Starting phenix.real_space_refine on Wed Mar 4 22:52:47 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6w1j_21511/03_2026/6w1j_21511_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/6w1j_21511/03_2026/6w1j_21511.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.92 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/6w1j_21511/03_2026/6w1j_21511.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6w1j_21511/03_2026/6w1j_21511.map" model { file = "/net/cci-nas-00/data/ceres_data/6w1j_21511/03_2026/6w1j_21511_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6w1j_21511/03_2026/6w1j_21511_neut.cif" } resolution = 2.92 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.002 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians S 50 5.16 5 Cl 1 4.86 5 C 11085 2.51 5 N 2710 2.21 5 O 3015 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 40 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 16861 Number of models: 1 Model: "" Number of chains: 25 Chain: "A" Number of atoms: 3255 Number of conformers: 1 Conformer: "" Number of residues, atoms: 393, 3255 Classifications: {'peptide': 393} Link IDs: {'PTRANS': 20, 'TRANS': 372} Chain breaks: 1 Chain: "B" Number of atoms: 3255 Number of conformers: 1 Conformer: "" Number of residues, atoms: 393, 3255 Classifications: {'peptide': 393} Link IDs: {'PTRANS': 20, 'TRANS': 372} Chain breaks: 1 Chain: "C" Number of atoms: 3255 Number of conformers: 1 Conformer: "" Number of residues, atoms: 393, 3255 Classifications: {'peptide': 393} Link IDs: {'PTRANS': 20, 'TRANS': 372} Chain breaks: 1 Chain: "D" Number of atoms: 3255 Number of conformers: 1 Conformer: "" Number of residues, atoms: 393, 3255 Classifications: {'peptide': 393} Link IDs: {'PTRANS': 20, 'TRANS': 372} Chain breaks: 1 Chain: "E" Number of atoms: 3255 Number of conformers: 1 Conformer: "" Number of residues, atoms: 393, 3255 Classifications: {'peptide': 393} Link IDs: {'PTRANS': 20, 'TRANS': 372} Chain breaks: 1 Chain: "F" 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: 7 Unresolved non-hydrogen chiralities: 2 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: 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: "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: 7 Unresolved non-hydrogen chiralities: 2 Chain: "J" 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: "K" 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: "L" 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: 7 Unresolved non-hydrogen chiralities: 2 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: 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: "O" 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: 7 Unresolved non-hydrogen chiralities: 2 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: 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: "R" 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: 7 Unresolved non-hydrogen chiralities: 2 Chain: "S" 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: "T" 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: "A" Number of atoms: 22 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 22 Unusual residues: {'S7Y': 1} Classifications: {'undetermined': 1} Chain: "B" Number of atoms: 22 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 22 Unusual residues: {'S7Y': 1} Classifications: {'undetermined': 1} Chain: "C" Number of atoms: 22 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 22 Unusual residues: {'S7Y': 1} Classifications: {'undetermined': 1} Chain: "D" Number of atoms: 23 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 23 Unusual residues: {' CL': 1, 'S7Y': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "E" Number of atoms: 22 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 22 Unusual residues: {'S7Y': 1} Classifications: {'undetermined': 1} Time building chain proxies: 3.68, per 1000 atoms: 0.22 Number of scatterers: 16861 At special positions: 0 Unit cell: (103.456, 106, 173.84, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) Cl 1 17.00 S 50 16.00 O 3015 8.00 N 2710 7.00 C 11085 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=5, symmetry=0 Simple disulfide: pdb=" SG CYS A 135 " - pdb=" SG CYS A 149 " distance=2.03 Simple disulfide: pdb=" SG CYS B 135 " - pdb=" SG CYS B 149 " distance=2.03 Simple disulfide: pdb=" SG CYS C 135 " - pdb=" SG CYS C 149 " distance=2.03 Simple disulfide: pdb=" SG CYS D 135 " - pdb=" SG CYS D 149 " distance=2.03 Simple disulfide: pdb=" SG CYS E 135 " - pdb=" SG CYS E 149 " 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=5, symmetry=0 Links applied BETA1-4 " NAG G 1 " - " NAG G 2 " " NAG G 2 " - " BMA G 3 " " NAG H 1 " - " NAG H 2 " " NAG J 1 " - " NAG J 2 " " NAG J 2 " - " BMA J 3 " " NAG K 1 " - " NAG K 2 " " NAG M 1 " - " NAG M 2 " " NAG M 2 " - " BMA M 3 " " NAG N 1 " - " NAG N 2 " " NAG P 1 " - " NAG P 2 " " NAG P 2 " - " BMA P 3 " " NAG Q 1 " - " NAG Q 2 " " NAG S 1 " - " NAG S 2 " " NAG S 2 " - " BMA S 3 " " NAG T 1 " - " NAG T 2 " NAG-ASN " NAG F 1 " - " ASN A 82 " " NAG G 1 " - " ASN A 164 " " NAG H 1 " - " ASN A 148 " " NAG I 1 " - " ASN B 82 " " NAG J 1 " - " ASN B 164 " " NAG K 1 " - " ASN B 148 " " NAG L 1 " - " ASN C 82 " " NAG M 1 " - " ASN C 164 " " NAG N 1 " - " ASN C 148 " " NAG O 1 " - " ASN D 82 " " NAG P 1 " - " ASN D 164 " " NAG Q 1 " - " ASN D 148 " " NAG R 1 " - " ASN E 82 " " NAG S 1 " - " ASN E 164 " " NAG T 1 " - " ASN E 148 " Number of additional bonds: simple=5, symmetry=0 Coordination: Other bonds: Time building additional restraints: 1.47 Conformation dependent library (CDL) restraints added in 675.1 milliseconds 3890 Ramachandran restraints generated. 1945 Oldfield, 0 Emsley, 1945 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3820 Finding SS restraints... Secondary structure from input PDB file: 58 helices and 10 sheets defined 44.2% alpha, 21.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.48 Creating SS restraints... Processing helix chain 'A' and resid 13 through 20 removed outlier: 3.548A pdb=" N ASP A 17 " --> pdb=" O LEU A 13 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N HIS A 18 " --> pdb=" O ARG A 14 " (cutoff:3.500A) Processing helix chain 'A' and resid 91 through 93 No H-bonds generated for 'chain 'A' and resid 91 through 93' Processing helix chain 'A' and resid 170 through 176 removed outlier: 3.531A pdb=" N SER A 176 " --> pdb=" O GLU A 172 " (cutoff:3.500A) Processing helix chain 'A' and resid 221 through 241 Proline residue: A 230 - end of helix removed outlier: 3.578A pdb=" N PHE A 233 " --> pdb=" O LEU A 229 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N MET A 235 " --> pdb=" O SER A 231 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N ASP A 238 " --> pdb=" O LEU A 234 " (cutoff:3.500A) Processing helix chain 'A' and resid 242 through 244 No H-bonds generated for 'chain 'A' and resid 242 through 244' Processing helix chain 'A' and resid 245 through 249 removed outlier: 4.095A pdb=" N GLY A 249 " --> pdb=" O PRO A 246 " (cutoff:3.500A) Processing helix chain 'A' and resid 250 through 273 removed outlier: 3.515A pdb=" N THR A 257 " --> pdb=" O SER A 253 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N PHE A 265 " --> pdb=" O GLY A 261 " (cutoff:3.500A) removed outlier: 3.885A pdb=" N ILE A 267 " --> pdb=" O SER A 263 " (cutoff:3.500A) removed outlier: 3.865A pdb=" N ILE A 268 " --> pdb=" O VAL A 264 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N ASP A 271 " --> pdb=" O ILE A 267 " (cutoff:3.500A) Processing helix chain 'A' and resid 281 through 283 No H-bonds generated for 'chain 'A' and resid 281 through 283' Processing helix chain 'A' and resid 284 through 306 removed outlier: 3.683A pdb=" N VAL A 288 " --> pdb=" O GLY A 284 " (cutoff:3.500A) removed outlier: 3.782A pdb=" N CYS A 290 " --> pdb=" O TYR A 286 " (cutoff:3.500A) removed outlier: 3.807A pdb=" N LEU A 294 " --> pdb=" O CYS A 290 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N VAL A 295 " --> pdb=" O MET A 291 " (cutoff:3.500A) removed outlier: 3.784A pdb=" N SER A 297 " --> pdb=" O LEU A 293 " (cutoff:3.500A) Processing helix chain 'A' and resid 317 through 326 removed outlier: 3.535A pdb=" N HIS A 323 " --> pdb=" O ASP A 319 " (cutoff:3.500A) removed outlier: 4.413A pdb=" N LEU A 324 " --> pdb=" O TRP A 320 " (cutoff:3.500A) Processing helix chain 'A' and resid 399 through 461 removed outlier: 4.048A pdb=" N LEU A 403 " --> pdb=" O VAL A 399 " (cutoff:3.500A) removed outlier: 3.939A pdb=" N GLN A 404 " --> pdb=" O ARG A 400 " (cutoff:3.500A) removed outlier: 4.039A pdb=" N GLU A 405 " --> pdb=" O GLY A 401 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N SER A 408 " --> pdb=" O GLN A 404 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N ARG A 420 " --> pdb=" O ARG A 416 " (cutoff:3.500A) removed outlier: 3.758A pdb=" N ALA A 423 " --> pdb=" O MET A 419 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N TRP A 426 " --> pdb=" O VAL A 422 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N TYR A 431 " --> pdb=" O LEU A 427 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N ASP A 434 " --> pdb=" O GLY A 430 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N SER A 449 " --> pdb=" O VAL A 445 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N TRP A 456 " --> pdb=" O LEU A 452 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N TRP A 459 " --> pdb=" O LEU A 455 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N TYR A 461 " --> pdb=" O SER A 457 " (cutoff:3.500A) Processing helix chain 'B' and resid 13 through 20 removed outlier: 3.548A pdb=" N ASP B 17 " --> pdb=" O LEU B 13 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N HIS B 18 " --> pdb=" O ARG B 14 " (cutoff:3.500A) Processing helix chain 'B' and resid 91 through 93 No H-bonds generated for 'chain 'B' and resid 91 through 93' Processing helix chain 'B' and resid 170 through 176 removed outlier: 3.532A pdb=" N SER B 176 " --> pdb=" O GLU B 172 " (cutoff:3.500A) Processing helix chain 'B' and resid 221 through 241 Proline residue: B 230 - end of helix removed outlier: 3.578A pdb=" N PHE B 233 " --> pdb=" O LEU B 229 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N MET B 235 " --> pdb=" O SER B 231 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N ASP B 238 " --> pdb=" O LEU B 234 " (cutoff:3.500A) Processing helix chain 'B' and resid 242 through 244 No H-bonds generated for 'chain 'B' and resid 242 through 244' Processing helix chain 'B' and resid 245 through 249 removed outlier: 4.095A pdb=" N GLY B 249 " --> pdb=" O PRO B 246 " (cutoff:3.500A) Processing helix chain 'B' and resid 250 through 273 removed outlier: 3.516A pdb=" N THR B 257 " --> pdb=" O SER B 253 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N PHE B 265 " --> pdb=" O GLY B 261 " (cutoff:3.500A) removed outlier: 3.885A pdb=" N ILE B 267 " --> pdb=" O SER B 263 " (cutoff:3.500A) removed outlier: 3.864A pdb=" N ILE B 268 " --> pdb=" O VAL B 264 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N ASP B 271 " --> pdb=" O ILE B 267 " (cutoff:3.500A) Processing helix chain 'B' and resid 281 through 283 No H-bonds generated for 'chain 'B' and resid 281 through 283' Processing helix chain 'B' and resid 284 through 306 removed outlier: 3.683A pdb=" N VAL B 288 " --> pdb=" O GLY B 284 " (cutoff:3.500A) removed outlier: 3.783A pdb=" N CYS B 290 " --> pdb=" O TYR B 286 " (cutoff:3.500A) removed outlier: 3.807A pdb=" N LEU B 294 " --> pdb=" O CYS B 290 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N VAL B 295 " --> pdb=" O MET B 291 " (cutoff:3.500A) removed outlier: 3.783A pdb=" N SER B 297 " --> pdb=" O LEU B 293 " (cutoff:3.500A) Processing helix chain 'B' and resid 317 through 326 removed outlier: 3.535A pdb=" N HIS B 323 " --> pdb=" O ASP B 319 " (cutoff:3.500A) removed outlier: 4.414A pdb=" N LEU B 324 " --> pdb=" O TRP B 320 " (cutoff:3.500A) Processing helix chain 'B' and resid 326 through 331 removed outlier: 3.693A pdb=" N ALA B 330 " --> pdb=" O LEU B 326 " (cutoff:3.500A) Processing helix chain 'B' and resid 399 through 461 removed outlier: 4.048A pdb=" N LEU B 403 " --> pdb=" O VAL B 399 " (cutoff:3.500A) removed outlier: 3.939A pdb=" N GLN B 404 " --> pdb=" O ARG B 400 " (cutoff:3.500A) removed outlier: 4.040A pdb=" N GLU B 405 " --> pdb=" O GLY B 401 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N SER B 408 " --> pdb=" O GLN B 404 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N ARG B 420 " --> pdb=" O ARG B 416 " (cutoff:3.500A) removed outlier: 3.757A pdb=" N ALA B 423 " --> pdb=" O MET B 419 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N TRP B 426 " --> pdb=" O VAL B 422 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N TYR B 431 " --> pdb=" O LEU B 427 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N ASP B 434 " --> pdb=" O GLY B 430 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N SER B 449 " --> pdb=" O VAL B 445 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N TRP B 456 " --> pdb=" O LEU B 452 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N TRP B 459 " --> pdb=" O LEU B 455 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N TYR B 461 " --> pdb=" O SER B 457 " (cutoff:3.500A) Processing helix chain 'C' and resid 13 through 20 removed outlier: 3.548A pdb=" N ASP C 17 " --> pdb=" O LEU C 13 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N HIS C 18 " --> pdb=" O ARG C 14 " (cutoff:3.500A) Processing helix chain 'C' and resid 91 through 93 No H-bonds generated for 'chain 'C' and resid 91 through 93' Processing helix chain 'C' and resid 170 through 176 removed outlier: 3.532A pdb=" N SER C 176 " --> pdb=" O GLU C 172 " (cutoff:3.500A) Processing helix chain 'C' and resid 221 through 241 Proline residue: C 230 - end of helix removed outlier: 3.578A pdb=" N PHE C 233 " --> pdb=" O LEU C 229 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N MET C 235 " --> pdb=" O SER C 231 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N ASP C 238 " --> pdb=" O LEU C 234 " (cutoff:3.500A) Processing helix chain 'C' and resid 242 through 244 No H-bonds generated for 'chain 'C' and resid 242 through 244' Processing helix chain 'C' and resid 245 through 249 removed outlier: 4.095A pdb=" N GLY C 249 " --> pdb=" O PRO C 246 " (cutoff:3.500A) Processing helix chain 'C' and resid 250 through 273 removed outlier: 3.516A pdb=" N THR C 257 " --> pdb=" O SER C 253 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N PHE C 265 " --> pdb=" O GLY C 261 " (cutoff:3.500A) removed outlier: 3.886A pdb=" N ILE C 267 " --> pdb=" O SER C 263 " (cutoff:3.500A) removed outlier: 3.864A pdb=" N ILE C 268 " --> pdb=" O VAL C 264 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N ASP C 271 " --> pdb=" O ILE C 267 " (cutoff:3.500A) Processing helix chain 'C' and resid 281 through 283 No H-bonds generated for 'chain 'C' and resid 281 through 283' Processing helix chain 'C' and resid 284 through 306 removed outlier: 3.684A pdb=" N VAL C 288 " --> pdb=" O GLY C 284 " (cutoff:3.500A) removed outlier: 3.783A pdb=" N CYS C 290 " --> pdb=" O TYR C 286 " (cutoff:3.500A) removed outlier: 3.807A pdb=" N LEU C 294 " --> pdb=" O CYS C 290 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N VAL C 295 " --> pdb=" O MET C 291 " (cutoff:3.500A) removed outlier: 3.783A pdb=" N SER C 297 " --> pdb=" O LEU C 293 " (cutoff:3.500A) Processing helix chain 'C' and resid 317 through 326 removed outlier: 3.535A pdb=" N HIS C 323 " --> pdb=" O ASP C 319 " (cutoff:3.500A) removed outlier: 4.414A pdb=" N LEU C 324 " --> pdb=" O TRP C 320 " (cutoff:3.500A) Processing helix chain 'C' and resid 326 through 331 removed outlier: 3.693A pdb=" N ALA C 330 " --> pdb=" O LEU C 326 " (cutoff:3.500A) Processing helix chain 'C' and resid 399 through 461 removed outlier: 4.047A pdb=" N LEU C 403 " --> pdb=" O VAL C 399 " (cutoff:3.500A) removed outlier: 3.939A pdb=" N GLN C 404 " --> pdb=" O ARG C 400 " (cutoff:3.500A) removed outlier: 4.039A pdb=" N GLU C 405 " --> pdb=" O GLY C 401 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N SER C 408 " --> pdb=" O GLN C 404 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N ARG C 420 " --> pdb=" O ARG C 416 " (cutoff:3.500A) removed outlier: 3.758A pdb=" N ALA C 423 " --> pdb=" O MET C 419 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N TRP C 426 " --> pdb=" O VAL C 422 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N TYR C 431 " --> pdb=" O LEU C 427 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N ASP C 434 " --> pdb=" O GLY C 430 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N SER C 449 " --> pdb=" O VAL C 445 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N TRP C 456 " --> pdb=" O LEU C 452 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N TRP C 459 " --> pdb=" O LEU C 455 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N TYR C 461 " --> pdb=" O SER C 457 " (cutoff:3.500A) Processing helix chain 'D' and resid 13 through 20 removed outlier: 3.549A pdb=" N ASP D 17 " --> pdb=" O LEU D 13 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N HIS D 18 " --> pdb=" O ARG D 14 " (cutoff:3.500A) Processing helix chain 'D' and resid 91 through 93 No H-bonds generated for 'chain 'D' and resid 91 through 93' Processing helix chain 'D' and resid 170 through 176 removed outlier: 3.531A pdb=" N SER D 176 " --> pdb=" O GLU D 172 " (cutoff:3.500A) Processing helix chain 'D' and resid 221 through 241 Proline residue: D 230 - end of helix removed outlier: 3.578A pdb=" N PHE D 233 " --> pdb=" O LEU D 229 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N MET D 235 " --> pdb=" O SER D 231 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N ASP D 238 " --> pdb=" O LEU D 234 " (cutoff:3.500A) Processing helix chain 'D' and resid 242 through 244 No H-bonds generated for 'chain 'D' and resid 242 through 244' Processing helix chain 'D' and resid 245 through 249 removed outlier: 4.095A pdb=" N GLY D 249 " --> pdb=" O PRO D 246 " (cutoff:3.500A) Processing helix chain 'D' and resid 250 through 273 removed outlier: 3.516A pdb=" N THR D 257 " --> pdb=" O SER D 253 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N PHE D 265 " --> pdb=" O GLY D 261 " (cutoff:3.500A) removed outlier: 3.886A pdb=" N ILE D 267 " --> pdb=" O SER D 263 " (cutoff:3.500A) removed outlier: 3.865A pdb=" N ILE D 268 " --> pdb=" O VAL D 264 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N ASP D 271 " --> pdb=" O ILE D 267 " (cutoff:3.500A) Processing helix chain 'D' and resid 281 through 283 No H-bonds generated for 'chain 'D' and resid 281 through 283' Processing helix chain 'D' and resid 284 through 306 removed outlier: 3.684A pdb=" N VAL D 288 " --> pdb=" O GLY D 284 " (cutoff:3.500A) removed outlier: 3.783A pdb=" N CYS D 290 " --> pdb=" O TYR D 286 " (cutoff:3.500A) removed outlier: 3.807A pdb=" N LEU D 294 " --> pdb=" O CYS D 290 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N VAL D 295 " --> pdb=" O MET D 291 " (cutoff:3.500A) removed outlier: 3.783A pdb=" N SER D 297 " --> pdb=" O LEU D 293 " (cutoff:3.500A) Processing helix chain 'D' and resid 317 through 326 removed outlier: 3.535A pdb=" N HIS D 323 " --> pdb=" O ASP D 319 " (cutoff:3.500A) removed outlier: 4.414A pdb=" N LEU D 324 " --> pdb=" O TRP D 320 " (cutoff:3.500A) Processing helix chain 'D' and resid 326 through 331 removed outlier: 3.692A pdb=" N ALA D 330 " --> pdb=" O LEU D 326 " (cutoff:3.500A) Processing helix chain 'D' and resid 399 through 461 removed outlier: 4.048A pdb=" N LEU D 403 " --> pdb=" O VAL D 399 " (cutoff:3.500A) removed outlier: 3.940A pdb=" N GLN D 404 " --> pdb=" O ARG D 400 " (cutoff:3.500A) removed outlier: 4.039A pdb=" N GLU D 405 " --> pdb=" O GLY D 401 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N SER D 408 " --> pdb=" O GLN D 404 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N ARG D 420 " --> pdb=" O ARG D 416 " (cutoff:3.500A) removed outlier: 3.756A pdb=" N ALA D 423 " --> pdb=" O MET D 419 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N TRP D 426 " --> pdb=" O VAL D 422 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N TYR D 431 " --> pdb=" O LEU D 427 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N ASP D 434 " --> pdb=" O GLY D 430 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N SER D 449 " --> pdb=" O VAL D 445 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N TRP D 456 " --> pdb=" O LEU D 452 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N TRP D 459 " --> pdb=" O LEU D 455 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N TYR D 461 " --> pdb=" O SER D 457 " (cutoff:3.500A) Processing helix chain 'E' and resid 13 through 20 removed outlier: 3.549A pdb=" N ASP E 17 " --> pdb=" O LEU E 13 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N HIS E 18 " --> pdb=" O ARG E 14 " (cutoff:3.500A) Processing helix chain 'E' and resid 91 through 93 No H-bonds generated for 'chain 'E' and resid 91 through 93' Processing helix chain 'E' and resid 170 through 176 removed outlier: 3.532A pdb=" N SER E 176 " --> pdb=" O GLU E 172 " (cutoff:3.500A) Processing helix chain 'E' and resid 221 through 241 Proline residue: E 230 - end of helix removed outlier: 3.578A pdb=" N PHE E 233 " --> pdb=" O LEU E 229 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N MET E 235 " --> pdb=" O SER E 231 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N ASP E 238 " --> pdb=" O LEU E 234 " (cutoff:3.500A) Processing helix chain 'E' and resid 242 through 244 No H-bonds generated for 'chain 'E' and resid 242 through 244' Processing helix chain 'E' and resid 245 through 249 removed outlier: 4.095A pdb=" N GLY E 249 " --> pdb=" O PRO E 246 " (cutoff:3.500A) Processing helix chain 'E' and resid 250 through 273 removed outlier: 3.516A pdb=" N THR E 257 " --> pdb=" O SER E 253 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N PHE E 265 " --> pdb=" O GLY E 261 " (cutoff:3.500A) removed outlier: 3.886A pdb=" N ILE E 267 " --> pdb=" O SER E 263 " (cutoff:3.500A) removed outlier: 3.864A pdb=" N ILE E 268 " --> pdb=" O VAL E 264 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N ASP E 271 " --> pdb=" O ILE E 267 " (cutoff:3.500A) Processing helix chain 'E' and resid 281 through 283 No H-bonds generated for 'chain 'E' and resid 281 through 283' Processing helix chain 'E' and resid 284 through 306 removed outlier: 3.684A pdb=" N VAL E 288 " --> pdb=" O GLY E 284 " (cutoff:3.500A) removed outlier: 3.782A pdb=" N CYS E 290 " --> pdb=" O TYR E 286 " (cutoff:3.500A) removed outlier: 3.808A pdb=" N LEU E 294 " --> pdb=" O CYS E 290 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N VAL E 295 " --> pdb=" O MET E 291 " (cutoff:3.500A) removed outlier: 3.783A pdb=" N SER E 297 " --> pdb=" O LEU E 293 " (cutoff:3.500A) Processing helix chain 'E' and resid 317 through 326 removed outlier: 3.535A pdb=" N HIS E 323 " --> pdb=" O ASP E 319 " (cutoff:3.500A) removed outlier: 4.414A pdb=" N LEU E 324 " --> pdb=" O TRP E 320 " (cutoff:3.500A) Processing helix chain 'E' and resid 399 through 461 removed outlier: 4.047A pdb=" N LEU E 403 " --> pdb=" O VAL E 399 " (cutoff:3.500A) removed outlier: 3.940A pdb=" N GLN E 404 " --> pdb=" O ARG E 400 " (cutoff:3.500A) removed outlier: 4.039A pdb=" N GLU E 405 " --> pdb=" O GLY E 401 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N SER E 408 " --> pdb=" O GLN E 404 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N ARG E 420 " --> pdb=" O ARG E 416 " (cutoff:3.500A) removed outlier: 3.758A pdb=" N ALA E 423 " --> pdb=" O MET E 419 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N TRP E 426 " --> pdb=" O VAL E 422 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N TYR E 431 " --> pdb=" O LEU E 427 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N ASP E 434 " --> pdb=" O GLY E 430 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N SER E 449 " --> pdb=" O VAL E 445 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N TRP E 456 " --> pdb=" O LEU E 452 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N TRP E 459 " --> pdb=" O LEU E 455 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N TYR E 461 " --> pdb=" O SER E 457 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 85 through 89 removed outlier: 6.851A pdb=" N TYR A 114 " --> pdb=" O TYR A 126 " (cutoff:3.500A) removed outlier: 5.395A pdb=" N TYR A 126 " --> pdb=" O TYR A 114 " (cutoff:3.500A) removed outlier: 4.173A pdb=" N GLU A 122 " --> pdb=" O HIS A 118 " (cutoff:3.500A) removed outlier: 7.050A pdb=" N TYR A 61 " --> pdb=" O ILE A 48 " (cutoff:3.500A) removed outlier: 5.817A pdb=" N ILE A 48 " --> pdb=" O TYR A 61 " (cutoff:3.500A) removed outlier: 8.081A pdb=" N TRP A 63 " --> pdb=" O TYR A 46 " (cutoff:3.500A) removed outlier: 7.061A pdb=" N TYR A 46 " --> pdb=" O TRP A 63 " (cutoff:3.500A) removed outlier: 8.134A pdb=" N ARG A 65 " --> pdb=" O ILE A 44 " (cutoff:3.500A) removed outlier: 8.052A pdb=" N ILE A 44 " --> pdb=" O ARG A 65 " (cutoff:3.500A) removed outlier: 8.392A pdb=" N TYR A 67 " --> pdb=" O ASP A 42 " (cutoff:3.500A) removed outlier: 8.414A pdb=" N ASP A 42 " --> pdb=" O TYR A 67 " (cutoff:3.500A) removed outlier: 8.974A pdb=" N THR A 69 " --> pdb=" O SER A 40 " (cutoff:3.500A) removed outlier: 9.768A pdb=" N SER A 40 " --> pdb=" O THR A 69 " (cutoff:3.500A) removed outlier: 6.303A pdb=" N THR A 37 " --> pdb=" O ASN A 164 " (cutoff:3.500A) removed outlier: 7.626A pdb=" N THR A 166 " --> pdb=" O THR A 37 " (cutoff:3.500A) removed outlier: 6.202A pdb=" N VAL A 39 " --> pdb=" O THR A 166 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 98 through 100 removed outlier: 4.010A pdb=" N SER A 155 " --> pdb=" O ALA A 208 " (cutoff:3.500A) removed outlier: 5.990A pdb=" N ALA A 208 " --> pdb=" O SER A 155 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N GLU A 191 " --> pdb=" O ILE A 215 " (cutoff:3.500A) removed outlier: 6.566A pdb=" N ARG A 217 " --> pdb=" O LEU A 189 " (cutoff:3.500A) removed outlier: 5.433A pdb=" N LEU A 189 " --> pdb=" O ARG A 217 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 85 through 89 removed outlier: 6.851A pdb=" N TYR B 114 " --> pdb=" O TYR B 126 " (cutoff:3.500A) removed outlier: 5.395A pdb=" N TYR B 126 " --> pdb=" O TYR B 114 " (cutoff:3.500A) removed outlier: 4.173A pdb=" N GLU B 122 " --> pdb=" O HIS B 118 " (cutoff:3.500A) removed outlier: 7.050A pdb=" N TYR B 61 " --> pdb=" O ILE B 48 " (cutoff:3.500A) removed outlier: 5.817A pdb=" N ILE B 48 " --> pdb=" O TYR B 61 " (cutoff:3.500A) removed outlier: 8.081A pdb=" N TRP B 63 " --> pdb=" O TYR B 46 " (cutoff:3.500A) removed outlier: 7.060A pdb=" N TYR B 46 " --> pdb=" O TRP B 63 " (cutoff:3.500A) removed outlier: 8.133A pdb=" N ARG B 65 " --> pdb=" O ILE B 44 " (cutoff:3.500A) removed outlier: 8.051A pdb=" N ILE B 44 " --> pdb=" O ARG B 65 " (cutoff:3.500A) removed outlier: 8.391A pdb=" N TYR B 67 " --> pdb=" O ASP B 42 " (cutoff:3.500A) removed outlier: 8.415A pdb=" N ASP B 42 " --> pdb=" O TYR B 67 " (cutoff:3.500A) removed outlier: 8.973A pdb=" N THR B 69 " --> pdb=" O SER B 40 " (cutoff:3.500A) removed outlier: 9.768A pdb=" N SER B 40 " --> pdb=" O THR B 69 " (cutoff:3.500A) removed outlier: 6.303A pdb=" N THR B 37 " --> pdb=" O ASN B 164 " (cutoff:3.500A) removed outlier: 7.626A pdb=" N THR B 166 " --> pdb=" O THR B 37 " (cutoff:3.500A) removed outlier: 6.202A pdb=" N VAL B 39 " --> pdb=" O THR B 166 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 98 through 100 removed outlier: 4.010A pdb=" N SER B 155 " --> pdb=" O ALA B 208 " (cutoff:3.500A) removed outlier: 5.991A pdb=" N ALA B 208 " --> pdb=" O SER B 155 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N GLU B 191 " --> pdb=" O ILE B 215 " (cutoff:3.500A) removed outlier: 6.567A pdb=" N ARG B 217 " --> pdb=" O LEU B 189 " (cutoff:3.500A) removed outlier: 5.433A pdb=" N LEU B 189 " --> pdb=" O ARG B 217 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'C' and resid 85 through 89 removed outlier: 6.851A pdb=" N TYR C 114 " --> pdb=" O TYR C 126 " (cutoff:3.500A) removed outlier: 5.395A pdb=" N TYR C 126 " --> pdb=" O TYR C 114 " (cutoff:3.500A) removed outlier: 4.173A pdb=" N GLU C 122 " --> pdb=" O HIS C 118 " (cutoff:3.500A) removed outlier: 7.050A pdb=" N TYR C 61 " --> pdb=" O ILE C 48 " (cutoff:3.500A) removed outlier: 5.817A pdb=" N ILE C 48 " --> pdb=" O TYR C 61 " (cutoff:3.500A) removed outlier: 8.082A pdb=" N TRP C 63 " --> pdb=" O TYR C 46 " (cutoff:3.500A) removed outlier: 7.060A pdb=" N TYR C 46 " --> pdb=" O TRP C 63 " (cutoff:3.500A) removed outlier: 8.134A pdb=" N ARG C 65 " --> pdb=" O ILE C 44 " (cutoff:3.500A) removed outlier: 8.050A pdb=" N ILE C 44 " --> pdb=" O ARG C 65 " (cutoff:3.500A) removed outlier: 8.391A pdb=" N TYR C 67 " --> pdb=" O ASP C 42 " (cutoff:3.500A) removed outlier: 8.415A pdb=" N ASP C 42 " --> pdb=" O TYR C 67 " (cutoff:3.500A) removed outlier: 8.973A pdb=" N THR C 69 " --> pdb=" O SER C 40 " (cutoff:3.500A) removed outlier: 9.768A pdb=" N SER C 40 " --> pdb=" O THR C 69 " (cutoff:3.500A) removed outlier: 6.302A pdb=" N THR C 37 " --> pdb=" O ASN C 164 " (cutoff:3.500A) removed outlier: 7.627A pdb=" N THR C 166 " --> pdb=" O THR C 37 " (cutoff:3.500A) removed outlier: 6.202A pdb=" N VAL C 39 " --> pdb=" O THR C 166 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'C' and resid 98 through 100 removed outlier: 4.010A pdb=" N SER C 155 " --> pdb=" O ALA C 208 " (cutoff:3.500A) removed outlier: 5.990A pdb=" N ALA C 208 " --> pdb=" O SER C 155 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N GLU C 191 " --> pdb=" O ILE C 215 " (cutoff:3.500A) removed outlier: 6.566A pdb=" N ARG C 217 " --> pdb=" O LEU C 189 " (cutoff:3.500A) removed outlier: 5.433A pdb=" N LEU C 189 " --> pdb=" O ARG C 217 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'D' and resid 85 through 89 removed outlier: 6.851A pdb=" N TYR D 114 " --> pdb=" O TYR D 126 " (cutoff:3.500A) removed outlier: 5.395A pdb=" N TYR D 126 " --> pdb=" O TYR D 114 " (cutoff:3.500A) removed outlier: 4.173A pdb=" N GLU D 122 " --> pdb=" O HIS D 118 " (cutoff:3.500A) removed outlier: 7.051A pdb=" N TYR D 61 " --> pdb=" O ILE D 48 " (cutoff:3.500A) removed outlier: 5.817A pdb=" N ILE D 48 " --> pdb=" O TYR D 61 " (cutoff:3.500A) removed outlier: 8.081A pdb=" N TRP D 63 " --> pdb=" O TYR D 46 " (cutoff:3.500A) removed outlier: 7.061A pdb=" N TYR D 46 " --> pdb=" O TRP D 63 " (cutoff:3.500A) removed outlier: 8.135A pdb=" N ARG D 65 " --> pdb=" O ILE D 44 " (cutoff:3.500A) removed outlier: 8.051A pdb=" N ILE D 44 " --> pdb=" O ARG D 65 " (cutoff:3.500A) removed outlier: 8.391A pdb=" N TYR D 67 " --> pdb=" O ASP D 42 " (cutoff:3.500A) removed outlier: 8.414A pdb=" N ASP D 42 " --> pdb=" O TYR D 67 " (cutoff:3.500A) removed outlier: 8.973A pdb=" N THR D 69 " --> pdb=" O SER D 40 " (cutoff:3.500A) removed outlier: 9.767A pdb=" N SER D 40 " --> pdb=" O THR D 69 " (cutoff:3.500A) removed outlier: 6.303A pdb=" N THR D 37 " --> pdb=" O ASN D 164 " (cutoff:3.500A) removed outlier: 7.627A pdb=" N THR D 166 " --> pdb=" O THR D 37 " (cutoff:3.500A) removed outlier: 6.202A pdb=" N VAL D 39 " --> pdb=" O THR D 166 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'D' and resid 98 through 100 removed outlier: 4.010A pdb=" N SER D 155 " --> pdb=" O ALA D 208 " (cutoff:3.500A) removed outlier: 5.990A pdb=" N ALA D 208 " --> pdb=" O SER D 155 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N GLU D 191 " --> pdb=" O ILE D 215 " (cutoff:3.500A) removed outlier: 6.566A pdb=" N ARG D 217 " --> pdb=" O LEU D 189 " (cutoff:3.500A) removed outlier: 5.432A pdb=" N LEU D 189 " --> pdb=" O ARG D 217 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'E' and resid 85 through 89 removed outlier: 6.851A pdb=" N TYR E 114 " --> pdb=" O TYR E 126 " (cutoff:3.500A) removed outlier: 5.396A pdb=" N TYR E 126 " --> pdb=" O TYR E 114 " (cutoff:3.500A) removed outlier: 4.174A pdb=" N GLU E 122 " --> pdb=" O HIS E 118 " (cutoff:3.500A) removed outlier: 7.050A pdb=" N TYR E 61 " --> pdb=" O ILE E 48 " (cutoff:3.500A) removed outlier: 5.817A pdb=" N ILE E 48 " --> pdb=" O TYR E 61 " (cutoff:3.500A) removed outlier: 8.081A pdb=" N TRP E 63 " --> pdb=" O TYR E 46 " (cutoff:3.500A) removed outlier: 7.061A pdb=" N TYR E 46 " --> pdb=" O TRP E 63 " (cutoff:3.500A) removed outlier: 8.134A pdb=" N ARG E 65 " --> pdb=" O ILE E 44 " (cutoff:3.500A) removed outlier: 8.052A pdb=" N ILE E 44 " --> pdb=" O ARG E 65 " (cutoff:3.500A) removed outlier: 8.391A pdb=" N TYR E 67 " --> pdb=" O ASP E 42 " (cutoff:3.500A) removed outlier: 8.414A pdb=" N ASP E 42 " --> pdb=" O TYR E 67 " (cutoff:3.500A) removed outlier: 8.974A pdb=" N THR E 69 " --> pdb=" O SER E 40 " (cutoff:3.500A) removed outlier: 9.768A pdb=" N SER E 40 " --> pdb=" O THR E 69 " (cutoff:3.500A) removed outlier: 6.303A pdb=" N THR E 37 " --> pdb=" O ASN E 164 " (cutoff:3.500A) removed outlier: 7.627A pdb=" N THR E 166 " --> pdb=" O THR E 37 " (cutoff:3.500A) removed outlier: 6.202A pdb=" N VAL E 39 " --> pdb=" O THR E 166 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'E' and resid 98 through 100 removed outlier: 4.010A pdb=" N SER E 155 " --> pdb=" O ALA E 208 " (cutoff:3.500A) removed outlier: 5.990A pdb=" N ALA E 208 " --> pdb=" O SER E 155 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N GLU E 191 " --> pdb=" O ILE E 215 " (cutoff:3.500A) removed outlier: 6.566A pdb=" N ARG E 217 " --> pdb=" O LEU E 189 " (cutoff:3.500A) removed outlier: 5.432A pdb=" N LEU E 189 " --> pdb=" O ARG E 217 " (cutoff:3.500A) 688 hydrogen bonds defined for protein. 2019 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: 2.41 Time building geometry restraints manager: 1.84 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: 4949 1.34 - 1.46: 3798 1.46 - 1.58: 8503 1.58 - 1.70: 0 1.70 - 1.82: 75 Bond restraints: 17325 Sorted by residual: bond pdb=" O S7Y A 508 " pdb=" C6 S7Y A 508 " ideal model delta sigma weight residual 1.229 1.439 -0.210 2.00e-02 2.50e+03 1.10e+02 bond pdb=" O S7Y C 508 " pdb=" C6 S7Y C 508 " ideal model delta sigma weight residual 1.229 1.438 -0.209 2.00e-02 2.50e+03 1.10e+02 bond pdb=" O S7Y D 508 " pdb=" C6 S7Y D 508 " ideal model delta sigma weight residual 1.229 1.438 -0.209 2.00e-02 2.50e+03 1.09e+02 bond pdb=" O S7Y B 508 " pdb=" C6 S7Y B 508 " ideal model delta sigma weight residual 1.229 1.438 -0.209 2.00e-02 2.50e+03 1.09e+02 bond pdb=" O S7Y E 508 " pdb=" C6 S7Y E 508 " ideal model delta sigma weight residual 1.229 1.438 -0.209 2.00e-02 2.50e+03 1.09e+02 ... (remaining 17320 not shown) Histogram of bond angle deviations from ideal: 0.00 - 6.13: 23595 6.13 - 12.27: 55 12.27 - 18.40: 25 18.40 - 24.53: 0 24.53 - 30.67: 5 Bond angle restraints: 23680 Sorted by residual: angle pdb=" C3 NAG P 1 " pdb=" C4 NAG P 1 " pdb=" O4 NAG P 1 " ideal model delta sigma weight residual 107.29 137.96 -30.67 3.00e+00 1.11e-01 1.04e+02 angle pdb=" C3 NAG S 1 " pdb=" C4 NAG S 1 " pdb=" O4 NAG S 1 " ideal model delta sigma weight residual 107.29 137.94 -30.65 3.00e+00 1.11e-01 1.04e+02 angle pdb=" C3 NAG M 1 " pdb=" C4 NAG M 1 " pdb=" O4 NAG M 1 " ideal model delta sigma weight residual 107.29 137.93 -30.64 3.00e+00 1.11e-01 1.04e+02 angle pdb=" C3 NAG G 1 " pdb=" C4 NAG G 1 " pdb=" O4 NAG G 1 " ideal model delta sigma weight residual 107.29 137.93 -30.64 3.00e+00 1.11e-01 1.04e+02 angle pdb=" C3 NAG J 1 " pdb=" C4 NAG J 1 " pdb=" O4 NAG J 1 " ideal model delta sigma weight residual 107.29 137.91 -30.62 3.00e+00 1.11e-01 1.04e+02 ... (remaining 23675 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 21.20: 10125 21.20 - 42.40: 400 42.40 - 63.60: 70 63.60 - 84.80: 35 84.80 - 106.00: 20 Dihedral angle restraints: 10650 sinusoidal: 4785 harmonic: 5865 Sorted by residual: dihedral pdb=" CA ASN E 141 " pdb=" C ASN E 141 " pdb=" N PHE E 142 " pdb=" CA PHE E 142 " ideal model delta harmonic sigma weight residual -180.00 -151.34 -28.66 0 5.00e+00 4.00e-02 3.29e+01 dihedral pdb=" CA ASN C 141 " pdb=" C ASN C 141 " pdb=" N PHE C 142 " pdb=" CA PHE C 142 " ideal model delta harmonic sigma weight residual -180.00 -151.36 -28.64 0 5.00e+00 4.00e-02 3.28e+01 dihedral pdb=" CA ASN D 141 " pdb=" C ASN D 141 " pdb=" N PHE D 142 " pdb=" CA PHE D 142 " ideal model delta harmonic sigma weight residual 180.00 -151.38 -28.62 0 5.00e+00 4.00e-02 3.28e+01 ... (remaining 10647 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.408: 2815 0.408 - 0.816: 0 0.816 - 1.225: 0 1.225 - 1.633: 0 1.633 - 2.041: 5 Chirality restraints: 2820 Sorted by residual: chirality pdb=" C4 NAG M 1 " pdb=" C3 NAG M 1 " pdb=" C5 NAG M 1 " pdb=" O4 NAG M 1 " both_signs ideal model delta sigma weight residual False -2.53 -0.49 -2.04 2.00e-01 2.50e+01 1.04e+02 chirality pdb=" C4 NAG G 1 " pdb=" C3 NAG G 1 " pdb=" C5 NAG G 1 " pdb=" O4 NAG G 1 " both_signs ideal model delta sigma weight residual False -2.53 -0.49 -2.04 2.00e-01 2.50e+01 1.04e+02 chirality pdb=" C4 NAG J 1 " pdb=" C3 NAG J 1 " pdb=" C5 NAG J 1 " pdb=" O4 NAG J 1 " both_signs ideal model delta sigma weight residual False -2.53 -0.49 -2.04 2.00e-01 2.50e+01 1.04e+02 ... (remaining 2817 not shown) Planarity restraints: 2865 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" N S7Y A 508 " 0.297 2.00e-02 2.50e+03 1.95e-01 5.73e+02 pdb=" O S7Y A 508 " 0.157 2.00e-02 2.50e+03 pdb=" C2 S7Y A 508 " -0.015 2.00e-02 2.50e+03 pdb=" C3 S7Y A 508 " 0.027 2.00e-02 2.50e+03 pdb=" C6 S7Y A 508 " -0.293 2.00e-02 2.50e+03 pdb=" C7 S7Y A 508 " -0.172 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" N S7Y E 508 " 0.297 2.00e-02 2.50e+03 1.95e-01 5.72e+02 pdb=" O S7Y E 508 " 0.157 2.00e-02 2.50e+03 pdb=" C2 S7Y E 508 " -0.015 2.00e-02 2.50e+03 pdb=" C3 S7Y E 508 " 0.027 2.00e-02 2.50e+03 pdb=" C6 S7Y E 508 " -0.293 2.00e-02 2.50e+03 pdb=" C7 S7Y E 508 " -0.172 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" N S7Y B 508 " 0.296 2.00e-02 2.50e+03 1.95e-01 5.72e+02 pdb=" O S7Y B 508 " 0.157 2.00e-02 2.50e+03 pdb=" C2 S7Y B 508 " -0.015 2.00e-02 2.50e+03 pdb=" C3 S7Y B 508 " 0.027 2.00e-02 2.50e+03 pdb=" C6 S7Y B 508 " -0.293 2.00e-02 2.50e+03 pdb=" C7 S7Y B 508 " -0.172 2.00e-02 2.50e+03 ... (remaining 2862 not shown) Histogram of nonbonded interaction distances: 2.34 - 2.85: 5290 2.85 - 3.36: 14111 3.36 - 3.87: 26883 3.87 - 4.39: 29694 4.39 - 4.90: 51652 Nonbonded interactions: 127630 Sorted by model distance: nonbonded pdb=" N ASP A 91 " pdb=" OD1 ASP A 91 " model vdw 2.337 3.120 nonbonded pdb=" N ASP B 91 " pdb=" OD1 ASP B 91 " model vdw 2.337 3.120 nonbonded pdb=" N ASP C 91 " pdb=" OD1 ASP C 91 " model vdw 2.339 3.120 nonbonded pdb=" N ASP E 91 " pdb=" OD1 ASP E 91 " model vdw 2.339 3.120 nonbonded pdb=" N ASP D 91 " pdb=" OD1 ASP D 91 " model vdw 2.339 3.120 ... (remaining 127625 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = (chain 'D' and resid 8 through 508) selection = chain 'E' } ncs_group { reference = (chain 'F' and (resid 1 or (resid 2 and (name C1 or name C2 or name C3 or name C \ 4 or name C5 or name C6 or name C7 or name C8 or name N2 or name O3 or name O4 o \ r name O5 or name O6 or name O7 )))) selection = (chain 'H' and ((resid 1 and (name C1 or name C2 or name C3 or name C4 or name C \ 5 or name C6 or name C7 or name C8 or name N2 or name O3 or name O5 or name O6 o \ r name O7 )) or resid 2)) selection = (chain 'I' and (resid 1 or (resid 2 and (name C1 or name C2 or name C3 or name C \ 4 or name C5 or name C6 or name C7 or name C8 or name N2 or name O3 or name O4 o \ r name O5 or name O6 or name O7 )))) selection = (chain 'K' and ((resid 1 and (name C1 or name C2 or name C3 or name C4 or name C \ 5 or name C6 or name C7 or name C8 or name N2 or name O3 or name O5 or name O6 o \ r name O7 )) or resid 2)) selection = (chain 'L' and (resid 1 or (resid 2 and (name C1 or name C2 or name C3 or name C \ 4 or name C5 or name C6 or name C7 or name C8 or name N2 or name O3 or name O4 o \ r name O5 or name O6 or name O7 )))) selection = (chain 'N' and ((resid 1 and (name C1 or name C2 or name C3 or name C4 or name C \ 5 or name C6 or name C7 or name C8 or name N2 or name O3 or name O5 or name O6 o \ r name O7 )) or resid 2)) selection = (chain 'O' and (resid 1 or (resid 2 and (name C1 or name C2 or name C3 or name C \ 4 or name C5 or name C6 or name C7 or name C8 or name N2 or name O3 or name O4 o \ r name O5 or name O6 or name O7 )))) selection = (chain 'Q' and ((resid 1 and (name C1 or name C2 or name C3 or name C4 or name C \ 5 or name C6 or name C7 or name C8 or name N2 or name O3 or name O5 or name O6 o \ r name O7 )) or resid 2)) selection = (chain 'R' and (resid 1 or (resid 2 and (name C1 or name C2 or name C3 or name C \ 4 or name C5 or name C6 or name C7 or name C8 or name N2 or name O3 or name O4 o \ r name O5 or name O6 or name O7 )))) selection = (chain 'T' and ((resid 1 and (name C1 or name C2 or name C3 or name C4 or name C \ 5 or name C6 or name C7 or name C8 or name N2 or name O3 or name O5 or name O6 o \ r name O7 )) or resid 2)) } ncs_group { reference = chain 'G' selection = chain 'J' selection = chain 'M' selection = chain 'P' selection = chain 'S' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.370 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.260 Check model and map are aligned: 0.050 Set scattering table: 0.040 Process input model: 14.250 Find NCS groups from input model: 0.310 Set up NCS constraints: 0.030 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: 0.000 Load rotamer database and sin/cos tables:7.920 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 25.230 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8490 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 : 0.010 0.210 17365 Z= 0.450 Angle : 1.390 48.504 23780 Z= 0.598 Chirality : 0.104 2.041 2820 Planarity : 0.011 0.195 2850 Dihedral : 13.559 105.996 6815 Min Nonbonded Distance : 2.337 Molprobity Statistics. All-atom Clashscore : 2.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.60 % Favored : 94.40 % Rotamer: Outliers : 0.82 % Allowed : 4.36 % Favored : 94.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -5.20 (0.14), residues: 1945 helix: -4.66 (0.06), residues: 835 sheet: -1.70 (0.21), residues: 440 loop : -2.56 (0.21), residues: 670 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG B 251 TYR 0.021 0.002 TYR B 67 PHE 0.024 0.003 PHE A 72 TRP 0.055 0.003 TRP A 168 HIS 0.017 0.002 HIS D 309 Details of bonding type rmsd covalent geometry : bond 0.00992 (17325) covalent geometry : angle 1.16700 (23680) SS BOND : bond 0.00037 ( 5) SS BOND : angle 1.36634 ( 10) hydrogen bonds : bond 0.30668 ( 688) hydrogen bonds : angle 9.45316 ( 2019) Misc. bond : bond 0.00059 ( 5) link_BETA1-4 : bond 0.04005 ( 15) link_BETA1-4 : angle 17.13465 ( 45) link_NAG-ASN : bond 0.00449 ( 15) link_NAG-ASN : angle 3.16598 ( 45) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3890 Ramachandran restraints generated. 1945 Oldfield, 0 Emsley, 1945 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3890 Ramachandran restraints generated. 1945 Oldfield, 0 Emsley, 1945 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 361 residues out of total 1835 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 346 time to evaluate : 0.603 Fit side-chains REVERT: A 197 LYS cc_start: 0.8581 (mttm) cc_final: 0.8302 (mtpp) REVERT: A 238 ASP cc_start: 0.8615 (t70) cc_final: 0.8117 (t70) REVERT: A 411 HIS cc_start: 0.8535 (t70) cc_final: 0.7753 (t70) REVERT: B 197 LYS cc_start: 0.8444 (mttm) cc_final: 0.8163 (mtpp) REVERT: B 238 ASP cc_start: 0.8816 (t70) cc_final: 0.8124 (t70) REVERT: B 411 HIS cc_start: 0.8396 (t70) cc_final: 0.7446 (t-90) REVERT: B 415 LYS cc_start: 0.8894 (mtpt) cc_final: 0.8623 (mtpm) REVERT: C 238 ASP cc_start: 0.8830 (t70) cc_final: 0.8211 (t0) REVERT: C 319 ASP cc_start: 0.7677 (t0) cc_final: 0.7475 (t0) REVERT: C 411 HIS cc_start: 0.8378 (t70) cc_final: 0.7733 (t70) REVERT: C 415 LYS cc_start: 0.8865 (mtpt) cc_final: 0.8524 (mtmp) REVERT: D 197 LYS cc_start: 0.8420 (mttm) cc_final: 0.8162 (mtpp) REVERT: D 238 ASP cc_start: 0.8799 (t70) cc_final: 0.7944 (t0) REVERT: D 411 HIS cc_start: 0.8565 (t70) cc_final: 0.8040 (t70) REVERT: E 197 LYS cc_start: 0.8423 (mttm) cc_final: 0.8143 (mtpp) REVERT: E 238 ASP cc_start: 0.8835 (t70) cc_final: 0.8369 (t70) REVERT: E 411 HIS cc_start: 0.8401 (t70) cc_final: 0.7446 (t70) REVERT: E 415 LYS cc_start: 0.8913 (mtpt) cc_final: 0.8512 (mtmp) outliers start: 15 outliers final: 1 residues processed: 356 average time/residue: 0.6482 time to fit residues: 253.8272 Evaluate side-chains 206 residues out of total 1835 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 205 time to evaluate : 0.604 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 268 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 195 random chunks: chunk 98 optimal weight: 0.7980 chunk 194 optimal weight: 6.9990 chunk 107 optimal weight: 8.9990 chunk 10 optimal weight: 7.9990 chunk 66 optimal weight: 10.0000 chunk 130 optimal weight: 2.9990 chunk 124 optimal weight: 0.9980 chunk 103 optimal weight: 1.9990 chunk 77 optimal weight: 4.9990 chunk 122 optimal weight: 0.9980 chunk 91 optimal weight: 2.9990 overall best weight: 1.5584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 55 ASN A 309 HIS B 55 ASN B 309 HIS C 55 ASN C 309 HIS D 55 ASN D 309 HIS E 55 ASN ** E 309 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3565 r_free = 0.3565 target = 0.119243 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2885 r_free = 0.2885 target = 0.076050 restraints weight = 25719.883| |-----------------------------------------------------------------------------| r_work (start): 0.2847 rms_B_bonded: 2.72 r_work: 0.2703 rms_B_bonded: 2.96 restraints_weight: 0.5000 r_work: 0.2561 rms_B_bonded: 4.66 restraints_weight: 0.2500 r_work (final): 0.2561 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8552 moved from start: 0.2137 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 17365 Z= 0.181 Angle : 0.732 7.115 23780 Z= 0.361 Chirality : 0.047 0.167 2820 Planarity : 0.006 0.045 2850 Dihedral : 10.857 66.667 2952 Min Nonbonded Distance : 2.419 Molprobity Statistics. All-atom Clashscore : 3.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.86 % Favored : 96.14 % Rotamer: Outliers : 3.98 % Allowed : 12.21 % Favored : 83.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.10 (0.17), residues: 1945 helix: -1.89 (0.15), residues: 790 sheet: -1.43 (0.21), residues: 450 loop : -2.43 (0.21), residues: 705 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG C 420 TYR 0.015 0.002 TYR A 126 PHE 0.018 0.001 PHE C 222 TRP 0.023 0.001 TRP B 168 HIS 0.003 0.001 HIS C 460 Details of bonding type rmsd covalent geometry : bond 0.00391 (17325) covalent geometry : angle 0.70859 (23680) SS BOND : bond 0.00557 ( 5) SS BOND : angle 1.43643 ( 10) hydrogen bonds : bond 0.08902 ( 688) hydrogen bonds : angle 5.31617 ( 2019) Misc. bond : bond 0.00055 ( 5) link_BETA1-4 : bond 0.00289 ( 15) link_BETA1-4 : angle 3.83065 ( 45) link_NAG-ASN : bond 0.00215 ( 15) link_NAG-ASN : angle 1.88912 ( 45) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3890 Ramachandran restraints generated. 1945 Oldfield, 0 Emsley, 1945 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3890 Ramachandran restraints generated. 1945 Oldfield, 0 Emsley, 1945 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 301 residues out of total 1835 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 73 poor density : 228 time to evaluate : 0.551 Fit side-chains REVERT: A 186 GLU cc_start: 0.7853 (tp30) cc_final: 0.7297 (tp30) REVERT: A 197 LYS cc_start: 0.8037 (mttm) cc_final: 0.7769 (mtpp) REVERT: A 238 ASP cc_start: 0.8822 (t70) cc_final: 0.8362 (t70) REVERT: A 420 ARG cc_start: 0.8739 (ttm-80) cc_final: 0.8319 (ttm170) REVERT: B 186 GLU cc_start: 0.7669 (tp30) cc_final: 0.7335 (tp30) REVERT: B 238 ASP cc_start: 0.9069 (t70) cc_final: 0.8695 (t70) REVERT: B 411 HIS cc_start: 0.7880 (t70) cc_final: 0.7641 (t-90) REVERT: B 418 GLU cc_start: 0.8627 (OUTLIER) cc_final: 0.8363 (tm-30) REVERT: C 186 GLU cc_start: 0.7744 (tp30) cc_final: 0.7508 (tp30) REVERT: C 195 GLN cc_start: 0.8512 (OUTLIER) cc_final: 0.8130 (tt0) REVERT: C 238 ASP cc_start: 0.9150 (t70) cc_final: 0.8565 (t70) REVERT: C 411 HIS cc_start: 0.7956 (t70) cc_final: 0.7706 (t70) REVERT: D 45 MET cc_start: 0.9615 (OUTLIER) cc_final: 0.9257 (tpp) REVERT: D 197 LYS cc_start: 0.7939 (mttm) cc_final: 0.7677 (mtpp) REVERT: D 238 ASP cc_start: 0.8958 (t70) cc_final: 0.8237 (t0) REVERT: E 186 GLU cc_start: 0.7692 (tp30) cc_final: 0.7289 (tp30) REVERT: E 197 LYS cc_start: 0.7931 (mttm) cc_final: 0.7677 (mtpp) REVERT: E 235 MET cc_start: 0.8906 (tpp) cc_final: 0.8691 (mmm) REVERT: E 238 ASP cc_start: 0.8923 (t70) cc_final: 0.8549 (t70) REVERT: E 411 HIS cc_start: 0.7953 (t70) cc_final: 0.7729 (t70) outliers start: 73 outliers final: 30 residues processed: 276 average time/residue: 0.4922 time to fit residues: 153.8882 Evaluate side-chains 233 residues out of total 1835 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 200 time to evaluate : 0.446 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 166 THR Chi-restraints excluded: chain A residue 225 VAL Chi-restraints excluded: chain A residue 236 VAL Chi-restraints excluded: chain B residue 116 TYR Chi-restraints excluded: chain B residue 221 LEU Chi-restraints excluded: chain B residue 225 VAL Chi-restraints excluded: chain B residue 228 LEU Chi-restraints excluded: chain B residue 231 SER Chi-restraints excluded: chain B residue 240 VAL Chi-restraints excluded: chain B residue 269 VAL Chi-restraints excluded: chain B residue 418 GLU Chi-restraints excluded: chain B residue 446 LEU Chi-restraints excluded: chain B residue 452 LEU Chi-restraints excluded: chain C residue 166 THR Chi-restraints excluded: chain C residue 195 GLN Chi-restraints excluded: chain C residue 221 LEU Chi-restraints excluded: chain C residue 225 VAL Chi-restraints excluded: chain C residue 231 SER Chi-restraints excluded: chain C residue 240 VAL Chi-restraints excluded: chain C residue 260 LEU Chi-restraints excluded: chain C residue 446 LEU Chi-restraints excluded: chain D residue 45 MET Chi-restraints excluded: chain D residue 221 LEU Chi-restraints excluded: chain D residue 225 VAL Chi-restraints excluded: chain D residue 231 SER Chi-restraints excluded: chain D residue 240 VAL Chi-restraints excluded: chain D residue 268 ILE Chi-restraints excluded: chain D residue 290 CYS Chi-restraints excluded: chain D residue 446 LEU Chi-restraints excluded: chain E residue 116 TYR Chi-restraints excluded: chain E residue 221 LEU Chi-restraints excluded: chain E residue 225 VAL Chi-restraints excluded: chain E residue 231 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 195 random chunks: chunk 10 optimal weight: 3.9990 chunk 58 optimal weight: 4.9990 chunk 165 optimal weight: 0.0770 chunk 137 optimal weight: 2.9990 chunk 61 optimal weight: 0.9990 chunk 129 optimal weight: 1.9990 chunk 41 optimal weight: 0.7980 chunk 186 optimal weight: 10.0000 chunk 124 optimal weight: 3.9990 chunk 94 optimal weight: 4.9990 chunk 20 optimal weight: 5.9990 overall best weight: 1.3744 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 309 HIS ** 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 = 0.3550 r_free = 0.3550 target = 0.118366 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.2841 r_free = 0.2841 target = 0.073990 restraints weight = 26181.787| |-----------------------------------------------------------------------------| r_work (start): 0.2821 rms_B_bonded: 2.82 r_work: 0.2678 rms_B_bonded: 3.01 restraints_weight: 0.5000 r_work: 0.2531 rms_B_bonded: 4.76 restraints_weight: 0.2500 r_work (final): 0.2531 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8532 moved from start: 0.2621 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 17365 Z= 0.156 Angle : 0.665 8.279 23780 Z= 0.323 Chirality : 0.047 0.187 2820 Planarity : 0.005 0.039 2850 Dihedral : 8.311 53.839 2952 Min Nonbonded Distance : 2.436 Molprobity Statistics. All-atom Clashscore : 3.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.37 % Favored : 95.63 % Rotamer: Outliers : 4.41 % Allowed : 13.73 % Favored : 81.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.87 (0.18), residues: 1945 helix: -0.40 (0.19), residues: 760 sheet: -1.20 (0.22), residues: 445 loop : -2.03 (0.22), residues: 740 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG E 420 TYR 0.015 0.001 TYR D 448 PHE 0.015 0.001 PHE B 222 TRP 0.017 0.001 TRP B 168 HIS 0.008 0.001 HIS D 411 Details of bonding type rmsd covalent geometry : bond 0.00341 (17325) covalent geometry : angle 0.63801 (23680) SS BOND : bond 0.00518 ( 5) SS BOND : angle 1.24442 ( 10) hydrogen bonds : bond 0.07329 ( 688) hydrogen bonds : angle 4.77731 ( 2019) Misc. bond : bond 0.00020 ( 5) link_BETA1-4 : bond 0.00397 ( 15) link_BETA1-4 : angle 3.98824 ( 45) link_NAG-ASN : bond 0.00265 ( 15) link_NAG-ASN : angle 1.76988 ( 45) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3890 Ramachandran restraints generated. 1945 Oldfield, 0 Emsley, 1945 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3890 Ramachandran restraints generated. 1945 Oldfield, 0 Emsley, 1945 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 301 residues out of total 1835 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 81 poor density : 220 time to evaluate : 0.658 Fit side-chains REVERT: A 186 GLU cc_start: 0.7880 (tp30) cc_final: 0.7258 (tp30) REVERT: A 197 LYS cc_start: 0.7947 (mttm) cc_final: 0.7700 (mtpp) REVERT: A 238 ASP cc_start: 0.8825 (t70) cc_final: 0.8426 (t70) REVERT: A 314 GLN cc_start: 0.7402 (mt0) cc_final: 0.7048 (mp10) REVERT: A 418 GLU cc_start: 0.8478 (OUTLIER) cc_final: 0.8166 (tm-30) REVERT: A 420 ARG cc_start: 0.8723 (ttm-80) cc_final: 0.8368 (ttm170) REVERT: B 186 GLU cc_start: 0.7766 (tp30) cc_final: 0.7271 (tp30) REVERT: B 238 ASP cc_start: 0.9049 (t70) cc_final: 0.8761 (t70) REVERT: B 314 GLN cc_start: 0.7606 (mt0) cc_final: 0.7206 (mp10) REVERT: B 411 HIS cc_start: 0.7863 (t70) cc_final: 0.7513 (t-90) REVERT: B 418 GLU cc_start: 0.8598 (OUTLIER) cc_final: 0.8277 (tm-30) REVERT: C 186 GLU cc_start: 0.7692 (tp30) cc_final: 0.7295 (tp30) REVERT: C 238 ASP cc_start: 0.9099 (t70) cc_final: 0.8535 (t0) REVERT: C 314 GLN cc_start: 0.7644 (mt0) cc_final: 0.7304 (mp10) REVERT: D 45 MET cc_start: 0.9628 (OUTLIER) cc_final: 0.9271 (tpp) REVERT: D 197 LYS cc_start: 0.7859 (mttm) cc_final: 0.7598 (mtpp) REVERT: D 238 ASP cc_start: 0.8901 (t70) cc_final: 0.8173 (t0) REVERT: D 420 ARG cc_start: 0.8753 (ttm170) cc_final: 0.8399 (ptp-110) REVERT: E 186 GLU cc_start: 0.7654 (tp30) cc_final: 0.7205 (tp30) REVERT: E 197 LYS cc_start: 0.7936 (mttm) cc_final: 0.7720 (mtpp) REVERT: E 238 ASP cc_start: 0.8933 (t70) cc_final: 0.8574 (t70) REVERT: E 411 HIS cc_start: 0.7917 (t70) cc_final: 0.7659 (m90) outliers start: 81 outliers final: 30 residues processed: 275 average time/residue: 0.4875 time to fit residues: 152.1225 Evaluate side-chains 225 residues out of total 1835 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 192 time to evaluate : 0.535 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 166 THR Chi-restraints excluded: chain A residue 229 LEU Chi-restraints excluded: chain A residue 236 VAL Chi-restraints excluded: chain A residue 240 VAL Chi-restraints excluded: chain A residue 321 LEU Chi-restraints excluded: chain A residue 418 GLU Chi-restraints excluded: chain A residue 446 LEU Chi-restraints excluded: chain B residue 116 TYR Chi-restraints excluded: chain B residue 166 THR Chi-restraints excluded: chain B residue 221 LEU Chi-restraints excluded: chain B residue 229 LEU Chi-restraints excluded: chain B residue 240 VAL Chi-restraints excluded: chain B residue 269 VAL Chi-restraints excluded: chain B residue 290 CYS Chi-restraints excluded: chain B residue 418 GLU Chi-restraints excluded: chain B residue 435 ARG Chi-restraints excluded: chain B residue 446 LEU Chi-restraints excluded: chain C residue 79 ASP Chi-restraints excluded: chain C residue 166 THR Chi-restraints excluded: chain C residue 221 LEU Chi-restraints excluded: chain C residue 240 VAL Chi-restraints excluded: chain C residue 260 LEU Chi-restraints excluded: chain C residue 269 VAL Chi-restraints excluded: chain C residue 290 CYS Chi-restraints excluded: chain C residue 446 LEU Chi-restraints excluded: chain D residue 45 MET Chi-restraints excluded: chain D residue 232 ILE Chi-restraints excluded: chain D residue 240 VAL Chi-restraints excluded: chain D residue 269 VAL Chi-restraints excluded: chain D residue 290 CYS Chi-restraints excluded: chain D residue 435 ARG Chi-restraints excluded: chain D residue 446 LEU Chi-restraints excluded: chain E residue 446 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 195 random chunks: chunk 103 optimal weight: 4.9990 chunk 186 optimal weight: 6.9990 chunk 181 optimal weight: 4.9990 chunk 4 optimal weight: 3.9990 chunk 108 optimal weight: 0.6980 chunk 69 optimal weight: 0.5980 chunk 65 optimal weight: 2.9990 chunk 22 optimal weight: 0.9990 chunk 191 optimal weight: 6.9990 chunk 152 optimal weight: 5.9990 chunk 0 optimal weight: 6.9990 overall best weight: 1.8586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 309 HIS ** 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 = 0.3531 r_free = 0.3531 target = 0.117084 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.2817 r_free = 0.2817 target = 0.072837 restraints weight = 26099.552| |-----------------------------------------------------------------------------| r_work (start): 0.2787 rms_B_bonded: 2.79 r_work: 0.2641 rms_B_bonded: 2.98 restraints_weight: 0.5000 r_work: 0.2497 rms_B_bonded: 4.67 restraints_weight: 0.2500 r_work (final): 0.2497 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8552 moved from start: 0.3025 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 17365 Z= 0.173 Angle : 0.658 8.288 23780 Z= 0.319 Chirality : 0.046 0.186 2820 Planarity : 0.004 0.039 2850 Dihedral : 7.145 54.505 2950 Min Nonbonded Distance : 2.452 Molprobity Statistics. All-atom Clashscore : 3.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.78 % Favored : 95.22 % Rotamer: Outliers : 4.47 % Allowed : 14.22 % Favored : 81.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.33 (0.19), residues: 1945 helix: 0.15 (0.19), residues: 790 sheet: -1.02 (0.22), residues: 445 loop : -1.86 (0.23), residues: 710 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG E 315 TYR 0.017 0.002 TYR D 448 PHE 0.028 0.002 PHE E 153 TRP 0.017 0.001 TRP E 456 HIS 0.008 0.001 HIS A 411 Details of bonding type rmsd covalent geometry : bond 0.00399 (17325) covalent geometry : angle 0.63302 (23680) SS BOND : bond 0.00590 ( 5) SS BOND : angle 1.34115 ( 10) hydrogen bonds : bond 0.06487 ( 688) hydrogen bonds : angle 4.60815 ( 2019) Misc. bond : bond 0.00019 ( 5) link_BETA1-4 : bond 0.00330 ( 15) link_BETA1-4 : angle 3.79551 ( 45) link_NAG-ASN : bond 0.00300 ( 15) link_NAG-ASN : angle 1.82597 ( 45) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3890 Ramachandran restraints generated. 1945 Oldfield, 0 Emsley, 1945 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3890 Ramachandran restraints generated. 1945 Oldfield, 0 Emsley, 1945 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 296 residues out of total 1835 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 82 poor density : 214 time to evaluate : 0.641 Fit side-chains revert: symmetry clash REVERT: A 186 GLU cc_start: 0.7924 (OUTLIER) cc_final: 0.7182 (tp30) REVERT: A 197 LYS cc_start: 0.8004 (mttm) cc_final: 0.7793 (mtpp) REVERT: A 238 ASP cc_start: 0.8867 (t70) cc_final: 0.8476 (t70) REVERT: A 314 GLN cc_start: 0.7481 (mt0) cc_final: 0.7140 (mp10) REVERT: A 411 HIS cc_start: 0.7745 (t70) cc_final: 0.7490 (m90) REVERT: A 420 ARG cc_start: 0.8682 (ttm-80) cc_final: 0.8452 (ptm160) REVERT: B 186 GLU cc_start: 0.7881 (tp30) cc_final: 0.7258 (tp30) REVERT: B 238 ASP cc_start: 0.9040 (t70) cc_final: 0.8431 (t0) REVERT: B 411 HIS cc_start: 0.7740 (t70) cc_final: 0.7478 (t-90) REVERT: B 420 ARG cc_start: 0.8730 (ttm-80) cc_final: 0.8497 (ptm160) REVERT: C 186 GLU cc_start: 0.7747 (tp30) cc_final: 0.7245 (tp30) REVERT: C 238 ASP cc_start: 0.9020 (t70) cc_final: 0.8541 (t0) REVERT: D 45 MET cc_start: 0.9610 (OUTLIER) cc_final: 0.9288 (tpp) REVERT: D 197 LYS cc_start: 0.7879 (mttm) cc_final: 0.7617 (mtpp) REVERT: D 238 ASP cc_start: 0.8957 (t70) cc_final: 0.8229 (t0) REVERT: D 314 GLN cc_start: 0.7142 (OUTLIER) cc_final: 0.6535 (pp30) REVERT: E 186 GLU cc_start: 0.7814 (tp30) cc_final: 0.7209 (tp30) REVERT: E 197 LYS cc_start: 0.8013 (mttm) cc_final: 0.7783 (mtpp) REVERT: E 238 ASP cc_start: 0.8962 (t70) cc_final: 0.8647 (t70) outliers start: 82 outliers final: 45 residues processed: 263 average time/residue: 0.4766 time to fit residues: 143.0899 Evaluate side-chains 239 residues out of total 1835 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 191 time to evaluate : 0.642 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 12 LEU Chi-restraints excluded: chain A residue 79 ASP Chi-restraints excluded: chain A residue 116 TYR Chi-restraints excluded: chain A residue 166 THR Chi-restraints excluded: chain A residue 186 GLU Chi-restraints excluded: chain A residue 229 LEU Chi-restraints excluded: chain A residue 236 VAL Chi-restraints excluded: chain A residue 240 VAL Chi-restraints excluded: chain A residue 445 VAL Chi-restraints excluded: chain A residue 450 ILE Chi-restraints excluded: chain B residue 12 LEU Chi-restraints excluded: chain B residue 79 ASP Chi-restraints excluded: chain B residue 116 TYR Chi-restraints excluded: chain B residue 166 THR Chi-restraints excluded: chain B residue 221 LEU Chi-restraints excluded: chain B residue 229 LEU Chi-restraints excluded: chain B residue 240 VAL Chi-restraints excluded: chain B residue 269 VAL Chi-restraints excluded: chain B residue 446 LEU Chi-restraints excluded: chain B residue 450 ILE Chi-restraints excluded: chain C residue 79 ASP Chi-restraints excluded: chain C residue 116 TYR Chi-restraints excluded: chain C residue 166 THR Chi-restraints excluded: chain C residue 221 LEU Chi-restraints excluded: chain C residue 240 VAL Chi-restraints excluded: chain C residue 260 LEU Chi-restraints excluded: chain C residue 269 VAL Chi-restraints excluded: chain C residue 290 CYS Chi-restraints excluded: chain C residue 435 ARG Chi-restraints excluded: chain D residue 12 LEU Chi-restraints excluded: chain D residue 45 MET Chi-restraints excluded: chain D residue 221 LEU Chi-restraints excluded: chain D residue 229 LEU Chi-restraints excluded: chain D residue 232 ILE Chi-restraints excluded: chain D residue 240 VAL Chi-restraints excluded: chain D residue 269 VAL Chi-restraints excluded: chain D residue 314 GLN Chi-restraints excluded: chain D residue 435 ARG Chi-restraints excluded: chain D residue 446 LEU Chi-restraints excluded: chain D residue 450 ILE Chi-restraints excluded: chain E residue 12 LEU Chi-restraints excluded: chain E residue 79 ASP Chi-restraints excluded: chain E residue 116 TYR Chi-restraints excluded: chain E residue 221 LEU Chi-restraints excluded: chain E residue 240 VAL Chi-restraints excluded: chain E residue 269 VAL Chi-restraints excluded: chain E residue 446 LEU Chi-restraints excluded: chain E residue 450 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 195 random chunks: chunk 157 optimal weight: 0.3980 chunk 137 optimal weight: 6.9990 chunk 25 optimal weight: 6.9990 chunk 104 optimal weight: 9.9990 chunk 39 optimal weight: 5.9990 chunk 175 optimal weight: 2.9990 chunk 184 optimal weight: 4.9990 chunk 46 optimal weight: 4.9990 chunk 109 optimal weight: 4.9990 chunk 35 optimal weight: 1.9990 chunk 132 optimal weight: 0.8980 overall best weight: 2.2586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 309 HIS ** 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 = 0.3517 r_free = 0.3517 target = 0.116190 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.2800 r_free = 0.2800 target = 0.072015 restraints weight = 25846.074| |-----------------------------------------------------------------------------| r_work (start): 0.2773 rms_B_bonded: 2.77 r_work: 0.2629 rms_B_bonded: 2.94 restraints_weight: 0.5000 r_work: 0.2484 rms_B_bonded: 4.63 restraints_weight: 0.2500 r_work (final): 0.2484 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8573 moved from start: 0.3181 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.033 17365 Z= 0.194 Angle : 0.664 8.183 23780 Z= 0.320 Chirality : 0.046 0.193 2820 Planarity : 0.004 0.039 2850 Dihedral : 6.924 54.758 2950 Min Nonbonded Distance : 2.442 Molprobity Statistics. All-atom Clashscore : 3.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.09 % Favored : 94.91 % Rotamer: Outliers : 4.41 % Allowed : 14.50 % Favored : 81.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.07 (0.19), residues: 1945 helix: 0.47 (0.20), residues: 785 sheet: -0.87 (0.23), residues: 445 loop : -1.87 (0.23), residues: 715 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D 328 TYR 0.017 0.002 TYR D 448 PHE 0.026 0.002 PHE E 153 TRP 0.019 0.001 TRP E 456 HIS 0.007 0.001 HIS D 411 Details of bonding type rmsd covalent geometry : bond 0.00460 (17325) covalent geometry : angle 0.63953 (23680) SS BOND : bond 0.00627 ( 5) SS BOND : angle 1.47196 ( 10) hydrogen bonds : bond 0.06284 ( 688) hydrogen bonds : angle 4.58059 ( 2019) Misc. bond : bond 0.00022 ( 5) link_BETA1-4 : bond 0.00351 ( 15) link_BETA1-4 : angle 3.69832 ( 45) link_NAG-ASN : bond 0.00286 ( 15) link_NAG-ASN : angle 1.87938 ( 45) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3890 Ramachandran restraints generated. 1945 Oldfield, 0 Emsley, 1945 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3890 Ramachandran restraints generated. 1945 Oldfield, 0 Emsley, 1945 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 271 residues out of total 1835 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 81 poor density : 190 time to evaluate : 0.673 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 186 GLU cc_start: 0.8001 (OUTLIER) cc_final: 0.7260 (tp30) REVERT: A 197 LYS cc_start: 0.7940 (mttm) cc_final: 0.7730 (mtpp) REVERT: A 238 ASP cc_start: 0.8882 (t70) cc_final: 0.8513 (t70) REVERT: A 314 GLN cc_start: 0.7471 (mt0) cc_final: 0.7110 (mp10) REVERT: A 420 ARG cc_start: 0.8669 (ttm-80) cc_final: 0.8455 (ptm160) REVERT: B 184 GLN cc_start: 0.8314 (tt0) cc_final: 0.8059 (tt0) REVERT: B 186 GLU cc_start: 0.7938 (OUTLIER) cc_final: 0.7202 (tp30) REVERT: B 238 ASP cc_start: 0.9037 (t70) cc_final: 0.8431 (t0) REVERT: B 420 ARG cc_start: 0.8683 (ttm-80) cc_final: 0.8465 (ptm160) REVERT: C 186 GLU cc_start: 0.7814 (tp30) cc_final: 0.7192 (tp30) REVERT: C 235 MET cc_start: 0.8833 (tpp) cc_final: 0.8602 (mmm) REVERT: C 238 ASP cc_start: 0.9036 (t70) cc_final: 0.8636 (t0) REVERT: D 45 MET cc_start: 0.9596 (OUTLIER) cc_final: 0.9281 (tpp) REVERT: D 197 LYS cc_start: 0.7907 (mttm) cc_final: 0.7651 (mtpp) REVERT: D 238 ASP cc_start: 0.9012 (t70) cc_final: 0.8308 (t0) REVERT: D 314 GLN cc_start: 0.7133 (OUTLIER) cc_final: 0.6532 (pp30) REVERT: D 420 ARG cc_start: 0.8662 (ttm170) cc_final: 0.8376 (ptp-110) REVERT: E 186 GLU cc_start: 0.7876 (OUTLIER) cc_final: 0.7134 (tp30) REVERT: E 197 LYS cc_start: 0.8019 (mttm) cc_final: 0.7780 (mtpp) REVERT: E 238 ASP cc_start: 0.8961 (t70) cc_final: 0.8393 (t0) REVERT: E 411 HIS cc_start: 0.7758 (m90) cc_final: 0.7514 (m90) outliers start: 81 outliers final: 49 residues processed: 240 average time/residue: 0.5026 time to fit residues: 137.1757 Evaluate side-chains 231 residues out of total 1835 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 177 time to evaluate : 0.625 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 12 LEU Chi-restraints excluded: chain A residue 79 ASP Chi-restraints excluded: chain A residue 116 TYR Chi-restraints excluded: chain A residue 166 THR Chi-restraints excluded: chain A residue 186 GLU Chi-restraints excluded: chain A residue 221 LEU Chi-restraints excluded: chain A residue 229 LEU Chi-restraints excluded: chain A residue 240 VAL Chi-restraints excluded: chain A residue 290 CYS Chi-restraints excluded: chain A residue 435 ARG Chi-restraints excluded: chain A residue 450 ILE Chi-restraints excluded: chain B residue 12 LEU Chi-restraints excluded: chain B residue 79 ASP Chi-restraints excluded: chain B residue 116 TYR Chi-restraints excluded: chain B residue 166 THR Chi-restraints excluded: chain B residue 186 GLU Chi-restraints excluded: chain B residue 221 LEU Chi-restraints excluded: chain B residue 228 LEU Chi-restraints excluded: chain B residue 229 LEU Chi-restraints excluded: chain B residue 240 VAL Chi-restraints excluded: chain B residue 269 VAL Chi-restraints excluded: chain B residue 290 CYS Chi-restraints excluded: chain B residue 435 ARG Chi-restraints excluded: chain B residue 450 ILE Chi-restraints excluded: chain C residue 12 LEU Chi-restraints excluded: chain C residue 79 ASP Chi-restraints excluded: chain C residue 166 THR Chi-restraints excluded: chain C residue 221 LEU Chi-restraints excluded: chain C residue 228 LEU Chi-restraints excluded: chain C residue 240 VAL Chi-restraints excluded: chain C residue 260 LEU Chi-restraints excluded: chain C residue 269 VAL Chi-restraints excluded: chain C residue 290 CYS Chi-restraints excluded: chain D residue 45 MET Chi-restraints excluded: chain D residue 79 ASP Chi-restraints excluded: chain D residue 221 LEU Chi-restraints excluded: chain D residue 229 LEU Chi-restraints excluded: chain D residue 232 ILE Chi-restraints excluded: chain D residue 240 VAL Chi-restraints excluded: chain D residue 269 VAL Chi-restraints excluded: chain D residue 290 CYS Chi-restraints excluded: chain D residue 314 GLN Chi-restraints excluded: chain D residue 435 ARG Chi-restraints excluded: chain D residue 450 ILE Chi-restraints excluded: chain E residue 12 LEU Chi-restraints excluded: chain E residue 79 ASP Chi-restraints excluded: chain E residue 116 TYR Chi-restraints excluded: chain E residue 186 GLU Chi-restraints excluded: chain E residue 221 LEU Chi-restraints excluded: chain E residue 240 VAL Chi-restraints excluded: chain E residue 269 VAL Chi-restraints excluded: chain E residue 290 CYS Chi-restraints excluded: chain E residue 433 LEU Chi-restraints excluded: chain E residue 446 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 195 random chunks: chunk 76 optimal weight: 8.9990 chunk 148 optimal weight: 4.9990 chunk 38 optimal weight: 5.9990 chunk 98 optimal weight: 5.9990 chunk 156 optimal weight: 2.9990 chunk 137 optimal weight: 4.9990 chunk 164 optimal weight: 0.9980 chunk 132 optimal weight: 0.9990 chunk 75 optimal weight: 0.7980 chunk 166 optimal weight: 0.9980 chunk 3 optimal weight: 3.9990 overall best weight: 1.3584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 309 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3529 r_free = 0.3529 target = 0.117055 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.2817 r_free = 0.2817 target = 0.072955 restraints weight = 25818.052| |-----------------------------------------------------------------------------| r_work (start): 0.2793 rms_B_bonded: 2.78 r_work: 0.2646 rms_B_bonded: 2.97 restraints_weight: 0.5000 r_work: 0.2501 rms_B_bonded: 4.66 restraints_weight: 0.2500 r_work (final): 0.2501 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8555 moved from start: 0.3345 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 17365 Z= 0.141 Angle : 0.621 7.687 23780 Z= 0.298 Chirality : 0.045 0.175 2820 Planarity : 0.004 0.035 2850 Dihedral : 6.472 53.692 2950 Min Nonbonded Distance : 2.393 Molprobity Statistics. All-atom Clashscore : 3.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.88 % Favored : 95.12 % Rotamer: Outliers : 4.47 % Allowed : 14.55 % Favored : 80.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.76 (0.19), residues: 1945 helix: 1.00 (0.20), residues: 755 sheet: -0.81 (0.24), residues: 425 loop : -1.84 (0.22), residues: 765 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 315 TYR 0.017 0.001 TYR C 448 PHE 0.016 0.001 PHE C 153 TRP 0.020 0.001 TRP A 456 HIS 0.007 0.001 HIS D 411 Details of bonding type rmsd covalent geometry : bond 0.00314 (17325) covalent geometry : angle 0.59783 (23680) SS BOND : bond 0.00494 ( 5) SS BOND : angle 1.28635 ( 10) hydrogen bonds : bond 0.05827 ( 688) hydrogen bonds : angle 4.47574 ( 2019) Misc. bond : bond 0.00002 ( 5) link_BETA1-4 : bond 0.00376 ( 15) link_BETA1-4 : angle 3.52799 ( 45) link_NAG-ASN : bond 0.00195 ( 15) link_NAG-ASN : angle 1.66320 ( 45) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3890 Ramachandran restraints generated. 1945 Oldfield, 0 Emsley, 1945 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3890 Ramachandran restraints generated. 1945 Oldfield, 0 Emsley, 1945 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 281 residues out of total 1835 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 82 poor density : 199 time to evaluate : 0.636 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 186 GLU cc_start: 0.7975 (OUTLIER) cc_final: 0.7224 (tp30) REVERT: A 197 LYS cc_start: 0.7923 (mttm) cc_final: 0.7722 (mtpp) REVERT: A 238 ASP cc_start: 0.8880 (t70) cc_final: 0.8547 (t70) REVERT: A 314 GLN cc_start: 0.7553 (mt0) cc_final: 0.7190 (mp10) REVERT: A 411 HIS cc_start: 0.7839 (m90) cc_final: 0.7628 (m90) REVERT: B 186 GLU cc_start: 0.7913 (OUTLIER) cc_final: 0.7212 (tp30) REVERT: B 238 ASP cc_start: 0.9040 (t70) cc_final: 0.8446 (t0) REVERT: C 186 GLU cc_start: 0.7835 (OUTLIER) cc_final: 0.7149 (tp30) REVERT: C 238 ASP cc_start: 0.9024 (t70) cc_final: 0.8617 (t0) REVERT: C 435 ARG cc_start: 0.7121 (OUTLIER) cc_final: 0.6831 (tpt170) REVERT: D 45 MET cc_start: 0.9598 (OUTLIER) cc_final: 0.9281 (tpp) REVERT: D 197 LYS cc_start: 0.7879 (mttm) cc_final: 0.7628 (mtpp) REVERT: D 238 ASP cc_start: 0.8983 (t70) cc_final: 0.8272 (t0) REVERT: D 314 GLN cc_start: 0.7126 (OUTLIER) cc_final: 0.6521 (pp30) REVERT: D 420 ARG cc_start: 0.8677 (ttm170) cc_final: 0.8402 (ptp-110) REVERT: E 186 GLU cc_start: 0.7820 (OUTLIER) cc_final: 0.7128 (tp30) REVERT: E 197 LYS cc_start: 0.7982 (mttm) cc_final: 0.7742 (mtpp) REVERT: E 238 ASP cc_start: 0.8972 (t70) cc_final: 0.8373 (t0) REVERT: E 411 HIS cc_start: 0.7696 (m90) cc_final: 0.7472 (m90) outliers start: 82 outliers final: 44 residues processed: 250 average time/residue: 0.4920 time to fit residues: 139.9551 Evaluate side-chains 233 residues out of total 1835 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 182 time to evaluate : 0.533 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 79 ASP Chi-restraints excluded: chain A residue 116 TYR Chi-restraints excluded: chain A residue 166 THR Chi-restraints excluded: chain A residue 186 GLU Chi-restraints excluded: chain A residue 221 LEU Chi-restraints excluded: chain A residue 229 LEU Chi-restraints excluded: chain A residue 236 VAL Chi-restraints excluded: chain A residue 240 VAL Chi-restraints excluded: chain A residue 260 LEU Chi-restraints excluded: chain A residue 290 CYS Chi-restraints excluded: chain A residue 435 ARG Chi-restraints excluded: chain A residue 450 ILE Chi-restraints excluded: chain B residue 79 ASP Chi-restraints excluded: chain B residue 116 TYR Chi-restraints excluded: chain B residue 166 THR Chi-restraints excluded: chain B residue 186 GLU Chi-restraints excluded: chain B residue 221 LEU Chi-restraints excluded: chain B residue 229 LEU Chi-restraints excluded: chain B residue 232 ILE Chi-restraints excluded: chain B residue 269 VAL Chi-restraints excluded: chain B residue 290 CYS Chi-restraints excluded: chain B residue 435 ARG Chi-restraints excluded: chain B residue 450 ILE Chi-restraints excluded: chain C residue 79 ASP Chi-restraints excluded: chain C residue 166 THR Chi-restraints excluded: chain C residue 186 GLU Chi-restraints excluded: chain C residue 221 LEU Chi-restraints excluded: chain C residue 229 LEU Chi-restraints excluded: chain C residue 260 LEU Chi-restraints excluded: chain C residue 269 VAL Chi-restraints excluded: chain C residue 290 CYS Chi-restraints excluded: chain C residue 435 ARG Chi-restraints excluded: chain C residue 450 ILE Chi-restraints excluded: chain D residue 12 LEU Chi-restraints excluded: chain D residue 45 MET Chi-restraints excluded: chain D residue 79 ASP Chi-restraints excluded: chain D residue 221 LEU Chi-restraints excluded: chain D residue 229 LEU Chi-restraints excluded: chain D residue 232 ILE Chi-restraints excluded: chain D residue 240 VAL Chi-restraints excluded: chain D residue 269 VAL Chi-restraints excluded: chain D residue 290 CYS Chi-restraints excluded: chain D residue 314 GLN Chi-restraints excluded: chain D residue 435 ARG Chi-restraints excluded: chain D residue 450 ILE Chi-restraints excluded: chain E residue 79 ASP Chi-restraints excluded: chain E residue 116 TYR Chi-restraints excluded: chain E residue 186 GLU Chi-restraints excluded: chain E residue 221 LEU Chi-restraints excluded: chain E residue 269 VAL Chi-restraints excluded: chain E residue 433 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 195 random chunks: chunk 105 optimal weight: 0.4980 chunk 87 optimal weight: 1.9990 chunk 168 optimal weight: 1.9990 chunk 25 optimal weight: 0.9990 chunk 97 optimal weight: 4.9990 chunk 15 optimal weight: 4.9990 chunk 30 optimal weight: 6.9990 chunk 114 optimal weight: 0.9990 chunk 123 optimal weight: 0.9990 chunk 149 optimal weight: 4.9990 chunk 190 optimal weight: 4.9990 overall best weight: 1.0988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3538 r_free = 0.3538 target = 0.117661 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.2829 r_free = 0.2829 target = 0.073515 restraints weight = 25790.231| |-----------------------------------------------------------------------------| r_work (start): 0.2803 rms_B_bonded: 2.80 r_work: 0.2657 rms_B_bonded: 2.97 restraints_weight: 0.5000 r_work: 0.2511 rms_B_bonded: 4.68 restraints_weight: 0.2500 r_work (final): 0.2511 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8547 moved from start: 0.3496 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 17365 Z= 0.128 Angle : 0.613 7.475 23780 Z= 0.293 Chirality : 0.045 0.167 2820 Planarity : 0.004 0.034 2850 Dihedral : 6.152 53.631 2950 Min Nonbonded Distance : 2.346 Molprobity Statistics. All-atom Clashscore : 3.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.78 % Favored : 95.22 % Rotamer: Outliers : 4.14 % Allowed : 15.37 % Favored : 80.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.57 (0.20), residues: 1945 helix: 1.21 (0.20), residues: 750 sheet: -0.70 (0.24), residues: 425 loop : -1.79 (0.22), residues: 770 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 420 TYR 0.018 0.001 TYR C 448 PHE 0.029 0.001 PHE D 412 TRP 0.022 0.001 TRP A 456 HIS 0.007 0.001 HIS D 411 Details of bonding type rmsd covalent geometry : bond 0.00278 (17325) covalent geometry : angle 0.59178 (23680) SS BOND : bond 0.00443 ( 5) SS BOND : angle 1.18377 ( 10) hydrogen bonds : bond 0.05514 ( 688) hydrogen bonds : angle 4.38450 ( 2019) Misc. bond : bond 0.00007 ( 5) link_BETA1-4 : bond 0.00395 ( 15) link_BETA1-4 : angle 3.39561 ( 45) link_NAG-ASN : bond 0.00193 ( 15) link_NAG-ASN : angle 1.52141 ( 45) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3890 Ramachandran restraints generated. 1945 Oldfield, 0 Emsley, 1945 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3890 Ramachandran restraints generated. 1945 Oldfield, 0 Emsley, 1945 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 266 residues out of total 1835 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 76 poor density : 190 time to evaluate : 0.624 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 186 GLU cc_start: 0.7969 (OUTLIER) cc_final: 0.7229 (tp30) REVERT: A 197 LYS cc_start: 0.7926 (mttm) cc_final: 0.7710 (mtpp) REVERT: A 238 ASP cc_start: 0.8884 (t70) cc_final: 0.8558 (t70) REVERT: A 314 GLN cc_start: 0.7577 (mt0) cc_final: 0.7150 (mp10) REVERT: A 420 ARG cc_start: 0.8652 (ttm-80) cc_final: 0.8320 (ptp-110) REVERT: A 435 ARG cc_start: 0.7377 (OUTLIER) cc_final: 0.7059 (tpt170) REVERT: B 186 GLU cc_start: 0.7756 (OUTLIER) cc_final: 0.7053 (tp30) REVERT: B 229 LEU cc_start: 0.8185 (OUTLIER) cc_final: 0.7755 (tm) REVERT: B 238 ASP cc_start: 0.9006 (t70) cc_final: 0.8450 (t0) REVERT: B 314 GLN cc_start: 0.7596 (mt0) cc_final: 0.7171 (mp10) REVERT: B 420 ARG cc_start: 0.8747 (ptm160) cc_final: 0.8521 (ptp-110) REVERT: B 435 ARG cc_start: 0.7232 (OUTLIER) cc_final: 0.6862 (tpt170) REVERT: C 91 ASP cc_start: 0.9058 (p0) cc_final: 0.8847 (p0) REVERT: C 186 GLU cc_start: 0.7736 (OUTLIER) cc_final: 0.7015 (tp30) REVERT: C 235 MET cc_start: 0.8854 (tpp) cc_final: 0.8623 (mmm) REVERT: C 238 ASP cc_start: 0.9015 (t70) cc_final: 0.8602 (t0) REVERT: C 435 ARG cc_start: 0.7096 (OUTLIER) cc_final: 0.6790 (tpt170) REVERT: D 45 MET cc_start: 0.9602 (OUTLIER) cc_final: 0.9283 (tpp) REVERT: D 197 LYS cc_start: 0.7879 (mttm) cc_final: 0.7632 (mtpp) REVERT: D 238 ASP cc_start: 0.8978 (t70) cc_final: 0.8289 (t0) REVERT: D 314 GLN cc_start: 0.7251 (OUTLIER) cc_final: 0.6654 (pp30) REVERT: D 420 ARG cc_start: 0.8653 (ttm170) cc_final: 0.8395 (ptp-110) REVERT: E 186 GLU cc_start: 0.7787 (OUTLIER) cc_final: 0.7096 (tp30) REVERT: E 197 LYS cc_start: 0.7960 (mttm) cc_final: 0.7722 (mtpp) REVERT: E 238 ASP cc_start: 0.8887 (t70) cc_final: 0.8320 (t0) outliers start: 76 outliers final: 42 residues processed: 236 average time/residue: 0.5060 time to fit residues: 135.5229 Evaluate side-chains 232 residues out of total 1835 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 180 time to evaluate : 0.420 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 12 LEU Chi-restraints excluded: chain A residue 79 ASP Chi-restraints excluded: chain A residue 116 TYR Chi-restraints excluded: chain A residue 166 THR Chi-restraints excluded: chain A residue 186 GLU Chi-restraints excluded: chain A residue 221 LEU Chi-restraints excluded: chain A residue 229 LEU Chi-restraints excluded: chain A residue 236 VAL Chi-restraints excluded: chain A residue 260 LEU Chi-restraints excluded: chain A residue 290 CYS Chi-restraints excluded: chain A residue 433 LEU Chi-restraints excluded: chain A residue 435 ARG Chi-restraints excluded: chain A residue 450 ILE Chi-restraints excluded: chain B residue 12 LEU Chi-restraints excluded: chain B residue 166 THR Chi-restraints excluded: chain B residue 186 GLU Chi-restraints excluded: chain B residue 221 LEU Chi-restraints excluded: chain B residue 229 LEU Chi-restraints excluded: chain B residue 269 VAL Chi-restraints excluded: chain B residue 290 CYS Chi-restraints excluded: chain B residue 435 ARG Chi-restraints excluded: chain C residue 12 LEU Chi-restraints excluded: chain C residue 79 ASP Chi-restraints excluded: chain C residue 166 THR Chi-restraints excluded: chain C residue 186 GLU Chi-restraints excluded: chain C residue 221 LEU Chi-restraints excluded: chain C residue 229 LEU Chi-restraints excluded: chain C residue 260 LEU Chi-restraints excluded: chain C residue 269 VAL Chi-restraints excluded: chain C residue 290 CYS Chi-restraints excluded: chain C residue 433 LEU Chi-restraints excluded: chain C residue 435 ARG Chi-restraints excluded: chain D residue 45 MET Chi-restraints excluded: chain D residue 79 ASP Chi-restraints excluded: chain D residue 116 TYR Chi-restraints excluded: chain D residue 221 LEU Chi-restraints excluded: chain D residue 229 LEU Chi-restraints excluded: chain D residue 232 ILE Chi-restraints excluded: chain D residue 240 VAL Chi-restraints excluded: chain D residue 269 VAL Chi-restraints excluded: chain D residue 314 GLN Chi-restraints excluded: chain D residue 435 ARG Chi-restraints excluded: chain E residue 12 LEU Chi-restraints excluded: chain E residue 79 ASP Chi-restraints excluded: chain E residue 116 TYR Chi-restraints excluded: chain E residue 186 GLU Chi-restraints excluded: chain E residue 221 LEU Chi-restraints excluded: chain E residue 229 LEU Chi-restraints excluded: chain E residue 269 VAL Chi-restraints excluded: chain E residue 433 LEU Chi-restraints excluded: chain E residue 435 ARG Chi-restraints excluded: chain E residue 450 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 195 random chunks: chunk 81 optimal weight: 3.9990 chunk 101 optimal weight: 0.7980 chunk 167 optimal weight: 5.9990 chunk 102 optimal weight: 1.9990 chunk 111 optimal weight: 5.9990 chunk 66 optimal weight: 0.8980 chunk 188 optimal weight: 8.9990 chunk 80 optimal weight: 3.9990 chunk 186 optimal weight: 0.2980 chunk 5 optimal weight: 3.9990 chunk 53 optimal weight: 5.9990 overall best weight: 1.5984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3530 r_free = 0.3530 target = 0.117034 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.2814 r_free = 0.2814 target = 0.072775 restraints weight = 25892.006| |-----------------------------------------------------------------------------| r_work (start): 0.2791 rms_B_bonded: 2.79 r_work: 0.2645 rms_B_bonded: 2.97 restraints_weight: 0.5000 r_work: 0.2499 rms_B_bonded: 4.65 restraints_weight: 0.2500 r_work (final): 0.2499 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8549 moved from start: 0.3553 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 17365 Z= 0.151 Angle : 0.630 8.137 23780 Z= 0.302 Chirality : 0.045 0.168 2820 Planarity : 0.004 0.036 2850 Dihedral : 6.080 54.454 2950 Min Nonbonded Distance : 2.302 Molprobity Statistics. All-atom Clashscore : 3.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.88 % Favored : 95.12 % Rotamer: Outliers : 3.65 % Allowed : 15.80 % Favored : 80.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.48 (0.20), residues: 1945 helix: 1.30 (0.20), residues: 750 sheet: -0.67 (0.24), residues: 425 loop : -1.74 (0.22), residues: 770 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 315 TYR 0.018 0.001 TYR C 448 PHE 0.027 0.002 PHE A 412 TRP 0.024 0.001 TRP E 456 HIS 0.006 0.001 HIS D 411 Details of bonding type rmsd covalent geometry : bond 0.00346 (17325) covalent geometry : angle 0.60992 (23680) SS BOND : bond 0.00532 ( 5) SS BOND : angle 1.26357 ( 10) hydrogen bonds : bond 0.05459 ( 688) hydrogen bonds : angle 4.35532 ( 2019) Misc. bond : bond 0.00008 ( 5) link_BETA1-4 : bond 0.00358 ( 15) link_BETA1-4 : angle 3.33830 ( 45) link_NAG-ASN : bond 0.00213 ( 15) link_NAG-ASN : angle 1.59818 ( 45) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3890 Ramachandran restraints generated. 1945 Oldfield, 0 Emsley, 1945 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3890 Ramachandran restraints generated. 1945 Oldfield, 0 Emsley, 1945 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 247 residues out of total 1835 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 180 time to evaluate : 0.697 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 186 GLU cc_start: 0.7968 (OUTLIER) cc_final: 0.7192 (tp30) REVERT: A 238 ASP cc_start: 0.8890 (t70) cc_final: 0.8548 (t70) REVERT: A 314 GLN cc_start: 0.7509 (mt0) cc_final: 0.7115 (mp10) REVERT: A 420 ARG cc_start: 0.8637 (ttm-80) cc_final: 0.8307 (ptp-110) REVERT: A 435 ARG cc_start: 0.7311 (OUTLIER) cc_final: 0.7015 (tpt170) REVERT: B 186 GLU cc_start: 0.7719 (OUTLIER) cc_final: 0.6983 (tp30) REVERT: B 238 ASP cc_start: 0.9023 (t70) cc_final: 0.8468 (t0) REVERT: B 435 ARG cc_start: 0.7177 (OUTLIER) cc_final: 0.6849 (tpt170) REVERT: C 91 ASP cc_start: 0.9058 (p0) cc_final: 0.8843 (p0) REVERT: C 186 GLU cc_start: 0.7690 (OUTLIER) cc_final: 0.6936 (tp30) REVERT: C 235 MET cc_start: 0.8839 (tpp) cc_final: 0.8623 (mmm) REVERT: C 238 ASP cc_start: 0.8982 (t70) cc_final: 0.8595 (t0) REVERT: C 435 ARG cc_start: 0.6999 (OUTLIER) cc_final: 0.6733 (tpt170) REVERT: D 45 MET cc_start: 0.9587 (OUTLIER) cc_final: 0.9251 (tpp) REVERT: D 197 LYS cc_start: 0.7914 (mttm) cc_final: 0.7665 (mtpp) REVERT: D 238 ASP cc_start: 0.8985 (t70) cc_final: 0.8308 (t0) REVERT: D 314 GLN cc_start: 0.7215 (OUTLIER) cc_final: 0.6640 (pp30) REVERT: D 420 ARG cc_start: 0.8631 (ttm170) cc_final: 0.8375 (ptp-110) REVERT: E 186 GLU cc_start: 0.7799 (OUTLIER) cc_final: 0.7078 (tp30) REVERT: E 197 LYS cc_start: 0.7951 (mttm) cc_final: 0.7722 (mtpp) REVERT: E 238 ASP cc_start: 0.8882 (t70) cc_final: 0.8336 (t0) outliers start: 67 outliers final: 47 residues processed: 220 average time/residue: 0.5414 time to fit residues: 134.2696 Evaluate side-chains 229 residues out of total 1835 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 173 time to evaluate : 0.634 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 12 LEU Chi-restraints excluded: chain A residue 79 ASP Chi-restraints excluded: chain A residue 116 TYR Chi-restraints excluded: chain A residue 166 THR Chi-restraints excluded: chain A residue 186 GLU Chi-restraints excluded: chain A residue 221 LEU Chi-restraints excluded: chain A residue 229 LEU Chi-restraints excluded: chain A residue 236 VAL Chi-restraints excluded: chain A residue 260 LEU Chi-restraints excluded: chain A residue 290 CYS Chi-restraints excluded: chain A residue 329 ILE Chi-restraints excluded: chain A residue 433 LEU Chi-restraints excluded: chain A residue 435 ARG Chi-restraints excluded: chain A residue 450 ILE Chi-restraints excluded: chain B residue 12 LEU Chi-restraints excluded: chain B residue 79 ASP Chi-restraints excluded: chain B residue 166 THR Chi-restraints excluded: chain B residue 186 GLU Chi-restraints excluded: chain B residue 221 LEU Chi-restraints excluded: chain B residue 228 LEU Chi-restraints excluded: chain B residue 229 LEU Chi-restraints excluded: chain B residue 232 ILE Chi-restraints excluded: chain B residue 269 VAL Chi-restraints excluded: chain B residue 435 ARG Chi-restraints excluded: chain B residue 450 ILE Chi-restraints excluded: chain C residue 12 LEU Chi-restraints excluded: chain C residue 79 ASP Chi-restraints excluded: chain C residue 166 THR Chi-restraints excluded: chain C residue 186 GLU Chi-restraints excluded: chain C residue 221 LEU Chi-restraints excluded: chain C residue 229 LEU Chi-restraints excluded: chain C residue 260 LEU Chi-restraints excluded: chain C residue 269 VAL Chi-restraints excluded: chain C residue 290 CYS Chi-restraints excluded: chain C residue 435 ARG Chi-restraints excluded: chain D residue 12 LEU Chi-restraints excluded: chain D residue 45 MET Chi-restraints excluded: chain D residue 79 ASP Chi-restraints excluded: chain D residue 116 TYR Chi-restraints excluded: chain D residue 221 LEU Chi-restraints excluded: chain D residue 229 LEU Chi-restraints excluded: chain D residue 232 ILE Chi-restraints excluded: chain D residue 240 VAL Chi-restraints excluded: chain D residue 269 VAL Chi-restraints excluded: chain D residue 314 GLN Chi-restraints excluded: chain D residue 435 ARG Chi-restraints excluded: chain D residue 450 ILE Chi-restraints excluded: chain E residue 12 LEU Chi-restraints excluded: chain E residue 79 ASP Chi-restraints excluded: chain E residue 116 TYR Chi-restraints excluded: chain E residue 186 GLU Chi-restraints excluded: chain E residue 221 LEU Chi-restraints excluded: chain E residue 269 VAL Chi-restraints excluded: chain E residue 433 LEU Chi-restraints excluded: chain E residue 435 ARG Chi-restraints excluded: chain E residue 450 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 195 random chunks: chunk 47 optimal weight: 2.9990 chunk 15 optimal weight: 0.8980 chunk 3 optimal weight: 4.9990 chunk 88 optimal weight: 0.2980 chunk 113 optimal weight: 5.9990 chunk 185 optimal weight: 1.9990 chunk 20 optimal weight: 1.9990 chunk 17 optimal weight: 0.7980 chunk 138 optimal weight: 3.9990 chunk 164 optimal weight: 1.9990 chunk 67 optimal weight: 0.9990 overall best weight: 0.9984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 184 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3547 r_free = 0.3547 target = 0.118289 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.2843 r_free = 0.2843 target = 0.074227 restraints weight = 25692.187| |-----------------------------------------------------------------------------| r_work (start): 0.2816 rms_B_bonded: 2.79 r_work: 0.2670 rms_B_bonded: 2.97 restraints_weight: 0.5000 r_work: 0.2525 rms_B_bonded: 4.67 restraints_weight: 0.2500 r_work (final): 0.2525 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8538 moved from start: 0.3695 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 17365 Z= 0.120 Angle : 0.604 8.017 23780 Z= 0.289 Chirality : 0.044 0.156 2820 Planarity : 0.004 0.033 2850 Dihedral : 5.799 53.321 2950 Min Nonbonded Distance : 2.282 Molprobity Statistics. All-atom Clashscore : 3.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.73 % Favored : 95.27 % Rotamer: Outliers : 3.38 % Allowed : 16.24 % Favored : 80.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.36 (0.20), residues: 1945 helix: 1.43 (0.20), residues: 750 sheet: -0.62 (0.24), residues: 425 loop : -1.69 (0.22), residues: 770 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG E 315 TYR 0.017 0.001 TYR E 448 PHE 0.018 0.001 PHE A 233 TRP 0.027 0.001 TRP D 456 HIS 0.006 0.001 HIS D 411 Details of bonding type rmsd covalent geometry : bond 0.00260 (17325) covalent geometry : angle 0.58428 (23680) SS BOND : bond 0.00407 ( 5) SS BOND : angle 1.19538 ( 10) hydrogen bonds : bond 0.05098 ( 688) hydrogen bonds : angle 4.26162 ( 2019) Misc. bond : bond 0.00012 ( 5) link_BETA1-4 : bond 0.00422 ( 15) link_BETA1-4 : angle 3.25379 ( 45) link_NAG-ASN : bond 0.00170 ( 15) link_NAG-ASN : angle 1.38829 ( 45) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3890 Ramachandran restraints generated. 1945 Oldfield, 0 Emsley, 1945 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3890 Ramachandran restraints generated. 1945 Oldfield, 0 Emsley, 1945 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 244 residues out of total 1835 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 182 time to evaluate : 0.613 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 186 GLU cc_start: 0.7939 (OUTLIER) cc_final: 0.7220 (tp30) REVERT: A 229 LEU cc_start: 0.8310 (OUTLIER) cc_final: 0.8051 (tm) REVERT: A 238 ASP cc_start: 0.8885 (t70) cc_final: 0.8564 (t70) REVERT: A 314 GLN cc_start: 0.7558 (mt0) cc_final: 0.7142 (mp10) REVERT: A 420 ARG cc_start: 0.8616 (ttm-80) cc_final: 0.8315 (ptp-110) REVERT: A 435 ARG cc_start: 0.7266 (OUTLIER) cc_final: 0.6934 (tpt170) REVERT: B 186 GLU cc_start: 0.7645 (OUTLIER) cc_final: 0.6948 (tp30) REVERT: B 229 LEU cc_start: 0.8160 (OUTLIER) cc_final: 0.7742 (tm) REVERT: B 238 ASP cc_start: 0.8998 (t70) cc_final: 0.8485 (t70) REVERT: B 314 GLN cc_start: 0.7658 (mt0) cc_final: 0.7194 (mp10) REVERT: B 435 ARG cc_start: 0.7163 (OUTLIER) cc_final: 0.6860 (tpt170) REVERT: C 91 ASP cc_start: 0.9058 (p0) cc_final: 0.8847 (p0) REVERT: C 186 GLU cc_start: 0.7677 (OUTLIER) cc_final: 0.6944 (tp30) REVERT: C 238 ASP cc_start: 0.8966 (t70) cc_final: 0.8574 (t0) REVERT: C 435 ARG cc_start: 0.6996 (OUTLIER) cc_final: 0.6715 (tpt170) REVERT: D 45 MET cc_start: 0.9598 (OUTLIER) cc_final: 0.9279 (tpp) REVERT: D 197 LYS cc_start: 0.7926 (mttm) cc_final: 0.7669 (mtpp) REVERT: D 238 ASP cc_start: 0.8972 (t70) cc_final: 0.8287 (t0) REVERT: D 314 GLN cc_start: 0.7267 (OUTLIER) cc_final: 0.6641 (pp30) REVERT: D 420 ARG cc_start: 0.8613 (ttm170) cc_final: 0.8400 (ptp-110) REVERT: E 186 GLU cc_start: 0.7718 (OUTLIER) cc_final: 0.7055 (tp30) REVERT: E 197 LYS cc_start: 0.7968 (mttm) cc_final: 0.7717 (mtpp) REVERT: E 238 ASP cc_start: 0.8863 (t70) cc_final: 0.8581 (t70) outliers start: 62 outliers final: 36 residues processed: 221 average time/residue: 0.5035 time to fit residues: 126.0806 Evaluate side-chains 217 residues out of total 1835 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 170 time to evaluate : 0.575 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 12 LEU Chi-restraints excluded: chain A residue 76 THR Chi-restraints excluded: chain A residue 79 ASP Chi-restraints excluded: chain A residue 116 TYR Chi-restraints excluded: chain A residue 166 THR Chi-restraints excluded: chain A residue 186 GLU Chi-restraints excluded: chain A residue 221 LEU Chi-restraints excluded: chain A residue 229 LEU Chi-restraints excluded: chain A residue 236 VAL Chi-restraints excluded: chain A residue 240 VAL Chi-restraints excluded: chain A residue 260 LEU Chi-restraints excluded: chain A residue 329 ILE Chi-restraints excluded: chain A residue 435 ARG Chi-restraints excluded: chain A residue 450 ILE Chi-restraints excluded: chain B residue 12 LEU Chi-restraints excluded: chain B residue 166 THR Chi-restraints excluded: chain B residue 186 GLU Chi-restraints excluded: chain B residue 221 LEU Chi-restraints excluded: chain B residue 229 LEU Chi-restraints excluded: chain B residue 240 VAL Chi-restraints excluded: chain B residue 269 VAL Chi-restraints excluded: chain B residue 435 ARG Chi-restraints excluded: chain C residue 12 LEU Chi-restraints excluded: chain C residue 166 THR Chi-restraints excluded: chain C residue 186 GLU Chi-restraints excluded: chain C residue 221 LEU Chi-restraints excluded: chain C residue 229 LEU Chi-restraints excluded: chain C residue 260 LEU Chi-restraints excluded: chain C residue 269 VAL Chi-restraints excluded: chain C residue 290 CYS Chi-restraints excluded: chain C residue 435 ARG Chi-restraints excluded: chain D residue 12 LEU Chi-restraints excluded: chain D residue 45 MET Chi-restraints excluded: chain D residue 116 TYR Chi-restraints excluded: chain D residue 221 LEU Chi-restraints excluded: chain D residue 229 LEU Chi-restraints excluded: chain D residue 232 ILE Chi-restraints excluded: chain D residue 269 VAL Chi-restraints excluded: chain D residue 314 GLN Chi-restraints excluded: chain D residue 435 ARG Chi-restraints excluded: chain E residue 12 LEU Chi-restraints excluded: chain E residue 116 TYR Chi-restraints excluded: chain E residue 186 GLU Chi-restraints excluded: chain E residue 221 LEU Chi-restraints excluded: chain E residue 269 VAL Chi-restraints excluded: chain E residue 433 LEU Chi-restraints excluded: chain E residue 435 ARG Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 195 random chunks: chunk 110 optimal weight: 20.0000 chunk 183 optimal weight: 3.9990 chunk 192 optimal weight: 2.9990 chunk 163 optimal weight: 0.7980 chunk 60 optimal weight: 0.0870 chunk 79 optimal weight: 2.9990 chunk 27 optimal weight: 2.9990 chunk 3 optimal weight: 5.9990 chunk 50 optimal weight: 3.9990 chunk 81 optimal weight: 3.9990 chunk 88 optimal weight: 1.9990 overall best weight: 1.7764 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 184 GLN C 184 GLN D 184 GLN ** E 311 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 = 0.3526 r_free = 0.3526 target = 0.116863 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.2810 r_free = 0.2810 target = 0.072541 restraints weight = 25631.302| |-----------------------------------------------------------------------------| r_work (start): 0.2791 rms_B_bonded: 2.78 r_work: 0.2645 rms_B_bonded: 2.95 restraints_weight: 0.5000 r_work: 0.2500 rms_B_bonded: 4.64 restraints_weight: 0.2500 r_work (final): 0.2500 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8555 moved from start: 0.3685 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.029 17365 Z= 0.159 Angle : 0.647 11.377 23780 Z= 0.309 Chirality : 0.045 0.163 2820 Planarity : 0.004 0.036 2850 Dihedral : 5.938 54.895 2950 Min Nonbonded Distance : 2.261 Molprobity Statistics. All-atom Clashscore : 3.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.19 % Favored : 94.81 % Rotamer: Outliers : 2.78 % Allowed : 17.00 % Favored : 80.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.36 (0.20), residues: 1945 helix: 1.43 (0.20), residues: 750 sheet: -0.60 (0.24), residues: 425 loop : -1.71 (0.22), residues: 770 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG D 315 TYR 0.018 0.001 TYR C 448 PHE 0.023 0.002 PHE A 233 TRP 0.031 0.001 TRP D 456 HIS 0.006 0.001 HIS D 411 Details of bonding type rmsd covalent geometry : bond 0.00373 (17325) covalent geometry : angle 0.62840 (23680) SS BOND : bond 0.00556 ( 5) SS BOND : angle 1.27978 ( 10) hydrogen bonds : bond 0.05293 ( 688) hydrogen bonds : angle 4.31031 ( 2019) Misc. bond : bond 0.00010 ( 5) link_BETA1-4 : bond 0.00354 ( 15) link_BETA1-4 : angle 3.25148 ( 45) link_NAG-ASN : bond 0.00209 ( 15) link_NAG-ASN : angle 1.57906 ( 45) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3890 Ramachandran restraints generated. 1945 Oldfield, 0 Emsley, 1945 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3890 Ramachandran restraints generated. 1945 Oldfield, 0 Emsley, 1945 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 223 residues out of total 1835 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 172 time to evaluate : 0.637 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 186 GLU cc_start: 0.7905 (OUTLIER) cc_final: 0.7121 (tp30) REVERT: A 238 ASP cc_start: 0.8902 (t70) cc_final: 0.8567 (t70) REVERT: A 314 GLN cc_start: 0.7522 (mt0) cc_final: 0.7057 (mp10) REVERT: A 420 ARG cc_start: 0.8616 (ttm-80) cc_final: 0.8298 (ptp-110) REVERT: A 435 ARG cc_start: 0.7219 (OUTLIER) cc_final: 0.6918 (tpt170) REVERT: B 186 GLU cc_start: 0.7683 (OUTLIER) cc_final: 0.6958 (tp30) REVERT: B 238 ASP cc_start: 0.9021 (t70) cc_final: 0.8462 (t0) REVERT: B 250 GLU cc_start: 0.8346 (mt-10) cc_final: 0.7992 (mp0) REVERT: B 435 ARG cc_start: 0.7203 (OUTLIER) cc_final: 0.6894 (tpt170) REVERT: C 91 ASP cc_start: 0.9062 (p0) cc_final: 0.8855 (p0) REVERT: C 186 GLU cc_start: 0.7624 (OUTLIER) cc_final: 0.6855 (tp30) REVERT: C 238 ASP cc_start: 0.8992 (t70) cc_final: 0.8593 (t0) REVERT: C 420 ARG cc_start: 0.8696 (ptm160) cc_final: 0.8495 (ptp-110) REVERT: C 435 ARG cc_start: 0.7014 (OUTLIER) cc_final: 0.6719 (tpt170) REVERT: D 45 MET cc_start: 0.9585 (OUTLIER) cc_final: 0.9275 (tpp) REVERT: D 197 LYS cc_start: 0.7951 (mttm) cc_final: 0.7691 (mtpp) REVERT: D 238 ASP cc_start: 0.8969 (t70) cc_final: 0.8300 (t0) REVERT: D 314 GLN cc_start: 0.7167 (OUTLIER) cc_final: 0.6666 (pp30) REVERT: D 420 ARG cc_start: 0.8636 (ttm170) cc_final: 0.8378 (ptp-110) REVERT: E 186 GLU cc_start: 0.7784 (OUTLIER) cc_final: 0.7050 (tp30) REVERT: E 197 LYS cc_start: 0.7954 (mttm) cc_final: 0.7721 (mtpp) REVERT: E 238 ASP cc_start: 0.8903 (t70) cc_final: 0.8622 (t70) outliers start: 51 outliers final: 31 residues processed: 201 average time/residue: 0.5384 time to fit residues: 121.4017 Evaluate side-chains 210 residues out of total 1835 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 170 time to evaluate : 0.546 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 79 ASP Chi-restraints excluded: chain A residue 116 TYR Chi-restraints excluded: chain A residue 166 THR Chi-restraints excluded: chain A residue 186 GLU Chi-restraints excluded: chain A residue 221 LEU Chi-restraints excluded: chain A residue 229 LEU Chi-restraints excluded: chain A residue 240 VAL Chi-restraints excluded: chain A residue 260 LEU Chi-restraints excluded: chain A residue 329 ILE Chi-restraints excluded: chain A residue 435 ARG Chi-restraints excluded: chain A residue 450 ILE Chi-restraints excluded: chain B residue 12 LEU Chi-restraints excluded: chain B residue 79 ASP Chi-restraints excluded: chain B residue 166 THR Chi-restraints excluded: chain B residue 186 GLU Chi-restraints excluded: chain B residue 221 LEU Chi-restraints excluded: chain B residue 229 LEU Chi-restraints excluded: chain B residue 269 VAL Chi-restraints excluded: chain B residue 435 ARG Chi-restraints excluded: chain C residue 12 LEU Chi-restraints excluded: chain C residue 79 ASP Chi-restraints excluded: chain C residue 166 THR Chi-restraints excluded: chain C residue 186 GLU Chi-restraints excluded: chain C residue 221 LEU Chi-restraints excluded: chain C residue 260 LEU Chi-restraints excluded: chain C residue 269 VAL Chi-restraints excluded: chain C residue 435 ARG Chi-restraints excluded: chain D residue 12 LEU Chi-restraints excluded: chain D residue 45 MET Chi-restraints excluded: chain D residue 221 LEU Chi-restraints excluded: chain D residue 229 LEU Chi-restraints excluded: chain D residue 269 VAL Chi-restraints excluded: chain D residue 314 GLN Chi-restraints excluded: chain D residue 435 ARG Chi-restraints excluded: chain E residue 12 LEU Chi-restraints excluded: chain E residue 116 TYR Chi-restraints excluded: chain E residue 186 GLU Chi-restraints excluded: chain E residue 221 LEU Chi-restraints excluded: chain E residue 269 VAL Chi-restraints excluded: chain E residue 435 ARG Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 195 random chunks: chunk 141 optimal weight: 6.9990 chunk 87 optimal weight: 0.9980 chunk 114 optimal weight: 0.9980 chunk 35 optimal weight: 7.9990 chunk 61 optimal weight: 0.9990 chunk 162 optimal weight: 3.9990 chunk 33 optimal weight: 5.9990 chunk 125 optimal weight: 1.9990 chunk 13 optimal weight: 0.8980 chunk 112 optimal weight: 7.9990 chunk 140 optimal weight: 0.8980 overall best weight: 0.9582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 184 GLN C 184 GLN ** D 311 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 311 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 = 0.3545 r_free = 0.3545 target = 0.118198 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.2853 r_free = 0.2853 target = 0.074692 restraints weight = 25706.563| |-----------------------------------------------------------------------------| r_work (start): 0.2821 rms_B_bonded: 2.75 r_work: 0.2677 rms_B_bonded: 2.93 restraints_weight: 0.5000 r_work: 0.2533 rms_B_bonded: 4.60 restraints_weight: 0.2500 r_work (final): 0.2533 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8498 moved from start: 0.3773 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 17365 Z= 0.121 Angle : 0.613 8.444 23780 Z= 0.293 Chirality : 0.044 0.154 2820 Planarity : 0.004 0.033 2850 Dihedral : 5.709 53.359 2950 Min Nonbonded Distance : 2.258 Molprobity Statistics. All-atom Clashscore : 3.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.94 % Favored : 95.06 % Rotamer: Outliers : 2.45 % Allowed : 17.38 % Favored : 80.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.26 (0.20), residues: 1945 helix: 1.54 (0.20), residues: 750 sheet: -0.59 (0.24), residues: 425 loop : -1.66 (0.22), residues: 770 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 322 TYR 0.016 0.001 TYR E 448 PHE 0.028 0.001 PHE C 412 TRP 0.030 0.001 TRP D 456 HIS 0.006 0.001 HIS D 411 Details of bonding type rmsd covalent geometry : bond 0.00267 (17325) covalent geometry : angle 0.59511 (23680) SS BOND : bond 0.00412 ( 5) SS BOND : angle 1.16719 ( 10) hydrogen bonds : bond 0.04948 ( 688) hydrogen bonds : angle 4.22626 ( 2019) Misc. bond : bond 0.00015 ( 5) link_BETA1-4 : bond 0.00436 ( 15) link_BETA1-4 : angle 3.19979 ( 45) link_NAG-ASN : bond 0.00160 ( 15) link_NAG-ASN : angle 1.37102 ( 45) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6084.45 seconds wall clock time: 104 minutes 2.45 seconds (6242.45 seconds total)