Starting phenix.real_space_refine on Tue Nov 18 21:16:08 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6a96_6998/11_2025/6a96_6998.cif Found real_map, /net/cci-nas-00/data/ceres_data/6a96_6998/11_2025/6a96_6998.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.51 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/6a96_6998/11_2025/6a96_6998.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6a96_6998/11_2025/6a96_6998.map" model { file = "/net/cci-nas-00/data/ceres_data/6a96_6998/11_2025/6a96_6998.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6a96_6998/11_2025/6a96_6998.cif" } resolution = 3.51 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= -0.023 sd= 0.837 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 160 atoms to isotropic. Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 92 5.16 5 C 11011 2.51 5 N 2753 2.21 5 O 3193 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 22 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5881/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 17049 Number of models: 1 Model: "" Number of chains: 19 Chain: "K" Number of atoms: 963 Number of conformers: 1 Conformer: "" Number of residues, atoms: 125, 963 Classifications: {'peptide': 125} Link IDs: {'PTRANS': 4, 'TRANS': 120} Chain: "L" Number of atoms: 957 Number of conformers: 1 Conformer: "" Number of residues, atoms: 124, 957 Classifications: {'peptide': 124} Link IDs: {'PTRANS': 4, 'TRANS': 119} Chain: "O" Number of atoms: 963 Number of conformers: 1 Conformer: "" Number of residues, atoms: 125, 963 Classifications: {'peptide': 125} Link IDs: {'PTRANS': 4, 'TRANS': 120} Chain: "B" Number of atoms: 2730 Number of conformers: 1 Conformer: "" Number of residues, atoms: 333, 2730 Classifications: {'peptide': 333} Link IDs: {'PCIS': 1, 'PTRANS': 13, 'TRANS': 318} Chain: "A" Number of atoms: 2706 Number of conformers: 1 Conformer: "" Number of residues, atoms: 337, 2706 Classifications: {'peptide': 337} Link IDs: {'PCIS': 1, 'PTRANS': 14, 'TRANS': 321} Chain: "E" Number of atoms: 2730 Number of conformers: 1 Conformer: "" Number of residues, atoms: 333, 2730 Classifications: {'peptide': 333} Link IDs: {'PCIS': 1, 'PTRANS': 13, 'TRANS': 318} Chain: "C" Number of atoms: 2730 Number of conformers: 1 Conformer: "" Number of residues, atoms: 333, 2730 Classifications: {'peptide': 333} Link IDs: {'PCIS': 1, 'PTRANS': 13, 'TRANS': 318} Chain: "D" Number of atoms: 2730 Number of conformers: 1 Conformer: "" Number of residues, atoms: 333, 2730 Classifications: {'peptide': 333} Link IDs: {'PCIS': 1, 'PTRANS': 13, 'TRANS': 318} Chain: "F" Number of atoms: 72 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 72 Unusual residues: {'BMA': 1, 'MAN': 3, 'NAG': 2} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 18 Unresolved non-hydrogen chiralities: 6 Chain: "G" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "H" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Chain: "I" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "J" Number of atoms: 72 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 72 Unusual residues: {'BMA': 1, 'MAN': 3, 'NAG': 2} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 18 Unresolved non-hydrogen chiralities: 6 Chain: "M" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "N" Number of atoms: 72 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 72 Unusual residues: {'BMA': 1, 'MAN': 3, 'NAG': 2} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 18 Unresolved non-hydrogen chiralities: 6 Chain: "P" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "Q" Number of atoms: 72 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 72 Unusual residues: {'BMA': 1, 'MAN': 3, 'NAG': 2} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 18 Unresolved non-hydrogen chiralities: 6 Chain: "R" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "B" Number of atoms: 7 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 7 Unusual residues: {'ABU': 1} Classifications: {'undetermined': 1} Time building chain proxies: 4.28, per 1000 atoms: 0.25 Number of scatterers: 17049 At special positions: 0 Unit cell: (130.54, 121.98, 144.45, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 92 16.00 O 3193 8.00 N 2753 7.00 C 11011 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=9, symmetry=0 Simple disulfide: pdb=" SG CYS K 22 " - pdb=" SG CYS K 96 " distance=2.03 Simple disulfide: pdb=" SG CYS L 22 " - pdb=" SG CYS L 96 " distance=2.03 Simple disulfide: pdb=" SG CYS O 22 " - pdb=" SG CYS O 96 " distance=2.04 Simple disulfide: pdb=" SG CYS B 136 " - pdb=" SG CYS B 150 " distance=2.03 Simple disulfide: pdb=" SG CYS A 142 " - pdb=" SG CYS A 156 " distance=2.04 Simple disulfide: pdb=" SG CYS A 237 " - pdb=" SG CYS A 296 " distance=2.04 Simple disulfide: pdb=" SG CYS E 136 " - pdb=" SG CYS E 150 " distance=2.03 Simple disulfide: pdb=" SG CYS C 136 " - pdb=" SG CYS C 150 " distance=2.03 Simple disulfide: pdb=" SG CYS D 136 " - pdb=" SG CYS D 150 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=6, symmetry=0 Links applied ALPHA1-3 " BMA F 3 " - " MAN F 6 " " MAN F 4 " - " MAN F 5 " " BMA H 3 " - " MAN H 4 " " BMA J 3 " - " MAN J 6 " " MAN J 4 " - " MAN J 5 " " BMA N 3 " - " MAN N 6 " " MAN N 4 " - " MAN N 5 " " BMA Q 3 " - " MAN Q 6 " " MAN Q 4 " - " MAN Q 5 " ALPHA1-6 " BMA F 3 " - " MAN F 4 " " BMA H 3 " - " MAN H 5 " " BMA J 3 " - " MAN J 4 " " BMA N 3 " - " MAN N 4 " " BMA Q 3 " - " MAN Q 4 " BETA1-4 " NAG F 1 " - " NAG F 2 " " NAG F 2 " - " BMA F 3 " " NAG G 1 " - " NAG G 2 " " NAG G 2 " - " BMA G 3 " " NAG H 1 " - " NAG H 2 " " NAG H 2 " - " BMA H 3 " " NAG I 1 " - " NAG I 2 " " NAG J 1 " - " NAG J 2 " " NAG J 2 " - " BMA J 3 " " NAG M 1 " - " NAG M 2 " " NAG M 2 " - " BMA M 3 " " NAG N 1 " - " NAG N 2 " " NAG N 2 " - " BMA N 3 " " NAG P 1 " - " NAG P 2 " " NAG P 2 " - " BMA P 3 " " NAG Q 1 " - " NAG Q 2 " " NAG Q 2 " - " BMA Q 3 " " NAG R 1 " - " NAG R 2 " " NAG R 2 " - " BMA R 3 " NAG-ASN " NAG F 1 " - " ASN B 149 " " NAG G 1 " - " ASN B 80 " " NAG H 1 " - " ASN A 114 " " NAG I 1 " - " ASN A 205 " " NAG J 1 " - " ASN E 149 " " NAG M 1 " - " ASN E 80 " " NAG N 1 " - " ASN C 149 " " NAG P 1 " - " ASN C 80 " " NAG Q 1 " - " ASN D 149 " " NAG R 1 " - " ASN D 80 " Number of additional bonds: simple=6, symmetry=0 Coordination: Other bonds: Time building additional restraints: 2.02 Conformation dependent library (CDL) restraints added in 774.7 milliseconds 4054 Ramachandran restraints generated. 2027 Oldfield, 0 Emsley, 2027 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3828 Finding SS restraints... Secondary structure from input PDB file: 60 helices and 26 sheets defined 33.6% alpha, 32.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.67 Creating SS restraints... Processing helix chain 'K' and resid 27 through 31 removed outlier: 3.772A pdb=" N ASN K 30 " --> pdb=" O HIS K 27 " (cutoff:3.500A) Processing helix chain 'K' and resid 87 through 91 removed outlier: 4.183A pdb=" N THR K 91 " --> pdb=" O PRO K 88 " (cutoff:3.500A) Processing helix chain 'K' and resid 108 through 112 Processing helix chain 'L' and resid 87 through 91 removed outlier: 3.841A pdb=" N THR L 91 " --> pdb=" O PRO L 88 " (cutoff:3.500A) Processing helix chain 'L' and resid 108 through 112 removed outlier: 3.631A pdb=" N ASN L 111 " --> pdb=" O TYR L 108 " (cutoff:3.500A) Processing helix chain 'O' and resid 27 through 31 removed outlier: 4.254A pdb=" N ASN O 30 " --> pdb=" O HIS O 27 " (cutoff:3.500A) removed outlier: 3.882A pdb=" N TYR O 31 " --> pdb=" O THR O 28 " (cutoff:3.500A) No H-bonds generated for 'chain 'O' and resid 27 through 31' Processing helix chain 'O' and resid 87 through 91 removed outlier: 4.051A pdb=" N THR O 91 " --> pdb=" O PRO O 88 " (cutoff:3.500A) Processing helix chain 'B' and resid 9 through 21 removed outlier: 3.904A pdb=" N LYS B 13 " --> pdb=" O MET B 9 " (cutoff:3.500A) removed outlier: 4.124A pdb=" N GLU B 14 " --> pdb=" O SER B 10 " (cutoff:3.500A) Processing helix chain 'B' and resid 84 through 91 removed outlier: 3.622A pdb=" N ASP B 89 " --> pdb=" O ARG B 86 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N LEU B 91 " --> pdb=" O ALA B 88 " (cutoff:3.500A) Processing helix chain 'B' and resid 220 through 225 Processing helix chain 'B' and resid 225 through 236 removed outlier: 3.609A pdb=" N SER B 229 " --> pdb=" O THR B 225 " (cutoff:3.500A) removed outlier: 3.977A pdb=" N THR B 233 " --> pdb=" O SER B 229 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N ILE B 234 " --> pdb=" O ILE B 230 " (cutoff:3.500A) Processing helix chain 'B' and resid 237 through 242 removed outlier: 4.392A pdb=" N TRP B 241 " --> pdb=" O TRP B 237 " (cutoff:3.500A) Processing helix chain 'B' and resid 243 through 245 No H-bonds generated for 'chain 'B' and resid 243 through 245' Processing helix chain 'B' and resid 246 through 267 removed outlier: 4.494A pdb=" N VAL B 251 " --> pdb=" O SER B 247 " (cutoff:3.500A) removed outlier: 4.701A pdb=" N ALA B 252 " --> pdb=" O ALA B 248 " (cutoff:3.500A) removed outlier: 3.821A pdb=" N LEU B 253 " --> pdb=" O ALA B 249 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N THR B 256 " --> pdb=" O ALA B 252 " (cutoff:3.500A) removed outlier: 3.841A pdb=" N VAL B 258 " --> pdb=" O GLY B 254 " (cutoff:3.500A) Processing helix chain 'B' and resid 268 through 272 Processing helix chain 'B' and resid 279 through 306 removed outlier: 3.515A pdb=" N MET B 283 " --> pdb=" O LYS B 279 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N VAL B 292 " --> pdb=" O CYS B 288 " (cutoff:3.500A) removed outlier: 4.228A pdb=" N TYR B 299 " --> pdb=" O ALA B 295 " (cutoff:3.500A) removed outlier: 3.764A pdb=" N PHE B 301 " --> pdb=" O LEU B 297 " (cutoff:3.500A) removed outlier: 3.941A pdb=" N TYR B 304 " --> pdb=" O ALA B 300 " (cutoff:3.500A) removed outlier: 3.832A pdb=" N ILE B 305 " --> pdb=" O PHE B 301 " (cutoff:3.500A) Processing helix chain 'B' and resid 309 through 428 removed outlier: 4.059A pdb=" N ALA B 313 " --> pdb=" O GLN B 309 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N ALA B 422 " --> pdb=" O ALA B 311 " (cutoff:3.500A) removed outlier: 4.778A pdb=" N ASP B 424 " --> pdb=" O ALA B 313 " (cutoff:3.500A) removed outlier: 4.795A pdb=" N ARG B 425 " --> pdb=" O ALA B 314 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N ARG B 428 " --> pdb=" O ASP B 424 " (cutoff:3.500A) Processing helix chain 'B' and resid 430 through 446 removed outlier: 4.668A pdb=" N SER B 436 " --> pdb=" O PRO B 432 " (cutoff:3.500A) removed outlier: 3.764A pdb=" N LEU B 444 " --> pdb=" O LEU B 440 " (cutoff:3.500A) removed outlier: 3.863A pdb=" N TYR B 446 " --> pdb=" O TYR B 442 " (cutoff:3.500A) Processing helix chain 'A' and resid 15 through 27 removed outlier: 3.508A pdb=" N ARG A 20 " --> pdb=" O THR A 16 " (cutoff:3.500A) Processing helix chain 'A' and resid 92 through 97 removed outlier: 3.738A pdb=" N LYS A 96 " --> pdb=" O LEU A 92 " (cutoff:3.500A) Processing helix chain 'A' and resid 228 through 233 Processing helix chain 'A' and resid 233 through 246 removed outlier: 3.554A pdb=" N CYS A 237 " --> pdb=" O THR A 233 " (cutoff:3.500A) Processing helix chain 'A' and resid 247 through 250 Processing helix chain 'A' and resid 256 through 277 removed outlier: 4.133A pdb=" N VAL A 260 " --> pdb=" O PRO A 256 " (cutoff:3.500A) removed outlier: 3.954A pdb=" N VAL A 263 " --> pdb=" O THR A 259 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N THR A 264 " --> pdb=" O VAL A 260 " (cutoff:3.500A) removed outlier: 3.834A pdb=" N VAL A 266 " --> pdb=" O GLY A 262 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N MET A 269 " --> pdb=" O THR A 265 " (cutoff:3.500A) Processing helix chain 'A' and resid 289 through 314 removed outlier: 4.357A pdb=" N VAL A 295 " --> pdb=" O TRP A 291 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N PHE A 299 " --> pdb=" O VAL A 295 " (cutoff:3.500A) removed outlier: 4.369A pdb=" N VAL A 300 " --> pdb=" O CYS A 296 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N PHE A 301 " --> pdb=" O TYR A 297 " (cutoff:3.500A) removed outlier: 4.143A pdb=" N ILE A 305 " --> pdb=" O PHE A 301 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N GLU A 306 " --> pdb=" O SER A 302 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N PHE A 307 " --> pdb=" O ALA A 303 " (cutoff:3.500A) removed outlier: 4.667A pdb=" N VAL A 310 " --> pdb=" O GLU A 306 " (cutoff:3.500A) removed outlier: 4.273A pdb=" N ASN A 311 " --> pdb=" O PHE A 307 " (cutoff:3.500A) removed outlier: 4.548A pdb=" N TYR A 312 " --> pdb=" O ALA A 308 " (cutoff:3.500A) Processing helix chain 'A' and resid 320 through 399 removed outlier: 4.307A pdb=" N LYS A 396 " --> pdb=" O ALA A 322 " (cutoff:3.500A) removed outlier: 3.744A pdb=" N ARG A 399 " --> pdb=" O ASP A 395 " (cutoff:3.500A) Processing helix chain 'A' and resid 401 through 418 removed outlier: 3.767A pdb=" N LEU A 411 " --> pdb=" O GLY A 407 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N ALA A 415 " --> pdb=" O LEU A 411 " (cutoff:3.500A) removed outlier: 3.916A pdb=" N TYR A 417 " --> pdb=" O TYR A 413 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N LEU A 418 " --> pdb=" O TRP A 414 " (cutoff:3.500A) Processing helix chain 'E' and resid 9 through 21 removed outlier: 3.904A pdb=" N LYS E 13 " --> pdb=" O MET E 9 " (cutoff:3.500A) removed outlier: 4.123A pdb=" N GLU E 14 " --> pdb=" O SER E 10 " (cutoff:3.500A) Processing helix chain 'E' and resid 84 through 91 removed outlier: 3.624A pdb=" N ASP E 89 " --> pdb=" O ARG E 86 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N LEU E 91 " --> pdb=" O ALA E 88 " (cutoff:3.500A) Processing helix chain 'E' and resid 220 through 225 Processing helix chain 'E' and resid 225 through 236 removed outlier: 3.609A pdb=" N SER E 229 " --> pdb=" O THR E 225 " (cutoff:3.500A) removed outlier: 3.977A pdb=" N THR E 233 " --> pdb=" O SER E 229 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N ILE E 234 " --> pdb=" O ILE E 230 " (cutoff:3.500A) Processing helix chain 'E' and resid 237 through 242 removed outlier: 4.391A pdb=" N TRP E 241 " --> pdb=" O TRP E 237 " (cutoff:3.500A) Processing helix chain 'E' and resid 243 through 245 No H-bonds generated for 'chain 'E' and resid 243 through 245' Processing helix chain 'E' and resid 246 through 267 removed outlier: 4.493A pdb=" N VAL E 251 " --> pdb=" O SER E 247 " (cutoff:3.500A) removed outlier: 4.701A pdb=" N ALA E 252 " --> pdb=" O ALA E 248 " (cutoff:3.500A) removed outlier: 3.821A pdb=" N LEU E 253 " --> pdb=" O ALA E 249 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N THR E 256 " --> pdb=" O ALA E 252 " (cutoff:3.500A) removed outlier: 3.841A pdb=" N VAL E 258 " --> pdb=" O GLY E 254 " (cutoff:3.500A) Processing helix chain 'E' and resid 268 through 272 Processing helix chain 'E' and resid 279 through 306 removed outlier: 3.516A pdb=" N MET E 283 " --> pdb=" O LYS E 279 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N VAL E 292 " --> pdb=" O CYS E 288 " (cutoff:3.500A) removed outlier: 4.228A pdb=" N TYR E 299 " --> pdb=" O ALA E 295 " (cutoff:3.500A) removed outlier: 3.764A pdb=" N PHE E 301 " --> pdb=" O LEU E 297 " (cutoff:3.500A) removed outlier: 3.942A pdb=" N TYR E 304 " --> pdb=" O ALA E 300 " (cutoff:3.500A) removed outlier: 3.833A pdb=" N ILE E 305 " --> pdb=" O PHE E 301 " (cutoff:3.500A) Processing helix chain 'E' and resid 309 through 428 removed outlier: 4.059A pdb=" N ALA E 313 " --> pdb=" O GLN E 309 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N ALA E 422 " --> pdb=" O ALA E 311 " (cutoff:3.500A) removed outlier: 4.778A pdb=" N ASP E 424 " --> pdb=" O ALA E 313 " (cutoff:3.500A) removed outlier: 4.795A pdb=" N ARG E 425 " --> pdb=" O ALA E 314 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N ARG E 428 " --> pdb=" O ASP E 424 " (cutoff:3.500A) Processing helix chain 'E' and resid 430 through 446 removed outlier: 4.668A pdb=" N SER E 436 " --> pdb=" O PRO E 432 " (cutoff:3.500A) removed outlier: 3.764A pdb=" N LEU E 444 " --> pdb=" O LEU E 440 " (cutoff:3.500A) removed outlier: 3.863A pdb=" N TYR E 446 " --> pdb=" O TYR E 442 " (cutoff:3.500A) Processing helix chain 'C' and resid 9 through 21 removed outlier: 3.903A pdb=" N LYS C 13 " --> pdb=" O MET C 9 " (cutoff:3.500A) removed outlier: 4.123A pdb=" N GLU C 14 " --> pdb=" O SER C 10 " (cutoff:3.500A) Processing helix chain 'C' and resid 84 through 91 removed outlier: 3.624A pdb=" N ASP C 89 " --> pdb=" O ARG C 86 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N LEU C 91 " --> pdb=" O ALA C 88 " (cutoff:3.500A) Processing helix chain 'C' and resid 220 through 225 Processing helix chain 'C' and resid 225 through 236 removed outlier: 3.608A pdb=" N SER C 229 " --> pdb=" O THR C 225 " (cutoff:3.500A) removed outlier: 3.977A pdb=" N THR C 233 " --> pdb=" O SER C 229 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N ILE C 234 " --> pdb=" O ILE C 230 " (cutoff:3.500A) Processing helix chain 'C' and resid 237 through 242 removed outlier: 4.392A pdb=" N TRP C 241 " --> pdb=" O TRP C 237 " (cutoff:3.500A) Processing helix chain 'C' and resid 243 through 245 No H-bonds generated for 'chain 'C' and resid 243 through 245' Processing helix chain 'C' and resid 246 through 267 removed outlier: 4.493A pdb=" N VAL C 251 " --> pdb=" O SER C 247 " (cutoff:3.500A) removed outlier: 4.699A pdb=" N ALA C 252 " --> pdb=" O ALA C 248 " (cutoff:3.500A) removed outlier: 3.821A pdb=" N LEU C 253 " --> pdb=" O ALA C 249 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N THR C 256 " --> pdb=" O ALA C 252 " (cutoff:3.500A) removed outlier: 3.841A pdb=" N VAL C 258 " --> pdb=" O GLY C 254 " (cutoff:3.500A) Processing helix chain 'C' and resid 268 through 272 Processing helix chain 'C' and resid 279 through 306 removed outlier: 3.516A pdb=" N MET C 283 " --> pdb=" O LYS C 279 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N VAL C 292 " --> pdb=" O CYS C 288 " (cutoff:3.500A) removed outlier: 4.227A pdb=" N TYR C 299 " --> pdb=" O ALA C 295 " (cutoff:3.500A) removed outlier: 3.765A pdb=" N PHE C 301 " --> pdb=" O LEU C 297 " (cutoff:3.500A) removed outlier: 3.941A pdb=" N TYR C 304 " --> pdb=" O ALA C 300 " (cutoff:3.500A) removed outlier: 3.833A pdb=" N ILE C 305 " --> pdb=" O PHE C 301 " (cutoff:3.500A) Processing helix chain 'C' and resid 309 through 428 removed outlier: 4.060A pdb=" N ALA C 313 " --> pdb=" O GLN C 309 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N ALA C 422 " --> pdb=" O ALA C 311 " (cutoff:3.500A) removed outlier: 4.778A pdb=" N ASP C 424 " --> pdb=" O ALA C 313 " (cutoff:3.500A) removed outlier: 4.796A pdb=" N ARG C 425 " --> pdb=" O ALA C 314 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N ARG C 428 " --> pdb=" O ASP C 424 " (cutoff:3.500A) Processing helix chain 'C' and resid 430 through 446 removed outlier: 4.668A pdb=" N SER C 436 " --> pdb=" O PRO C 432 " (cutoff:3.500A) removed outlier: 3.764A pdb=" N LEU C 444 " --> pdb=" O LEU C 440 " (cutoff:3.500A) removed outlier: 3.863A pdb=" N TYR C 446 " --> pdb=" O TYR C 442 " (cutoff:3.500A) Processing helix chain 'D' and resid 9 through 21 removed outlier: 3.904A pdb=" N LYS D 13 " --> pdb=" O MET D 9 " (cutoff:3.500A) removed outlier: 4.123A pdb=" N GLU D 14 " --> pdb=" O SER D 10 " (cutoff:3.500A) Processing helix chain 'D' and resid 84 through 91 removed outlier: 3.623A pdb=" N ASP D 89 " --> pdb=" O ARG D 86 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N LEU D 91 " --> pdb=" O ALA D 88 " (cutoff:3.500A) Processing helix chain 'D' and resid 220 through 225 Processing helix chain 'D' and resid 225 through 236 removed outlier: 3.610A pdb=" N SER D 229 " --> pdb=" O THR D 225 " (cutoff:3.500A) removed outlier: 3.977A pdb=" N THR D 233 " --> pdb=" O SER D 229 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N ILE D 234 " --> pdb=" O ILE D 230 " (cutoff:3.500A) Processing helix chain 'D' and resid 237 through 242 removed outlier: 4.391A pdb=" N TRP D 241 " --> pdb=" O TRP D 237 " (cutoff:3.500A) Processing helix chain 'D' and resid 243 through 245 No H-bonds generated for 'chain 'D' and resid 243 through 245' Processing helix chain 'D' and resid 246 through 267 removed outlier: 4.493A pdb=" N VAL D 251 " --> pdb=" O SER D 247 " (cutoff:3.500A) removed outlier: 4.701A pdb=" N ALA D 252 " --> pdb=" O ALA D 248 " (cutoff:3.500A) removed outlier: 3.822A pdb=" N LEU D 253 " --> pdb=" O ALA D 249 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N THR D 256 " --> pdb=" O ALA D 252 " (cutoff:3.500A) removed outlier: 3.842A pdb=" N VAL D 258 " --> pdb=" O GLY D 254 " (cutoff:3.500A) Processing helix chain 'D' and resid 268 through 272 Processing helix chain 'D' and resid 279 through 306 removed outlier: 3.517A pdb=" N MET D 283 " --> pdb=" O LYS D 279 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N VAL D 292 " --> pdb=" O CYS D 288 " (cutoff:3.500A) removed outlier: 4.228A pdb=" N TYR D 299 " --> pdb=" O ALA D 295 " (cutoff:3.500A) removed outlier: 3.765A pdb=" N PHE D 301 " --> pdb=" O LEU D 297 " (cutoff:3.500A) removed outlier: 3.941A pdb=" N TYR D 304 " --> pdb=" O ALA D 300 " (cutoff:3.500A) removed outlier: 3.833A pdb=" N ILE D 305 " --> pdb=" O PHE D 301 " (cutoff:3.500A) Processing helix chain 'D' and resid 309 through 428 removed outlier: 4.059A pdb=" N ALA D 313 " --> pdb=" O GLN D 309 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N ALA D 422 " --> pdb=" O ALA D 311 " (cutoff:3.500A) removed outlier: 4.778A pdb=" N ASP D 424 " --> pdb=" O ALA D 313 " (cutoff:3.500A) removed outlier: 4.796A pdb=" N ARG D 425 " --> pdb=" O ALA D 314 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N ARG D 428 " --> pdb=" O ASP D 424 " (cutoff:3.500A) Processing helix chain 'D' and resid 430 through 446 removed outlier: 4.668A pdb=" N SER D 436 " --> pdb=" O PRO D 432 " (cutoff:3.500A) removed outlier: 3.765A pdb=" N LEU D 444 " --> pdb=" O LEU D 440 " (cutoff:3.500A) removed outlier: 3.863A pdb=" N TYR D 446 " --> pdb=" O TYR D 442 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'K' and resid 5 through 7 removed outlier: 3.503A pdb=" N GLN K 5 " --> pdb=" O ALA K 23 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'K' and resid 11 through 12 removed outlier: 3.730A pdb=" N VAL K 12 " --> pdb=" O THR K 122 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA2 Processing sheet with id=AA3, first strand: chain 'K' and resid 17 through 19 Processing sheet with id=AA4, first strand: chain 'K' and resid 58 through 60 removed outlier: 4.158A pdb=" N GLY K 49 " --> pdb=" O TRP K 36 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N MET K 34 " --> pdb=" O ILE K 51 " (cutoff:3.500A) removed outlier: 4.176A pdb=" N ILE K 33 " --> pdb=" O LYS K 99 " (cutoff:3.500A) removed outlier: 3.828A pdb=" N CYS K 96 " --> pdb=" O GLY K 116 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'L' and resid 6 through 7 Processing sheet with id=AA6, first strand: chain 'L' and resid 11 through 13 removed outlier: 7.417A pdb=" N VAL L 12 " --> pdb=" O SER L 124 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA6 Processing sheet with id=AA7, first strand: chain 'L' and resid 58 through 60 removed outlier: 5.197A pdb=" N PHE L 47 " --> pdb=" O ARG L 38 " (cutoff:3.500A) removed outlier: 6.015A pdb=" N ARG L 38 " --> pdb=" O PHE L 47 " (cutoff:3.500A) removed outlier: 4.219A pdb=" N GLY L 49 " --> pdb=" O TRP L 36 " (cutoff:3.500A) removed outlier: 3.950A pdb=" N MET L 34 " --> pdb=" O ILE L 51 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'O' and resid 3 through 7 Processing sheet with id=AA9, first strand: chain 'O' and resid 11 through 13 removed outlier: 6.925A pdb=" N VAL O 12 " --> pdb=" O SER O 124 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'O' and resid 58 through 60 removed outlier: 5.493A pdb=" N PHE O 47 " --> pdb=" O ARG O 38 " (cutoff:3.500A) removed outlier: 6.181A pdb=" N ARG O 38 " --> pdb=" O PHE O 47 " (cutoff:3.500A) removed outlier: 4.433A pdb=" N GLY O 49 " --> pdb=" O TRP O 36 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N MET O 34 " --> pdb=" O ILE O 51 " (cutoff:3.500A) removed outlier: 4.085A pdb=" N ILE O 33 " --> pdb=" O LYS O 99 " (cutoff:3.500A) removed outlier: 3.769A pdb=" N CYS O 96 " --> pdb=" O GLY O 116 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'B' and resid 82 through 83 removed outlier: 4.365A pdb=" N ILE B 116 " --> pdb=" O LEU B 83 " (cutoff:3.500A) removed outlier: 6.804A pdb=" N ASP B 56 " --> pdb=" O VAL B 50 " (cutoff:3.500A) removed outlier: 4.755A pdb=" N VAL B 50 " --> pdb=" O ASP B 56 " (cutoff:3.500A) removed outlier: 6.681A pdb=" N THR B 58 " --> pdb=" O ASP B 48 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N SER B 46 " --> pdb=" O THR B 60 " (cutoff:3.500A) removed outlier: 6.286A pdb=" N TYR B 62 " --> pdb=" O ILE B 44 " (cutoff:3.500A) removed outlier: 5.387A pdb=" N ILE B 44 " --> pdb=" O TYR B 62 " (cutoff:3.500A) removed outlier: 7.252A pdb=" N GLN B 64 " --> pdb=" O ILE B 42 " (cutoff:3.500A) removed outlier: 5.485A pdb=" N ILE B 42 " --> pdb=" O GLN B 64 " (cutoff:3.500A) removed outlier: 6.421A pdb=" N TYR B 66 " --> pdb=" O MET B 40 " (cutoff:3.500A) removed outlier: 5.803A pdb=" N MET B 40 " --> pdb=" O TYR B 66 " (cutoff:3.500A) removed outlier: 8.859A pdb=" N ARG B 68 " --> pdb=" O VAL B 38 " (cutoff:3.500A) removed outlier: 8.440A pdb=" N VAL B 38 " --> pdb=" O ARG B 68 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'B' and resid 101 through 106 removed outlier: 7.097A pdb=" N THR B 133 " --> pdb=" O LYS B 102 " (cutoff:3.500A) removed outlier: 4.727A pdb=" N SER B 104 " --> pdb=" O THR B 131 " (cutoff:3.500A) removed outlier: 7.212A pdb=" N THR B 131 " --> pdb=" O SER B 104 " (cutoff:3.500A) removed outlier: 5.097A pdb=" N VAL B 106 " --> pdb=" O ARG B 129 " (cutoff:3.500A) removed outlier: 7.852A pdb=" N ARG B 129 " --> pdb=" O VAL B 106 " (cutoff:3.500A) removed outlier: 6.804A pdb=" N ASP B 56 " --> pdb=" O VAL B 50 " (cutoff:3.500A) removed outlier: 4.755A pdb=" N VAL B 50 " --> pdb=" O ASP B 56 " (cutoff:3.500A) removed outlier: 6.681A pdb=" N THR B 58 " --> pdb=" O ASP B 48 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N SER B 46 " --> pdb=" O THR B 60 " (cutoff:3.500A) removed outlier: 6.286A pdb=" N TYR B 62 " --> pdb=" O ILE B 44 " (cutoff:3.500A) removed outlier: 5.387A pdb=" N ILE B 44 " --> pdb=" O TYR B 62 " (cutoff:3.500A) removed outlier: 7.252A pdb=" N GLN B 64 " --> pdb=" O ILE B 42 " (cutoff:3.500A) removed outlier: 5.485A pdb=" N ILE B 42 " --> pdb=" O GLN B 64 " (cutoff:3.500A) removed outlier: 6.421A pdb=" N TYR B 66 " --> pdb=" O MET B 40 " (cutoff:3.500A) removed outlier: 5.803A pdb=" N MET B 40 " --> pdb=" O TYR B 66 " (cutoff:3.500A) removed outlier: 8.859A pdb=" N ARG B 68 " --> pdb=" O VAL B 38 " (cutoff:3.500A) removed outlier: 8.440A pdb=" N VAL B 38 " --> pdb=" O ARG B 68 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'B' and resid 97 through 98 removed outlier: 3.651A pdb=" N CYS B 150 " --> pdb=" O PHE B 212 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N PHE B 212 " --> pdb=" O CYS B 150 " (cutoff:3.500A) removed outlier: 3.995A pdb=" N ARG B 207 " --> pdb=" O ARG B 196 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N SER B 211 " --> pdb=" O ARG B 192 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N ARG B 213 " --> pdb=" O GLU B 190 " (cutoff:3.500A) removed outlier: 5.189A pdb=" N GLU B 190 " --> pdb=" O ARG B 213 " (cutoff:3.500A) removed outlier: 6.572A pdb=" N LYS B 215 " --> pdb=" O ILE B 188 " (cutoff:3.500A) removed outlier: 5.640A pdb=" N ILE B 188 " --> pdb=" O LYS B 215 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'A' and resid 56 through 57 removed outlier: 3.705A pdb=" N GLU A 62 " --> pdb=" O SER A 57 " (cutoff:3.500A) removed outlier: 4.652A pdb=" N LYS A 74 " --> pdb=" O GLN A 43 " (cutoff:3.500A) removed outlier: 6.575A pdb=" N GLN A 43 " --> pdb=" O LYS A 74 " (cutoff:3.500A) removed outlier: 6.774A pdb=" N THR A 42 " --> pdb=" O VAL A 171 " (cutoff:3.500A) removed outlier: 7.731A pdb=" N VAL A 173 " --> pdb=" O THR A 42 " (cutoff:3.500A) removed outlier: 5.934A pdb=" N VAL A 44 " --> pdb=" O VAL A 173 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'A' and resid 107 through 110 removed outlier: 6.588A pdb=" N GLY A 107 " --> pdb=" O GLU A 141 " (cutoff:3.500A) removed outlier: 7.047A pdb=" N GLU A 141 " --> pdb=" O GLY A 107 " (cutoff:3.500A) removed outlier: 3.781A pdb=" N LYS A 109 " --> pdb=" O SER A 139 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N TRP A 73 " --> pdb=" O LEU A 130 " (cutoff:3.500A) removed outlier: 3.745A pdb=" N VAL A 67 " --> pdb=" O LEU A 136 " (cutoff:3.500A) removed outlier: 4.652A pdb=" N LYS A 74 " --> pdb=" O GLN A 43 " (cutoff:3.500A) removed outlier: 6.575A pdb=" N GLN A 43 " --> pdb=" O LYS A 74 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'A' and resid 87 through 89 removed outlier: 4.026A pdb=" N LEU A 122 " --> pdb=" O LEU A 89 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'A' and resid 159 through 161 removed outlier: 3.897A pdb=" N THR A 200 " --> pdb=" O HIS A 219 " (cutoff:3.500A) removed outlier: 3.988A pdb=" N GLY A 198 " --> pdb=" O HIS A 221 " (cutoff:3.500A) removed outlier: 6.406A pdb=" N LYS A 223 " --> pdb=" O LEU A 196 " (cutoff:3.500A) removed outlier: 5.229A pdb=" N LEU A 196 " --> pdb=" O LYS A 223 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'E' and resid 82 through 83 removed outlier: 4.366A pdb=" N ILE E 116 " --> pdb=" O LEU E 83 " (cutoff:3.500A) removed outlier: 6.805A pdb=" N ASP E 56 " --> pdb=" O VAL E 50 " (cutoff:3.500A) removed outlier: 4.755A pdb=" N VAL E 50 " --> pdb=" O ASP E 56 " (cutoff:3.500A) removed outlier: 6.681A pdb=" N THR E 58 " --> pdb=" O ASP E 48 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N SER E 46 " --> pdb=" O THR E 60 " (cutoff:3.500A) removed outlier: 6.287A pdb=" N TYR E 62 " --> pdb=" O ILE E 44 " (cutoff:3.500A) removed outlier: 5.386A pdb=" N ILE E 44 " --> pdb=" O TYR E 62 " (cutoff:3.500A) removed outlier: 7.252A pdb=" N GLN E 64 " --> pdb=" O ILE E 42 " (cutoff:3.500A) removed outlier: 5.486A pdb=" N ILE E 42 " --> pdb=" O GLN E 64 " (cutoff:3.500A) removed outlier: 6.421A pdb=" N TYR E 66 " --> pdb=" O MET E 40 " (cutoff:3.500A) removed outlier: 5.803A pdb=" N MET E 40 " --> pdb=" O TYR E 66 " (cutoff:3.500A) removed outlier: 8.859A pdb=" N ARG E 68 " --> pdb=" O VAL E 38 " (cutoff:3.500A) removed outlier: 8.440A pdb=" N VAL E 38 " --> pdb=" O ARG E 68 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'E' and resid 101 through 106 removed outlier: 7.097A pdb=" N THR E 133 " --> pdb=" O LYS E 102 " (cutoff:3.500A) removed outlier: 4.727A pdb=" N SER E 104 " --> pdb=" O THR E 131 " (cutoff:3.500A) removed outlier: 7.211A pdb=" N THR E 131 " --> pdb=" O SER E 104 " (cutoff:3.500A) removed outlier: 5.097A pdb=" N VAL E 106 " --> pdb=" O ARG E 129 " (cutoff:3.500A) removed outlier: 7.852A pdb=" N ARG E 129 " --> pdb=" O VAL E 106 " (cutoff:3.500A) removed outlier: 6.805A pdb=" N ASP E 56 " --> pdb=" O VAL E 50 " (cutoff:3.500A) removed outlier: 4.755A pdb=" N VAL E 50 " --> pdb=" O ASP E 56 " (cutoff:3.500A) removed outlier: 6.681A pdb=" N THR E 58 " --> pdb=" O ASP E 48 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N SER E 46 " --> pdb=" O THR E 60 " (cutoff:3.500A) removed outlier: 6.287A pdb=" N TYR E 62 " --> pdb=" O ILE E 44 " (cutoff:3.500A) removed outlier: 5.386A pdb=" N ILE E 44 " --> pdb=" O TYR E 62 " (cutoff:3.500A) removed outlier: 7.252A pdb=" N GLN E 64 " --> pdb=" O ILE E 42 " (cutoff:3.500A) removed outlier: 5.486A pdb=" N ILE E 42 " --> pdb=" O GLN E 64 " (cutoff:3.500A) removed outlier: 6.421A pdb=" N TYR E 66 " --> pdb=" O MET E 40 " (cutoff:3.500A) removed outlier: 5.803A pdb=" N MET E 40 " --> pdb=" O TYR E 66 " (cutoff:3.500A) removed outlier: 8.859A pdb=" N ARG E 68 " --> pdb=" O VAL E 38 " (cutoff:3.500A) removed outlier: 8.440A pdb=" N VAL E 38 " --> pdb=" O ARG E 68 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'E' and resid 97 through 98 removed outlier: 3.650A pdb=" N CYS E 150 " --> pdb=" O PHE E 212 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N PHE E 212 " --> pdb=" O CYS E 150 " (cutoff:3.500A) removed outlier: 3.994A pdb=" N ARG E 207 " --> pdb=" O ARG E 196 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N SER E 211 " --> pdb=" O ARG E 192 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N ARG E 213 " --> pdb=" O GLU E 190 " (cutoff:3.500A) removed outlier: 5.189A pdb=" N GLU E 190 " --> pdb=" O ARG E 213 " (cutoff:3.500A) removed outlier: 6.573A pdb=" N LYS E 215 " --> pdb=" O ILE E 188 " (cutoff:3.500A) removed outlier: 5.640A pdb=" N ILE E 188 " --> pdb=" O LYS E 215 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'C' and resid 82 through 83 removed outlier: 4.367A pdb=" N ILE C 116 " --> pdb=" O LEU C 83 " (cutoff:3.500A) removed outlier: 6.804A pdb=" N ASP C 56 " --> pdb=" O VAL C 50 " (cutoff:3.500A) removed outlier: 4.754A pdb=" N VAL C 50 " --> pdb=" O ASP C 56 " (cutoff:3.500A) removed outlier: 6.682A pdb=" N THR C 58 " --> pdb=" O ASP C 48 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N SER C 46 " --> pdb=" O THR C 60 " (cutoff:3.500A) removed outlier: 6.288A pdb=" N TYR C 62 " --> pdb=" O ILE C 44 " (cutoff:3.500A) removed outlier: 5.387A pdb=" N ILE C 44 " --> pdb=" O TYR C 62 " (cutoff:3.500A) removed outlier: 7.251A pdb=" N GLN C 64 " --> pdb=" O ILE C 42 " (cutoff:3.500A) removed outlier: 5.484A pdb=" N ILE C 42 " --> pdb=" O GLN C 64 " (cutoff:3.500A) removed outlier: 6.421A pdb=" N TYR C 66 " --> pdb=" O MET C 40 " (cutoff:3.500A) removed outlier: 5.803A pdb=" N MET C 40 " --> pdb=" O TYR C 66 " (cutoff:3.500A) removed outlier: 8.860A pdb=" N ARG C 68 " --> pdb=" O VAL C 38 " (cutoff:3.500A) removed outlier: 8.440A pdb=" N VAL C 38 " --> pdb=" O ARG C 68 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'C' and resid 101 through 106 removed outlier: 7.097A pdb=" N THR C 133 " --> pdb=" O LYS C 102 " (cutoff:3.500A) removed outlier: 4.727A pdb=" N SER C 104 " --> pdb=" O THR C 131 " (cutoff:3.500A) removed outlier: 7.212A pdb=" N THR C 131 " --> pdb=" O SER C 104 " (cutoff:3.500A) removed outlier: 5.097A pdb=" N VAL C 106 " --> pdb=" O ARG C 129 " (cutoff:3.500A) removed outlier: 7.853A pdb=" N ARG C 129 " --> pdb=" O VAL C 106 " (cutoff:3.500A) removed outlier: 6.804A pdb=" N ASP C 56 " --> pdb=" O VAL C 50 " (cutoff:3.500A) removed outlier: 4.754A pdb=" N VAL C 50 " --> pdb=" O ASP C 56 " (cutoff:3.500A) removed outlier: 6.682A pdb=" N THR C 58 " --> pdb=" O ASP C 48 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N SER C 46 " --> pdb=" O THR C 60 " (cutoff:3.500A) removed outlier: 6.288A pdb=" N TYR C 62 " --> pdb=" O ILE C 44 " (cutoff:3.500A) removed outlier: 5.387A pdb=" N ILE C 44 " --> pdb=" O TYR C 62 " (cutoff:3.500A) removed outlier: 7.251A pdb=" N GLN C 64 " --> pdb=" O ILE C 42 " (cutoff:3.500A) removed outlier: 5.484A pdb=" N ILE C 42 " --> pdb=" O GLN C 64 " (cutoff:3.500A) removed outlier: 6.421A pdb=" N TYR C 66 " --> pdb=" O MET C 40 " (cutoff:3.500A) removed outlier: 5.803A pdb=" N MET C 40 " --> pdb=" O TYR C 66 " (cutoff:3.500A) removed outlier: 8.860A pdb=" N ARG C 68 " --> pdb=" O VAL C 38 " (cutoff:3.500A) removed outlier: 8.440A pdb=" N VAL C 38 " --> pdb=" O ARG C 68 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'C' and resid 97 through 98 removed outlier: 3.650A pdb=" N CYS C 150 " --> pdb=" O PHE C 212 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N PHE C 212 " --> pdb=" O CYS C 150 " (cutoff:3.500A) removed outlier: 3.994A pdb=" N ARG C 207 " --> pdb=" O ARG C 196 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N SER C 211 " --> pdb=" O ARG C 192 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N ARG C 213 " --> pdb=" O GLU C 190 " (cutoff:3.500A) removed outlier: 5.190A pdb=" N GLU C 190 " --> pdb=" O ARG C 213 " (cutoff:3.500A) removed outlier: 6.573A pdb=" N LYS C 215 " --> pdb=" O ILE C 188 " (cutoff:3.500A) removed outlier: 5.639A pdb=" N ILE C 188 " --> pdb=" O LYS C 215 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'D' and resid 82 through 83 removed outlier: 4.365A pdb=" N ILE D 116 " --> pdb=" O LEU D 83 " (cutoff:3.500A) removed outlier: 6.805A pdb=" N ASP D 56 " --> pdb=" O VAL D 50 " (cutoff:3.500A) removed outlier: 4.754A pdb=" N VAL D 50 " --> pdb=" O ASP D 56 " (cutoff:3.500A) removed outlier: 6.682A pdb=" N THR D 58 " --> pdb=" O ASP D 48 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N SER D 46 " --> pdb=" O THR D 60 " (cutoff:3.500A) removed outlier: 6.286A pdb=" N TYR D 62 " --> pdb=" O ILE D 44 " (cutoff:3.500A) removed outlier: 5.387A pdb=" N ILE D 44 " --> pdb=" O TYR D 62 " (cutoff:3.500A) removed outlier: 7.251A pdb=" N GLN D 64 " --> pdb=" O ILE D 42 " (cutoff:3.500A) removed outlier: 5.485A pdb=" N ILE D 42 " --> pdb=" O GLN D 64 " (cutoff:3.500A) removed outlier: 6.421A pdb=" N TYR D 66 " --> pdb=" O MET D 40 " (cutoff:3.500A) removed outlier: 5.803A pdb=" N MET D 40 " --> pdb=" O TYR D 66 " (cutoff:3.500A) removed outlier: 8.859A pdb=" N ARG D 68 " --> pdb=" O VAL D 38 " (cutoff:3.500A) removed outlier: 8.440A pdb=" N VAL D 38 " --> pdb=" O ARG D 68 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'D' and resid 101 through 106 removed outlier: 7.098A pdb=" N THR D 133 " --> pdb=" O LYS D 102 " (cutoff:3.500A) removed outlier: 4.726A pdb=" N SER D 104 " --> pdb=" O THR D 131 " (cutoff:3.500A) removed outlier: 7.212A pdb=" N THR D 131 " --> pdb=" O SER D 104 " (cutoff:3.500A) removed outlier: 5.097A pdb=" N VAL D 106 " --> pdb=" O ARG D 129 " (cutoff:3.500A) removed outlier: 7.853A pdb=" N ARG D 129 " --> pdb=" O VAL D 106 " (cutoff:3.500A) removed outlier: 6.805A pdb=" N ASP D 56 " --> pdb=" O VAL D 50 " (cutoff:3.500A) removed outlier: 4.754A pdb=" N VAL D 50 " --> pdb=" O ASP D 56 " (cutoff:3.500A) removed outlier: 6.682A pdb=" N THR D 58 " --> pdb=" O ASP D 48 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N SER D 46 " --> pdb=" O THR D 60 " (cutoff:3.500A) removed outlier: 6.286A pdb=" N TYR D 62 " --> pdb=" O ILE D 44 " (cutoff:3.500A) removed outlier: 5.387A pdb=" N ILE D 44 " --> pdb=" O TYR D 62 " (cutoff:3.500A) removed outlier: 7.251A pdb=" N GLN D 64 " --> pdb=" O ILE D 42 " (cutoff:3.500A) removed outlier: 5.485A pdb=" N ILE D 42 " --> pdb=" O GLN D 64 " (cutoff:3.500A) removed outlier: 6.421A pdb=" N TYR D 66 " --> pdb=" O MET D 40 " (cutoff:3.500A) removed outlier: 5.803A pdb=" N MET D 40 " --> pdb=" O TYR D 66 " (cutoff:3.500A) removed outlier: 8.859A pdb=" N ARG D 68 " --> pdb=" O VAL D 38 " (cutoff:3.500A) removed outlier: 8.440A pdb=" N VAL D 38 " --> pdb=" O ARG D 68 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'D' and resid 97 through 98 removed outlier: 3.651A pdb=" N CYS D 150 " --> pdb=" O PHE D 212 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N PHE D 212 " --> pdb=" O CYS D 150 " (cutoff:3.500A) removed outlier: 3.994A pdb=" N ARG D 207 " --> pdb=" O ARG D 196 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N SER D 211 " --> pdb=" O ARG D 192 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N ARG D 213 " --> pdb=" O GLU D 190 " (cutoff:3.500A) removed outlier: 5.190A pdb=" N GLU D 190 " --> pdb=" O ARG D 213 " (cutoff:3.500A) removed outlier: 6.573A pdb=" N LYS D 215 " --> pdb=" O ILE D 188 " (cutoff:3.500A) removed outlier: 5.640A pdb=" N ILE D 188 " --> pdb=" O LYS D 215 " (cutoff:3.500A) 631 hydrogen bonds defined for protein. 1749 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 3.08 Time building geometry restraints manager: 2.44 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 5173 1.34 - 1.46: 4848 1.46 - 1.59: 7306 1.59 - 1.71: 0 1.71 - 1.84: 158 Bond restraints: 17485 Sorted by residual: bond pdb=" C1 NAG I 2 " pdb=" O5 NAG I 2 " ideal model delta sigma weight residual 1.406 1.479 -0.073 2.00e-02 2.50e+03 1.35e+01 bond pdb=" C1 MAN H 4 " pdb=" C2 MAN H 4 " ideal model delta sigma weight residual 1.526 1.587 -0.061 2.00e-02 2.50e+03 9.31e+00 bond pdb=" C5 MAN N 5 " pdb=" O5 MAN N 5 " ideal model delta sigma weight residual 1.418 1.474 -0.056 2.00e-02 2.50e+03 7.74e+00 bond pdb=" C3 BMA N 3 " pdb=" O3 BMA N 3 " ideal model delta sigma weight residual 1.406 1.462 -0.056 2.00e-02 2.50e+03 7.71e+00 bond pdb=" C5 MAN J 5 " pdb=" O5 MAN J 5 " ideal model delta sigma weight residual 1.418 1.474 -0.056 2.00e-02 2.50e+03 7.70e+00 ... (remaining 17480 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.08: 22596 2.08 - 4.17: 959 4.17 - 6.25: 163 6.25 - 8.33: 43 8.33 - 10.41: 16 Bond angle restraints: 23777 Sorted by residual: angle pdb=" C LYS K 65 " pdb=" N ASP K 66 " pdb=" CA ASP K 66 " ideal model delta sigma weight residual 121.54 131.31 -9.77 1.91e+00 2.74e-01 2.62e+01 angle pdb=" C MET A 84 " pdb=" N GLN A 85 " pdb=" CA GLN A 85 " ideal model delta sigma weight residual 121.54 129.36 -7.82 1.91e+00 2.74e-01 1.68e+01 angle pdb=" CB MET A 115 " pdb=" CG MET A 115 " pdb=" SD MET A 115 " ideal model delta sigma weight residual 112.70 102.29 10.41 3.00e+00 1.11e-01 1.21e+01 angle pdb=" C2 NAG I 1 " pdb=" N2 NAG I 1 " pdb=" C7 NAG I 1 " ideal model delta sigma weight residual 124.56 134.18 -9.62 3.00e+00 1.11e-01 1.03e+01 angle pdb=" C2 NAG Q 2 " pdb=" N2 NAG Q 2 " pdb=" C7 NAG Q 2 " ideal model delta sigma weight residual 124.56 134.05 -9.49 3.00e+00 1.11e-01 1.00e+01 ... (remaining 23772 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 23.87: 10326 23.87 - 47.74: 276 47.74 - 71.61: 75 71.61 - 95.48: 66 95.48 - 119.34: 41 Dihedral angle restraints: 10784 sinusoidal: 4787 harmonic: 5997 Sorted by residual: dihedral pdb=" CB CYS A 237 " pdb=" SG CYS A 237 " pdb=" SG CYS A 296 " pdb=" CB CYS A 296 " ideal model delta sinusoidal sigma weight residual 93.00 141.02 -48.02 1 1.00e+01 1.00e-02 3.18e+01 dihedral pdb=" CA PHE O 37 " pdb=" C PHE O 37 " pdb=" N ARG O 38 " pdb=" CA ARG O 38 " ideal model delta harmonic sigma weight residual 180.00 152.72 27.28 0 5.00e+00 4.00e-02 2.98e+01 dihedral pdb=" CA TYR D 66 " pdb=" C TYR D 66 " pdb=" N TRP D 67 " pdb=" CA TRP D 67 " ideal model delta harmonic sigma weight residual 180.00 154.12 25.88 0 5.00e+00 4.00e-02 2.68e+01 ... (remaining 10781 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.140: 2703 0.140 - 0.281: 48 0.281 - 0.421: 13 0.421 - 0.561: 1 0.561 - 0.701: 1 Chirality restraints: 2766 Sorted by residual: chirality pdb=" C1 NAG I 1 " pdb=" ND2 ASN A 205 " pdb=" C2 NAG I 1 " pdb=" O5 NAG I 1 " both_signs ideal model delta sigma weight residual False -2.40 -1.70 -0.70 2.00e-01 2.50e+01 1.23e+01 chirality pdb=" CB VAL K 64 " pdb=" CA VAL K 64 " pdb=" CG1 VAL K 64 " pdb=" CG2 VAL K 64 " both_signs ideal model delta sigma weight residual False -2.63 -2.17 -0.46 2.00e-01 2.50e+01 5.22e+00 chirality pdb=" C2 NAG J 2 " pdb=" C1 NAG J 2 " pdb=" C3 NAG J 2 " pdb=" N2 NAG J 2 " both_signs ideal model delta sigma weight residual False -2.49 -2.09 -0.41 2.00e-01 2.50e+01 4.10e+00 ... (remaining 2763 not shown) Planarity restraints: 2923 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C PHE B 431 " 0.046 5.00e-02 4.00e+02 6.85e-02 7.50e+00 pdb=" N PRO B 432 " -0.118 5.00e-02 4.00e+02 pdb=" CA PRO B 432 " 0.034 5.00e-02 4.00e+02 pdb=" CD PRO B 432 " 0.039 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PHE D 431 " -0.046 5.00e-02 4.00e+02 6.84e-02 7.49e+00 pdb=" N PRO D 432 " 0.118 5.00e-02 4.00e+02 pdb=" CA PRO D 432 " -0.034 5.00e-02 4.00e+02 pdb=" CD PRO D 432 " -0.039 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PHE E 431 " -0.045 5.00e-02 4.00e+02 6.84e-02 7.48e+00 pdb=" N PRO E 432 " 0.118 5.00e-02 4.00e+02 pdb=" CA PRO E 432 " -0.034 5.00e-02 4.00e+02 pdb=" CD PRO E 432 " -0.039 5.00e-02 4.00e+02 ... (remaining 2920 not shown) Histogram of nonbonded interaction distances: 2.16 - 2.71: 728 2.71 - 3.25: 16064 3.25 - 3.80: 26882 3.80 - 4.35: 32068 4.35 - 4.90: 53214 Nonbonded interactions: 128956 Sorted by model distance: nonbonded pdb=" OG1 THR C 110 " pdb=" O THR D 96 " model vdw 2.158 3.040 nonbonded pdb=" OG1 THR B 110 " pdb=" O THR C 96 " model vdw 2.193 3.040 nonbonded pdb=" O2 BMA H 3 " pdb=" O6 MAN H 5 " model vdw 2.247 3.040 nonbonded pdb=" OG SER L 7 " pdb=" OG SER L 21 " model vdw 2.266 3.040 nonbonded pdb=" O PRO A 256 " pdb=" OG1 THR A 259 " model vdw 2.270 3.040 ... (remaining 128951 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 'B' and resid 8 through 447) selection = chain 'C' selection = chain 'D' selection = chain 'E' } ncs_group { reference = chain 'F' selection = chain 'J' selection = chain 'N' selection = chain 'Q' } ncs_group { reference = chain 'G' selection = chain 'M' selection = chain 'P' selection = chain 'R' } ncs_group { reference = (chain 'K' and resid 1 through 124) selection = chain 'L' selection = (chain 'O' and resid 1 through 124) } 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 group one per residue 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: 1.090 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.030 Construct map_model_manager: 0.010 Extract box with map and model: 0.300 Check model and map are aligned: 0.050 Set scattering table: 0.050 Process input model: 17.520 Find NCS groups from input model: 0.310 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.320 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 20.740 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7753 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 : 0.012 0.883 17543 Z= 0.924 Angle : 1.123 24.273 23924 Z= 0.528 Chirality : 0.063 0.701 2766 Planarity : 0.007 0.068 2913 Dihedral : 16.063 119.344 6929 Min Nonbonded Distance : 2.158 Molprobity Statistics. All-atom Clashscore : 6.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.30 % Favored : 92.70 % Rotamer: Outliers : 0.22 % Allowed : 1.57 % Favored : 98.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.02 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.71 (0.16), residues: 2027 helix: -3.69 (0.13), residues: 395 sheet: -2.02 (0.21), residues: 551 loop : -2.17 (0.18), residues: 1081 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.001 ARG B 169 TYR 0.024 0.003 TYR K 108 PHE 0.023 0.003 PHE O 37 TRP 0.025 0.003 TRP B 92 HIS 0.011 0.002 HIS A 113 Details of bonding type rmsd covalent geometry : bond 0.00790 (17485) covalent geometry : angle 1.01743 (23777) SS BOND : bond 0.00501 ( 9) SS BOND : angle 1.48816 ( 18) hydrogen bonds : bond 0.31622 ( 569) hydrogen bonds : angle 10.08708 ( 1749) Misc. bond : bond 0.45774 ( 6) link_ALPHA1-3 : bond 0.00663 ( 9) link_ALPHA1-3 : angle 4.76735 ( 27) link_ALPHA1-6 : bond 0.00175 ( 5) link_ALPHA1-6 : angle 1.86249 ( 15) link_BETA1-4 : bond 0.01651 ( 19) link_BETA1-4 : angle 6.40736 ( 57) link_NAG-ASN : bond 0.01675 ( 10) link_NAG-ASN : angle 9.14140 ( 30) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4054 Ramachandran restraints generated. 2027 Oldfield, 0 Emsley, 2027 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4054 Ramachandran restraints generated. 2027 Oldfield, 0 Emsley, 2027 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 870 residues out of total 1787 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 866 time to evaluate : 0.659 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: K 11 LEU cc_start: 0.9576 (pp) cc_final: 0.9064 (tp) REVERT: K 18 LEU cc_start: 0.8930 (tm) cc_final: 0.8553 (tm) REVERT: K 39 GLN cc_start: 0.8278 (mm110) cc_final: 0.8003 (mm110) REVERT: K 73 ASP cc_start: 0.7495 (t0) cc_final: 0.6052 (t0) REVERT: K 74 ASN cc_start: 0.9253 (t0) cc_final: 0.9010 (t0) REVERT: K 76 LYS cc_start: 0.9402 (mttt) cc_final: 0.9168 (mtmm) REVERT: K 81 LEU cc_start: 0.7669 (mp) cc_final: 0.6851 (mp) REVERT: K 82 GLU cc_start: 0.9020 (tt0) cc_final: 0.8778 (tt0) REVERT: K 83 MET cc_start: 0.8436 (mpm) cc_final: 0.8150 (mpp) REVERT: K 90 ASP cc_start: 0.9125 (m-30) cc_final: 0.8905 (m-30) REVERT: K 95 TYR cc_start: 0.8571 (m-80) cc_final: 0.8345 (m-80) REVERT: L 43 LYS cc_start: 0.8977 (tttt) cc_final: 0.8619 (tttm) REVERT: L 48 VAL cc_start: 0.9184 (m) cc_final: 0.8930 (m) REVERT: O 22 CYS cc_start: 0.3909 (t) cc_final: 0.3575 (t) REVERT: O 30 ASN cc_start: 0.9054 (p0) cc_final: 0.8396 (p0) REVERT: O 36 TRP cc_start: 0.8709 (m100) cc_final: 0.8399 (m100) REVERT: O 58 THR cc_start: 0.9113 (p) cc_final: 0.8890 (t) REVERT: O 85 ASN cc_start: 0.8720 (m110) cc_final: 0.8174 (m-40) REVERT: O 87 LYS cc_start: 0.9197 (mtpp) cc_final: 0.8962 (mtpp) REVERT: O 89 GLU cc_start: 0.8931 (pt0) cc_final: 0.8620 (pm20) REVERT: O 99 LYS cc_start: 0.8225 (ttpm) cc_final: 0.7878 (tttp) REVERT: O 101 ARG cc_start: 0.8997 (ttm110) cc_final: 0.8780 (ttm110) REVERT: O 103 SER cc_start: 0.7950 (t) cc_final: 0.7213 (m) REVERT: O 115 TRP cc_start: 0.7017 (m-10) cc_final: 0.6771 (m-10) REVERT: B 21 LYS cc_start: 0.9540 (tttt) cc_final: 0.9296 (ptmt) REVERT: B 30 ASP cc_start: 0.9082 (m-30) cc_final: 0.8135 (t0) REVERT: B 37 CYS cc_start: 0.8206 (t) cc_final: 0.6905 (t) REVERT: B 40 MET cc_start: 0.7937 (mtm) cc_final: 0.7525 (mtt) REVERT: B 46 SER cc_start: 0.9294 (p) cc_final: 0.9010 (p) REVERT: B 49 MET cc_start: 0.9181 (ptm) cc_final: 0.8511 (ppp) REVERT: B 55 MET cc_start: 0.9359 (mtt) cc_final: 0.8591 (mmm) REVERT: B 89 ASP cc_start: 0.9007 (m-30) cc_final: 0.8759 (m-30) REVERT: B 90 GLN cc_start: 0.9150 (mt0) cc_final: 0.8596 (mp10) REVERT: B 95 ASP cc_start: 0.8433 (p0) cc_final: 0.8117 (p0) REVERT: B 115 MET cc_start: 0.8357 (ttp) cc_final: 0.8143 (ttp) REVERT: B 165 GLU cc_start: 0.8579 (mm-30) cc_final: 0.8361 (tm-30) REVERT: B 168 TRP cc_start: 0.9387 (m100) cc_final: 0.8963 (m100) REVERT: B 208 LEU cc_start: 0.8770 (mt) cc_final: 0.8550 (mp) REVERT: B 215 LYS cc_start: 0.8807 (tttt) cc_final: 0.8601 (ttpt) REVERT: B 229 SER cc_start: 0.9349 (m) cc_final: 0.8948 (t) REVERT: B 230 ILE cc_start: 0.9376 (mt) cc_final: 0.9176 (mt) REVERT: B 261 MET cc_start: 0.9562 (mmm) cc_final: 0.9180 (mmp) REVERT: A 20 ARG cc_start: 0.9293 (mtt180) cc_final: 0.8956 (mtp-110) REVERT: A 75 ASP cc_start: 0.8484 (t0) cc_final: 0.8157 (t70) REVERT: A 90 ASN cc_start: 0.8605 (t0) cc_final: 0.8105 (t0) REVERT: A 98 TRP cc_start: 0.8941 (t60) cc_final: 0.8683 (t60) REVERT: A 125 GLU cc_start: 0.8575 (mt-10) cc_final: 0.8274 (mm-30) REVERT: A 193 GLN cc_start: 0.8145 (tt0) cc_final: 0.7648 (tp-100) REVERT: A 225 LYS cc_start: 0.8695 (mmtt) cc_final: 0.8481 (mmmt) REVERT: E 14 GLU cc_start: 0.9029 (pt0) cc_final: 0.8788 (pp20) REVERT: E 24 ASP cc_start: 0.8956 (t0) cc_final: 0.8542 (t70) REVERT: E 49 MET cc_start: 0.9131 (ptm) cc_final: 0.8326 (ppp) REVERT: E 97 TYR cc_start: 0.8706 (p90) cc_final: 0.8227 (p90) REVERT: E 208 LEU cc_start: 0.9145 (mt) cc_final: 0.8502 (mt) REVERT: E 312 ARG cc_start: 0.7961 (tpp-160) cc_final: 0.7620 (ttt180) REVERT: C 44 ILE cc_start: 0.9139 (mt) cc_final: 0.8932 (mp) REVERT: C 119 HIS cc_start: 0.8829 (m90) cc_final: 0.8474 (m90) REVERT: C 148 GLN cc_start: 0.7883 (mm-40) cc_final: 0.7558 (mm110) REVERT: C 151 THR cc_start: 0.9679 (p) cc_final: 0.9453 (t) REVERT: C 163 ASP cc_start: 0.8976 (m-30) cc_final: 0.8352 (p0) REVERT: C 191 HIS cc_start: 0.7909 (m-70) cc_final: 0.7552 (m-70) REVERT: C 217 ASN cc_start: 0.8734 (m-40) cc_final: 0.8461 (m110) REVERT: C 224 GLN cc_start: 0.8920 (mm110) cc_final: 0.8579 (mp10) REVERT: C 226 TYR cc_start: 0.9378 (m-10) cc_final: 0.8967 (m-10) REVERT: C 227 MET cc_start: 0.8687 (mtt) cc_final: 0.8374 (mmt) REVERT: C 229 SER cc_start: 0.9596 (m) cc_final: 0.9389 (p) REVERT: C 261 MET cc_start: 0.9157 (mmm) cc_final: 0.8391 (mmm) REVERT: C 282 ASP cc_start: 0.8991 (m-30) cc_final: 0.8315 (m-30) REVERT: C 288 CYS cc_start: 0.9500 (m) cc_final: 0.8068 (t) REVERT: C 289 PHE cc_start: 0.8846 (t80) cc_final: 0.8549 (t80) REVERT: C 303 ASN cc_start: 0.8875 (t160) cc_final: 0.8552 (m-40) REVERT: C 444 LEU cc_start: 0.9392 (mt) cc_final: 0.9128 (mt) REVERT: D 13 LYS cc_start: 0.9402 (tttm) cc_final: 0.9077 (tttp) REVERT: D 17 ASP cc_start: 0.9343 (m-30) cc_final: 0.9125 (m-30) REVERT: D 55 MET cc_start: 0.9364 (mtt) cc_final: 0.8922 (mtp) REVERT: D 85 ASN cc_start: 0.8884 (p0) cc_final: 0.8466 (p0) REVERT: D 100 ASN cc_start: 0.8394 (p0) cc_final: 0.8131 (p0) REVERT: D 137 MET cc_start: 0.9127 (mmm) cc_final: 0.8811 (mmm) REVERT: D 190 GLU cc_start: 0.8328 (tt0) cc_final: 0.7888 (tm-30) REVERT: D 191 HIS cc_start: 0.7815 (m-70) cc_final: 0.7152 (m-70) REVERT: D 208 LEU cc_start: 0.8585 (mt) cc_final: 0.8352 (mp) REVERT: D 235 LEU cc_start: 0.8580 (mp) cc_final: 0.8345 (tt) REVERT: D 261 MET cc_start: 0.8832 (mmm) cc_final: 0.8581 (tpp) REVERT: D 282 ASP cc_start: 0.9107 (m-30) cc_final: 0.8740 (m-30) REVERT: D 299 TYR cc_start: 0.6468 (t80) cc_final: 0.6204 (t80) outliers start: 4 outliers final: 1 residues processed: 870 average time/residue: 0.1513 time to fit residues: 191.2089 Evaluate side-chains 513 residues out of total 1787 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 512 time to evaluate : 0.655 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 38 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 201 random chunks: chunk 98 optimal weight: 2.9990 chunk 194 optimal weight: 0.9990 chunk 107 optimal weight: 4.9990 chunk 10 optimal weight: 0.9980 chunk 66 optimal weight: 9.9990 chunk 130 optimal weight: 0.9980 chunk 124 optimal weight: 10.0000 chunk 103 optimal weight: 0.6980 chunk 200 optimal weight: 3.9990 chunk 77 optimal weight: 0.6980 chunk 122 optimal weight: 1.9990 overall best weight: 0.8782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** K 1 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 120 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 27 HIS O 77 ASN ** B 185 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 193 GLN A 232 GLN E 113 ASN ** E 191 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 265 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 303 ASN C 64 GLN C 113 ASN C 303 ASN D 197 ASN D 224 GLN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3633 r_free = 0.3633 target = 0.095195 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3404 r_free = 0.3404 target = 0.080782 restraints weight = 49815.164| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3449 r_free = 0.3449 target = 0.083702 restraints weight = 24114.976| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3480 r_free = 0.3480 target = 0.085657 restraints weight = 14231.994| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.3501 r_free = 0.3501 target = 0.086982 restraints weight = 9446.930| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 37)----------------| | r_work = 0.3515 r_free = 0.3515 target = 0.087897 restraints weight = 6851.475| |-----------------------------------------------------------------------------| r_work (final): 0.3488 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7814 moved from start: 0.3641 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 17543 Z= 0.176 Angle : 0.985 18.169 23924 Z= 0.451 Chirality : 0.052 0.399 2766 Planarity : 0.007 0.149 2913 Dihedral : 17.456 107.260 3155 Min Nonbonded Distance : 2.170 Molprobity Statistics. All-atom Clashscore : 12.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.09 % Favored : 95.91 % Rotamer: Outliers : 3.86 % Allowed : 16.45 % Favored : 79.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.02 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.47 (0.18), residues: 2027 helix: -1.63 (0.21), residues: 431 sheet: -1.40 (0.22), residues: 528 loop : -1.71 (0.19), residues: 1068 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG E 196 TYR 0.022 0.002 TYR E 442 PHE 0.029 0.002 PHE L 68 TRP 0.014 0.001 TRP E 67 HIS 0.004 0.001 HIS E 107 Details of bonding type rmsd covalent geometry : bond 0.00367 (17485) covalent geometry : angle 0.90814 (23777) SS BOND : bond 0.00921 ( 9) SS BOND : angle 4.03208 ( 18) hydrogen bonds : bond 0.06171 ( 569) hydrogen bonds : angle 6.13556 ( 1749) Misc. bond : bond 0.00208 ( 6) link_ALPHA1-3 : bond 0.01102 ( 9) link_ALPHA1-3 : angle 4.06945 ( 27) link_ALPHA1-6 : bond 0.01413 ( 5) link_ALPHA1-6 : angle 2.29910 ( 15) link_BETA1-4 : bond 0.00847 ( 19) link_BETA1-4 : angle 4.99683 ( 57) link_NAG-ASN : bond 0.00647 ( 10) link_NAG-ASN : angle 6.74440 ( 30) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4054 Ramachandran restraints generated. 2027 Oldfield, 0 Emsley, 2027 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4054 Ramachandran restraints generated. 2027 Oldfield, 0 Emsley, 2027 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 665 residues out of total 1787 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 596 time to evaluate : 0.689 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: K 4 LEU cc_start: 0.9337 (mm) cc_final: 0.9106 (mm) REVERT: K 18 LEU cc_start: 0.8964 (OUTLIER) cc_final: 0.8601 (tm) REVERT: K 34 MET cc_start: 0.8220 (mtt) cc_final: 0.7868 (mtm) REVERT: K 46 GLU cc_start: 0.9372 (OUTLIER) cc_final: 0.9007 (mp0) REVERT: K 73 ASP cc_start: 0.6877 (t0) cc_final: 0.6377 (t0) REVERT: K 83 MET cc_start: 0.8807 (mpm) cc_final: 0.8253 (mpp) REVERT: K 89 GLU cc_start: 0.9213 (mp0) cc_final: 0.8903 (pm20) REVERT: K 90 ASP cc_start: 0.9099 (m-30) cc_final: 0.8816 (m-30) REVERT: L 1 GLN cc_start: 0.9125 (mm-40) cc_final: 0.8070 (mp10) REVERT: L 34 MET cc_start: 0.8570 (mtm) cc_final: 0.8244 (mtp) REVERT: L 65 LYS cc_start: 0.9646 (tppt) cc_final: 0.9335 (tppt) REVERT: O 4 LEU cc_start: 0.7680 (mt) cc_final: 0.7471 (mt) REVERT: O 18 LEU cc_start: 0.9298 (tt) cc_final: 0.9058 (tt) REVERT: O 30 ASN cc_start: 0.8952 (p0) cc_final: 0.8638 (p0) REVERT: O 36 TRP cc_start: 0.8689 (m100) cc_final: 0.8178 (m100) REVERT: O 52 SER cc_start: 0.8874 (t) cc_final: 0.8657 (p) REVERT: O 85 ASN cc_start: 0.8705 (m110) cc_final: 0.8170 (m-40) REVERT: O 89 GLU cc_start: 0.8938 (pt0) cc_final: 0.8663 (pm20) REVERT: O 99 LYS cc_start: 0.8352 (ttpm) cc_final: 0.7720 (tttm) REVERT: O 101 ARG cc_start: 0.8975 (ttm110) cc_final: 0.8746 (ttm110) REVERT: O 103 SER cc_start: 0.7666 (t) cc_final: 0.7192 (m) REVERT: O 111 ASN cc_start: 0.9107 (m-40) cc_final: 0.8571 (t0) REVERT: B 21 LYS cc_start: 0.9487 (tttt) cc_final: 0.9217 (ptmt) REVERT: B 30 ASP cc_start: 0.9119 (m-30) cc_final: 0.8241 (t0) REVERT: B 37 CYS cc_start: 0.8326 (t) cc_final: 0.7006 (t) REVERT: B 49 MET cc_start: 0.9109 (ptm) cc_final: 0.8534 (ppp) REVERT: B 69 ASP cc_start: 0.9286 (t0) cc_final: 0.8890 (t70) REVERT: B 89 ASP cc_start: 0.8939 (m-30) cc_final: 0.8717 (m-30) REVERT: B 90 GLN cc_start: 0.9063 (mt0) cc_final: 0.8558 (mp10) REVERT: B 95 ASP cc_start: 0.8541 (p0) cc_final: 0.8194 (p0) REVERT: B 101 ASP cc_start: 0.8825 (p0) cc_final: 0.8379 (t70) REVERT: B 208 LEU cc_start: 0.8837 (mt) cc_final: 0.8506 (mt) REVERT: B 229 SER cc_start: 0.9198 (m) cc_final: 0.8740 (t) REVERT: A 90 ASN cc_start: 0.8696 (t0) cc_final: 0.8074 (t0) REVERT: A 98 TRP cc_start: 0.9033 (t60) cc_final: 0.8673 (t60) REVERT: A 115 MET cc_start: 0.6440 (tmm) cc_final: 0.6235 (tmm) REVERT: A 282 LYS cc_start: 0.8585 (tptt) cc_final: 0.8298 (tptt) REVERT: A 306 GLU cc_start: 0.8221 (tm-30) cc_final: 0.7985 (tm-30) REVERT: E 9 MET cc_start: 0.9031 (tpp) cc_final: 0.8830 (tpp) REVERT: E 13 LYS cc_start: 0.8849 (pttt) cc_final: 0.8477 (ttmt) REVERT: E 14 GLU cc_start: 0.9052 (pt0) cc_final: 0.8623 (pp20) REVERT: E 24 ASP cc_start: 0.8856 (t0) cc_final: 0.8508 (t70) REVERT: E 49 MET cc_start: 0.9109 (ptm) cc_final: 0.8453 (ppp) REVERT: E 61 MET cc_start: 0.9271 (ptp) cc_final: 0.8191 (pmm) REVERT: E 97 TYR cc_start: 0.8818 (p90) cc_final: 0.8484 (p90) REVERT: E 153 GLU cc_start: 0.8351 (mt-10) cc_final: 0.7822 (mt-10) REVERT: E 208 LEU cc_start: 0.9329 (mt) cc_final: 0.8797 (mt) REVERT: E 282 ASP cc_start: 0.8700 (m-30) cc_final: 0.8418 (m-30) REVERT: E 312 ARG cc_start: 0.7764 (tpp-160) cc_final: 0.7542 (ttt180) REVERT: E 428 ARG cc_start: 0.7229 (ptp90) cc_final: 0.6553 (ptm160) REVERT: E 435 PHE cc_start: 0.8691 (t80) cc_final: 0.8482 (t80) REVERT: E 439 ASN cc_start: 0.8704 (m-40) cc_final: 0.8401 (m110) REVERT: C 49 MET cc_start: 0.8539 (OUTLIER) cc_final: 0.8056 (ptm) REVERT: C 55 MET cc_start: 0.9091 (mmm) cc_final: 0.8638 (ttm) REVERT: C 208 LEU cc_start: 0.9468 (mt) cc_final: 0.9253 (mt) REVERT: C 224 GLN cc_start: 0.8698 (mm110) cc_final: 0.8427 (mm110) REVERT: C 226 TYR cc_start: 0.9167 (m-10) cc_final: 0.8759 (m-10) REVERT: C 229 SER cc_start: 0.9528 (m) cc_final: 0.9239 (p) REVERT: C 261 MET cc_start: 0.9202 (mmm) cc_final: 0.8874 (mmt) REVERT: C 282 ASP cc_start: 0.8871 (m-30) cc_final: 0.8669 (m-30) REVERT: C 289 PHE cc_start: 0.8918 (t80) cc_final: 0.8608 (t80) REVERT: C 303 ASN cc_start: 0.8747 (t0) cc_final: 0.8378 (m110) REVERT: C 433 PHE cc_start: 0.8469 (m-80) cc_final: 0.8250 (m-10) REVERT: D 17 ASP cc_start: 0.9288 (m-30) cc_final: 0.9055 (m-30) REVERT: D 55 MET cc_start: 0.9413 (mtt) cc_final: 0.8975 (mmm) REVERT: D 103 LYS cc_start: 0.8311 (OUTLIER) cc_final: 0.8107 (mmtt) REVERT: D 137 MET cc_start: 0.9108 (mmm) cc_final: 0.8713 (mmm) REVERT: D 190 GLU cc_start: 0.8164 (tt0) cc_final: 0.7493 (tm-30) REVERT: D 191 HIS cc_start: 0.7509 (m-70) cc_final: 0.7031 (m-70) REVERT: D 235 LEU cc_start: 0.8691 (mp) cc_final: 0.8323 (tt) REVERT: D 250 ARG cc_start: 0.7641 (ttm170) cc_final: 0.7189 (mtm180) REVERT: D 282 ASP cc_start: 0.9373 (m-30) cc_final: 0.9128 (m-30) REVERT: D 298 GLU cc_start: 0.8349 (tm-30) cc_final: 0.8078 (tm-30) outliers start: 69 outliers final: 38 residues processed: 629 average time/residue: 0.1406 time to fit residues: 132.5106 Evaluate side-chains 544 residues out of total 1787 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 502 time to evaluate : 0.668 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain K residue 7 SER Chi-restraints excluded: chain K residue 18 LEU Chi-restraints excluded: chain K residue 46 GLU Chi-restraints excluded: chain L residue 20 LEU Chi-restraints excluded: chain L residue 57 SER Chi-restraints excluded: chain L residue 91 THR Chi-restraints excluded: chain L residue 106 LEU Chi-restraints excluded: chain O residue 120 GLN Chi-restraints excluded: chain B residue 93 VAL Chi-restraints excluded: chain B residue 99 LEU Chi-restraints excluded: chain B residue 259 LEU Chi-restraints excluded: chain B residue 268 LEU Chi-restraints excluded: chain B residue 288 CYS Chi-restraints excluded: chain A residue 30 ASP Chi-restraints excluded: chain A residue 156 CYS Chi-restraints excluded: chain A residue 237 CYS Chi-restraints excluded: chain A residue 287 THR Chi-restraints excluded: chain A residue 394 ILE Chi-restraints excluded: chain A residue 418 LEU Chi-restraints excluded: chain E residue 42 ILE Chi-restraints excluded: chain E residue 44 ILE Chi-restraints excluded: chain E residue 125 LEU Chi-restraints excluded: chain E residue 156 SER Chi-restraints excluded: chain E residue 198 VAL Chi-restraints excluded: chain E residue 265 ASN Chi-restraints excluded: chain C residue 37 CYS Chi-restraints excluded: chain C residue 48 ASP Chi-restraints excluded: chain C residue 49 MET Chi-restraints excluded: chain C residue 69 ASP Chi-restraints excluded: chain C residue 175 VAL Chi-restraints excluded: chain C residue 194 VAL Chi-restraints excluded: chain C residue 440 LEU Chi-restraints excluded: chain D residue 99 LEU Chi-restraints excluded: chain D residue 103 LYS Chi-restraints excluded: chain D residue 113 ASN Chi-restraints excluded: chain D residue 125 LEU Chi-restraints excluded: chain D residue 188 ILE Chi-restraints excluded: chain D residue 194 VAL Chi-restraints excluded: chain D residue 198 VAL Chi-restraints excluded: chain D residue 212 PHE Chi-restraints excluded: chain D residue 268 LEU Chi-restraints excluded: chain D residue 285 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 201 random chunks: chunk 50 optimal weight: 2.9990 chunk 30 optimal weight: 10.0000 chunk 15 optimal weight: 6.9990 chunk 105 optimal weight: 5.9990 chunk 67 optimal weight: 5.9990 chunk 152 optimal weight: 0.4980 chunk 197 optimal weight: 0.5980 chunk 35 optimal weight: 3.9990 chunk 194 optimal weight: 3.9990 chunk 33 optimal weight: 7.9990 chunk 59 optimal weight: 3.9990 overall best weight: 2.4186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** K 1 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 120 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 30 ASN L 111 ASN B 191 HIS B 303 ASN ** A 193 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 278 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 317 GLN ** E 185 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 191 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 265 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 309 GLN C 64 GLN C 265 ASN D 224 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3550 r_free = 0.3550 target = 0.090505 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3316 r_free = 0.3316 target = 0.076509 restraints weight = 52157.988| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3360 r_free = 0.3360 target = 0.079221 restraints weight = 25705.687| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3389 r_free = 0.3389 target = 0.081034 restraints weight = 15551.551| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3410 r_free = 0.3410 target = 0.082325 restraints weight = 10546.018| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3422 r_free = 0.3422 target = 0.083096 restraints weight = 7651.975| |-----------------------------------------------------------------------------| r_work (final): 0.3413 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7907 moved from start: 0.4426 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 17543 Z= 0.202 Angle : 0.931 18.669 23924 Z= 0.420 Chirality : 0.050 0.380 2766 Planarity : 0.006 0.179 2913 Dihedral : 15.626 102.347 3154 Min Nonbonded Distance : 2.159 Molprobity Statistics. All-atom Clashscore : 12.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.23 % Favored : 94.77 % Rotamer: Outliers : 4.81 % Allowed : 19.19 % Favored : 75.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.02 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % 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: -1.81 (0.19), residues: 2027 helix: -0.65 (0.23), residues: 456 sheet: -1.03 (0.21), residues: 586 loop : -1.50 (0.21), residues: 985 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG D 196 TYR 0.033 0.002 TYR D 244 PHE 0.024 0.002 PHE D 293 TRP 0.019 0.002 TRP E 67 HIS 0.012 0.001 HIS A 221 Details of bonding type rmsd covalent geometry : bond 0.00438 (17485) covalent geometry : angle 0.86491 (23777) SS BOND : bond 0.00745 ( 9) SS BOND : angle 3.02443 ( 18) hydrogen bonds : bond 0.04885 ( 569) hydrogen bonds : angle 5.48297 ( 1749) Misc. bond : bond 0.00308 ( 6) link_ALPHA1-3 : bond 0.01304 ( 9) link_ALPHA1-3 : angle 3.88149 ( 27) link_ALPHA1-6 : bond 0.01248 ( 5) link_ALPHA1-6 : angle 2.69328 ( 15) link_BETA1-4 : bond 0.00988 ( 19) link_BETA1-4 : angle 4.61861 ( 57) link_NAG-ASN : bond 0.00450 ( 10) link_NAG-ASN : angle 5.94160 ( 30) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4054 Ramachandran restraints generated. 2027 Oldfield, 0 Emsley, 2027 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4054 Ramachandran restraints generated. 2027 Oldfield, 0 Emsley, 2027 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 627 residues out of total 1787 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 86 poor density : 541 time to evaluate : 0.596 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: K 18 LEU cc_start: 0.8980 (OUTLIER) cc_final: 0.8584 (tm) REVERT: K 45 ARG cc_start: 0.8659 (ptt180) cc_final: 0.7725 (ptp-170) REVERT: K 46 GLU cc_start: 0.9410 (OUTLIER) cc_final: 0.9111 (mp0) REVERT: K 73 ASP cc_start: 0.7020 (t0) cc_final: 0.6340 (t0) REVERT: K 76 LYS cc_start: 0.9377 (mttt) cc_final: 0.9151 (mttp) REVERT: K 80 TYR cc_start: 0.9055 (m-10) cc_final: 0.8843 (m-10) REVERT: K 83 MET cc_start: 0.8855 (mpm) cc_final: 0.8323 (mpp) REVERT: K 89 GLU cc_start: 0.9242 (mp0) cc_final: 0.8921 (pm20) REVERT: K 90 ASP cc_start: 0.9079 (m-30) cc_final: 0.8833 (m-30) REVERT: L 1 GLN cc_start: 0.9180 (mm-40) cc_final: 0.8163 (mp10) REVERT: L 4 LEU cc_start: 0.8637 (mt) cc_final: 0.8287 (mt) REVERT: L 29 PHE cc_start: 0.8832 (t80) cc_final: 0.8405 (t80) REVERT: L 38 ARG cc_start: 0.8609 (mtm180) cc_final: 0.8340 (mtm180) REVERT: O 4 LEU cc_start: 0.7785 (mt) cc_final: 0.7520 (mt) REVERT: O 18 LEU cc_start: 0.9352 (tt) cc_final: 0.9137 (tt) REVERT: O 30 ASN cc_start: 0.8890 (p0) cc_final: 0.8562 (p0) REVERT: O 52 SER cc_start: 0.8952 (t) cc_final: 0.8656 (p) REVERT: O 85 ASN cc_start: 0.8932 (m110) cc_final: 0.8254 (m-40) REVERT: O 89 GLU cc_start: 0.8943 (pt0) cc_final: 0.8687 (pm20) REVERT: O 91 THR cc_start: 0.8675 (t) cc_final: 0.8348 (m) REVERT: O 99 LYS cc_start: 0.8368 (ttpm) cc_final: 0.7807 (tttp) REVERT: O 101 ARG cc_start: 0.8986 (ttm110) cc_final: 0.8665 (ttm110) REVERT: O 103 SER cc_start: 0.7803 (t) cc_final: 0.7566 (m) REVERT: B 21 LYS cc_start: 0.9508 (tttt) cc_final: 0.9211 (ptmt) REVERT: B 30 ASP cc_start: 0.9067 (m-30) cc_final: 0.8214 (t0) REVERT: B 40 MET cc_start: 0.7402 (mtm) cc_final: 0.6347 (mpp) REVERT: B 49 MET cc_start: 0.9118 (ptm) cc_final: 0.8483 (ppp) REVERT: B 55 MET cc_start: 0.8902 (mmm) cc_final: 0.8351 (mmm) REVERT: B 69 ASP cc_start: 0.9302 (t0) cc_final: 0.8973 (t70) REVERT: B 85 ASN cc_start: 0.9052 (p0) cc_final: 0.8838 (p0) REVERT: B 86 ARG cc_start: 0.9416 (tpp80) cc_final: 0.8675 (mmm160) REVERT: B 90 GLN cc_start: 0.9123 (mt0) cc_final: 0.8625 (mp10) REVERT: B 95 ASP cc_start: 0.8814 (p0) cc_final: 0.8493 (p0) REVERT: B 101 ASP cc_start: 0.8813 (OUTLIER) cc_final: 0.8329 (t70) REVERT: B 200 PHE cc_start: 0.8671 (m-10) cc_final: 0.8453 (m-10) REVERT: B 208 LEU cc_start: 0.8938 (mt) cc_final: 0.8628 (mt) REVERT: B 229 SER cc_start: 0.9231 (m) cc_final: 0.8761 (t) REVERT: A 23 ASP cc_start: 0.9407 (m-30) cc_final: 0.8873 (p0) REVERT: A 31 ASN cc_start: 0.9359 (p0) cc_final: 0.9039 (p0) REVERT: A 45 ARG cc_start: 0.8873 (OUTLIER) cc_final: 0.8453 (tpp80) REVERT: A 62 GLU cc_start: 0.8624 (pt0) cc_final: 0.8215 (pt0) REVERT: A 90 ASN cc_start: 0.8881 (t0) cc_final: 0.8295 (t0) REVERT: A 98 TRP cc_start: 0.9180 (t60) cc_final: 0.8778 (t60) REVERT: A 115 MET cc_start: 0.6761 (tmm) cc_final: 0.6553 (tmm) REVERT: A 225 LYS cc_start: 0.8560 (mmmt) cc_final: 0.8240 (mmmt) REVERT: A 289 MET cc_start: 0.9115 (tpp) cc_final: 0.8839 (tpt) REVERT: E 14 GLU cc_start: 0.9091 (pt0) cc_final: 0.8783 (pp20) REVERT: E 24 ASP cc_start: 0.8881 (t0) cc_final: 0.8547 (t70) REVERT: E 49 MET cc_start: 0.9099 (ptm) cc_final: 0.8301 (ppp) REVERT: E 97 TYR cc_start: 0.8927 (p90) cc_final: 0.8619 (p90) REVERT: E 99 LEU cc_start: 0.9303 (tp) cc_final: 0.8946 (mt) REVERT: E 153 GLU cc_start: 0.8449 (mt-10) cc_final: 0.7787 (mt-10) REVERT: E 155 GLU cc_start: 0.8827 (mt-10) cc_final: 0.7967 (mt-10) REVERT: E 208 LEU cc_start: 0.9424 (mt) cc_final: 0.9116 (mt) REVERT: E 312 ARG cc_start: 0.7899 (tpp-160) cc_final: 0.7635 (mtt180) REVERT: E 428 ARG cc_start: 0.7586 (ptp90) cc_final: 0.6755 (ptm160) REVERT: E 439 ASN cc_start: 0.8798 (m-40) cc_final: 0.8594 (m-40) REVERT: C 49 MET cc_start: 0.8593 (OUTLIER) cc_final: 0.8171 (ptm) REVERT: C 55 MET cc_start: 0.8861 (mmm) cc_final: 0.8521 (ttm) REVERT: C 97 TYR cc_start: 0.9124 (p90) cc_final: 0.8905 (p90) REVERT: C 112 LYS cc_start: 0.9150 (mtpp) cc_final: 0.8498 (ttmm) REVERT: C 153 GLU cc_start: 0.8734 (mt-10) cc_final: 0.8321 (tp30) REVERT: C 162 ASP cc_start: 0.9168 (m-30) cc_final: 0.8541 (t70) REVERT: C 173 LYS cc_start: 0.9370 (mmtm) cc_final: 0.9123 (mmtm) REVERT: C 179 GLU cc_start: 0.9030 (mp0) cc_final: 0.8800 (mp0) REVERT: C 208 LEU cc_start: 0.9367 (mt) cc_final: 0.9048 (mt) REVERT: C 226 TYR cc_start: 0.9126 (m-10) cc_final: 0.8886 (m-10) REVERT: C 229 SER cc_start: 0.9455 (m) cc_final: 0.9239 (p) REVERT: C 261 MET cc_start: 0.9142 (mmm) cc_final: 0.8882 (mmt) REVERT: C 279 LYS cc_start: 0.9289 (mtpt) cc_final: 0.8892 (mtmm) REVERT: C 282 ASP cc_start: 0.9115 (m-30) cc_final: 0.8348 (m-30) REVERT: C 289 PHE cc_start: 0.9065 (t80) cc_final: 0.8786 (t80) REVERT: C 303 ASN cc_start: 0.8546 (t0) cc_final: 0.8115 (m-40) REVERT: D 17 ASP cc_start: 0.9294 (m-30) cc_final: 0.9040 (m-30) REVERT: D 28 ARG cc_start: 0.8840 (ptt90) cc_final: 0.8533 (ppt90) REVERT: D 55 MET cc_start: 0.9523 (mtt) cc_final: 0.9105 (mmm) REVERT: D 100 ASN cc_start: 0.8355 (p0) cc_final: 0.7394 (p0) REVERT: D 137 MET cc_start: 0.9039 (mmm) cc_final: 0.8700 (mmm) REVERT: D 138 MET cc_start: 0.9578 (mmt) cc_final: 0.9108 (mmt) REVERT: D 153 GLU cc_start: 0.8312 (mt-10) cc_final: 0.7574 (mt-10) REVERT: D 165 GLU cc_start: 0.8552 (mm-30) cc_final: 0.8253 (mm-30) REVERT: D 190 GLU cc_start: 0.8175 (tt0) cc_final: 0.7558 (tm-30) REVERT: D 191 HIS cc_start: 0.7483 (m-70) cc_final: 0.6662 (m-70) REVERT: D 208 LEU cc_start: 0.8655 (mp) cc_final: 0.8394 (mt) REVERT: D 235 LEU cc_start: 0.8616 (mp) cc_final: 0.8300 (tt) REVERT: D 279 LYS cc_start: 0.8787 (mptt) cc_final: 0.8515 (mptt) REVERT: D 282 ASP cc_start: 0.9312 (m-30) cc_final: 0.8925 (m-30) outliers start: 86 outliers final: 48 residues processed: 586 average time/residue: 0.1341 time to fit residues: 118.3643 Evaluate side-chains 548 residues out of total 1787 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 495 time to evaluate : 0.657 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain K residue 7 SER Chi-restraints excluded: chain K residue 11 LEU Chi-restraints excluded: chain K residue 18 LEU Chi-restraints excluded: chain K residue 28 THR Chi-restraints excluded: chain K residue 46 GLU Chi-restraints excluded: chain K residue 122 THR Chi-restraints excluded: chain L residue 20 LEU Chi-restraints excluded: chain L residue 57 SER Chi-restraints excluded: chain L residue 91 THR Chi-restraints excluded: chain L residue 93 VAL Chi-restraints excluded: chain L residue 106 LEU Chi-restraints excluded: chain O residue 28 THR Chi-restraints excluded: chain O residue 120 GLN Chi-restraints excluded: chain B residue 46 SER Chi-restraints excluded: chain B residue 93 VAL Chi-restraints excluded: chain B residue 101 ASP Chi-restraints excluded: chain B residue 212 PHE Chi-restraints excluded: chain B residue 259 LEU Chi-restraints excluded: chain B residue 268 LEU Chi-restraints excluded: chain B residue 288 CYS Chi-restraints excluded: chain A residue 30 ASP Chi-restraints excluded: chain A residue 45 ARG Chi-restraints excluded: chain A residue 117 THR Chi-restraints excluded: chain A residue 131 LEU Chi-restraints excluded: chain A residue 156 CYS Chi-restraints excluded: chain A residue 189 SER Chi-restraints excluded: chain A residue 195 HIS Chi-restraints excluded: chain A residue 237 CYS Chi-restraints excluded: chain A residue 243 LEU Chi-restraints excluded: chain A residue 287 THR Chi-restraints excluded: chain A residue 418 LEU Chi-restraints excluded: chain E residue 38 VAL Chi-restraints excluded: chain E residue 44 ILE Chi-restraints excluded: chain E residue 125 LEU Chi-restraints excluded: chain E residue 156 SER Chi-restraints excluded: chain E residue 198 VAL Chi-restraints excluded: chain E residue 265 ASN Chi-restraints excluded: chain C residue 49 MET Chi-restraints excluded: chain C residue 69 ASP Chi-restraints excluded: chain C residue 175 VAL Chi-restraints excluded: chain C residue 181 ILE Chi-restraints excluded: chain C residue 194 VAL Chi-restraints excluded: chain C residue 247 SER Chi-restraints excluded: chain C residue 440 LEU Chi-restraints excluded: chain D residue 99 LEU Chi-restraints excluded: chain D residue 103 LYS Chi-restraints excluded: chain D residue 113 ASN Chi-restraints excluded: chain D residue 188 ILE Chi-restraints excluded: chain D residue 198 VAL Chi-restraints excluded: chain D residue 212 PHE Chi-restraints excluded: chain D residue 268 LEU Chi-restraints excluded: chain D residue 281 ILE Chi-restraints excluded: chain D residue 440 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 201 random chunks: chunk 81 optimal weight: 1.9990 chunk 74 optimal weight: 0.9990 chunk 188 optimal weight: 3.9990 chunk 173 optimal weight: 3.9990 chunk 55 optimal weight: 7.9990 chunk 107 optimal weight: 6.9990 chunk 87 optimal weight: 2.9990 chunk 64 optimal weight: 0.9980 chunk 170 optimal weight: 0.7980 chunk 164 optimal weight: 0.9990 chunk 100 optimal weight: 10.0000 overall best weight: 1.1586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: K 1 GLN K 120 GLN L 111 ASN ** B 191 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 193 GLN ** A 278 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 191 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 265 ASN ** 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 = 0.3569 r_free = 0.3569 target = 0.091975 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3336 r_free = 0.3336 target = 0.077947 restraints weight = 51617.703| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3383 r_free = 0.3383 target = 0.080763 restraints weight = 25368.125| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3411 r_free = 0.3411 target = 0.082580 restraints weight = 15166.510| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3432 r_free = 0.3432 target = 0.083903 restraints weight = 10300.720| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3446 r_free = 0.3446 target = 0.084749 restraints weight = 7469.844| |-----------------------------------------------------------------------------| r_work (final): 0.3436 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7889 moved from start: 0.4829 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 17543 Z= 0.143 Angle : 0.886 20.569 23924 Z= 0.392 Chirality : 0.049 0.388 2766 Planarity : 0.005 0.155 2913 Dihedral : 13.815 97.958 3154 Min Nonbonded Distance : 2.262 Molprobity Statistics. All-atom Clashscore : 10.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.70 % Favored : 96.30 % Rotamer: Outliers : 4.70 % Allowed : 21.04 % Favored : 74.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.02 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.53 (0.19), residues: 2027 helix: -0.21 (0.24), residues: 456 sheet: -0.91 (0.22), residues: 561 loop : -1.40 (0.20), residues: 1010 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG D 196 TYR 0.029 0.002 TYR D 299 PHE 0.021 0.002 PHE D 289 TRP 0.016 0.001 TRP D 67 HIS 0.010 0.001 HIS B 191 Details of bonding type rmsd covalent geometry : bond 0.00305 (17485) covalent geometry : angle 0.82411 (23777) SS BOND : bond 0.00402 ( 9) SS BOND : angle 2.52397 ( 18) hydrogen bonds : bond 0.04155 ( 569) hydrogen bonds : angle 5.08789 ( 1749) Misc. bond : bond 0.00311 ( 6) link_ALPHA1-3 : bond 0.01441 ( 9) link_ALPHA1-3 : angle 4.33172 ( 27) link_ALPHA1-6 : bond 0.01500 ( 5) link_ALPHA1-6 : angle 2.65128 ( 15) link_BETA1-4 : bond 0.01057 ( 19) link_BETA1-4 : angle 4.28940 ( 57) link_NAG-ASN : bond 0.00526 ( 10) link_NAG-ASN : angle 5.33181 ( 30) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4054 Ramachandran restraints generated. 2027 Oldfield, 0 Emsley, 2027 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4054 Ramachandran restraints generated. 2027 Oldfield, 0 Emsley, 2027 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 631 residues out of total 1787 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 84 poor density : 547 time to evaluate : 0.672 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: K 18 LEU cc_start: 0.8994 (OUTLIER) cc_final: 0.8570 (tm) REVERT: K 36 TRP cc_start: 0.8730 (m100) cc_final: 0.8427 (m100) REVERT: K 37 PHE cc_start: 0.9004 (m-80) cc_final: 0.8648 (m-80) REVERT: K 45 ARG cc_start: 0.8614 (ptt180) cc_final: 0.7588 (ptp-170) REVERT: K 73 ASP cc_start: 0.7088 (t0) cc_final: 0.6716 (t0) REVERT: K 83 MET cc_start: 0.8864 (mpm) cc_final: 0.8185 (mpp) REVERT: K 89 GLU cc_start: 0.9238 (mp0) cc_final: 0.8902 (pm20) REVERT: K 90 ASP cc_start: 0.9081 (m-30) cc_final: 0.8876 (m-30) REVERT: L 1 GLN cc_start: 0.9184 (mm-40) cc_final: 0.8203 (mp10) REVERT: L 4 LEU cc_start: 0.8829 (mt) cc_final: 0.8620 (mt) REVERT: L 83 MET cc_start: 0.8195 (pmt) cc_final: 0.6897 (ppp) REVERT: O 18 LEU cc_start: 0.9267 (tt) cc_final: 0.8939 (tt) REVERT: O 30 ASN cc_start: 0.8666 (p0) cc_final: 0.8357 (p0) REVERT: O 36 TRP cc_start: 0.8849 (m100) cc_final: 0.8519 (m100) REVERT: O 52 SER cc_start: 0.8840 (t) cc_final: 0.8639 (p) REVERT: O 67 ARG cc_start: 0.7603 (mtp180) cc_final: 0.7210 (mtp180) REVERT: O 84 ASN cc_start: 0.7642 (t0) cc_final: 0.7343 (t0) REVERT: O 87 LYS cc_start: 0.9393 (mtpp) cc_final: 0.9010 (mtpp) REVERT: O 89 GLU cc_start: 0.8913 (pt0) cc_final: 0.8649 (pm20) REVERT: O 91 THR cc_start: 0.8463 (t) cc_final: 0.8087 (m) REVERT: O 99 LYS cc_start: 0.8359 (ttpm) cc_final: 0.7446 (tttp) REVERT: O 101 ARG cc_start: 0.8892 (ttm110) cc_final: 0.8606 (ttm110) REVERT: O 103 SER cc_start: 0.7820 (t) cc_final: 0.7102 (m) REVERT: O 108 TYR cc_start: 0.9021 (m-80) cc_final: 0.8787 (m-80) REVERT: O 111 ASN cc_start: 0.8999 (t0) cc_final: 0.8270 (t0) REVERT: B 21 LYS cc_start: 0.9492 (tttt) cc_final: 0.9178 (ptmt) REVERT: B 30 ASP cc_start: 0.9007 (m-30) cc_final: 0.8208 (t0) REVERT: B 49 MET cc_start: 0.9109 (ptm) cc_final: 0.8562 (ppp) REVERT: B 67 TRP cc_start: 0.8483 (p90) cc_final: 0.8106 (p90) REVERT: B 69 ASP cc_start: 0.9249 (t0) cc_final: 0.8889 (t70) REVERT: B 86 ARG cc_start: 0.9387 (tpp80) cc_final: 0.9098 (tpp80) REVERT: B 89 ASP cc_start: 0.9038 (m-30) cc_final: 0.8834 (m-30) REVERT: B 90 GLN cc_start: 0.9125 (mt0) cc_final: 0.8642 (mp10) REVERT: B 95 ASP cc_start: 0.8844 (p0) cc_final: 0.8522 (p0) REVERT: B 101 ASP cc_start: 0.8784 (OUTLIER) cc_final: 0.8352 (t70) REVERT: B 102 LYS cc_start: 0.9398 (mtmt) cc_final: 0.9159 (mtmt) REVERT: B 190 GLU cc_start: 0.8655 (mt-10) cc_final: 0.8372 (mt-10) REVERT: B 192 ARG cc_start: 0.8206 (mtm-85) cc_final: 0.7831 (mtm-85) REVERT: B 200 PHE cc_start: 0.8731 (m-10) cc_final: 0.8468 (m-10) REVERT: B 229 SER cc_start: 0.9248 (m) cc_final: 0.8688 (t) REVERT: A 31 ASN cc_start: 0.9368 (p0) cc_final: 0.8992 (p0) REVERT: A 45 ARG cc_start: 0.8888 (OUTLIER) cc_final: 0.8455 (tpp80) REVERT: A 61 MET cc_start: 0.9064 (mtt) cc_final: 0.8748 (mtt) REVERT: A 90 ASN cc_start: 0.9011 (t0) cc_final: 0.8427 (t0) REVERT: A 98 TRP cc_start: 0.9190 (t60) cc_final: 0.8814 (t60) REVERT: A 102 THR cc_start: 0.9104 (OUTLIER) cc_final: 0.8896 (p) REVERT: A 225 LYS cc_start: 0.8765 (mmmt) cc_final: 0.8434 (mmmt) REVERT: A 239 MET cc_start: 0.8669 (mtt) cc_final: 0.8380 (mtm) REVERT: E 14 GLU cc_start: 0.9018 (pt0) cc_final: 0.8813 (pp20) REVERT: E 24 ASP cc_start: 0.8750 (t0) cc_final: 0.8524 (t70) REVERT: E 36 VAL cc_start: 0.9078 (p) cc_final: 0.8210 (m) REVERT: E 49 MET cc_start: 0.9086 (ptm) cc_final: 0.8293 (ppp) REVERT: E 137 MET cc_start: 0.8905 (mmm) cc_final: 0.8665 (mmm) REVERT: E 164 ILE cc_start: 0.9044 (mt) cc_final: 0.8348 (mp) REVERT: E 207 ARG cc_start: 0.8774 (ttm-80) cc_final: 0.8218 (ttm-80) REVERT: E 208 LEU cc_start: 0.9353 (mt) cc_final: 0.9125 (mp) REVERT: E 237 TRP cc_start: 0.7636 (m-10) cc_final: 0.7219 (m-10) REVERT: E 282 ASP cc_start: 0.8722 (m-30) cc_final: 0.8437 (m-30) REVERT: E 312 ARG cc_start: 0.7870 (tpp-160) cc_final: 0.7573 (ttt180) REVERT: E 428 ARG cc_start: 0.7555 (ptp90) cc_final: 0.6786 (ptm160) REVERT: E 439 ASN cc_start: 0.8673 (m-40) cc_final: 0.8465 (m-40) REVERT: C 49 MET cc_start: 0.8597 (OUTLIER) cc_final: 0.8118 (ptm) REVERT: C 84 ASP cc_start: 0.8500 (t0) cc_final: 0.8281 (t0) REVERT: C 85 ASN cc_start: 0.9038 (p0) cc_final: 0.8761 (p0) REVERT: C 112 LYS cc_start: 0.9195 (mtpp) cc_final: 0.8686 (ttmm) REVERT: C 162 ASP cc_start: 0.9161 (m-30) cc_final: 0.8506 (t70) REVERT: C 173 LYS cc_start: 0.9403 (mmtm) cc_final: 0.9157 (mmtm) REVERT: C 208 LEU cc_start: 0.9262 (mt) cc_final: 0.8816 (mp) REVERT: C 224 GLN cc_start: 0.8775 (mm110) cc_final: 0.8201 (mm110) REVERT: C 226 TYR cc_start: 0.9211 (m-10) cc_final: 0.8900 (m-10) REVERT: C 261 MET cc_start: 0.9126 (mmm) cc_final: 0.8865 (mmt) REVERT: C 279 LYS cc_start: 0.9276 (mtpt) cc_final: 0.8912 (mtmm) REVERT: C 282 ASP cc_start: 0.9115 (m-30) cc_final: 0.8248 (m-30) REVERT: D 17 ASP cc_start: 0.9280 (m-30) cc_final: 0.9013 (m-30) REVERT: D 55 MET cc_start: 0.9524 (mtt) cc_final: 0.9116 (mmm) REVERT: D 100 ASN cc_start: 0.8395 (p0) cc_final: 0.7426 (p0) REVERT: D 137 MET cc_start: 0.8920 (mmm) cc_final: 0.8640 (mmm) REVERT: D 138 MET cc_start: 0.9552 (mmt) cc_final: 0.9177 (tpp) REVERT: D 190 GLU cc_start: 0.8192 (tt0) cc_final: 0.7566 (tm-30) REVERT: D 191 HIS cc_start: 0.7155 (m-70) cc_final: 0.6500 (m-70) REVERT: D 207 ARG cc_start: 0.7951 (ttm170) cc_final: 0.7578 (ttm170) REVERT: D 208 LEU cc_start: 0.8656 (mp) cc_final: 0.8417 (mt) REVERT: D 235 LEU cc_start: 0.8617 (mp) cc_final: 0.8327 (tt) REVERT: D 279 LYS cc_start: 0.8774 (mptt) cc_final: 0.8460 (mptt) REVERT: D 282 ASP cc_start: 0.9270 (m-30) cc_final: 0.8951 (m-30) REVERT: D 299 TYR cc_start: 0.7603 (t80) cc_final: 0.7169 (t80) REVERT: D 423 ILE cc_start: 0.8524 (tp) cc_final: 0.8293 (tt) outliers start: 84 outliers final: 52 residues processed: 587 average time/residue: 0.1341 time to fit residues: 118.7194 Evaluate side-chains 567 residues out of total 1787 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 510 time to evaluate : 0.648 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain K residue 7 SER Chi-restraints excluded: chain K residue 11 LEU Chi-restraints excluded: chain K residue 18 LEU Chi-restraints excluded: chain L residue 20 LEU Chi-restraints excluded: chain L residue 91 THR Chi-restraints excluded: chain L residue 93 VAL Chi-restraints excluded: chain L residue 106 LEU Chi-restraints excluded: chain O residue 78 THR Chi-restraints excluded: chain B residue 38 VAL Chi-restraints excluded: chain B residue 101 ASP Chi-restraints excluded: chain B residue 136 CYS Chi-restraints excluded: chain B residue 138 MET Chi-restraints excluded: chain B residue 189 VAL Chi-restraints excluded: chain B residue 212 PHE Chi-restraints excluded: chain B residue 244 TYR Chi-restraints excluded: chain B residue 255 ILE Chi-restraints excluded: chain B residue 259 LEU Chi-restraints excluded: chain B residue 268 LEU Chi-restraints excluded: chain B residue 288 CYS Chi-restraints excluded: chain B residue 437 LEU Chi-restraints excluded: chain A residue 25 LEU Chi-restraints excluded: chain A residue 30 ASP Chi-restraints excluded: chain A residue 45 ARG Chi-restraints excluded: chain A residue 58 ASP Chi-restraints excluded: chain A residue 102 THR Chi-restraints excluded: chain A residue 131 LEU Chi-restraints excluded: chain A residue 156 CYS Chi-restraints excluded: chain A residue 189 SER Chi-restraints excluded: chain A residue 193 GLN Chi-restraints excluded: chain A residue 195 HIS Chi-restraints excluded: chain A residue 237 CYS Chi-restraints excluded: chain A residue 243 LEU Chi-restraints excluded: chain A residue 287 THR Chi-restraints excluded: chain A residue 418 LEU Chi-restraints excluded: chain E residue 38 VAL Chi-restraints excluded: chain E residue 40 MET Chi-restraints excluded: chain E residue 125 LEU Chi-restraints excluded: chain E residue 156 SER Chi-restraints excluded: chain E residue 198 VAL Chi-restraints excluded: chain E residue 225 THR Chi-restraints excluded: chain E residue 265 ASN Chi-restraints excluded: chain C residue 12 VAL Chi-restraints excluded: chain C residue 49 MET Chi-restraints excluded: chain C residue 69 ASP Chi-restraints excluded: chain C residue 91 LEU Chi-restraints excluded: chain C residue 165 GLU Chi-restraints excluded: chain C residue 175 VAL Chi-restraints excluded: chain C residue 181 ILE Chi-restraints excluded: chain C residue 194 VAL Chi-restraints excluded: chain D residue 99 LEU Chi-restraints excluded: chain D residue 125 LEU Chi-restraints excluded: chain D residue 188 ILE Chi-restraints excluded: chain D residue 198 VAL Chi-restraints excluded: chain D residue 212 PHE Chi-restraints excluded: chain D residue 264 ILE Chi-restraints excluded: chain D residue 268 LEU Chi-restraints excluded: chain D residue 440 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 201 random chunks: chunk 25 optimal weight: 8.9990 chunk 27 optimal weight: 7.9990 chunk 77 optimal weight: 3.9990 chunk 170 optimal weight: 1.9990 chunk 71 optimal weight: 6.9990 chunk 175 optimal weight: 4.9990 chunk 11 optimal weight: 5.9990 chunk 69 optimal weight: 0.5980 chunk 68 optimal weight: 5.9990 chunk 91 optimal weight: 0.0670 chunk 50 optimal weight: 5.9990 overall best weight: 2.3324 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: K 111 ASN L 111 ASN ** B 185 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 191 HIS A 193 GLN ** A 278 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 191 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 265 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 303 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3520 r_free = 0.3520 target = 0.089211 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3287 r_free = 0.3287 target = 0.075377 restraints weight = 52268.273| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.3332 r_free = 0.3332 target = 0.078071 restraints weight = 25792.518| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3361 r_free = 0.3361 target = 0.079855 restraints weight = 15444.206| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.3383 r_free = 0.3383 target = 0.081144 restraints weight = 10414.623| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3396 r_free = 0.3396 target = 0.081991 restraints weight = 7611.989| |-----------------------------------------------------------------------------| r_work (final): 0.3388 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7942 moved from start: 0.5137 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 17543 Z= 0.191 Angle : 0.899 20.144 23924 Z= 0.401 Chirality : 0.048 0.366 2766 Planarity : 0.005 0.149 2913 Dihedral : 12.461 97.122 3154 Min Nonbonded Distance : 2.211 Molprobity Statistics. All-atom Clashscore : 12.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.98 % Favored : 95.02 % Rotamer: Outliers : 5.60 % Allowed : 21.88 % Favored : 72.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.02 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.39 (0.19), residues: 2027 helix: -0.06 (0.24), residues: 464 sheet: -0.74 (0.22), residues: 573 loop : -1.41 (0.21), residues: 990 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG D 196 TYR 0.023 0.002 TYR E 299 PHE 0.018 0.002 PHE L 29 TRP 0.020 0.002 TRP E 67 HIS 0.005 0.001 HIS B 119 Details of bonding type rmsd covalent geometry : bond 0.00414 (17485) covalent geometry : angle 0.84170 (23777) SS BOND : bond 0.00481 ( 9) SS BOND : angle 2.46045 ( 18) hydrogen bonds : bond 0.04098 ( 569) hydrogen bonds : angle 5.00753 ( 1749) Misc. bond : bond 0.00267 ( 6) link_ALPHA1-3 : bond 0.01402 ( 9) link_ALPHA1-3 : angle 4.03064 ( 27) link_ALPHA1-6 : bond 0.01281 ( 5) link_ALPHA1-6 : angle 3.03226 ( 15) link_BETA1-4 : bond 0.00975 ( 19) link_BETA1-4 : angle 4.16220 ( 57) link_NAG-ASN : bond 0.00465 ( 10) link_NAG-ASN : angle 5.15894 ( 30) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4054 Ramachandran restraints generated. 2027 Oldfield, 0 Emsley, 2027 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4054 Ramachandran restraints generated. 2027 Oldfield, 0 Emsley, 2027 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 621 residues out of total 1787 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 100 poor density : 521 time to evaluate : 0.697 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: K 36 TRP cc_start: 0.8736 (m100) cc_final: 0.8512 (m100) REVERT: K 45 ARG cc_start: 0.8528 (ptt180) cc_final: 0.7948 (ptp-170) REVERT: K 73 ASP cc_start: 0.7330 (t0) cc_final: 0.7088 (t0) REVERT: K 89 GLU cc_start: 0.9252 (mp0) cc_final: 0.8916 (pm20) REVERT: K 99 LYS cc_start: 0.8967 (ttpt) cc_final: 0.8440 (tttt) REVERT: K 111 ASN cc_start: 0.9155 (OUTLIER) cc_final: 0.8907 (t0) REVERT: L 1 GLN cc_start: 0.9164 (mm-40) cc_final: 0.8245 (mp10) REVERT: L 4 LEU cc_start: 0.8842 (mt) cc_final: 0.8635 (mt) REVERT: L 29 PHE cc_start: 0.8759 (t80) cc_final: 0.8521 (t80) REVERT: L 83 MET cc_start: 0.8204 (pmt) cc_final: 0.6971 (ppp) REVERT: O 30 ASN cc_start: 0.8669 (p0) cc_final: 0.7934 (p0) REVERT: O 36 TRP cc_start: 0.8809 (m100) cc_final: 0.8534 (m100) REVERT: O 67 ARG cc_start: 0.7716 (mtp180) cc_final: 0.6377 (mtp180) REVERT: O 84 ASN cc_start: 0.7767 (t0) cc_final: 0.6691 (t0) REVERT: O 85 ASN cc_start: 0.9003 (m110) cc_final: 0.8022 (p0) REVERT: O 89 GLU cc_start: 0.8921 (pt0) cc_final: 0.8686 (pm20) REVERT: O 99 LYS cc_start: 0.8360 (ttpm) cc_final: 0.7692 (tttp) REVERT: O 101 ARG cc_start: 0.8929 (ttm110) cc_final: 0.8717 (ttm110) REVERT: O 103 SER cc_start: 0.7916 (t) cc_final: 0.7469 (m) REVERT: O 108 TYR cc_start: 0.9036 (m-80) cc_final: 0.8810 (m-80) REVERT: O 111 ASN cc_start: 0.9037 (t0) cc_final: 0.8596 (t0) REVERT: B 21 LYS cc_start: 0.9487 (tttt) cc_final: 0.9184 (ptmt) REVERT: B 30 ASP cc_start: 0.9030 (m-30) cc_final: 0.8276 (t0) REVERT: B 49 MET cc_start: 0.9150 (ptm) cc_final: 0.8556 (ppp) REVERT: B 55 MET cc_start: 0.8911 (mmm) cc_final: 0.7812 (mmm) REVERT: B 67 TRP cc_start: 0.8564 (p90) cc_final: 0.8193 (p90) REVERT: B 69 ASP cc_start: 0.9293 (t0) cc_final: 0.8981 (t70) REVERT: B 86 ARG cc_start: 0.9389 (tpp80) cc_final: 0.8663 (mmm160) REVERT: B 90 GLN cc_start: 0.9128 (mt0) cc_final: 0.8644 (mp10) REVERT: B 95 ASP cc_start: 0.8850 (p0) cc_final: 0.8539 (p0) REVERT: B 101 ASP cc_start: 0.8768 (OUTLIER) cc_final: 0.8300 (t70) REVERT: B 102 LYS cc_start: 0.9368 (OUTLIER) cc_final: 0.9115 (mtmt) REVERT: B 138 MET cc_start: 0.7643 (OUTLIER) cc_final: 0.6530 (mpp) REVERT: B 147 GLU cc_start: 0.9005 (mm-30) cc_final: 0.8715 (mm-30) REVERT: B 182 GLU cc_start: 0.7889 (pm20) cc_final: 0.7572 (pm20) REVERT: B 192 ARG cc_start: 0.8221 (mtm-85) cc_final: 0.7795 (mtm-85) REVERT: B 229 SER cc_start: 0.9294 (m) cc_final: 0.9011 (p) REVERT: A 23 ASP cc_start: 0.9349 (m-30) cc_final: 0.8865 (p0) REVERT: A 31 ASN cc_start: 0.9418 (p0) cc_final: 0.9021 (p0) REVERT: A 45 ARG cc_start: 0.8873 (OUTLIER) cc_final: 0.8433 (tpp80) REVERT: A 90 ASN cc_start: 0.9149 (t0) cc_final: 0.8621 (t0) REVERT: A 98 TRP cc_start: 0.9240 (t60) cc_final: 0.8854 (t60) REVERT: A 102 THR cc_start: 0.9215 (OUTLIER) cc_final: 0.9010 (p) REVERT: A 192 ASN cc_start: 0.9066 (OUTLIER) cc_final: 0.8865 (p0) REVERT: A 204 GLU cc_start: 0.8722 (tp30) cc_final: 0.8493 (tt0) REVERT: A 225 LYS cc_start: 0.8833 (mmmt) cc_final: 0.8507 (mmmt) REVERT: E 24 ASP cc_start: 0.8833 (t0) cc_final: 0.8601 (t0) REVERT: E 36 VAL cc_start: 0.8905 (p) cc_final: 0.8316 (m) REVERT: E 49 MET cc_start: 0.9096 (ptm) cc_final: 0.8357 (ppp) REVERT: E 55 MET cc_start: 0.9285 (ttm) cc_final: 0.9049 (ttm) REVERT: E 155 GLU cc_start: 0.8543 (mt-10) cc_final: 0.8293 (mt-10) REVERT: E 207 ARG cc_start: 0.8928 (ttm-80) cc_final: 0.8701 (ttm-80) REVERT: E 208 LEU cc_start: 0.9350 (mt) cc_final: 0.9138 (mp) REVERT: E 237 TRP cc_start: 0.7670 (m-10) cc_final: 0.7377 (m-10) REVERT: E 282 ASP cc_start: 0.8722 (m-30) cc_final: 0.8448 (m-30) REVERT: E 312 ARG cc_start: 0.7938 (tpp-160) cc_final: 0.7641 (mtt180) REVERT: E 428 ARG cc_start: 0.7639 (ptp90) cc_final: 0.7112 (ptm160) REVERT: C 49 MET cc_start: 0.8588 (OUTLIER) cc_final: 0.8115 (ptm) REVERT: C 55 MET cc_start: 0.9017 (ttm) cc_final: 0.8734 (tpp) REVERT: C 84 ASP cc_start: 0.8641 (t0) cc_final: 0.8221 (t0) REVERT: C 112 LYS cc_start: 0.9244 (mtpp) cc_final: 0.8738 (ttpp) REVERT: C 153 GLU cc_start: 0.8866 (OUTLIER) cc_final: 0.8349 (tp30) REVERT: C 162 ASP cc_start: 0.9199 (m-30) cc_final: 0.8525 (t70) REVERT: C 173 LYS cc_start: 0.9427 (mmtm) cc_final: 0.9156 (mmtm) REVERT: C 207 ARG cc_start: 0.8948 (ttm-80) cc_final: 0.8723 (ttm-80) REVERT: C 279 LYS cc_start: 0.9276 (mtpt) cc_final: 0.8876 (mtmm) REVERT: C 282 ASP cc_start: 0.9149 (m-30) cc_final: 0.8268 (m-30) REVERT: C 303 ASN cc_start: 0.7851 (OUTLIER) cc_final: 0.7354 (m-40) REVERT: D 17 ASP cc_start: 0.9290 (m-30) cc_final: 0.8969 (m-30) REVERT: D 28 ARG cc_start: 0.8892 (ptt90) cc_final: 0.8501 (ppt90) REVERT: D 49 MET cc_start: 0.9121 (ppp) cc_final: 0.8592 (ppp) REVERT: D 55 MET cc_start: 0.9545 (mtt) cc_final: 0.9146 (mmm) REVERT: D 100 ASN cc_start: 0.8452 (p0) cc_final: 0.7511 (p0) REVERT: D 137 MET cc_start: 0.8930 (mmm) cc_final: 0.8693 (mmm) REVERT: D 138 MET cc_start: 0.9582 (mmt) cc_final: 0.9147 (tpp) REVERT: D 153 GLU cc_start: 0.8423 (mt-10) cc_final: 0.7500 (mt-10) REVERT: D 190 GLU cc_start: 0.8246 (tt0) cc_final: 0.7600 (tm-30) REVERT: D 191 HIS cc_start: 0.7247 (m-70) cc_final: 0.6526 (m-70) REVERT: D 207 ARG cc_start: 0.8097 (ttm170) cc_final: 0.7613 (ttm170) REVERT: D 235 LEU cc_start: 0.8628 (mp) cc_final: 0.8340 (tt) REVERT: D 279 LYS cc_start: 0.8804 (mptt) cc_final: 0.8403 (mptt) REVERT: D 282 ASP cc_start: 0.9215 (m-30) cc_final: 0.8936 (m-30) REVERT: D 299 TYR cc_start: 0.7614 (t80) cc_final: 0.7249 (t80) REVERT: D 423 ILE cc_start: 0.8519 (tp) cc_final: 0.8295 (tt) outliers start: 100 outliers final: 67 residues processed: 573 average time/residue: 0.1322 time to fit residues: 113.7306 Evaluate side-chains 573 residues out of total 1787 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 77 poor density : 496 time to evaluate : 0.623 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain K residue 20 LEU Chi-restraints excluded: chain K residue 28 THR Chi-restraints excluded: chain K residue 38 ARG Chi-restraints excluded: chain K residue 111 ASN Chi-restraints excluded: chain K residue 122 THR Chi-restraints excluded: chain L residue 20 LEU Chi-restraints excluded: chain L residue 57 SER Chi-restraints excluded: chain L residue 91 THR Chi-restraints excluded: chain L residue 106 LEU Chi-restraints excluded: chain O residue 37 PHE Chi-restraints excluded: chain O residue 113 ASP Chi-restraints excluded: chain B residue 38 VAL Chi-restraints excluded: chain B residue 46 SER Chi-restraints excluded: chain B residue 101 ASP Chi-restraints excluded: chain B residue 102 LYS Chi-restraints excluded: chain B residue 138 MET Chi-restraints excluded: chain B residue 189 VAL Chi-restraints excluded: chain B residue 210 LEU Chi-restraints excluded: chain B residue 212 PHE Chi-restraints excluded: chain B residue 255 ILE Chi-restraints excluded: chain B residue 259 LEU Chi-restraints excluded: chain B residue 268 LEU Chi-restraints excluded: chain B residue 285 LEU Chi-restraints excluded: chain B residue 288 CYS Chi-restraints excluded: chain B residue 303 ASN Chi-restraints excluded: chain B residue 437 LEU Chi-restraints excluded: chain A residue 30 ASP Chi-restraints excluded: chain A residue 45 ARG Chi-restraints excluded: chain A residue 51 THR Chi-restraints excluded: chain A residue 58 ASP Chi-restraints excluded: chain A residue 102 THR Chi-restraints excluded: chain A residue 117 THR Chi-restraints excluded: chain A residue 131 LEU Chi-restraints excluded: chain A residue 134 MET Chi-restraints excluded: chain A residue 156 CYS Chi-restraints excluded: chain A residue 189 SER Chi-restraints excluded: chain A residue 192 ASN Chi-restraints excluded: chain A residue 237 CYS Chi-restraints excluded: chain A residue 243 LEU Chi-restraints excluded: chain A residue 287 THR Chi-restraints excluded: chain A residue 304 LEU Chi-restraints excluded: chain A residue 411 LEU Chi-restraints excluded: chain A residue 418 LEU Chi-restraints excluded: chain E residue 38 VAL Chi-restraints excluded: chain E residue 40 MET Chi-restraints excluded: chain E residue 99 LEU Chi-restraints excluded: chain E residue 100 ASN Chi-restraints excluded: chain E residue 125 LEU Chi-restraints excluded: chain E residue 156 SER Chi-restraints excluded: chain E residue 198 VAL Chi-restraints excluded: chain E residue 225 THR Chi-restraints excluded: chain C residue 12 VAL Chi-restraints excluded: chain C residue 49 MET Chi-restraints excluded: chain C residue 69 ASP Chi-restraints excluded: chain C residue 91 LEU Chi-restraints excluded: chain C residue 153 GLU Chi-restraints excluded: chain C residue 165 GLU Chi-restraints excluded: chain C residue 175 VAL Chi-restraints excluded: chain C residue 181 ILE Chi-restraints excluded: chain C residue 194 VAL Chi-restraints excluded: chain C residue 247 SER Chi-restraints excluded: chain C residue 285 LEU Chi-restraints excluded: chain C residue 303 ASN Chi-restraints excluded: chain C residue 425 ARG Chi-restraints excluded: chain C residue 437 LEU Chi-restraints excluded: chain D residue 38 VAL Chi-restraints excluded: chain D residue 99 LEU Chi-restraints excluded: chain D residue 125 LEU Chi-restraints excluded: chain D residue 188 ILE Chi-restraints excluded: chain D residue 198 VAL Chi-restraints excluded: chain D residue 212 PHE Chi-restraints excluded: chain D residue 236 SER Chi-restraints excluded: chain D residue 264 ILE Chi-restraints excluded: chain D residue 268 LEU Chi-restraints excluded: chain D residue 275 ILE Chi-restraints excluded: chain D residue 439 ASN Chi-restraints excluded: chain D residue 440 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 201 random chunks: chunk 109 optimal weight: 0.0970 chunk 140 optimal weight: 0.9980 chunk 21 optimal weight: 7.9990 chunk 32 optimal weight: 5.9990 chunk 104 optimal weight: 0.9980 chunk 30 optimal weight: 7.9990 chunk 96 optimal weight: 0.6980 chunk 115 optimal weight: 0.4980 chunk 129 optimal weight: 3.9990 chunk 13 optimal weight: 9.9990 chunk 141 optimal weight: 3.9990 overall best weight: 0.6578 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** L 111 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 191 HIS A 278 ASN ** E 191 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 265 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 303 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3564 r_free = 0.3564 target = 0.091966 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3334 r_free = 0.3334 target = 0.077971 restraints weight = 51083.413| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 48)----------------| | r_work = 0.3379 r_free = 0.3379 target = 0.080759 restraints weight = 25164.608| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3407 r_free = 0.3407 target = 0.082559 restraints weight = 15061.240| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3427 r_free = 0.3427 target = 0.083806 restraints weight = 10188.131| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 39)----------------| | r_work = 0.3443 r_free = 0.3443 target = 0.084713 restraints weight = 7524.322| |-----------------------------------------------------------------------------| r_work (final): 0.3427 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7899 moved from start: 0.5371 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 17543 Z= 0.139 Angle : 0.871 21.044 23924 Z= 0.385 Chirality : 0.049 0.448 2766 Planarity : 0.005 0.124 2913 Dihedral : 10.925 96.494 3154 Min Nonbonded Distance : 2.325 Molprobity Statistics. All-atom Clashscore : 10.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.45 % Favored : 96.55 % Rotamer: Outliers : 4.20 % Allowed : 24.12 % Favored : 71.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.02 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.28 (0.19), residues: 2027 helix: -0.09 (0.24), residues: 472 sheet: -0.66 (0.22), residues: 558 loop : -1.27 (0.20), residues: 997 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.027 0.001 ARG D 196 TYR 0.023 0.001 TYR E 299 PHE 0.016 0.001 PHE K 37 TRP 0.017 0.001 TRP E 67 HIS 0.004 0.001 HIS B 119 Details of bonding type rmsd covalent geometry : bond 0.00295 (17485) covalent geometry : angle 0.81761 (23777) SS BOND : bond 0.00443 ( 9) SS BOND : angle 2.09372 ( 18) hydrogen bonds : bond 0.03719 ( 569) hydrogen bonds : angle 4.76386 ( 1749) Misc. bond : bond 0.00197 ( 6) link_ALPHA1-3 : bond 0.01475 ( 9) link_ALPHA1-3 : angle 4.19941 ( 27) link_ALPHA1-6 : bond 0.01670 ( 5) link_ALPHA1-6 : angle 2.62749 ( 15) link_BETA1-4 : bond 0.01078 ( 19) link_BETA1-4 : angle 3.88861 ( 57) link_NAG-ASN : bond 0.00460 ( 10) link_NAG-ASN : angle 4.90935 ( 30) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4054 Ramachandran restraints generated. 2027 Oldfield, 0 Emsley, 2027 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4054 Ramachandran restraints generated. 2027 Oldfield, 0 Emsley, 2027 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 625 residues out of total 1787 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 75 poor density : 550 time to evaluate : 0.622 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: K 36 TRP cc_start: 0.8719 (m100) cc_final: 0.8478 (m100) REVERT: K 45 ARG cc_start: 0.8477 (ptt180) cc_final: 0.7711 (ptp-170) REVERT: K 73 ASP cc_start: 0.7294 (t0) cc_final: 0.7074 (t0) REVERT: K 89 GLU cc_start: 0.9210 (mp0) cc_final: 0.8878 (pm20) REVERT: K 99 LYS cc_start: 0.9192 (ttpt) cc_final: 0.8656 (tttt) REVERT: L 1 GLN cc_start: 0.9163 (mm-40) cc_final: 0.8279 (mp10) REVERT: L 29 PHE cc_start: 0.8749 (t80) cc_final: 0.8444 (t80) REVERT: L 30 ASN cc_start: 0.9350 (m110) cc_final: 0.8764 (p0) REVERT: L 83 MET cc_start: 0.8214 (pmt) cc_final: 0.6949 (ppp) REVERT: L 99 LYS cc_start: 0.9053 (ptpp) cc_final: 0.8759 (ptpp) REVERT: L 103 SER cc_start: 0.7988 (m) cc_final: 0.7711 (m) REVERT: L 120 GLN cc_start: 0.7942 (tp-100) cc_final: 0.7609 (tp-100) REVERT: O 30 ASN cc_start: 0.8686 (p0) cc_final: 0.7904 (p0) REVERT: O 36 TRP cc_start: 0.8676 (m100) cc_final: 0.8213 (m100) REVERT: O 38 ARG cc_start: 0.8817 (ttp-170) cc_final: 0.8393 (mtm110) REVERT: O 67 ARG cc_start: 0.7616 (mtp180) cc_final: 0.7092 (mtp180) REVERT: O 77 ASN cc_start: 0.9479 (m-40) cc_final: 0.9252 (p0) REVERT: O 84 ASN cc_start: 0.7738 (t0) cc_final: 0.7296 (t0) REVERT: O 85 ASN cc_start: 0.8881 (m110) cc_final: 0.7938 (m110) REVERT: O 89 GLU cc_start: 0.8932 (pt0) cc_final: 0.8681 (pm20) REVERT: O 99 LYS cc_start: 0.8415 (ttpm) cc_final: 0.7485 (tttp) REVERT: O 103 SER cc_start: 0.8065 (t) cc_final: 0.7475 (m) REVERT: O 106 LEU cc_start: 0.7789 (pt) cc_final: 0.7558 (mp) REVERT: O 111 ASN cc_start: 0.9010 (t0) cc_final: 0.8335 (t0) REVERT: B 21 LYS cc_start: 0.9474 (tttt) cc_final: 0.9252 (tmmt) REVERT: B 30 ASP cc_start: 0.8977 (m-30) cc_final: 0.8217 (t0) REVERT: B 49 MET cc_start: 0.9104 (ptm) cc_final: 0.8574 (ppp) REVERT: B 55 MET cc_start: 0.9015 (mmm) cc_final: 0.8556 (mmm) REVERT: B 67 TRP cc_start: 0.8482 (p90) cc_final: 0.8165 (p90) REVERT: B 69 ASP cc_start: 0.9212 (t0) cc_final: 0.8948 (t70) REVERT: B 86 ARG cc_start: 0.9376 (tpp80) cc_final: 0.9004 (tpp80) REVERT: B 90 GLN cc_start: 0.9115 (mt0) cc_final: 0.8649 (mp10) REVERT: B 95 ASP cc_start: 0.8833 (p0) cc_final: 0.8525 (p0) REVERT: B 101 ASP cc_start: 0.8701 (OUTLIER) cc_final: 0.8235 (t70) REVERT: B 102 LYS cc_start: 0.9408 (mtmt) cc_final: 0.9161 (mtmt) REVERT: B 182 GLU cc_start: 0.7784 (pm20) cc_final: 0.7519 (pm20) REVERT: B 190 GLU cc_start: 0.8603 (mt-10) cc_final: 0.8279 (mt-10) REVERT: B 192 ARG cc_start: 0.8231 (mtm-85) cc_final: 0.7788 (mtm-85) REVERT: B 229 SER cc_start: 0.9244 (m) cc_final: 0.8912 (p) REVERT: B 301 PHE cc_start: 0.5974 (OUTLIER) cc_final: 0.5700 (m-80) REVERT: A 23 ASP cc_start: 0.9304 (m-30) cc_final: 0.8853 (p0) REVERT: A 31 ASN cc_start: 0.9391 (p0) cc_final: 0.8989 (p0) REVERT: A 45 ARG cc_start: 0.8906 (OUTLIER) cc_final: 0.8475 (tpp80) REVERT: A 61 MET cc_start: 0.9081 (mtt) cc_final: 0.8829 (mtt) REVERT: A 87 LEU cc_start: 0.9527 (mt) cc_final: 0.9312 (mm) REVERT: A 90 ASN cc_start: 0.9131 (t0) cc_final: 0.8703 (t0) REVERT: A 98 TRP cc_start: 0.9184 (t60) cc_final: 0.8825 (t60) REVERT: A 102 THR cc_start: 0.9164 (OUTLIER) cc_final: 0.8900 (p) REVERT: A 225 LYS cc_start: 0.8841 (mmmt) cc_final: 0.8439 (mmmt) REVERT: A 239 MET cc_start: 0.8587 (mtt) cc_final: 0.8282 (mtm) REVERT: A 264 THR cc_start: 0.9013 (m) cc_final: 0.8770 (p) REVERT: E 49 MET cc_start: 0.9071 (ptm) cc_final: 0.8289 (ppp) REVERT: E 153 GLU cc_start: 0.8498 (mt-10) cc_final: 0.8275 (mt-10) REVERT: E 155 GLU cc_start: 0.8595 (mt-10) cc_final: 0.8321 (mt-10) REVERT: E 208 LEU cc_start: 0.9300 (mt) cc_final: 0.9083 (mp) REVERT: E 282 ASP cc_start: 0.8737 (m-30) cc_final: 0.8435 (m-30) REVERT: E 312 ARG cc_start: 0.7809 (tpp-160) cc_final: 0.7484 (mtt180) REVERT: E 428 ARG cc_start: 0.7505 (ptp90) cc_final: 0.6878 (ptm160) REVERT: C 49 MET cc_start: 0.8585 (OUTLIER) cc_final: 0.8014 (ptm) REVERT: C 55 MET cc_start: 0.9046 (ttm) cc_final: 0.8692 (tpp) REVERT: C 84 ASP cc_start: 0.8600 (t0) cc_final: 0.8291 (t0) REVERT: C 112 LYS cc_start: 0.9199 (mtpp) cc_final: 0.8900 (mtpp) REVERT: C 153 GLU cc_start: 0.8835 (OUTLIER) cc_final: 0.8193 (tp30) REVERT: C 162 ASP cc_start: 0.9156 (m-30) cc_final: 0.8526 (t70) REVERT: C 209 SER cc_start: 0.9623 (t) cc_final: 0.8794 (t) REVERT: C 279 LYS cc_start: 0.9283 (mtpt) cc_final: 0.8877 (mtmm) REVERT: C 282 ASP cc_start: 0.9130 (m-30) cc_final: 0.8187 (m-30) REVERT: C 303 ASN cc_start: 0.7228 (OUTLIER) cc_final: 0.6928 (m-40) REVERT: D 13 LYS cc_start: 0.9226 (tttm) cc_final: 0.8915 (tttp) REVERT: D 17 ASP cc_start: 0.9238 (m-30) cc_final: 0.8913 (m-30) REVERT: D 28 ARG cc_start: 0.8848 (ptt90) cc_final: 0.8508 (ppt90) REVERT: D 49 MET cc_start: 0.9201 (ppp) cc_final: 0.8597 (ppp) REVERT: D 55 MET cc_start: 0.9538 (mtt) cc_final: 0.9106 (mmm) REVERT: D 100 ASN cc_start: 0.8449 (p0) cc_final: 0.7548 (p0) REVERT: D 137 MET cc_start: 0.8920 (mmm) cc_final: 0.8578 (mmm) REVERT: D 138 MET cc_start: 0.9553 (mmt) cc_final: 0.9160 (tpp) REVERT: D 153 GLU cc_start: 0.8351 (mt-10) cc_final: 0.6956 (mt-10) REVERT: D 190 GLU cc_start: 0.8204 (tt0) cc_final: 0.7659 (tm-30) REVERT: D 191 HIS cc_start: 0.6918 (m-70) cc_final: 0.6391 (m-70) REVERT: D 207 ARG cc_start: 0.8118 (ttm170) cc_final: 0.7096 (ttm170) REVERT: D 235 LEU cc_start: 0.8642 (mp) cc_final: 0.8351 (tt) REVERT: D 279 LYS cc_start: 0.8792 (mptt) cc_final: 0.8456 (mptt) REVERT: D 282 ASP cc_start: 0.9185 (m-30) cc_final: 0.8928 (m-30) REVERT: D 299 TYR cc_start: 0.7601 (t80) cc_final: 0.7226 (t80) REVERT: D 423 ILE cc_start: 0.8615 (tp) cc_final: 0.8337 (tt) outliers start: 75 outliers final: 51 residues processed: 587 average time/residue: 0.1324 time to fit residues: 116.8634 Evaluate side-chains 563 residues out of total 1787 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 505 time to evaluate : 0.665 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain K residue 38 ARG Chi-restraints excluded: chain K residue 122 THR Chi-restraints excluded: chain L residue 20 LEU Chi-restraints excluded: chain L residue 57 SER Chi-restraints excluded: chain L residue 84 ASN Chi-restraints excluded: chain L residue 91 THR Chi-restraints excluded: chain L residue 106 LEU Chi-restraints excluded: chain L residue 123 VAL Chi-restraints excluded: chain O residue 113 ASP Chi-restraints excluded: chain B residue 38 VAL Chi-restraints excluded: chain B residue 46 SER Chi-restraints excluded: chain B residue 101 ASP Chi-restraints excluded: chain B residue 138 MET Chi-restraints excluded: chain B residue 210 LEU Chi-restraints excluded: chain B residue 212 PHE Chi-restraints excluded: chain B residue 255 ILE Chi-restraints excluded: chain B residue 259 LEU Chi-restraints excluded: chain B residue 268 LEU Chi-restraints excluded: chain B residue 301 PHE Chi-restraints excluded: chain B residue 303 ASN Chi-restraints excluded: chain A residue 30 ASP Chi-restraints excluded: chain A residue 45 ARG Chi-restraints excluded: chain A residue 51 THR Chi-restraints excluded: chain A residue 58 ASP Chi-restraints excluded: chain A residue 102 THR Chi-restraints excluded: chain A residue 156 CYS Chi-restraints excluded: chain A residue 195 HIS Chi-restraints excluded: chain A residue 237 CYS Chi-restraints excluded: chain A residue 243 LEU Chi-restraints excluded: chain A residue 287 THR Chi-restraints excluded: chain A residue 411 LEU Chi-restraints excluded: chain A residue 418 LEU Chi-restraints excluded: chain E residue 38 VAL Chi-restraints excluded: chain E residue 40 MET Chi-restraints excluded: chain E residue 99 LEU Chi-restraints excluded: chain E residue 125 LEU Chi-restraints excluded: chain E residue 156 SER Chi-restraints excluded: chain E residue 198 VAL Chi-restraints excluded: chain E residue 225 THR Chi-restraints excluded: chain C residue 12 VAL Chi-restraints excluded: chain C residue 49 MET Chi-restraints excluded: chain C residue 69 ASP Chi-restraints excluded: chain C residue 91 LEU Chi-restraints excluded: chain C residue 125 LEU Chi-restraints excluded: chain C residue 153 GLU Chi-restraints excluded: chain C residue 165 GLU Chi-restraints excluded: chain C residue 181 ILE Chi-restraints excluded: chain C residue 223 LEU Chi-restraints excluded: chain C residue 247 SER Chi-restraints excluded: chain C residue 303 ASN Chi-restraints excluded: chain D residue 38 VAL Chi-restraints excluded: chain D residue 99 LEU Chi-restraints excluded: chain D residue 198 VAL Chi-restraints excluded: chain D residue 212 PHE Chi-restraints excluded: chain D residue 234 ILE Chi-restraints excluded: chain D residue 264 ILE Chi-restraints excluded: chain D residue 268 LEU Chi-restraints excluded: chain D residue 440 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 201 random chunks: chunk 31 optimal weight: 0.9990 chunk 37 optimal weight: 3.9990 chunk 115 optimal weight: 1.9990 chunk 22 optimal weight: 7.9990 chunk 59 optimal weight: 1.9990 chunk 195 optimal weight: 4.9990 chunk 120 optimal weight: 8.9990 chunk 41 optimal weight: 3.9990 chunk 98 optimal weight: 0.9980 chunk 71 optimal weight: 3.9990 chunk 146 optimal weight: 7.9990 overall best weight: 1.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: K 30 ASN ** K 120 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 111 ASN ** B 185 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 191 HIS E 148 GLN ** E 191 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 265 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 303 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3525 r_free = 0.3525 target = 0.089611 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3291 r_free = 0.3291 target = 0.075694 restraints weight = 51908.636| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3336 r_free = 0.3336 target = 0.078451 restraints weight = 25589.050| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3364 r_free = 0.3364 target = 0.080229 restraints weight = 15283.470| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3385 r_free = 0.3385 target = 0.081476 restraints weight = 10313.865| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3400 r_free = 0.3400 target = 0.082353 restraints weight = 7651.889| |-----------------------------------------------------------------------------| r_work (final): 0.3388 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7933 moved from start: 0.5571 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 17543 Z= 0.176 Angle : 0.899 20.060 23924 Z= 0.399 Chirality : 0.049 0.431 2766 Planarity : 0.005 0.166 2913 Dihedral : 10.277 98.378 3154 Min Nonbonded Distance : 2.158 Molprobity Statistics. All-atom Clashscore : 12.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.13 % Favored : 94.87 % Rotamer: Outliers : 4.87 % Allowed : 24.73 % Favored : 70.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.02 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.18 (0.19), residues: 2027 helix: 0.15 (0.24), residues: 472 sheet: -0.55 (0.22), residues: 578 loop : -1.36 (0.21), residues: 977 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.027 0.001 ARG D 196 TYR 0.020 0.001 TYR B 299 PHE 0.016 0.001 PHE D 293 TRP 0.019 0.002 TRP E 67 HIS 0.005 0.001 HIS B 119 Details of bonding type rmsd covalent geometry : bond 0.00388 (17485) covalent geometry : angle 0.84996 (23777) SS BOND : bond 0.00428 ( 9) SS BOND : angle 2.16130 ( 18) hydrogen bonds : bond 0.03825 ( 569) hydrogen bonds : angle 4.76419 ( 1749) Misc. bond : bond 0.00235 ( 6) link_ALPHA1-3 : bond 0.01458 ( 9) link_ALPHA1-3 : angle 3.96030 ( 27) link_ALPHA1-6 : bond 0.01439 ( 5) link_ALPHA1-6 : angle 2.62348 ( 15) link_BETA1-4 : bond 0.01014 ( 19) link_BETA1-4 : angle 3.79322 ( 57) link_NAG-ASN : bond 0.00570 ( 10) link_NAG-ASN : angle 4.85606 ( 30) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4054 Ramachandran restraints generated. 2027 Oldfield, 0 Emsley, 2027 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4054 Ramachandran restraints generated. 2027 Oldfield, 0 Emsley, 2027 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 598 residues out of total 1787 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 87 poor density : 511 time to evaluate : 0.662 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: K 36 TRP cc_start: 0.8752 (m100) cc_final: 0.8532 (m100) REVERT: K 45 ARG cc_start: 0.8556 (ptt180) cc_final: 0.7821 (ptp-170) REVERT: K 89 GLU cc_start: 0.9231 (mp0) cc_final: 0.8908 (pm20) REVERT: L 1 GLN cc_start: 0.9186 (mm-40) cc_final: 0.8307 (mp10) REVERT: L 4 LEU cc_start: 0.8755 (mt) cc_final: 0.8206 (mt) REVERT: L 30 ASN cc_start: 0.9372 (m110) cc_final: 0.8789 (p0) REVERT: L 83 MET cc_start: 0.8279 (pmt) cc_final: 0.7102 (ppp) REVERT: L 111 ASN cc_start: 0.9265 (m-40) cc_final: 0.8959 (m-40) REVERT: L 120 GLN cc_start: 0.7921 (tp-100) cc_final: 0.7589 (tp-100) REVERT: O 30 ASN cc_start: 0.8787 (p0) cc_final: 0.7883 (p0) REVERT: O 36 TRP cc_start: 0.8680 (m100) cc_final: 0.8244 (m100) REVERT: O 67 ARG cc_start: 0.7744 (mtp180) cc_final: 0.6679 (mtp180) REVERT: O 84 ASN cc_start: 0.7688 (t0) cc_final: 0.6349 (t0) REVERT: O 85 ASN cc_start: 0.8932 (m110) cc_final: 0.7938 (p0) REVERT: O 89 GLU cc_start: 0.8979 (pt0) cc_final: 0.8699 (pm20) REVERT: O 99 LYS cc_start: 0.8517 (ttpm) cc_final: 0.7812 (tttp) REVERT: O 103 SER cc_start: 0.8024 (t) cc_final: 0.7014 (t) REVERT: O 111 ASN cc_start: 0.9025 (t0) cc_final: 0.8458 (t0) REVERT: B 21 LYS cc_start: 0.9475 (tttt) cc_final: 0.9256 (tmmt) REVERT: B 30 ASP cc_start: 0.9008 (m-30) cc_final: 0.8281 (t0) REVERT: B 49 MET cc_start: 0.9148 (ptm) cc_final: 0.8558 (ppp) REVERT: B 55 MET cc_start: 0.9191 (mmm) cc_final: 0.8991 (tpt) REVERT: B 67 TRP cc_start: 0.8589 (p90) cc_final: 0.8209 (p90) REVERT: B 86 ARG cc_start: 0.9428 (tpp80) cc_final: 0.9003 (tpp80) REVERT: B 90 GLN cc_start: 0.9162 (mt0) cc_final: 0.8691 (mp10) REVERT: B 95 ASP cc_start: 0.8932 (p0) cc_final: 0.8634 (p0) REVERT: B 101 ASP cc_start: 0.8651 (OUTLIER) cc_final: 0.8236 (t70) REVERT: B 102 LYS cc_start: 0.9389 (mtmt) cc_final: 0.9131 (mtmt) REVERT: B 147 GLU cc_start: 0.8985 (mm-30) cc_final: 0.8679 (mm-30) REVERT: B 182 GLU cc_start: 0.7903 (pm20) cc_final: 0.7495 (pm20) REVERT: B 192 ARG cc_start: 0.8242 (mtm-85) cc_final: 0.7881 (mtm-85) REVERT: B 229 SER cc_start: 0.9259 (m) cc_final: 0.8938 (p) REVERT: B 286 MET cc_start: 0.9047 (tpt) cc_final: 0.8748 (tpt) REVERT: B 426 TRP cc_start: 0.7126 (OUTLIER) cc_final: 0.6230 (m-10) REVERT: A 31 ASN cc_start: 0.9410 (p0) cc_final: 0.8985 (p0) REVERT: A 45 ARG cc_start: 0.8852 (OUTLIER) cc_final: 0.8301 (tpp80) REVERT: A 87 LEU cc_start: 0.9517 (mt) cc_final: 0.9316 (mm) REVERT: A 90 ASN cc_start: 0.9214 (t0) cc_final: 0.8775 (t0) REVERT: A 98 TRP cc_start: 0.9217 (t60) cc_final: 0.8813 (t60) REVERT: A 186 GLU cc_start: 0.8409 (pm20) cc_final: 0.8181 (pm20) REVERT: A 190 ARG cc_start: 0.8235 (ptp-170) cc_final: 0.7935 (ptt-90) REVERT: A 225 LYS cc_start: 0.8803 (mmmt) cc_final: 0.8387 (mmmt) REVERT: A 264 THR cc_start: 0.8963 (m) cc_final: 0.8694 (p) REVERT: E 49 MET cc_start: 0.9086 (ptm) cc_final: 0.8255 (ppp) REVERT: E 282 ASP cc_start: 0.8732 (m-30) cc_final: 0.8434 (m-30) REVERT: E 312 ARG cc_start: 0.7874 (tpp-160) cc_final: 0.7510 (ttt180) REVERT: E 428 ARG cc_start: 0.7628 (ptp90) cc_final: 0.7141 (ptm160) REVERT: C 49 MET cc_start: 0.8643 (OUTLIER) cc_final: 0.7937 (ptm) REVERT: C 64 GLN cc_start: 0.9172 (mm110) cc_final: 0.8870 (mm110) REVERT: C 84 ASP cc_start: 0.8612 (t0) cc_final: 0.8276 (t0) REVERT: C 112 LYS cc_start: 0.9261 (mtpp) cc_final: 0.8717 (ttmm) REVERT: C 153 GLU cc_start: 0.8899 (OUTLIER) cc_final: 0.8580 (tp30) REVERT: C 261 MET cc_start: 0.9052 (mmt) cc_final: 0.8658 (tpt) REVERT: C 279 LYS cc_start: 0.9250 (mtpt) cc_final: 0.8921 (mtmm) REVERT: C 282 ASP cc_start: 0.9145 (m-30) cc_final: 0.8455 (m-30) REVERT: C 288 CYS cc_start: 0.9366 (OUTLIER) cc_final: 0.8460 (t) REVERT: C 303 ASN cc_start: 0.7284 (OUTLIER) cc_final: 0.7056 (m110) REVERT: D 13 LYS cc_start: 0.9317 (tttm) cc_final: 0.8894 (tttp) REVERT: D 17 ASP cc_start: 0.9266 (m-30) cc_final: 0.8901 (m-30) REVERT: D 28 ARG cc_start: 0.8925 (ptt90) cc_final: 0.8518 (ppt90) REVERT: D 49 MET cc_start: 0.9267 (ppp) cc_final: 0.8535 (ppp) REVERT: D 55 MET cc_start: 0.9565 (mtt) cc_final: 0.9128 (mmm) REVERT: D 100 ASN cc_start: 0.8520 (p0) cc_final: 0.7599 (p0) REVERT: D 137 MET cc_start: 0.8898 (mmm) cc_final: 0.8617 (mmm) REVERT: D 138 MET cc_start: 0.9545 (mmt) cc_final: 0.9088 (mmt) REVERT: D 153 GLU cc_start: 0.8451 (mt-10) cc_final: 0.7424 (mt-10) REVERT: D 190 GLU cc_start: 0.8286 (tt0) cc_final: 0.7673 (tm-30) REVERT: D 191 HIS cc_start: 0.7018 (m-70) cc_final: 0.6463 (m-70) REVERT: D 207 ARG cc_start: 0.8048 (ttm170) cc_final: 0.7181 (ttm170) REVERT: D 235 LEU cc_start: 0.8612 (mp) cc_final: 0.8321 (tt) REVERT: D 279 LYS cc_start: 0.8795 (mptt) cc_final: 0.8360 (mptt) REVERT: D 282 ASP cc_start: 0.9182 (m-30) cc_final: 0.8871 (m-30) REVERT: D 299 TYR cc_start: 0.7685 (t80) cc_final: 0.7249 (t80) outliers start: 87 outliers final: 63 residues processed: 563 average time/residue: 0.1304 time to fit residues: 110.8493 Evaluate side-chains 564 residues out of total 1787 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 494 time to evaluate : 0.670 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain K residue 11 LEU Chi-restraints excluded: chain K residue 38 ARG Chi-restraints excluded: chain K residue 122 THR Chi-restraints excluded: chain L residue 20 LEU Chi-restraints excluded: chain L residue 84 ASN Chi-restraints excluded: chain L residue 91 THR Chi-restraints excluded: chain L residue 106 LEU Chi-restraints excluded: chain L residue 123 VAL Chi-restraints excluded: chain O residue 113 ASP Chi-restraints excluded: chain B residue 101 ASP Chi-restraints excluded: chain B residue 136 CYS Chi-restraints excluded: chain B residue 138 MET Chi-restraints excluded: chain B residue 210 LEU Chi-restraints excluded: chain B residue 212 PHE Chi-restraints excluded: chain B residue 255 ILE Chi-restraints excluded: chain B residue 259 LEU Chi-restraints excluded: chain B residue 268 LEU Chi-restraints excluded: chain B residue 285 LEU Chi-restraints excluded: chain B residue 426 TRP Chi-restraints excluded: chain B residue 437 LEU Chi-restraints excluded: chain A residue 30 ASP Chi-restraints excluded: chain A residue 45 ARG Chi-restraints excluded: chain A residue 58 ASP Chi-restraints excluded: chain A residue 130 LEU Chi-restraints excluded: chain A residue 131 LEU Chi-restraints excluded: chain A residue 156 CYS Chi-restraints excluded: chain A residue 189 SER Chi-restraints excluded: chain A residue 195 HIS Chi-restraints excluded: chain A residue 243 LEU Chi-restraints excluded: chain A residue 287 THR Chi-restraints excluded: chain A residue 304 LEU Chi-restraints excluded: chain A residue 411 LEU Chi-restraints excluded: chain A residue 418 LEU Chi-restraints excluded: chain E residue 38 VAL Chi-restraints excluded: chain E residue 40 MET Chi-restraints excluded: chain E residue 99 LEU Chi-restraints excluded: chain E residue 100 ASN Chi-restraints excluded: chain E residue 125 LEU Chi-restraints excluded: chain E residue 148 GLN Chi-restraints excluded: chain E residue 156 SER Chi-restraints excluded: chain E residue 198 VAL Chi-restraints excluded: chain E residue 218 ILE Chi-restraints excluded: chain E residue 225 THR Chi-restraints excluded: chain C residue 12 VAL Chi-restraints excluded: chain C residue 25 ILE Chi-restraints excluded: chain C residue 36 VAL Chi-restraints excluded: chain C residue 49 MET Chi-restraints excluded: chain C residue 69 ASP Chi-restraints excluded: chain C residue 91 LEU Chi-restraints excluded: chain C residue 125 LEU Chi-restraints excluded: chain C residue 153 GLU Chi-restraints excluded: chain C residue 181 ILE Chi-restraints excluded: chain C residue 194 VAL Chi-restraints excluded: chain C residue 223 LEU Chi-restraints excluded: chain C residue 247 SER Chi-restraints excluded: chain C residue 288 CYS Chi-restraints excluded: chain C residue 289 PHE Chi-restraints excluded: chain C residue 303 ASN Chi-restraints excluded: chain C residue 425 ARG Chi-restraints excluded: chain C residue 437 LEU Chi-restraints excluded: chain C residue 440 LEU Chi-restraints excluded: chain D residue 38 VAL Chi-restraints excluded: chain D residue 145 LEU Chi-restraints excluded: chain D residue 188 ILE Chi-restraints excluded: chain D residue 198 VAL Chi-restraints excluded: chain D residue 212 PHE Chi-restraints excluded: chain D residue 234 ILE Chi-restraints excluded: chain D residue 236 SER Chi-restraints excluded: chain D residue 264 ILE Chi-restraints excluded: chain D residue 440 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 201 random chunks: chunk 72 optimal weight: 9.9990 chunk 49 optimal weight: 4.9990 chunk 173 optimal weight: 6.9990 chunk 14 optimal weight: 4.9990 chunk 17 optimal weight: 7.9990 chunk 114 optimal weight: 6.9990 chunk 40 optimal weight: 3.9990 chunk 47 optimal weight: 5.9990 chunk 61 optimal weight: 0.2980 chunk 6 optimal weight: 3.9990 chunk 27 optimal weight: 7.9990 overall best weight: 3.6588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** K 120 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 191 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 148 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 191 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 265 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 303 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3472 r_free = 0.3472 target = 0.086524 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3238 r_free = 0.3238 target = 0.073013 restraints weight = 53363.483| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3283 r_free = 0.3283 target = 0.075625 restraints weight = 26377.997| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3311 r_free = 0.3311 target = 0.077354 restraints weight = 15873.891| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3332 r_free = 0.3332 target = 0.078586 restraints weight = 10798.606| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.3347 r_free = 0.3347 target = 0.079435 restraints weight = 7868.869| |-----------------------------------------------------------------------------| r_work (final): 0.3337 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8006 moved from start: 0.5800 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.062 17543 Z= 0.264 Angle : 0.949 16.497 23924 Z= 0.432 Chirality : 0.051 0.412 2766 Planarity : 0.005 0.082 2913 Dihedral : 10.251 102.151 3154 Min Nonbonded Distance : 2.269 Molprobity Statistics. All-atom Clashscore : 15.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.51 % Favored : 93.49 % Rotamer: Outliers : 5.54 % Allowed : 24.01 % Favored : 70.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.02 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.37 (0.19), residues: 2027 helix: -0.02 (0.23), residues: 472 sheet: -0.71 (0.21), residues: 599 loop : -1.45 (0.21), residues: 956 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG E 196 TYR 0.023 0.002 TYR A 163 PHE 0.021 0.002 PHE E 291 TRP 0.025 0.002 TRP A 291 HIS 0.006 0.002 HIS E 107 Details of bonding type rmsd covalent geometry : bond 0.00573 (17485) covalent geometry : angle 0.90177 (23777) SS BOND : bond 0.00739 ( 9) SS BOND : angle 2.79676 ( 18) hydrogen bonds : bond 0.04269 ( 569) hydrogen bonds : angle 4.92762 ( 1749) Misc. bond : bond 0.00739 ( 6) link_ALPHA1-3 : bond 0.01172 ( 9) link_ALPHA1-3 : angle 3.91374 ( 27) link_ALPHA1-6 : bond 0.00931 ( 5) link_ALPHA1-6 : angle 2.56934 ( 15) link_BETA1-4 : bond 0.00960 ( 19) link_BETA1-4 : angle 3.77141 ( 57) link_NAG-ASN : bond 0.00553 ( 10) link_NAG-ASN : angle 5.05269 ( 30) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4054 Ramachandran restraints generated. 2027 Oldfield, 0 Emsley, 2027 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4054 Ramachandran restraints generated. 2027 Oldfield, 0 Emsley, 2027 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 589 residues out of total 1787 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 99 poor density : 490 time to evaluate : 0.677 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: K 36 TRP cc_start: 0.8819 (m100) cc_final: 0.8577 (m100) REVERT: K 81 LEU cc_start: 0.7861 (mp) cc_final: 0.7605 (mp) REVERT: K 89 GLU cc_start: 0.9239 (mp0) cc_final: 0.8909 (pm20) REVERT: K 102 TYR cc_start: 0.9122 (m-80) cc_final: 0.8898 (m-10) REVERT: L 1 GLN cc_start: 0.9196 (mm-40) cc_final: 0.8337 (mp10) REVERT: L 4 LEU cc_start: 0.8798 (mt) cc_final: 0.8276 (mt) REVERT: L 29 PHE cc_start: 0.8698 (t80) cc_final: 0.8301 (t80) REVERT: L 30 ASN cc_start: 0.9371 (m110) cc_final: 0.8862 (p0) REVERT: L 83 MET cc_start: 0.8228 (pmt) cc_final: 0.7213 (ppp) REVERT: L 111 ASN cc_start: 0.9360 (m-40) cc_final: 0.9133 (m-40) REVERT: O 30 ASN cc_start: 0.8757 (p0) cc_final: 0.7984 (p0) REVERT: O 36 TRP cc_start: 0.8774 (m100) cc_final: 0.8304 (m100) REVERT: O 84 ASN cc_start: 0.7927 (t0) cc_final: 0.6761 (t0) REVERT: O 85 ASN cc_start: 0.9010 (m110) cc_final: 0.8200 (p0) REVERT: O 99 LYS cc_start: 0.8649 (ttpm) cc_final: 0.7577 (tttp) REVERT: O 103 SER cc_start: 0.8202 (t) cc_final: 0.6778 (t) REVERT: O 106 LEU cc_start: 0.7826 (pt) cc_final: 0.7546 (pp) REVERT: O 111 ASN cc_start: 0.9051 (t0) cc_final: 0.8219 (t0) REVERT: B 21 LYS cc_start: 0.9480 (tttt) cc_final: 0.9272 (tmmt) REVERT: B 30 ASP cc_start: 0.9048 (m-30) cc_final: 0.8213 (t0) REVERT: B 49 MET cc_start: 0.9163 (ptm) cc_final: 0.8500 (ppp) REVERT: B 90 GLN cc_start: 0.9193 (mt0) cc_final: 0.8730 (mp10) REVERT: B 95 ASP cc_start: 0.9062 (p0) cc_final: 0.8739 (p0) REVERT: B 101 ASP cc_start: 0.8622 (OUTLIER) cc_final: 0.8254 (p0) REVERT: B 182 GLU cc_start: 0.7992 (pm20) cc_final: 0.7541 (pm20) REVERT: B 192 ARG cc_start: 0.8325 (mtm-85) cc_final: 0.7959 (mtm-85) REVERT: B 224 GLN cc_start: 0.9444 (tp40) cc_final: 0.9004 (tp40) REVERT: B 229 SER cc_start: 0.9290 (m) cc_final: 0.8989 (p) REVERT: B 286 MET cc_start: 0.9076 (tpt) cc_final: 0.8772 (tpt) REVERT: B 426 TRP cc_start: 0.7035 (OUTLIER) cc_final: 0.6052 (m-10) REVERT: A 31 ASN cc_start: 0.9462 (p0) cc_final: 0.9029 (p0) REVERT: A 45 ARG cc_start: 0.8856 (OUTLIER) cc_final: 0.8430 (tpp80) REVERT: A 61 MET cc_start: 0.9072 (mtt) cc_final: 0.8795 (mtt) REVERT: A 90 ASN cc_start: 0.9294 (t0) cc_final: 0.8970 (t0) REVERT: A 98 TRP cc_start: 0.9231 (t60) cc_final: 0.8793 (t60) REVERT: A 190 ARG cc_start: 0.8166 (ptp-170) cc_final: 0.7775 (ptt-90) REVERT: A 225 LYS cc_start: 0.8815 (mmmt) cc_final: 0.8460 (mmmt) REVERT: A 239 MET cc_start: 0.8690 (mtt) cc_final: 0.8396 (mtm) REVERT: A 264 THR cc_start: 0.9079 (m) cc_final: 0.8822 (p) REVERT: E 49 MET cc_start: 0.9105 (ptm) cc_final: 0.8284 (ppp) REVERT: E 153 GLU cc_start: 0.8556 (mt-10) cc_final: 0.7662 (mt-10) REVERT: E 182 GLU cc_start: 0.8038 (mm-30) cc_final: 0.7690 (mm-30) REVERT: E 207 ARG cc_start: 0.8854 (ttm-80) cc_final: 0.7348 (ttm-80) REVERT: E 282 ASP cc_start: 0.8839 (m-30) cc_final: 0.8526 (m-30) REVERT: E 312 ARG cc_start: 0.7821 (tpp-160) cc_final: 0.7405 (ttt180) REVERT: E 428 ARG cc_start: 0.7643 (ptp90) cc_final: 0.7339 (ptm160) REVERT: C 49 MET cc_start: 0.8606 (OUTLIER) cc_final: 0.8032 (ptm) REVERT: C 55 MET cc_start: 0.8989 (ttm) cc_final: 0.8530 (tpp) REVERT: C 64 GLN cc_start: 0.9206 (mm110) cc_final: 0.8796 (mm-40) REVERT: C 84 ASP cc_start: 0.8724 (t0) cc_final: 0.8416 (t0) REVERT: C 112 LYS cc_start: 0.9323 (mtpp) cc_final: 0.8742 (ttmm) REVERT: C 153 GLU cc_start: 0.8912 (OUTLIER) cc_final: 0.8602 (tp30) REVERT: C 179 GLU cc_start: 0.8962 (mp0) cc_final: 0.8655 (mp0) REVERT: C 261 MET cc_start: 0.9106 (mmt) cc_final: 0.8771 (mmm) REVERT: C 279 LYS cc_start: 0.9279 (mtpt) cc_final: 0.8955 (mtmm) REVERT: C 282 ASP cc_start: 0.9121 (m-30) cc_final: 0.8405 (m-30) REVERT: C 288 CYS cc_start: 0.9295 (OUTLIER) cc_final: 0.8626 (t) REVERT: D 13 LYS cc_start: 0.9340 (tttm) cc_final: 0.8954 (tttp) REVERT: D 17 ASP cc_start: 0.9278 (m-30) cc_final: 0.8951 (m-30) REVERT: D 28 ARG cc_start: 0.8937 (ptt90) cc_final: 0.8562 (ppt90) REVERT: D 49 MET cc_start: 0.9295 (ppp) cc_final: 0.8887 (ppp) REVERT: D 55 MET cc_start: 0.9565 (mtt) cc_final: 0.9155 (mmm) REVERT: D 100 ASN cc_start: 0.8615 (p0) cc_final: 0.7790 (p0) REVERT: D 137 MET cc_start: 0.8884 (mmm) cc_final: 0.8571 (mmm) REVERT: D 138 MET cc_start: 0.9450 (mmt) cc_final: 0.9006 (mmt) REVERT: D 153 GLU cc_start: 0.8490 (mt-10) cc_final: 0.7907 (mt-10) REVERT: D 190 GLU cc_start: 0.8309 (tt0) cc_final: 0.7540 (tm-30) REVERT: D 191 HIS cc_start: 0.7427 (m-70) cc_final: 0.6565 (m-70) REVERT: D 207 ARG cc_start: 0.8110 (ttm170) cc_final: 0.7557 (ttm170) REVERT: D 217 ASN cc_start: 0.9049 (m-40) cc_final: 0.8824 (t0) REVERT: D 235 LEU cc_start: 0.8636 (mp) cc_final: 0.8305 (tt) REVERT: D 279 LYS cc_start: 0.8833 (mptt) cc_final: 0.8233 (mptt) REVERT: D 282 ASP cc_start: 0.9205 (m-30) cc_final: 0.8900 (m-30) REVERT: D 299 TYR cc_start: 0.7700 (t80) cc_final: 0.7250 (t80) outliers start: 99 outliers final: 77 residues processed: 547 average time/residue: 0.1292 time to fit residues: 107.4922 Evaluate side-chains 565 residues out of total 1787 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 83 poor density : 482 time to evaluate : 0.625 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain K residue 7 SER Chi-restraints excluded: chain K residue 11 LEU Chi-restraints excluded: chain K residue 28 THR Chi-restraints excluded: chain K residue 38 ARG Chi-restraints excluded: chain K residue 122 THR Chi-restraints excluded: chain L residue 20 LEU Chi-restraints excluded: chain L residue 57 SER Chi-restraints excluded: chain L residue 84 ASN Chi-restraints excluded: chain L residue 91 THR Chi-restraints excluded: chain L residue 106 LEU Chi-restraints excluded: chain O residue 113 ASP Chi-restraints excluded: chain B residue 38 VAL Chi-restraints excluded: chain B residue 101 ASP Chi-restraints excluded: chain B residue 136 CYS Chi-restraints excluded: chain B residue 189 VAL Chi-restraints excluded: chain B residue 212 PHE Chi-restraints excluded: chain B residue 255 ILE Chi-restraints excluded: chain B residue 259 LEU Chi-restraints excluded: chain B residue 261 MET Chi-restraints excluded: chain B residue 268 LEU Chi-restraints excluded: chain B residue 285 LEU Chi-restraints excluded: chain B residue 288 CYS Chi-restraints excluded: chain B residue 426 TRP Chi-restraints excluded: chain A residue 30 ASP Chi-restraints excluded: chain A residue 45 ARG Chi-restraints excluded: chain A residue 51 THR Chi-restraints excluded: chain A residue 58 ASP Chi-restraints excluded: chain A residue 130 LEU Chi-restraints excluded: chain A residue 131 LEU Chi-restraints excluded: chain A residue 156 CYS Chi-restraints excluded: chain A residue 189 SER Chi-restraints excluded: chain A residue 195 HIS Chi-restraints excluded: chain A residue 243 LEU Chi-restraints excluded: chain A residue 263 VAL Chi-restraints excluded: chain A residue 270 THR Chi-restraints excluded: chain A residue 287 THR Chi-restraints excluded: chain A residue 304 LEU Chi-restraints excluded: chain A residue 411 LEU Chi-restraints excluded: chain A residue 418 LEU Chi-restraints excluded: chain E residue 25 ILE Chi-restraints excluded: chain E residue 38 VAL Chi-restraints excluded: chain E residue 40 MET Chi-restraints excluded: chain E residue 100 ASN Chi-restraints excluded: chain E residue 125 LEU Chi-restraints excluded: chain E residue 156 SER Chi-restraints excluded: chain E residue 198 VAL Chi-restraints excluded: chain E residue 215 LYS Chi-restraints excluded: chain E residue 225 THR Chi-restraints excluded: chain E residue 227 MET Chi-restraints excluded: chain E residue 435 PHE Chi-restraints excluded: chain C residue 12 VAL Chi-restraints excluded: chain C residue 25 ILE Chi-restraints excluded: chain C residue 36 VAL Chi-restraints excluded: chain C residue 49 MET Chi-restraints excluded: chain C residue 69 ASP Chi-restraints excluded: chain C residue 91 LEU Chi-restraints excluded: chain C residue 125 LEU Chi-restraints excluded: chain C residue 153 GLU Chi-restraints excluded: chain C residue 181 ILE Chi-restraints excluded: chain C residue 194 VAL Chi-restraints excluded: chain C residue 223 LEU Chi-restraints excluded: chain C residue 247 SER Chi-restraints excluded: chain C residue 255 ILE Chi-restraints excluded: chain C residue 259 LEU Chi-restraints excluded: chain C residue 285 LEU Chi-restraints excluded: chain C residue 288 CYS Chi-restraints excluded: chain C residue 289 PHE Chi-restraints excluded: chain C residue 425 ARG Chi-restraints excluded: chain C residue 437 LEU Chi-restraints excluded: chain C residue 440 LEU Chi-restraints excluded: chain D residue 38 VAL Chi-restraints excluded: chain D residue 125 LEU Chi-restraints excluded: chain D residue 145 LEU Chi-restraints excluded: chain D residue 188 ILE Chi-restraints excluded: chain D residue 198 VAL Chi-restraints excluded: chain D residue 212 PHE Chi-restraints excluded: chain D residue 234 ILE Chi-restraints excluded: chain D residue 236 SER Chi-restraints excluded: chain D residue 242 ILE Chi-restraints excluded: chain D residue 264 ILE Chi-restraints excluded: chain D residue 278 VAL Chi-restraints excluded: chain D residue 439 ASN Chi-restraints excluded: chain D residue 440 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 201 random chunks: chunk 5 optimal weight: 4.9990 chunk 28 optimal weight: 0.1980 chunk 48 optimal weight: 2.9990 chunk 197 optimal weight: 2.9990 chunk 121 optimal weight: 0.0000 chunk 168 optimal weight: 2.9990 chunk 19 optimal weight: 0.9980 chunk 65 optimal weight: 0.9990 chunk 137 optimal weight: 0.7980 chunk 119 optimal weight: 0.9990 chunk 175 optimal weight: 3.9990 overall best weight: 0.5986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: K 30 ASN K 111 ASN ** K 120 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 191 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 148 GLN ** E 185 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 191 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 265 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 185 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3533 r_free = 0.3533 target = 0.090206 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3302 r_free = 0.3302 target = 0.076360 restraints weight = 51356.488| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3347 r_free = 0.3347 target = 0.079100 restraints weight = 25146.409| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3375 r_free = 0.3375 target = 0.080906 restraints weight = 15044.248| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3392 r_free = 0.3392 target = 0.081985 restraints weight = 10114.546| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3408 r_free = 0.3408 target = 0.082977 restraints weight = 7709.100| |-----------------------------------------------------------------------------| r_work (final): 0.3400 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7919 moved from start: 0.5971 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 17543 Z= 0.142 Angle : 0.919 19.488 23924 Z= 0.411 Chirality : 0.050 0.410 2766 Planarity : 0.005 0.151 2913 Dihedral : 9.613 101.424 3154 Min Nonbonded Distance : 2.259 Molprobity Statistics. All-atom Clashscore : 12.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.09 % Favored : 95.91 % Rotamer: Outliers : 3.30 % Allowed : 26.69 % Favored : 70.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.02 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.06 (0.19), residues: 2027 helix: 0.16 (0.24), residues: 468 sheet: -0.36 (0.22), residues: 557 loop : -1.29 (0.20), residues: 1002 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.021 0.001 ARG D 196 TYR 0.019 0.001 TYR E 220 PHE 0.019 0.001 PHE L 29 TRP 0.016 0.001 TRP E 237 HIS 0.005 0.001 HIS B 119 Details of bonding type rmsd covalent geometry : bond 0.00310 (17485) covalent geometry : angle 0.87579 (23777) SS BOND : bond 0.00708 ( 9) SS BOND : angle 2.32836 ( 18) hydrogen bonds : bond 0.03715 ( 569) hydrogen bonds : angle 4.69766 ( 1749) Misc. bond : bond 0.00136 ( 6) link_ALPHA1-3 : bond 0.01554 ( 9) link_ALPHA1-3 : angle 3.99956 ( 27) link_ALPHA1-6 : bond 0.01152 ( 5) link_ALPHA1-6 : angle 1.77319 ( 15) link_BETA1-4 : bond 0.00920 ( 19) link_BETA1-4 : angle 3.59138 ( 57) link_NAG-ASN : bond 0.00537 ( 10) link_NAG-ASN : angle 4.66421 ( 30) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4054 Ramachandran restraints generated. 2027 Oldfield, 0 Emsley, 2027 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4054 Ramachandran restraints generated. 2027 Oldfield, 0 Emsley, 2027 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 581 residues out of total 1787 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 522 time to evaluate : 0.720 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: K 45 ARG cc_start: 0.8425 (ptt180) cc_final: 0.8025 (ptp-170) REVERT: K 89 GLU cc_start: 0.9219 (mp0) cc_final: 0.8878 (pm20) REVERT: K 99 LYS cc_start: 0.9131 (ttpt) cc_final: 0.8355 (tttt) REVERT: K 102 TYR cc_start: 0.9066 (m-80) cc_final: 0.8863 (m-10) REVERT: K 111 ASN cc_start: 0.9106 (t160) cc_final: 0.8759 (t0) REVERT: L 1 GLN cc_start: 0.9224 (mm-40) cc_final: 0.8380 (mp10) REVERT: L 29 PHE cc_start: 0.8679 (t80) cc_final: 0.8251 (t80) REVERT: L 30 ASN cc_start: 0.9351 (m110) cc_final: 0.8776 (p0) REVERT: L 39 GLN cc_start: 0.9022 (tt0) cc_final: 0.8356 (tp40) REVERT: L 83 MET cc_start: 0.8308 (pmt) cc_final: 0.7123 (ppp) REVERT: L 120 GLN cc_start: 0.7918 (tp-100) cc_final: 0.7627 (tp-100) REVERT: O 30 ASN cc_start: 0.8780 (p0) cc_final: 0.7869 (p0) REVERT: O 36 TRP cc_start: 0.8650 (m100) cc_final: 0.8095 (m100) REVERT: O 65 LYS cc_start: 0.9331 (tptp) cc_final: 0.9087 (tptp) REVERT: O 67 ARG cc_start: 0.7938 (mtp180) cc_final: 0.6879 (mtp180) REVERT: O 84 ASN cc_start: 0.7812 (t0) cc_final: 0.6555 (t0) REVERT: O 85 ASN cc_start: 0.8893 (m110) cc_final: 0.7752 (p0) REVERT: O 87 LYS cc_start: 0.9279 (mtpp) cc_final: 0.8963 (mtpp) REVERT: O 89 GLU cc_start: 0.8867 (pm20) cc_final: 0.8545 (pm20) REVERT: O 99 LYS cc_start: 0.8509 (ttpm) cc_final: 0.7532 (tttp) REVERT: O 103 SER cc_start: 0.7966 (t) cc_final: 0.6596 (t) REVERT: O 111 ASN cc_start: 0.9005 (t0) cc_final: 0.8205 (t0) REVERT: B 17 ASP cc_start: 0.8825 (m-30) cc_final: 0.8343 (m-30) REVERT: B 30 ASP cc_start: 0.8959 (m-30) cc_final: 0.8174 (t0) REVERT: B 49 MET cc_start: 0.9128 (ptm) cc_final: 0.8524 (ppp) REVERT: B 55 MET cc_start: 0.9465 (tpt) cc_final: 0.9262 (tpt) REVERT: B 67 TRP cc_start: 0.8536 (p90) cc_final: 0.8119 (p90) REVERT: B 86 ARG cc_start: 0.9399 (tpp80) cc_final: 0.8927 (tpp80) REVERT: B 90 GLN cc_start: 0.9154 (mt0) cc_final: 0.8678 (mp10) REVERT: B 95 ASP cc_start: 0.8975 (p0) cc_final: 0.8577 (p0) REVERT: B 101 ASP cc_start: 0.8583 (p0) cc_final: 0.8253 (p0) REVERT: B 182 GLU cc_start: 0.7749 (pm20) cc_final: 0.7413 (pm20) REVERT: B 192 ARG cc_start: 0.8223 (mtm-85) cc_final: 0.7857 (mtm-85) REVERT: B 229 SER cc_start: 0.9292 (m) cc_final: 0.8977 (p) REVERT: B 426 TRP cc_start: 0.6983 (OUTLIER) cc_final: 0.5997 (m-10) REVERT: A 31 ASN cc_start: 0.9440 (p0) cc_final: 0.8937 (p0) REVERT: A 45 ARG cc_start: 0.8866 (OUTLIER) cc_final: 0.8339 (tpp80) REVERT: A 61 MET cc_start: 0.9064 (mtt) cc_final: 0.8805 (mtt) REVERT: A 71 GLN cc_start: 0.9265 (mt0) cc_final: 0.8946 (mp10) REVERT: A 87 LEU cc_start: 0.9526 (mt) cc_final: 0.9323 (mm) REVERT: A 90 ASN cc_start: 0.9239 (t0) cc_final: 0.8922 (t0) REVERT: A 98 TRP cc_start: 0.9207 (t60) cc_final: 0.8857 (t60) REVERT: A 225 LYS cc_start: 0.8829 (mmmt) cc_final: 0.8431 (mmmt) REVERT: A 239 MET cc_start: 0.8627 (mtt) cc_final: 0.8317 (mtm) REVERT: A 264 THR cc_start: 0.9028 (m) cc_final: 0.8787 (p) REVERT: E 49 MET cc_start: 0.9058 (ptm) cc_final: 0.8317 (ppp) REVERT: E 153 GLU cc_start: 0.8498 (mt-10) cc_final: 0.8034 (mt-10) REVERT: E 207 ARG cc_start: 0.8632 (ttm-80) cc_final: 0.7476 (ttm-80) REVERT: E 282 ASP cc_start: 0.8830 (m-30) cc_final: 0.8511 (m-30) REVERT: E 312 ARG cc_start: 0.7759 (tpp-160) cc_final: 0.7344 (ttt180) REVERT: E 428 ARG cc_start: 0.7531 (ptp90) cc_final: 0.7284 (ttt-90) REVERT: C 49 MET cc_start: 0.8615 (OUTLIER) cc_final: 0.8107 (ptm) REVERT: C 55 MET cc_start: 0.9048 (ttm) cc_final: 0.8602 (tpp) REVERT: C 64 GLN cc_start: 0.9216 (mm110) cc_final: 0.8944 (mm-40) REVERT: C 84 ASP cc_start: 0.8652 (t0) cc_final: 0.8411 (t0) REVERT: C 85 ASN cc_start: 0.9074 (p0) cc_final: 0.8812 (p0) REVERT: C 112 LYS cc_start: 0.9283 (mtpp) cc_final: 0.8623 (ttmm) REVERT: C 179 GLU cc_start: 0.8973 (mp0) cc_final: 0.8701 (mp0) REVERT: C 209 SER cc_start: 0.9637 (t) cc_final: 0.9274 (p) REVERT: C 279 LYS cc_start: 0.9312 (mtpt) cc_final: 0.9000 (mtmm) REVERT: C 282 ASP cc_start: 0.9134 (m-30) cc_final: 0.8441 (m-30) REVERT: C 303 ASN cc_start: 0.7289 (m-40) cc_final: 0.6932 (m110) REVERT: D 13 LYS cc_start: 0.9256 (tttm) cc_final: 0.8834 (tttp) REVERT: D 14 GLU cc_start: 0.9423 (pt0) cc_final: 0.8924 (tm-30) REVERT: D 17 ASP cc_start: 0.9293 (m-30) cc_final: 0.8947 (m-30) REVERT: D 18 LYS cc_start: 0.9644 (mmmm) cc_final: 0.9398 (mtpp) REVERT: D 28 ARG cc_start: 0.8887 (ptt90) cc_final: 0.8521 (ppt90) REVERT: D 49 MET cc_start: 0.9299 (ppp) cc_final: 0.8846 (ppp) REVERT: D 55 MET cc_start: 0.9570 (mtt) cc_final: 0.9130 (mmm) REVERT: D 84 ASP cc_start: 0.9214 (t70) cc_final: 0.8991 (t0) REVERT: D 85 ASN cc_start: 0.9199 (p0) cc_final: 0.8854 (p0) REVERT: D 100 ASN cc_start: 0.8665 (p0) cc_final: 0.7809 (p0) REVERT: D 137 MET cc_start: 0.8939 (mmm) cc_final: 0.8626 (mmm) REVERT: D 138 MET cc_start: 0.9503 (mmt) cc_final: 0.9084 (mmt) REVERT: D 153 GLU cc_start: 0.8429 (mt-10) cc_final: 0.8106 (mt-10) REVERT: D 190 GLU cc_start: 0.8306 (tt0) cc_final: 0.7645 (tm-30) REVERT: D 191 HIS cc_start: 0.7063 (m-70) cc_final: 0.6351 (m-70) REVERT: D 215 LYS cc_start: 0.9484 (tttm) cc_final: 0.9239 (tptm) REVERT: D 235 LEU cc_start: 0.8610 (mp) cc_final: 0.8315 (tt) REVERT: D 279 LYS cc_start: 0.8829 (mptt) cc_final: 0.8382 (mptt) REVERT: D 282 ASP cc_start: 0.9155 (m-30) cc_final: 0.8874 (m-30) REVERT: D 299 TYR cc_start: 0.7645 (t80) cc_final: 0.7197 (t80) outliers start: 59 outliers final: 47 residues processed: 557 average time/residue: 0.1349 time to fit residues: 112.9022 Evaluate side-chains 551 residues out of total 1787 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 501 time to evaluate : 0.708 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain K residue 7 SER Chi-restraints excluded: chain K residue 11 LEU Chi-restraints excluded: chain K residue 122 THR Chi-restraints excluded: chain L residue 20 LEU Chi-restraints excluded: chain L residue 57 SER Chi-restraints excluded: chain L residue 84 ASN Chi-restraints excluded: chain L residue 91 THR Chi-restraints excluded: chain L residue 106 LEU Chi-restraints excluded: chain O residue 113 ASP Chi-restraints excluded: chain B residue 212 PHE Chi-restraints excluded: chain B residue 255 ILE Chi-restraints excluded: chain B residue 259 LEU Chi-restraints excluded: chain B residue 268 LEU Chi-restraints excluded: chain B residue 426 TRP Chi-restraints excluded: chain A residue 30 ASP Chi-restraints excluded: chain A residue 45 ARG Chi-restraints excluded: chain A residue 51 THR Chi-restraints excluded: chain A residue 58 ASP Chi-restraints excluded: chain A residue 130 LEU Chi-restraints excluded: chain A residue 156 CYS Chi-restraints excluded: chain A residue 189 SER Chi-restraints excluded: chain A residue 195 HIS Chi-restraints excluded: chain A residue 243 LEU Chi-restraints excluded: chain A residue 411 LEU Chi-restraints excluded: chain A residue 418 LEU Chi-restraints excluded: chain E residue 38 VAL Chi-restraints excluded: chain E residue 40 MET Chi-restraints excluded: chain E residue 100 ASN Chi-restraints excluded: chain E residue 125 LEU Chi-restraints excluded: chain E residue 148 GLN Chi-restraints excluded: chain E residue 156 SER Chi-restraints excluded: chain E residue 198 VAL Chi-restraints excluded: chain E residue 225 THR Chi-restraints excluded: chain E residue 227 MET Chi-restraints excluded: chain E residue 265 ASN Chi-restraints excluded: chain C residue 12 VAL Chi-restraints excluded: chain C residue 25 ILE Chi-restraints excluded: chain C residue 36 VAL Chi-restraints excluded: chain C residue 49 MET Chi-restraints excluded: chain C residue 69 ASP Chi-restraints excluded: chain C residue 91 LEU Chi-restraints excluded: chain C residue 223 LEU Chi-restraints excluded: chain C residue 247 SER Chi-restraints excluded: chain D residue 38 VAL Chi-restraints excluded: chain D residue 145 LEU Chi-restraints excluded: chain D residue 198 VAL Chi-restraints excluded: chain D residue 212 PHE Chi-restraints excluded: chain D residue 236 SER Chi-restraints excluded: chain D residue 278 VAL Chi-restraints excluded: chain D residue 440 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 201 random chunks: chunk 153 optimal weight: 10.0000 chunk 134 optimal weight: 3.9990 chunk 13 optimal weight: 4.9990 chunk 190 optimal weight: 3.9990 chunk 104 optimal weight: 0.9980 chunk 1 optimal weight: 0.5980 chunk 105 optimal weight: 0.9980 chunk 85 optimal weight: 0.7980 chunk 4 optimal weight: 5.9990 chunk 80 optimal weight: 9.9990 chunk 184 optimal weight: 0.9980 overall best weight: 0.8780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** K 120 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 191 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 148 GLN ** E 185 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 191 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 265 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 439 ASN ** D 185 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 = 0.3541 r_free = 0.3541 target = 0.090595 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3313 r_free = 0.3313 target = 0.076769 restraints weight = 51021.896| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3357 r_free = 0.3357 target = 0.079483 restraints weight = 25034.465| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3387 r_free = 0.3387 target = 0.081339 restraints weight = 14995.687| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3405 r_free = 0.3405 target = 0.082513 restraints weight = 10053.426| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 36)----------------| | r_work = 0.3420 r_free = 0.3420 target = 0.083418 restraints weight = 7418.698| |-----------------------------------------------------------------------------| r_work (final): 0.3406 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7910 moved from start: 0.6151 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.058 17543 Z= 0.149 Angle : 0.941 18.130 23924 Z= 0.423 Chirality : 0.050 0.431 2766 Planarity : 0.006 0.165 2913 Dihedral : 9.364 101.812 3154 Min Nonbonded Distance : 2.276 Molprobity Statistics. All-atom Clashscore : 12.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.29 % Favored : 95.71 % Rotamer: Outliers : 3.19 % Allowed : 27.14 % Favored : 69.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.02 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.05 (0.19), residues: 2027 helix: 0.16 (0.24), residues: 472 sheet: -0.13 (0.24), residues: 482 loop : -1.37 (0.20), residues: 1073 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.039 0.001 ARG E 196 TYR 0.017 0.001 TYR B 244 PHE 0.018 0.001 PHE L 29 TRP 0.032 0.002 TRP K 36 HIS 0.004 0.001 HIS B 119 Details of bonding type rmsd covalent geometry : bond 0.00333 (17485) covalent geometry : angle 0.90028 (23777) SS BOND : bond 0.00643 ( 9) SS BOND : angle 2.23513 ( 18) hydrogen bonds : bond 0.03691 ( 569) hydrogen bonds : angle 4.69099 ( 1749) Misc. bond : bond 0.00355 ( 6) link_ALPHA1-3 : bond 0.01542 ( 9) link_ALPHA1-3 : angle 3.85664 ( 27) link_ALPHA1-6 : bond 0.00974 ( 5) link_ALPHA1-6 : angle 1.78147 ( 15) link_BETA1-4 : bond 0.01019 ( 19) link_BETA1-4 : angle 3.52924 ( 57) link_NAG-ASN : bond 0.00612 ( 10) link_NAG-ASN : angle 4.72635 ( 30) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4054 Ramachandran restraints generated. 2027 Oldfield, 0 Emsley, 2027 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4054 Ramachandran restraints generated. 2027 Oldfield, 0 Emsley, 2027 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 580 residues out of total 1787 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 523 time to evaluate : 0.672 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: K 45 ARG cc_start: 0.8522 (ptt180) cc_final: 0.8082 (ptp-170) REVERT: K 89 GLU cc_start: 0.9201 (mp0) cc_final: 0.8858 (pm20) REVERT: K 99 LYS cc_start: 0.9157 (ttpt) cc_final: 0.8473 (tttt) REVERT: K 102 TYR cc_start: 0.9124 (m-80) cc_final: 0.8911 (m-10) REVERT: K 111 ASN cc_start: 0.9135 (t160) cc_final: 0.8798 (t0) REVERT: L 1 GLN cc_start: 0.9217 (mm-40) cc_final: 0.8378 (mp10) REVERT: L 29 PHE cc_start: 0.8657 (t80) cc_final: 0.8203 (t80) REVERT: L 30 ASN cc_start: 0.9351 (m110) cc_final: 0.8769 (p0) REVERT: L 38 ARG cc_start: 0.8880 (mtm180) cc_final: 0.8660 (mtm180) REVERT: L 39 GLN cc_start: 0.9016 (tt0) cc_final: 0.8355 (tp40) REVERT: L 83 MET cc_start: 0.8270 (pmt) cc_final: 0.7244 (ppp) REVERT: L 99 LYS cc_start: 0.9058 (ptpp) cc_final: 0.8726 (ptpp) REVERT: L 111 ASN cc_start: 0.9256 (m-40) cc_final: 0.9006 (m-40) REVERT: O 30 ASN cc_start: 0.8751 (p0) cc_final: 0.7893 (p0) REVERT: O 36 TRP cc_start: 0.8629 (m100) cc_final: 0.8031 (m100) REVERT: O 65 LYS cc_start: 0.9313 (tptp) cc_final: 0.9033 (tptt) REVERT: O 67 ARG cc_start: 0.7906 (mtp180) cc_final: 0.6916 (mtp180) REVERT: O 84 ASN cc_start: 0.7835 (t0) cc_final: 0.6683 (t0) REVERT: O 85 ASN cc_start: 0.8883 (m110) cc_final: 0.7773 (p0) REVERT: O 99 LYS cc_start: 0.8549 (ttpm) cc_final: 0.7627 (tttp) REVERT: O 103 SER cc_start: 0.7962 (t) cc_final: 0.6667 (t) REVERT: O 106 LEU cc_start: 0.7651 (pt) cc_final: 0.7184 (mp) REVERT: O 111 ASN cc_start: 0.8972 (t0) cc_final: 0.8243 (t0) REVERT: B 30 ASP cc_start: 0.8933 (m-30) cc_final: 0.8173 (t70) REVERT: B 49 MET cc_start: 0.9126 (ptm) cc_final: 0.8542 (ppp) REVERT: B 55 MET cc_start: 0.9451 (tpt) cc_final: 0.9240 (tpt) REVERT: B 67 TRP cc_start: 0.8518 (p90) cc_final: 0.8155 (p90) REVERT: B 86 ARG cc_start: 0.9394 (tpp80) cc_final: 0.8915 (tpp80) REVERT: B 90 GLN cc_start: 0.9154 (mt0) cc_final: 0.8680 (mp10) REVERT: B 95 ASP cc_start: 0.9009 (p0) cc_final: 0.8609 (p0) REVERT: B 182 GLU cc_start: 0.7754 (pm20) cc_final: 0.7401 (pm20) REVERT: B 192 ARG cc_start: 0.8230 (mtm-85) cc_final: 0.7894 (mtm-85) REVERT: B 227 MET cc_start: 0.9055 (mmp) cc_final: 0.8270 (mmp) REVERT: B 229 SER cc_start: 0.9294 (m) cc_final: 0.8988 (p) REVERT: B 426 TRP cc_start: 0.6875 (OUTLIER) cc_final: 0.5899 (m-10) REVERT: A 31 ASN cc_start: 0.9412 (p0) cc_final: 0.8875 (p0) REVERT: A 45 ARG cc_start: 0.8845 (OUTLIER) cc_final: 0.8306 (tpp80) REVERT: A 61 MET cc_start: 0.9053 (mtt) cc_final: 0.8500 (ttm) REVERT: A 71 GLN cc_start: 0.9226 (mt0) cc_final: 0.8915 (mp10) REVERT: A 90 ASN cc_start: 0.9227 (t0) cc_final: 0.8922 (t0) REVERT: A 98 TRP cc_start: 0.9214 (t60) cc_final: 0.8812 (t60) REVERT: A 225 LYS cc_start: 0.8799 (mmmt) cc_final: 0.8420 (mmmt) REVERT: A 239 MET cc_start: 0.8626 (mtt) cc_final: 0.8280 (mtm) REVERT: A 264 THR cc_start: 0.8977 (m) cc_final: 0.8763 (p) REVERT: E 49 MET cc_start: 0.9050 (ptm) cc_final: 0.8342 (ppp) REVERT: E 153 GLU cc_start: 0.8432 (mt-10) cc_final: 0.7078 (mt-10) REVERT: E 207 ARG cc_start: 0.8462 (ttm-80) cc_final: 0.7264 (ttm-80) REVERT: E 282 ASP cc_start: 0.8783 (m-30) cc_final: 0.8469 (m-30) REVERT: E 312 ARG cc_start: 0.7780 (tpp-160) cc_final: 0.7352 (ttt180) REVERT: E 428 ARG cc_start: 0.7493 (ptp90) cc_final: 0.7263 (ttt-90) REVERT: E 444 LEU cc_start: 0.8634 (mt) cc_final: 0.8212 (pp) REVERT: C 49 MET cc_start: 0.8610 (OUTLIER) cc_final: 0.8068 (ptm) REVERT: C 55 MET cc_start: 0.9024 (ttm) cc_final: 0.8583 (tpp) REVERT: C 64 GLN cc_start: 0.9190 (mm110) cc_final: 0.8900 (mm110) REVERT: C 84 ASP cc_start: 0.8623 (t0) cc_final: 0.8341 (t0) REVERT: C 112 LYS cc_start: 0.9283 (mtpp) cc_final: 0.8674 (ttmm) REVERT: C 207 ARG cc_start: 0.9169 (ttm-80) cc_final: 0.8847 (ttm-80) REVERT: C 209 SER cc_start: 0.9467 (t) cc_final: 0.9200 (t) REVERT: C 279 LYS cc_start: 0.9308 (mtpt) cc_final: 0.9025 (mtmm) REVERT: C 282 ASP cc_start: 0.9140 (m-30) cc_final: 0.8452 (m-30) REVERT: C 303 ASN cc_start: 0.7086 (m-40) cc_final: 0.6869 (m110) REVERT: D 13 LYS cc_start: 0.9256 (tttm) cc_final: 0.8865 (tttp) REVERT: D 14 GLU cc_start: 0.9398 (pt0) cc_final: 0.8917 (tm-30) REVERT: D 17 ASP cc_start: 0.9279 (m-30) cc_final: 0.8943 (m-30) REVERT: D 28 ARG cc_start: 0.8943 (ptt90) cc_final: 0.8560 (ppt90) REVERT: D 49 MET cc_start: 0.9294 (ppp) cc_final: 0.8837 (ppp) REVERT: D 55 MET cc_start: 0.9591 (mtt) cc_final: 0.9152 (mmm) REVERT: D 61 MET cc_start: 0.9027 (ptm) cc_final: 0.8748 (ptm) REVERT: D 85 ASN cc_start: 0.9171 (p0) cc_final: 0.8832 (p0) REVERT: D 100 ASN cc_start: 0.8662 (p0) cc_final: 0.7836 (p0) REVERT: D 137 MET cc_start: 0.8923 (mmm) cc_final: 0.8607 (mmm) REVERT: D 138 MET cc_start: 0.9496 (mmt) cc_final: 0.9068 (mmt) REVERT: D 190 GLU cc_start: 0.8269 (tt0) cc_final: 0.7679 (tm-30) REVERT: D 191 HIS cc_start: 0.6978 (m-70) cc_final: 0.6555 (m170) REVERT: D 215 LYS cc_start: 0.9487 (tttm) cc_final: 0.9188 (tptm) REVERT: D 235 LEU cc_start: 0.8613 (mp) cc_final: 0.8311 (tt) REVERT: D 279 LYS cc_start: 0.8821 (mptt) cc_final: 0.8379 (mptt) REVERT: D 282 ASP cc_start: 0.9121 (m-30) cc_final: 0.8837 (m-30) REVERT: D 299 TYR cc_start: 0.7670 (t80) cc_final: 0.7207 (t80) outliers start: 57 outliers final: 52 residues processed: 555 average time/residue: 0.1376 time to fit residues: 115.3177 Evaluate side-chains 558 residues out of total 1787 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 503 time to evaluate : 0.649 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain K residue 122 THR Chi-restraints excluded: chain L residue 20 LEU Chi-restraints excluded: chain L residue 57 SER Chi-restraints excluded: chain L residue 84 ASN Chi-restraints excluded: chain L residue 91 THR Chi-restraints excluded: chain L residue 106 LEU Chi-restraints excluded: chain L residue 123 VAL Chi-restraints excluded: chain O residue 4 LEU Chi-restraints excluded: chain O residue 37 PHE Chi-restraints excluded: chain O residue 113 ASP Chi-restraints excluded: chain B residue 212 PHE Chi-restraints excluded: chain B residue 255 ILE Chi-restraints excluded: chain B residue 259 LEU Chi-restraints excluded: chain B residue 268 LEU Chi-restraints excluded: chain B residue 426 TRP Chi-restraints excluded: chain A residue 30 ASP Chi-restraints excluded: chain A residue 45 ARG Chi-restraints excluded: chain A residue 51 THR Chi-restraints excluded: chain A residue 58 ASP Chi-restraints excluded: chain A residue 130 LEU Chi-restraints excluded: chain A residue 156 CYS Chi-restraints excluded: chain A residue 189 SER Chi-restraints excluded: chain A residue 195 HIS Chi-restraints excluded: chain A residue 243 LEU Chi-restraints excluded: chain A residue 248 PHE Chi-restraints excluded: chain A residue 411 LEU Chi-restraints excluded: chain A residue 418 LEU Chi-restraints excluded: chain E residue 38 VAL Chi-restraints excluded: chain E residue 40 MET Chi-restraints excluded: chain E residue 100 ASN Chi-restraints excluded: chain E residue 125 LEU Chi-restraints excluded: chain E residue 148 GLN Chi-restraints excluded: chain E residue 156 SER Chi-restraints excluded: chain E residue 198 VAL Chi-restraints excluded: chain E residue 208 LEU Chi-restraints excluded: chain E residue 225 THR Chi-restraints excluded: chain E residue 227 MET Chi-restraints excluded: chain E residue 265 ASN Chi-restraints excluded: chain C residue 12 VAL Chi-restraints excluded: chain C residue 25 ILE Chi-restraints excluded: chain C residue 36 VAL Chi-restraints excluded: chain C residue 49 MET Chi-restraints excluded: chain C residue 69 ASP Chi-restraints excluded: chain C residue 91 LEU Chi-restraints excluded: chain C residue 223 LEU Chi-restraints excluded: chain C residue 247 SER Chi-restraints excluded: chain C residue 285 LEU Chi-restraints excluded: chain D residue 38 VAL Chi-restraints excluded: chain D residue 125 LEU Chi-restraints excluded: chain D residue 145 LEU Chi-restraints excluded: chain D residue 198 VAL Chi-restraints excluded: chain D residue 212 PHE Chi-restraints excluded: chain D residue 236 SER Chi-restraints excluded: chain D residue 278 VAL Chi-restraints excluded: chain D residue 440 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 201 random chunks: chunk 161 optimal weight: 4.9990 chunk 73 optimal weight: 1.9990 chunk 25 optimal weight: 0.0050 chunk 68 optimal weight: 2.9990 chunk 99 optimal weight: 2.9990 chunk 28 optimal weight: 0.0000 chunk 171 optimal weight: 9.9990 chunk 196 optimal weight: 7.9990 chunk 125 optimal weight: 3.9990 chunk 144 optimal weight: 2.9990 chunk 172 optimal weight: 5.9990 overall best weight: 1.6004 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** K 120 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 148 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 191 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 148 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 185 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 191 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 265 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 191 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 185 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3524 r_free = 0.3524 target = 0.089697 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3297 r_free = 0.3297 target = 0.076005 restraints weight = 51828.660| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3341 r_free = 0.3341 target = 0.078713 restraints weight = 25439.685| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3370 r_free = 0.3370 target = 0.080502 restraints weight = 15205.551| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3389 r_free = 0.3389 target = 0.081703 restraints weight = 10226.153| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3403 r_free = 0.3403 target = 0.082579 restraints weight = 7580.376| |-----------------------------------------------------------------------------| r_work (final): 0.3390 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7930 moved from start: 0.6246 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.065 17543 Z= 0.162 Angle : 0.940 19.329 23924 Z= 0.424 Chirality : 0.050 0.403 2766 Planarity : 0.005 0.147 2913 Dihedral : 9.263 100.352 3154 Min Nonbonded Distance : 2.273 Molprobity Statistics. All-atom Clashscore : 13.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.54 % Favored : 95.46 % Rotamer: Outliers : 3.25 % Allowed : 27.53 % Favored : 69.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.02 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.04 (0.19), residues: 2027 helix: 0.14 (0.24), residues: 472 sheet: -0.22 (0.23), residues: 509 loop : -1.31 (0.20), residues: 1046 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.017 0.001 ARG E 196 TYR 0.015 0.001 TYR B 244 PHE 0.017 0.001 PHE L 29 TRP 0.026 0.002 TRP K 36 HIS 0.005 0.001 HIS B 119 Details of bonding type rmsd covalent geometry : bond 0.00365 (17485) covalent geometry : angle 0.89985 (23777) SS BOND : bond 0.00723 ( 9) SS BOND : angle 2.40803 ( 18) hydrogen bonds : bond 0.03635 ( 569) hydrogen bonds : angle 4.65634 ( 1749) Misc. bond : bond 0.00474 ( 6) link_ALPHA1-3 : bond 0.01468 ( 9) link_ALPHA1-3 : angle 3.78135 ( 27) link_ALPHA1-6 : bond 0.00825 ( 5) link_ALPHA1-6 : angle 1.89297 ( 15) link_BETA1-4 : bond 0.00878 ( 19) link_BETA1-4 : angle 3.47588 ( 57) link_NAG-ASN : bond 0.00621 ( 10) link_NAG-ASN : angle 4.60051 ( 30) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3859.83 seconds wall clock time: 67 minutes 9.03 seconds (4029.03 seconds total)