Starting phenix.real_space_refine on Tue Nov 18 20:16:43 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6w1j_21511/11_2025/6w1j_21511_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/6w1j_21511/11_2025/6w1j_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 { model { file = "/net/cci-nas-00/data/ceres_data/6w1j_21511/11_2025/6w1j_21511_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6w1j_21511/11_2025/6w1j_21511_neut.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/6w1j_21511/11_2025/6w1j_21511.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6w1j_21511/11_2025/6w1j_21511.map" } 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-2.0-5881/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 16861 Number of models: 1 Model: "" Number of chains: 6 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: "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: "A" 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: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' CL': 1} Classifications: {'undetermined': 1} Restraints were copied for chains: B, C, D, E, I, L, O, R, J, M, P, S, K, N, Q, T Time building chain proxies: 3.76, 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: 1.57 Conformation dependent library (CDL) restraints added in 723.8 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: 0.59 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: 2.52 Time building geometry restraints manager: 1.98 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: 1.870 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: 0.010 Extract box with map and model: 0.330 Check model and map are aligned: 0.060 Set scattering table: 0.050 Process input model: 15.950 Find NCS groups from input model: 0.450 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:6.550 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 25.300 ------------------------------------------------------------------------------- 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 : 0.790 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: 0.6911 time to fit residues: 271.0838 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 : 0.671 ------------------------------------------------------------------------------- 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 = 0.119307 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.2859 r_free = 0.2859 target = 0.074810 restraints weight = 25807.135| |-----------------------------------------------------------------------------| r_work (start): 0.2840 rms_B_bonded: 2.80 r_work: 0.2700 rms_B_bonded: 3.00 restraints_weight: 0.5000 r_work: 0.2557 rms_B_bonded: 4.73 restraints_weight: 0.2500 r_work (final): 0.2557 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8551 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 : 10.856 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 : 0.775 Fit side-chains REVERT: A 186 GLU cc_start: 0.7856 (tp30) cc_final: 0.7298 (tp30) REVERT: A 197 LYS cc_start: 0.8033 (mttm) cc_final: 0.7767 (mtpp) REVERT: A 238 ASP cc_start: 0.8821 (t70) cc_final: 0.8361 (t70) REVERT: A 420 ARG cc_start: 0.8739 (ttm-80) cc_final: 0.8319 (ttm170) REVERT: B 186 GLU cc_start: 0.7671 (tp30) cc_final: 0.7335 (tp30) REVERT: B 238 ASP cc_start: 0.9073 (t70) cc_final: 0.8699 (t70) REVERT: B 411 HIS cc_start: 0.7877 (t70) cc_final: 0.7639 (t-90) REVERT: B 418 GLU cc_start: 0.8627 (OUTLIER) cc_final: 0.8362 (tm-30) REVERT: C 186 GLU cc_start: 0.7745 (tp30) cc_final: 0.7507 (tp30) REVERT: C 195 GLN cc_start: 0.8513 (OUTLIER) cc_final: 0.8131 (tt0) REVERT: C 238 ASP cc_start: 0.9150 (t70) cc_final: 0.8564 (t70) REVERT: C 411 HIS cc_start: 0.7954 (t70) cc_final: 0.7703 (t70) REVERT: D 45 MET cc_start: 0.9615 (OUTLIER) cc_final: 0.9258 (tpp) REVERT: D 197 LYS cc_start: 0.7938 (mttm) cc_final: 0.7677 (mtpp) REVERT: D 238 ASP cc_start: 0.8958 (t70) cc_final: 0.8239 (t0) REVERT: E 186 GLU cc_start: 0.7695 (tp30) cc_final: 0.7290 (tp30) REVERT: E 197 LYS cc_start: 0.7928 (mttm) cc_final: 0.7675 (mtpp) REVERT: E 235 MET cc_start: 0.8902 (tpp) cc_final: 0.8687 (mmm) REVERT: E 238 ASP cc_start: 0.8922 (t70) cc_final: 0.8549 (t70) REVERT: E 411 HIS cc_start: 0.7951 (t70) cc_final: 0.7728 (t70) outliers start: 73 outliers final: 30 residues processed: 276 average time/residue: 0.5472 time to fit residues: 170.7688 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 : 0.668 ------------------------------------------------------------------------------- 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: 3.9990 chunk 165 optimal weight: 0.6980 chunk 137 optimal weight: 2.9990 chunk 61 optimal weight: 0.9990 chunk 129 optimal weight: 0.8980 chunk 41 optimal weight: 2.9990 chunk 186 optimal weight: 9.9990 chunk 124 optimal weight: 3.9990 chunk 94 optimal weight: 4.9990 chunk 20 optimal weight: 5.9990 overall best weight: 1.7186 ------------------------------------------------------------------------------- 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 = 0.3540 r_free = 0.3540 target = 0.117705 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.2830 r_free = 0.2830 target = 0.073334 restraints weight = 26190.325| |-----------------------------------------------------------------------------| r_work (start): 0.2804 rms_B_bonded: 2.81 r_work: 0.2658 rms_B_bonded: 3.00 restraints_weight: 0.5000 r_work: 0.2512 rms_B_bonded: 4.73 restraints_weight: 0.2500 r_work (final): 0.2512 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8556 moved from start: 0.2673 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.062 17365 Z= 0.174 Angle : 0.677 8.508 23780 Z= 0.329 Chirality : 0.047 0.198 2820 Planarity : 0.005 0.040 2850 Dihedral : 8.247 54.197 2952 Min Nonbonded Distance : 2.427 Molprobity Statistics. All-atom Clashscore : 3.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.37 % Favored : 95.63 % Rotamer: Outliers : 4.52 % Allowed : 13.46 % Favored : 82.02 % 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: -1.78 (0.18), residues: 1945 helix: -0.30 (0.19), residues: 760 sheet: -1.16 (0.22), residues: 445 loop : -2.02 (0.22), residues: 740 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG E 420 TYR 0.016 0.001 TYR D 448 PHE 0.019 0.002 PHE E 153 TRP 0.018 0.001 TRP B 456 HIS 0.009 0.001 HIS D 411 Details of bonding type rmsd covalent geometry : bond 0.00395 (17325) covalent geometry : angle 0.64995 (23680) SS BOND : bond 0.00565 ( 5) SS BOND : angle 1.32100 ( 10) hydrogen bonds : bond 0.07273 ( 688) hydrogen bonds : angle 4.76145 ( 2019) Misc. bond : bond 0.00028 ( 5) link_BETA1-4 : bond 0.00408 ( 15) link_BETA1-4 : angle 4.01750 ( 45) link_NAG-ASN : bond 0.00279 ( 15) link_NAG-ASN : angle 1.89303 ( 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 306 residues out of total 1835 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 83 poor density : 223 time to evaluate : 0.695 Fit side-chains REVERT: A 186 GLU cc_start: 0.7911 (tp30) cc_final: 0.7266 (tp30) REVERT: A 197 LYS cc_start: 0.7968 (mttm) cc_final: 0.7711 (mtpp) REVERT: A 238 ASP cc_start: 0.8836 (t70) cc_final: 0.8428 (t70) REVERT: A 314 GLN cc_start: 0.7428 (mt0) cc_final: 0.7077 (mp10) REVERT: A 418 GLU cc_start: 0.8496 (OUTLIER) cc_final: 0.8189 (tm-30) REVERT: A 420 ARG cc_start: 0.8727 (ttm-80) cc_final: 0.8360 (ttm170) REVERT: B 186 GLU cc_start: 0.7836 (tp30) cc_final: 0.7328 (tp30) REVERT: B 238 ASP cc_start: 0.9081 (t70) cc_final: 0.8476 (t70) REVERT: B 314 GLN cc_start: 0.7641 (mt0) cc_final: 0.7230 (mp10) REVERT: B 315 ARG cc_start: 0.7162 (tmt170) cc_final: 0.6931 (tmt170) REVERT: B 411 HIS cc_start: 0.7808 (t70) cc_final: 0.7480 (t-90) REVERT: B 418 GLU cc_start: 0.8602 (OUTLIER) cc_final: 0.8282 (tm-30) REVERT: C 184 GLN cc_start: 0.8068 (tt0) cc_final: 0.7829 (tt0) REVERT: C 186 GLU cc_start: 0.7705 (tp30) cc_final: 0.7270 (tp30) REVERT: C 235 MET cc_start: 0.8799 (tpp) cc_final: 0.8592 (mmm) REVERT: C 238 ASP cc_start: 0.9078 (t70) cc_final: 0.8553 (t0) REVERT: D 45 MET cc_start: 0.9623 (OUTLIER) cc_final: 0.9272 (tpp) REVERT: D 197 LYS cc_start: 0.7882 (mttm) cc_final: 0.7614 (mtpp) REVERT: D 238 ASP cc_start: 0.8912 (t70) cc_final: 0.8194 (t0) REVERT: D 420 ARG cc_start: 0.8765 (ttm170) cc_final: 0.8432 (ptp-110) REVERT: E 186 GLU cc_start: 0.7687 (tp30) cc_final: 0.7198 (tp30) REVERT: E 197 LYS cc_start: 0.8014 (mttm) cc_final: 0.7793 (mtpp) REVERT: E 238 ASP cc_start: 0.8953 (t70) cc_final: 0.8607 (t70) REVERT: E 411 HIS cc_start: 0.7929 (t70) cc_final: 0.7625 (t70) outliers start: 83 outliers final: 35 residues processed: 278 average time/residue: 0.4960 time to fit residues: 157.4601 Evaluate side-chains 232 residues out of total 1835 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 194 time to evaluate : 0.743 ------------------------------------------------------------------------------- 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 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 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 B residue 453 VAL 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 229 LEU Chi-restraints excluded: chain D residue 232 ILE Chi-restraints excluded: chain D residue 240 VAL Chi-restraints excluded: chain D residue 268 ILE 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 285 VAL 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: 10.0000 chunk 181 optimal weight: 5.9990 chunk 4 optimal weight: 3.9990 chunk 108 optimal weight: 0.9980 chunk 69 optimal weight: 2.9990 chunk 65 optimal weight: 8.9990 chunk 22 optimal weight: 0.6980 chunk 191 optimal weight: 1.9990 chunk 152 optimal weight: 0.9980 chunk 0 optimal weight: 5.9990 overall best weight: 1.5384 ------------------------------------------------------------------------------- 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 = 0.3538 r_free = 0.3538 target = 0.117657 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.2828 r_free = 0.2828 target = 0.073440 restraints weight = 26069.922| |-----------------------------------------------------------------------------| r_work (start): 0.2803 rms_B_bonded: 2.80 r_work: 0.2656 rms_B_bonded: 2.99 restraints_weight: 0.5000 r_work: 0.2511 rms_B_bonded: 4.70 restraints_weight: 0.2500 r_work (final): 0.2511 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8553 moved from start: 0.3011 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 17365 Z= 0.154 Angle : 0.638 8.055 23780 Z= 0.309 Chirality : 0.046 0.179 2820 Planarity : 0.004 0.037 2850 Dihedral : 7.134 53.867 2952 Min Nonbonded Distance : 2.458 Molprobity Statistics. All-atom Clashscore : 3.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.27 % Favored : 95.73 % Rotamer: Outliers : 4.58 % Allowed : 14.33 % 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: -1.29 (0.19), residues: 1945 helix: 0.21 (0.19), residues: 785 sheet: -1.01 (0.22), residues: 445 loop : -1.85 (0.23), residues: 715 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 315 TYR 0.015 0.001 TYR C 448 PHE 0.024 0.002 PHE E 153 TRP 0.018 0.001 TRP E 456 HIS 0.010 0.001 HIS A 411 Details of bonding type rmsd covalent geometry : bond 0.00347 (17325) covalent geometry : angle 0.61318 (23680) SS BOND : bond 0.00500 ( 5) SS BOND : angle 1.25572 ( 10) hydrogen bonds : bond 0.06402 ( 688) hydrogen bonds : angle 4.58959 ( 2019) Misc. bond : bond 0.00011 ( 5) link_BETA1-4 : bond 0.00319 ( 15) link_BETA1-4 : angle 3.76684 ( 45) link_NAG-ASN : bond 0.00229 ( 15) link_NAG-ASN : angle 1.69299 ( 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 297 residues out of total 1835 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 84 poor density : 213 time to evaluate : 0.681 Fit side-chains revert: symmetry clash REVERT: A 186 GLU cc_start: 0.7921 (OUTLIER) cc_final: 0.7153 (tp30) REVERT: A 197 LYS cc_start: 0.7957 (mttm) cc_final: 0.7722 (mtpp) REVERT: A 238 ASP cc_start: 0.8859 (t70) cc_final: 0.8468 (t70) REVERT: A 314 GLN cc_start: 0.7482 (mt0) cc_final: 0.7141 (mp10) REVERT: A 411 HIS cc_start: 0.7685 (t70) cc_final: 0.7447 (m90) REVERT: A 420 ARG cc_start: 0.8688 (ttm-80) cc_final: 0.8448 (ptm160) REVERT: B 186 GLU cc_start: 0.7866 (tp30) cc_final: 0.7219 (tp30) REVERT: B 238 ASP cc_start: 0.9034 (t70) cc_final: 0.8440 (t0) REVERT: B 411 HIS cc_start: 0.7705 (t70) cc_final: 0.7479 (t-90) REVERT: B 420 ARG cc_start: 0.8733 (ttm-80) cc_final: 0.8508 (ptm160) REVERT: C 184 GLN cc_start: 0.8152 (tt0) cc_final: 0.7879 (tt0) REVERT: C 186 GLU cc_start: 0.7723 (tp30) cc_final: 0.7199 (tp30) REVERT: C 238 ASP cc_start: 0.9081 (t70) cc_final: 0.8603 (t0) REVERT: D 45 MET cc_start: 0.9618 (OUTLIER) cc_final: 0.9290 (tpp) REVERT: D 197 LYS cc_start: 0.7869 (mttm) cc_final: 0.7608 (mtpp) REVERT: D 238 ASP cc_start: 0.8945 (t70) cc_final: 0.8205 (t0) REVERT: D 314 GLN cc_start: 0.7150 (OUTLIER) cc_final: 0.6521 (pp30) REVERT: E 186 GLU cc_start: 0.7758 (tp30) cc_final: 0.7143 (tp30) REVERT: E 197 LYS cc_start: 0.7973 (mttm) cc_final: 0.7741 (mtpp) REVERT: E 238 ASP cc_start: 0.8966 (t70) cc_final: 0.8642 (t70) outliers start: 84 outliers final: 43 residues processed: 262 average time/residue: 0.5014 time to fit residues: 149.7173 Evaluate side-chains 238 residues out of total 1835 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 192 time to evaluate : 0.734 ------------------------------------------------------------------------------- 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 450 ILE Chi-restraints excluded: chain B residue 12 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 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 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 321 LEU 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 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: 0.8980 chunk 137 optimal weight: 5.9990 chunk 25 optimal weight: 6.9990 chunk 104 optimal weight: 10.0000 chunk 39 optimal weight: 6.9990 chunk 175 optimal weight: 8.9990 chunk 184 optimal weight: 3.9990 chunk 46 optimal weight: 5.9990 chunk 109 optimal weight: 10.0000 chunk 35 optimal weight: 6.9990 chunk 132 optimal weight: 2.9990 overall best weight: 3.9788 ------------------------------------------------------------------------------- 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 = 0.3485 r_free = 0.3485 target = 0.114081 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.2748 r_free = 0.2748 target = 0.069333 restraints weight = 26062.605| |-----------------------------------------------------------------------------| r_work (start): 0.2722 rms_B_bonded: 2.79 r_work: 0.2578 rms_B_bonded: 2.93 restraints_weight: 0.5000 r_work: 0.2434 rms_B_bonded: 4.58 restraints_weight: 0.2500 r_work (final): 0.2434 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8608 moved from start: 0.3215 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.048 17365 Z= 0.316 Angle : 0.760 8.679 23780 Z= 0.369 Chirality : 0.050 0.214 2820 Planarity : 0.005 0.044 2850 Dihedral : 7.475 56.832 2950 Min Nonbonded Distance : 2.399 Molprobity Statistics. All-atom Clashscore : 4.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.35 % Favored : 94.65 % Rotamer: Outliers : 5.40 % Allowed : 13.90 % Favored : 80.71 % 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: -1.09 (0.19), residues: 1945 helix: 0.59 (0.20), residues: 760 sheet: -0.82 (0.23), residues: 425 loop : -2.00 (0.21), residues: 760 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG C 420 TYR 0.024 0.002 TYR E 67 PHE 0.042 0.003 PHE C 153 TRP 0.021 0.002 TRP E 456 HIS 0.007 0.001 HIS A 411 Details of bonding type rmsd covalent geometry : bond 0.00772 (17325) covalent geometry : angle 0.73450 (23680) SS BOND : bond 0.00897 ( 5) SS BOND : angle 1.88116 ( 10) hydrogen bonds : bond 0.06812 ( 688) hydrogen bonds : angle 4.78164 ( 2019) Misc. bond : bond 0.00054 ( 5) link_BETA1-4 : bond 0.00457 ( 15) link_BETA1-4 : angle 3.84578 ( 45) link_NAG-ASN : bond 0.00474 ( 15) link_NAG-ASN : angle 2.32264 ( 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 284 residues out of total 1835 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 99 poor density : 185 time to evaluate : 0.683 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 186 GLU cc_start: 0.8077 (OUTLIER) cc_final: 0.7228 (tp30) REVERT: A 197 LYS cc_start: 0.7979 (mttm) cc_final: 0.7747 (mtpp) REVERT: A 238 ASP cc_start: 0.8947 (t70) cc_final: 0.8615 (t70) REVERT: A 411 HIS cc_start: 0.7705 (t70) cc_final: 0.7467 (m90) REVERT: B 186 GLU cc_start: 0.8013 (OUTLIER) cc_final: 0.7170 (tp30) REVERT: B 238 ASP cc_start: 0.9075 (t70) cc_final: 0.8524 (t0) REVERT: C 184 GLN cc_start: 0.8403 (tt0) cc_final: 0.8121 (tp40) REVERT: C 186 GLU cc_start: 0.7967 (OUTLIER) cc_final: 0.7221 (tp30) REVERT: C 235 MET cc_start: 0.8767 (mmm) cc_final: 0.8389 (mmm) REVERT: C 238 ASP cc_start: 0.9055 (t70) cc_final: 0.8700 (t0) REVERT: D 45 MET cc_start: 0.9577 (OUTLIER) cc_final: 0.9254 (tpp) REVERT: D 197 LYS cc_start: 0.7998 (mttm) cc_final: 0.7733 (mtpp) REVERT: D 238 ASP cc_start: 0.8994 (t70) cc_final: 0.8362 (t0) REVERT: D 314 GLN cc_start: 0.7209 (OUTLIER) cc_final: 0.6604 (pp30) REVERT: E 186 GLU cc_start: 0.8067 (OUTLIER) cc_final: 0.7231 (tp30) REVERT: E 197 LYS cc_start: 0.8047 (mttm) cc_final: 0.7826 (mtpp) REVERT: E 238 ASP cc_start: 0.8996 (t70) cc_final: 0.8435 (t0) REVERT: E 411 HIS cc_start: 0.7792 (m90) cc_final: 0.7536 (m90) outliers start: 99 outliers final: 53 residues processed: 242 average time/residue: 0.4881 time to fit residues: 135.2020 Evaluate side-chains 234 residues out of total 1835 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 175 time to evaluate : 0.664 ------------------------------------------------------------------------------- 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 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 446 LEU 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 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 446 LEU Chi-restraints excluded: chain B residue 450 ILE Chi-restraints excluded: chain B residue 458 ILE Chi-restraints excluded: chain C residue 79 ASP Chi-restraints excluded: chain C residue 186 GLU Chi-restraints excluded: chain C residue 221 LEU Chi-restraints excluded: chain C residue 228 LEU Chi-restraints excluded: chain C residue 234 LEU Chi-restraints excluded: chain C residue 240 VAL Chi-restraints excluded: chain C residue 260 LEU Chi-restraints excluded: chain C residue 264 VAL Chi-restraints excluded: chain C residue 269 VAL Chi-restraints excluded: chain C residue 435 ARG Chi-restraints excluded: chain C residue 443 LEU Chi-restraints excluded: chain C residue 446 LEU Chi-restraints excluded: chain C residue 450 ILE Chi-restraints excluded: chain C residue 458 ILE 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 446 LEU Chi-restraints excluded: chain D residue 450 ILE Chi-restraints excluded: chain D residue 458 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 232 ILE Chi-restraints excluded: chain E residue 240 VAL Chi-restraints excluded: chain E residue 269 VAL Chi-restraints excluded: chain E residue 433 LEU Chi-restraints excluded: chain E residue 446 LEU Chi-restraints excluded: chain E residue 450 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 195 random chunks: chunk 76 optimal weight: 7.9990 chunk 148 optimal weight: 8.9990 chunk 38 optimal weight: 7.9990 chunk 98 optimal weight: 1.9990 chunk 156 optimal weight: 0.0970 chunk 137 optimal weight: 0.9990 chunk 164 optimal weight: 0.9980 chunk 132 optimal weight: 1.9990 chunk 75 optimal weight: 0.9990 chunk 166 optimal weight: 0.5980 chunk 3 optimal weight: 3.9990 overall best weight: 0.7382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 314 GLN D 311 GLN E 309 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3535 r_free = 0.3535 target = 0.117577 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.2828 r_free = 0.2828 target = 0.073531 restraints weight = 25800.973| |-----------------------------------------------------------------------------| r_work (start): 0.2800 rms_B_bonded: 2.79 r_work: 0.2653 rms_B_bonded: 2.97 restraints_weight: 0.5000 r_work: 0.2508 rms_B_bonded: 4.67 restraints_weight: 0.2500 r_work (final): 0.2508 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8547 moved from start: 0.3416 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 17365 Z= 0.121 Angle : 0.617 7.741 23780 Z= 0.295 Chirality : 0.044 0.168 2820 Planarity : 0.004 0.033 2850 Dihedral : 6.523 52.202 2950 Min Nonbonded Distance : 2.374 Molprobity Statistics. All-atom Clashscore : 3.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.47 % Favored : 95.53 % Rotamer: Outliers : 3.71 % Allowed : 15.69 % Favored : 80.60 % 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: 0.96 (0.20), residues: 755 sheet: -0.78 (0.24), residues: 425 loop : -1.81 (0.22), residues: 765 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 315 TYR 0.016 0.001 TYR B 448 PHE 0.014 0.001 PHE C 233 TRP 0.020 0.001 TRP A 456 HIS 0.007 0.001 HIS C 411 Details of bonding type rmsd covalent geometry : bond 0.00248 (17325) covalent geometry : angle 0.59334 (23680) SS BOND : bond 0.00412 ( 5) SS BOND : angle 1.25053 ( 10) hydrogen bonds : bond 0.05706 ( 688) hydrogen bonds : angle 4.51714 ( 2019) Misc. bond : bond 0.00016 ( 5) link_BETA1-4 : bond 0.00445 ( 15) link_BETA1-4 : angle 3.57782 ( 45) link_NAG-ASN : bond 0.00173 ( 15) link_NAG-ASN : angle 1.59626 ( 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 274 residues out of total 1835 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 206 time to evaluate : 0.678 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 186 GLU cc_start: 0.8000 (OUTLIER) cc_final: 0.7260 (tp30) REVERT: A 238 ASP cc_start: 0.8899 (t70) cc_final: 0.8559 (t70) REVERT: A 314 GLN cc_start: 0.7510 (mt0) cc_final: 0.7169 (mp10) REVERT: B 186 GLU cc_start: 0.7906 (OUTLIER) cc_final: 0.7195 (tp30) REVERT: B 238 ASP cc_start: 0.9037 (t70) cc_final: 0.8445 (t0) REVERT: B 333 LEU cc_start: 0.7911 (OUTLIER) cc_final: 0.7703 (mm) REVERT: C 184 GLN cc_start: 0.8192 (tt0) cc_final: 0.7840 (tp40) REVERT: C 186 GLU cc_start: 0.7706 (OUTLIER) cc_final: 0.7076 (tp30) REVERT: C 238 ASP cc_start: 0.9001 (t70) cc_final: 0.8582 (t0) REVERT: C 435 ARG cc_start: 0.7111 (OUTLIER) cc_final: 0.6818 (tpt170) REVERT: D 45 MET cc_start: 0.9586 (OUTLIER) cc_final: 0.9270 (tpp) REVERT: D 197 LYS cc_start: 0.7858 (mttm) cc_final: 0.7606 (mtpp) REVERT: D 238 ASP cc_start: 0.8990 (t70) cc_final: 0.8303 (t0) REVERT: D 291 MET cc_start: 0.8638 (tpt) cc_final: 0.8433 (tpt) REVERT: D 314 GLN cc_start: 0.7234 (OUTLIER) cc_final: 0.6639 (pp30) REVERT: D 420 ARG cc_start: 0.8619 (ttm170) cc_final: 0.8390 (ptp-110) REVERT: E 186 GLU cc_start: 0.7820 (OUTLIER) cc_final: 0.7118 (tp30) REVERT: E 197 LYS cc_start: 0.7950 (mttm) cc_final: 0.7714 (mtpp) REVERT: E 238 ASP cc_start: 0.8917 (t70) cc_final: 0.8591 (t70) outliers start: 68 outliers final: 32 residues processed: 250 average time/residue: 0.5015 time to fit residues: 142.6929 Evaluate side-chains 228 residues out of total 1835 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 188 time to evaluate : 0.571 ------------------------------------------------------------------------------- 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 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 435 ARG Chi-restraints excluded: chain A residue 450 ILE 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 333 LEU Chi-restraints excluded: chain B residue 435 ARG Chi-restraints excluded: chain C residue 116 TYR 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 415 LYS Chi-restraints excluded: chain C residue 435 ARG 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 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 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 Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 195 random chunks: chunk 105 optimal weight: 5.9990 chunk 87 optimal weight: 0.0980 chunk 168 optimal weight: 1.9990 chunk 25 optimal weight: 1.9990 chunk 97 optimal weight: 7.9990 chunk 15 optimal weight: 4.9990 chunk 30 optimal weight: 8.9990 chunk 114 optimal weight: 6.9990 chunk 123 optimal weight: 2.9990 chunk 149 optimal weight: 0.0010 chunk 190 optimal weight: 4.9990 overall best weight: 1.4192 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 311 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3525 r_free = 0.3525 target = 0.116800 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2814 r_free = 0.2814 target = 0.072813 restraints weight = 25900.795| |-----------------------------------------------------------------------------| r_work (start): 0.2788 rms_B_bonded: 2.79 r_work: 0.2640 rms_B_bonded: 2.96 restraints_weight: 0.5000 r_work: 0.2496 rms_B_bonded: 4.65 restraints_weight: 0.2500 r_work (final): 0.2496 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8567 moved from start: 0.3521 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= 0.145 Angle : 0.623 7.584 23780 Z= 0.299 Chirality : 0.045 0.174 2820 Planarity : 0.004 0.036 2850 Dihedral : 6.380 53.988 2950 Min Nonbonded Distance : 2.332 Molprobity Statistics. All-atom Clashscore : 3.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.99 % Favored : 95.01 % Rotamer: Outliers : 4.03 % Allowed : 15.64 % Favored : 80.33 % 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: 1.18 (0.20), residues: 750 sheet: -0.68 (0.24), residues: 425 loop : -1.77 (0.22), residues: 770 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D 315 TYR 0.017 0.001 TYR E 448 PHE 0.027 0.002 PHE D 412 TRP 0.022 0.001 TRP A 456 HIS 0.006 0.001 HIS A 411 Details of bonding type rmsd covalent geometry : bond 0.00327 (17325) covalent geometry : angle 0.60075 (23680) SS BOND : bond 0.00492 ( 5) SS BOND : angle 1.26303 ( 10) hydrogen bonds : bond 0.05649 ( 688) hydrogen bonds : angle 4.41945 ( 2019) Misc. bond : bond 0.00006 ( 5) link_BETA1-4 : bond 0.00372 ( 15) link_BETA1-4 : angle 3.46730 ( 45) link_NAG-ASN : bond 0.00217 ( 15) link_NAG-ASN : angle 1.62589 ( 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 260 residues out of total 1835 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 74 poor density : 186 time to evaluate : 0.733 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 186 GLU cc_start: 0.7981 (OUTLIER) cc_final: 0.7230 (tp30) REVERT: A 238 ASP cc_start: 0.8911 (t70) cc_final: 0.8583 (t70) REVERT: B 186 GLU cc_start: 0.7986 (OUTLIER) cc_final: 0.7242 (tp30) REVERT: B 238 ASP cc_start: 0.9048 (t70) cc_final: 0.8459 (t0) REVERT: B 420 ARG cc_start: 0.8737 (ptm160) cc_final: 0.8470 (ptp-110) REVERT: B 435 ARG cc_start: 0.7270 (OUTLIER) cc_final: 0.6867 (tpt170) REVERT: C 162 ASP cc_start: 0.8895 (m-30) cc_final: 0.8672 (m-30) REVERT: C 186 GLU cc_start: 0.7735 (OUTLIER) cc_final: 0.7076 (tp30) REVERT: C 235 MET cc_start: 0.8777 (mmm) cc_final: 0.8398 (mmm) REVERT: C 238 ASP cc_start: 0.9030 (t70) cc_final: 0.8654 (t0) REVERT: C 435 ARG cc_start: 0.7033 (OUTLIER) cc_final: 0.6802 (tpt170) REVERT: D 45 MET cc_start: 0.9591 (OUTLIER) cc_final: 0.9276 (tpp) REVERT: D 197 LYS cc_start: 0.7918 (mttm) cc_final: 0.7666 (mtpp) REVERT: D 238 ASP cc_start: 0.8997 (t70) cc_final: 0.8313 (t0) REVERT: D 314 GLN cc_start: 0.7236 (OUTLIER) cc_final: 0.6647 (pp30) REVERT: D 411 HIS cc_start: 0.7922 (m90) cc_final: 0.7642 (m90) REVERT: D 420 ARG cc_start: 0.8619 (ttm170) cc_final: 0.8390 (ptp-110) REVERT: E 186 GLU cc_start: 0.7863 (OUTLIER) cc_final: 0.7118 (tp30) REVERT: E 197 LYS cc_start: 0.7973 (mttm) cc_final: 0.7740 (mtpp) REVERT: E 238 ASP cc_start: 0.8898 (t70) cc_final: 0.8598 (t70) REVERT: E 411 HIS cc_start: 0.7776 (m90) cc_final: 0.7528 (m90) outliers start: 74 outliers final: 39 residues processed: 230 average time/residue: 0.5067 time to fit residues: 132.6355 Evaluate side-chains 224 residues out of total 1835 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 177 time to evaluate : 0.705 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 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 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 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 166 THR Chi-restraints excluded: chain C residue 186 GLU Chi-restraints excluded: chain C residue 221 LEU Chi-restraints excluded: chain C residue 234 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 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 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 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 450 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 195 random chunks: chunk 81 optimal weight: 4.9990 chunk 101 optimal weight: 0.7980 chunk 167 optimal weight: 2.9990 chunk 102 optimal weight: 5.9990 chunk 111 optimal weight: 5.9990 chunk 66 optimal weight: 2.9990 chunk 188 optimal weight: 20.0000 chunk 80 optimal weight: 3.9990 chunk 186 optimal weight: 6.9990 chunk 5 optimal weight: 2.9990 chunk 53 optimal weight: 3.9990 overall best weight: 2.7588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 311 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3501 r_free = 0.3501 target = 0.115114 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.2775 r_free = 0.2775 target = 0.070631 restraints weight = 26084.873| |-----------------------------------------------------------------------------| r_work (start): 0.2752 rms_B_bonded: 2.78 r_work: 0.2607 rms_B_bonded: 2.94 restraints_weight: 0.5000 r_work: 0.2464 rms_B_bonded: 4.60 restraints_weight: 0.2500 r_work (final): 0.2464 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8575 moved from start: 0.3550 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.035 17365 Z= 0.224 Angle : 0.680 7.748 23780 Z= 0.328 Chirality : 0.047 0.183 2820 Planarity : 0.004 0.040 2850 Dihedral : 6.568 55.325 2950 Min Nonbonded Distance : 2.287 Molprobity Statistics. All-atom Clashscore : 4.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.99 % Favored : 95.01 % Rotamer: Outliers : 4.14 % Allowed : 15.53 % Favored : 80.33 % 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: -0.61 (0.19), residues: 1945 helix: 1.19 (0.20), residues: 750 sheet: -0.69 (0.24), residues: 425 loop : -1.84 (0.22), residues: 770 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 315 TYR 0.019 0.002 TYR E 448 PHE 0.024 0.002 PHE C 153 TRP 0.025 0.001 TRP A 456 HIS 0.006 0.001 HIS A 411 Details of bonding type rmsd covalent geometry : bond 0.00538 (17325) covalent geometry : angle 0.65808 (23680) SS BOND : bond 0.00706 ( 5) SS BOND : angle 1.54658 ( 10) hydrogen bonds : bond 0.05923 ( 688) hydrogen bonds : angle 4.52570 ( 2019) Misc. bond : bond 0.00020 ( 5) link_BETA1-4 : bond 0.00317 ( 15) link_BETA1-4 : angle 3.50902 ( 45) link_NAG-ASN : bond 0.00293 ( 15) link_NAG-ASN : angle 1.92491 ( 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 252 residues out of total 1835 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 76 poor density : 176 time to evaluate : 0.685 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 186 GLU cc_start: 0.7999 (OUTLIER) cc_final: 0.6639 (tp30) REVERT: A 238 ASP cc_start: 0.8936 (t70) cc_final: 0.8633 (t70) REVERT: B 186 GLU cc_start: 0.8014 (OUTLIER) cc_final: 0.7212 (tp30) REVERT: B 238 ASP cc_start: 0.9045 (t70) cc_final: 0.8482 (t0) REVERT: B 435 ARG cc_start: 0.7249 (OUTLIER) cc_final: 0.6857 (tpt170) REVERT: C 186 GLU cc_start: 0.7837 (OUTLIER) cc_final: 0.7098 (tp30) REVERT: C 235 MET cc_start: 0.8778 (mmm) cc_final: 0.8392 (mmm) REVERT: C 238 ASP cc_start: 0.9027 (t70) cc_final: 0.8609 (t0) REVERT: C 435 ARG cc_start: 0.7008 (OUTLIER) cc_final: 0.6796 (tpt170) REVERT: D 45 MET cc_start: 0.9582 (OUTLIER) cc_final: 0.9264 (tpp) REVERT: D 197 LYS cc_start: 0.7954 (mttm) cc_final: 0.7693 (mtpp) REVERT: D 235 MET cc_start: 0.8930 (tpp) cc_final: 0.8648 (mmt) REVERT: D 238 ASP cc_start: 0.8950 (t70) cc_final: 0.8308 (t0) REVERT: D 311 GLN cc_start: 0.6114 (OUTLIER) cc_final: 0.5633 (pp30) REVERT: D 314 GLN cc_start: 0.7316 (OUTLIER) cc_final: 0.6730 (pp30) REVERT: D 411 HIS cc_start: 0.7892 (m90) cc_final: 0.7665 (m90) REVERT: D 420 ARG cc_start: 0.8601 (OUTLIER) cc_final: 0.8333 (ptp-110) REVERT: E 186 GLU cc_start: 0.7956 (OUTLIER) cc_final: 0.7156 (tp30) REVERT: E 197 LYS cc_start: 0.7976 (mttm) cc_final: 0.7730 (mtpp) REVERT: E 238 ASP cc_start: 0.8909 (t70) cc_final: 0.8358 (t0) REVERT: E 411 HIS cc_start: 0.7744 (m90) cc_final: 0.7504 (m90) outliers start: 76 outliers final: 44 residues processed: 222 average time/residue: 0.5235 time to fit residues: 131.2741 Evaluate side-chains 226 residues out of total 1835 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 172 time to evaluate : 0.619 ------------------------------------------------------------------------------- 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 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 446 LEU 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 290 CYS Chi-restraints excluded: chain B residue 435 ARG 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 166 THR Chi-restraints excluded: chain C residue 186 GLU Chi-restraints excluded: chain C residue 221 LEU Chi-restraints excluded: chain C residue 234 LEU Chi-restraints excluded: chain C residue 260 LEU Chi-restraints excluded: chain C residue 269 VAL Chi-restraints excluded: chain C residue 433 LEU Chi-restraints excluded: chain C residue 435 ARG Chi-restraints excluded: chain C residue 450 ILE 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 269 VAL Chi-restraints excluded: chain D residue 311 GLN Chi-restraints excluded: chain D residue 314 GLN Chi-restraints excluded: chain D residue 420 ARG 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 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: 0.9980 chunk 15 optimal weight: 2.9990 chunk 3 optimal weight: 4.9990 chunk 88 optimal weight: 0.9980 chunk 113 optimal weight: 7.9990 chunk 185 optimal weight: 2.9990 chunk 20 optimal weight: 0.9980 chunk 17 optimal weight: 3.9990 chunk 138 optimal weight: 6.9990 chunk 164 optimal weight: 0.9980 chunk 67 optimal weight: 3.9990 overall best weight: 1.3982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 184 GLN D 311 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3520 r_free = 0.3520 target = 0.116359 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.2806 r_free = 0.2806 target = 0.072241 restraints weight = 25797.577| |-----------------------------------------------------------------------------| r_work (start): 0.2782 rms_B_bonded: 2.79 r_work: 0.2635 rms_B_bonded: 2.96 restraints_weight: 0.5000 r_work: 0.2492 rms_B_bonded: 4.63 restraints_weight: 0.2500 r_work (final): 0.2492 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8561 moved from start: 0.3627 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= 0.144 Angle : 0.632 8.039 23780 Z= 0.304 Chirality : 0.045 0.170 2820 Planarity : 0.004 0.035 2850 Dihedral : 6.270 53.863 2950 Min Nonbonded Distance : 2.276 Molprobity Statistics. All-atom Clashscore : 3.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.94 % Favored : 95.06 % Rotamer: Outliers : 3.54 % Allowed : 16.24 % 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: -0.49 (0.20), residues: 1945 helix: 1.30 (0.20), residues: 750 sheet: -0.65 (0.24), residues: 425 loop : -1.78 (0.22), residues: 770 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 315 TYR 0.017 0.001 TYR B 448 PHE 0.031 0.002 PHE E 412 TRP 0.025 0.001 TRP D 456 HIS 0.005 0.001 HIS C 411 Details of bonding type rmsd covalent geometry : bond 0.00327 (17325) covalent geometry : angle 0.61066 (23680) SS BOND : bond 0.00506 ( 5) SS BOND : angle 1.33354 ( 10) hydrogen bonds : bond 0.05549 ( 688) hydrogen bonds : angle 4.42777 ( 2019) Misc. bond : bond 0.00010 ( 5) link_BETA1-4 : bond 0.00408 ( 15) link_BETA1-4 : angle 3.44552 ( 45) link_NAG-ASN : bond 0.00161 ( 15) link_NAG-ASN : angle 1.68740 ( 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 242 residues out of total 1835 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 177 time to evaluate : 0.668 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 186 GLU cc_start: 0.7964 (OUTLIER) cc_final: 0.7183 (tp30) REVERT: A 238 ASP cc_start: 0.8942 (t70) cc_final: 0.8634 (t70) REVERT: A 435 ARG cc_start: 0.7229 (OUTLIER) cc_final: 0.6903 (tpt170) REVERT: B 186 GLU cc_start: 0.7945 (OUTLIER) cc_final: 0.7183 (tp30) REVERT: B 238 ASP cc_start: 0.9023 (t70) cc_final: 0.8447 (t0) REVERT: B 435 ARG cc_start: 0.7238 (OUTLIER) cc_final: 0.6856 (tpt170) REVERT: C 162 ASP cc_start: 0.8863 (m-30) cc_final: 0.8651 (m-30) REVERT: C 186 GLU cc_start: 0.7661 (OUTLIER) cc_final: 0.6925 (tp30) REVERT: C 235 MET cc_start: 0.8786 (mmm) cc_final: 0.8436 (mmm) REVERT: C 238 ASP cc_start: 0.9014 (t70) cc_final: 0.8636 (t0) REVERT: C 435 ARG cc_start: 0.6987 (OUTLIER) cc_final: 0.6729 (tpt170) REVERT: D 45 MET cc_start: 0.9580 (OUTLIER) cc_final: 0.9270 (tpp) REVERT: D 197 LYS cc_start: 0.7932 (mttm) cc_final: 0.7674 (mtpp) REVERT: D 238 ASP cc_start: 0.8940 (t70) cc_final: 0.8304 (t0) REVERT: D 314 GLN cc_start: 0.7330 (OUTLIER) cc_final: 0.6772 (pp30) REVERT: D 420 ARG cc_start: 0.8614 (OUTLIER) cc_final: 0.8390 (ptp-110) REVERT: E 186 GLU cc_start: 0.7850 (OUTLIER) cc_final: 0.7091 (tp30) REVERT: E 197 LYS cc_start: 0.7961 (mttm) cc_final: 0.7730 (mtpp) REVERT: E 238 ASP cc_start: 0.8914 (t70) cc_final: 0.8635 (t70) outliers start: 65 outliers final: 39 residues processed: 213 average time/residue: 0.5507 time to fit residues: 132.0898 Evaluate side-chains 220 residues out of total 1835 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 171 time to evaluate : 0.568 ------------------------------------------------------------------------------- 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 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 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 240 VAL 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 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 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 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 420 ARG 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 229 LEU Chi-restraints excluded: chain E residue 269 VAL Chi-restraints excluded: chain E residue 435 ARG Chi-restraints excluded: chain E residue 450 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 195 random chunks: chunk 110 optimal weight: 30.0000 chunk 183 optimal weight: 5.9990 chunk 192 optimal weight: 0.8980 chunk 163 optimal weight: 0.9990 chunk 60 optimal weight: 3.9990 chunk 79 optimal weight: 2.9990 chunk 27 optimal weight: 10.0000 chunk 3 optimal weight: 4.9990 chunk 50 optimal weight: 5.9990 chunk 81 optimal weight: 4.9990 chunk 88 optimal weight: 1.9990 overall best weight: 2.1788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 184 GLN D 311 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3510 r_free = 0.3510 target = 0.115705 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.2792 r_free = 0.2792 target = 0.071529 restraints weight = 25746.940| |-----------------------------------------------------------------------------| r_work (start): 0.2765 rms_B_bonded: 2.77 r_work: 0.2619 rms_B_bonded: 2.93 restraints_weight: 0.5000 r_work: 0.2475 rms_B_bonded: 4.59 restraints_weight: 0.2500 r_work (final): 0.2475 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8584 moved from start: 0.3645 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.030 17365 Z= 0.185 Angle : 0.665 8.104 23780 Z= 0.319 Chirality : 0.046 0.176 2820 Planarity : 0.004 0.038 2850 Dihedral : 6.305 54.783 2950 Min Nonbonded Distance : 2.253 Molprobity Statistics. All-atom Clashscore : 4.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.83 % Favored : 95.17 % Rotamer: Outliers : 3.05 % Allowed : 16.68 % Favored : 80.27 % 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: -0.49 (0.20), residues: 1945 helix: 1.31 (0.20), residues: 750 sheet: -0.64 (0.24), residues: 425 loop : -1.80 (0.22), residues: 770 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 322 TYR 0.019 0.002 TYR B 448 PHE 0.019 0.002 PHE A 233 TRP 0.028 0.001 TRP D 456 HIS 0.005 0.001 HIS C 411 Details of bonding type rmsd covalent geometry : bond 0.00438 (17325) covalent geometry : angle 0.64352 (23680) SS BOND : bond 0.00604 ( 5) SS BOND : angle 1.43660 ( 10) hydrogen bonds : bond 0.05651 ( 688) hydrogen bonds : angle 4.45409 ( 2019) Misc. bond : bond 0.00012 ( 5) link_BETA1-4 : bond 0.00346 ( 15) link_BETA1-4 : angle 3.44519 ( 45) link_NAG-ASN : bond 0.00222 ( 15) link_NAG-ASN : angle 1.76338 ( 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 231 residues out of total 1835 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 175 time to evaluate : 0.667 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 186 GLU cc_start: 0.7964 (OUTLIER) cc_final: 0.7145 (tp30) REVERT: A 238 ASP cc_start: 0.8958 (t70) cc_final: 0.8658 (t70) REVERT: A 435 ARG cc_start: 0.7235 (OUTLIER) cc_final: 0.6912 (tpt170) REVERT: B 186 GLU cc_start: 0.7989 (OUTLIER) cc_final: 0.7206 (tp30) REVERT: B 238 ASP cc_start: 0.9043 (t70) cc_final: 0.8473 (t0) REVERT: B 250 GLU cc_start: 0.8333 (OUTLIER) cc_final: 0.7991 (mp0) REVERT: B 435 ARG cc_start: 0.7267 (OUTLIER) cc_final: 0.6873 (tpt170) REVERT: C 162 ASP cc_start: 0.8886 (m-30) cc_final: 0.8664 (m-30) REVERT: C 186 GLU cc_start: 0.7675 (OUTLIER) cc_final: 0.6924 (tp30) REVERT: C 235 MET cc_start: 0.8793 (mmm) cc_final: 0.8435 (mmm) REVERT: C 238 ASP cc_start: 0.9038 (t70) cc_final: 0.8667 (t0) REVERT: C 435 ARG cc_start: 0.7002 (OUTLIER) cc_final: 0.6784 (tpt170) REVERT: D 45 MET cc_start: 0.9587 (OUTLIER) cc_final: 0.9264 (tpp) REVERT: D 197 LYS cc_start: 0.7965 (mttm) cc_final: 0.7712 (mtpp) REVERT: D 238 ASP cc_start: 0.8952 (t70) cc_final: 0.8324 (t0) REVERT: D 311 GLN cc_start: 0.6055 (OUTLIER) cc_final: 0.5674 (pp30) REVERT: D 314 GLN cc_start: 0.7289 (OUTLIER) cc_final: 0.6738 (pp30) REVERT: D 420 ARG cc_start: 0.8620 (OUTLIER) cc_final: 0.8389 (ptp-110) REVERT: E 186 GLU cc_start: 0.7920 (OUTLIER) cc_final: 0.7143 (tp30) REVERT: E 197 LYS cc_start: 0.7984 (mttm) cc_final: 0.7751 (mtpp) REVERT: E 238 ASP cc_start: 0.8927 (t70) cc_final: 0.8645 (t70) outliers start: 56 outliers final: 39 residues processed: 206 average time/residue: 0.5614 time to fit residues: 130.0430 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 : 0.674 ------------------------------------------------------------------------------- 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 186 GLU Chi-restraints excluded: chain A residue 221 LEU Chi-restraints excluded: chain A residue 229 LEU 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 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 250 GLU Chi-restraints excluded: chain B residue 269 VAL Chi-restraints excluded: chain B residue 333 LEU 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 260 LEU Chi-restraints excluded: chain C residue 269 VAL 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 184 GLN 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 311 GLN Chi-restraints excluded: chain D residue 314 GLN Chi-restraints excluded: chain D residue 420 ARG 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 229 LEU Chi-restraints excluded: chain E residue 269 VAL Chi-restraints excluded: chain E residue 435 ARG Chi-restraints excluded: chain E residue 450 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 195 random chunks: chunk 141 optimal weight: 0.7980 chunk 87 optimal weight: 0.5980 chunk 114 optimal weight: 0.7980 chunk 35 optimal weight: 0.9980 chunk 61 optimal weight: 0.9990 chunk 162 optimal weight: 3.9990 chunk 33 optimal weight: 0.9990 chunk 125 optimal weight: 0.6980 chunk 13 optimal weight: 0.3980 chunk 112 optimal weight: 1.9990 chunk 140 optimal weight: 0.9980 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 184 GLN D 184 GLN D 311 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3534 r_free = 0.3534 target = 0.117394 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.2827 r_free = 0.2827 target = 0.073398 restraints weight = 25721.098| |-----------------------------------------------------------------------------| r_work (start): 0.2800 rms_B_bonded: 2.78 r_work: 0.2653 rms_B_bonded: 2.96 restraints_weight: 0.5000 r_work: 0.2508 rms_B_bonded: 4.65 restraints_weight: 0.2500 r_work (final): 0.2508 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8551 moved from start: 0.3738 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.040 17365 Z= 0.118 Angle : 0.620 7.927 23780 Z= 0.297 Chirality : 0.044 0.162 2820 Planarity : 0.004 0.033 2850 Dihedral : 5.988 53.248 2950 Min Nonbonded Distance : 2.256 Molprobity Statistics. All-atom Clashscore : 3.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.78 % Favored : 95.22 % Rotamer: Outliers : 2.83 % Allowed : 16.95 % 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: -0.43 (0.20), residues: 1945 helix: 1.35 (0.20), residues: 760 sheet: -0.63 (0.24), residues: 425 loop : -1.78 (0.22), residues: 760 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 315 TYR 0.018 0.001 TYR B 448 PHE 0.034 0.001 PHE E 412 TRP 0.029 0.001 TRP D 456 HIS 0.005 0.001 HIS C 411 Details of bonding type rmsd covalent geometry : bond 0.00243 (17325) covalent geometry : angle 0.60024 (23680) SS BOND : bond 0.00389 ( 5) SS BOND : angle 1.18029 ( 10) hydrogen bonds : bond 0.05227 ( 688) hydrogen bonds : angle 4.35551 ( 2019) Misc. bond : bond 0.00017 ( 5) link_BETA1-4 : bond 0.00418 ( 15) link_BETA1-4 : angle 3.34690 ( 45) link_NAG-ASN : bond 0.00158 ( 15) link_NAG-ASN : angle 1.50104 ( 45) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6461.76 seconds wall clock time: 110 minutes 27.91 seconds (6627.91 seconds total)