 Evaluate side-chains 693 residues out of total 2607 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 94 poor density : 599 time to evaluate : 0.996 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 77 GLU Chi-restraints excluded: chain A residue 87 THR Chi-restraints excluded: chain A residue 88 THR Chi-restraints excluded: chain A residue 106 SER Chi-restraints excluded: chain A residue 206 GLN Chi-restraints excluded: chain A residue 208 SER Chi-restraints excluded: chain B residue 23 GLN Chi-restraints excluded: chain B residue 31 CYS Chi-restraints excluded: chain B residue 49 VAL Chi-restraints excluded: chain B residue 50 GLU Chi-restraints excluded: chain B residue 82 VAL Chi-restraints excluded: chain B residue 99 ILE Chi-restraints excluded: chain B residue 223 SER Chi-restraints excluded: chain B residue 272 GLN Chi-restraints excluded: chain C residue 43 GLU Chi-restraints excluded: chain C residue 50 GLU Chi-restraints excluded: chain C residue 81 LEU Chi-restraints excluded: chain C residue 99 ILE Chi-restraints excluded: chain C residue 104 THR Chi-restraints excluded: chain C residue 176 GLU Chi-restraints excluded: chain C residue 187 ASP Chi-restraints excluded: chain D residue 27 ARG Chi-restraints excluded: chain D residue 97 SER Chi-restraints excluded: chain D residue 121 SER Chi-restraints excluded: chain D residue 125 MET Chi-restraints excluded: chain D residue 128 GLU Chi-restraints excluded: chain D residue 161 ASP Chi-restraints excluded: chain D residue 187 ASP Chi-restraints excluded: chain D residue 222 ASP Chi-restraints excluded: chain D residue 272 GLN Chi-restraints excluded: chain D residue 273 VAL Chi-restraints excluded: chain D residue 274 ASP Chi-restraints excluded: chain D residue 330 ASN Chi-restraints excluded: chain E residue 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 255 LEU Chi-restraints excluded: chain E residue 273 VAL Chi-restraints excluded: chain E residue 296 SER Chi-restraints excluded: chain E residue 334 VAL Chi-restraints excluded: chain F residue 26 SER Chi-restraints excluded: chain F residue 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 158 MET Chi-restraints excluded: chain F residue 161 ASP Chi-restraints excluded: chain F residue 206 GLN Chi-restraints excluded: chain F residue 222 ASP Chi-restraints excluded: chain F residue 272 GLN Chi-restraints excluded: chain F residue 273 VAL Chi-restraints excluded: chain F residue 297 THR Chi-restraints excluded: chain F residue 319 CYS Chi-restraints excluded: chain G residue 38 VAL Chi-restraints excluded: chain G residue 43 GLU Chi-restraints excluded: chain G residue 91 GLU Chi-restraints excluded: chain G residue 94 GLN Chi-restraints excluded: chain G residue 97 SER Chi-restraints excluded: chain G residue 125 MET Chi-restraints excluded: chain G residue 161 ASP Chi-restraints excluded: chain G residue 206 GLN Chi-restraints excluded: chain G residue 272 GLN Chi-restraints excluded: chain H residue 64 LYS Chi-restraints excluded: chain H residue 142 VAL Chi-restraints excluded: chain H residue 306 ARG Chi-restraints excluded: chain H residue 308 GLU Chi-restraints excluded: chain I residue 28 LEU Chi-restraints excluded: chain I residue 90 THR Chi-restraints excluded: chain I residue 97 SER Chi-restraints excluded: chain I residue 99 ILE Chi-restraints excluded: chain I residue 109 LEU Chi-restraints excluded: chain I residue 121 SER Chi-restraints excluded: chain I residue 130 ARG Chi-restraints excluded: chain I residue 149 ASP Chi-restraints excluded: chain I residue 183 SER Chi-restraints excluded: chain I residue 201 THR Chi-restraints excluded: chain I residue 212 VAL Chi-restraints excluded: chain I residue 214 SER Chi-restraints excluded: chain I residue 261 VAL Chi-restraints excluded: chain J residue 58 LYS Chi-restraints excluded: chain J residue 77 GLU Chi-restraints excluded: chain J residue 88 THR Chi-restraints excluded: chain J residue 97 SER Chi-restraints excluded: chain J residue 130 ARG Chi-restraints excluded: chain J residue 187 ASP Chi-restraints excluded: chain J residue 214 SER Chi-restraints excluded: chain J residue 222 ASP Chi-restraints excluded: chain J residue 239 SER Chi-restraints excluded: chain J residue 255 LEU Chi-restraints excluded: chain J residue 261 VAL Chi-restraints excluded: chain J residue 272 GLN Chi-restraints excluded: chain J residue 300 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 323 random chunks: chunk 32 optimal weight: 10.0000 chunk 150 optimal weight: 0.7980 chunk 115 optimal weight: 0.6980 chunk 225 optimal weight: 1.9990 chunk 288 optimal weight: 1.9990 chunk 157 optimal weight: 0.6980 chunk 314 optimal weight: 8.9990 chunk 236 optimal weight: 0.3980 chunk 121 optimal weight: 2.9990 chunk 114 optimal weight: 1.9990 chunk 320 optimal weight: 2.9990 overall best weight: 0.9182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 272 GLN B 242 GLN ** C 145 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 272 GLN D 145 GLN E 145 GLN F 23 GLN H 34 ASN ** H 145 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 290 ASN ** I 145 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 94 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3673 r_free = 0.3673 target = 0.147748 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3284 r_free = 0.3284 target = 0.113583 restraints weight = 32007.728| |-----------------------------------------------------------------------------| r_work (start): 0.3278 rms_B_bonded: 2.01 r_work: 0.3158 rms_B_bonded: 2.67 restraints_weight: 0.5000 r_work: 0.3028 rms_B_bonded: 4.39 restraints_weight: 0.2500 r_work (final): 0.3028 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8020 moved from start: 0.3397 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 26875 Z= 0.120 Angle : 0.472 8.011 36550 Z= 0.250 Chirality : 0.039 0.147 4139 Planarity : 0.003 0.039 4521 Dihedral : 13.690 143.670 4454 Min Nonbonded Distance : 2.238 Molprobity Statistics. All-atom Clashscore : 6.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.72 % Favored : 98.28 % Rotamer: Outliers : 3.80 % Allowed : 23.01 % Favored : 73.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.32 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.16 (0.14), residues: 3196 helix: 0.88 (0.14), residues: 1390 sheet: 0.05 (0.27), residues: 380 loop : -1.12 (0.15), residues: 1426 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG D 215 TYR 0.008 0.001 TYR H 301 PHE 0.014 0.001 PHE F 126 HIS 0.006 0.001 HIS A 138 Details of bonding type rmsd covalent geometry : bond 0.00267 (26875) covalent geometry : angle 0.47232 (36550) hydrogen bonds : bond 0.03087 ( 1159) hydrogen bonds : angle 4.23064 ( 3100) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6392 Ramachandran restraints generated. 3196 Oldfield, 0 Emsley, 3196 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6392 Ramachandran restraints generated. 3196 Oldfield, 0 Emsley, 3196 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 718 residues out of total 2607 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 99 poor density : 619 time to evaluate : 0.934 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 40 LYS cc_start: 0.7319 (mtpp) cc_final: 0.6302 (mtpt) REVERT: A 42 GLU cc_start: 0.6824 (pt0) cc_final: 0.6581 (pt0) REVERT: A 66 ILE cc_start: 0.6831 (mm) cc_final: 0.6611 (tp) REVERT: A 68 GLU cc_start: 0.6786 (mt-10) cc_final: 0.6221 (tm-30) REVERT: A 70 LYS cc_start: 0.6687 (ttpt) cc_final: 0.6430 (ttpt) REVERT: A 84 MET cc_start: 0.8908 (mtp) cc_final: 0.8651 (mtp) REVERT: A 107 LYS cc_start: 0.7170 (mmtm) cc_final: 0.6765 (mttm) REVERT: A 206 GLN cc_start: 0.7544 (OUTLIER) cc_final: 0.6976 (mt0) REVERT: A 210 MET cc_start: 0.8150 (mtp) cc_final: 0.7438 (mtp) REVERT: A 247 ARG cc_start: 0.7047 (mtp-110) cc_final: 0.6481 (mmm-85) REVERT: A 254 ARG cc_start: 0.7410 (ttp80) cc_final: 0.7092 (tmt90) REVERT: A 303 ARG cc_start: 0.7579 (mtp180) cc_final: 0.7349 (mtm110) REVERT: A 308 GLU cc_start: 0.7215 (pt0) cc_final: 0.6638 (tt0) REVERT: A 329 ILE cc_start: 0.8565 (mt) cc_final: 0.7968 (mt) REVERT: B 42 GLU cc_start: 0.7164 (mt-10) cc_final: 0.6600 (mt-10) REVERT: B 43 GLU cc_start: 0.7472 (mt-10) cc_final: 0.7109 (mt-10) REVERT: B 72 ASP cc_start: 0.7527 (m-30) cc_final: 0.7229 (m-30) REVERT: B 95 ARG cc_start: 0.7915 (ttp80) cc_final: 0.7508 (ttt-90) REVERT: B 100 ILE cc_start: 0.9123 (mp) cc_final: 0.8854 (pp) REVERT: B 107 LYS cc_start: 0.7773 (mmtm) cc_final: 0.6880 (ptpt) REVERT: B 145 GLN cc_start: 0.8295 (mt0) cc_final: 0.8063 (mp10) REVERT: B 206 GLN cc_start: 0.7491 (mt0) cc_final: 0.7207 (mt0) REVERT: B 306 ARG cc_start: 0.7900 (mmm-85) cc_final: 0.7272 (ptm-80) REVERT: B 332 ASP cc_start: 0.8764 (p0) cc_final: 0.8378 (p0) REVERT: C 94 GLN cc_start: 0.7787 (mm-40) cc_final: 0.6997 (tm-30) REVERT: C 95 ARG cc_start: 0.8262 (ttp80) cc_final: 0.7578 (ttp-170) REVERT: C 107 LYS cc_start: 0.8264 (mmtm) cc_final: 0.7646 (ptmt) REVERT: C 145 GLN cc_start: 0.8749 (mp10) cc_final: 0.8110 (mp10) REVERT: C 154 GLU cc_start: 0.7684 (mt-10) cc_final: 0.6951 (mt-10) REVERT: C 181 SER cc_start: 0.8770 (t) cc_final: 0.8497 (p) REVERT: C 202 GLN cc_start: 0.7842 (mm-40) cc_final: 0.7461 (mt0) REVERT: D 27 ARG cc_start: 0.8299 (OUTLIER) cc_final: 0.7157 (mtp180) REVERT: D 30 GLN cc_start: 0.7551 (mt0) cc_final: 0.7316 (mp10) REVERT: D 57 LYS cc_start: 0.7933 (tttp) cc_final: 0.7644 (ttpt) REVERT: D 94 GLN cc_start: 0.7767 (mm-40) cc_final: 0.6967 (tm-30) REVERT: D 107 LYS cc_start: 0.8318 (mmtm) cc_final: 0.7934 (mtmt) REVERT: D 111 LYS cc_start: 0.8430 (OUTLIER) cc_final: 0.8038 (ttmt) REVERT: D 187 ASP cc_start: 0.9051 (OUTLIER) cc_final: 0.8712 (t70) REVERT: D 247 ARG cc_start: 0.7996 (mtp-110) cc_final: 0.7787 (ttt-90) REVERT: D 334 VAL cc_start: 0.9203 (t) cc_final: 0.8964 (p) REVERT: E 57 LYS cc_start: 0.8399 (tptm) cc_final: 0.8012 (tttt) REVERT: E 68 GLU cc_start: 0.8003 (mp0) cc_final: 0.7748 (tp30) REVERT: E 107 LYS cc_start: 0.8007 (mmtm) cc_final: 0.7602 (mtmt) REVERT: E 145 GLN cc_start: 0.8975 (OUTLIER) cc_final: 0.8617 (mp10) REVERT: E 149 ASP cc_start: 0.8265 (t70) cc_final: 0.7852 (t70) REVERT: E 176 GLU cc_start: 0.8363 (mm-30) cc_final: 0.7820 (tt0) REVERT: E 215 ARG cc_start: 0.8177 (tpt-90) cc_final: 0.7920 (tmt90) REVERT: F 23 GLN cc_start: 0.8429 (mt0) cc_final: 0.8186 (mt0) REVERT: F 27 ARG cc_start: 0.8418 (mtp180) cc_final: 0.8203 (mmm160) REVERT: F 39 LYS cc_start: 0.7401 (mttt) cc_final: 0.6583 (mtmt) REVERT: F 43 GLU cc_start: 0.7942 (mt-10) cc_final: 0.7389 (mp0) REVERT: F 68 GLU cc_start: 0.8191 (mt-10) cc_final: 0.7686 (mp0) REVERT: F 80 LYS cc_start: 0.8218 (mtpt) cc_final: 0.8007 (mtmm) REVERT: F 95 ARG cc_start: 0.8169 (ttp80) cc_final: 0.7866 (ttp-110) REVERT: F 202 GLN cc_start: 0.8183 (mm-40) cc_final: 0.7810 (mt0) REVERT: F 206 GLN cc_start: 0.8678 (OUTLIER) cc_final: 0.7870 (mt0) REVERT: G 39 LYS cc_start: 0.7797 (mttt) cc_final: 0.7414 (mtpp) REVERT: G 94 GLN cc_start: 0.7867 (OUTLIER) cc_final: 0.7462 (tp-100) REVERT: G 107 LYS cc_start: 0.7917 (mmtm) cc_final: 0.6950 (ttmt) REVERT: G 111 LYS cc_start: 0.8316 (ttpp) cc_final: 0.8056 (mtpp) REVERT: G 125 MET cc_start: 0.9006 (OUTLIER) cc_final: 0.8533 (mtm) REVERT: G 130 ARG cc_start: 0.8425 (ptp90) cc_final: 0.8176 (ptt-90) REVERT: G 176 GLU cc_start: 0.8155 (mm-30) cc_final: 0.7800 (mm-30) REVERT: G 187 ASP cc_start: 0.8372 (m-30) cc_final: 0.8143 (m-30) REVERT: G 191 TYR cc_start: 0.9492 (t80) cc_final: 0.9249 (t80) REVERT: G 202 GLN cc_start: 0.8120 (mm-40) cc_final: 0.7855 (mt0) REVERT: G 206 GLN cc_start: 0.8883 (OUTLIER) cc_final: 0.8353 (mt0) REVERT: G 247 ARG cc_start: 0.8214 (mtp-110) cc_final: 0.7993 (mtp85) REVERT: G 306 ARG cc_start: 0.7858 (ttm110) cc_final: 0.7015 (tmm160) REVERT: G 308 GLU cc_start: 0.8228 (pm20) cc_final: 0.7898 (pm20) REVERT: H 27 ARG cc_start: 0.7634 (mtp-110) cc_final: 0.7359 (tmt170) REVERT: H 39 LYS cc_start: 0.7614 (mttt) cc_final: 0.7199 (mtmm) REVERT: H 94 GLN cc_start: 0.8442 (mm-40) cc_final: 0.8102 (tp40) REVERT: H 96 ARG cc_start: 0.7799 (ttt90) cc_final: 0.7249 (ttt90) REVERT: H 149 ASP cc_start: 0.7897 (t0) cc_final: 0.7325 (p0) REVERT: H 206 GLN cc_start: 0.8733 (OUTLIER) cc_final: 0.8386 (mt0) REVERT: H 210 MET cc_start: 0.8507 (mtp) cc_final: 0.8306 (mtm) REVERT: H 247 ARG cc_start: 0.7976 (mtp-110) cc_final: 0.7453 (mmm160) REVERT: H 254 ARG cc_start: 0.8044 (ttt-90) cc_final: 0.7615 (tmm-80) REVERT: H 257 ASP cc_start: 0.8520 (m-30) cc_final: 0.8030 (m-30) REVERT: I 27 ARG cc_start: 0.7662 (OUTLIER) cc_final: 0.7394 (tmt-80) REVERT: I 39 LYS cc_start: 0.7850 (mttt) cc_final: 0.7520 (mmmm) REVERT: I 40 LYS cc_start: 0.7703 (mtpp) cc_final: 0.7315 (mttp) REVERT: I 43 GLU cc_start: 0.7644 (mt-10) cc_final: 0.7311 (tp30) REVERT: I 109 LEU cc_start: 0.8722 (OUTLIER) cc_final: 0.8353 (mp) REVERT: I 110 ASP cc_start: 0.8682 (m-30) cc_final: 0.8387 (m-30) REVERT: I 154 GLU cc_start: 0.8030 (mt-10) cc_final: 0.7378 (mm-30) REVERT: I 176 GLU cc_start: 0.7293 (mm-30) cc_final: 0.7054 (tm-30) REVERT: I 215 ARG cc_start: 0.8326 (tmm160) cc_final: 0.8096 (tmm160) REVERT: I 332 ASP cc_start: 0.8318 (p0) cc_final: 0.8003 (p0) REVERT: J 39 LYS cc_start: 0.6756 (mttt) cc_final: 0.6052 (mmmt) REVERT: J 40 LYS cc_start: 0.7007 (mtpp) cc_final: 0.6420 (mttt) REVERT: J 42 GLU cc_start: 0.7152 (tp30) cc_final: 0.6526 (tt0) REVERT: J 50 GLU cc_start: 0.7773 (mp0) cc_final: 0.6795 (mp0) REVERT: J 73 LYS cc_start: 0.6560 (mttt) cc_final: 0.5973 (tptt) REVERT: J 77 GLU cc_start: 0.7448 (OUTLIER) cc_final: 0.6804 (mp0) REVERT: J 110 ASP cc_start: 0.8206 (m-30) cc_final: 0.7900 (m-30) REVERT: J 154 GLU cc_start: 0.8105 (mt-10) cc_final: 0.7368 (mm-30) REVERT: J 177 ARG cc_start: 0.8351 (OUTLIER) cc_final: 0.7674 (ttt180) REVERT: J 184 ASP cc_start: 0.8644 (m-30) cc_final: 0.8317 (m-30) REVERT: J 187 ASP cc_start: 0.8146 (OUTLIER) cc_final: 0.7354 (m-30) REVERT: J 222 ASP cc_start: 0.8620 (OUTLIER) cc_final: 0.8326 (t0) REVERT: J 299 ARG cc_start: 0.8650 (mtm180) cc_final: 0.8226 (mtt-85) REVERT: J 308 GLU cc_start: 0.7970 (pm20) cc_final: 0.6983 (mt-10) REVERT: J 332 ASP cc_start: 0.8574 (p0) cc_final: 0.8183 (p0) outliers start: 99 outliers final: 52 residues processed: 668 average time/residue: 0.7472 time to fit residues: 565.8778 Evaluate side-chains 660 residues out of total 2607 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 592 time to evaluate : 0.974 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 87 THR Chi-restraints excluded: chain A residue 88 THR Chi-restraints excluded: chain A residue 206 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 113 LEU Chi-restraints excluded: chain B residue 272 GLN Chi-restraints excluded: chain C residue 43 GLU Chi-restraints excluded: chain C residue 128 GLU Chi-restraints excluded: chain C residue 330 ASN Chi-restraints excluded: chain D residue 27 ARG Chi-restraints excluded: chain D residue 97 SER Chi-restraints excluded: chain D residue 111 LYS Chi-restraints excluded: chain D residue 128 GLU Chi-restraints excluded: chain D residue 161 ASP Chi-restraints excluded: chain D residue 187 ASP Chi-restraints excluded: chain D residue 237 GLU Chi-restraints excluded: chain D residue 272 GLN Chi-restraints excluded: chain D residue 274 ASP Chi-restraints excluded: chain D residue 330 ASN Chi-restraints excluded: chain E residue 48 THR Chi-restraints excluded: chain E residue 87 THR Chi-restraints excluded: chain E residue 112 LEU Chi-restraints excluded: chain E residue 125 MET Chi-restraints excluded: chain E residue 145 GLN Chi-restraints excluded: chain E residue 161 ASP Chi-restraints excluded: chain E residue 273 VAL Chi-restraints excluded: chain E residue 296 SER Chi-restraints excluded: chain E residue 334 VAL 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 149 ASP Chi-restraints excluded: chain F residue 158 MET Chi-restraints excluded: chain F residue 206 GLN Chi-restraints excluded: chain F residue 272 GLN Chi-restraints excluded: chain F residue 297 THR Chi-restraints excluded: chain G residue 38 VAL Chi-restraints excluded: chain G residue 94 GLN Chi-restraints excluded: chain G residue 125 MET Chi-restraints excluded: chain G residue 161 ASP Chi-restraints excluded: chain G residue 206 GLN Chi-restraints excluded: chain G residue 272 GLN Chi-restraints excluded: chain H residue 26 SER Chi-restraints excluded: chain H residue 82 VAL Chi-restraints excluded: chain H residue 142 VAL Chi-restraints excluded: chain H residue 206 GLN Chi-restraints excluded: chain H residue 272 GLN Chi-restraints excluded: chain H residue 308 GLU Chi-restraints excluded: chain I residue 27 ARG Chi-restraints excluded: chain I residue 28 LEU Chi-restraints excluded: chain I residue 90 THR Chi-restraints excluded: chain I residue 99 ILE Chi-restraints excluded: chain I residue 109 LEU Chi-restraints excluded: chain I residue 121 SER Chi-restraints excluded: chain I residue 183 SER Chi-restraints excluded: chain I residue 201 THR Chi-restraints excluded: chain I residue 212 VAL Chi-restraints excluded: chain I residue 214 SER Chi-restraints excluded: chain J residue 77 GLU Chi-restraints excluded: chain J residue 130 ARG Chi-restraints excluded: chain J residue 177 ARG Chi-restraints excluded: chain J residue 187 ASP Chi-restraints excluded: chain J residue 222 ASP Chi-restraints excluded: chain J residue 239 SER Chi-restraints excluded: chain J residue 272 GLN Chi-restraints excluded: chain J residue 300 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 323 random chunks: chunk 36 optimal weight: 9.9990 chunk 40 optimal weight: 6.9990 chunk 153 optimal weight: 0.0770 chunk 77 optimal weight: 0.9990 chunk 309 optimal weight: 9.9990 chunk 67 optimal weight: 3.9990 chunk 279 optimal weight: 20.0000 chunk 272 optimal weight: 0.9980 chunk 213 optimal weight: 4.9990 chunk 298 optimal weight: 3.9990 chunk 132 optimal weight: 0.9980 overall best weight: 1.4142 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 272 GLN C 145 GLN ** D 145 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 145 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 34 ASN ** H 145 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 145 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 135 GLN J 242 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3661 r_free = 0.3661 target = 0.146535 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3268 r_free = 0.3268 target = 0.112366 restraints weight = 32042.735| |-----------------------------------------------------------------------------| r_work (start): 0.3239 rms_B_bonded: 2.00 r_work: 0.3118 rms_B_bonded: 2.67 restraints_weight: 0.5000 r_work: 0.2990 rms_B_bonded: 4.36 restraints_weight: 0.2500 r_work (final): 0.2990 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8034 moved from start: 0.3432 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 26875 Z= 0.149 Angle : 0.490 8.158 36550 Z= 0.259 Chirality : 0.039 0.141 4139 Planarity : 0.003 0.039 4521 Dihedral : 13.650 142.673 4454 Min Nonbonded Distance : 2.238 Molprobity Statistics. All-atom Clashscore : 6.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.25 % Favored : 97.75 % Rotamer: Outliers : 3.95 % Allowed : 23.28 % Favored : 72.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.32 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.03 (0.14), residues: 3196 helix: 1.02 (0.14), residues: 1390 sheet: 0.16 (0.27), residues: 380 loop : -1.00 (0.15), residues: 1426 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG D 215 TYR 0.011 0.001 TYR G 315 PHE 0.014 0.001 PHE F 126 HIS 0.006 0.001 HIS A 138 Details of bonding type rmsd covalent geometry : bond 0.00338 (26875) covalent geometry : angle 0.49039 (36550) hydrogen bonds : bond 0.03345 ( 1159) hydrogen bonds : angle 4.22746 ( 3100) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6392 Ramachandran restraints generated. 3196 Oldfield, 0 Emsley, 3196 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6392 Ramachandran restraints generated. 3196 Oldfield, 0 Emsley, 3196 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 710 residues out of total 2607 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 103 poor density : 607 time to evaluate : 0.796 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 40 LYS cc_start: 0.7317 (mtpp) cc_final: 0.6311 (mtpt) REVERT: A 42 GLU cc_start: 0.6834 (pt0) cc_final: 0.6594 (pt0) REVERT: A 66 ILE cc_start: 0.6829 (mm) cc_final: 0.6614 (tp) REVERT: A 68 GLU cc_start: 0.6810 (mt-10) cc_final: 0.6237 (tm-30) REVERT: A 70 LYS cc_start: 0.6762 (ttpt) cc_final: 0.6402 (ttpt) REVERT: A 107 LYS cc_start: 0.7176 (mmtm) cc_final: 0.6770 (mttm) REVERT: A 210 MET cc_start: 0.8177 (mtp) cc_final: 0.7195 (mtp) REVERT: A 247 ARG cc_start: 0.7355 (mtp-110) cc_final: 0.6662 (mmm-85) REVERT: A 254 ARG cc_start: 0.7416 (ttp80) cc_final: 0.7117 (tmt90) REVERT: A 303 ARG cc_start: 0.7597 (mtp180) cc_final: 0.7352 (mtm110) REVERT: A 308 GLU cc_start: 0.7233 (pt0) cc_final: 0.6588 (tt0) REVERT: A 329 ILE cc_start: 0.8543 (mt) cc_final: 0.7963 (mt) REVERT: B 40 LYS cc_start: 0.6912 (mtpp) cc_final: 0.5790 (mtmt) REVERT: B 42 GLU cc_start: 0.7153 (mt-10) cc_final: 0.6590 (mt-10) REVERT: B 43 GLU cc_start: 0.7521 (mt-10) cc_final: 0.7145 (mt-10) REVERT: B 72 ASP cc_start: 0.7553 (m-30) cc_final: 0.7244 (m-30) REVERT: B 88 THR cc_start: 0.9117 (OUTLIER) cc_final: 0.8815 (p) REVERT: B 95 ARG cc_start: 0.7895 (ttp80) cc_final: 0.7475 (ttt-90) REVERT: B 100 ILE cc_start: 0.9120 (mp) cc_final: 0.8842 (pp) REVERT: B 107 LYS cc_start: 0.7820 (mmtm) cc_final: 0.6887 (ptpt) REVERT: B 206 GLN cc_start: 0.7504 (mt0) cc_final: 0.7258 (mt0) REVERT: B 332 ASP cc_start: 0.8781 (p0) cc_final: 0.8376 (p0) REVERT: C 33 ILE cc_start: 0.8596 (mm) cc_final: 0.8352 (mm) REVERT: C 94 GLN cc_start: 0.7790 (mm-40) cc_final: 0.7005 (tm-30) REVERT: C 95 ARG cc_start: 0.8166 (ttp80) cc_final: 0.7476 (ttp-170) REVERT: C 107 LYS cc_start: 0.8317 (mmtm) cc_final: 0.7644 (ptmt) REVERT: C 145 GLN cc_start: 0.8893 (OUTLIER) cc_final: 0.8296 (mp10) REVERT: C 154 GLU cc_start: 0.7677 (mt-10) cc_final: 0.6953 (mt-10) REVERT: C 181 SER cc_start: 0.8687 (t) cc_final: 0.8227 (p) REVERT: C 187 ASP cc_start: 0.8683 (OUTLIER) cc_final: 0.8481 (m-30) REVERT: C 202 GLN cc_start: 0.7854 (mm-40) cc_final: 0.7454 (mt0) REVERT: D 27 ARG cc_start: 0.8325 (OUTLIER) cc_final: 0.7405 (mtp180) REVERT: D 30 GLN cc_start: 0.7549 (mt0) cc_final: 0.7321 (mp10) REVERT: D 94 GLN cc_start: 0.7787 (mm-40) cc_final: 0.6987 (tm-30) REVERT: D 107 LYS cc_start: 0.8320 (mmtm) cc_final: 0.7931 (mtmt) REVERT: D 111 LYS cc_start: 0.8462 (OUTLIER) cc_final: 0.8078 (ttmt) REVERT: D 187 ASP cc_start: 0.9066 (OUTLIER) cc_final: 0.8716 (t70) REVERT: E 27 ARG cc_start: 0.8449 (mtp180) cc_final: 0.8206 (ttt-90) REVERT: E 57 LYS cc_start: 0.8477 (tptm) cc_final: 0.8107 (tttt) REVERT: E 68 GLU cc_start: 0.8065 (mp0) cc_final: 0.7684 (tp30) REVERT: E 107 LYS cc_start: 0.8007 (mmtm) cc_final: 0.7604 (mtmt) REVERT: E 149 ASP cc_start: 0.8266 (t70) cc_final: 0.7865 (t70) REVERT: E 176 GLU cc_start: 0.8350 (mm-30) cc_final: 0.7812 (tt0) REVERT: E 243 MET cc_start: 0.8914 (OUTLIER) cc_final: 0.8617 (mtt) REVERT: F 23 GLN cc_start: 0.8438 (mt0) cc_final: 0.8183 (mt0) REVERT: F 27 ARG cc_start: 0.8423 (mtp180) cc_final: 0.8171 (mmm160) REVERT: F 39 LYS cc_start: 0.7518 (mttt) cc_final: 0.6711 (mtmt) REVERT: F 43 GLU cc_start: 0.7904 (mt-10) cc_final: 0.7381 (mp0) REVERT: F 68 GLU cc_start: 0.8200 (mt-10) cc_final: 0.7672 (mp0) REVERT: F 80 LYS cc_start: 0.8181 (mtpt) cc_final: 0.7978 (mtmm) REVERT: F 95 ARG cc_start: 0.8162 (ttp80) cc_final: 0.7892 (ttp-110) REVERT: F 202 GLN cc_start: 0.8185 (mm-40) cc_final: 0.7740 (mt0) REVERT: F 206 GLN cc_start: 0.8683 (OUTLIER) cc_final: 0.7866 (mt0) REVERT: G 39 LYS cc_start: 0.7695 (mttt) cc_final: 0.7312 (mtpp) REVERT: G 94 GLN cc_start: 0.7870 (OUTLIER) cc_final: 0.7471 (tp-100) REVERT: G 107 LYS cc_start: 0.7931 (mmtm) cc_final: 0.6943 (ttmm) REVERT: G 111 LYS cc_start: 0.8301 (ttpp) cc_final: 0.8052 (mtpp) REVERT: G 176 GLU cc_start: 0.8159 (mm-30) cc_final: 0.7801 (mm-30) REVERT: G 202 GLN cc_start: 0.8155 (mm-40) cc_final: 0.7909 (mt0) REVERT: G 206 GLN cc_start: 0.8961 (OUTLIER) cc_final: 0.8415 (mt0) REVERT: G 247 ARG cc_start: 0.8203 (mtp-110) cc_final: 0.7984 (mtp85) REVERT: G 306 ARG cc_start: 0.7804 (ttm110) cc_final: 0.6955 (tmm160) REVERT: G 308 GLU cc_start: 0.8211 (pm20) cc_final: 0.7879 (pm20) REVERT: H 39 LYS cc_start: 0.7643 (mttt) cc_final: 0.7221 (mtmm) REVERT: H 40 LYS cc_start: 0.7615 (mtpp) cc_final: 0.7336 (mtpt) REVERT: H 94 GLN cc_start: 0.8392 (mm-40) cc_final: 0.8027 (tp40) REVERT: H 206 GLN cc_start: 0.8669 (OUTLIER) cc_final: 0.8290 (mt0) REVERT: H 210 MET cc_start: 0.8578 (mtp) cc_final: 0.8377 (mtm) REVERT: H 247 ARG cc_start: 0.8001 (mtp-110) cc_final: 0.7325 (mmm160) REVERT: H 254 ARG cc_start: 0.8112 (ttt-90) cc_final: 0.7771 (tmm-80) REVERT: I 27 ARG cc_start: 0.8178 (OUTLIER) cc_final: 0.7828 (tmt-80) REVERT: I 39 LYS cc_start: 0.7929 (mttt) cc_final: 0.7602 (mmmm) REVERT: I 40 LYS cc_start: 0.7700 (mtpp) cc_final: 0.7307 (mttp) REVERT: I 43 GLU cc_start: 0.7620 (mt-10) cc_final: 0.7255 (tp30) REVERT: I 109 LEU cc_start: 0.8759 (OUTLIER) cc_final: 0.8400 (mp) REVERT: I 211 MET cc_start: 0.8508 (OUTLIER) cc_final: 0.8082 (mtt) REVERT: I 332 ASP cc_start: 0.8377 (p0) cc_final: 0.8129 (p0) REVERT: J 39 LYS cc_start: 0.6912 (mttt) cc_final: 0.6260 (mmmt) REVERT: J 40 LYS cc_start: 0.6992 (mtpp) cc_final: 0.6481 (mttt) REVERT: J 42 GLU cc_start: 0.7209 (tp30) cc_final: 0.6488 (tt0) REVERT: J 50 GLU cc_start: 0.7837 (mp0) cc_final: 0.6967 (mp0) REVERT: J 73 LYS cc_start: 0.6559 (mttt) cc_final: 0.5962 (tptt) REVERT: J 77 GLU cc_start: 0.7424 (OUTLIER) cc_final: 0.6788 (mp0) REVERT: J 110 ASP cc_start: 0.8247 (m-30) cc_final: 0.7909 (m-30) REVERT: J 177 ARG cc_start: 0.8350 (OUTLIER) cc_final: 0.7793 (ttt180) REVERT: J 184 ASP cc_start: 0.8644 (m-30) cc_final: 0.8327 (m-30) REVERT: J 187 ASP cc_start: 0.8139 (OUTLIER) cc_final: 0.7379 (m-30) REVERT: J 215 ARG cc_start: 0.6984 (tpt-90) cc_final: 0.6710 (tpt-90) REVERT: J 222 ASP cc_start: 0.8598 (OUTLIER) cc_final: 0.8305 (t0) REVERT: J 299 ARG cc_start: 0.8646 (mtm180) cc_final: 0.8220 (mtt-85) REVERT: J 308 GLU cc_start: 0.7966 (pm20) cc_final: 0.6929 (mt-10) outliers start: 103 outliers final: 59 residues processed: 658 average time/residue: 0.7581 time to fit residues: 565.9121 Evaluate side-chains 665 residues out of total 2607 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 77 poor density : 588 time to evaluate : 0.978 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 87 THR Chi-restraints excluded: chain A residue 88 THR Chi-restraints excluded: chain A residue 128 GLU Chi-restraints excluded: chain 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 223 SER Chi-restraints excluded: chain B residue 334 VAL Chi-restraints excluded: chain C residue 43 GLU Chi-restraints excluded: chain C residue 145 GLN Chi-restraints excluded: chain C residue 187 ASP Chi-restraints excluded: chain C residue 330 ASN Chi-restraints excluded: chain D residue 27 ARG Chi-restraints excluded: chain D residue 97 SER Chi-restraints excluded: chain D residue 111 LYS Chi-restraints excluded: chain D residue 128 GLU Chi-restraints excluded: chain D residue 161 ASP Chi-restraints excluded: chain D residue 181 SER Chi-restraints excluded: chain D residue 187 ASP Chi-restraints excluded: chain D residue 274 ASP Chi-restraints excluded: chain D residue 330 ASN Chi-restraints excluded: chain E residue 48 THR Chi-restraints excluded: chain E residue 87 THR Chi-restraints excluded: chain E residue 112 LEU Chi-restraints excluded: chain E residue 125 MET Chi-restraints excluded: chain E residue 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 E residue 334 VAL Chi-restraints excluded: chain F residue 97 SER Chi-restraints excluded: chain F residue 112 LEU Chi-restraints excluded: chain F residue 125 MET Chi-restraints excluded: chain F residue 145 GLN Chi-restraints excluded: chain F residue 158 MET Chi-restraints excluded: chain F residue 161 ASP Chi-restraints excluded: chain F residue 206 GLN Chi-restraints excluded: chain F residue 272 GLN Chi-restraints excluded: chain F residue 273 VAL Chi-restraints excluded: chain F residue 297 THR Chi-restraints excluded: chain G residue 38 VAL Chi-restraints excluded: chain G residue 94 GLN Chi-restraints excluded: chain G residue 97 SER Chi-restraints excluded: chain G residue 130 ARG Chi-restraints excluded: chain G residue 161 ASP Chi-restraints excluded: chain G residue 206 GLN Chi-restraints excluded: chain G residue 272 GLN Chi-restraints excluded: chain H residue 26 SER Chi-restraints excluded: chain H residue 82 VAL Chi-restraints excluded: chain H residue 142 VAL Chi-restraints excluded: chain H residue 206 GLN Chi-restraints excluded: chain H residue 272 GLN Chi-restraints excluded: chain H residue 308 GLU Chi-restraints excluded: chain I residue 27 ARG Chi-restraints excluded: chain I residue 28 LEU Chi-restraints excluded: chain I residue 90 THR Chi-restraints excluded: chain I residue 99 ILE Chi-restraints excluded: chain I residue 109 LEU Chi-restraints excluded: chain I residue 121 SER Chi-restraints excluded: chain I residue 183 SER Chi-restraints excluded: chain I residue 201 THR Chi-restraints excluded: chain I residue 211 MET 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 177 ARG Chi-restraints excluded: chain J residue 187 ASP Chi-restraints excluded: chain J residue 222 ASP Chi-restraints excluded: chain J residue 239 SER Chi-restraints excluded: chain J residue 272 GLN Chi-restraints excluded: chain J residue 300 LEU 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 21 optimal weight: 5.9990 chunk 48 optimal weight: 5.9990 chunk 165 optimal weight: 2.9990 chunk 218 optimal weight: 10.0000 chunk 200 optimal weight: 4.9990 chunk 164 optimal weight: 2.9990 chunk 234 optimal weight: 3.9990 chunk 129 optimal weight: 2.9990 chunk 126 optimal weight: 2.9990 chunk 160 optimal weight: 0.9990 chunk 288 optimal weight: 0.9990 overall best weight: 2.1990 ------------------------------------------------------------------------------- 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 H 23 GLN H 34 ASN 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 = 0.3641 r_free = 0.3641 target = 0.144679 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3243 r_free = 0.3243 target = 0.110466 restraints weight = 32376.129| |-----------------------------------------------------------------------------| r_work (start): 0.3216 rms_B_bonded: 2.01 r_work: 0.3095 rms_B_bonded: 2.66 restraints_weight: 0.5000 r_work: 0.2965 rms_B_bonded: 4.35 restraints_weight: 0.2500 r_work (final): 0.2965 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8063 moved from start: 0.3430 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.050 26875 Z= 0.201 Angle : 0.535 8.610 36550 Z= 0.280 Chirality : 0.041 0.153 4139 Planarity : 0.004 0.039 4521 Dihedral : 13.687 142.579 4454 Min Nonbonded Distance : 2.200 Molprobity Statistics. All-atom Clashscore : 6.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.22 % Favored : 97.78 % Rotamer: Outliers : 4.14 % Allowed : 23.21 % Favored : 72.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.32 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.01 (0.14), residues: 3196 helix: 1.05 (0.14), residues: 1370 sheet: 0.20 (0.27), residues: 380 loop : -1.06 (0.15), residues: 1446 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG B 130 TYR 0.015 0.001 TYR G 315 PHE 0.014 0.001 PHE F 126 HIS 0.006 0.001 HIS E 294 Details of bonding type rmsd covalent geometry : bond 0.00462 (26875) covalent geometry : angle 0.53468 (36550) hydrogen bonds : bond 0.03788 ( 1159) hydrogen bonds : angle 4.35832 ( 3100) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6392 Ramachandran restraints generated. 3196 Oldfield, 0 Emsley, 3196 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6392 Ramachandran restraints generated. 3196 Oldfield, 0 Emsley, 3196 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 704 residues out of total 2607 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 108 poor density : 596 time to evaluate : 0.843 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 37 ASP cc_start: 0.7825 (m-30) cc_final: 0.7438 (m-30) REVERT: A 40 LYS cc_start: 0.7333 (mtpp) cc_final: 0.6314 (mtpt) REVERT: A 42 GLU cc_start: 0.6958 (pt0) cc_final: 0.6705 (pt0) REVERT: A 66 ILE cc_start: 0.6932 (mm) cc_final: 0.6686 (tp) REVERT: A 68 GLU cc_start: 0.6836 (mt-10) cc_final: 0.6194 (tm-30) REVERT: A 70 LYS cc_start: 0.6670 (ttpt) cc_final: 0.6230 (ttpt) REVERT: A 72 ASP cc_start: 0.6904 (m-30) cc_final: 0.6679 (m-30) REVERT: A 107 LYS cc_start: 0.7176 (mmtm) cc_final: 0.6818 (mtmm) REVERT: A 247 ARG cc_start: 0.7383 (mtp-110) cc_final: 0.6687 (mmm-85) REVERT: A 254 ARG cc_start: 0.7440 (ttp80) cc_final: 0.7091 (tmt90) REVERT: A 303 ARG cc_start: 0.7538 (mtp180) cc_final: 0.6969 (mtm180) REVERT: A 308 GLU cc_start: 0.7284 (pt0) cc_final: 0.6494 (tt0) REVERT: A 329 ILE cc_start: 0.8583 (mt) cc_final: 0.7835 (mt) REVERT: B 40 LYS cc_start: 0.6962 (mtpp) cc_final: 0.5835 (mtmt) REVERT: B 42 GLU cc_start: 0.7170 (mt-10) cc_final: 0.6678 (mt-10) REVERT: B 43 GLU cc_start: 0.7547 (mt-10) cc_final: 0.7212 (mt-10) REVERT: B 72 ASP cc_start: 0.7508 (m-30) cc_final: 0.7191 (m-30) REVERT: B 88 THR cc_start: 0.9122 (OUTLIER) cc_final: 0.8818 (p) REVERT: B 95 ARG cc_start: 0.7885 (ttp80) cc_final: 0.7430 (ttt-90) REVERT: B 100 ILE cc_start: 0.9127 (mp) cc_final: 0.8826 (pp) REVERT: B 107 LYS cc_start: 0.7795 (mmtm) cc_final: 0.6927 (ptpt) REVERT: B 145 GLN cc_start: 0.8434 (mp10) cc_final: 0.8200 (mp10) REVERT: B 332 ASP cc_start: 0.8825 (p0) cc_final: 0.8399 (p0) REVERT: C 33 ILE cc_start: 0.8687 (mm) cc_final: 0.8422 (mm) REVERT: C 94 GLN cc_start: 0.7837 (mm-40) cc_final: 0.7141 (tm-30) REVERT: C 95 ARG cc_start: 0.8261 (ttp80) cc_final: 0.7566 (ttp-170) REVERT: C 107 LYS cc_start: 0.8352 (mmtm) cc_final: 0.7647 (ptmt) REVERT: C 145 GLN cc_start: 0.8797 (mp10) cc_final: 0.8224 (mp10) REVERT: C 154 GLU cc_start: 0.7679 (mt-10) cc_final: 0.6954 (mt-10) REVERT: C 181 SER cc_start: 0.8897 (t) cc_final: 0.8598 (p) REVERT: C 202 GLN cc_start: 0.7795 (mm-40) cc_final: 0.7501 (mt0) REVERT: C 243 MET cc_start: 0.8559 (mtt) cc_final: 0.8172 (mtm) REVERT: D 27 ARG cc_start: 0.8365 (OUTLIER) cc_final: 0.7696 (mtp180) REVERT: D 30 GLN cc_start: 0.7620 (mt0) cc_final: 0.7359 (mp10) REVERT: D 37 ASP cc_start: 0.7350 (m-30) cc_final: 0.6854 (m-30) REVERT: D 94 GLN cc_start: 0.7789 (mm-40) cc_final: 0.6982 (tm-30) REVERT: D 107 LYS cc_start: 0.8340 (mmtm) cc_final: 0.7950 (mtmt) REVERT: D 111 LYS cc_start: 0.8468 (OUTLIER) cc_final: 0.8079 (ttmt) REVERT: D 187 ASP cc_start: 0.9078 (OUTLIER) cc_final: 0.8724 (t70) REVERT: E 27 ARG cc_start: 0.8510 (mtp180) cc_final: 0.8212 (ttt-90) REVERT: E 57 LYS cc_start: 0.8508 (tptm) cc_final: 0.8134 (tttt) REVERT: E 68 GLU cc_start: 0.8111 (mp0) cc_final: 0.7723 (tp30) REVERT: E 107 LYS cc_start: 0.8023 (mmtm) cc_final: 0.7621 (mtmt) REVERT: E 145 GLN cc_start: 0.8954 (OUTLIER) cc_final: 0.8538 (mp10) REVERT: E 176 GLU cc_start: 0.8389 (mm-30) cc_final: 0.7846 (tt0) REVERT: E 243 MET cc_start: 0.8905 (OUTLIER) cc_final: 0.8638 (mtt) REVERT: F 39 LYS cc_start: 0.7718 (mttt) cc_final: 0.6950 (mtmt) REVERT: F 43 GLU cc_start: 0.7991 (mt-10) cc_final: 0.7440 (mp0) REVERT: F 68 GLU cc_start: 0.8189 (mt-10) cc_final: 0.7646 (mp0) REVERT: F 95 ARG cc_start: 0.8183 (ttp80) cc_final: 0.7889 (ttp-110) REVERT: F 202 GLN cc_start: 0.8227 (mm-40) cc_final: 0.7773 (mt0) REVERT: F 206 GLN cc_start: 0.8665 (OUTLIER) cc_final: 0.7807 (mt0) REVERT: G 39 LYS cc_start: 0.7722 (mttt) cc_final: 0.7322 (mtpp) REVERT: G 91 GLU cc_start: 0.8249 (OUTLIER) cc_final: 0.7855 (tt0) REVERT: G 94 GLN cc_start: 0.7889 (OUTLIER) cc_final: 0.7510 (tp-100) REVERT: G 107 LYS cc_start: 0.7989 (mmtm) cc_final: 0.7029 (ttmm) REVERT: G 111 LYS cc_start: 0.8363 (ttpp) cc_final: 0.8133 (mtpp) REVERT: G 125 MET cc_start: 0.9018 (mtm) cc_final: 0.8638 (ptp) REVERT: G 176 GLU cc_start: 0.8176 (mm-30) cc_final: 0.7859 (mm-30) REVERT: G 187 ASP cc_start: 0.8255 (m-30) cc_final: 0.7928 (m-30) REVERT: G 202 GLN cc_start: 0.8102 (mm-40) cc_final: 0.7848 (mt0) REVERT: G 206 GLN cc_start: 0.9001 (OUTLIER) cc_final: 0.8427 (mt0) REVERT: G 247 ARG cc_start: 0.8228 (mtp-110) cc_final: 0.8010 (mtp85) REVERT: G 306 ARG cc_start: 0.7750 (ttm110) cc_final: 0.6900 (tmm160) REVERT: G 308 GLU cc_start: 0.8197 (pm20) cc_final: 0.7851 (pm20) REVERT: H 27 ARG cc_start: 0.7673 (mtp-110) cc_final: 0.7280 (tmt170) REVERT: H 30 GLN cc_start: 0.8221 (mt0) cc_final: 0.7708 (mm-40) REVERT: H 39 LYS cc_start: 0.7746 (mttt) cc_final: 0.7325 (mtmm) REVERT: H 206 GLN cc_start: 0.8739 (OUTLIER) cc_final: 0.8322 (mt0) REVERT: H 247 ARG cc_start: 0.8038 (mtp-110) cc_final: 0.7386 (mmm160) REVERT: H 254 ARG cc_start: 0.8135 (ttt-90) cc_final: 0.7710 (tmm-80) REVERT: H 306 ARG cc_start: 0.7407 (OUTLIER) cc_final: 0.7132 (ttt-90) REVERT: I 27 ARG cc_start: 0.7860 (OUTLIER) cc_final: 0.7534 (tmt-80) REVERT: I 39 LYS cc_start: 0.7942 (mttt) cc_final: 0.7621 (mmmm) REVERT: I 40 LYS cc_start: 0.7806 (mtpp) cc_final: 0.7373 (mttp) REVERT: I 43 GLU cc_start: 0.7691 (mt-10) cc_final: 0.7323 (tp30) REVERT: I 211 MET cc_start: 0.8352 (OUTLIER) cc_final: 0.7781 (mtt) REVERT: I 247 ARG cc_start: 0.7916 (mtp85) cc_final: 0.7372 (ttt180) REVERT: I 332 ASP cc_start: 0.8409 (p0) cc_final: 0.8146 (p0) REVERT: J 39 LYS cc_start: 0.6943 (mttt) cc_final: 0.6230 (mmmt) REVERT: J 40 LYS cc_start: 0.7063 (mtpp) cc_final: 0.6168 (mttt) REVERT: J 42 GLU cc_start: 0.7211 (tp30) cc_final: 0.6495 (tt0) REVERT: J 43 GLU cc_start: 0.6877 (OUTLIER) cc_final: 0.6297 (pp20) REVERT: J 50 GLU cc_start: 0.7893 (mp0) cc_final: 0.7111 (mp0) REVERT: J 73 LYS cc_start: 0.6591 (mttt) cc_final: 0.6000 (tptt) REVERT: J 77 GLU cc_start: 0.7436 (OUTLIER) cc_final: 0.6780 (mp0) REVERT: J 177 ARG cc_start: 0.8297 (OUTLIER) cc_final: 0.7703 (ttt180) REVERT: J 184 ASP cc_start: 0.8603 (m-30) cc_final: 0.8344 (m-30) REVERT: J 187 ASP cc_start: 0.8200 (OUTLIER) cc_final: 0.7926 (t70) REVERT: J 215 ARG cc_start: 0.7054 (tpt-90) cc_final: 0.6667 (tpt-90) REVERT: J 222 ASP cc_start: 0.8679 (OUTLIER) cc_final: 0.8397 (t0) REVERT: J 231 ASP cc_start: 0.8368 (m-30) cc_final: 0.8092 (m-30) REVERT: J 299 ARG cc_start: 0.8720 (mtm180) cc_final: 0.8421 (mtm180) REVERT: J 308 GLU cc_start: 0.7956 (pm20) cc_final: 0.6927 (mt-10) outliers start: 108 outliers final: 60 residues processed: 652 average time/residue: 0.6948 time to fit residues: 514.0640 Evaluate side-chains 664 residues out of total 2607 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 79 poor density : 585 time to evaluate : 1.003 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 87 THR Chi-restraints excluded: chain A residue 88 THR Chi-restraints excluded: chain A residue 128 GLU Chi-restraints excluded: chain A residue 208 SER Chi-restraints excluded: chain B residue 23 GLN Chi-restraints excluded: chain B residue 31 CYS Chi-restraints excluded: chain B residue 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 B residue 334 VAL Chi-restraints excluded: chain C residue 43 GLU Chi-restraints excluded: chain C residue 128 GLU Chi-restraints excluded: chain C residue 330 ASN Chi-restraints excluded: chain D residue 27 ARG Chi-restraints excluded: chain D residue 97 SER Chi-restraints excluded: chain D residue 111 LYS Chi-restraints excluded: chain D residue 121 SER 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 273 VAL 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 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 E residue 334 VAL Chi-restraints excluded: chain F residue 97 SER Chi-restraints excluded: chain F residue 112 LEU Chi-restraints excluded: chain F residue 125 MET Chi-restraints excluded: chain F residue 145 GLN Chi-restraints excluded: chain F residue 158 MET Chi-restraints excluded: chain F residue 161 ASP Chi-restraints excluded: chain F residue 206 GLN Chi-restraints excluded: chain F residue 272 GLN Chi-restraints excluded: chain F residue 273 VAL Chi-restraints excluded: chain F residue 297 THR Chi-restraints excluded: chain G residue 38 VAL Chi-restraints excluded: chain G residue 91 GLU Chi-restraints excluded: chain G residue 94 GLN Chi-restraints excluded: chain G residue 97 SER Chi-restraints excluded: chain G residue 161 ASP Chi-restraints excluded: chain G residue 206 GLN Chi-restraints excluded: chain G residue 272 GLN Chi-restraints excluded: chain G residue 319 CYS Chi-restraints excluded: chain H residue 26 SER Chi-restraints excluded: chain H residue 68 GLU Chi-restraints excluded: chain H residue 82 VAL Chi-restraints excluded: chain H residue 142 VAL Chi-restraints excluded: chain H residue 206 GLN Chi-restraints excluded: chain H residue 208 SER Chi-restraints excluded: chain H residue 272 GLN Chi-restraints excluded: chain H residue 306 ARG Chi-restraints excluded: chain H residue 308 GLU Chi-restraints excluded: chain I residue 27 ARG Chi-restraints excluded: chain I residue 28 LEU Chi-restraints excluded: chain I residue 90 THR Chi-restraints excluded: chain I residue 97 SER Chi-restraints excluded: chain I residue 99 ILE Chi-restraints excluded: chain I residue 121 SER Chi-restraints excluded: chain I residue 183 SER Chi-restraints excluded: chain I residue 201 THR Chi-restraints excluded: chain I residue 211 MET 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 177 ARG Chi-restraints excluded: chain J residue 187 ASP Chi-restraints excluded: chain J residue 222 ASP Chi-restraints excluded: chain J residue 239 SER Chi-restraints excluded: chain J residue 272 GLN Chi-restraints excluded: chain J residue 300 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 323 random chunks: chunk 133 optimal weight: 0.9980 chunk 103 optimal weight: 0.8980 chunk 144 optimal weight: 2.9990 chunk 171 optimal weight: 1.9990 chunk 295 optimal weight: 0.9980 chunk 79 optimal weight: 4.9990 chunk 127 optimal weight: 0.6980 chunk 251 optimal weight: 0.8980 chunk 186 optimal weight: 10.0000 chunk 202 optimal weight: 1.9990 chunk 111 optimal weight: 1.9990 overall best weight: 0.8980 ------------------------------------------------------------------------------- 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** D 242 GLN ** E 145 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 23 GLN H 34 ASN ** H 145 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 290 ASN ** I 145 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3680 r_free = 0.3680 target = 0.148303 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3291 r_free = 0.3291 target = 0.114192 restraints weight = 32120.964| |-----------------------------------------------------------------------------| r_work (start): 0.3284 rms_B_bonded: 2.01 r_work: 0.3164 rms_B_bonded: 2.68 restraints_weight: 0.5000 r_work: 0.3035 rms_B_bonded: 4.40 restraints_weight: 0.2500 r_work (final): 0.3035 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8011 moved from start: 0.3616 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.056 26875 Z= 0.121 Angle : 0.480 7.912 36550 Z= 0.254 Chirality : 0.039 0.174 4139 Planarity : 0.003 0.041 4521 Dihedral : 13.628 143.145 4454 Min Nonbonded Distance : 2.251 Molprobity Statistics. All-atom Clashscore : 6.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.81 % Favored : 98.19 % Rotamer: Outliers : 2.95 % Allowed : 24.70 % Favored : 72.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.32 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.23 (0.15), residues: 3196 helix: 1.23 (0.14), residues: 1370 sheet: 0.28 (0.27), residues: 380 loop : -0.92 (0.15), residues: 1446 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG B 130 TYR 0.010 0.001 TYR G 315 PHE 0.016 0.001 PHE J 259 HIS 0.006 0.001 HIS A 138 Details of bonding type rmsd covalent geometry : bond 0.00271 (26875) covalent geometry : angle 0.48038 (36550) hydrogen bonds : bond 0.03069 ( 1159) hydrogen bonds : angle 4.18236 ( 3100) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6392 Ramachandran restraints generated. 3196 Oldfield, 0 Emsley, 3196 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6392 Ramachandran restraints generated. 3196 Oldfield, 0 Emsley, 3196 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 686 residues out of total 2607 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 77 poor density : 609 time to evaluate : 0.890 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 40 LYS cc_start: 0.7316 (mtpp) cc_final: 0.6299 (mtpt) REVERT: A 42 GLU cc_start: 0.6900 (pt0) cc_final: 0.6650 (pt0) REVERT: A 66 ILE cc_start: 0.6922 (mm) cc_final: 0.6676 (tp) REVERT: A 68 GLU cc_start: 0.6765 (mt-10) cc_final: 0.6210 (tm-30) REVERT: A 70 LYS cc_start: 0.6785 (ttpt) cc_final: 0.6489 (ttpt) REVERT: A 107 LYS cc_start: 0.7140 (mmtm) cc_final: 0.6908 (tptt) REVERT: A 210 MET cc_start: 0.8238 (mtm) cc_final: 0.7515 (mtp) REVERT: A 247 ARG cc_start: 0.7054 (mtp-110) cc_final: 0.6491 (mmm-85) REVERT: A 251 MET cc_start: 0.7995 (mtp) cc_final: 0.7667 (mtp) REVERT: A 254 ARG cc_start: 0.7383 (ttp80) cc_final: 0.7100 (tmt90) REVERT: A 303 ARG cc_start: 0.7511 (mtp180) cc_final: 0.6928 (mtm180) REVERT: A 308 GLU cc_start: 0.7174 (pt0) cc_final: 0.6532 (tt0) REVERT: A 329 ILE cc_start: 0.8526 (mt) cc_final: 0.7929 (mt) REVERT: B 37 ASP cc_start: 0.6724 (m-30) cc_final: 0.6290 (m-30) REVERT: B 40 LYS cc_start: 0.6884 (mtpp) cc_final: 0.5780 (mtmt) REVERT: B 42 GLU cc_start: 0.7102 (mt-10) cc_final: 0.6548 (mt-10) REVERT: B 43 GLU cc_start: 0.7493 (mt-10) cc_final: 0.7138 (mt-10) REVERT: B 72 ASP cc_start: 0.7526 (m-30) cc_final: 0.7312 (m-30) REVERT: B 88 THR cc_start: 0.9067 (OUTLIER) cc_final: 0.8779 (p) REVERT: B 95 ARG cc_start: 0.7867 (ttp80) cc_final: 0.7411 (ttt-90) REVERT: B 100 ILE cc_start: 0.9139 (mp) cc_final: 0.8883 (pp) REVERT: B 107 LYS cc_start: 0.7775 (mmtm) cc_final: 0.6907 (ptpt) REVERT: B 206 GLN cc_start: 0.7499 (mt0) cc_final: 0.7274 (mt0) REVERT: B 306 ARG cc_start: 0.7923 (mmm-85) cc_final: 0.7247 (ptm-80) REVERT: B 332 ASP cc_start: 0.8823 (p0) cc_final: 0.8468 (p0) REVERT: C 33 ILE cc_start: 0.8595 (mm) cc_final: 0.8340 (mm) REVERT: C 94 GLN cc_start: 0.7810 (mm-40) cc_final: 0.6991 (tm-30) REVERT: C 95 ARG cc_start: 0.8089 (ttp80) cc_final: 0.7401 (ttp-170) REVERT: C 107 LYS cc_start: 0.8312 (mmtm) cc_final: 0.7640 (ptmt) REVERT: C 145 GLN cc_start: 0.8484 (mp10) cc_final: 0.7724 (mp10) REVERT: C 154 GLU cc_start: 0.7623 (mt-10) cc_final: 0.6944 (mt-10) REVERT: C 181 SER cc_start: 0.8665 (t) cc_final: 0.8190 (p) REVERT: C 187 ASP cc_start: 0.8661 (OUTLIER) cc_final: 0.8451 (m-30) REVERT: C 202 GLN cc_start: 0.7689 (mm-40) cc_final: 0.7423 (mt0) REVERT: C 243 MET cc_start: 0.8525 (mtt) cc_final: 0.8161 (mtm) REVERT: D 27 ARG cc_start: 0.8298 (OUTLIER) cc_final: 0.7411 (mtp180) REVERT: D 94 GLN cc_start: 0.7771 (mm-40) cc_final: 0.6966 (tm-30) REVERT: D 107 LYS cc_start: 0.8322 (mmtm) cc_final: 0.7930 (mtmt) REVERT: D 111 LYS cc_start: 0.8412 (OUTLIER) cc_final: 0.8019 (ttmt) REVERT: D 187 ASP cc_start: 0.9042 (OUTLIER) cc_final: 0.8696 (t70) REVERT: D 215 ARG cc_start: 0.7983 (tpt-90) cc_final: 0.7765 (tpt-90) REVERT: E 57 LYS cc_start: 0.8480 (tptm) cc_final: 0.8121 (tttt) REVERT: E 68 GLU cc_start: 0.8078 (mp0) cc_final: 0.7700 (tp30) REVERT: E 107 LYS cc_start: 0.8000 (mmtm) cc_final: 0.7599 (mtmt) REVERT: E 176 GLU cc_start: 0.8338 (mm-30) cc_final: 0.7789 (tt0) REVERT: E 243 MET cc_start: 0.8895 (OUTLIER) cc_final: 0.8620 (mtt) REVERT: E 306 ARG cc_start: 0.7678 (ttp-110) cc_final: 0.7343 (tmm160) REVERT: F 27 ARG cc_start: 0.8430 (mtp180) cc_final: 0.7976 (mmm160) REVERT: F 39 LYS cc_start: 0.7363 (mttt) cc_final: 0.6615 (mtmt) REVERT: F 43 GLU cc_start: 0.7909 (mt-10) cc_final: 0.7350 (mp0) REVERT: F 68 GLU cc_start: 0.8162 (mt-10) cc_final: 0.7668 (mp0) REVERT: F 202 GLN cc_start: 0.8183 (mm-40) cc_final: 0.7747 (mt0) REVERT: F 206 GLN cc_start: 0.8658 (OUTLIER) cc_final: 0.7839 (mt0) REVERT: G 39 LYS cc_start: 0.7696 (mttt) cc_final: 0.7301 (mtpp) REVERT: G 94 GLN cc_start: 0.7852 (OUTLIER) cc_final: 0.7456 (tp-100) REVERT: G 107 LYS cc_start: 0.7965 (mmtm) cc_final: 0.7004 (ttmm) REVERT: G 111 LYS cc_start: 0.8286 (ttpp) cc_final: 0.8043 (mtpp) REVERT: G 125 MET cc_start: 0.9032 (mtm) cc_final: 0.8636 (ptp) REVERT: G 130 ARG cc_start: 0.8398 (OUTLIER) cc_final: 0.8102 (ptt-90) REVERT: G 176 GLU cc_start: 0.8167 (mm-30) cc_final: 0.7808 (mm-30) REVERT: G 187 ASP cc_start: 0.8247 (m-30) cc_final: 0.7884 (m-30) REVERT: G 202 GLN cc_start: 0.8101 (mm-40) cc_final: 0.7849 (mt0) REVERT: G 206 GLN cc_start: 0.8990 (OUTLIER) cc_final: 0.8422 (mt0) REVERT: G 247 ARG cc_start: 0.8200 (mtp-110) cc_final: 0.7982 (mtp85) REVERT: G 306 ARG cc_start: 0.7776 (ttm110) cc_final: 0.6921 (tmm160) REVERT: G 308 GLU cc_start: 0.8193 (pm20) cc_final: 0.7872 (pm20) REVERT: H 27 ARG cc_start: 0.7633 (mtp-110) cc_final: 0.7297 (tmt170) REVERT: H 30 GLN cc_start: 0.8196 (mt0) cc_final: 0.7660 (mm-40) REVERT: H 39 LYS cc_start: 0.7659 (mttt) cc_final: 0.7204 (mtmm) REVERT: H 40 LYS cc_start: 0.7740 (mtpp) cc_final: 0.7442 (mtpt) REVERT: H 149 ASP cc_start: 0.8029 (t0) cc_final: 0.7443 (p0) REVERT: H 206 GLN cc_start: 0.8752 (OUTLIER) cc_final: 0.8413 (mt0) REVERT: H 247 ARG cc_start: 0.7968 (mtp-110) cc_final: 0.7441 (mmm160) REVERT: H 254 ARG cc_start: 0.8100 (ttt-90) cc_final: 0.7611 (tmm-80) REVERT: H 306 ARG cc_start: 0.7390 (OUTLIER) cc_final: 0.7134 (ttt-90) REVERT: I 27 ARG cc_start: 0.7484 (OUTLIER) cc_final: 0.7087 (tmt-80) REVERT: I 39 LYS cc_start: 0.7911 (mttt) cc_final: 0.7570 (mmmm) REVERT: I 40 LYS cc_start: 0.7693 (mtpp) cc_final: 0.7300 (mttp) REVERT: I 154 GLU cc_start: 0.8037 (mt-10) cc_final: 0.7362 (mm-30) REVERT: I 247 ARG cc_start: 0.7974 (mtp85) cc_final: 0.7437 (ttt180) REVERT: I 332 ASP cc_start: 0.8376 (p0) cc_final: 0.8118 (p0) REVERT: J 39 LYS cc_start: 0.6898 (mttt) cc_final: 0.6198 (mmmt) REVERT: J 40 LYS cc_start: 0.7026 (mtpp) cc_final: 0.6165 (mttt) REVERT: J 42 GLU cc_start: 0.7204 (tp30) cc_final: 0.6450 (tt0) REVERT: J 43 GLU cc_start: 0.6890 (OUTLIER) cc_final: 0.6351 (pp20) REVERT: J 50 GLU cc_start: 0.7832 (mp0) cc_final: 0.7029 (mp0) REVERT: J 73 LYS cc_start: 0.6529 (mttt) cc_final: 0.5930 (tptt) REVERT: J 77 GLU cc_start: 0.7374 (OUTLIER) cc_final: 0.6731 (mp0) REVERT: J 95 ARG cc_start: 0.7927 (ttp-170) cc_final: 0.7656 (ttm110) REVERT: J 110 ASP cc_start: 0.8203 (m-30) cc_final: 0.7866 (m-30) REVERT: J 154 GLU cc_start: 0.8029 (mt-10) cc_final: 0.7220 (mm-30) REVERT: J 177 ARG cc_start: 0.8247 (OUTLIER) cc_final: 0.7598 (ttt180) REVERT: J 184 ASP cc_start: 0.8632 (m-30) cc_final: 0.8312 (m-30) REVERT: J 187 ASP cc_start: 0.8038 (OUTLIER) cc_final: 0.7262 (m-30) REVERT: J 211 MET cc_start: 0.8681 (mtt) cc_final: 0.8457 (mtt) REVERT: J 215 ARG cc_start: 0.6896 (tpt-90) cc_final: 0.6598 (tpt-90) REVERT: J 222 ASP cc_start: 0.8585 (OUTLIER) cc_final: 0.8233 (t0) REVERT: J 299 ARG cc_start: 0.8649 (mtm180) cc_final: 0.8209 (mtt-85) REVERT: J 308 GLU cc_start: 0.7954 (pm20) cc_final: 0.6920 (mt-10) outliers start: 77 outliers final: 44 residues processed: 648 average time/residue: 0.7234 time to fit residues: 532.8351 Evaluate side-chains 643 residues out of total 2607 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 581 time to evaluate : 0.877 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 43 GLU Chi-restraints excluded: chain C residue 128 GLU Chi-restraints excluded: chain C residue 187 ASP Chi-restraints excluded: chain C residue 330 ASN Chi-restraints excluded: chain D residue 27 ARG Chi-restraints excluded: chain D residue 97 SER Chi-restraints excluded: chain D residue 111 LYS 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 273 VAL Chi-restraints excluded: chain E residue 296 SER Chi-restraints excluded: chain E residue 334 VAL 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 158 MET Chi-restraints excluded: chain F residue 206 GLN Chi-restraints excluded: chain F residue 272 GLN Chi-restraints excluded: chain F residue 273 VAL Chi-restraints excluded: chain F residue 297 THR Chi-restraints excluded: chain G residue 38 VAL Chi-restraints excluded: chain G residue 94 GLN Chi-restraints excluded: chain G residue 130 ARG Chi-restraints excluded: chain G residue 161 ASP Chi-restraints excluded: chain G residue 206 GLN Chi-restraints excluded: chain G residue 272 GLN Chi-restraints excluded: chain H residue 82 VAL Chi-restraints excluded: chain H residue 142 VAL Chi-restraints excluded: chain H residue 206 GLN Chi-restraints excluded: chain H residue 272 GLN Chi-restraints excluded: chain H residue 306 ARG Chi-restraints excluded: chain H residue 308 GLU Chi-restraints excluded: chain I residue 27 ARG Chi-restraints excluded: chain I residue 90 THR Chi-restraints excluded: chain I residue 99 ILE 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 177 ARG Chi-restraints excluded: chain J residue 187 ASP Chi-restraints excluded: chain J residue 222 ASP Chi-restraints excluded: chain J residue 239 SER Chi-restraints excluded: chain J residue 272 GLN Chi-restraints excluded: chain J residue 300 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 323 random chunks: chunk 313 optimal weight: 20.0000 chunk 56 optimal weight: 0.4980 chunk 27 optimal weight: 6.9990 chunk 234 optimal weight: 5.9990 chunk 262 optimal weight: 0.0030 chunk 203 optimal weight: 2.9990 chunk 200 optimal weight: 1.9990 chunk 167 optimal weight: 0.5980 chunk 60 optimal weight: 1.9990 chunk 111 optimal weight: 2.9990 chunk 39 optimal weight: 0.2980 overall best weight: 0.6792 ------------------------------------------------------------------------------- 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 145 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 145 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 145 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 23 GLN H 34 ASN ** H 145 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 = 0.3696 r_free = 0.3696 target = 0.149741 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3310 r_free = 0.3310 target = 0.115641 restraints weight = 31842.513| |-----------------------------------------------------------------------------| r_work (start): 0.3306 rms_B_bonded: 2.01 r_work: 0.3186 rms_B_bonded: 2.68 restraints_weight: 0.5000 r_work: 0.3058 rms_B_bonded: 4.41 restraints_weight: 0.2500 r_work (final): 0.3058 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7996 moved from start: 0.3744 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.051 26875 Z= 0.111 Angle : 0.475 8.305 36550 Z= 0.251 Chirality : 0.039 0.190 4139 Planarity : 0.003 0.042 4521 Dihedral : 13.568 141.665 4454 Min Nonbonded Distance : 2.247 Molprobity Statistics. All-atom Clashscore : 6.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.88 % Favored : 98.12 % Rotamer: Outliers : 2.76 % Allowed : 25.51 % Favored : 71.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.32 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.42 (0.15), residues: 3196 helix: 1.39 (0.14), residues: 1370 sheet: 0.36 (0.27), residues: 380 loop : -0.82 (0.15), residues: 1446 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG B 130 TYR 0.012 0.001 TYR G 315 PHE 0.014 0.001 PHE F 126 HIS 0.006 0.001 HIS A 138 Details of bonding type rmsd covalent geometry : bond 0.00248 (26875) covalent geometry : angle 0.47514 (36550) hydrogen bonds : bond 0.02909 ( 1159) hydrogen bonds : angle 4.09510 ( 3100) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6392 Ramachandran restraints generated. 3196 Oldfield, 0 Emsley, 3196 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6392 Ramachandran restraints generated. 3196 Oldfield, 0 Emsley, 3196 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 672 residues out of total 2607 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 72 poor density : 600 time to evaluate : 0.954 Fit side-chains revert: symmetry clash REVERT: A 29 GLU cc_start: 0.7160 (mt-10) cc_final: 0.6943 (mm-30) REVERT: A 33 ILE cc_start: 0.8024 (mp) cc_final: 0.7287 (mm) REVERT: A 40 LYS cc_start: 0.7325 (mtpp) cc_final: 0.6327 (mtpt) REVERT: A 42 GLU cc_start: 0.6778 (pt0) cc_final: 0.6539 (pt0) REVERT: A 66 ILE cc_start: 0.6917 (mm) cc_final: 0.6683 (tp) REVERT: A 68 GLU cc_start: 0.6742 (mt-10) cc_final: 0.6193 (tm-30) REVERT: A 70 LYS cc_start: 0.6745 (ttpt) cc_final: 0.6544 (ttpt) REVERT: A 107 LYS cc_start: 0.7128 (mmtm) cc_final: 0.6899 (tptt) REVERT: A 210 MET cc_start: 0.8211 (mtm) cc_final: 0.7524 (mtp) REVERT: A 247 ARG cc_start: 0.7056 (mtp-110) cc_final: 0.6506 (mmm-85) REVERT: A 251 MET cc_start: 0.7994 (mtp) cc_final: 0.7657 (mtp) REVERT: A 254 ARG cc_start: 0.7396 (ttp80) cc_final: 0.7158 (tmt90) REVERT: A 303 ARG cc_start: 0.7622 (mtp180) cc_final: 0.7041 (mtm180) REVERT: A 308 GLU cc_start: 0.7132 (pt0) cc_final: 0.6508 (tt0) REVERT: A 329 ILE cc_start: 0.8515 (mt) cc_final: 0.7838 (mt) REVERT: B 37 ASP cc_start: 0.6570 (m-30) cc_final: 0.5828 (m-30) REVERT: B 42 GLU cc_start: 0.7067 (mt-10) cc_final: 0.6512 (mt-10) REVERT: B 43 GLU cc_start: 0.7530 (mt-10) cc_final: 0.7134 (mt-10) REVERT: B 88 THR cc_start: 0.9071 (OUTLIER) cc_final: 0.8836 (p) REVERT: B 95 ARG cc_start: 0.7918 (ttp80) cc_final: 0.7500 (ttt-90) REVERT: B 100 ILE cc_start: 0.9165 (mp) cc_final: 0.8945 (pp) REVERT: B 107 LYS cc_start: 0.7789 (mmtm) cc_final: 0.6911 (ptpt) REVERT: B 206 GLN cc_start: 0.7498 (mt0) cc_final: 0.7277 (mt0) REVERT: B 225 THR cc_start: 0.9186 (p) cc_final: 0.8947 (p) REVERT: B 274 ASP cc_start: 0.5708 (t0) cc_final: 0.4768 (p0) REVERT: B 306 ARG cc_start: 0.7940 (mmm-85) cc_final: 0.7260 (ptm-80) REVERT: B 332 ASP cc_start: 0.8779 (p0) cc_final: 0.8400 (p0) REVERT: C 94 GLN cc_start: 0.7804 (mm-40) cc_final: 0.6971 (tm-30) REVERT: C 95 ARG cc_start: 0.8068 (ttp80) cc_final: 0.7423 (ttp-170) REVERT: C 107 LYS cc_start: 0.8338 (mmtm) cc_final: 0.7650 (ptmt) REVERT: C 145 GLN cc_start: 0.8486 (mp10) cc_final: 0.7784 (mp10) REVERT: C 154 GLU cc_start: 0.7604 (mt-10) cc_final: 0.6949 (mt-10) REVERT: C 181 SER cc_start: 0.8649 (t) cc_final: 0.8167 (p) REVERT: C 222 ASP cc_start: 0.8798 (t70) cc_final: 0.8366 (t70) REVERT: C 243 MET cc_start: 0.8544 (mtt) cc_final: 0.8188 (mtm) REVERT: D 27 ARG cc_start: 0.8241 (OUTLIER) cc_final: 0.7140 (mtp180) REVERT: D 94 GLN cc_start: 0.7766 (mm-40) cc_final: 0.6963 (tm-30) REVERT: D 107 LYS cc_start: 0.8316 (mmtm) cc_final: 0.7919 (mtmt) REVERT: D 111 LYS cc_start: 0.8392 (OUTLIER) cc_final: 0.7970 (ttmt) REVERT: D 187 ASP cc_start: 0.9032 (OUTLIER) cc_final: 0.8684 (t70) REVERT: D 206 GLN cc_start: 0.8133 (OUTLIER) cc_final: 0.7692 (mm-40) REVERT: D 215 ARG cc_start: 0.7882 (tpt-90) cc_final: 0.7618 (tpt-90) REVERT: D 306 ARG cc_start: 0.7580 (ttp-110) cc_final: 0.7123 (ttm110) REVERT: D 338 LYS cc_start: 0.7742 (ttmm) cc_final: 0.7534 (mttp) REVERT: E 27 ARG cc_start: 0.8287 (ttt-90) cc_final: 0.7771 (tpt-90) REVERT: E 57 LYS cc_start: 0.8473 (tptm) cc_final: 0.8112 (tttt) REVERT: E 68 GLU cc_start: 0.7939 (mp0) cc_final: 0.7562 (tp30) REVERT: E 107 LYS cc_start: 0.8015 (mmtm) cc_final: 0.7575 (mtmt) REVERT: E 176 GLU cc_start: 0.8309 (mm-30) cc_final: 0.7754 (tt0) REVERT: E 243 MET cc_start: 0.8912 (OUTLIER) cc_final: 0.8570 (mtt) REVERT: E 306 ARG cc_start: 0.7663 (ttp-110) cc_final: 0.7355 (tmm160) REVERT: F 27 ARG cc_start: 0.8408 (mtp180) cc_final: 0.8055 (ttt-90) REVERT: F 39 LYS cc_start: 0.7279 (mttt) cc_final: 0.6431 (mtpp) REVERT: F 43 GLU cc_start: 0.8038 (mt-10) cc_final: 0.7421 (mp0) REVERT: F 68 GLU cc_start: 0.8281 (mt-10) cc_final: 0.7824 (mp0) REVERT: F 176 GLU cc_start: 0.8214 (mm-30) cc_final: 0.7999 (mm-30) REVERT: F 202 GLN cc_start: 0.8164 (mm-40) cc_final: 0.7690 (mt0) REVERT: F 206 GLN cc_start: 0.8643 (OUTLIER) cc_final: 0.7831 (mt0) REVERT: G 39 LYS cc_start: 0.7709 (mttt) cc_final: 0.7312 (mtpp) REVERT: G 94 GLN cc_start: 0.7847 (mm-40) cc_final: 0.7447 (tp-100) REVERT: G 107 LYS cc_start: 0.7960 (mmtm) cc_final: 0.7000 (ttmm) REVERT: G 111 LYS cc_start: 0.8259 (ttpp) cc_final: 0.8012 (mtpp) REVERT: G 125 MET cc_start: 0.9012 (mtm) cc_final: 0.8626 (ptp) REVERT: G 130 ARG cc_start: 0.8399 (OUTLIER) cc_final: 0.8118 (ptt-90) REVERT: G 176 GLU cc_start: 0.8127 (mm-30) cc_final: 0.7774 (mm-30) REVERT: G 187 ASP cc_start: 0.8358 (m-30) cc_final: 0.8018 (m-30) REVERT: G 206 GLN cc_start: 0.8946 (OUTLIER) cc_final: 0.8378 (mt0) REVERT: G 247 ARG cc_start: 0.8191 (mtp-110) cc_final: 0.7975 (mtp85) REVERT: G 306 ARG cc_start: 0.7782 (ttm110) cc_final: 0.6930 (tmm160) REVERT: G 308 GLU cc_start: 0.8163 (pm20) cc_final: 0.7837 (pm20) REVERT: H 27 ARG cc_start: 0.7640 (OUTLIER) cc_final: 0.7409 (tmt170) REVERT: H 30 GLN cc_start: 0.7956 (mt0) cc_final: 0.7450 (mm-40) REVERT: H 39 LYS cc_start: 0.7656 (mttt) cc_final: 0.7205 (mtmm) REVERT: H 40 LYS cc_start: 0.7705 (mtpp) cc_final: 0.7425 (mtpt) REVERT: H 94 GLN cc_start: 0.8385 (mm-40) cc_final: 0.8022 (tp40) REVERT: H 149 ASP cc_start: 0.7945 (t0) cc_final: 0.7434 (p0) REVERT: H 206 GLN cc_start: 0.8719 (OUTLIER) cc_final: 0.8375 (mt0) REVERT: H 247 ARG cc_start: 0.7955 (mtp-110) cc_final: 0.7428 (mmm160) REVERT: H 254 ARG cc_start: 0.8073 (ttt-90) cc_final: 0.7701 (tmm-80) REVERT: I 27 ARG cc_start: 0.7447 (OUTLIER) cc_final: 0.7129 (tmt-80) REVERT: I 37 ASP cc_start: 0.7928 (m-30) cc_final: 0.7635 (m-30) REVERT: I 39 LYS cc_start: 0.7917 (mttt) cc_final: 0.7599 (mmmm) REVERT: I 40 LYS cc_start: 0.7749 (mtpp) cc_final: 0.7291 (mttp) REVERT: I 43 GLU cc_start: 0.7659 (mt-10) cc_final: 0.7271 (tp30) REVERT: I 80 LYS cc_start: 0.8011 (OUTLIER) cc_final: 0.7806 (ttmt) REVERT: I 154 GLU cc_start: 0.7939 (mt-10) cc_final: 0.7390 (mm-30) REVERT: I 247 ARG cc_start: 0.8018 (mtp85) cc_final: 0.7469 (ttt180) REVERT: I 332 ASP cc_start: 0.8289 (p0) cc_final: 0.8038 (p0) REVERT: J 39 LYS cc_start: 0.6876 (mttt) cc_final: 0.6200 (mmmt) REVERT: J 40 LYS cc_start: 0.7033 (mtpp) cc_final: 0.6168 (mttt) REVERT: J 42 GLU cc_start: 0.7208 (tp30) cc_final: 0.6470 (tt0) REVERT: J 43 GLU cc_start: 0.6872 (OUTLIER) cc_final: 0.6409 (pp20) REVERT: J 50 GLU cc_start: 0.7764 (mp0) cc_final: 0.6976 (mp0) REVERT: J 73 LYS cc_start: 0.6523 (mttt) cc_final: 0.5925 (tptt) REVERT: J 77 GLU cc_start: 0.7356 (OUTLIER) cc_final: 0.6689 (mp0) REVERT: J 95 ARG cc_start: 0.7967 (ttp-170) cc_final: 0.7703 (ttm110) REVERT: J 110 ASP cc_start: 0.8203 (m-30) cc_final: 0.7860 (m-30) REVERT: J 154 GLU cc_start: 0.8029 (mt-10) cc_final: 0.7554 (mm-30) REVERT: J 184 ASP cc_start: 0.8630 (m-30) cc_final: 0.8387 (m-30) REVERT: J 215 ARG cc_start: 0.6883 (tpt-90) cc_final: 0.6607 (tpt-90) REVERT: J 222 ASP cc_start: 0.8467 (OUTLIER) cc_final: 0.8173 (t0) REVERT: J 299 ARG cc_start: 0.8666 (mtm180) cc_final: 0.8337 (mtt-85) REVERT: J 308 GLU cc_start: 0.7994 (pm20) cc_final: 0.6993 (mt-10) outliers start: 72 outliers final: 41 residues processed: 634 average time/residue: 0.6826 time to fit residues: 492.0594 Evaluate side-chains 648 residues out of total 2607 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 591 time to evaluate : 0.621 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 43 GLU Chi-restraints excluded: chain C residue 128 GLU Chi-restraints excluded: chain C residue 330 ASN Chi-restraints excluded: chain D residue 27 ARG Chi-restraints excluded: chain D residue 111 LYS Chi-restraints excluded: chain D residue 128 GLU Chi-restraints excluded: chain D residue 161 ASP Chi-restraints excluded: chain D residue 187 ASP Chi-restraints excluded: chain D residue 206 GLN Chi-restraints excluded: chain D residue 330 ASN Chi-restraints excluded: chain E residue 48 THR Chi-restraints excluded: chain E residue 125 MET Chi-restraints excluded: chain E residue 161 ASP Chi-restraints excluded: chain E residue 243 MET Chi-restraints excluded: chain E residue 273 VAL Chi-restraints excluded: chain E residue 296 SER Chi-restraints excluded: chain E residue 334 VAL 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 149 ASP Chi-restraints excluded: chain F residue 206 GLN Chi-restraints excluded: chain F residue 272 GLN Chi-restraints excluded: chain F residue 273 VAL Chi-restraints excluded: chain F residue 297 THR Chi-restraints excluded: chain G residue 38 VAL Chi-restraints excluded: chain G residue 130 ARG Chi-restraints excluded: chain G residue 161 ASP Chi-restraints excluded: chain G residue 206 GLN Chi-restraints excluded: chain G residue 272 GLN Chi-restraints excluded: chain H residue 26 SER Chi-restraints excluded: chain H residue 27 ARG Chi-restraints excluded: chain H residue 82 VAL Chi-restraints excluded: chain H residue 142 VAL Chi-restraints excluded: chain H residue 206 GLN Chi-restraints excluded: chain H residue 213 GLU Chi-restraints excluded: chain H residue 272 GLN Chi-restraints excluded: chain H residue 308 GLU Chi-restraints excluded: chain I residue 27 ARG Chi-restraints excluded: chain I residue 80 LYS Chi-restraints excluded: chain I residue 90 THR Chi-restraints excluded: chain I residue 99 ILE 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 222 ASP Chi-restraints excluded: chain J residue 239 SER Chi-restraints excluded: chain J residue 272 GLN Chi-restraints excluded: chain J residue 300 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 323 random chunks: chunk 236 optimal weight: 2.9990 chunk 165 optimal weight: 4.9990 chunk 50 optimal weight: 5.9990 chunk 162 optimal weight: 6.9990 chunk 183 optimal weight: 4.9990 chunk 320 optimal weight: 4.9990 chunk 244 optimal weight: 4.9990 chunk 108 optimal weight: 3.9990 chunk 300 optimal weight: 0.1980 chunk 151 optimal weight: 0.9990 chunk 43 optimal weight: 0.9990 overall best weight: 1.8388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 272 GLN B 272 GLN ** C 145 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 145 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 145 GLN ** 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** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3660 r_free = 0.3660 target = 0.146365 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3266 r_free = 0.3266 target = 0.112144 restraints weight = 32037.940| |-----------------------------------------------------------------------------| r_work (start): 0.3237 rms_B_bonded: 2.01 r_work: 0.3115 rms_B_bonded: 2.68 restraints_weight: 0.5000 r_work: 0.2985 rms_B_bonded: 4.39 restraints_weight: 0.2500 r_work (final): 0.2985 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8045 moved from start: 0.3639 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.056 26875 Z= 0.177 Angle : 0.518 8.149 36550 Z= 0.274 Chirality : 0.041 0.159 4139 Planarity : 0.004 0.042 4521 Dihedral : 13.615 140.819 4454 Min Nonbonded Distance : 2.218 Molprobity Statistics. All-atom Clashscore : 6.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.50 % Favored : 97.50 % Rotamer: Outliers : 2.80 % Allowed : 25.58 % Favored : 71.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.32 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.32 (0.15), residues: 3196 helix: 1.30 (0.14), residues: 1370 sheet: 0.33 (0.27), residues: 380 loop : -0.86 (0.15), residues: 1446 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG B 130 TYR 0.019 0.001 TYR G 315 PHE 0.015 0.001 PHE F 126 HIS 0.006 0.001 HIS E 294 Details of bonding type rmsd covalent geometry : bond 0.00409 (26875) covalent geometry : angle 0.51799 (36550) hydrogen bonds : bond 0.03518 ( 1159) hydrogen bonds : angle 4.21625 ( 3100) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 12709.07 seconds wall clock time: 216 minutes 17.47 seconds (12977.47 seconds total)