Starting phenix.real_space_refine on Sat May 24 11:23:46 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8jyu_36731/05_2025/8jyu_36731.cif Found real_map, /net/cci-nas-00/data/ceres_data/8jyu_36731/05_2025/8jyu_36731.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.19 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8jyu_36731/05_2025/8jyu_36731.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8jyu_36731/05_2025/8jyu_36731.map" model { file = "/net/cci-nas-00/data/ceres_data/8jyu_36731/05_2025/8jyu_36731.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8jyu_36731/05_2025/8jyu_36731.cif" } resolution = 2.19 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.002 sd= 0.176 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians P 6 5.49 5 Mg 6 5.21 5 S 108 5.16 5 C 16374 2.51 5 N 4266 2.21 5 O 4782 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 48 residue(s): 0.08s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/chem_data/mon_lib" Total number of atoms: 25542 Number of models: 1 Model: "" Number of chains: 12 Chain: "A" Number of atoms: 4222 Number of conformers: 1 Conformer: "" Number of residues, atoms: 530, 4222 Classifications: {'peptide': 530} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PCIS': 1, 'PTRANS': 22, 'TRANS': 506} Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 8 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ASN:plan1': 1} Unresolved non-hydrogen planarities: 3 Chain: "D" Number of atoms: 4222 Number of conformers: 1 Conformer: "" Number of residues, atoms: 530, 4222 Classifications: {'peptide': 530} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PCIS': 1, 'PTRANS': 22, 'TRANS': 506} Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 8 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ASN:plan1': 1} Unresolved non-hydrogen planarities: 3 Chain: "B" Number of atoms: 4222 Number of conformers: 1 Conformer: "" Number of residues, atoms: 530, 4222 Classifications: {'peptide': 530} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PCIS': 1, 'PTRANS': 22, 'TRANS': 506} Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 8 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ASN:plan1': 1} Unresolved non-hydrogen planarities: 3 Chain: "C" Number of atoms: 4222 Number of conformers: 1 Conformer: "" Number of residues, atoms: 530, 4222 Classifications: {'peptide': 530} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PCIS': 1, 'PTRANS': 22, 'TRANS': 506} Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 8 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ASN:plan1': 1} Unresolved non-hydrogen planarities: 3 Chain: "E" Number of atoms: 4222 Number of conformers: 1 Conformer: "" Number of residues, atoms: 530, 4222 Classifications: {'peptide': 530} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PCIS': 1, 'PTRANS': 22, 'TRANS': 506} Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 8 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ASN:plan1': 1} Unresolved non-hydrogen planarities: 3 Chain: "F" Number of atoms: 4222 Number of conformers: 1 Conformer: "" Number of residues, atoms: 530, 4222 Classifications: {'peptide': 530} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PCIS': 1, 'PTRANS': 22, 'TRANS': 506} Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 8 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ASN:plan1': 1} Unresolved non-hydrogen planarities: 3 Chain: "A" Number of atoms: 35 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 35 Unusual residues: {' MG': 1, 'DKA': 1} Classifications: {'RNA': 1, 'undetermined': 2} Modifications used: {'rna3p': 1} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 1 Chain: "D" Number of atoms: 35 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 35 Unusual residues: {' MG': 1, 'DKA': 1} Classifications: {'RNA': 1, 'undetermined': 2} Modifications used: {'rna3p': 1} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 1 Chain: "B" Number of atoms: 35 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 35 Unusual residues: {' MG': 1, 'DKA': 1} Classifications: {'RNA': 1, 'undetermined': 2} Modifications used: {'rna3p': 1} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 1 Chain: "C" Number of atoms: 35 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 35 Unusual residues: {' MG': 1, 'DKA': 1} Classifications: {'RNA': 1, 'undetermined': 2} Modifications used: {'rna3p': 1} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 1 Chain: "E" Number of atoms: 35 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 35 Unusual residues: {' MG': 1, 'DKA': 1} Classifications: {'RNA': 1, 'undetermined': 2} Modifications used: {'rna3p': 1} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 1 Chain: "F" Number of atoms: 35 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 35 Unusual residues: {' MG': 1, 'DKA': 1} Classifications: {'RNA': 1, 'undetermined': 2} Modifications used: {'rna3p': 1} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 1 Time building chain proxies: 13.97, per 1000 atoms: 0.55 Number of scatterers: 25542 At special positions: 0 Unit cell: (162.75, 154.38, 95.79, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 108 16.00 P 6 15.00 Mg 6 11.99 O 4782 8.00 N 4266 7.00 C 16374 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=6, symmetry=0 Number of additional bonds: simple=6, symmetry=0 Coordination: Other bonds: Time building additional restraints: 6.16 Conformation dependent library (CDL) restraints added in 3.1 seconds 6336 Ramachandran restraints generated. 3168 Oldfield, 0 Emsley, 3168 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5964 Finding SS restraints... Secondary structure from input PDB file: 138 helices and 36 sheets defined 39.4% alpha, 17.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 3.33 Creating SS restraints... Processing helix chain 'A' and resid 14 through 21 Processing helix chain 'A' and resid 41 through 58 Processing helix chain 'A' and resid 73 through 86 Proline residue: A 84 - end of helix Processing helix chain 'A' and resid 98 through 110 Processing helix chain 'A' and resid 120 through 128 removed outlier: 3.628A pdb=" N GLN A 126 " --> pdb=" O PRO A 122 " (cutoff:3.500A) removed outlier: 3.805A pdb=" N ILE A 127 " --> pdb=" O ILE A 123 " (cutoff:3.500A) Processing helix chain 'A' and resid 129 through 131 No H-bonds generated for 'chain 'A' and resid 129 through 131' Processing helix chain 'A' and resid 146 through 154 Processing helix chain 'A' and resid 189 through 203 Processing helix chain 'A' and resid 226 through 231 Processing helix chain 'A' and resid 231 through 240 Processing helix chain 'A' and resid 250 through 262 Processing helix chain 'A' and resid 269 through 279 Processing helix chain 'A' and resid 280 through 283 removed outlier: 3.515A pdb=" N LYS A 283 " --> pdb=" O PRO A 280 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 280 through 283' Processing helix chain 'A' and resid 300 through 309 Processing helix chain 'A' and resid 321 through 324 removed outlier: 4.327A pdb=" N GLY A 324 " --> pdb=" O SER A 321 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 321 through 324' Processing helix chain 'A' and resid 333 through 338 removed outlier: 3.508A pdb=" N GLU A 338 " --> pdb=" O PRO A 334 " (cutoff:3.500A) Processing helix chain 'A' and resid 340 through 349 Processing helix chain 'A' and resid 395 through 402 Processing helix chain 'A' and resid 403 through 406 removed outlier: 3.690A pdb=" N TYR A 406 " --> pdb=" O ARG A 403 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 403 through 406' Processing helix chain 'A' and resid 439 through 448 removed outlier: 3.879A pdb=" N LEU A 443 " --> pdb=" O SER A 439 " (cutoff:3.500A) Processing helix chain 'A' and resid 483 through 492 Processing helix chain 'A' and resid 503 through 508 removed outlier: 4.700A pdb=" N LYS A 508 " --> pdb=" O ALA A 504 " (cutoff:3.500A) Processing helix chain 'A' and resid 524 through 531 removed outlier: 3.639A pdb=" N LEU A 531 " --> pdb=" O GLU A 527 " (cutoff:3.500A) Processing helix chain 'D' and resid 14 through 21 Processing helix chain 'D' and resid 41 through 58 Processing helix chain 'D' and resid 73 through 86 Proline residue: D 84 - end of helix Processing helix chain 'D' and resid 98 through 110 Processing helix chain 'D' and resid 120 through 128 removed outlier: 3.628A pdb=" N GLN D 126 " --> pdb=" O PRO D 122 " (cutoff:3.500A) removed outlier: 3.805A pdb=" N ILE D 127 " --> pdb=" O ILE D 123 " (cutoff:3.500A) Processing helix chain 'D' and resid 129 through 131 No H-bonds generated for 'chain 'D' and resid 129 through 131' Processing helix chain 'D' and resid 146 through 154 Processing helix chain 'D' and resid 189 through 203 Processing helix chain 'D' and resid 226 through 231 Processing helix chain 'D' and resid 231 through 240 Processing helix chain 'D' and resid 250 through 262 Processing helix chain 'D' and resid 269 through 279 Processing helix chain 'D' and resid 280 through 283 removed outlier: 3.515A pdb=" N LYS D 283 " --> pdb=" O PRO D 280 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 280 through 283' Processing helix chain 'D' and resid 300 through 309 Processing helix chain 'D' and resid 321 through 324 removed outlier: 4.327A pdb=" N GLY D 324 " --> pdb=" O SER D 321 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 321 through 324' Processing helix chain 'D' and resid 333 through 338 removed outlier: 3.507A pdb=" N GLU D 338 " --> pdb=" O PRO D 334 " (cutoff:3.500A) Processing helix chain 'D' and resid 340 through 349 Processing helix chain 'D' and resid 395 through 402 Processing helix chain 'D' and resid 403 through 406 removed outlier: 3.690A pdb=" N TYR D 406 " --> pdb=" O ARG D 403 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 403 through 406' Processing helix chain 'D' and resid 439 through 448 removed outlier: 3.879A pdb=" N LEU D 443 " --> pdb=" O SER D 439 " (cutoff:3.500A) Processing helix chain 'D' and resid 483 through 492 Processing helix chain 'D' and resid 503 through 508 removed outlier: 4.700A pdb=" N LYS D 508 " --> pdb=" O ALA D 504 " (cutoff:3.500A) Processing helix chain 'D' and resid 524 through 531 removed outlier: 3.640A pdb=" N LEU D 531 " --> pdb=" O GLU D 527 " (cutoff:3.500A) Processing helix chain 'B' and resid 14 through 21 Processing helix chain 'B' and resid 41 through 58 Processing helix chain 'B' and resid 73 through 86 Proline residue: B 84 - end of helix Processing helix chain 'B' and resid 98 through 110 Processing helix chain 'B' and resid 120 through 128 removed outlier: 3.628A pdb=" N GLN B 126 " --> pdb=" O PRO B 122 " (cutoff:3.500A) removed outlier: 3.805A pdb=" N ILE B 127 " --> pdb=" O ILE B 123 " (cutoff:3.500A) Processing helix chain 'B' and resid 129 through 131 No H-bonds generated for 'chain 'B' and resid 129 through 131' Processing helix chain 'B' and resid 146 through 154 Processing helix chain 'B' and resid 189 through 203 Processing helix chain 'B' and resid 226 through 231 Processing helix chain 'B' and resid 231 through 240 Processing helix chain 'B' and resid 250 through 262 Processing helix chain 'B' and resid 269 through 279 Processing helix chain 'B' and resid 280 through 283 removed outlier: 3.515A pdb=" N LYS B 283 " --> pdb=" O PRO B 280 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 280 through 283' Processing helix chain 'B' and resid 300 through 309 Processing helix chain 'B' and resid 321 through 324 removed outlier: 4.327A pdb=" N GLY B 324 " --> pdb=" O SER B 321 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 321 through 324' Processing helix chain 'B' and resid 333 through 338 removed outlier: 3.508A pdb=" N GLU B 338 " --> pdb=" O PRO B 334 " (cutoff:3.500A) Processing helix chain 'B' and resid 340 through 349 Processing helix chain 'B' and resid 395 through 402 Processing helix chain 'B' and resid 403 through 406 removed outlier: 3.690A pdb=" N TYR B 406 " --> pdb=" O ARG B 403 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 403 through 406' Processing helix chain 'B' and resid 439 through 448 removed outlier: 3.878A pdb=" N LEU B 443 " --> pdb=" O SER B 439 " (cutoff:3.500A) Processing helix chain 'B' and resid 483 through 492 Processing helix chain 'B' and resid 503 through 508 removed outlier: 4.700A pdb=" N LYS B 508 " --> pdb=" O ALA B 504 " (cutoff:3.500A) Processing helix chain 'B' and resid 524 through 531 removed outlier: 3.639A pdb=" N LEU B 531 " --> pdb=" O GLU B 527 " (cutoff:3.500A) Processing helix chain 'C' and resid 14 through 21 Processing helix chain 'C' and resid 41 through 58 Processing helix chain 'C' and resid 73 through 86 Proline residue: C 84 - end of helix Processing helix chain 'C' and resid 98 through 110 Processing helix chain 'C' and resid 120 through 128 removed outlier: 3.628A pdb=" N GLN C 126 " --> pdb=" O PRO C 122 " (cutoff:3.500A) removed outlier: 3.805A pdb=" N ILE C 127 " --> pdb=" O ILE C 123 " (cutoff:3.500A) Processing helix chain 'C' and resid 129 through 131 No H-bonds generated for 'chain 'C' and resid 129 through 131' Processing helix chain 'C' and resid 146 through 154 Processing helix chain 'C' and resid 189 through 203 Processing helix chain 'C' and resid 226 through 231 Processing helix chain 'C' and resid 231 through 240 Processing helix chain 'C' and resid 250 through 262 Processing helix chain 'C' and resid 269 through 279 Processing helix chain 'C' and resid 280 through 283 removed outlier: 3.515A pdb=" N LYS C 283 " --> pdb=" O PRO C 280 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 280 through 283' Processing helix chain 'C' and resid 300 through 309 Processing helix chain 'C' and resid 321 through 324 removed outlier: 4.327A pdb=" N GLY C 324 " --> pdb=" O SER C 321 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 321 through 324' Processing helix chain 'C' and resid 333 through 338 removed outlier: 3.508A pdb=" N GLU C 338 " --> pdb=" O PRO C 334 " (cutoff:3.500A) Processing helix chain 'C' and resid 340 through 349 Processing helix chain 'C' and resid 395 through 402 Processing helix chain 'C' and resid 403 through 406 removed outlier: 3.690A pdb=" N TYR C 406 " --> pdb=" O ARG C 403 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 403 through 406' Processing helix chain 'C' and resid 439 through 448 removed outlier: 3.879A pdb=" N LEU C 443 " --> pdb=" O SER C 439 " (cutoff:3.500A) Processing helix chain 'C' and resid 483 through 492 Processing helix chain 'C' and resid 503 through 508 removed outlier: 4.699A pdb=" N LYS C 508 " --> pdb=" O ALA C 504 " (cutoff:3.500A) Processing helix chain 'C' and resid 524 through 531 removed outlier: 3.638A pdb=" N LEU C 531 " --> pdb=" O GLU C 527 " (cutoff:3.500A) Processing helix chain 'E' and resid 14 through 21 Processing helix chain 'E' and resid 41 through 58 Processing helix chain 'E' and resid 73 through 86 Proline residue: E 84 - end of helix Processing helix chain 'E' and resid 98 through 110 Processing helix chain 'E' and resid 120 through 128 removed outlier: 3.629A pdb=" N GLN E 126 " --> pdb=" O PRO E 122 " (cutoff:3.500A) removed outlier: 3.805A pdb=" N ILE E 127 " --> pdb=" O ILE E 123 " (cutoff:3.500A) Processing helix chain 'E' and resid 129 through 131 No H-bonds generated for 'chain 'E' and resid 129 through 131' Processing helix chain 'E' and resid 146 through 154 Processing helix chain 'E' and resid 189 through 203 Processing helix chain 'E' and resid 226 through 231 Processing helix chain 'E' and resid 231 through 240 Processing helix chain 'E' and resid 250 through 262 Processing helix chain 'E' and resid 269 through 279 Processing helix chain 'E' and resid 280 through 283 removed outlier: 3.515A pdb=" N LYS E 283 " --> pdb=" O PRO E 280 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 280 through 283' Processing helix chain 'E' and resid 300 through 309 Processing helix chain 'E' and resid 321 through 324 removed outlier: 4.328A pdb=" N GLY E 324 " --> pdb=" O SER E 321 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 321 through 324' Processing helix chain 'E' and resid 333 through 338 removed outlier: 3.507A pdb=" N GLU E 338 " --> pdb=" O PRO E 334 " (cutoff:3.500A) Processing helix chain 'E' and resid 340 through 349 Processing helix chain 'E' and resid 395 through 402 Processing helix chain 'E' and resid 403 through 406 removed outlier: 3.690A pdb=" N TYR E 406 " --> pdb=" O ARG E 403 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 403 through 406' Processing helix chain 'E' and resid 439 through 448 removed outlier: 3.879A pdb=" N LEU E 443 " --> pdb=" O SER E 439 " (cutoff:3.500A) Processing helix chain 'E' and resid 483 through 492 Processing helix chain 'E' and resid 503 through 508 removed outlier: 4.700A pdb=" N LYS E 508 " --> pdb=" O ALA E 504 " (cutoff:3.500A) Processing helix chain 'E' and resid 524 through 531 removed outlier: 3.638A pdb=" N LEU E 531 " --> pdb=" O GLU E 527 " (cutoff:3.500A) Processing helix chain 'F' and resid 14 through 21 Processing helix chain 'F' and resid 41 through 58 Processing helix chain 'F' and resid 73 through 86 Proline residue: F 84 - end of helix Processing helix chain 'F' and resid 98 through 110 Processing helix chain 'F' and resid 120 through 128 removed outlier: 3.628A pdb=" N GLN F 126 " --> pdb=" O PRO F 122 " (cutoff:3.500A) removed outlier: 3.806A pdb=" N ILE F 127 " --> pdb=" O ILE F 123 " (cutoff:3.500A) Processing helix chain 'F' and resid 129 through 131 No H-bonds generated for 'chain 'F' and resid 129 through 131' Processing helix chain 'F' and resid 146 through 154 Processing helix chain 'F' and resid 189 through 203 Processing helix chain 'F' and resid 226 through 231 Processing helix chain 'F' and resid 231 through 240 Processing helix chain 'F' and resid 250 through 262 Processing helix chain 'F' and resid 269 through 279 Processing helix chain 'F' and resid 280 through 283 removed outlier: 3.515A pdb=" N LYS F 283 " --> pdb=" O PRO F 280 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 280 through 283' Processing helix chain 'F' and resid 300 through 309 Processing helix chain 'F' and resid 321 through 324 removed outlier: 4.327A pdb=" N GLY F 324 " --> pdb=" O SER F 321 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 321 through 324' Processing helix chain 'F' and resid 333 through 338 removed outlier: 3.508A pdb=" N GLU F 338 " --> pdb=" O PRO F 334 " (cutoff:3.500A) Processing helix chain 'F' and resid 340 through 349 Processing helix chain 'F' and resid 395 through 402 Processing helix chain 'F' and resid 403 through 406 removed outlier: 3.690A pdb=" N TYR F 406 " --> pdb=" O ARG F 403 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 403 through 406' Processing helix chain 'F' and resid 439 through 448 removed outlier: 3.879A pdb=" N LEU F 443 " --> pdb=" O SER F 439 " (cutoff:3.500A) Processing helix chain 'F' and resid 483 through 492 Processing helix chain 'F' and resid 503 through 508 removed outlier: 4.700A pdb=" N LYS F 508 " --> pdb=" O ALA F 504 " (cutoff:3.500A) Processing helix chain 'F' and resid 524 through 531 removed outlier: 3.639A pdb=" N LEU F 531 " --> pdb=" O GLU F 527 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 37 through 40 removed outlier: 6.615A pdb=" N GLU A 30 " --> pdb=" O GLN A 243 " (cutoff:3.500A) removed outlier: 8.056A pdb=" N TYR A 245 " --> pdb=" O GLU A 30 " (cutoff:3.500A) removed outlier: 6.599A pdb=" N VAL A 32 " --> pdb=" O TYR A 245 " (cutoff:3.500A) removed outlier: 6.335A pdb=" N TYR A 218 " --> pdb=" O VAL A 244 " (cutoff:3.500A) removed outlier: 5.995A pdb=" N ILE A 217 " --> pdb=" O PHE A 265 " (cutoff:3.500A) removed outlier: 8.458A pdb=" N HIS A 267 " --> pdb=" O ILE A 217 " (cutoff:3.500A) removed outlier: 7.811A pdb=" N MET A 219 " --> pdb=" O HIS A 267 " (cutoff:3.500A) removed outlier: 7.062A pdb=" N ALA A 316 " --> pdb=" O ILE A 329 " (cutoff:3.500A) removed outlier: 4.849A pdb=" N ILE A 329 " --> pdb=" O ALA A 316 " (cutoff:3.500A) removed outlier: 6.770A pdb=" N TYR A 318 " --> pdb=" O LEU A 327 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 136 through 140 removed outlier: 6.479A pdb=" N ILE A 114 " --> pdb=" O VAL A 138 " (cutoff:3.500A) removed outlier: 7.172A pdb=" N LEU A 140 " --> pdb=" O ILE A 114 " (cutoff:3.500A) removed outlier: 6.676A pdb=" N ILE A 116 " --> pdb=" O LEU A 140 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N ILE A 113 " --> pdb=" O THR A 65 " (cutoff:3.500A) removed outlier: 4.695A pdb=" N TYR A 174 " --> pdb=" O MET A 92 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 359 through 363 removed outlier: 5.108A pdb=" N ASP A 411 " --> pdb=" O ILE A 380 " (cutoff:3.500A) removed outlier: 8.841A pdb=" N VAL A 382 " --> pdb=" O THR A 409 " (cutoff:3.500A) removed outlier: 7.166A pdb=" N THR A 409 " --> pdb=" O VAL A 382 " (cutoff:3.500A) removed outlier: 6.553A pdb=" N HIS A 414 " --> pdb=" O ILE A 423 " (cutoff:3.500A) removed outlier: 5.353A pdb=" N ILE A 423 " --> pdb=" O HIS A 414 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 431 through 433 removed outlier: 3.779A pdb=" N ILE A 433 " --> pdb=" O GLU A 436 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 453 through 458 removed outlier: 6.464A pdb=" N THR A 475 " --> pdb=" O SER A 454 " (cutoff:3.500A) removed outlier: 4.264A pdb=" N VAL A 456 " --> pdb=" O LEU A 473 " (cutoff:3.500A) removed outlier: 6.638A pdb=" N LEU A 473 " --> pdb=" O VAL A 456 " (cutoff:3.500A) removed outlier: 6.222A pdb=" N ALA A 472 " --> pdb=" O LYS A 510 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 461 through 463 Processing sheet with id=AA7, first strand: chain 'D' and resid 37 through 40 removed outlier: 6.616A pdb=" N GLU D 30 " --> pdb=" O GLN D 243 " (cutoff:3.500A) removed outlier: 8.056A pdb=" N TYR D 245 " --> pdb=" O GLU D 30 " (cutoff:3.500A) removed outlier: 6.599A pdb=" N VAL D 32 " --> pdb=" O TYR D 245 " (cutoff:3.500A) removed outlier: 6.335A pdb=" N TYR D 218 " --> pdb=" O VAL D 244 " (cutoff:3.500A) removed outlier: 5.995A pdb=" N ILE D 217 " --> pdb=" O PHE D 265 " (cutoff:3.500A) removed outlier: 8.459A pdb=" N HIS D 267 " --> pdb=" O ILE D 217 " (cutoff:3.500A) removed outlier: 7.811A pdb=" N MET D 219 " --> pdb=" O HIS D 267 " (cutoff:3.500A) removed outlier: 7.062A pdb=" N ALA D 316 " --> pdb=" O ILE D 329 " (cutoff:3.500A) removed outlier: 4.849A pdb=" N ILE D 329 " --> pdb=" O ALA D 316 " (cutoff:3.500A) removed outlier: 6.770A pdb=" N TYR D 318 " --> pdb=" O LEU D 327 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'D' and resid 136 through 140 removed outlier: 6.478A pdb=" N ILE D 114 " --> pdb=" O VAL D 138 " (cutoff:3.500A) removed outlier: 7.173A pdb=" N LEU D 140 " --> pdb=" O ILE D 114 " (cutoff:3.500A) removed outlier: 6.675A pdb=" N ILE D 116 " --> pdb=" O LEU D 140 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N ILE D 113 " --> pdb=" O THR D 65 " (cutoff:3.500A) removed outlier: 4.696A pdb=" N TYR D 174 " --> pdb=" O MET D 92 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'D' and resid 359 through 363 removed outlier: 5.109A pdb=" N ASP D 411 " --> pdb=" O ILE D 380 " (cutoff:3.500A) removed outlier: 8.841A pdb=" N VAL D 382 " --> pdb=" O THR D 409 " (cutoff:3.500A) removed outlier: 7.166A pdb=" N THR D 409 " --> pdb=" O VAL D 382 " (cutoff:3.500A) removed outlier: 6.553A pdb=" N HIS D 414 " --> pdb=" O ILE D 423 " (cutoff:3.500A) removed outlier: 5.352A pdb=" N ILE D 423 " --> pdb=" O HIS D 414 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'D' and resid 431 through 433 removed outlier: 3.778A pdb=" N ILE D 433 " --> pdb=" O GLU D 436 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'D' and resid 453 through 458 removed outlier: 6.463A pdb=" N THR D 475 " --> pdb=" O SER D 454 " (cutoff:3.500A) removed outlier: 4.264A pdb=" N VAL D 456 " --> pdb=" O LEU D 473 " (cutoff:3.500A) removed outlier: 6.638A pdb=" N LEU D 473 " --> pdb=" O VAL D 456 " (cutoff:3.500A) removed outlier: 6.223A pdb=" N ALA D 472 " --> pdb=" O LYS D 510 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'D' and resid 461 through 463 Processing sheet with id=AB4, first strand: chain 'B' and resid 37 through 40 removed outlier: 6.615A pdb=" N GLU B 30 " --> pdb=" O GLN B 243 " (cutoff:3.500A) removed outlier: 8.055A pdb=" N TYR B 245 " --> pdb=" O GLU B 30 " (cutoff:3.500A) removed outlier: 6.598A pdb=" N VAL B 32 " --> pdb=" O TYR B 245 " (cutoff:3.500A) removed outlier: 6.335A pdb=" N TYR B 218 " --> pdb=" O VAL B 244 " (cutoff:3.500A) removed outlier: 5.995A pdb=" N ILE B 217 " --> pdb=" O PHE B 265 " (cutoff:3.500A) removed outlier: 8.458A pdb=" N HIS B 267 " --> pdb=" O ILE B 217 " (cutoff:3.500A) removed outlier: 7.811A pdb=" N MET B 219 " --> pdb=" O HIS B 267 " (cutoff:3.500A) removed outlier: 7.062A pdb=" N ALA B 316 " --> pdb=" O ILE B 329 " (cutoff:3.500A) removed outlier: 4.849A pdb=" N ILE B 329 " --> pdb=" O ALA B 316 " (cutoff:3.500A) removed outlier: 6.770A pdb=" N TYR B 318 " --> pdb=" O LEU B 327 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'B' and resid 136 through 140 removed outlier: 6.479A pdb=" N ILE B 114 " --> pdb=" O VAL B 138 " (cutoff:3.500A) removed outlier: 7.172A pdb=" N LEU B 140 " --> pdb=" O ILE B 114 " (cutoff:3.500A) removed outlier: 6.675A pdb=" N ILE B 116 " --> pdb=" O LEU B 140 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N ILE B 113 " --> pdb=" O THR B 65 " (cutoff:3.500A) removed outlier: 4.695A pdb=" N TYR B 174 " --> pdb=" O MET B 92 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'B' and resid 359 through 363 removed outlier: 5.109A pdb=" N ASP B 411 " --> pdb=" O ILE B 380 " (cutoff:3.500A) removed outlier: 8.841A pdb=" N VAL B 382 " --> pdb=" O THR B 409 " (cutoff:3.500A) removed outlier: 7.166A pdb=" N THR B 409 " --> pdb=" O VAL B 382 " (cutoff:3.500A) removed outlier: 6.553A pdb=" N HIS B 414 " --> pdb=" O ILE B 423 " (cutoff:3.500A) removed outlier: 5.353A pdb=" N ILE B 423 " --> pdb=" O HIS B 414 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'B' and resid 431 through 433 removed outlier: 3.779A pdb=" N ILE B 433 " --> pdb=" O GLU B 436 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'B' and resid 453 through 458 removed outlier: 6.463A pdb=" N THR B 475 " --> pdb=" O SER B 454 " (cutoff:3.500A) removed outlier: 4.264A pdb=" N VAL B 456 " --> pdb=" O LEU B 473 " (cutoff:3.500A) removed outlier: 6.638A pdb=" N LEU B 473 " --> pdb=" O VAL B 456 " (cutoff:3.500A) removed outlier: 6.222A pdb=" N ALA B 472 " --> pdb=" O LYS B 510 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'B' and resid 461 through 463 Processing sheet with id=AC1, first strand: chain 'C' and resid 37 through 40 removed outlier: 6.617A pdb=" N GLU C 30 " --> pdb=" O GLN C 243 " (cutoff:3.500A) removed outlier: 8.056A pdb=" N TYR C 245 " --> pdb=" O GLU C 30 " (cutoff:3.500A) removed outlier: 6.599A pdb=" N VAL C 32 " --> pdb=" O TYR C 245 " (cutoff:3.500A) removed outlier: 6.335A pdb=" N TYR C 218 " --> pdb=" O VAL C 244 " (cutoff:3.500A) removed outlier: 5.995A pdb=" N ILE C 217 " --> pdb=" O PHE C 265 " (cutoff:3.500A) removed outlier: 8.458A pdb=" N HIS C 267 " --> pdb=" O ILE C 217 " (cutoff:3.500A) removed outlier: 7.811A pdb=" N MET C 219 " --> pdb=" O HIS C 267 " (cutoff:3.500A) removed outlier: 7.062A pdb=" N ALA C 316 " --> pdb=" O ILE C 329 " (cutoff:3.500A) removed outlier: 4.849A pdb=" N ILE C 329 " --> pdb=" O ALA C 316 " (cutoff:3.500A) removed outlier: 6.770A pdb=" N TYR C 318 " --> pdb=" O LEU C 327 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'C' and resid 136 through 140 removed outlier: 6.479A pdb=" N ILE C 114 " --> pdb=" O VAL C 138 " (cutoff:3.500A) removed outlier: 7.173A pdb=" N LEU C 140 " --> pdb=" O ILE C 114 " (cutoff:3.500A) removed outlier: 6.675A pdb=" N ILE C 116 " --> pdb=" O LEU C 140 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N ILE C 113 " --> pdb=" O THR C 65 " (cutoff:3.500A) removed outlier: 4.695A pdb=" N TYR C 174 " --> pdb=" O MET C 92 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'C' and resid 359 through 363 removed outlier: 5.108A pdb=" N ASP C 411 " --> pdb=" O ILE C 380 " (cutoff:3.500A) removed outlier: 8.842A pdb=" N VAL C 382 " --> pdb=" O THR C 409 " (cutoff:3.500A) removed outlier: 7.166A pdb=" N THR C 409 " --> pdb=" O VAL C 382 " (cutoff:3.500A) removed outlier: 6.553A pdb=" N HIS C 414 " --> pdb=" O ILE C 423 " (cutoff:3.500A) removed outlier: 5.352A pdb=" N ILE C 423 " --> pdb=" O HIS C 414 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'C' and resid 431 through 433 removed outlier: 3.779A pdb=" N ILE C 433 " --> pdb=" O GLU C 436 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'C' and resid 453 through 458 removed outlier: 6.464A pdb=" N THR C 475 " --> pdb=" O SER C 454 " (cutoff:3.500A) removed outlier: 4.264A pdb=" N VAL C 456 " --> pdb=" O LEU C 473 " (cutoff:3.500A) removed outlier: 6.638A pdb=" N LEU C 473 " --> pdb=" O VAL C 456 " (cutoff:3.500A) removed outlier: 6.223A pdb=" N ALA C 472 " --> pdb=" O LYS C 510 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'C' and resid 461 through 463 Processing sheet with id=AC7, first strand: chain 'E' and resid 37 through 40 removed outlier: 6.615A pdb=" N GLU E 30 " --> pdb=" O GLN E 243 " (cutoff:3.500A) removed outlier: 8.056A pdb=" N TYR E 245 " --> pdb=" O GLU E 30 " (cutoff:3.500A) removed outlier: 6.598A pdb=" N VAL E 32 " --> pdb=" O TYR E 245 " (cutoff:3.500A) removed outlier: 6.336A pdb=" N TYR E 218 " --> pdb=" O VAL E 244 " (cutoff:3.500A) removed outlier: 5.995A pdb=" N ILE E 217 " --> pdb=" O PHE E 265 " (cutoff:3.500A) removed outlier: 8.458A pdb=" N HIS E 267 " --> pdb=" O ILE E 217 " (cutoff:3.500A) removed outlier: 7.811A pdb=" N MET E 219 " --> pdb=" O HIS E 267 " (cutoff:3.500A) removed outlier: 7.061A pdb=" N ALA E 316 " --> pdb=" O ILE E 329 " (cutoff:3.500A) removed outlier: 4.848A pdb=" N ILE E 329 " --> pdb=" O ALA E 316 " (cutoff:3.500A) removed outlier: 6.769A pdb=" N TYR E 318 " --> pdb=" O LEU E 327 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'E' and resid 136 through 140 removed outlier: 6.479A pdb=" N ILE E 114 " --> pdb=" O VAL E 138 " (cutoff:3.500A) removed outlier: 7.173A pdb=" N LEU E 140 " --> pdb=" O ILE E 114 " (cutoff:3.500A) removed outlier: 6.676A pdb=" N ILE E 116 " --> pdb=" O LEU E 140 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N ILE E 113 " --> pdb=" O THR E 65 " (cutoff:3.500A) removed outlier: 4.695A pdb=" N TYR E 174 " --> pdb=" O MET E 92 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'E' and resid 359 through 363 removed outlier: 5.108A pdb=" N ASP E 411 " --> pdb=" O ILE E 380 " (cutoff:3.500A) removed outlier: 8.841A pdb=" N VAL E 382 " --> pdb=" O THR E 409 " (cutoff:3.500A) removed outlier: 7.166A pdb=" N THR E 409 " --> pdb=" O VAL E 382 " (cutoff:3.500A) removed outlier: 6.553A pdb=" N HIS E 414 " --> pdb=" O ILE E 423 " (cutoff:3.500A) removed outlier: 5.353A pdb=" N ILE E 423 " --> pdb=" O HIS E 414 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'E' and resid 431 through 433 removed outlier: 3.779A pdb=" N ILE E 433 " --> pdb=" O GLU E 436 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'E' and resid 453 through 458 removed outlier: 6.464A pdb=" N THR E 475 " --> pdb=" O SER E 454 " (cutoff:3.500A) removed outlier: 4.264A pdb=" N VAL E 456 " --> pdb=" O LEU E 473 " (cutoff:3.500A) removed outlier: 6.638A pdb=" N LEU E 473 " --> pdb=" O VAL E 456 " (cutoff:3.500A) removed outlier: 6.222A pdb=" N ALA E 472 " --> pdb=" O LYS E 510 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'E' and resid 461 through 463 Processing sheet with id=AD4, first strand: chain 'F' and resid 37 through 40 removed outlier: 6.615A pdb=" N GLU F 30 " --> pdb=" O GLN F 243 " (cutoff:3.500A) removed outlier: 8.056A pdb=" N TYR F 245 " --> pdb=" O GLU F 30 " (cutoff:3.500A) removed outlier: 6.599A pdb=" N VAL F 32 " --> pdb=" O TYR F 245 " (cutoff:3.500A) removed outlier: 6.336A pdb=" N TYR F 218 " --> pdb=" O VAL F 244 " (cutoff:3.500A) removed outlier: 5.996A pdb=" N ILE F 217 " --> pdb=" O PHE F 265 " (cutoff:3.500A) removed outlier: 8.458A pdb=" N HIS F 267 " --> pdb=" O ILE F 217 " (cutoff:3.500A) removed outlier: 7.811A pdb=" N MET F 219 " --> pdb=" O HIS F 267 " (cutoff:3.500A) removed outlier: 7.061A pdb=" N ALA F 316 " --> pdb=" O ILE F 329 " (cutoff:3.500A) removed outlier: 4.849A pdb=" N ILE F 329 " --> pdb=" O ALA F 316 " (cutoff:3.500A) removed outlier: 6.769A pdb=" N TYR F 318 " --> pdb=" O LEU F 327 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'F' and resid 136 through 140 removed outlier: 6.479A pdb=" N ILE F 114 " --> pdb=" O VAL F 138 " (cutoff:3.500A) removed outlier: 7.172A pdb=" N LEU F 140 " --> pdb=" O ILE F 114 " (cutoff:3.500A) removed outlier: 6.675A pdb=" N ILE F 116 " --> pdb=" O LEU F 140 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N ILE F 113 " --> pdb=" O THR F 65 " (cutoff:3.500A) removed outlier: 4.696A pdb=" N TYR F 174 " --> pdb=" O MET F 92 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'F' and resid 359 through 363 removed outlier: 5.108A pdb=" N ASP F 411 " --> pdb=" O ILE F 380 " (cutoff:3.500A) removed outlier: 8.841A pdb=" N VAL F 382 " --> pdb=" O THR F 409 " (cutoff:3.500A) removed outlier: 7.166A pdb=" N THR F 409 " --> pdb=" O VAL F 382 " (cutoff:3.500A) removed outlier: 6.554A pdb=" N HIS F 414 " --> pdb=" O ILE F 423 " (cutoff:3.500A) removed outlier: 5.353A pdb=" N ILE F 423 " --> pdb=" O HIS F 414 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'F' and resid 431 through 433 removed outlier: 3.778A pdb=" N ILE F 433 " --> pdb=" O GLU F 436 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'F' and resid 453 through 458 removed outlier: 6.464A pdb=" N THR F 475 " --> pdb=" O SER F 454 " (cutoff:3.500A) removed outlier: 4.264A pdb=" N VAL F 456 " --> pdb=" O LEU F 473 " (cutoff:3.500A) removed outlier: 6.637A pdb=" N LEU F 473 " --> pdb=" O VAL F 456 " (cutoff:3.500A) removed outlier: 6.222A pdb=" N ALA F 472 " --> pdb=" O LYS F 510 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'F' and resid 461 through 463 948 hydrogen bonds defined for protein. 2682 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: 10.14 Time building geometry restraints manager: 7.24 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.31: 4321 1.31 - 1.44: 6695 1.44 - 1.56: 14904 1.56 - 1.69: 6 1.69 - 1.81: 192 Bond restraints: 26118 Sorted by residual: bond pdb=" CA PHE C 81 " pdb=" C PHE C 81 " ideal model delta sigma weight residual 1.525 1.477 0.048 1.02e-02 9.61e+03 2.26e+01 bond pdb=" CA PHE D 81 " pdb=" C PHE D 81 " ideal model delta sigma weight residual 1.525 1.477 0.048 1.02e-02 9.61e+03 2.26e+01 bond pdb=" CA PHE B 81 " pdb=" C PHE B 81 " ideal model delta sigma weight residual 1.525 1.477 0.048 1.02e-02 9.61e+03 2.25e+01 bond pdb=" CA PHE E 81 " pdb=" C PHE E 81 " ideal model delta sigma weight residual 1.525 1.477 0.048 1.02e-02 9.61e+03 2.23e+01 bond pdb=" CA PHE A 81 " pdb=" C PHE A 81 " ideal model delta sigma weight residual 1.525 1.477 0.048 1.02e-02 9.61e+03 2.22e+01 ... (remaining 26113 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.16: 34817 2.16 - 4.31: 478 4.31 - 6.47: 108 6.47 - 8.63: 15 8.63 - 10.78: 6 Bond angle restraints: 35424 Sorted by residual: angle pdb=" N TYR B 249 " pdb=" CA TYR B 249 " pdb=" C TYR B 249 " ideal model delta sigma weight residual 109.15 119.93 -10.78 1.44e+00 4.82e-01 5.61e+01 angle pdb=" N TYR C 249 " pdb=" CA TYR C 249 " pdb=" C TYR C 249 " ideal model delta sigma weight residual 109.15 119.92 -10.77 1.44e+00 4.82e-01 5.60e+01 angle pdb=" N TYR E 249 " pdb=" CA TYR E 249 " pdb=" C TYR E 249 " ideal model delta sigma weight residual 109.15 119.91 -10.76 1.44e+00 4.82e-01 5.59e+01 angle pdb=" N TYR D 249 " pdb=" CA TYR D 249 " pdb=" C TYR D 249 " ideal model delta sigma weight residual 109.15 119.91 -10.76 1.44e+00 4.82e-01 5.58e+01 angle pdb=" N TYR A 249 " pdb=" CA TYR A 249 " pdb=" C TYR A 249 " ideal model delta sigma weight residual 109.15 119.91 -10.76 1.44e+00 4.82e-01 5.58e+01 ... (remaining 35419 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.94: 14324 17.94 - 35.89: 949 35.89 - 53.83: 267 53.83 - 71.78: 60 71.78 - 89.72: 36 Dihedral angle restraints: 15636 sinusoidal: 6366 harmonic: 9270 Sorted by residual: dihedral pdb=" CA PRO F 325 " pdb=" C PRO F 325 " pdb=" N ILE F 326 " pdb=" CA ILE F 326 " ideal model delta harmonic sigma weight residual -180.00 -160.71 -19.29 0 5.00e+00 4.00e-02 1.49e+01 dihedral pdb=" CA PRO D 325 " pdb=" C PRO D 325 " pdb=" N ILE D 326 " pdb=" CA ILE D 326 " ideal model delta harmonic sigma weight residual 180.00 -160.74 -19.26 0 5.00e+00 4.00e-02 1.48e+01 dihedral pdb=" CA PRO A 325 " pdb=" C PRO A 325 " pdb=" N ILE A 326 " pdb=" CA ILE A 326 " ideal model delta harmonic sigma weight residual -180.00 -160.75 -19.25 0 5.00e+00 4.00e-02 1.48e+01 ... (remaining 15633 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.079: 3530 0.079 - 0.159: 454 0.159 - 0.238: 0 0.238 - 0.317: 0 0.317 - 0.396: 18 Chirality restraints: 4002 Sorted by residual: chirality pdb=" CA PHE C 81 " pdb=" N PHE C 81 " pdb=" C PHE C 81 " pdb=" CB PHE C 81 " both_signs ideal model delta sigma weight residual False 2.51 2.11 0.40 2.00e-01 2.50e+01 3.93e+00 chirality pdb=" CA PHE E 81 " pdb=" N PHE E 81 " pdb=" C PHE E 81 " pdb=" CB PHE E 81 " both_signs ideal model delta sigma weight residual False 2.51 2.12 0.40 2.00e-01 2.50e+01 3.90e+00 chirality pdb=" CA PHE D 81 " pdb=" N PHE D 81 " pdb=" C PHE D 81 " pdb=" CB PHE D 81 " both_signs ideal model delta sigma weight residual False 2.51 2.12 0.39 2.00e-01 2.50e+01 3.90e+00 ... (remaining 3999 not shown) Planarity restraints: 4494 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA GLU C 78 " -0.015 2.00e-02 2.50e+03 3.06e-02 9.36e+00 pdb=" C GLU C 78 " 0.053 2.00e-02 2.50e+03 pdb=" O GLU C 78 " -0.020 2.00e-02 2.50e+03 pdb=" N CYS C 79 " -0.018 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLU B 78 " 0.015 2.00e-02 2.50e+03 3.06e-02 9.36e+00 pdb=" C GLU B 78 " -0.053 2.00e-02 2.50e+03 pdb=" O GLU B 78 " 0.020 2.00e-02 2.50e+03 pdb=" N CYS B 79 " 0.018 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLU D 78 " 0.015 2.00e-02 2.50e+03 3.06e-02 9.34e+00 pdb=" C GLU D 78 " -0.053 2.00e-02 2.50e+03 pdb=" O GLU D 78 " 0.020 2.00e-02 2.50e+03 pdb=" N CYS D 79 " 0.018 2.00e-02 2.50e+03 ... (remaining 4491 not shown) Histogram of nonbonded interaction distances: 2.23 - 2.76: 4101 2.76 - 3.30: 24752 3.30 - 3.83: 45681 3.83 - 4.37: 57715 4.37 - 4.90: 93277 Nonbonded interactions: 225526 Sorted by model distance: nonbonded pdb="MG MG F 601 " pdb=" O2P AMP F 602 " model vdw 2.229 2.170 nonbonded pdb="MG MG B 601 " pdb=" O2P AMP B 602 " model vdw 2.229 2.170 nonbonded pdb="MG MG D 601 " pdb=" O2P AMP D 602 " model vdw 2.229 2.170 nonbonded pdb="MG MG A 601 " pdb=" O1P AMP A 602 " model vdw 2.230 2.170 nonbonded pdb="MG MG C 601 " pdb=" O1P AMP C 602 " model vdw 2.230 2.170 ... (remaining 225521 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: 0.20 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'C' selection = chain 'B' selection = chain 'E' selection = chain 'D' selection = chain 'F' } 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: 1.500 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 1.140 Check model and map are aligned: 0.200 Set scattering table: 0.270 Process input model: 56.140 Find NCS groups from input model: 0.490 Set up NCS constraints: 0.110 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:11.140 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 71.020 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6975 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 : 0.004 0.062 26124 Z= 0.253 Angle : 0.658 10.784 35424 Z= 0.394 Chirality : 0.050 0.396 4002 Planarity : 0.004 0.039 4494 Dihedral : 14.446 89.722 9672 Min Nonbonded Distance : 2.229 Molprobity Statistics. All-atom Clashscore : 6.37 Ramachandran Plot: Outliers : 0.19 % Allowed : 4.32 % Favored : 95.49 % Rotamer: Outliers : 0.14 % Allowed : 7.22 % Favored : 92.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.35 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.10 (0.15), residues: 3168 helix: 1.25 (0.17), residues: 1050 sheet: 0.03 (0.21), residues: 576 loop : -0.72 (0.16), residues: 1542 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP C 386 HIS 0.002 0.001 HIS B 408 PHE 0.011 0.001 PHE C 161 TYR 0.012 0.001 TYR B 80 ARG 0.002 0.000 ARG B 529 Details of bonding type rmsd hydrogen bonds : bond 0.19172 ( 948) hydrogen bonds : angle 7.51129 ( 2682) covalent geometry : bond 0.00390 (26118) covalent geometry : angle 0.65773 (35424) Misc. bond : bond 0.00044 ( 6) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6336 Ramachandran restraints generated. 3168 Oldfield, 0 Emsley, 3168 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6336 Ramachandran restraints generated. 3168 Oldfield, 0 Emsley, 3168 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 410 residues out of total 2790 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 406 time to evaluate : 2.709 Fit side-chains REVERT: A 28 GLU cc_start: 0.6917 (mm-30) cc_final: 0.6695 (mp0) REVERT: A 42 LYS cc_start: 0.7118 (ttpp) cc_final: 0.6734 (ttpp) REVERT: A 61 LYS cc_start: 0.6927 (mtmm) cc_final: 0.5971 (mmtm) REVERT: A 100 GLU cc_start: 0.6435 (tp30) cc_final: 0.5923 (tp30) REVERT: A 112 ASP cc_start: 0.7812 (m-30) cc_final: 0.7608 (m-30) REVERT: A 145 GLU cc_start: 0.5641 (mm-30) cc_final: 0.5259 (mp0) REVERT: A 150 ARG cc_start: 0.6339 (mtm110) cc_final: 0.6127 (mtm-85) REVERT: A 158 GLU cc_start: 0.7531 (mm-30) cc_final: 0.7080 (mp0) REVERT: A 160 ASN cc_start: 0.7479 (m-40) cc_final: 0.7261 (m-40) REVERT: A 197 MET cc_start: 0.7883 (mmp) cc_final: 0.6507 (mtp) REVERT: A 256 ASN cc_start: 0.7290 (t0) cc_final: 0.6905 (t0) REVERT: A 285 MET cc_start: 0.7144 (mtp) cc_final: 0.6935 (mtp) REVERT: A 309 GLU cc_start: 0.7012 (mt-10) cc_final: 0.6704 (mt-10) REVERT: A 343 GLN cc_start: 0.7059 (mt0) cc_final: 0.6560 (mt0) REVERT: A 366 ASP cc_start: 0.5427 (m-30) cc_final: 0.5180 (m-30) REVERT: A 399 LYS cc_start: 0.6883 (ttmm) cc_final: 0.5926 (tmmt) REVERT: A 461 MET cc_start: 0.3195 (OUTLIER) cc_final: 0.2213 (mpp) REVERT: D 42 LYS cc_start: 0.6930 (ttpp) cc_final: 0.6608 (ttpp) REVERT: D 61 LYS cc_start: 0.7030 (mtmm) cc_final: 0.6003 (mmtt) REVERT: D 100 GLU cc_start: 0.6353 (tp30) cc_final: 0.5283 (mp0) REVERT: D 118 GLU cc_start: 0.7106 (pt0) cc_final: 0.6493 (pp20) REVERT: D 145 GLU cc_start: 0.5585 (mm-30) cc_final: 0.5200 (mp0) REVERT: D 150 ARG cc_start: 0.6432 (mtm110) cc_final: 0.6204 (mtm-85) REVERT: D 158 GLU cc_start: 0.7540 (mm-30) cc_final: 0.6308 (tm-30) REVERT: D 160 ASN cc_start: 0.7300 (m-40) cc_final: 0.7023 (m-40) REVERT: D 197 MET cc_start: 0.7804 (mmp) cc_final: 0.6427 (mtm) REVERT: D 248 LYS cc_start: 0.7494 (tttp) cc_final: 0.7211 (tttm) REVERT: D 262 LYS cc_start: 0.7306 (mmtm) cc_final: 0.6858 (mptt) REVERT: D 285 MET cc_start: 0.6924 (mtp) cc_final: 0.6617 (mtp) REVERT: D 344 GLN cc_start: 0.7851 (mt0) cc_final: 0.7486 (mt0) REVERT: D 346 GLU cc_start: 0.6990 (tp30) cc_final: 0.6757 (tp30) REVERT: D 399 LYS cc_start: 0.6912 (ttmm) cc_final: 0.6095 (tmmt) REVERT: D 403 ARG cc_start: 0.7464 (ttp-110) cc_final: 0.7219 (ttp80) REVERT: D 461 MET cc_start: 0.2999 (ppp) cc_final: 0.2436 (mpp) REVERT: B 42 LYS cc_start: 0.7130 (ttpp) cc_final: 0.6730 (ttpp) REVERT: B 61 LYS cc_start: 0.6927 (mtmm) cc_final: 0.5969 (mmtm) REVERT: B 100 GLU cc_start: 0.6359 (tp30) cc_final: 0.6112 (tp30) REVERT: B 112 ASP cc_start: 0.7769 (m-30) cc_final: 0.7569 (m-30) REVERT: B 145 GLU cc_start: 0.5645 (mm-30) cc_final: 0.5290 (mp0) REVERT: B 150 ARG cc_start: 0.6339 (mtm110) cc_final: 0.6131 (mtm-85) REVERT: B 158 GLU cc_start: 0.7531 (mm-30) cc_final: 0.7079 (mp0) REVERT: B 160 ASN cc_start: 0.7481 (m-40) cc_final: 0.7265 (m-40) REVERT: B 197 MET cc_start: 0.7840 (mmp) cc_final: 0.6488 (mtp) REVERT: B 248 LYS cc_start: 0.7512 (tttp) cc_final: 0.7214 (tttm) REVERT: B 256 ASN cc_start: 0.7278 (t0) cc_final: 0.6860 (t0) REVERT: B 285 MET cc_start: 0.7151 (mtp) cc_final: 0.6932 (mtp) REVERT: B 309 GLU cc_start: 0.7022 (mt-10) cc_final: 0.6712 (mt-10) REVERT: B 343 GLN cc_start: 0.7052 (mt0) cc_final: 0.6566 (mt0) REVERT: B 366 ASP cc_start: 0.5447 (m-30) cc_final: 0.5196 (m-30) REVERT: B 399 LYS cc_start: 0.6900 (ttmm) cc_final: 0.5952 (tmmt) REVERT: B 461 MET cc_start: 0.3037 (OUTLIER) cc_final: 0.2095 (mpp) REVERT: C 28 GLU cc_start: 0.6768 (mm-30) cc_final: 0.6489 (mp0) REVERT: C 42 LYS cc_start: 0.7042 (ttpp) cc_final: 0.6740 (tmtp) REVERT: C 61 LYS cc_start: 0.7144 (mtmm) cc_final: 0.6153 (mmtm) REVERT: C 100 GLU cc_start: 0.6519 (tp30) cc_final: 0.5294 (mp0) REVERT: C 118 GLU cc_start: 0.7061 (pt0) cc_final: 0.6409 (pp20) REVERT: C 136 ARG cc_start: 0.7739 (ttt180) cc_final: 0.7352 (tpt-90) REVERT: C 145 GLU cc_start: 0.5648 (mm-30) cc_final: 0.5208 (mp0) REVERT: C 150 ARG cc_start: 0.6272 (mtm110) cc_final: 0.5894 (mtm110) REVERT: C 151 LEU cc_start: 0.7668 (mt) cc_final: 0.7410 (mt) REVERT: C 158 GLU cc_start: 0.7438 (mm-30) cc_final: 0.7035 (mp0) REVERT: C 165 ASP cc_start: 0.7933 (t0) cc_final: 0.7681 (t0) REVERT: C 197 MET cc_start: 0.7712 (mmp) cc_final: 0.6705 (mtp) REVERT: C 248 LYS cc_start: 0.7605 (tttp) cc_final: 0.7339 (tttm) REVERT: C 274 HIS cc_start: 0.7553 (t70) cc_final: 0.7296 (t70) REVERT: C 309 GLU cc_start: 0.7174 (mt-10) cc_final: 0.6834 (mt-10) REVERT: C 335 GLU cc_start: 0.5675 (mp0) cc_final: 0.5393 (tm-30) REVERT: C 343 GLN cc_start: 0.6730 (mt0) cc_final: 0.6127 (mt0) REVERT: C 344 GLN cc_start: 0.7892 (mt0) cc_final: 0.7431 (mt0) REVERT: C 366 ASP cc_start: 0.5334 (m-30) cc_final: 0.5116 (m-30) REVERT: C 399 LYS cc_start: 0.6771 (ttmm) cc_final: 0.5792 (tmmt) REVERT: C 403 ARG cc_start: 0.7570 (ttp-110) cc_final: 0.7274 (tmm160) REVERT: C 461 MET cc_start: 0.2941 (OUTLIER) cc_final: 0.2014 (mmt) REVERT: E 42 LYS cc_start: 0.6934 (ttpp) cc_final: 0.6603 (ttpp) REVERT: E 61 LYS cc_start: 0.7067 (mtmm) cc_final: 0.6050 (mmtt) REVERT: E 100 GLU cc_start: 0.6358 (tp30) cc_final: 0.5289 (mp0) REVERT: E 118 GLU cc_start: 0.7093 (pt0) cc_final: 0.6482 (pp20) REVERT: E 145 GLU cc_start: 0.5587 (mm-30) cc_final: 0.5167 (mp0) REVERT: E 150 ARG cc_start: 0.6404 (mtm110) cc_final: 0.6175 (mtm-85) REVERT: E 158 GLU cc_start: 0.7487 (mm-30) cc_final: 0.6310 (tm-30) REVERT: E 160 ASN cc_start: 0.7306 (m-40) cc_final: 0.7040 (m-40) REVERT: E 197 MET cc_start: 0.7827 (mmp) cc_final: 0.6436 (mtm) REVERT: E 248 LYS cc_start: 0.7485 (tttp) cc_final: 0.7198 (tttm) REVERT: E 285 MET cc_start: 0.6889 (mtp) cc_final: 0.6588 (mtp) REVERT: E 344 GLN cc_start: 0.7851 (mt0) cc_final: 0.7493 (mt0) REVERT: E 346 GLU cc_start: 0.6992 (tp30) cc_final: 0.6756 (tp30) REVERT: E 399 LYS cc_start: 0.6994 (ttmm) cc_final: 0.6160 (tmmt) REVERT: E 403 ARG cc_start: 0.7418 (ttp-110) cc_final: 0.7173 (ttp80) REVERT: E 461 MET cc_start: 0.3019 (ppp) cc_final: 0.2427 (mpp) REVERT: F 28 GLU cc_start: 0.6768 (mm-30) cc_final: 0.6490 (mp0) REVERT: F 42 LYS cc_start: 0.7039 (ttpp) cc_final: 0.6737 (tmtp) REVERT: F 61 LYS cc_start: 0.7146 (mtmm) cc_final: 0.6156 (mmtm) REVERT: F 100 GLU cc_start: 0.6517 (tp30) cc_final: 0.5292 (mp0) REVERT: F 118 GLU cc_start: 0.7066 (pt0) cc_final: 0.6411 (pp20) REVERT: F 136 ARG cc_start: 0.7749 (ttt180) cc_final: 0.7375 (tpt-90) REVERT: F 145 GLU cc_start: 0.5565 (mm-30) cc_final: 0.5147 (mp0) REVERT: F 150 ARG cc_start: 0.6271 (mtm110) cc_final: 0.5890 (mtm110) REVERT: F 151 LEU cc_start: 0.7669 (mt) cc_final: 0.7418 (mt) REVERT: F 158 GLU cc_start: 0.7436 (mm-30) cc_final: 0.7035 (mp0) REVERT: F 165 ASP cc_start: 0.7930 (t0) cc_final: 0.7689 (t0) REVERT: F 197 MET cc_start: 0.7697 (mmp) cc_final: 0.6681 (mtp) REVERT: F 248 LYS cc_start: 0.7599 (tttp) cc_final: 0.7330 (tttm) REVERT: F 274 HIS cc_start: 0.7545 (t70) cc_final: 0.7314 (t70) REVERT: F 309 GLU cc_start: 0.7163 (mt-10) cc_final: 0.6840 (mt-10) REVERT: F 335 GLU cc_start: 0.5703 (mp0) cc_final: 0.5401 (tm-30) REVERT: F 343 GLN cc_start: 0.6659 (mt0) cc_final: 0.6056 (mt0) REVERT: F 344 GLN cc_start: 0.7877 (mt0) cc_final: 0.7424 (mt0) REVERT: F 366 ASP cc_start: 0.5399 (m-30) cc_final: 0.5174 (m-30) REVERT: F 399 LYS cc_start: 0.6767 (ttmm) cc_final: 0.5787 (tmmt) REVERT: F 403 ARG cc_start: 0.7569 (ttp-110) cc_final: 0.7271 (tmm160) REVERT: F 461 MET cc_start: 0.2939 (OUTLIER) cc_final: 0.2014 (mmt) outliers start: 4 outliers final: 0 residues processed: 406 average time/residue: 1.7968 time to fit residues: 818.5964 Evaluate side-chains 351 residues out of total 2790 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 347 time to evaluate : 2.752 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 461 MET Chi-restraints excluded: chain B residue 461 MET Chi-restraints excluded: chain C residue 461 MET Chi-restraints excluded: chain F residue 461 MET Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 318 random chunks: chunk 268 optimal weight: 6.9990 chunk 241 optimal weight: 8.9990 chunk 133 optimal weight: 0.1980 chunk 82 optimal weight: 8.9990 chunk 162 optimal weight: 6.9990 chunk 128 optimal weight: 2.9990 chunk 249 optimal weight: 10.0000 chunk 96 optimal weight: 6.9990 chunk 151 optimal weight: 6.9990 chunk 185 optimal weight: 6.9990 chunk 288 optimal weight: 0.0770 overall best weight: 3.4544 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 206 ASN A 226 HIS A 344 GLN A 532 HIS D 226 HIS D 395 ASN D 532 HIS B 206 ASN B 226 HIS B 344 GLN B 532 HIS C 206 ASN C 226 HIS C 532 HIS E 226 HIS E 395 ASN E 532 HIS F 206 ASN F 226 HIS F 532 HIS Total number of N/Q/H flips: 20 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4143 r_free = 0.4143 target = 0.197939 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 69)----------------| | r_work = 0.3362 r_free = 0.3362 target = 0.125909 restraints weight = 17022.497| |-----------------------------------------------------------------------------| r_work (start): 0.3342 rms_B_bonded: 1.35 r_work: 0.3140 rms_B_bonded: 2.06 restraints_weight: 0.5000 r_work: 0.3029 rms_B_bonded: 2.97 restraints_weight: 0.2500 r_work (final): 0.3029 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8049 moved from start: 0.1678 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.043 26124 Z= 0.241 Angle : 0.749 9.417 35424 Z= 0.392 Chirality : 0.052 0.224 4002 Planarity : 0.005 0.038 4494 Dihedral : 7.450 59.194 3534 Min Nonbonded Distance : 2.169 Molprobity Statistics. All-atom Clashscore : 5.61 Ramachandran Plot: Outliers : 0.19 % Allowed : 4.23 % Favored : 95.58 % Rotamer: Outliers : 1.30 % Allowed : 8.01 % Favored : 90.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.35 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.23 (0.14), residues: 3168 helix: 0.63 (0.15), residues: 1104 sheet: -0.47 (0.21), residues: 576 loop : -0.51 (0.16), residues: 1488 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP F 402 HIS 0.007 0.002 HIS E 74 PHE 0.023 0.003 PHE A 187 TYR 0.031 0.003 TYR A 245 ARG 0.005 0.001 ARG A 190 Details of bonding type rmsd hydrogen bonds : bond 0.07036 ( 948) hydrogen bonds : angle 6.54844 ( 2682) covalent geometry : bond 0.00507 (26118) covalent geometry : angle 0.74923 (35424) Misc. bond : bond 0.00401 ( 6) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6336 Ramachandran restraints generated. 3168 Oldfield, 0 Emsley, 3168 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6336 Ramachandran restraints generated. 3168 Oldfield, 0 Emsley, 3168 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 368 residues out of total 2790 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 332 time to evaluate : 2.808 Fit side-chains REVERT: A 42 LYS cc_start: 0.8419 (ttpp) cc_final: 0.8206 (tmmt) REVERT: A 61 LYS cc_start: 0.8188 (mtmm) cc_final: 0.7497 (mmtm) REVERT: A 112 ASP cc_start: 0.8508 (m-30) cc_final: 0.8273 (m-30) REVERT: A 144 GLU cc_start: 0.6708 (pm20) cc_final: 0.6374 (pm20) REVERT: A 158 GLU cc_start: 0.8210 (mm-30) cc_final: 0.7899 (mp0) REVERT: A 197 MET cc_start: 0.8934 (mmp) cc_final: 0.8192 (mtp) REVERT: A 256 ASN cc_start: 0.8074 (t0) cc_final: 0.7772 (t0) REVERT: A 283 LYS cc_start: 0.7451 (mmtm) cc_final: 0.7224 (mptt) REVERT: A 309 GLU cc_start: 0.7793 (mt-10) cc_final: 0.7559 (mt-10) REVERT: A 335 GLU cc_start: 0.6583 (mp0) cc_final: 0.6165 (tm-30) REVERT: A 343 GLN cc_start: 0.7806 (mt0) cc_final: 0.7540 (mt0) REVERT: A 366 ASP cc_start: 0.7027 (m-30) cc_final: 0.6813 (m-30) REVERT: A 375 GLU cc_start: 0.7157 (pt0) cc_final: 0.6829 (pm20) REVERT: A 399 LYS cc_start: 0.8042 (ttmm) cc_final: 0.7425 (tmmt) REVERT: D 61 LYS cc_start: 0.8195 (mtmm) cc_final: 0.7533 (mmtt) REVERT: D 100 GLU cc_start: 0.7982 (tp30) cc_final: 0.7274 (mp0) REVERT: D 158 GLU cc_start: 0.8220 (mm-30) cc_final: 0.7485 (tm-30) REVERT: D 197 MET cc_start: 0.8867 (mmp) cc_final: 0.8154 (mtp) REVERT: D 285 MET cc_start: 0.7606 (mtp) cc_final: 0.7256 (mtp) REVERT: D 338 GLU cc_start: 0.7157 (mt-10) cc_final: 0.6301 (mm-30) REVERT: D 346 GLU cc_start: 0.7777 (tp30) cc_final: 0.7516 (tp30) REVERT: D 375 GLU cc_start: 0.7109 (pt0) cc_final: 0.6718 (pm20) REVERT: D 399 LYS cc_start: 0.7988 (ttmm) cc_final: 0.7435 (tmmt) REVERT: B 42 LYS cc_start: 0.8417 (ttpp) cc_final: 0.8204 (tmmt) REVERT: B 61 LYS cc_start: 0.8185 (mtmm) cc_final: 0.7493 (mmtm) REVERT: B 112 ASP cc_start: 0.8515 (m-30) cc_final: 0.8279 (m-30) REVERT: B 144 GLU cc_start: 0.6723 (pm20) cc_final: 0.6404 (pm20) REVERT: B 158 GLU cc_start: 0.8204 (mm-30) cc_final: 0.7892 (mp0) REVERT: B 197 MET cc_start: 0.8931 (mmp) cc_final: 0.8188 (mtp) REVERT: B 256 ASN cc_start: 0.8080 (t0) cc_final: 0.7782 (t0) REVERT: B 309 GLU cc_start: 0.7794 (mt-10) cc_final: 0.7559 (mt-10) REVERT: B 335 GLU cc_start: 0.6626 (mp0) cc_final: 0.6225 (tm-30) REVERT: B 343 GLN cc_start: 0.7802 (mt0) cc_final: 0.7519 (mt0) REVERT: B 366 ASP cc_start: 0.7039 (m-30) cc_final: 0.6834 (m-30) REVERT: B 375 GLU cc_start: 0.7139 (pt0) cc_final: 0.6811 (pm20) REVERT: B 399 LYS cc_start: 0.8058 (ttmm) cc_final: 0.7441 (tmmt) REVERT: C 61 LYS cc_start: 0.8306 (mtmm) cc_final: 0.7593 (mmtm) REVERT: C 100 GLU cc_start: 0.8043 (tp30) cc_final: 0.7287 (mp0) REVERT: C 133 THR cc_start: 0.6600 (OUTLIER) cc_final: 0.6333 (t) REVERT: C 145 GLU cc_start: 0.6795 (mm-30) cc_final: 0.6467 (mp0) REVERT: C 150 ARG cc_start: 0.7405 (mtm110) cc_final: 0.7011 (mtm110) REVERT: C 158 GLU cc_start: 0.8225 (mm-30) cc_final: 0.7901 (mp0) REVERT: C 197 MET cc_start: 0.8978 (mmp) cc_final: 0.8200 (mtp) REVERT: C 274 HIS cc_start: 0.8153 (t70) cc_final: 0.7943 (t70) REVERT: C 283 LYS cc_start: 0.7401 (mmtm) cc_final: 0.7200 (mppt) REVERT: C 338 GLU cc_start: 0.7126 (mt-10) cc_final: 0.6330 (mm-30) REVERT: C 343 GLN cc_start: 0.7574 (mt0) cc_final: 0.7197 (mt0) REVERT: C 375 GLU cc_start: 0.7102 (pt0) cc_final: 0.6727 (pm20) REVERT: C 399 LYS cc_start: 0.7966 (ttmm) cc_final: 0.7253 (tmmt) REVERT: E 61 LYS cc_start: 0.8199 (mtmm) cc_final: 0.7535 (mmtt) REVERT: E 100 GLU cc_start: 0.7975 (tp30) cc_final: 0.7257 (mp0) REVERT: E 158 GLU cc_start: 0.8212 (mm-30) cc_final: 0.7493 (tm-30) REVERT: E 197 MET cc_start: 0.8870 (mmp) cc_final: 0.8156 (mtp) REVERT: E 285 MET cc_start: 0.7613 (mtp) cc_final: 0.7317 (mtp) REVERT: E 338 GLU cc_start: 0.7145 (mt-10) cc_final: 0.6294 (mm-30) REVERT: E 346 GLU cc_start: 0.7781 (tp30) cc_final: 0.7518 (tp30) REVERT: E 375 GLU cc_start: 0.7112 (pt0) cc_final: 0.6720 (pm20) REVERT: E 399 LYS cc_start: 0.7985 (ttmm) cc_final: 0.7436 (tmmt) REVERT: F 61 LYS cc_start: 0.8318 (mtmm) cc_final: 0.7589 (mmtm) REVERT: F 100 GLU cc_start: 0.8042 (tp30) cc_final: 0.7285 (mp0) REVERT: F 118 GLU cc_start: 0.8012 (pt0) cc_final: 0.7564 (pp20) REVERT: F 133 THR cc_start: 0.6602 (OUTLIER) cc_final: 0.6336 (t) REVERT: F 145 GLU cc_start: 0.6774 (mm-30) cc_final: 0.6449 (mp0) REVERT: F 150 ARG cc_start: 0.7410 (mtm110) cc_final: 0.7016 (mtm110) REVERT: F 158 GLU cc_start: 0.8236 (mm-30) cc_final: 0.7952 (mp0) REVERT: F 197 MET cc_start: 0.8976 (mmp) cc_final: 0.8204 (mtp) REVERT: F 274 HIS cc_start: 0.8160 (t70) cc_final: 0.7949 (t70) REVERT: F 335 GLU cc_start: 0.6628 (mp0) cc_final: 0.6241 (tm-30) REVERT: F 338 GLU cc_start: 0.7128 (mt-10) cc_final: 0.6343 (mm-30) REVERT: F 343 GLN cc_start: 0.7572 (mt0) cc_final: 0.7202 (mt0) REVERT: F 375 GLU cc_start: 0.7110 (pt0) cc_final: 0.6735 (pm20) REVERT: F 399 LYS cc_start: 0.7961 (ttmm) cc_final: 0.7246 (tmmt) outliers start: 36 outliers final: 22 residues processed: 360 average time/residue: 1.6596 time to fit residues: 674.7259 Evaluate side-chains 337 residues out of total 2790 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 313 time to evaluate : 2.660 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 111 ASP Chi-restraints excluded: chain A residue 118 GLU Chi-restraints excluded: chain A residue 221 ILE Chi-restraints excluded: chain A residue 227 VAL Chi-restraints excluded: chain A residue 461 MET Chi-restraints excluded: chain D residue 111 ASP Chi-restraints excluded: chain D residue 221 ILE Chi-restraints excluded: chain D residue 227 VAL Chi-restraints excluded: chain B residue 111 ASP Chi-restraints excluded: chain B residue 118 GLU Chi-restraints excluded: chain B residue 221 ILE Chi-restraints excluded: chain B residue 227 VAL Chi-restraints excluded: chain B residue 461 MET Chi-restraints excluded: chain C residue 133 THR Chi-restraints excluded: chain C residue 221 ILE Chi-restraints excluded: chain C residue 227 VAL Chi-restraints excluded: chain C residue 461 MET Chi-restraints excluded: chain E residue 111 ASP Chi-restraints excluded: chain E residue 221 ILE Chi-restraints excluded: chain E residue 227 VAL Chi-restraints excluded: chain F residue 133 THR Chi-restraints excluded: chain F residue 221 ILE Chi-restraints excluded: chain F residue 227 VAL Chi-restraints excluded: chain F residue 461 MET Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 318 random chunks: chunk 46 optimal weight: 5.9990 chunk 14 optimal weight: 0.6980 chunk 142 optimal weight: 8.9990 chunk 285 optimal weight: 10.0000 chunk 161 optimal weight: 0.8980 chunk 228 optimal weight: 0.7980 chunk 193 optimal weight: 6.9990 chunk 218 optimal weight: 9.9990 chunk 96 optimal weight: 9.9990 chunk 233 optimal weight: 4.9990 chunk 160 optimal weight: 6.9990 overall best weight: 2.6784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 126 GLN A 154 GLN D 343 GLN B 126 GLN B 154 GLN C 154 GLN C 160 ASN C 368 ASN E 343 GLN F 154 GLN F 368 ASN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4145 r_free = 0.4145 target = 0.198276 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 65)----------------| | r_work = 0.3372 r_free = 0.3372 target = 0.127293 restraints weight = 17009.160| |-----------------------------------------------------------------------------| r_work (start): 0.3337 rms_B_bonded: 1.41 r_work: 0.3117 rms_B_bonded: 2.32 restraints_weight: 0.5000 r_work: 0.3007 rms_B_bonded: 3.38 restraints_weight: 0.2500 r_work (final): 0.3007 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8102 moved from start: 0.1932 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 26124 Z= 0.200 Angle : 0.693 8.819 35424 Z= 0.362 Chirality : 0.050 0.210 4002 Planarity : 0.005 0.038 4494 Dihedral : 7.374 59.297 3534 Min Nonbonded Distance : 2.367 Molprobity Statistics. All-atom Clashscore : 5.96 Ramachandran Plot: Outliers : 0.19 % Allowed : 3.82 % Favored : 95.99 % Rotamer: Outliers : 1.73 % Allowed : 8.30 % Favored : 89.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.35 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.25 (0.14), residues: 3168 helix: 0.64 (0.15), residues: 1104 sheet: -0.57 (0.20), residues: 576 loop : -0.51 (0.16), residues: 1488 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP F 402 HIS 0.005 0.001 HIS E 39 PHE 0.022 0.002 PHE F 81 TYR 0.027 0.002 TYR B 245 ARG 0.004 0.001 ARG B 47 Details of bonding type rmsd hydrogen bonds : bond 0.06392 ( 948) hydrogen bonds : angle 6.28358 ( 2682) covalent geometry : bond 0.00415 (26118) covalent geometry : angle 0.69284 (35424) Misc. bond : bond 0.00410 ( 6) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6336 Ramachandran restraints generated. 3168 Oldfield, 0 Emsley, 3168 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6336 Ramachandran restraints generated. 3168 Oldfield, 0 Emsley, 3168 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 366 residues out of total 2790 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 318 time to evaluate : 2.715 Fit side-chains REVERT: A 42 LYS cc_start: 0.8507 (ttpp) cc_final: 0.8296 (tmmt) REVERT: A 61 LYS cc_start: 0.8234 (mtmm) cc_final: 0.7517 (mmtm) REVERT: A 112 ASP cc_start: 0.8544 (m-30) cc_final: 0.8264 (m-30) REVERT: A 158 GLU cc_start: 0.8217 (mm-30) cc_final: 0.7908 (mp0) REVERT: A 197 MET cc_start: 0.9021 (mmp) cc_final: 0.8284 (mtp) REVERT: A 256 ASN cc_start: 0.8075 (t0) cc_final: 0.7823 (t0) REVERT: A 335 GLU cc_start: 0.6665 (mp0) cc_final: 0.6106 (tm-30) REVERT: A 343 GLN cc_start: 0.7814 (mt0) cc_final: 0.7533 (mt0) REVERT: A 366 ASP cc_start: 0.6994 (m-30) cc_final: 0.6770 (m-30) REVERT: A 375 GLU cc_start: 0.7207 (pt0) cc_final: 0.6850 (pm20) REVERT: A 399 LYS cc_start: 0.8110 (ttmm) cc_final: 0.7476 (tmmt) REVERT: D 61 LYS cc_start: 0.8214 (mtmm) cc_final: 0.7526 (mmtt) REVERT: D 100 GLU cc_start: 0.8063 (tp30) cc_final: 0.7339 (mp0) REVERT: D 158 GLU cc_start: 0.8183 (mm-30) cc_final: 0.7565 (tm-30) REVERT: D 197 MET cc_start: 0.8910 (mmp) cc_final: 0.8194 (mtp) REVERT: D 262 LYS cc_start: 0.8208 (mmtp) cc_final: 0.7935 (mmmt) REVERT: D 285 MET cc_start: 0.7596 (mtp) cc_final: 0.7258 (mtp) REVERT: D 335 GLU cc_start: 0.6761 (mp0) cc_final: 0.6270 (tm-30) REVERT: D 338 GLU cc_start: 0.7103 (mt-10) cc_final: 0.6180 (mm-30) REVERT: D 346 GLU cc_start: 0.7869 (tp30) cc_final: 0.7559 (tp30) REVERT: D 375 GLU cc_start: 0.7153 (pt0) cc_final: 0.6794 (pm20) REVERT: D 399 LYS cc_start: 0.8094 (ttmm) cc_final: 0.7547 (tmmt) REVERT: B 42 LYS cc_start: 0.8509 (ttpp) cc_final: 0.8296 (tmmt) REVERT: B 61 LYS cc_start: 0.8240 (mtmm) cc_final: 0.7524 (mmtm) REVERT: B 112 ASP cc_start: 0.8547 (m-30) cc_final: 0.8266 (m-30) REVERT: B 158 GLU cc_start: 0.8213 (mm-30) cc_final: 0.7898 (mp0) REVERT: B 197 MET cc_start: 0.9014 (mmp) cc_final: 0.8275 (mtp) REVERT: B 256 ASN cc_start: 0.8058 (t0) cc_final: 0.7799 (t0) REVERT: B 335 GLU cc_start: 0.6670 (mp0) cc_final: 0.6128 (tm-30) REVERT: B 343 GLN cc_start: 0.7812 (mt0) cc_final: 0.7540 (mt0) REVERT: B 366 ASP cc_start: 0.6984 (m-30) cc_final: 0.6763 (m-30) REVERT: B 375 GLU cc_start: 0.7171 (pt0) cc_final: 0.6824 (pm20) REVERT: B 399 LYS cc_start: 0.8123 (ttmm) cc_final: 0.7490 (tmmt) REVERT: C 61 LYS cc_start: 0.8346 (mtmm) cc_final: 0.7603 (mmtm) REVERT: C 100 GLU cc_start: 0.8053 (tp30) cc_final: 0.7330 (mp0) REVERT: C 133 THR cc_start: 0.6651 (OUTLIER) cc_final: 0.6382 (t) REVERT: C 145 GLU cc_start: 0.6853 (mm-30) cc_final: 0.6448 (mp0) REVERT: C 150 ARG cc_start: 0.7419 (mtm110) cc_final: 0.7016 (mtm110) REVERT: C 158 GLU cc_start: 0.8206 (mm-30) cc_final: 0.7967 (mp0) REVERT: C 197 MET cc_start: 0.9045 (mmp) cc_final: 0.8280 (mtp) REVERT: C 274 HIS cc_start: 0.8202 (t70) cc_final: 0.7992 (t70) REVERT: C 335 GLU cc_start: 0.6775 (mp0) cc_final: 0.6203 (tm-30) REVERT: C 338 GLU cc_start: 0.7018 (mt-10) cc_final: 0.6285 (mm-30) REVERT: C 343 GLN cc_start: 0.7573 (mt0) cc_final: 0.7184 (mt0) REVERT: C 366 ASP cc_start: 0.6678 (OUTLIER) cc_final: 0.6476 (m-30) REVERT: C 375 GLU cc_start: 0.7133 (pt0) cc_final: 0.6763 (pm20) REVERT: C 399 LYS cc_start: 0.8080 (ttmm) cc_final: 0.7363 (tmmt) REVERT: E 61 LYS cc_start: 0.8250 (mtmm) cc_final: 0.7554 (mmtt) REVERT: E 100 GLU cc_start: 0.8049 (tp30) cc_final: 0.7329 (mp0) REVERT: E 158 GLU cc_start: 0.8180 (mm-30) cc_final: 0.7570 (tm-30) REVERT: E 197 MET cc_start: 0.8920 (mmp) cc_final: 0.8198 (mtp) REVERT: E 262 LYS cc_start: 0.8206 (mmtm) cc_final: 0.7919 (mmmt) REVERT: E 285 MET cc_start: 0.7593 (mtp) cc_final: 0.7256 (mtp) REVERT: E 335 GLU cc_start: 0.6773 (mp0) cc_final: 0.6275 (tm-30) REVERT: E 338 GLU cc_start: 0.7092 (mt-10) cc_final: 0.6172 (mm-30) REVERT: E 346 GLU cc_start: 0.7872 (tp30) cc_final: 0.7562 (tp30) REVERT: E 375 GLU cc_start: 0.7132 (pt0) cc_final: 0.6766 (pm20) REVERT: E 399 LYS cc_start: 0.8101 (ttmm) cc_final: 0.7549 (tmmt) REVERT: F 61 LYS cc_start: 0.8335 (mtmm) cc_final: 0.7594 (mmtm) REVERT: F 100 GLU cc_start: 0.8058 (tp30) cc_final: 0.7328 (mp0) REVERT: F 118 GLU cc_start: 0.8026 (pt0) cc_final: 0.7639 (pp20) REVERT: F 133 THR cc_start: 0.6634 (OUTLIER) cc_final: 0.6363 (t) REVERT: F 145 GLU cc_start: 0.6839 (mm-30) cc_final: 0.6437 (mp0) REVERT: F 150 ARG cc_start: 0.7420 (mtm110) cc_final: 0.7019 (mtm110) REVERT: F 158 GLU cc_start: 0.8232 (mm-30) cc_final: 0.7983 (mp0) REVERT: F 197 MET cc_start: 0.9043 (mmp) cc_final: 0.8273 (mtp) REVERT: F 274 HIS cc_start: 0.8208 (t70) cc_final: 0.7996 (t70) REVERT: F 335 GLU cc_start: 0.6764 (mp0) cc_final: 0.6195 (tm-30) REVERT: F 338 GLU cc_start: 0.7018 (mt-10) cc_final: 0.6282 (mm-30) REVERT: F 343 GLN cc_start: 0.7561 (mt0) cc_final: 0.7168 (mt0) REVERT: F 375 GLU cc_start: 0.7127 (pt0) cc_final: 0.6759 (pm20) REVERT: F 399 LYS cc_start: 0.8088 (ttmm) cc_final: 0.7374 (tmmt) outliers start: 48 outliers final: 35 residues processed: 356 average time/residue: 1.5906 time to fit residues: 641.3682 Evaluate side-chains 349 residues out of total 2790 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 311 time to evaluate : 2.806 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 111 ASP Chi-restraints excluded: chain A residue 118 GLU Chi-restraints excluded: chain A residue 221 ILE Chi-restraints excluded: chain A residue 227 VAL Chi-restraints excluded: chain A residue 459 ILE Chi-restraints excluded: chain A residue 461 MET Chi-restraints excluded: chain D residue 111 ASP Chi-restraints excluded: chain D residue 118 GLU Chi-restraints excluded: chain D residue 221 ILE Chi-restraints excluded: chain D residue 227 VAL Chi-restraints excluded: chain D residue 272 ILE Chi-restraints excluded: chain D residue 459 ILE Chi-restraints excluded: chain D residue 461 MET Chi-restraints excluded: chain B residue 111 ASP Chi-restraints excluded: chain B residue 118 GLU Chi-restraints excluded: chain B residue 221 ILE Chi-restraints excluded: chain B residue 227 VAL Chi-restraints excluded: chain B residue 459 ILE Chi-restraints excluded: chain B residue 461 MET Chi-restraints excluded: chain C residue 118 GLU Chi-restraints excluded: chain C residue 133 THR Chi-restraints excluded: chain C residue 221 ILE Chi-restraints excluded: chain C residue 227 VAL Chi-restraints excluded: chain C residue 366 ASP Chi-restraints excluded: chain C residue 459 ILE Chi-restraints excluded: chain C residue 461 MET Chi-restraints excluded: chain E residue 111 ASP Chi-restraints excluded: chain E residue 118 GLU Chi-restraints excluded: chain E residue 221 ILE Chi-restraints excluded: chain E residue 227 VAL Chi-restraints excluded: chain E residue 272 ILE Chi-restraints excluded: chain E residue 459 ILE Chi-restraints excluded: chain E residue 461 MET Chi-restraints excluded: chain F residue 133 THR Chi-restraints excluded: chain F residue 221 ILE Chi-restraints excluded: chain F residue 227 VAL Chi-restraints excluded: chain F residue 459 ILE Chi-restraints excluded: chain F residue 461 MET Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 318 random chunks: chunk 114 optimal weight: 3.9990 chunk 78 optimal weight: 7.9990 chunk 291 optimal weight: 5.9990 chunk 273 optimal weight: 1.9990 chunk 236 optimal weight: 5.9990 chunk 89 optimal weight: 0.9980 chunk 281 optimal weight: 3.9990 chunk 305 optimal weight: 9.9990 chunk 285 optimal weight: 0.9990 chunk 54 optimal weight: 0.8980 chunk 183 optimal weight: 3.9990 overall best weight: 1.7786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 154 GLN D 343 GLN B 154 GLN C 154 GLN C 160 ASN E 343 GLN F 154 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4156 r_free = 0.4156 target = 0.199449 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 66)----------------| | r_work = 0.3396 r_free = 0.3396 target = 0.129407 restraints weight = 17180.381| |-----------------------------------------------------------------------------| r_work (start): 0.3358 rms_B_bonded: 1.53 r_work: 0.3133 rms_B_bonded: 2.38 restraints_weight: 0.5000 r_work: 0.3022 rms_B_bonded: 3.49 restraints_weight: 0.2500 r_work (final): 0.3022 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8077 moved from start: 0.1993 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 26124 Z= 0.157 Angle : 0.640 8.331 35424 Z= 0.335 Chirality : 0.047 0.208 4002 Planarity : 0.004 0.036 4494 Dihedral : 7.258 58.857 3534 Min Nonbonded Distance : 2.390 Molprobity Statistics. All-atom Clashscore : 6.10 Ramachandran Plot: Outliers : 0.19 % Allowed : 4.17 % Favored : 95.64 % Rotamer: Outliers : 1.23 % Allowed : 9.27 % Favored : 89.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.35 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.19 (0.15), residues: 3168 helix: 0.79 (0.16), residues: 1104 sheet: -0.53 (0.21), residues: 576 loop : -0.55 (0.16), residues: 1488 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP C 402 HIS 0.004 0.001 HIS E 39 PHE 0.020 0.002 PHE F 81 TYR 0.023 0.002 TYR A 245 ARG 0.003 0.000 ARG A 47 Details of bonding type rmsd hydrogen bonds : bond 0.05605 ( 948) hydrogen bonds : angle 6.05320 ( 2682) covalent geometry : bond 0.00322 (26118) covalent geometry : angle 0.63952 (35424) Misc. bond : bond 0.00268 ( 6) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6336 Ramachandran restraints generated. 3168 Oldfield, 0 Emsley, 3168 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6336 Ramachandran restraints generated. 3168 Oldfield, 0 Emsley, 3168 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 357 residues out of total 2790 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 323 time to evaluate : 2.738 Fit side-chains REVERT: A 42 LYS cc_start: 0.8479 (ttpp) cc_final: 0.8268 (ttpp) REVERT: A 61 LYS cc_start: 0.8207 (mtmm) cc_final: 0.7494 (mmtm) REVERT: A 112 ASP cc_start: 0.8532 (m-30) cc_final: 0.8254 (m-30) REVERT: A 158 GLU cc_start: 0.8193 (mm-30) cc_final: 0.7905 (mp0) REVERT: A 197 MET cc_start: 0.8973 (mmp) cc_final: 0.8218 (mtp) REVERT: A 256 ASN cc_start: 0.8055 (t0) cc_final: 0.7810 (t0) REVERT: A 335 GLU cc_start: 0.6620 (mp0) cc_final: 0.6005 (tm-30) REVERT: A 343 GLN cc_start: 0.7788 (mt0) cc_final: 0.7495 (mt0) REVERT: A 366 ASP cc_start: 0.6941 (m-30) cc_final: 0.6718 (m-30) REVERT: A 375 GLU cc_start: 0.7230 (pt0) cc_final: 0.6890 (pm20) REVERT: A 399 LYS cc_start: 0.8135 (ttmm) cc_final: 0.7484 (tmmt) REVERT: D 61 LYS cc_start: 0.8182 (mtmm) cc_final: 0.7533 (mmtm) REVERT: D 100 GLU cc_start: 0.8105 (tp30) cc_final: 0.7350 (mp0) REVERT: D 158 GLU cc_start: 0.8170 (mm-30) cc_final: 0.7540 (tm-30) REVERT: D 197 MET cc_start: 0.8959 (mmp) cc_final: 0.8178 (mtp) REVERT: D 278 SER cc_start: 0.8156 (m) cc_final: 0.7906 (p) REVERT: D 285 MET cc_start: 0.7543 (mtp) cc_final: 0.7200 (mtp) REVERT: D 335 GLU cc_start: 0.6709 (mp0) cc_final: 0.6156 (tm-30) REVERT: D 338 GLU cc_start: 0.6993 (mt-10) cc_final: 0.6011 (mm-30) REVERT: D 346 GLU cc_start: 0.7849 (tp30) cc_final: 0.7594 (tp30) REVERT: D 399 LYS cc_start: 0.8058 (ttmm) cc_final: 0.7542 (tmmt) REVERT: B 42 LYS cc_start: 0.8478 (ttpp) cc_final: 0.8267 (ttpp) REVERT: B 61 LYS cc_start: 0.8208 (mtmm) cc_final: 0.7494 (mmtm) REVERT: B 112 ASP cc_start: 0.8536 (m-30) cc_final: 0.8255 (m-30) REVERT: B 158 GLU cc_start: 0.8197 (mm-30) cc_final: 0.7903 (mp0) REVERT: B 197 MET cc_start: 0.8967 (mmp) cc_final: 0.8210 (mtp) REVERT: B 256 ASN cc_start: 0.8079 (t0) cc_final: 0.7830 (t0) REVERT: B 335 GLU cc_start: 0.6658 (mp0) cc_final: 0.6052 (tm-30) REVERT: B 343 GLN cc_start: 0.7788 (mt0) cc_final: 0.7457 (mt0) REVERT: B 366 ASP cc_start: 0.6950 (m-30) cc_final: 0.6732 (m-30) REVERT: B 375 GLU cc_start: 0.7220 (pt0) cc_final: 0.6889 (pm20) REVERT: B 399 LYS cc_start: 0.8155 (ttmm) cc_final: 0.7502 (tmmt) REVERT: C 61 LYS cc_start: 0.8293 (mtmm) cc_final: 0.7567 (mmtm) REVERT: C 100 GLU cc_start: 0.8056 (tp30) cc_final: 0.7296 (mp0) REVERT: C 133 THR cc_start: 0.6540 (OUTLIER) cc_final: 0.6279 (t) REVERT: C 150 ARG cc_start: 0.7350 (mtm110) cc_final: 0.7070 (mtm110) REVERT: C 158 GLU cc_start: 0.8163 (mm-30) cc_final: 0.7906 (mp0) REVERT: C 197 MET cc_start: 0.9043 (mmp) cc_final: 0.8272 (mtp) REVERT: C 274 HIS cc_start: 0.8200 (t70) cc_final: 0.7988 (t70) REVERT: C 283 LYS cc_start: 0.7295 (mmtm) cc_final: 0.6937 (mppt) REVERT: C 335 GLU cc_start: 0.6728 (mp0) cc_final: 0.6101 (tm-30) REVERT: C 338 GLU cc_start: 0.6862 (mt-10) cc_final: 0.6071 (mm-30) REVERT: C 343 GLN cc_start: 0.7510 (mt0) cc_final: 0.7118 (mt0) REVERT: C 375 GLU cc_start: 0.7106 (pt0) cc_final: 0.6719 (pm20) REVERT: C 399 LYS cc_start: 0.8044 (ttmm) cc_final: 0.7334 (tmmt) REVERT: C 461 MET cc_start: 0.2655 (OUTLIER) cc_final: 0.1957 (mtt) REVERT: E 61 LYS cc_start: 0.8189 (mtmm) cc_final: 0.7536 (mmtm) REVERT: E 100 GLU cc_start: 0.8106 (tp30) cc_final: 0.7349 (mp0) REVERT: E 158 GLU cc_start: 0.8160 (mm-30) cc_final: 0.7545 (tm-30) REVERT: E 197 MET cc_start: 0.8962 (mmp) cc_final: 0.8185 (mtp) REVERT: E 262 LYS cc_start: 0.8201 (mmtm) cc_final: 0.7913 (mmmt) REVERT: E 278 SER cc_start: 0.8139 (m) cc_final: 0.7888 (p) REVERT: E 285 MET cc_start: 0.7549 (mtp) cc_final: 0.7212 (mtp) REVERT: E 335 GLU cc_start: 0.6721 (mp0) cc_final: 0.6153 (tm-30) REVERT: E 338 GLU cc_start: 0.6991 (mt-10) cc_final: 0.6011 (mm-30) REVERT: E 346 GLU cc_start: 0.7865 (tp30) cc_final: 0.7607 (tp30) REVERT: E 399 LYS cc_start: 0.8066 (ttmm) cc_final: 0.7545 (tmmt) REVERT: F 61 LYS cc_start: 0.8286 (mtmm) cc_final: 0.7565 (mmtm) REVERT: F 100 GLU cc_start: 0.8051 (tp30) cc_final: 0.7300 (mp0) REVERT: F 118 GLU cc_start: 0.8033 (pt0) cc_final: 0.7614 (pp20) REVERT: F 133 THR cc_start: 0.6556 (OUTLIER) cc_final: 0.6269 (t) REVERT: F 150 ARG cc_start: 0.7357 (mtm110) cc_final: 0.7080 (mtm110) REVERT: F 158 GLU cc_start: 0.8201 (mm-30) cc_final: 0.7970 (mp0) REVERT: F 197 MET cc_start: 0.9046 (mmp) cc_final: 0.8275 (mtp) REVERT: F 274 HIS cc_start: 0.8205 (t70) cc_final: 0.7988 (t70) REVERT: F 335 GLU cc_start: 0.6713 (mp0) cc_final: 0.6103 (tm-30) REVERT: F 338 GLU cc_start: 0.6841 (mt-10) cc_final: 0.6048 (mm-30) REVERT: F 343 GLN cc_start: 0.7511 (mt0) cc_final: 0.7122 (mt0) REVERT: F 375 GLU cc_start: 0.7105 (pt0) cc_final: 0.6711 (pm20) REVERT: F 399 LYS cc_start: 0.8037 (ttmm) cc_final: 0.7336 (tmmt) REVERT: F 461 MET cc_start: 0.2660 (OUTLIER) cc_final: 0.1909 (mtt) outliers start: 34 outliers final: 29 residues processed: 349 average time/residue: 1.6163 time to fit residues: 638.6552 Evaluate side-chains 343 residues out of total 2790 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 310 time to evaluate : 2.722 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 111 ASP Chi-restraints excluded: chain A residue 118 GLU Chi-restraints excluded: chain A residue 227 VAL Chi-restraints excluded: chain A residue 461 MET Chi-restraints excluded: chain D residue 111 ASP Chi-restraints excluded: chain D residue 118 GLU Chi-restraints excluded: chain D residue 221 ILE Chi-restraints excluded: chain D residue 227 VAL Chi-restraints excluded: chain D residue 272 ILE Chi-restraints excluded: chain D residue 459 ILE Chi-restraints excluded: chain D residue 461 MET Chi-restraints excluded: chain B residue 111 ASP Chi-restraints excluded: chain B residue 118 GLU Chi-restraints excluded: chain B residue 221 ILE Chi-restraints excluded: chain B residue 227 VAL Chi-restraints excluded: chain B residue 461 MET Chi-restraints excluded: chain C residue 118 GLU Chi-restraints excluded: chain C residue 133 THR Chi-restraints excluded: chain C residue 221 ILE Chi-restraints excluded: chain C residue 227 VAL Chi-restraints excluded: chain C residue 272 ILE Chi-restraints excluded: chain C residue 461 MET Chi-restraints excluded: chain E residue 111 ASP Chi-restraints excluded: chain E residue 118 GLU Chi-restraints excluded: chain E residue 221 ILE Chi-restraints excluded: chain E residue 227 VAL Chi-restraints excluded: chain E residue 272 ILE Chi-restraints excluded: chain E residue 461 MET Chi-restraints excluded: chain F residue 133 THR Chi-restraints excluded: chain F residue 221 ILE Chi-restraints excluded: chain F residue 227 VAL Chi-restraints excluded: chain F residue 272 ILE Chi-restraints excluded: chain F residue 461 MET Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 318 random chunks: chunk 303 optimal weight: 2.9990 chunk 67 optimal weight: 9.9990 chunk 217 optimal weight: 3.9990 chunk 183 optimal weight: 8.9990 chunk 131 optimal weight: 6.9990 chunk 244 optimal weight: 5.9990 chunk 0 optimal weight: 10.0000 chunk 216 optimal weight: 2.9990 chunk 40 optimal weight: 5.9990 chunk 234 optimal weight: 0.9980 chunk 286 optimal weight: 0.9980 overall best weight: 2.3986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 343 GLN C 154 GLN C 160 ASN E 343 GLN F 126 GLN F 154 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4144 r_free = 0.4144 target = 0.198230 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 70)----------------| | r_work = 0.3404 r_free = 0.3404 target = 0.130145 restraints weight = 17058.585| |-----------------------------------------------------------------------------| r_work (start): 0.3377 rms_B_bonded: 1.46 r_work: 0.3140 rms_B_bonded: 2.21 restraints_weight: 0.5000 r_work: 0.3029 rms_B_bonded: 3.21 restraints_weight: 0.2500 r_work (final): 0.3029 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8102 moved from start: 0.2117 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 26124 Z= 0.188 Angle : 0.680 8.651 35424 Z= 0.355 Chirality : 0.049 0.220 4002 Planarity : 0.005 0.036 4494 Dihedral : 7.430 58.968 3534 Min Nonbonded Distance : 2.347 Molprobity Statistics. All-atom Clashscore : 6.23 Ramachandran Plot: Outliers : 0.19 % Allowed : 4.20 % Favored : 95.61 % Rotamer: Outliers : 1.77 % Allowed : 9.13 % Favored : 89.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.35 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.26 (0.15), residues: 3168 helix: 0.70 (0.15), residues: 1104 sheet: -0.61 (0.21), residues: 576 loop : -0.56 (0.16), residues: 1488 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP C 402 HIS 0.005 0.001 HIS E 39 PHE 0.024 0.002 PHE C 81 TYR 0.025 0.002 TYR B 245 ARG 0.003 0.000 ARG B 47 Details of bonding type rmsd hydrogen bonds : bond 0.06134 ( 948) hydrogen bonds : angle 6.17067 ( 2682) covalent geometry : bond 0.00387 (26118) covalent geometry : angle 0.67979 (35424) Misc. bond : bond 0.00381 ( 6) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6336 Ramachandran restraints generated. 3168 Oldfield, 0 Emsley, 3168 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6336 Ramachandran restraints generated. 3168 Oldfield, 0 Emsley, 3168 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 359 residues out of total 2790 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 310 time to evaluate : 2.720 Fit side-chains REVERT: A 42 LYS cc_start: 0.8479 (ttpp) cc_final: 0.8257 (tmmt) REVERT: A 61 LYS cc_start: 0.8248 (mtmm) cc_final: 0.7553 (mmtm) REVERT: A 158 GLU cc_start: 0.8172 (mm-30) cc_final: 0.7928 (mp0) REVERT: A 197 MET cc_start: 0.8977 (mmp) cc_final: 0.8241 (mtp) REVERT: A 256 ASN cc_start: 0.8075 (t0) cc_final: 0.7802 (t0) REVERT: A 335 GLU cc_start: 0.6693 (mp0) cc_final: 0.6112 (tm-30) REVERT: A 343 GLN cc_start: 0.7835 (mt0) cc_final: 0.7557 (mt0) REVERT: A 366 ASP cc_start: 0.7079 (m-30) cc_final: 0.6856 (m-30) REVERT: A 375 GLU cc_start: 0.7256 (pt0) cc_final: 0.6944 (pm20) REVERT: A 399 LYS cc_start: 0.8253 (ttmm) cc_final: 0.7590 (tmmt) REVERT: D 61 LYS cc_start: 0.8203 (mtmm) cc_final: 0.7575 (mmtm) REVERT: D 100 GLU cc_start: 0.8104 (tp30) cc_final: 0.7383 (mp0) REVERT: D 158 GLU cc_start: 0.8190 (mm-30) cc_final: 0.7596 (tm-30) REVERT: D 197 MET cc_start: 0.8936 (mmp) cc_final: 0.8219 (mtp) REVERT: D 278 SER cc_start: 0.8213 (m) cc_final: 0.7979 (p) REVERT: D 285 MET cc_start: 0.7601 (mtp) cc_final: 0.7246 (mtp) REVERT: D 335 GLU cc_start: 0.6751 (mp0) cc_final: 0.6245 (tm-30) REVERT: D 338 GLU cc_start: 0.7050 (mt-10) cc_final: 0.6095 (mm-30) REVERT: D 346 GLU cc_start: 0.7804 (tp30) cc_final: 0.7565 (tp30) REVERT: D 399 LYS cc_start: 0.8085 (ttmm) cc_final: 0.7574 (tmmt) REVERT: B 42 LYS cc_start: 0.8480 (ttpp) cc_final: 0.8256 (tmmt) REVERT: B 61 LYS cc_start: 0.8247 (mtmm) cc_final: 0.7555 (mmtm) REVERT: B 158 GLU cc_start: 0.8176 (mm-30) cc_final: 0.7928 (mp0) REVERT: B 197 MET cc_start: 0.8974 (mmp) cc_final: 0.8235 (mtp) REVERT: B 256 ASN cc_start: 0.8090 (t0) cc_final: 0.7851 (t0) REVERT: B 335 GLU cc_start: 0.6716 (mp0) cc_final: 0.6142 (tm-30) REVERT: B 343 GLN cc_start: 0.7835 (mt0) cc_final: 0.7558 (mt0) REVERT: B 366 ASP cc_start: 0.7044 (m-30) cc_final: 0.6830 (m-30) REVERT: B 375 GLU cc_start: 0.7249 (pt0) cc_final: 0.6940 (pm20) REVERT: B 399 LYS cc_start: 0.8265 (ttmm) cc_final: 0.7600 (tmmt) REVERT: C 61 LYS cc_start: 0.8314 (mtmm) cc_final: 0.7610 (mmtm) REVERT: C 100 GLU cc_start: 0.8059 (tp30) cc_final: 0.7341 (mp0) REVERT: C 133 THR cc_start: 0.6728 (OUTLIER) cc_final: 0.6466 (t) REVERT: C 150 ARG cc_start: 0.7412 (mtm110) cc_final: 0.7010 (mtm110) REVERT: C 158 GLU cc_start: 0.8126 (mm-30) cc_final: 0.7905 (mp0) REVERT: C 197 MET cc_start: 0.9064 (mmp) cc_final: 0.8307 (mtp) REVERT: C 274 HIS cc_start: 0.8241 (t70) cc_final: 0.8021 (t70) REVERT: C 283 LYS cc_start: 0.7479 (mmtm) cc_final: 0.7125 (mppt) REVERT: C 335 GLU cc_start: 0.6783 (mp0) cc_final: 0.6192 (tm-30) REVERT: C 338 GLU cc_start: 0.6945 (mt-10) cc_final: 0.6188 (mm-30) REVERT: C 343 GLN cc_start: 0.7592 (mt0) cc_final: 0.7164 (mt0) REVERT: C 375 GLU cc_start: 0.7150 (pt0) cc_final: 0.6784 (pm20) REVERT: C 399 LYS cc_start: 0.8192 (ttmm) cc_final: 0.7465 (tmmt) REVERT: E 61 LYS cc_start: 0.8213 (mtmm) cc_final: 0.7581 (mmtm) REVERT: E 100 GLU cc_start: 0.8089 (tp30) cc_final: 0.7377 (mp0) REVERT: E 158 GLU cc_start: 0.8183 (mm-30) cc_final: 0.7595 (tm-30) REVERT: E 197 MET cc_start: 0.8937 (mmp) cc_final: 0.8220 (mtp) REVERT: E 262 LYS cc_start: 0.8275 (mmtm) cc_final: 0.7983 (mmmt) REVERT: E 278 SER cc_start: 0.8212 (m) cc_final: 0.7975 (p) REVERT: E 285 MET cc_start: 0.7593 (mtp) cc_final: 0.7241 (mtp) REVERT: E 335 GLU cc_start: 0.6755 (mp0) cc_final: 0.6256 (tm-30) REVERT: E 338 GLU cc_start: 0.7040 (mt-10) cc_final: 0.6094 (mm-30) REVERT: E 346 GLU cc_start: 0.7812 (tp30) cc_final: 0.7572 (tp30) REVERT: E 366 ASP cc_start: 0.6766 (OUTLIER) cc_final: 0.6494 (m-30) REVERT: E 399 LYS cc_start: 0.8085 (ttmm) cc_final: 0.7571 (tmmt) REVERT: F 61 LYS cc_start: 0.8311 (mtmm) cc_final: 0.7608 (mmtm) REVERT: F 100 GLU cc_start: 0.8056 (tp30) cc_final: 0.7341 (mp0) REVERT: F 118 GLU cc_start: 0.8035 (pt0) cc_final: 0.7683 (pp20) REVERT: F 133 THR cc_start: 0.6723 (OUTLIER) cc_final: 0.6457 (t) REVERT: F 150 ARG cc_start: 0.7405 (mtm110) cc_final: 0.7006 (mtm110) REVERT: F 158 GLU cc_start: 0.8161 (mm-30) cc_final: 0.7921 (mp0) REVERT: F 197 MET cc_start: 0.9063 (mmp) cc_final: 0.8303 (mtp) REVERT: F 274 HIS cc_start: 0.8241 (t70) cc_final: 0.8016 (t70) REVERT: F 335 GLU cc_start: 0.6782 (mp0) cc_final: 0.6182 (tm-30) REVERT: F 338 GLU cc_start: 0.6954 (mt-10) cc_final: 0.6189 (mm-30) REVERT: F 343 GLN cc_start: 0.7578 (mt0) cc_final: 0.7147 (mt0) REVERT: F 375 GLU cc_start: 0.7152 (pt0) cc_final: 0.6785 (pm20) REVERT: F 399 LYS cc_start: 0.8171 (ttmm) cc_final: 0.7455 (tmmt) outliers start: 49 outliers final: 38 residues processed: 347 average time/residue: 1.5664 time to fit residues: 617.9238 Evaluate side-chains 349 residues out of total 2790 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 308 time to evaluate : 2.629 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 111 ASP Chi-restraints excluded: chain A residue 118 GLU Chi-restraints excluded: chain A residue 221 ILE Chi-restraints excluded: chain A residue 227 VAL Chi-restraints excluded: chain A residue 459 ILE Chi-restraints excluded: chain A residue 461 MET Chi-restraints excluded: chain D residue 111 ASP Chi-restraints excluded: chain D residue 118 GLU Chi-restraints excluded: chain D residue 221 ILE Chi-restraints excluded: chain D residue 227 VAL Chi-restraints excluded: chain D residue 272 ILE Chi-restraints excluded: chain D residue 459 ILE Chi-restraints excluded: chain D residue 461 MET Chi-restraints excluded: chain B residue 111 ASP Chi-restraints excluded: chain B residue 118 GLU Chi-restraints excluded: chain B residue 221 ILE Chi-restraints excluded: chain B residue 227 VAL Chi-restraints excluded: chain B residue 459 ILE Chi-restraints excluded: chain B residue 461 MET Chi-restraints excluded: chain C residue 118 GLU Chi-restraints excluded: chain C residue 133 THR Chi-restraints excluded: chain C residue 221 ILE Chi-restraints excluded: chain C residue 227 VAL Chi-restraints excluded: chain C residue 272 ILE Chi-restraints excluded: chain C residue 459 ILE Chi-restraints excluded: chain C residue 461 MET Chi-restraints excluded: chain E residue 111 ASP Chi-restraints excluded: chain E residue 118 GLU Chi-restraints excluded: chain E residue 133 THR Chi-restraints excluded: chain E residue 221 ILE Chi-restraints excluded: chain E residue 227 VAL Chi-restraints excluded: chain E residue 272 ILE Chi-restraints excluded: chain E residue 366 ASP Chi-restraints excluded: chain E residue 459 ILE Chi-restraints excluded: chain E residue 461 MET Chi-restraints excluded: chain F residue 133 THR Chi-restraints excluded: chain F residue 221 ILE Chi-restraints excluded: chain F residue 227 VAL Chi-restraints excluded: chain F residue 272 ILE Chi-restraints excluded: chain F residue 459 ILE Chi-restraints excluded: chain F residue 461 MET Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 318 random chunks: chunk 167 optimal weight: 0.0000 chunk 223 optimal weight: 8.9990 chunk 41 optimal weight: 0.7980 chunk 86 optimal weight: 8.9990 chunk 289 optimal weight: 0.0570 chunk 15 optimal weight: 1.9990 chunk 221 optimal weight: 2.9990 chunk 282 optimal weight: 2.9990 chunk 62 optimal weight: 0.5980 chunk 124 optimal weight: 0.5980 chunk 165 optimal weight: 8.9990 overall best weight: 0.4102 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 126 GLN D 343 GLN C 126 GLN C 154 GLN C 160 ASN E 343 GLN F 154 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4254 r_free = 0.4254 target = 0.207984 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 75)----------------| | r_work = 0.3836 r_free = 0.3836 target = 0.164485 restraints weight = 17391.420| |-----------------------------------------------------------------------------| r_work (start): 0.3818 rms_B_bonded: 0.82 r_work: 0.3462 rms_B_bonded: 2.04 restraints_weight: 0.5000 r_work: 0.3289 rms_B_bonded: 4.65 restraints_weight: 0.2500 r_work (final): 0.3289 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8112 moved from start: 0.2041 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 26124 Z= 0.105 Angle : 0.560 7.475 35424 Z= 0.293 Chirality : 0.044 0.164 4002 Planarity : 0.003 0.036 4494 Dihedral : 6.739 57.103 3534 Min Nonbonded Distance : 2.507 Molprobity Statistics. All-atom Clashscore : 6.06 Ramachandran Plot: Outliers : 0.19 % Allowed : 4.04 % Favored : 95.77 % Rotamer: Outliers : 1.44 % Allowed : 9.60 % Favored : 88.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.35 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.03 (0.15), residues: 3168 helix: 0.97 (0.16), residues: 1122 sheet: -0.27 (0.22), residues: 546 loop : -0.52 (0.16), residues: 1500 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP D 402 HIS 0.003 0.001 HIS E 39 PHE 0.016 0.001 PHE B 81 TYR 0.010 0.001 TYR B 245 ARG 0.001 0.000 ARG A 47 Details of bonding type rmsd hydrogen bonds : bond 0.04241 ( 948) hydrogen bonds : angle 5.59138 ( 2682) covalent geometry : bond 0.00206 (26118) covalent geometry : angle 0.56003 (35424) Misc. bond : bond 0.00099 ( 6) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6336 Ramachandran restraints generated. 3168 Oldfield, 0 Emsley, 3168 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6336 Ramachandran restraints generated. 3168 Oldfield, 0 Emsley, 3168 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 359 residues out of total 2790 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 319 time to evaluate : 2.784 Fit side-chains REVERT: A 61 LYS cc_start: 0.8389 (mtmm) cc_final: 0.7990 (mmtm) REVERT: A 112 ASP cc_start: 0.8710 (m-30) cc_final: 0.8440 (m-30) REVERT: A 197 MET cc_start: 0.9028 (mmp) cc_final: 0.8439 (mtp) REVERT: A 399 LYS cc_start: 0.8432 (ttmm) cc_final: 0.8046 (tmmt) REVERT: A 461 MET cc_start: 0.2541 (OUTLIER) cc_final: 0.1497 (mtp) REVERT: D 61 LYS cc_start: 0.8477 (mtmm) cc_final: 0.8064 (mmtm) REVERT: D 100 GLU cc_start: 0.8514 (tp30) cc_final: 0.7992 (mp0) REVERT: D 158 GLU cc_start: 0.8378 (mm-30) cc_final: 0.8036 (tm-30) REVERT: D 197 MET cc_start: 0.9006 (mmp) cc_final: 0.8349 (mtp) REVERT: D 285 MET cc_start: 0.7814 (mtp) cc_final: 0.7494 (mtp) REVERT: D 338 GLU cc_start: 0.7458 (mt-10) cc_final: 0.6747 (mm-30) REVERT: D 399 LYS cc_start: 0.8272 (ttmm) cc_final: 0.8028 (tmmt) REVERT: D 461 MET cc_start: 0.2097 (OUTLIER) cc_final: 0.1812 (mpp) REVERT: B 61 LYS cc_start: 0.8388 (mtmm) cc_final: 0.8000 (mmtm) REVERT: B 112 ASP cc_start: 0.8715 (m-30) cc_final: 0.8452 (m-30) REVERT: B 197 MET cc_start: 0.9023 (mmp) cc_final: 0.8431 (mtp) REVERT: B 399 LYS cc_start: 0.8434 (ttmm) cc_final: 0.8052 (tmmt) REVERT: B 461 MET cc_start: 0.2501 (OUTLIER) cc_final: 0.1510 (mtp) REVERT: C 61 LYS cc_start: 0.8452 (mtmm) cc_final: 0.8043 (mmtm) REVERT: C 100 GLU cc_start: 0.8429 (tp30) cc_final: 0.7936 (mp0) REVERT: C 150 ARG cc_start: 0.7833 (mtm110) cc_final: 0.7602 (mtm110) REVERT: C 197 MET cc_start: 0.9071 (mmp) cc_final: 0.8418 (mtp) REVERT: C 335 GLU cc_start: 0.7008 (mp0) cc_final: 0.6795 (tm-30) REVERT: C 338 GLU cc_start: 0.7375 (mt-10) cc_final: 0.6777 (mm-30) REVERT: C 344 GLN cc_start: 0.8633 (mt0) cc_final: 0.8284 (mt0) REVERT: C 365 GLU cc_start: 0.7245 (mp0) cc_final: 0.6632 (mp0) REVERT: C 399 LYS cc_start: 0.8359 (ttmm) cc_final: 0.7973 (tmmt) REVERT: C 461 MET cc_start: 0.2254 (OUTLIER) cc_final: 0.1633 (mtt) REVERT: E 61 LYS cc_start: 0.8453 (mtmm) cc_final: 0.8060 (mmtm) REVERT: E 100 GLU cc_start: 0.8497 (tp30) cc_final: 0.7972 (mp0) REVERT: E 158 GLU cc_start: 0.8372 (mm-30) cc_final: 0.8031 (tm-30) REVERT: E 197 MET cc_start: 0.9009 (mmp) cc_final: 0.8356 (mtp) REVERT: E 262 LYS cc_start: 0.8503 (mmtm) cc_final: 0.8303 (mmmt) REVERT: E 285 MET cc_start: 0.7832 (mtp) cc_final: 0.7524 (mtp) REVERT: E 338 GLU cc_start: 0.7465 (mt-10) cc_final: 0.6759 (mm-30) REVERT: E 399 LYS cc_start: 0.8282 (ttmm) cc_final: 0.8017 (tmmt) REVERT: E 461 MET cc_start: 0.2062 (OUTLIER) cc_final: 0.1812 (mpp) REVERT: F 61 LYS cc_start: 0.8458 (mtmm) cc_final: 0.8066 (mmtm) REVERT: F 100 GLU cc_start: 0.8431 (tp30) cc_final: 0.7947 (mp0) REVERT: F 118 GLU cc_start: 0.8380 (pt0) cc_final: 0.8141 (pp20) REVERT: F 150 ARG cc_start: 0.7810 (mtm110) cc_final: 0.7578 (mtm110) REVERT: F 165 ASP cc_start: 0.9011 (t0) cc_final: 0.8721 (t0) REVERT: F 197 MET cc_start: 0.9073 (mmp) cc_final: 0.8417 (mtp) REVERT: F 335 GLU cc_start: 0.6995 (mp0) cc_final: 0.6792 (tm-30) REVERT: F 338 GLU cc_start: 0.7374 (mt-10) cc_final: 0.6773 (mm-30) REVERT: F 343 GLN cc_start: 0.8025 (mt0) cc_final: 0.7784 (mt0) REVERT: F 344 GLN cc_start: 0.8630 (mt0) cc_final: 0.8277 (mt0) REVERT: F 365 GLU cc_start: 0.7193 (mp0) cc_final: 0.6561 (mp0) REVERT: F 399 LYS cc_start: 0.8341 (ttmm) cc_final: 0.7956 (tmmt) REVERT: F 461 MET cc_start: 0.2172 (OUTLIER) cc_final: 0.1562 (mtt) outliers start: 40 outliers final: 20 residues processed: 350 average time/residue: 1.6540 time to fit residues: 665.4943 Evaluate side-chains 324 residues out of total 2790 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 298 time to evaluate : 2.995 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 227 VAL Chi-restraints excluded: chain A residue 459 ILE Chi-restraints excluded: chain A residue 461 MET Chi-restraints excluded: chain A residue 469 VAL Chi-restraints excluded: chain D residue 118 GLU Chi-restraints excluded: chain D residue 227 VAL Chi-restraints excluded: chain D residue 461 MET Chi-restraints excluded: chain D residue 469 VAL Chi-restraints excluded: chain B residue 227 VAL Chi-restraints excluded: chain B residue 459 ILE Chi-restraints excluded: chain B residue 461 MET Chi-restraints excluded: chain B residue 469 VAL Chi-restraints excluded: chain C residue 227 VAL Chi-restraints excluded: chain C residue 272 ILE Chi-restraints excluded: chain C residue 459 ILE Chi-restraints excluded: chain C residue 461 MET Chi-restraints excluded: chain C residue 469 VAL Chi-restraints excluded: chain E residue 118 GLU Chi-restraints excluded: chain E residue 227 VAL Chi-restraints excluded: chain E residue 459 ILE Chi-restraints excluded: chain E residue 461 MET Chi-restraints excluded: chain F residue 227 VAL Chi-restraints excluded: chain F residue 272 ILE Chi-restraints excluded: chain F residue 459 ILE Chi-restraints excluded: chain F residue 461 MET Chi-restraints excluded: chain F residue 469 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 318 random chunks: chunk 315 optimal weight: 7.9990 chunk 27 optimal weight: 10.0000 chunk 193 optimal weight: 10.0000 chunk 61 optimal weight: 1.9990 chunk 185 optimal weight: 10.0000 chunk 230 optimal weight: 8.9990 chunk 54 optimal weight: 0.7980 chunk 105 optimal weight: 4.9990 chunk 226 optimal weight: 9.9990 chunk 1 optimal weight: 0.5980 chunk 43 optimal weight: 4.9990 overall best weight: 2.6786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 343 GLN A 448 HIS D 343 GLN B 343 GLN C 154 GLN C 160 ASN C 343 GLN E 343 GLN F 154 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4143 r_free = 0.4143 target = 0.197953 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 65)----------------| | r_work = 0.3375 r_free = 0.3375 target = 0.126811 restraints weight = 17076.301| |-----------------------------------------------------------------------------| r_work (start): 0.3354 rms_B_bonded: 1.30 r_work: 0.3134 rms_B_bonded: 2.20 restraints_weight: 0.5000 r_work: 0.3026 rms_B_bonded: 3.18 restraints_weight: 0.2500 r_work (final): 0.3026 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8066 moved from start: 0.2242 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 26124 Z= 0.200 Angle : 0.687 8.499 35424 Z= 0.358 Chirality : 0.049 0.232 4002 Planarity : 0.005 0.038 4494 Dihedral : 7.354 59.588 3534 Min Nonbonded Distance : 2.337 Molprobity Statistics. All-atom Clashscore : 6.51 Ramachandran Plot: Outliers : 0.19 % Allowed : 4.42 % Favored : 95.39 % Rotamer: Outliers : 1.95 % Allowed : 9.78 % Favored : 88.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.35 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.11 (0.15), residues: 3168 helix: 0.82 (0.16), residues: 1104 sheet: -0.43 (0.21), residues: 546 loop : -0.51 (0.16), residues: 1518 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP B 402 HIS 0.006 0.001 HIS F 39 PHE 0.024 0.002 PHE F 81 TYR 0.023 0.003 TYR A 245 ARG 0.004 0.001 ARG A 190 Details of bonding type rmsd hydrogen bonds : bond 0.06128 ( 948) hydrogen bonds : angle 6.06655 ( 2682) covalent geometry : bond 0.00417 (26118) covalent geometry : angle 0.68701 (35424) Misc. bond : bond 0.00420 ( 6) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6336 Ramachandran restraints generated. 3168 Oldfield, 0 Emsley, 3168 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6336 Ramachandran restraints generated. 3168 Oldfield, 0 Emsley, 3168 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 367 residues out of total 2790 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 313 time to evaluate : 2.726 Fit side-chains REVERT: A 61 LYS cc_start: 0.8218 (mtmm) cc_final: 0.7509 (mmtm) REVERT: A 197 MET cc_start: 0.8951 (mmp) cc_final: 0.8191 (mtp) REVERT: A 366 ASP cc_start: 0.6990 (OUTLIER) cc_final: 0.6655 (m-30) REVERT: A 375 GLU cc_start: 0.7222 (pt0) cc_final: 0.6884 (pm20) REVERT: A 399 LYS cc_start: 0.8268 (ttmm) cc_final: 0.7567 (tmmt) REVERT: D 61 LYS cc_start: 0.8182 (mtmm) cc_final: 0.7535 (mmtm) REVERT: D 100 GLU cc_start: 0.8064 (tp30) cc_final: 0.7323 (mp0) REVERT: D 158 GLU cc_start: 0.8173 (mm-30) cc_final: 0.7574 (tm-30) REVERT: D 197 MET cc_start: 0.8924 (mmp) cc_final: 0.8191 (mtp) REVERT: D 285 MET cc_start: 0.7576 (mtp) cc_final: 0.7248 (mtp) REVERT: D 338 GLU cc_start: 0.7045 (mt-10) cc_final: 0.6090 (mm-30) REVERT: D 366 ASP cc_start: 0.6703 (OUTLIER) cc_final: 0.6440 (m-30) REVERT: D 375 GLU cc_start: 0.7130 (pt0) cc_final: 0.6774 (pm20) REVERT: D 399 LYS cc_start: 0.8097 (ttmm) cc_final: 0.7561 (tmmt) REVERT: B 61 LYS cc_start: 0.8219 (mtmm) cc_final: 0.7508 (mmtm) REVERT: B 197 MET cc_start: 0.8951 (mmp) cc_final: 0.8189 (mtp) REVERT: B 366 ASP cc_start: 0.6987 (OUTLIER) cc_final: 0.6650 (m-30) REVERT: B 375 GLU cc_start: 0.7216 (pt0) cc_final: 0.6880 (pm20) REVERT: B 399 LYS cc_start: 0.8279 (ttmm) cc_final: 0.7565 (tmmt) REVERT: C 61 LYS cc_start: 0.8302 (mtmm) cc_final: 0.7569 (mmtm) REVERT: C 100 GLU cc_start: 0.8018 (tp30) cc_final: 0.7285 (mp0) REVERT: C 133 THR cc_start: 0.6725 (OUTLIER) cc_final: 0.6444 (t) REVERT: C 150 ARG cc_start: 0.7373 (mtm110) cc_final: 0.6945 (mtm110) REVERT: C 197 MET cc_start: 0.9052 (mmp) cc_final: 0.8277 (mtp) REVERT: C 283 LYS cc_start: 0.7488 (mmtm) cc_final: 0.7134 (mppt) REVERT: C 335 GLU cc_start: 0.6812 (mp0) cc_final: 0.6237 (tm-30) REVERT: C 338 GLU cc_start: 0.6929 (mt-10) cc_final: 0.6175 (mm-30) REVERT: C 343 GLN cc_start: 0.7588 (mt0) cc_final: 0.7236 (mt0) REVERT: C 366 ASP cc_start: 0.6649 (OUTLIER) cc_final: 0.6440 (m-30) REVERT: C 375 GLU cc_start: 0.7109 (pt0) cc_final: 0.6747 (pm20) REVERT: C 399 LYS cc_start: 0.8128 (ttmm) cc_final: 0.7383 (tmmt) REVERT: C 461 MET cc_start: 0.2503 (OUTLIER) cc_final: 0.1676 (mtt) REVERT: E 61 LYS cc_start: 0.8179 (mtmm) cc_final: 0.7536 (mmtm) REVERT: E 100 GLU cc_start: 0.8054 (tp30) cc_final: 0.7317 (mp0) REVERT: E 158 GLU cc_start: 0.8159 (mm-30) cc_final: 0.7565 (tm-30) REVERT: E 197 MET cc_start: 0.8929 (mmp) cc_final: 0.8198 (mtp) REVERT: E 262 LYS cc_start: 0.8162 (mmtm) cc_final: 0.7910 (mmmt) REVERT: E 285 MET cc_start: 0.7578 (mtp) cc_final: 0.7248 (mtp) REVERT: E 338 GLU cc_start: 0.7022 (mt-10) cc_final: 0.6072 (mm-30) REVERT: E 366 ASP cc_start: 0.6730 (OUTLIER) cc_final: 0.6443 (m-30) REVERT: E 375 GLU cc_start: 0.7133 (pt0) cc_final: 0.6775 (pm20) REVERT: E 399 LYS cc_start: 0.8098 (ttmm) cc_final: 0.7562 (tmmt) REVERT: F 42 LYS cc_start: 0.8330 (tmtp) cc_final: 0.7997 (ttpp) REVERT: F 61 LYS cc_start: 0.8293 (mtmm) cc_final: 0.7560 (mmtm) REVERT: F 100 GLU cc_start: 0.8017 (tp30) cc_final: 0.7284 (mp0) REVERT: F 118 GLU cc_start: 0.7956 (pt0) cc_final: 0.7602 (pp20) REVERT: F 133 THR cc_start: 0.6721 (OUTLIER) cc_final: 0.6435 (t) REVERT: F 150 ARG cc_start: 0.7333 (mtm110) cc_final: 0.6911 (mtm110) REVERT: F 197 MET cc_start: 0.9052 (mmp) cc_final: 0.8274 (mtp) REVERT: F 335 GLU cc_start: 0.6823 (mp0) cc_final: 0.6232 (tm-30) REVERT: F 338 GLU cc_start: 0.6919 (mt-10) cc_final: 0.6107 (mm-30) REVERT: F 343 GLN cc_start: 0.7575 (mt0) cc_final: 0.7142 (mt0) REVERT: F 375 GLU cc_start: 0.7119 (pt0) cc_final: 0.6756 (pm20) REVERT: F 399 LYS cc_start: 0.8126 (ttmm) cc_final: 0.7390 (tmmt) REVERT: F 461 MET cc_start: 0.2447 (OUTLIER) cc_final: 0.1652 (mtt) outliers start: 54 outliers final: 38 residues processed: 349 average time/residue: 1.5220 time to fit residues: 603.8675 Evaluate side-chains 352 residues out of total 2790 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 305 time to evaluate : 2.744 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 111 ASP Chi-restraints excluded: chain A residue 118 GLU Chi-restraints excluded: chain A residue 221 ILE Chi-restraints excluded: chain A residue 227 VAL Chi-restraints excluded: chain A residue 366 ASP Chi-restraints excluded: chain A residue 459 ILE Chi-restraints excluded: chain A residue 461 MET Chi-restraints excluded: chain A residue 469 VAL Chi-restraints excluded: chain D residue 111 ASP Chi-restraints excluded: chain D residue 118 GLU Chi-restraints excluded: chain D residue 227 VAL Chi-restraints excluded: chain D residue 306 SER Chi-restraints excluded: chain D residue 366 ASP Chi-restraints excluded: chain D residue 459 ILE Chi-restraints excluded: chain D residue 461 MET Chi-restraints excluded: chain D residue 469 VAL Chi-restraints excluded: chain B residue 111 ASP Chi-restraints excluded: chain B residue 118 GLU Chi-restraints excluded: chain B residue 221 ILE Chi-restraints excluded: chain B residue 227 VAL Chi-restraints excluded: chain B residue 366 ASP Chi-restraints excluded: chain B residue 459 ILE Chi-restraints excluded: chain B residue 461 MET Chi-restraints excluded: chain B residue 469 VAL Chi-restraints excluded: chain C residue 133 THR Chi-restraints excluded: chain C residue 221 ILE Chi-restraints excluded: chain C residue 227 VAL Chi-restraints excluded: chain C residue 272 ILE Chi-restraints excluded: chain C residue 366 ASP Chi-restraints excluded: chain C residue 459 ILE Chi-restraints excluded: chain C residue 461 MET Chi-restraints excluded: chain C residue 469 VAL Chi-restraints excluded: chain E residue 111 ASP Chi-restraints excluded: chain E residue 118 GLU Chi-restraints excluded: chain E residue 133 THR Chi-restraints excluded: chain E residue 227 VAL Chi-restraints excluded: chain E residue 306 SER Chi-restraints excluded: chain E residue 366 ASP Chi-restraints excluded: chain E residue 459 ILE Chi-restraints excluded: chain E residue 461 MET Chi-restraints excluded: chain F residue 133 THR Chi-restraints excluded: chain F residue 221 ILE Chi-restraints excluded: chain F residue 227 VAL Chi-restraints excluded: chain F residue 272 ILE Chi-restraints excluded: chain F residue 459 ILE Chi-restraints excluded: chain F residue 461 MET Chi-restraints excluded: chain F residue 469 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 318 random chunks: chunk 21 optimal weight: 3.9990 chunk 120 optimal weight: 7.9990 chunk 25 optimal weight: 3.9990 chunk 79 optimal weight: 7.9990 chunk 19 optimal weight: 1.9990 chunk 35 optimal weight: 2.9990 chunk 304 optimal weight: 7.9990 chunk 50 optimal weight: 1.9990 chunk 170 optimal weight: 8.9990 chunk 28 optimal weight: 4.9990 chunk 81 optimal weight: 4.9990 overall best weight: 2.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 154 GLN D 343 GLN C 154 GLN C 160 ASN E 154 GLN E 343 GLN F 154 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4139 r_free = 0.4139 target = 0.197474 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 65)----------------| | r_work = 0.3381 r_free = 0.3381 target = 0.127480 restraints weight = 16982.436| |-----------------------------------------------------------------------------| r_work (start): 0.3361 rms_B_bonded: 1.31 r_work: 0.3135 rms_B_bonded: 2.12 restraints_weight: 0.5000 r_work: 0.3023 rms_B_bonded: 3.12 restraints_weight: 0.2500 r_work (final): 0.3023 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8052 moved from start: 0.2313 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.041 26124 Z= 0.215 Angle : 0.711 9.069 35424 Z= 0.371 Chirality : 0.050 0.242 4002 Planarity : 0.005 0.038 4494 Dihedral : 7.479 59.191 3534 Min Nonbonded Distance : 2.350 Molprobity Statistics. All-atom Clashscore : 6.45 Ramachandran Plot: Outliers : 0.19 % Allowed : 4.36 % Favored : 95.45 % Rotamer: Outliers : 1.91 % Allowed : 9.78 % Favored : 88.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.35 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.24 (0.14), residues: 3168 helix: 0.69 (0.15), residues: 1098 sheet: -0.58 (0.21), residues: 546 loop : -0.52 (0.15), residues: 1524 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP A 402 HIS 0.006 0.001 HIS D 39 PHE 0.025 0.002 PHE F 81 TYR 0.026 0.003 TYR A 245 ARG 0.004 0.001 ARG A 47 Details of bonding type rmsd hydrogen bonds : bond 0.06376 ( 948) hydrogen bonds : angle 6.15768 ( 2682) covalent geometry : bond 0.00451 (26118) covalent geometry : angle 0.71064 (35424) Misc. bond : bond 0.00436 ( 6) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6336 Ramachandran restraints generated. 3168 Oldfield, 0 Emsley, 3168 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6336 Ramachandran restraints generated. 3168 Oldfield, 0 Emsley, 3168 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 361 residues out of total 2790 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 308 time to evaluate : 2.731 Fit side-chains REVERT: A 61 LYS cc_start: 0.8203 (mtmm) cc_final: 0.7492 (mmtm) REVERT: A 197 MET cc_start: 0.8924 (mmp) cc_final: 0.8159 (mtp) REVERT: A 366 ASP cc_start: 0.6972 (OUTLIER) cc_final: 0.6640 (m-30) REVERT: A 375 GLU cc_start: 0.7192 (pt0) cc_final: 0.6850 (pm20) REVERT: A 399 LYS cc_start: 0.8224 (ttmm) cc_final: 0.7536 (tmmt) REVERT: D 61 LYS cc_start: 0.8156 (mtmm) cc_final: 0.7511 (mmtm) REVERT: D 100 GLU cc_start: 0.8006 (tp30) cc_final: 0.7261 (mp0) REVERT: D 158 GLU cc_start: 0.8153 (mm-30) cc_final: 0.7553 (tm-30) REVERT: D 197 MET cc_start: 0.8878 (mmp) cc_final: 0.8138 (mtp) REVERT: D 262 LYS cc_start: 0.8235 (mmtm) cc_final: 0.8002 (mmmt) REVERT: D 285 MET cc_start: 0.7550 (mtp) cc_final: 0.7197 (mtp) REVERT: D 338 GLU cc_start: 0.6991 (mt-10) cc_final: 0.6007 (mm-30) REVERT: D 366 ASP cc_start: 0.6692 (OUTLIER) cc_final: 0.6430 (m-30) REVERT: D 375 GLU cc_start: 0.7141 (pt0) cc_final: 0.6793 (pm20) REVERT: D 399 LYS cc_start: 0.8130 (ttmm) cc_final: 0.7573 (tmmt) REVERT: B 61 LYS cc_start: 0.8202 (mtmm) cc_final: 0.7492 (mmtm) REVERT: B 144 GLU cc_start: 0.6524 (pm20) cc_final: 0.6175 (pm20) REVERT: B 197 MET cc_start: 0.8920 (mmp) cc_final: 0.8151 (mtp) REVERT: B 366 ASP cc_start: 0.6960 (OUTLIER) cc_final: 0.6624 (m-30) REVERT: B 375 GLU cc_start: 0.7192 (pt0) cc_final: 0.6852 (pm20) REVERT: B 399 LYS cc_start: 0.8232 (ttmm) cc_final: 0.7539 (tmmt) REVERT: B 461 MET cc_start: 0.2733 (OUTLIER) cc_final: 0.1702 (mmm) REVERT: C 61 LYS cc_start: 0.8290 (mtmm) cc_final: 0.7554 (mmtm) REVERT: C 100 GLU cc_start: 0.8001 (tp30) cc_final: 0.7257 (mp0) REVERT: C 133 THR cc_start: 0.6810 (OUTLIER) cc_final: 0.6487 (t) REVERT: C 150 ARG cc_start: 0.7356 (mtm110) cc_final: 0.6918 (mtm110) REVERT: C 197 MET cc_start: 0.9022 (mmp) cc_final: 0.8257 (mtp) REVERT: C 283 LYS cc_start: 0.7403 (mmtm) cc_final: 0.7052 (mppt) REVERT: C 335 GLU cc_start: 0.6718 (mp0) cc_final: 0.6076 (tm-30) REVERT: C 338 GLU cc_start: 0.6870 (mt-10) cc_final: 0.6052 (mm-30) REVERT: C 343 GLN cc_start: 0.7529 (mt0) cc_final: 0.7140 (mt0) REVERT: C 366 ASP cc_start: 0.6618 (OUTLIER) cc_final: 0.6407 (m-30) REVERT: C 375 GLU cc_start: 0.7065 (pt0) cc_final: 0.6665 (pm20) REVERT: C 399 LYS cc_start: 0.8141 (ttmm) cc_final: 0.7370 (tmmt) REVERT: C 461 MET cc_start: 0.2607 (OUTLIER) cc_final: 0.1859 (mmm) REVERT: E 61 LYS cc_start: 0.8163 (mtmm) cc_final: 0.7517 (mmtm) REVERT: E 100 GLU cc_start: 0.8034 (tp30) cc_final: 0.7283 (mp0) REVERT: E 158 GLU cc_start: 0.8140 (mm-30) cc_final: 0.7555 (tm-30) REVERT: E 197 MET cc_start: 0.8884 (mmp) cc_final: 0.8145 (mtp) REVERT: E 262 LYS cc_start: 0.8212 (mmtm) cc_final: 0.7929 (mmmt) REVERT: E 285 MET cc_start: 0.7551 (mtp) cc_final: 0.7195 (mtp) REVERT: E 338 GLU cc_start: 0.6987 (mt-10) cc_final: 0.6005 (mm-30) REVERT: E 366 ASP cc_start: 0.6717 (OUTLIER) cc_final: 0.6447 (m-30) REVERT: E 375 GLU cc_start: 0.7131 (pt0) cc_final: 0.6780 (pm20) REVERT: E 399 LYS cc_start: 0.8126 (ttmm) cc_final: 0.7575 (tmmt) REVERT: F 61 LYS cc_start: 0.8284 (mtmm) cc_final: 0.7551 (mmtm) REVERT: F 100 GLU cc_start: 0.7998 (tp30) cc_final: 0.7253 (mp0) REVERT: F 118 GLU cc_start: 0.7973 (pt0) cc_final: 0.7617 (pp20) REVERT: F 133 THR cc_start: 0.6799 (OUTLIER) cc_final: 0.6473 (t) REVERT: F 150 ARG cc_start: 0.7350 (mtm110) cc_final: 0.6916 (mtm110) REVERT: F 197 MET cc_start: 0.9023 (mmp) cc_final: 0.8254 (mtp) REVERT: F 335 GLU cc_start: 0.6707 (mp0) cc_final: 0.6065 (tm-30) REVERT: F 338 GLU cc_start: 0.6861 (mt-10) cc_final: 0.6045 (mm-30) REVERT: F 343 GLN cc_start: 0.7501 (mt0) cc_final: 0.7057 (mt0) REVERT: F 375 GLU cc_start: 0.7065 (pt0) cc_final: 0.6667 (pm20) REVERT: F 399 LYS cc_start: 0.8140 (ttmm) cc_final: 0.7383 (tmmt) REVERT: F 461 MET cc_start: 0.2630 (OUTLIER) cc_final: 0.1866 (mmm) outliers start: 53 outliers final: 40 residues processed: 346 average time/residue: 1.5399 time to fit residues: 606.8159 Evaluate side-chains 353 residues out of total 2790 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 303 time to evaluate : 3.188 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 111 ASP Chi-restraints excluded: chain A residue 118 GLU Chi-restraints excluded: chain A residue 221 ILE Chi-restraints excluded: chain A residue 227 VAL Chi-restraints excluded: chain A residue 366 ASP Chi-restraints excluded: chain A residue 459 ILE Chi-restraints excluded: chain A residue 461 MET Chi-restraints excluded: chain A residue 469 VAL Chi-restraints excluded: chain D residue 111 ASP Chi-restraints excluded: chain D residue 118 GLU Chi-restraints excluded: chain D residue 221 ILE Chi-restraints excluded: chain D residue 227 VAL Chi-restraints excluded: chain D residue 306 SER Chi-restraints excluded: chain D residue 366 ASP Chi-restraints excluded: chain D residue 459 ILE Chi-restraints excluded: chain D residue 469 VAL Chi-restraints excluded: chain B residue 111 ASP Chi-restraints excluded: chain B residue 118 GLU Chi-restraints excluded: chain B residue 221 ILE Chi-restraints excluded: chain B residue 227 VAL Chi-restraints excluded: chain B residue 366 ASP Chi-restraints excluded: chain B residue 459 ILE Chi-restraints excluded: chain B residue 461 MET Chi-restraints excluded: chain B residue 469 VAL Chi-restraints excluded: chain C residue 118 GLU Chi-restraints excluded: chain C residue 133 THR Chi-restraints excluded: chain C residue 221 ILE Chi-restraints excluded: chain C residue 227 VAL Chi-restraints excluded: chain C residue 272 ILE Chi-restraints excluded: chain C residue 366 ASP Chi-restraints excluded: chain C residue 459 ILE Chi-restraints excluded: chain C residue 461 MET Chi-restraints excluded: chain C residue 469 VAL Chi-restraints excluded: chain E residue 111 ASP Chi-restraints excluded: chain E residue 118 GLU Chi-restraints excluded: chain E residue 133 THR Chi-restraints excluded: chain E residue 221 ILE Chi-restraints excluded: chain E residue 227 VAL Chi-restraints excluded: chain E residue 306 SER Chi-restraints excluded: chain E residue 366 ASP Chi-restraints excluded: chain E residue 459 ILE Chi-restraints excluded: chain E residue 461 MET Chi-restraints excluded: chain E residue 469 VAL Chi-restraints excluded: chain F residue 133 THR Chi-restraints excluded: chain F residue 221 ILE Chi-restraints excluded: chain F residue 227 VAL Chi-restraints excluded: chain F residue 272 ILE Chi-restraints excluded: chain F residue 459 ILE Chi-restraints excluded: chain F residue 461 MET Chi-restraints excluded: chain F residue 469 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 318 random chunks: chunk 223 optimal weight: 0.6980 chunk 52 optimal weight: 5.9990 chunk 291 optimal weight: 7.9990 chunk 304 optimal weight: 6.9990 chunk 284 optimal weight: 1.9990 chunk 307 optimal weight: 7.9990 chunk 262 optimal weight: 10.0000 chunk 191 optimal weight: 2.9990 chunk 35 optimal weight: 2.9990 chunk 20 optimal weight: 6.9990 chunk 207 optimal weight: 3.9990 overall best weight: 2.5388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 343 GLN D 154 GLN D 343 GLN B 343 GLN B 448 HIS C 154 GLN C 160 ASN C 206 ASN E 154 GLN E 343 GLN F 154 GLN F 206 ASN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4145 r_free = 0.4145 target = 0.198099 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 67)----------------| | r_work = 0.3389 r_free = 0.3389 target = 0.128599 restraints weight = 17154.087| |-----------------------------------------------------------------------------| r_work (start): 0.3353 rms_B_bonded: 1.42 r_work: 0.3153 rms_B_bonded: 2.08 restraints_weight: 0.5000 r_work: 0.3041 rms_B_bonded: 3.01 restraints_weight: 0.2500 r_work (final): 0.3041 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7995 moved from start: 0.2333 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 26124 Z= 0.192 Angle : 0.683 8.653 35424 Z= 0.356 Chirality : 0.049 0.236 4002 Planarity : 0.005 0.040 4494 Dihedral : 7.417 59.373 3534 Min Nonbonded Distance : 2.366 Molprobity Statistics. All-atom Clashscore : 6.55 Ramachandran Plot: Outliers : 0.19 % Allowed : 4.29 % Favored : 95.52 % Rotamer: Outliers : 1.80 % Allowed : 10.14 % Favored : 88.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.35 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.24 (0.14), residues: 3168 helix: 0.71 (0.15), residues: 1098 sheet: -0.60 (0.21), residues: 546 loop : -0.54 (0.15), residues: 1524 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP D 402 HIS 0.005 0.001 HIS E 39 PHE 0.024 0.002 PHE F 81 TYR 0.025 0.002 TYR A 245 ARG 0.004 0.000 ARG A 47 Details of bonding type rmsd hydrogen bonds : bond 0.06058 ( 948) hydrogen bonds : angle 6.09643 ( 2682) covalent geometry : bond 0.00401 (26118) covalent geometry : angle 0.68254 (35424) Misc. bond : bond 0.00377 ( 6) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6336 Ramachandran restraints generated. 3168 Oldfield, 0 Emsley, 3168 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6336 Ramachandran restraints generated. 3168 Oldfield, 0 Emsley, 3168 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 357 residues out of total 2790 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 307 time to evaluate : 2.787 Fit side-chains REVERT: A 61 LYS cc_start: 0.8140 (mtmm) cc_final: 0.7405 (mmtm) REVERT: A 197 MET cc_start: 0.8881 (mmp) cc_final: 0.8089 (mtp) REVERT: A 366 ASP cc_start: 0.6889 (OUTLIER) cc_final: 0.6560 (m-30) REVERT: A 375 GLU cc_start: 0.7148 (pt0) cc_final: 0.6801 (pm20) REVERT: A 399 LYS cc_start: 0.8184 (ttmm) cc_final: 0.7464 (tmmt) REVERT: D 61 LYS cc_start: 0.8120 (mtmm) cc_final: 0.7458 (mmtm) REVERT: D 100 GLU cc_start: 0.7981 (tp30) cc_final: 0.7216 (mp0) REVERT: D 158 GLU cc_start: 0.8128 (mm-30) cc_final: 0.7528 (tm-30) REVERT: D 197 MET cc_start: 0.8838 (mmp) cc_final: 0.8086 (mtp) REVERT: D 262 LYS cc_start: 0.8189 (mmtm) cc_final: 0.7949 (mmmt) REVERT: D 285 MET cc_start: 0.7540 (mtp) cc_final: 0.7150 (mtp) REVERT: D 338 GLU cc_start: 0.6963 (mt-10) cc_final: 0.5982 (mm-30) REVERT: D 366 ASP cc_start: 0.6648 (OUTLIER) cc_final: 0.6386 (m-30) REVERT: D 375 GLU cc_start: 0.7044 (pt0) cc_final: 0.6674 (pm20) REVERT: D 399 LYS cc_start: 0.8095 (ttmm) cc_final: 0.7532 (tmmt) REVERT: B 61 LYS cc_start: 0.8142 (mtmm) cc_final: 0.7404 (mmtm) REVERT: B 144 GLU cc_start: 0.6484 (pm20) cc_final: 0.6140 (pm20) REVERT: B 197 MET cc_start: 0.8876 (mmp) cc_final: 0.8080 (mtp) REVERT: B 366 ASP cc_start: 0.6891 (OUTLIER) cc_final: 0.6560 (m-30) REVERT: B 375 GLU cc_start: 0.7144 (pt0) cc_final: 0.6796 (pm20) REVERT: B 399 LYS cc_start: 0.8191 (ttmm) cc_final: 0.7473 (tmmt) REVERT: C 61 LYS cc_start: 0.8243 (mtmm) cc_final: 0.7486 (mmtm) REVERT: C 100 GLU cc_start: 0.7940 (tp30) cc_final: 0.7180 (mp0) REVERT: C 133 THR cc_start: 0.6671 (OUTLIER) cc_final: 0.6347 (t) REVERT: C 150 ARG cc_start: 0.7271 (mtm110) cc_final: 0.6828 (mtm110) REVERT: C 197 MET cc_start: 0.8996 (mmp) cc_final: 0.8190 (mtp) REVERT: C 283 LYS cc_start: 0.7393 (mmtm) cc_final: 0.7040 (mppt) REVERT: C 335 GLU cc_start: 0.6693 (mp0) cc_final: 0.6048 (tm-30) REVERT: C 338 GLU cc_start: 0.6846 (mt-10) cc_final: 0.6031 (mm-30) REVERT: C 343 GLN cc_start: 0.7481 (mt0) cc_final: 0.7091 (mt0) REVERT: C 366 ASP cc_start: 0.6575 (OUTLIER) cc_final: 0.6365 (m-30) REVERT: C 375 GLU cc_start: 0.7089 (pt0) cc_final: 0.6717 (pm20) REVERT: C 399 LYS cc_start: 0.8090 (ttmm) cc_final: 0.7297 (tmmt) REVERT: C 461 MET cc_start: 0.2605 (OUTLIER) cc_final: 0.1858 (mmm) REVERT: E 61 LYS cc_start: 0.8122 (mtmm) cc_final: 0.7460 (mmtm) REVERT: E 100 GLU cc_start: 0.7970 (tp30) cc_final: 0.7217 (mp0) REVERT: E 158 GLU cc_start: 0.8114 (mm-30) cc_final: 0.7527 (tm-30) REVERT: E 197 MET cc_start: 0.8845 (mmp) cc_final: 0.8094 (mtp) REVERT: E 262 LYS cc_start: 0.8178 (mmtm) cc_final: 0.7870 (mmmt) REVERT: E 285 MET cc_start: 0.7541 (mtp) cc_final: 0.7150 (mtp) REVERT: E 338 GLU cc_start: 0.6953 (mt-10) cc_final: 0.5972 (mm-30) REVERT: E 366 ASP cc_start: 0.6715 (OUTLIER) cc_final: 0.6476 (m-30) REVERT: E 375 GLU cc_start: 0.7041 (pt0) cc_final: 0.6672 (pm20) REVERT: E 399 LYS cc_start: 0.8095 (ttmm) cc_final: 0.7530 (tmmt) REVERT: F 61 LYS cc_start: 0.8235 (mtmm) cc_final: 0.7481 (mmtm) REVERT: F 100 GLU cc_start: 0.7935 (tp30) cc_final: 0.7175 (mp0) REVERT: F 118 GLU cc_start: 0.7913 (pt0) cc_final: 0.7542 (pp20) REVERT: F 133 THR cc_start: 0.6664 (OUTLIER) cc_final: 0.6339 (t) REVERT: F 150 ARG cc_start: 0.7270 (mtm110) cc_final: 0.6827 (mtm110) REVERT: F 197 MET cc_start: 0.8998 (mmp) cc_final: 0.8181 (mtp) REVERT: F 335 GLU cc_start: 0.6676 (mp0) cc_final: 0.6034 (tm-30) REVERT: F 338 GLU cc_start: 0.6853 (mt-10) cc_final: 0.6029 (mm-30) REVERT: F 343 GLN cc_start: 0.7463 (mt0) cc_final: 0.7020 (mt0) REVERT: F 375 GLU cc_start: 0.7091 (pt0) cc_final: 0.6694 (pm20) REVERT: F 399 LYS cc_start: 0.8085 (ttmm) cc_final: 0.7305 (tmmt) REVERT: F 430 MET cc_start: 0.6243 (mmm) cc_final: 0.6006 (mmm) REVERT: F 461 MET cc_start: 0.2635 (OUTLIER) cc_final: 0.1867 (mmm) outliers start: 50 outliers final: 36 residues processed: 346 average time/residue: 1.6344 time to fit residues: 643.7048 Evaluate side-chains 347 residues out of total 2790 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 302 time to evaluate : 2.928 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 111 ASP Chi-restraints excluded: chain A residue 118 GLU Chi-restraints excluded: chain A residue 221 ILE Chi-restraints excluded: chain A residue 227 VAL Chi-restraints excluded: chain A residue 366 ASP Chi-restraints excluded: chain A residue 459 ILE Chi-restraints excluded: chain A residue 461 MET Chi-restraints excluded: chain A residue 469 VAL Chi-restraints excluded: chain D residue 111 ASP Chi-restraints excluded: chain D residue 118 GLU Chi-restraints excluded: chain D residue 221 ILE Chi-restraints excluded: chain D residue 227 VAL Chi-restraints excluded: chain D residue 366 ASP Chi-restraints excluded: chain D residue 459 ILE Chi-restraints excluded: chain B residue 111 ASP Chi-restraints excluded: chain B residue 118 GLU Chi-restraints excluded: chain B residue 221 ILE Chi-restraints excluded: chain B residue 227 VAL Chi-restraints excluded: chain B residue 366 ASP Chi-restraints excluded: chain B residue 459 ILE Chi-restraints excluded: chain B residue 461 MET Chi-restraints excluded: chain B residue 469 VAL Chi-restraints excluded: chain C residue 118 GLU Chi-restraints excluded: chain C residue 133 THR Chi-restraints excluded: chain C residue 221 ILE Chi-restraints excluded: chain C residue 227 VAL Chi-restraints excluded: chain C residue 272 ILE Chi-restraints excluded: chain C residue 366 ASP Chi-restraints excluded: chain C residue 459 ILE Chi-restraints excluded: chain C residue 461 MET Chi-restraints excluded: chain C residue 469 VAL Chi-restraints excluded: chain E residue 111 ASP Chi-restraints excluded: chain E residue 118 GLU Chi-restraints excluded: chain E residue 133 THR Chi-restraints excluded: chain E residue 221 ILE Chi-restraints excluded: chain E residue 227 VAL Chi-restraints excluded: chain E residue 366 ASP Chi-restraints excluded: chain E residue 459 ILE Chi-restraints excluded: chain F residue 133 THR Chi-restraints excluded: chain F residue 221 ILE Chi-restraints excluded: chain F residue 227 VAL Chi-restraints excluded: chain F residue 272 ILE Chi-restraints excluded: chain F residue 459 ILE Chi-restraints excluded: chain F residue 461 MET Chi-restraints excluded: chain F residue 469 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 318 random chunks: chunk 263 optimal weight: 0.0980 chunk 244 optimal weight: 7.9990 chunk 256 optimal weight: 7.9990 chunk 236 optimal weight: 5.9990 chunk 23 optimal weight: 0.9990 chunk 315 optimal weight: 30.0000 chunk 200 optimal weight: 0.5980 chunk 173 optimal weight: 8.9990 chunk 1 optimal weight: 1.9990 chunk 240 optimal weight: 8.9990 chunk 103 optimal weight: 20.0000 overall best weight: 1.9386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 154 GLN D 154 GLN D 343 GLN B 154 GLN B 343 GLN C 154 GLN C 160 ASN E 126 GLN E 154 GLN E 343 GLN F 154 GLN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4153 r_free = 0.4153 target = 0.198919 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 71)----------------| | r_work = 0.3414 r_free = 0.3414 target = 0.130669 restraints weight = 17124.243| |-----------------------------------------------------------------------------| r_work (start): 0.3394 rms_B_bonded: 1.48 r_work: 0.3176 rms_B_bonded: 2.05 restraints_weight: 0.5000 r_work: 0.3066 rms_B_bonded: 2.96 restraints_weight: 0.2500 r_work (final): 0.3066 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8042 moved from start: 0.2338 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 26124 Z= 0.166 Angle : 0.656 8.541 35424 Z= 0.342 Chirality : 0.048 0.230 4002 Planarity : 0.004 0.036 4494 Dihedral : 7.333 59.129 3534 Min Nonbonded Distance : 2.396 Molprobity Statistics. All-atom Clashscore : 6.51 Ramachandran Plot: Outliers : 0.19 % Allowed : 4.01 % Favored : 95.80 % Rotamer: Outliers : 1.62 % Allowed : 10.57 % Favored : 87.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.35 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.17 (0.15), residues: 3168 helix: 0.80 (0.16), residues: 1098 sheet: -0.58 (0.21), residues: 546 loop : -0.52 (0.16), residues: 1524 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP D 402 HIS 0.005 0.001 HIS E 39 PHE 0.023 0.002 PHE F 81 TYR 0.023 0.002 TYR A 245 ARG 0.003 0.000 ARG B 47 Details of bonding type rmsd hydrogen bonds : bond 0.05681 ( 948) hydrogen bonds : angle 5.97639 ( 2682) covalent geometry : bond 0.00342 (26118) covalent geometry : angle 0.65619 (35424) Misc. bond : bond 0.00301 ( 6) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6336 Ramachandran restraints generated. 3168 Oldfield, 0 Emsley, 3168 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6336 Ramachandran restraints generated. 3168 Oldfield, 0 Emsley, 3168 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 348 residues out of total 2790 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 303 time to evaluate : 2.750 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 61 LYS cc_start: 0.8179 (mtmm) cc_final: 0.7502 (mmtm) REVERT: A 197 MET cc_start: 0.8921 (mmp) cc_final: 0.8164 (mtp) REVERT: A 366 ASP cc_start: 0.6926 (OUTLIER) cc_final: 0.6593 (m-30) REVERT: A 399 LYS cc_start: 0.8182 (ttmm) cc_final: 0.7528 (tmmt) REVERT: D 61 LYS cc_start: 0.8167 (mtmm) cc_final: 0.7559 (mmtm) REVERT: D 100 GLU cc_start: 0.8061 (tp30) cc_final: 0.7339 (mp0) REVERT: D 158 GLU cc_start: 0.8146 (mm-30) cc_final: 0.7621 (tm-30) REVERT: D 197 MET cc_start: 0.8847 (mmp) cc_final: 0.8140 (mtp) REVERT: D 262 LYS cc_start: 0.8183 (mmtm) cc_final: 0.7961 (mmmt) REVERT: D 285 MET cc_start: 0.7560 (mtp) cc_final: 0.7200 (mtp) REVERT: D 338 GLU cc_start: 0.7005 (mt-10) cc_final: 0.6045 (mm-30) REVERT: D 399 LYS cc_start: 0.8123 (ttmm) cc_final: 0.7633 (tmmt) REVERT: B 61 LYS cc_start: 0.8189 (mtmm) cc_final: 0.7516 (mmtm) REVERT: B 144 GLU cc_start: 0.6515 (pm20) cc_final: 0.6184 (pm20) REVERT: B 197 MET cc_start: 0.8915 (mmp) cc_final: 0.8155 (mtp) REVERT: B 248 LYS cc_start: 0.8317 (tttm) cc_final: 0.8058 (tttp) REVERT: B 366 ASP cc_start: 0.6920 (OUTLIER) cc_final: 0.6586 (m-30) REVERT: B 399 LYS cc_start: 0.8180 (ttmm) cc_final: 0.7536 (tmmt) REVERT: C 61 LYS cc_start: 0.8290 (mtmm) cc_final: 0.7586 (mmtm) REVERT: C 100 GLU cc_start: 0.7997 (tp30) cc_final: 0.7294 (mp0) REVERT: C 133 THR cc_start: 0.6665 (OUTLIER) cc_final: 0.6357 (t) REVERT: C 150 ARG cc_start: 0.7313 (mtm110) cc_final: 0.7006 (mtm110) REVERT: C 197 MET cc_start: 0.8995 (mmp) cc_final: 0.8231 (mtp) REVERT: C 283 LYS cc_start: 0.7355 (mmtm) cc_final: 0.7013 (mppt) REVERT: C 335 GLU cc_start: 0.6755 (mp0) cc_final: 0.6118 (tm-30) REVERT: C 338 GLU cc_start: 0.6852 (mt-10) cc_final: 0.6074 (mm-30) REVERT: C 365 GLU cc_start: 0.6901 (mp0) cc_final: 0.6691 (mp0) REVERT: C 375 GLU cc_start: 0.7095 (pt0) cc_final: 0.6722 (pm20) REVERT: C 399 LYS cc_start: 0.8129 (ttmm) cc_final: 0.7405 (tmmt) REVERT: C 430 MET cc_start: 0.6246 (mmm) cc_final: 0.6021 (mmm) REVERT: C 461 MET cc_start: 0.2566 (OUTLIER) cc_final: 0.1840 (mmm) REVERT: E 61 LYS cc_start: 0.8168 (mtmm) cc_final: 0.7558 (mmtm) REVERT: E 100 GLU cc_start: 0.8052 (tp30) cc_final: 0.7341 (mp0) REVERT: E 158 GLU cc_start: 0.8134 (mm-30) cc_final: 0.7618 (tm-30) REVERT: E 197 MET cc_start: 0.8850 (mmp) cc_final: 0.8145 (mtp) REVERT: E 262 LYS cc_start: 0.8154 (mmtm) cc_final: 0.7885 (mmmt) REVERT: E 285 MET cc_start: 0.7563 (mtp) cc_final: 0.7200 (mtp) REVERT: E 338 GLU cc_start: 0.6994 (mt-10) cc_final: 0.6033 (mm-30) REVERT: E 399 LYS cc_start: 0.8128 (ttmm) cc_final: 0.7629 (tmmt) REVERT: F 61 LYS cc_start: 0.8281 (mtmm) cc_final: 0.7579 (mmtm) REVERT: F 100 GLU cc_start: 0.7997 (tp30) cc_final: 0.7292 (mp0) REVERT: F 118 GLU cc_start: 0.7946 (pt0) cc_final: 0.7594 (pp20) REVERT: F 133 THR cc_start: 0.6659 (OUTLIER) cc_final: 0.6349 (t) REVERT: F 150 ARG cc_start: 0.7311 (mtm110) cc_final: 0.7004 (mtm110) REVERT: F 197 MET cc_start: 0.9004 (mmp) cc_final: 0.8230 (mtp) REVERT: F 335 GLU cc_start: 0.6735 (mp0) cc_final: 0.6098 (tm-30) REVERT: F 338 GLU cc_start: 0.6844 (mt-10) cc_final: 0.6058 (mm-30) REVERT: F 343 GLN cc_start: 0.7531 (mt0) cc_final: 0.7096 (mt0) REVERT: F 365 GLU cc_start: 0.6872 (mp0) cc_final: 0.6655 (mp0) REVERT: F 375 GLU cc_start: 0.7100 (pt0) cc_final: 0.6730 (pm20) REVERT: F 399 LYS cc_start: 0.8122 (ttmm) cc_final: 0.7412 (tmmt) REVERT: F 430 MET cc_start: 0.6238 (mmm) cc_final: 0.6007 (mmm) REVERT: F 461 MET cc_start: 0.2627 (OUTLIER) cc_final: 0.1869 (mmm) outliers start: 45 outliers final: 36 residues processed: 337 average time/residue: 1.5649 time to fit residues: 598.1257 Evaluate side-chains 341 residues out of total 2790 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 299 time to evaluate : 2.711 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 118 GLU Chi-restraints excluded: chain A residue 221 ILE Chi-restraints excluded: chain A residue 227 VAL Chi-restraints excluded: chain A residue 366 ASP Chi-restraints excluded: chain A residue 459 ILE Chi-restraints excluded: chain A residue 461 MET Chi-restraints excluded: chain A residue 469 VAL Chi-restraints excluded: chain D residue 111 ASP Chi-restraints excluded: chain D residue 118 GLU Chi-restraints excluded: chain D residue 221 ILE Chi-restraints excluded: chain D residue 227 VAL Chi-restraints excluded: chain D residue 459 ILE Chi-restraints excluded: chain D residue 461 MET Chi-restraints excluded: chain D residue 469 VAL Chi-restraints excluded: chain B residue 111 ASP Chi-restraints excluded: chain B residue 118 GLU Chi-restraints excluded: chain B residue 221 ILE Chi-restraints excluded: chain B residue 227 VAL Chi-restraints excluded: chain B residue 366 ASP Chi-restraints excluded: chain B residue 459 ILE Chi-restraints excluded: chain B residue 461 MET Chi-restraints excluded: chain B residue 469 VAL Chi-restraints excluded: chain C residue 118 GLU Chi-restraints excluded: chain C residue 133 THR Chi-restraints excluded: chain C residue 221 ILE Chi-restraints excluded: chain C residue 227 VAL Chi-restraints excluded: chain C residue 272 ILE Chi-restraints excluded: chain C residue 459 ILE Chi-restraints excluded: chain C residue 461 MET Chi-restraints excluded: chain E residue 111 ASP Chi-restraints excluded: chain E residue 118 GLU Chi-restraints excluded: chain E residue 133 THR Chi-restraints excluded: chain E residue 221 ILE Chi-restraints excluded: chain E residue 227 VAL Chi-restraints excluded: chain E residue 459 ILE Chi-restraints excluded: chain E residue 461 MET Chi-restraints excluded: chain F residue 133 THR Chi-restraints excluded: chain F residue 221 ILE Chi-restraints excluded: chain F residue 227 VAL Chi-restraints excluded: chain F residue 272 ILE Chi-restraints excluded: chain F residue 459 ILE Chi-restraints excluded: chain F residue 461 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 318 random chunks: chunk 269 optimal weight: 0.9990 chunk 133 optimal weight: 0.7980 chunk 62 optimal weight: 1.9990 chunk 260 optimal weight: 6.9990 chunk 107 optimal weight: 3.9990 chunk 44 optimal weight: 5.9990 chunk 41 optimal weight: 0.7980 chunk 127 optimal weight: 0.0570 chunk 173 optimal weight: 7.9990 chunk 225 optimal weight: 0.0270 chunk 38 optimal weight: 0.5980 overall best weight: 0.4556 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 154 GLN A 343 GLN D 343 GLN B 154 GLN B 343 GLN C 154 GLN C 160 ASN C 343 GLN E 154 GLN E 343 GLN F 154 GLN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4107 r_free = 0.4107 target = 0.197518 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3334 r_free = 0.3334 target = 0.125593 restraints weight = 17106.189| |-----------------------------------------------------------------------------| r_work (start): 0.3313 rms_B_bonded: 1.74 r_work: 0.3138 rms_B_bonded: 2.05 restraints_weight: 0.5000 r_work: 0.3020 rms_B_bonded: 3.06 restraints_weight: 0.2500 r_work (final): 0.3020 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7798 moved from start: 0.2283 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 26124 Z= 0.106 Angle : 0.568 7.757 35424 Z= 0.297 Chirality : 0.045 0.174 4002 Planarity : 0.003 0.034 4494 Dihedral : 6.800 57.323 3534 Min Nonbonded Distance : 2.501 Molprobity Statistics. All-atom Clashscore : 6.20 Ramachandran Plot: Outliers : 0.19 % Allowed : 4.10 % Favored : 95.71 % Rotamer: Outliers : 1.12 % Allowed : 11.22 % Favored : 87.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.35 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.01 (0.15), residues: 3168 helix: 0.97 (0.16), residues: 1122 sheet: -0.37 (0.21), residues: 546 loop : -0.51 (0.16), residues: 1500 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP D 402 HIS 0.003 0.001 HIS C 91 PHE 0.017 0.001 PHE B 81 TYR 0.009 0.001 TYR F 80 ARG 0.002 0.000 ARG A 47 Details of bonding type rmsd hydrogen bonds : bond 0.04207 ( 948) hydrogen bonds : angle 5.53279 ( 2682) covalent geometry : bond 0.00211 (26118) covalent geometry : angle 0.56760 (35424) Misc. bond : bond 0.00097 ( 6) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 25841.02 seconds wall clock time: 444 minutes 1.32 seconds (26641.32 seconds total)