Starting phenix.real_space_refine on Sun Jun 22 01:03:17 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8jyu_36731/06_2025/8jyu_36731.cif Found real_map, /net/cci-nas-00/data/ceres_data/8jyu_36731/06_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_36731/06_2025/8jyu_36731.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8jyu_36731/06_2025/8jyu_36731.map" model { file = "/net/cci-nas-00/data/ceres_data/8jyu_36731/06_2025/8jyu_36731.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8jyu_36731/06_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): 0.07s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/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, 'AMP%rna3p': 1, 'DKA': 1} Classifications: {'RNA_mixed': 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, 'AMP%rna3p': 1, 'DKA': 1} Classifications: {'RNA_mixed': 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, 'AMP%rna3p': 1, 'DKA': 1} Classifications: {'RNA_mixed': 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, 'AMP%rna3p': 1, 'DKA': 1} Classifications: {'RNA_mixed': 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, 'AMP%rna3p': 1, 'DKA': 1} Classifications: {'RNA_mixed': 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, 'AMP%rna3p': 1, 'DKA': 1} Classifications: {'RNA_mixed': 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: 15.07, per 1000 atoms: 0.59 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: 6.58 Conformation dependent library (CDL) restraints added in 3.2 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: 3.82 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: 10.30 Time building geometry restraints manager: 7.73 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: 34769 2.16 - 4.31: 502 4.31 - 6.47: 120 6.47 - 8.63: 21 8.63 - 10.78: 12 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: 3524 0.079 - 0.159: 454 0.159 - 0.238: 0 0.238 - 0.317: 6 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: 0.21 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: 2.470 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: 1.010 Check model and map are aligned: 0.170 Set scattering table: 0.260 Process input model: 59.830 Find NCS groups from input model: 0.560 Set up NCS constraints: 0.130 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:13.580 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 78.040 ------------------------------------------------------------------------------- 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= 0.255 Angle : 0.690 10.784 35424 Z= 0.400 Chirality : 0.051 0.396 4002 Planarity : 0.004 0.039 4494 Dihedral : 14.449 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 0.00396 (26118) covalent geometry : angle 0.69018 (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 : 2.806 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: 1.6735 time to fit residues: 765.2810 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 : 2.674 ------------------------------------------------------------------------------- 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: 7.9990 chunk 133 optimal weight: 0.1980 chunk 82 optimal weight: 7.9990 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 = 0.197950 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3390 r_free = 0.3390 target = 0.128512 restraints weight = 17030.332| |-----------------------------------------------------------------------------| r_work (start): 0.3362 rms_B_bonded: 1.58 r_work: 0.3097 rms_B_bonded: 2.38 restraints_weight: 0.5000 r_work: 0.2986 rms_B_bonded: 3.45 restraints_weight: 0.2500 r_work (final): 0.2986 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8050 moved from start: 0.1630 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.044 26124 Z= 0.241 Angle : 0.763 9.443 35424 Z= 0.393 Chirality : 0.052 0.223 4002 Planarity : 0.005 0.038 4494 Dihedral : 7.321 59.295 3534 Min Nonbonded Distance : 2.182 Molprobity Statistics. All-atom Clashscore : 5.61 Ramachandran Plot: Outliers : 0.19 % Allowed : 4.20 % Favored : 95.61 % Rotamer: Outliers : 1.30 % Allowed : 7.90 % Favored : 90.80 % 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: -0.20 (0.14), residues: 3168 helix: 0.66 (0.15), residues: 1104 sheet: -0.45 (0.21), residues: 576 loop : -0.51 (0.16), residues: 1488 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP C 402 HIS 0.007 0.002 HIS E 74 PHE 0.024 0.003 PHE C 81 TYR 0.031 0.003 TYR A 245 ARG 0.005 0.001 ARG A 190 Details of bonding type rmsd hydrogen bonds : bond 0.07142 ( 948) hydrogen bonds : angle 6.55494 ( 2682) covalent geometry : bond 0.00507 (26118) covalent geometry : angle 0.76297 (35424) Misc. bond : bond 0.00379 ( 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 : 2.805 Fit side-chains REVERT: A 42 LYS cc_start: 0.8448 (ttpp) cc_final: 0.8217 (tmmt) REVERT: A 61 LYS cc_start: 0.8140 (mtmm) cc_final: 0.7426 (mmtm) REVERT: A 112 ASP cc_start: 0.8516 (m-30) cc_final: 0.8258 (m-30) REVERT: A 144 GLU cc_start: 0.6638 (pm20) cc_final: 0.6275 (pm20) REVERT: A 158 GLU cc_start: 0.8237 (mm-30) cc_final: 0.7912 (mp0) REVERT: A 197 MET cc_start: 0.8947 (mmp) cc_final: 0.8184 (mtp) REVERT: A 256 ASN cc_start: 0.8084 (t0) cc_final: 0.7794 (t0) REVERT: A 309 GLU cc_start: 0.7785 (mt-10) cc_final: 0.7547 (mt-10) REVERT: A 335 GLU cc_start: 0.6545 (mp0) cc_final: 0.6054 (tm-30) REVERT: A 343 GLN cc_start: 0.7763 (mt0) cc_final: 0.7472 (mt0) REVERT: A 366 ASP cc_start: 0.6963 (m-30) cc_final: 0.6744 (m-30) REVERT: A 375 GLU cc_start: 0.7148 (pt0) cc_final: 0.6794 (pm20) REVERT: A 399 LYS cc_start: 0.8052 (ttmm) cc_final: 0.7385 (tmmt) REVERT: D 42 LYS cc_start: 0.8308 (ttpp) cc_final: 0.8092 (ttpp) REVERT: D 61 LYS cc_start: 0.8177 (mtmm) cc_final: 0.7470 (mmtt) REVERT: D 89 LYS cc_start: 0.8854 (mtpt) cc_final: 0.8630 (mttt) REVERT: D 100 GLU cc_start: 0.8021 (tp30) cc_final: 0.7233 (mp0) REVERT: D 158 GLU cc_start: 0.8247 (mm-30) cc_final: 0.7446 (tm-30) REVERT: D 197 MET cc_start: 0.8908 (mmp) cc_final: 0.8170 (mtp) REVERT: D 285 MET cc_start: 0.7566 (mtp) cc_final: 0.7216 (mtp) REVERT: D 338 GLU cc_start: 0.7131 (mt-10) cc_final: 0.6222 (mm-30) REVERT: D 346 GLU cc_start: 0.7780 (tp30) cc_final: 0.7512 (tp30) REVERT: D 375 GLU cc_start: 0.7137 (pt0) cc_final: 0.6741 (pm20) REVERT: D 399 LYS cc_start: 0.8001 (ttmm) cc_final: 0.7383 (tmmt) REVERT: B 61 LYS cc_start: 0.8138 (mtmm) cc_final: 0.7419 (mmtm) REVERT: B 112 ASP cc_start: 0.8526 (m-30) cc_final: 0.8265 (m-30) REVERT: B 144 GLU cc_start: 0.6660 (pm20) cc_final: 0.6309 (pm20) REVERT: B 158 GLU cc_start: 0.8229 (mm-30) cc_final: 0.7903 (mp0) REVERT: B 197 MET cc_start: 0.8945 (mmp) cc_final: 0.8180 (mtp) REVERT: B 256 ASN cc_start: 0.8044 (t0) cc_final: 0.7748 (t0) REVERT: B 309 GLU cc_start: 0.7791 (mt-10) cc_final: 0.7540 (mt-10) REVERT: B 335 GLU cc_start: 0.6597 (mp0) cc_final: 0.6144 (tm-30) REVERT: B 343 GLN cc_start: 0.7756 (mt0) cc_final: 0.7445 (mt0) REVERT: B 366 ASP cc_start: 0.6977 (m-30) cc_final: 0.6766 (m-30) REVERT: B 375 GLU cc_start: 0.7122 (pt0) cc_final: 0.6775 (pm20) REVERT: B 399 LYS cc_start: 0.8071 (ttmm) cc_final: 0.7404 (tmmt) REVERT: C 61 LYS cc_start: 0.8294 (mtmm) cc_final: 0.7531 (mmtm) REVERT: C 100 GLU cc_start: 0.8080 (tp30) cc_final: 0.7260 (mp0) REVERT: C 133 THR cc_start: 0.6472 (OUTLIER) cc_final: 0.6199 (t) REVERT: C 136 ARG cc_start: 0.8432 (ttt180) cc_final: 0.8144 (tpt-90) REVERT: C 145 GLU cc_start: 0.6696 (mm-30) cc_final: 0.6328 (mp0) REVERT: C 150 ARG cc_start: 0.7452 (mtm110) cc_final: 0.7048 (mtm110) REVERT: C 158 GLU cc_start: 0.8250 (mm-30) cc_final: 0.7919 (mp0) REVERT: C 197 MET cc_start: 0.8999 (mmp) cc_final: 0.8203 (mtp) REVERT: C 274 HIS cc_start: 0.8113 (t70) cc_final: 0.7897 (t70) REVERT: C 283 LYS cc_start: 0.7311 (mmtm) cc_final: 0.7092 (mppt) REVERT: C 338 GLU cc_start: 0.7108 (mt-10) cc_final: 0.6292 (mm-30) REVERT: C 343 GLN cc_start: 0.7517 (mt0) cc_final: 0.7108 (mt0) REVERT: C 375 GLU cc_start: 0.7063 (pt0) cc_final: 0.6656 (pm20) REVERT: C 399 LYS cc_start: 0.7998 (ttmm) cc_final: 0.7231 (tmmt) REVERT: E 42 LYS cc_start: 0.8293 (ttpp) cc_final: 0.8089 (ttpp) REVERT: E 61 LYS cc_start: 0.8178 (mtmm) cc_final: 0.7475 (mmtt) REVERT: E 100 GLU cc_start: 0.8010 (tp30) cc_final: 0.7230 (mp0) REVERT: E 158 GLU cc_start: 0.8234 (mm-30) cc_final: 0.7454 (tm-30) REVERT: E 197 MET cc_start: 0.8908 (mmp) cc_final: 0.8167 (mtp) REVERT: E 285 MET cc_start: 0.7572 (mtp) cc_final: 0.7259 (mtp) REVERT: E 338 GLU cc_start: 0.7123 (mt-10) cc_final: 0.6220 (mm-30) REVERT: E 346 GLU cc_start: 0.7781 (tp30) cc_final: 0.7512 (tp30) REVERT: E 375 GLU cc_start: 0.7147 (pt0) cc_final: 0.6745 (pm20) REVERT: E 399 LYS cc_start: 0.8009 (ttmm) cc_final: 0.7412 (tmmt) REVERT: F 61 LYS cc_start: 0.8286 (mtmm) cc_final: 0.7518 (mmtm) REVERT: F 100 GLU cc_start: 0.8083 (tp30) cc_final: 0.7263 (mp0) REVERT: F 133 THR cc_start: 0.6436 (OUTLIER) cc_final: 0.6164 (t) REVERT: F 136 ARG cc_start: 0.8430 (ttt180) cc_final: 0.8142 (tpt-90) REVERT: F 145 GLU cc_start: 0.6670 (mm-30) cc_final: 0.6313 (mp0) REVERT: F 150 ARG cc_start: 0.7443 (mtm110) cc_final: 0.7039 (mtm110) REVERT: F 158 GLU cc_start: 0.8265 (mm-30) cc_final: 0.7924 (mp0) REVERT: F 197 MET cc_start: 0.8999 (mmp) cc_final: 0.8201 (mtp) REVERT: F 274 HIS cc_start: 0.8117 (t70) cc_final: 0.7901 (t70) REVERT: F 283 LYS cc_start: 0.7327 (mmtm) cc_final: 0.7109 (mppt) REVERT: F 335 GLU cc_start: 0.6585 (mp0) cc_final: 0.6142 (tm-30) REVERT: F 338 GLU cc_start: 0.7112 (mt-10) cc_final: 0.6292 (mm-30) REVERT: F 343 GLN cc_start: 0.7511 (mt0) cc_final: 0.7110 (mt0) REVERT: F 375 GLU cc_start: 0.7061 (pt0) cc_final: 0.6654 (pm20) REVERT: F 399 LYS cc_start: 0.7979 (ttmm) cc_final: 0.7216 (tmmt) outliers start: 36 outliers final: 22 residues processed: 360 average time/residue: 1.6676 time to fit residues: 679.7608 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 : 3.350 ------------------------------------------------------------------------------- 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: 3.9990 chunk 14 optimal weight: 1.9990 chunk 142 optimal weight: 8.9990 chunk 285 optimal weight: 9.9990 chunk 161 optimal weight: 0.9990 chunk 228 optimal weight: 0.4980 chunk 193 optimal weight: 6.9990 chunk 218 optimal weight: 10.0000 chunk 96 optimal weight: 9.9990 chunk 233 optimal weight: 0.9990 chunk 160 optimal weight: 2.9990 overall best weight: 1.4988 ------------------------------------------------------------------------------- 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 C 368 ASN E 343 GLN E 368 ASN F 154 GLN F 368 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4161 r_free = 0.4161 target = 0.199908 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3412 r_free = 0.3412 target = 0.130019 restraints weight = 17160.124| |-----------------------------------------------------------------------------| r_work (start): 0.3390 rms_B_bonded: 1.28 r_work: 0.3173 rms_B_bonded: 2.15 restraints_weight: 0.5000 r_work: 0.3064 rms_B_bonded: 3.09 restraints_weight: 0.2500 r_work (final): 0.3064 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8022 moved from start: 0.1732 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 26124 Z= 0.147 Angle : 0.639 8.206 35424 Z= 0.330 Chirality : 0.047 0.199 4002 Planarity : 0.004 0.036 4494 Dihedral : 6.909 59.901 3534 Min Nonbonded Distance : 2.287 Molprobity Statistics. All-atom Clashscore : 6.02 Ramachandran Plot: Outliers : 0.19 % Allowed : 3.79 % Favored : 96.02 % Rotamer: Outliers : 1.59 % Allowed : 8.48 % Favored : 89.94 % 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: -0.12 (0.15), residues: 3168 helix: 0.85 (0.16), residues: 1104 sheet: -0.47 (0.21), residues: 576 loop : -0.52 (0.16), residues: 1488 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP C 402 HIS 0.004 0.001 HIS D 39 PHE 0.019 0.002 PHE C 81 TYR 0.022 0.002 TYR B 245 ARG 0.003 0.000 ARG A 47 Details of bonding type rmsd hydrogen bonds : bond 0.05500 ( 948) hydrogen bonds : angle 6.07059 ( 2682) covalent geometry : bond 0.00297 (26118) covalent geometry : angle 0.63923 (35424) Misc. bond : bond 0.00205 ( 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 371 residues out of total 2790 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 327 time to evaluate : 2.630 Fit side-chains REVERT: A 61 LYS cc_start: 0.8168 (mtmm) cc_final: 0.7485 (mmtm) REVERT: A 112 ASP cc_start: 0.8492 (m-30) cc_final: 0.8223 (m-30) REVERT: A 158 GLU cc_start: 0.8137 (mm-30) cc_final: 0.7845 (mp0) REVERT: A 197 MET cc_start: 0.8963 (mmp) cc_final: 0.8200 (mtp) REVERT: A 256 ASN cc_start: 0.8099 (t0) cc_final: 0.7816 (t0) REVERT: A 309 GLU cc_start: 0.7766 (mt-10) cc_final: 0.7520 (mt-10) REVERT: A 335 GLU cc_start: 0.6612 (mp0) cc_final: 0.6158 (tm-30) REVERT: A 343 GLN cc_start: 0.7769 (mt0) cc_final: 0.7454 (mt0) REVERT: A 366 ASP cc_start: 0.6855 (m-30) cc_final: 0.6640 (m-30) REVERT: A 375 GLU cc_start: 0.7120 (pt0) cc_final: 0.6764 (pm20) REVERT: A 399 LYS cc_start: 0.7992 (ttmm) cc_final: 0.7378 (tmmt) REVERT: D 61 LYS cc_start: 0.8209 (mtmm) cc_final: 0.7516 (mmtt) REVERT: D 89 LYS cc_start: 0.8794 (mtpt) cc_final: 0.8563 (ttmm) REVERT: D 100 GLU cc_start: 0.7990 (tp30) cc_final: 0.7275 (mp0) REVERT: D 158 GLU cc_start: 0.8219 (mm-30) cc_final: 0.7594 (tm-30) REVERT: D 197 MET cc_start: 0.8882 (mmp) cc_final: 0.8135 (mtp) REVERT: D 278 SER cc_start: 0.8160 (m) cc_final: 0.7902 (p) REVERT: D 285 MET cc_start: 0.7534 (mtp) cc_final: 0.7258 (mtp) REVERT: D 338 GLU cc_start: 0.7118 (mt-10) cc_final: 0.6270 (mm-30) REVERT: D 346 GLU cc_start: 0.7784 (tp30) cc_final: 0.7478 (tp30) REVERT: D 399 LYS cc_start: 0.8048 (ttmm) cc_final: 0.7513 (tmmt) REVERT: B 61 LYS cc_start: 0.8173 (mtmm) cc_final: 0.7487 (mmtm) REVERT: B 112 ASP cc_start: 0.8497 (m-30) cc_final: 0.8230 (m-30) REVERT: B 158 GLU cc_start: 0.8141 (mm-30) cc_final: 0.7849 (mp0) REVERT: B 197 MET cc_start: 0.8965 (mmp) cc_final: 0.8201 (mtp) REVERT: B 256 ASN cc_start: 0.8097 (t0) cc_final: 0.7813 (t0) REVERT: B 309 GLU cc_start: 0.7767 (mt-10) cc_final: 0.7519 (mt-10) REVERT: B 335 GLU cc_start: 0.6622 (mp0) cc_final: 0.6176 (tm-30) REVERT: B 343 GLN cc_start: 0.7772 (mt0) cc_final: 0.7488 (mt0) REVERT: B 366 ASP cc_start: 0.6858 (m-30) cc_final: 0.6649 (m-30) REVERT: B 375 GLU cc_start: 0.7101 (pt0) cc_final: 0.6748 (pm20) REVERT: B 399 LYS cc_start: 0.8005 (ttmm) cc_final: 0.7390 (tmmt) REVERT: C 61 LYS cc_start: 0.8287 (mtmm) cc_final: 0.7571 (mmtm) REVERT: C 100 GLU cc_start: 0.7951 (tp30) cc_final: 0.7244 (mp0) REVERT: C 133 THR cc_start: 0.6245 (OUTLIER) cc_final: 0.6032 (t) REVERT: C 145 GLU cc_start: 0.6793 (mm-30) cc_final: 0.6458 (mp0) REVERT: C 150 ARG cc_start: 0.7271 (mtm110) cc_final: 0.6905 (mtm110) REVERT: C 158 GLU cc_start: 0.8168 (mm-30) cc_final: 0.7908 (mp0) REVERT: C 197 MET cc_start: 0.8983 (mmp) cc_final: 0.8207 (mtp) REVERT: C 274 HIS cc_start: 0.8159 (t70) cc_final: 0.7957 (t70) REVERT: C 335 GLU cc_start: 0.6623 (mp0) cc_final: 0.6126 (tm-30) REVERT: C 338 GLU cc_start: 0.7076 (mt-10) cc_final: 0.6274 (mm-30) REVERT: C 343 GLN cc_start: 0.7558 (mt0) cc_final: 0.7157 (mt0) REVERT: C 375 GLU cc_start: 0.7043 (pt0) cc_final: 0.6658 (pm20) REVERT: C 399 LYS cc_start: 0.7974 (ttmm) cc_final: 0.7257 (tmmt) REVERT: E 61 LYS cc_start: 0.8221 (mtmm) cc_final: 0.7525 (mmtt) REVERT: E 100 GLU cc_start: 0.7984 (tp30) cc_final: 0.7276 (mp0) REVERT: E 158 GLU cc_start: 0.8196 (mm-30) cc_final: 0.7576 (tm-30) REVERT: E 197 MET cc_start: 0.8887 (mmp) cc_final: 0.8138 (mtp) REVERT: E 278 SER cc_start: 0.8152 (m) cc_final: 0.7895 (p) REVERT: E 285 MET cc_start: 0.7537 (mtp) cc_final: 0.7255 (mtp) REVERT: E 338 GLU cc_start: 0.7135 (mt-10) cc_final: 0.6193 (mm-30) REVERT: E 346 GLU cc_start: 0.7840 (tp30) cc_final: 0.7555 (tp30) REVERT: E 399 LYS cc_start: 0.8062 (ttmm) cc_final: 0.7528 (tmmt) REVERT: F 61 LYS cc_start: 0.8282 (mtmm) cc_final: 0.7571 (mmtm) REVERT: F 100 GLU cc_start: 0.7952 (tp30) cc_final: 0.7247 (mp0) REVERT: F 133 THR cc_start: 0.6242 (OUTLIER) cc_final: 0.6029 (t) REVERT: F 145 GLU cc_start: 0.6762 (mm-30) cc_final: 0.6436 (mp0) REVERT: F 150 ARG cc_start: 0.7277 (mtm110) cc_final: 0.6912 (mtm110) REVERT: F 158 GLU cc_start: 0.8187 (mm-30) cc_final: 0.7917 (mp0) REVERT: F 197 MET cc_start: 0.8993 (mmp) cc_final: 0.8211 (mtp) REVERT: F 283 LYS cc_start: 0.7486 (mmtm) cc_final: 0.7207 (mppt) REVERT: F 335 GLU cc_start: 0.6596 (mp0) cc_final: 0.6202 (tm-30) REVERT: F 338 GLU cc_start: 0.7087 (mt-10) cc_final: 0.6297 (mm-30) REVERT: F 343 GLN cc_start: 0.7550 (mt0) cc_final: 0.7147 (mt0) REVERT: F 375 GLU cc_start: 0.7044 (pt0) cc_final: 0.6660 (pm20) REVERT: F 399 LYS cc_start: 0.7969 (ttmm) cc_final: 0.7260 (tmmt) REVERT: F 403 ARG cc_start: 0.7949 (ttp-110) cc_final: 0.7716 (ttp80) outliers start: 44 outliers final: 29 residues processed: 363 average time/residue: 1.6158 time to fit residues: 664.8833 Evaluate side-chains 340 residues out of total 2790 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 309 time to evaluate : 2.944 ------------------------------------------------------------------------------- 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 461 MET Chi-restraints excluded: chain B residue 111 ASP Chi-restraints excluded: chain B residue 118 GLU 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 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 306 SER Chi-restraints excluded: chain E residue 461 MET Chi-restraints excluded: chain F residue 118 GLU 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=4.00 ------------------------------------------------------------------------------- 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: 9.9990 chunk 273 optimal weight: 4.9990 chunk 236 optimal weight: 6.9990 chunk 89 optimal weight: 7.9990 chunk 281 optimal weight: 0.9980 chunk 305 optimal weight: 0.5980 chunk 285 optimal weight: 1.9990 chunk 54 optimal weight: 0.5980 chunk 183 optimal weight: 7.9990 overall best weight: 1.6384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 126 GLN D 343 GLN B 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 = 0.4159 r_free = 0.4159 target = 0.199684 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3419 r_free = 0.3419 target = 0.131419 restraints weight = 17217.079| |-----------------------------------------------------------------------------| r_work (start): 0.3370 rms_B_bonded: 1.33 r_work: 0.3174 rms_B_bonded: 2.07 restraints_weight: 0.5000 r_work: 0.3064 rms_B_bonded: 2.99 restraints_weight: 0.2500 r_work (final): 0.3064 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7968 moved from start: 0.1910 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 26124 Z= 0.153 Angle : 0.650 8.368 35424 Z= 0.335 Chirality : 0.048 0.205 4002 Planarity : 0.004 0.036 4494 Dihedral : 6.988 59.949 3534 Min Nonbonded Distance : 2.301 Molprobity Statistics. All-atom Clashscore : 6.14 Ramachandran Plot: Outliers : 0.19 % Allowed : 4.23 % Favored : 95.58 % Rotamer: Outliers : 1.80 % Allowed : 8.77 % Favored : 89.43 % 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: -0.12 (0.15), residues: 3168 helix: 0.86 (0.16), residues: 1104 sheet: -0.47 (0.21), residues: 576 loop : -0.55 (0.16), residues: 1488 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP C 402 HIS 0.005 0.001 HIS E 39 PHE 0.020 0.002 PHE C 81 TYR 0.022 0.002 TYR A 245 ARG 0.003 0.000 ARG B 47 Details of bonding type rmsd hydrogen bonds : bond 0.05531 ( 948) hydrogen bonds : angle 6.02659 ( 2682) covalent geometry : bond 0.00310 (26118) covalent geometry : angle 0.64968 (35424) Misc. bond : bond 0.00254 ( 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 363 residues out of total 2790 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 313 time to evaluate : 2.627 Fit side-chains REVERT: A 61 LYS cc_start: 0.8087 (mtmm) cc_final: 0.7387 (mmtm) REVERT: A 112 ASP cc_start: 0.8448 (m-30) cc_final: 0.8165 (m-30) REVERT: A 158 GLU cc_start: 0.8099 (mm-30) cc_final: 0.7777 (mp0) REVERT: A 197 MET cc_start: 0.8914 (mmp) cc_final: 0.8132 (mtp) REVERT: A 256 ASN cc_start: 0.7945 (t0) cc_final: 0.7693 (t0) REVERT: A 335 GLU cc_start: 0.6607 (mp0) cc_final: 0.6055 (tm-30) REVERT: A 343 GLN cc_start: 0.7734 (mt0) cc_final: 0.7449 (mt0) REVERT: A 366 ASP cc_start: 0.6913 (m-30) cc_final: 0.6694 (m-30) REVERT: A 375 GLU cc_start: 0.7143 (pt0) cc_final: 0.6810 (pm20) REVERT: A 399 LYS cc_start: 0.7987 (ttmm) cc_final: 0.7324 (tmmt) REVERT: D 42 LYS cc_start: 0.8382 (ttpp) cc_final: 0.8165 (ttpp) REVERT: D 61 LYS cc_start: 0.8163 (mtmm) cc_final: 0.7486 (mmtm) REVERT: D 89 LYS cc_start: 0.8759 (mtpt) cc_final: 0.8513 (ttmm) REVERT: D 100 GLU cc_start: 0.7913 (tp30) cc_final: 0.7187 (mp0) REVERT: D 158 GLU cc_start: 0.8079 (mm-30) cc_final: 0.7504 (tm-30) REVERT: D 197 MET cc_start: 0.8860 (mmp) cc_final: 0.8008 (mtp) REVERT: D 285 MET cc_start: 0.7520 (mtp) cc_final: 0.7260 (mtp) REVERT: D 335 GLU cc_start: 0.6722 (mp0) cc_final: 0.6224 (tm-30) REVERT: D 338 GLU cc_start: 0.7055 (mt-10) cc_final: 0.6125 (mm-30) REVERT: D 346 GLU cc_start: 0.7732 (tp30) cc_final: 0.7452 (tp30) REVERT: D 375 GLU cc_start: 0.7106 (pt0) cc_final: 0.6731 (pm20) REVERT: D 399 LYS cc_start: 0.7993 (ttmm) cc_final: 0.7424 (tmmt) REVERT: B 61 LYS cc_start: 0.8098 (mtmm) cc_final: 0.7396 (mmtm) REVERT: B 112 ASP cc_start: 0.8462 (m-30) cc_final: 0.8181 (m-30) REVERT: B 158 GLU cc_start: 0.8099 (mm-30) cc_final: 0.7779 (mp0) REVERT: B 197 MET cc_start: 0.8912 (mmp) cc_final: 0.8128 (mtp) REVERT: B 256 ASN cc_start: 0.7952 (t0) cc_final: 0.7696 (t0) REVERT: B 335 GLU cc_start: 0.6598 (mp0) cc_final: 0.6049 (tm-30) REVERT: B 343 GLN cc_start: 0.7737 (mt0) cc_final: 0.7437 (mt0) REVERT: B 366 ASP cc_start: 0.6901 (m-30) cc_final: 0.6685 (m-30) REVERT: B 375 GLU cc_start: 0.7138 (pt0) cc_final: 0.6806 (pm20) REVERT: B 399 LYS cc_start: 0.7999 (ttmm) cc_final: 0.7332 (tmmt) REVERT: C 42 LYS cc_start: 0.8260 (tmtp) cc_final: 0.7890 (ttpp) REVERT: C 61 LYS cc_start: 0.8253 (mtmm) cc_final: 0.7499 (mmtm) REVERT: C 100 GLU cc_start: 0.7884 (tp30) cc_final: 0.7141 (mp0) REVERT: C 133 THR cc_start: 0.6386 (OUTLIER) cc_final: 0.6114 (t) REVERT: C 145 GLU cc_start: 0.6769 (mm-30) cc_final: 0.6391 (mp0) REVERT: C 150 ARG cc_start: 0.7211 (mtm110) cc_final: 0.6775 (mtm110) REVERT: C 158 GLU cc_start: 0.8103 (mm-30) cc_final: 0.7823 (mp0) REVERT: C 197 MET cc_start: 0.8944 (mmp) cc_final: 0.8151 (mtp) REVERT: C 274 HIS cc_start: 0.8139 (t70) cc_final: 0.7933 (t70) REVERT: C 335 GLU cc_start: 0.6648 (mp0) cc_final: 0.6115 (tm-30) REVERT: C 338 GLU cc_start: 0.6938 (mt-10) cc_final: 0.6201 (mm-30) REVERT: C 343 GLN cc_start: 0.7452 (mt0) cc_final: 0.6994 (mt0) REVERT: C 366 ASP cc_start: 0.6499 (OUTLIER) cc_final: 0.6279 (m-30) REVERT: C 375 GLU cc_start: 0.7074 (pt0) cc_final: 0.6684 (pm20) REVERT: C 399 LYS cc_start: 0.7958 (ttmm) cc_final: 0.7220 (tmmt) REVERT: E 42 LYS cc_start: 0.8380 (ttpp) cc_final: 0.8163 (ttpp) REVERT: E 61 LYS cc_start: 0.8143 (mtmm) cc_final: 0.7464 (mmtm) REVERT: E 100 GLU cc_start: 0.7907 (tp30) cc_final: 0.7186 (mp0) REVERT: E 158 GLU cc_start: 0.8073 (mm-30) cc_final: 0.7508 (tm-30) REVERT: E 197 MET cc_start: 0.8866 (mmp) cc_final: 0.8013 (mtp) REVERT: E 248 LYS cc_start: 0.8306 (tttm) cc_final: 0.8080 (tttm) REVERT: E 285 MET cc_start: 0.7534 (mtp) cc_final: 0.7256 (mtp) REVERT: E 335 GLU cc_start: 0.6743 (mp0) cc_final: 0.6241 (tm-30) REVERT: E 338 GLU cc_start: 0.7063 (mt-10) cc_final: 0.6104 (mm-30) REVERT: E 346 GLU cc_start: 0.7746 (tp30) cc_final: 0.7437 (tp30) REVERT: E 375 GLU cc_start: 0.7108 (pt0) cc_final: 0.6731 (pm20) REVERT: E 399 LYS cc_start: 0.8000 (ttmm) cc_final: 0.7432 (tmmt) REVERT: F 42 LYS cc_start: 0.8266 (tmtp) cc_final: 0.7898 (ttpp) REVERT: F 61 LYS cc_start: 0.8243 (mtmm) cc_final: 0.7492 (mmtm) REVERT: F 100 GLU cc_start: 0.7881 (tp30) cc_final: 0.7140 (mp0) REVERT: F 133 THR cc_start: 0.6376 (OUTLIER) cc_final: 0.6102 (t) REVERT: F 145 GLU cc_start: 0.6776 (mm-30) cc_final: 0.6416 (mp0) REVERT: F 150 ARG cc_start: 0.7237 (mtm110) cc_final: 0.6807 (mtm110) REVERT: F 158 GLU cc_start: 0.8142 (mm-30) cc_final: 0.7871 (mp0) REVERT: F 197 MET cc_start: 0.8954 (mmp) cc_final: 0.8158 (mtp) REVERT: F 283 LYS cc_start: 0.7460 (mmtm) cc_final: 0.7100 (mppt) REVERT: F 335 GLU cc_start: 0.6636 (mp0) cc_final: 0.6100 (tm-30) REVERT: F 338 GLU cc_start: 0.6930 (mt-10) cc_final: 0.6188 (mm-30) REVERT: F 343 GLN cc_start: 0.7434 (mt0) cc_final: 0.6978 (mt0) REVERT: F 375 GLU cc_start: 0.7086 (pt0) cc_final: 0.6703 (pm20) REVERT: F 399 LYS cc_start: 0.7959 (ttmm) cc_final: 0.7221 (tmmt) outliers start: 50 outliers final: 38 residues processed: 351 average time/residue: 1.5690 time to fit residues: 629.2363 Evaluate side-chains 346 residues out of total 2790 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 305 time to evaluate : 3.053 ------------------------------------------------------------------------------- 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 306 SER 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 306 SER Chi-restraints excluded: chain E residue 459 ILE Chi-restraints excluded: chain E residue 461 MET Chi-restraints excluded: chain F residue 118 GLU 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=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 318 random chunks: chunk 303 optimal weight: 2.9990 chunk 67 optimal weight: 10.0000 chunk 217 optimal weight: 4.9990 chunk 183 optimal weight: 3.9990 chunk 131 optimal weight: 6.9990 chunk 244 optimal weight: 2.9990 chunk 0 optimal weight: 10.0000 chunk 216 optimal weight: 1.9990 chunk 40 optimal weight: 1.9990 chunk 234 optimal weight: 2.9990 chunk 286 optimal weight: 6.9990 overall best weight: 2.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4146 r_free = 0.4146 target = 0.198191 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3396 r_free = 0.3396 target = 0.129173 restraints weight = 17064.241| |-----------------------------------------------------------------------------| r_work (start): 0.3351 rms_B_bonded: 1.42 r_work: 0.3111 rms_B_bonded: 2.36 restraints_weight: 0.5000 r_work: 0.3002 rms_B_bonded: 3.42 restraints_weight: 0.2500 r_work (final): 0.3002 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8072 moved from start: 0.2094 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 26124 Z= 0.198 Angle : 0.711 8.849 35424 Z= 0.365 Chirality : 0.050 0.225 4002 Planarity : 0.005 0.037 4494 Dihedral : 7.316 59.111 3534 Min Nonbonded Distance : 2.294 Molprobity Statistics. All-atom Clashscore : 6.20 Ramachandran Plot: Outliers : 0.19 % Allowed : 4.36 % Favored : 95.45 % Rotamer: Outliers : 1.77 % Allowed : 9.05 % Favored : 89.18 % 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 (0.15), residues: 3168 helix: 0.71 (0.15), residues: 1104 sheet: -0.58 (0.21), residues: 576 loop : -0.55 (0.16), residues: 1488 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP B 402 HIS 0.005 0.001 HIS D 39 PHE 0.024 0.002 PHE F 81 TYR 0.025 0.002 TYR A 245 ARG 0.004 0.001 ARG A 47 Details of bonding type rmsd hydrogen bonds : bond 0.06234 ( 948) hydrogen bonds : angle 6.20170 ( 2682) covalent geometry : bond 0.00411 (26118) covalent geometry : angle 0.71131 (35424) Misc. bond : bond 0.00397 ( 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 358 residues out of total 2790 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 309 time to evaluate : 2.999 Fit side-chains REVERT: A 61 LYS cc_start: 0.8189 (mtmm) cc_final: 0.7453 (mmtm) REVERT: A 158 GLU cc_start: 0.8204 (mm-30) cc_final: 0.7897 (mp0) REVERT: A 197 MET cc_start: 0.8975 (mmp) cc_final: 0.8216 (mtp) REVERT: A 256 ASN cc_start: 0.8044 (t0) cc_final: 0.7792 (t0) REVERT: A 335 GLU cc_start: 0.6682 (mp0) cc_final: 0.6062 (tm-30) REVERT: A 343 GLN cc_start: 0.7819 (mt0) cc_final: 0.7535 (mt0) REVERT: A 366 ASP cc_start: 0.7006 (m-30) cc_final: 0.6792 (m-30) REVERT: A 375 GLU cc_start: 0.7225 (pt0) cc_final: 0.6900 (pm20) REVERT: A 399 LYS cc_start: 0.8188 (ttmm) cc_final: 0.7488 (tmmt) REVERT: D 61 LYS cc_start: 0.8194 (mtmm) cc_final: 0.7555 (mmtm) REVERT: D 89 LYS cc_start: 0.8834 (mtpt) cc_final: 0.8626 (mttt) REVERT: D 100 GLU cc_start: 0.8076 (tp30) cc_final: 0.7310 (mp0) REVERT: D 158 GLU cc_start: 0.8191 (mm-30) cc_final: 0.7507 (tm-30) REVERT: D 197 MET cc_start: 0.8933 (mmp) cc_final: 0.8153 (mtp) REVERT: D 262 LYS cc_start: 0.8254 (mmtm) cc_final: 0.8017 (mmmt) REVERT: D 285 MET cc_start: 0.7618 (mtp) cc_final: 0.7262 (mtp) REVERT: D 335 GLU cc_start: 0.6721 (mp0) cc_final: 0.6263 (tm-30) REVERT: D 338 GLU cc_start: 0.7054 (mt-10) cc_final: 0.6090 (mm-30) REVERT: D 346 GLU cc_start: 0.7807 (tp30) cc_final: 0.7527 (tp30) REVERT: D 366 ASP cc_start: 0.6841 (OUTLIER) cc_final: 0.6590 (m-30) REVERT: D 399 LYS cc_start: 0.8101 (ttmm) cc_final: 0.7554 (tmmt) REVERT: B 61 LYS cc_start: 0.8206 (mtmm) cc_final: 0.7460 (mmtm) REVERT: B 158 GLU cc_start: 0.8216 (mm-30) cc_final: 0.7901 (mp0) REVERT: B 197 MET cc_start: 0.8970 (mmp) cc_final: 0.8205 (mtp) REVERT: B 256 ASN cc_start: 0.8045 (t0) cc_final: 0.7793 (t0) REVERT: B 335 GLU cc_start: 0.6695 (mp0) cc_final: 0.6086 (tm-30) REVERT: B 343 GLN cc_start: 0.7821 (mt0) cc_final: 0.7496 (mt0) REVERT: B 366 ASP cc_start: 0.6998 (m-30) cc_final: 0.6783 (m-30) REVERT: B 375 GLU cc_start: 0.7214 (pt0) cc_final: 0.6893 (pm20) REVERT: B 399 LYS cc_start: 0.8211 (ttmm) cc_final: 0.7505 (tmmt) REVERT: C 42 LYS cc_start: 0.8409 (tmtp) cc_final: 0.8038 (ttpp) REVERT: C 61 LYS cc_start: 0.8295 (mtmm) cc_final: 0.7541 (mmtm) REVERT: C 100 GLU cc_start: 0.8032 (tp30) cc_final: 0.7267 (mp0) REVERT: C 133 THR cc_start: 0.6688 (OUTLIER) cc_final: 0.6400 (t) REVERT: C 150 ARG cc_start: 0.7376 (mtm110) cc_final: 0.6965 (mtm110) REVERT: C 158 GLU cc_start: 0.8138 (mm-30) cc_final: 0.7889 (mp0) REVERT: C 197 MET cc_start: 0.9039 (mmp) cc_final: 0.8267 (mtp) REVERT: C 274 HIS cc_start: 0.8188 (t70) cc_final: 0.7961 (t70) REVERT: C 283 LYS cc_start: 0.7440 (mmtm) cc_final: 0.7082 (mppt) REVERT: C 335 GLU cc_start: 0.6782 (mp0) cc_final: 0.6159 (tm-30) REVERT: C 338 GLU cc_start: 0.6946 (mt-10) cc_final: 0.6173 (mm-30) REVERT: C 343 GLN cc_start: 0.7544 (mt0) cc_final: 0.7107 (mt0) REVERT: C 375 GLU cc_start: 0.7082 (pt0) cc_final: 0.6712 (pm20) REVERT: C 399 LYS cc_start: 0.8049 (ttmm) cc_final: 0.7320 (tmmt) REVERT: E 61 LYS cc_start: 0.8202 (mtmm) cc_final: 0.7500 (mmtt) REVERT: E 100 GLU cc_start: 0.8057 (tp30) cc_final: 0.7290 (mp0) REVERT: E 158 GLU cc_start: 0.8184 (mm-30) cc_final: 0.7511 (tm-30) REVERT: E 197 MET cc_start: 0.8938 (mmp) cc_final: 0.8154 (mtp) REVERT: E 262 LYS cc_start: 0.8289 (mmtm) cc_final: 0.8048 (mmmt) REVERT: E 285 MET cc_start: 0.7573 (mtp) cc_final: 0.7214 (mtp) REVERT: E 335 GLU cc_start: 0.6743 (mp0) cc_final: 0.6227 (tm-30) REVERT: E 338 GLU cc_start: 0.7045 (mt-10) cc_final: 0.6086 (mm-30) REVERT: E 346 GLU cc_start: 0.7869 (tp30) cc_final: 0.7598 (tp30) REVERT: E 399 LYS cc_start: 0.8083 (ttmm) cc_final: 0.7512 (tmmt) REVERT: F 42 LYS cc_start: 0.8405 (tmtp) cc_final: 0.8034 (ttpp) REVERT: F 61 LYS cc_start: 0.8287 (mtmm) cc_final: 0.7535 (mmtm) REVERT: F 100 GLU cc_start: 0.8026 (tp30) cc_final: 0.7264 (mp0) REVERT: F 133 THR cc_start: 0.6686 (OUTLIER) cc_final: 0.6399 (t) REVERT: F 150 ARG cc_start: 0.7365 (mtm110) cc_final: 0.6953 (mtm110) REVERT: F 158 GLU cc_start: 0.8157 (mm-30) cc_final: 0.7893 (mp0) REVERT: F 197 MET cc_start: 0.9042 (mmp) cc_final: 0.8266 (mtp) REVERT: F 283 LYS cc_start: 0.7452 (mmtm) cc_final: 0.7097 (mppt) REVERT: F 335 GLU cc_start: 0.6794 (mp0) cc_final: 0.6165 (tm-30) REVERT: F 338 GLU cc_start: 0.6962 (mt-10) cc_final: 0.6183 (mm-30) REVERT: F 343 GLN cc_start: 0.7535 (mt0) cc_final: 0.7097 (mt0) REVERT: F 375 GLU cc_start: 0.7139 (pt0) cc_final: 0.6765 (pm20) REVERT: F 399 LYS cc_start: 0.8053 (ttmm) cc_final: 0.7315 (tmmt) outliers start: 49 outliers final: 37 residues processed: 346 average time/residue: 1.5513 time to fit residues: 611.9488 Evaluate side-chains 347 residues out of total 2790 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 307 time to evaluate : 2.617 ------------------------------------------------------------------------------- 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 366 ASP 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 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 459 ILE Chi-restraints excluded: chain E residue 461 MET Chi-restraints excluded: chain F residue 118 GLU 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 318 random chunks: chunk 167 optimal weight: 0.9990 chunk 223 optimal weight: 4.9990 chunk 41 optimal weight: 0.8980 chunk 86 optimal weight: 6.9990 chunk 289 optimal weight: 0.4980 chunk 15 optimal weight: 0.7980 chunk 221 optimal weight: 0.4980 chunk 282 optimal weight: 0.8980 chunk 62 optimal weight: 0.9990 chunk 124 optimal weight: 0.6980 chunk 165 optimal weight: 7.9990 overall best weight: 0.6780 ------------------------------------------------------------------------------- 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 154 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4243 r_free = 0.4243 target = 0.206841 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3833 r_free = 0.3833 target = 0.164354 restraints weight = 17329.488| |-----------------------------------------------------------------------------| r_work (start): 0.3817 rms_B_bonded: 0.80 r_work: 0.3452 rms_B_bonded: 1.91 restraints_weight: 0.5000 r_work: 0.3220 rms_B_bonded: 4.77 restraints_weight: 0.2500 r_work (final): 0.3220 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8153 moved from start: 0.2023 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 26124 Z= 0.113 Angle : 0.587 7.678 35424 Z= 0.303 Chirality : 0.045 0.180 4002 Planarity : 0.004 0.036 4494 Dihedral : 6.594 59.116 3534 Min Nonbonded Distance : 2.397 Molprobity Statistics. All-atom Clashscore : 5.82 Ramachandran Plot: Outliers : 0.19 % Allowed : 4.04 % Favored : 95.77 % Rotamer: Outliers : 1.55 % Allowed : 9.60 % Favored : 88.85 % 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: -0.02 (0.15), residues: 3168 helix: 0.93 (0.16), residues: 1122 sheet: -0.34 (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 E 402 HIS 0.003 0.001 HIS D 39 PHE 0.018 0.001 PHE C 81 TYR 0.013 0.001 TYR A 245 ARG 0.002 0.000 ARG B 47 Details of bonding type rmsd hydrogen bonds : bond 0.04503 ( 948) hydrogen bonds : angle 5.67008 ( 2682) covalent geometry : bond 0.00224 (26118) covalent geometry : angle 0.58669 (35424) Misc. bond : bond 0.00132 ( 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 357 residues out of total 2790 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 314 time to evaluate : 2.866 Fit side-chains REVERT: A 61 LYS cc_start: 0.8328 (mtmm) cc_final: 0.7703 (mmtm) REVERT: A 112 ASP cc_start: 0.8657 (m-30) cc_final: 0.8381 (m-30) REVERT: A 197 MET cc_start: 0.9041 (mmp) cc_final: 0.8424 (mtp) REVERT: A 335 GLU cc_start: 0.7000 (mp0) cc_final: 0.6544 (tm-30) REVERT: A 343 GLN cc_start: 0.8125 (mt0) cc_final: 0.7852 (mt0) REVERT: A 399 LYS cc_start: 0.8426 (ttmm) cc_final: 0.7838 (tmmt) REVERT: D 61 LYS cc_start: 0.8486 (mtmm) cc_final: 0.7876 (mmtm) REVERT: D 89 LYS cc_start: 0.8928 (mtpt) cc_final: 0.8688 (ttmm) REVERT: D 100 GLU cc_start: 0.8477 (tp30) cc_final: 0.7781 (mp0) REVERT: D 158 GLU cc_start: 0.8423 (mm-30) cc_final: 0.7810 (tm-30) REVERT: D 197 MET cc_start: 0.8989 (mmp) cc_final: 0.8305 (mtp) REVERT: D 285 MET cc_start: 0.7680 (mtp) cc_final: 0.7315 (mtp) REVERT: D 335 GLU cc_start: 0.7124 (mp0) cc_final: 0.6670 (tm-30) REVERT: D 338 GLU cc_start: 0.7362 (mt-10) cc_final: 0.6456 (mm-30) REVERT: D 346 GLU cc_start: 0.8428 (tp30) cc_final: 0.8177 (tp30) REVERT: D 399 LYS cc_start: 0.8274 (ttmm) cc_final: 0.7844 (tmmt) REVERT: D 461 MET cc_start: 0.2289 (OUTLIER) cc_final: 0.1923 (mpp) REVERT: B 61 LYS cc_start: 0.8350 (mtmm) cc_final: 0.7706 (mmtm) REVERT: B 112 ASP cc_start: 0.8660 (m-30) cc_final: 0.8372 (m-30) REVERT: B 197 MET cc_start: 0.9037 (mmp) cc_final: 0.8420 (mtp) REVERT: B 248 LYS cc_start: 0.8594 (tttm) cc_final: 0.8351 (tttp) REVERT: B 335 GLU cc_start: 0.7025 (mp0) cc_final: 0.6541 (tm-30) REVERT: B 343 GLN cc_start: 0.8129 (mt0) cc_final: 0.7857 (mt0) REVERT: B 399 LYS cc_start: 0.8434 (ttmm) cc_final: 0.7852 (tmmt) REVERT: C 61 LYS cc_start: 0.8476 (mtmm) cc_final: 0.7830 (mmtm) REVERT: C 100 GLU cc_start: 0.8434 (tp30) cc_final: 0.7772 (mp0) REVERT: C 133 THR cc_start: 0.6526 (OUTLIER) cc_final: 0.6313 (t) REVERT: C 150 ARG cc_start: 0.7786 (mtm110) cc_final: 0.7522 (mtm110) REVERT: C 197 MET cc_start: 0.9090 (mmp) cc_final: 0.8429 (mtp) REVERT: C 262 LYS cc_start: 0.8270 (mmtp) cc_final: 0.8038 (mmmm) REVERT: C 283 LYS cc_start: 0.7597 (mmtm) cc_final: 0.7267 (mppt) REVERT: C 335 GLU cc_start: 0.6932 (mp0) cc_final: 0.6390 (tm-30) REVERT: C 338 GLU cc_start: 0.7247 (mt-10) cc_final: 0.6465 (mm-30) REVERT: C 343 GLN cc_start: 0.7875 (mt0) cc_final: 0.7561 (mt0) REVERT: C 344 GLN cc_start: 0.8557 (mt0) cc_final: 0.8184 (mt0) REVERT: C 365 GLU cc_start: 0.7181 (mp0) cc_final: 0.6523 (mp0) REVERT: C 375 GLU cc_start: 0.7256 (pt0) cc_final: 0.6909 (pm20) REVERT: C 399 LYS cc_start: 0.8267 (ttmm) cc_final: 0.7677 (tmmt) REVERT: C 461 MET cc_start: 0.2476 (OUTLIER) cc_final: 0.1678 (mtt) REVERT: E 61 LYS cc_start: 0.8485 (mtmm) cc_final: 0.7883 (mmtm) REVERT: E 100 GLU cc_start: 0.8478 (tp30) cc_final: 0.7778 (mp0) REVERT: E 158 GLU cc_start: 0.8411 (mm-30) cc_final: 0.7842 (tm-30) REVERT: E 197 MET cc_start: 0.9004 (mmp) cc_final: 0.8320 (mtp) REVERT: E 278 SER cc_start: 0.8262 (m) cc_final: 0.8061 (p) REVERT: E 285 MET cc_start: 0.7694 (mtp) cc_final: 0.7326 (mtp) REVERT: E 335 GLU cc_start: 0.7112 (mp0) cc_final: 0.6626 (tm-30) REVERT: E 338 GLU cc_start: 0.7359 (mt-10) cc_final: 0.6461 (mm-30) REVERT: E 346 GLU cc_start: 0.8317 (tp30) cc_final: 0.8090 (tp30) REVERT: E 399 LYS cc_start: 0.8284 (ttmm) cc_final: 0.7832 (tmmt) REVERT: E 461 MET cc_start: 0.2291 (OUTLIER) cc_final: 0.1904 (mpp) REVERT: F 61 LYS cc_start: 0.8468 (mtmm) cc_final: 0.7837 (mmtm) REVERT: F 100 GLU cc_start: 0.8437 (tp30) cc_final: 0.7773 (mp0) REVERT: F 133 THR cc_start: 0.6518 (OUTLIER) cc_final: 0.6305 (t) REVERT: F 150 ARG cc_start: 0.7756 (mtm110) cc_final: 0.7489 (mtm110) REVERT: F 197 MET cc_start: 0.9091 (mmp) cc_final: 0.8429 (mtp) REVERT: F 262 LYS cc_start: 0.8268 (mmtp) cc_final: 0.8035 (mmmm) REVERT: F 283 LYS cc_start: 0.7700 (mmtm) cc_final: 0.7365 (mppt) REVERT: F 335 GLU cc_start: 0.6905 (mp0) cc_final: 0.6366 (tm-30) REVERT: F 338 GLU cc_start: 0.7316 (mt-10) cc_final: 0.6576 (mm-30) REVERT: F 343 GLN cc_start: 0.7862 (mt0) cc_final: 0.7544 (mt0) REVERT: F 344 GLN cc_start: 0.8549 (mt0) cc_final: 0.8175 (mt0) REVERT: F 365 GLU cc_start: 0.7123 (mp0) cc_final: 0.6438 (mp0) REVERT: F 375 GLU cc_start: 0.7251 (pt0) cc_final: 0.6910 (pm20) REVERT: F 399 LYS cc_start: 0.8279 (ttmm) cc_final: 0.7681 (tmmt) REVERT: F 461 MET cc_start: 0.2553 (OUTLIER) cc_final: 0.1727 (mtt) outliers start: 43 outliers final: 23 residues processed: 349 average time/residue: 1.5659 time to fit residues: 632.4169 Evaluate side-chains 328 residues out of total 2790 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 299 time to evaluate : 2.885 ------------------------------------------------------------------------------- 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 306 SER Chi-restraints excluded: chain D residue 459 ILE Chi-restraints excluded: chain D residue 461 MET 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 133 THR Chi-restraints excluded: chain C residue 227 VAL 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 133 THR Chi-restraints excluded: chain E residue 227 VAL Chi-restraints excluded: chain E residue 306 SER 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 227 VAL 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: 0.9980 chunk 27 optimal weight: 9.9990 chunk 193 optimal weight: 10.0000 chunk 61 optimal weight: 0.6980 chunk 185 optimal weight: 7.9990 chunk 230 optimal weight: 7.9990 chunk 54 optimal weight: 0.6980 chunk 105 optimal weight: 7.9990 chunk 226 optimal weight: 9.9990 chunk 1 optimal weight: 0.6980 chunk 43 optimal weight: 10.0000 overall best weight: 2.2182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4215 r_free = 0.4215 target = 0.203550 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3796 r_free = 0.3796 target = 0.160749 restraints weight = 17131.560| |-----------------------------------------------------------------------------| r_work (start): 0.3782 rms_B_bonded: 0.81 r_work: 0.3401 rms_B_bonded: 2.00 restraints_weight: 0.5000 r_work: 0.3203 rms_B_bonded: 4.85 restraints_weight: 0.2500 r_work (final): 0.3203 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8210 moved from start: 0.2160 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.030 26124 Z= 0.178 Angle : 0.677 8.494 35424 Z= 0.347 Chirality : 0.049 0.220 4002 Planarity : 0.004 0.037 4494 Dihedral : 7.051 59.502 3534 Min Nonbonded Distance : 2.320 Molprobity Statistics. All-atom Clashscore : 6.08 Ramachandran Plot: Outliers : 0.19 % Allowed : 4.48 % Favored : 95.33 % Rotamer: Outliers : 1.80 % Allowed : 9.92 % 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: -0.08 (0.15), residues: 3168 helix: 0.87 (0.16), residues: 1104 sheet: -0.42 (0.21), residues: 546 loop : -0.52 (0.16), residues: 1518 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP C 402 HIS 0.005 0.001 HIS E 39 PHE 0.022 0.002 PHE F 81 TYR 0.022 0.002 TYR A 245 ARG 0.003 0.000 ARG B 47 Details of bonding type rmsd hydrogen bonds : bond 0.05822 ( 948) hydrogen bonds : angle 5.99745 ( 2682) covalent geometry : bond 0.00368 (26118) covalent geometry : angle 0.67663 (35424) Misc. bond : bond 0.00353 ( 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 360 residues out of total 2790 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 310 time to evaluate : 4.052 Fit side-chains REVERT: A 61 LYS cc_start: 0.8493 (mtmm) cc_final: 0.8030 (mmtm) REVERT: A 197 MET cc_start: 0.9066 (mmp) cc_final: 0.8487 (mtp) REVERT: A 335 GLU cc_start: 0.7115 (mp0) cc_final: 0.6814 (tm-30) REVERT: A 343 GLN cc_start: 0.8261 (mt0) cc_final: 0.8060 (mt0) REVERT: A 366 ASP cc_start: 0.7616 (OUTLIER) cc_final: 0.7299 (m-30) REVERT: A 399 LYS cc_start: 0.8515 (ttmm) cc_final: 0.8079 (tmmt) REVERT: D 61 LYS cc_start: 0.8507 (mtmm) cc_final: 0.8070 (mmtm) REVERT: D 89 LYS cc_start: 0.8920 (mtpt) cc_final: 0.8671 (ttmm) REVERT: D 100 GLU cc_start: 0.8556 (tp30) cc_final: 0.7983 (mp0) REVERT: D 158 GLU cc_start: 0.8479 (mm-30) cc_final: 0.7998 (tm-30) REVERT: D 197 MET cc_start: 0.9061 (mmp) cc_final: 0.8468 (mtp) REVERT: D 285 MET cc_start: 0.7855 (mtp) cc_final: 0.7568 (mtp) REVERT: D 338 GLU cc_start: 0.7475 (mt-10) cc_final: 0.6723 (mm-30) REVERT: D 366 ASP cc_start: 0.7391 (OUTLIER) cc_final: 0.7133 (m-30) REVERT: D 399 LYS cc_start: 0.8335 (ttmm) cc_final: 0.8045 (tmmt) REVERT: D 461 MET cc_start: 0.2195 (OUTLIER) cc_final: 0.1865 (mpp) REVERT: B 61 LYS cc_start: 0.8500 (mtmm) cc_final: 0.8048 (mmtm) REVERT: B 197 MET cc_start: 0.9074 (mmp) cc_final: 0.8490 (mtp) REVERT: B 335 GLU cc_start: 0.7112 (mp0) cc_final: 0.6821 (tm-30) REVERT: B 343 GLN cc_start: 0.8259 (mt0) cc_final: 0.8050 (mt0) REVERT: B 366 ASP cc_start: 0.7609 (OUTLIER) cc_final: 0.7289 (m-30) REVERT: B 399 LYS cc_start: 0.8518 (ttmm) cc_final: 0.8087 (tmmt) REVERT: C 42 LYS cc_start: 0.8679 (tmtp) cc_final: 0.8478 (ttpp) REVERT: C 61 LYS cc_start: 0.8511 (mtmm) cc_final: 0.8016 (mmtm) REVERT: C 100 GLU cc_start: 0.8511 (tp30) cc_final: 0.7960 (mp0) REVERT: C 133 THR cc_start: 0.7115 (OUTLIER) cc_final: 0.6906 (t) REVERT: C 150 ARG cc_start: 0.7930 (mtm110) cc_final: 0.7704 (mtm110) REVERT: C 197 MET cc_start: 0.9174 (mmp) cc_final: 0.8559 (mtp) REVERT: C 283 LYS cc_start: 0.7925 (mmtm) cc_final: 0.7639 (mppt) REVERT: C 335 GLU cc_start: 0.7108 (mp0) cc_final: 0.6799 (tm-30) REVERT: C 338 GLU cc_start: 0.7383 (mt-10) cc_final: 0.6791 (mm-30) REVERT: C 343 GLN cc_start: 0.8076 (mt0) cc_final: 0.7819 (mt0) REVERT: C 375 GLU cc_start: 0.7409 (pt0) cc_final: 0.7157 (pm20) REVERT: C 399 LYS cc_start: 0.8405 (ttmm) cc_final: 0.7971 (tmmt) REVERT: E 61 LYS cc_start: 0.8493 (mtmm) cc_final: 0.8091 (mmtm) REVERT: E 100 GLU cc_start: 0.8563 (tp30) cc_final: 0.7982 (mp0) REVERT: E 158 GLU cc_start: 0.8469 (mm-30) cc_final: 0.7990 (tm-30) REVERT: E 197 MET cc_start: 0.9062 (mmp) cc_final: 0.8485 (mtp) REVERT: E 285 MET cc_start: 0.7865 (mtp) cc_final: 0.7574 (mtp) REVERT: E 335 GLU cc_start: 0.7122 (mp0) cc_final: 0.6909 (tm-30) REVERT: E 338 GLU cc_start: 0.7444 (mt-10) cc_final: 0.6697 (mm-30) REVERT: E 366 ASP cc_start: 0.7296 (OUTLIER) cc_final: 0.7035 (m-30) REVERT: E 399 LYS cc_start: 0.8335 (ttmm) cc_final: 0.8042 (tmmt) REVERT: F 61 LYS cc_start: 0.8486 (mtmm) cc_final: 0.8010 (mmtm) REVERT: F 100 GLU cc_start: 0.8507 (tp30) cc_final: 0.7967 (mp0) REVERT: F 133 THR cc_start: 0.7117 (OUTLIER) cc_final: 0.6906 (t) REVERT: F 150 ARG cc_start: 0.7912 (mtm110) cc_final: 0.7682 (mtm110) REVERT: F 197 MET cc_start: 0.9179 (mmp) cc_final: 0.8561 (mtp) REVERT: F 283 LYS cc_start: 0.7921 (mmtm) cc_final: 0.7635 (mppt) REVERT: F 335 GLU cc_start: 0.7110 (mp0) cc_final: 0.6808 (tm-30) REVERT: F 338 GLU cc_start: 0.7409 (mt-10) cc_final: 0.6817 (mm-30) REVERT: F 343 GLN cc_start: 0.8076 (mt0) cc_final: 0.7747 (mt0) REVERT: F 375 GLU cc_start: 0.7447 (pt0) cc_final: 0.7187 (pm20) REVERT: F 399 LYS cc_start: 0.8420 (ttmm) cc_final: 0.7982 (tmmt) REVERT: F 461 MET cc_start: 0.2201 (OUTLIER) cc_final: 0.1447 (mtt) outliers start: 50 outliers final: 38 residues processed: 346 average time/residue: 2.0600 time to fit residues: 811.8243 Evaluate side-chains 346 residues out of total 2790 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 300 time to evaluate : 2.883 ------------------------------------------------------------------------------- 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 133 THR 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 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 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 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 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 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: 10.0000 chunk 25 optimal weight: 3.9990 chunk 79 optimal weight: 8.9990 chunk 19 optimal weight: 1.9990 chunk 35 optimal weight: 3.9990 chunk 304 optimal weight: 4.9990 chunk 50 optimal weight: 2.9990 chunk 170 optimal weight: 8.9990 chunk 28 optimal weight: 4.9990 chunk 81 optimal weight: 5.9990 overall best weight: 3.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 448 HIS D 343 GLN C 126 GLN C 154 GLN C 160 ASN E 343 GLN F 126 GLN F 154 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4143 r_free = 0.4143 target = 0.197675 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 76)----------------| | r_work = 0.3353 r_free = 0.3353 target = 0.125642 restraints weight = 16973.101| |-----------------------------------------------------------------------------| r_work (start): 0.3306 rms_B_bonded: 1.34 r_work: 0.3134 rms_B_bonded: 2.05 restraints_weight: 0.5000 r_work: 0.3024 rms_B_bonded: 2.97 restraints_weight: 0.2500 r_work (final): 0.3024 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8010 moved from start: 0.2317 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= 0.236 Angle : 0.757 9.327 35424 Z= 0.388 Chirality : 0.052 0.236 4002 Planarity : 0.005 0.042 4494 Dihedral : 7.442 59.500 3534 Min Nonbonded Distance : 2.316 Molprobity Statistics. All-atom Clashscore : 6.63 Ramachandran Plot: Outliers : 0.19 % Allowed : 4.36 % Favored : 95.45 % Rotamer: Outliers : 2.02 % Allowed : 9.74 % Favored : 88.24 % 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: -0.27 (0.14), residues: 3168 helix: 0.65 (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 0.014 0.002 TRP A 402 HIS 0.006 0.002 HIS E 39 PHE 0.026 0.003 PHE F 81 TYR 0.027 0.003 TYR A 245 ARG 0.005 0.001 ARG B 47 Details of bonding type rmsd hydrogen bonds : bond 0.06633 ( 948) hydrogen bonds : angle 6.24159 ( 2682) covalent geometry : bond 0.00497 (26118) covalent geometry : angle 0.75663 (35424) Misc. bond : bond 0.00502 ( 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 353 residues out of total 2790 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 297 time to evaluate : 2.686 Fit side-chains REVERT: A 61 LYS cc_start: 0.8168 (mtmm) cc_final: 0.7441 (mmtm) REVERT: A 197 MET cc_start: 0.8912 (mmp) cc_final: 0.8127 (mtp) REVERT: A 335 GLU cc_start: 0.6759 (mp0) cc_final: 0.6118 (tm-30) REVERT: A 343 GLN cc_start: 0.7774 (mt0) cc_final: 0.7491 (mt0) REVERT: A 366 ASP cc_start: 0.6906 (OUTLIER) cc_final: 0.6585 (m-30) REVERT: A 375 GLU cc_start: 0.7122 (OUTLIER) cc_final: 0.6542 (pm20) REVERT: A 399 LYS cc_start: 0.8200 (ttmm) cc_final: 0.7490 (tmmt) REVERT: A 461 MET cc_start: 0.2588 (OUTLIER) cc_final: 0.1587 (mmm) REVERT: D 61 LYS cc_start: 0.8126 (mtmm) cc_final: 0.7520 (mmtm) REVERT: D 89 LYS cc_start: 0.8790 (mtpt) cc_final: 0.8580 (mttt) REVERT: D 100 GLU cc_start: 0.7979 (tp30) cc_final: 0.7220 (mp0) REVERT: D 158 GLU cc_start: 0.8111 (mm-30) cc_final: 0.7511 (tm-30) REVERT: D 197 MET cc_start: 0.8825 (mmp) cc_final: 0.8071 (mtp) REVERT: D 285 MET cc_start: 0.7601 (mtp) cc_final: 0.7236 (mtp) REVERT: D 338 GLU cc_start: 0.6987 (mt-10) cc_final: 0.6026 (mm-30) REVERT: D 366 ASP cc_start: 0.6808 (OUTLIER) cc_final: 0.6560 (m-30) REVERT: D 375 GLU cc_start: 0.7081 (pt0) cc_final: 0.6726 (pm20) REVERT: D 399 LYS cc_start: 0.8089 (ttmm) cc_final: 0.7508 (tmmt) REVERT: B 61 LYS cc_start: 0.8175 (mtmm) cc_final: 0.7439 (mmtm) REVERT: B 197 MET cc_start: 0.8909 (mmp) cc_final: 0.8120 (mtp) REVERT: B 248 LYS cc_start: 0.8307 (tttm) cc_final: 0.8093 (tttp) REVERT: B 335 GLU cc_start: 0.6773 (mp0) cc_final: 0.6130 (tm-30) REVERT: B 343 GLN cc_start: 0.7786 (mt0) cc_final: 0.7505 (mt0) REVERT: B 366 ASP cc_start: 0.6897 (OUTLIER) cc_final: 0.6574 (m-30) REVERT: B 375 GLU cc_start: 0.7115 (OUTLIER) cc_final: 0.6534 (pm20) REVERT: B 399 LYS cc_start: 0.8202 (ttmm) cc_final: 0.7489 (tmmt) REVERT: C 42 LYS cc_start: 0.8287 (tmtp) cc_final: 0.7931 (ttpp) REVERT: C 61 LYS cc_start: 0.8271 (mtmm) cc_final: 0.7516 (mmtm) REVERT: C 100 GLU cc_start: 0.7926 (tp30) cc_final: 0.7174 (mp0) REVERT: C 133 THR cc_start: 0.6757 (OUTLIER) cc_final: 0.6480 (t) REVERT: C 150 ARG cc_start: 0.7317 (mtm110) cc_final: 0.6887 (mtm110) REVERT: C 197 MET cc_start: 0.8968 (mmp) cc_final: 0.8197 (mtp) REVERT: C 283 LYS cc_start: 0.7445 (mmtm) cc_final: 0.7084 (mppt) REVERT: C 335 GLU cc_start: 0.6728 (mp0) cc_final: 0.6109 (tm-30) REVERT: C 338 GLU cc_start: 0.6937 (mt-10) cc_final: 0.6169 (mm-30) REVERT: C 343 GLN cc_start: 0.7485 (mt0) cc_final: 0.7062 (mt0) REVERT: C 366 ASP cc_start: 0.6602 (OUTLIER) cc_final: 0.6392 (m-30) REVERT: C 375 GLU cc_start: 0.7012 (pt0) cc_final: 0.6622 (pm20) REVERT: C 399 LYS cc_start: 0.8075 (ttmm) cc_final: 0.7308 (tmmt) REVERT: E 61 LYS cc_start: 0.8148 (mtmm) cc_final: 0.7475 (mmtt) REVERT: E 100 GLU cc_start: 0.7987 (tp30) cc_final: 0.7222 (mp0) REVERT: E 158 GLU cc_start: 0.8106 (mm-30) cc_final: 0.7517 (tm-30) REVERT: E 197 MET cc_start: 0.8833 (mmp) cc_final: 0.8079 (mtp) REVERT: E 285 MET cc_start: 0.7602 (mtp) cc_final: 0.7237 (mtp) REVERT: E 335 GLU cc_start: 0.6668 (mp0) cc_final: 0.6246 (tm-30) REVERT: E 338 GLU cc_start: 0.6985 (mt-10) cc_final: 0.6016 (mm-30) REVERT: E 366 ASP cc_start: 0.6703 (OUTLIER) cc_final: 0.6450 (m-30) REVERT: E 375 GLU cc_start: 0.7066 (pt0) cc_final: 0.6715 (pm20) REVERT: E 399 LYS cc_start: 0.8090 (ttmm) cc_final: 0.7514 (tmmt) REVERT: F 42 LYS cc_start: 0.8391 (ttpp) cc_final: 0.8133 (tmtm) REVERT: F 61 LYS cc_start: 0.8255 (mtmm) cc_final: 0.7497 (mmtm) REVERT: F 100 GLU cc_start: 0.7927 (tp30) cc_final: 0.7162 (mp0) REVERT: F 133 THR cc_start: 0.6752 (OUTLIER) cc_final: 0.6473 (t) REVERT: F 150 ARG cc_start: 0.7293 (mtm110) cc_final: 0.6859 (mtm110) REVERT: F 197 MET cc_start: 0.8977 (mmp) cc_final: 0.8188 (mtp) REVERT: F 283 LYS cc_start: 0.7436 (mmtm) cc_final: 0.7078 (mppt) REVERT: F 335 GLU cc_start: 0.6707 (mp0) cc_final: 0.6088 (tm-30) REVERT: F 338 GLU cc_start: 0.6875 (mt-10) cc_final: 0.6085 (mm-30) REVERT: F 343 GLN cc_start: 0.7484 (mt0) cc_final: 0.7051 (mt0) REVERT: F 375 GLU cc_start: 0.7020 (pt0) cc_final: 0.6631 (pm20) REVERT: F 399 LYS cc_start: 0.8097 (ttmm) cc_final: 0.7324 (tmmt) REVERT: F 461 MET cc_start: 0.2622 (OUTLIER) cc_final: 0.1855 (mmm) outliers start: 56 outliers final: 38 residues processed: 335 average time/residue: 1.5230 time to fit residues: 581.8485 Evaluate side-chains 345 residues out of total 2790 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 296 time to evaluate : 3.099 ------------------------------------------------------------------------------- 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 375 GLU 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 133 THR 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 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 375 GLU 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 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 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 F residue 118 GLU 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 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: 5.9990 chunk 52 optimal weight: 5.9990 chunk 291 optimal weight: 4.9990 chunk 304 optimal weight: 6.9990 chunk 284 optimal weight: 1.9990 chunk 307 optimal weight: 0.4980 chunk 262 optimal weight: 10.0000 chunk 191 optimal weight: 1.9990 chunk 35 optimal weight: 1.9990 chunk 20 optimal weight: 5.9990 chunk 207 optimal weight: 0.7980 overall best weight: 1.4586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 343 GLN C 160 ASN E 154 GLN E 343 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4161 r_free = 0.4161 target = 0.199748 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 66)----------------| | r_work = 0.3440 r_free = 0.3440 target = 0.133061 restraints weight = 17243.242| |-----------------------------------------------------------------------------| r_work (start): 0.3406 rms_B_bonded: 1.37 r_work: 0.3146 rms_B_bonded: 2.38 restraints_weight: 0.5000 r_work: 0.3037 rms_B_bonded: 3.47 restraints_weight: 0.2500 r_work (final): 0.3037 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8061 moved from start: 0.2246 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= 0.145 Angle : 0.641 8.824 35424 Z= 0.329 Chirality : 0.047 0.212 4002 Planarity : 0.004 0.036 4494 Dihedral : 7.001 59.287 3534 Min Nonbonded Distance : 2.398 Molprobity Statistics. All-atom Clashscore : 6.63 Ramachandran Plot: Outliers : 0.19 % Allowed : 3.85 % Favored : 95.96 % Rotamer: Outliers : 1.48 % Allowed : 10.35 % Favored : 88.17 % 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: 0.88 (0.16), residues: 1098 sheet: -0.50 (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 E 402 HIS 0.004 0.001 HIS D 39 PHE 0.021 0.002 PHE F 81 TYR 0.020 0.002 TYR A 245 ARG 0.002 0.000 ARG B 47 Details of bonding type rmsd hydrogen bonds : bond 0.05304 ( 948) hydrogen bonds : angle 5.88541 ( 2682) covalent geometry : bond 0.00296 (26118) covalent geometry : angle 0.64135 (35424) Misc. bond : bond 0.00231 ( 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 345 residues out of total 2790 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 304 time to evaluate : 3.697 Fit side-chains revert: symmetry clash REVERT: A 61 LYS cc_start: 0.8190 (mtmm) cc_final: 0.7454 (mmtm) REVERT: A 112 ASP cc_start: 0.8507 (m-30) cc_final: 0.8216 (m-30) REVERT: A 197 MET cc_start: 0.8956 (mmp) cc_final: 0.8204 (mtp) REVERT: A 335 GLU cc_start: 0.6763 (mp0) cc_final: 0.6127 (tm-30) REVERT: A 343 GLN cc_start: 0.7792 (mt0) cc_final: 0.7510 (mt0) REVERT: A 399 LYS cc_start: 0.8266 (ttmm) cc_final: 0.7555 (tmmt) REVERT: D 61 LYS cc_start: 0.8176 (mtmm) cc_final: 0.7516 (mmtm) REVERT: D 89 LYS cc_start: 0.8828 (mtpt) cc_final: 0.8555 (ttmm) REVERT: D 100 GLU cc_start: 0.8052 (tp30) cc_final: 0.7319 (mp0) REVERT: D 158 GLU cc_start: 0.8206 (mm-30) cc_final: 0.7588 (tm-30) REVERT: D 197 MET cc_start: 0.8917 (mmp) cc_final: 0.8170 (mtp) REVERT: D 285 MET cc_start: 0.7553 (mtp) cc_final: 0.7240 (mtp) REVERT: D 338 GLU cc_start: 0.7058 (mt-10) cc_final: 0.6086 (mm-30) REVERT: D 375 GLU cc_start: 0.7112 (pt0) cc_final: 0.6771 (pm20) REVERT: D 399 LYS cc_start: 0.8134 (ttmm) cc_final: 0.7608 (tmmt) REVERT: B 61 LYS cc_start: 0.8199 (mtmm) cc_final: 0.7462 (mmtm) REVERT: B 112 ASP cc_start: 0.8516 (m-30) cc_final: 0.8233 (m-30) REVERT: B 197 MET cc_start: 0.8951 (mmp) cc_final: 0.8195 (mtp) REVERT: B 335 GLU cc_start: 0.6776 (mp0) cc_final: 0.6137 (tm-30) REVERT: B 343 GLN cc_start: 0.7795 (mt0) cc_final: 0.7514 (mt0) REVERT: B 399 LYS cc_start: 0.8271 (ttmm) cc_final: 0.7560 (tmmt) REVERT: C 42 LYS cc_start: 0.8372 (tmtp) cc_final: 0.8019 (ttpp) REVERT: C 61 LYS cc_start: 0.8297 (mtmm) cc_final: 0.7555 (mmtm) REVERT: C 100 GLU cc_start: 0.8046 (tp30) cc_final: 0.7301 (mp0) REVERT: C 133 THR cc_start: 0.6552 (OUTLIER) cc_final: 0.6327 (t) REVERT: C 150 ARG cc_start: 0.7388 (mtm110) cc_final: 0.7072 (mtm110) REVERT: C 197 MET cc_start: 0.9038 (mmp) cc_final: 0.8273 (mtp) REVERT: C 283 LYS cc_start: 0.7361 (mmtm) cc_final: 0.7016 (mppt) REVERT: C 335 GLU cc_start: 0.6806 (mp0) cc_final: 0.6121 (tm-30) REVERT: C 338 GLU cc_start: 0.6916 (mt-10) cc_final: 0.6151 (mm-30) REVERT: C 343 GLN cc_start: 0.7548 (mt0) cc_final: 0.7183 (mt0) REVERT: C 365 GLU cc_start: 0.6857 (mp0) cc_final: 0.6134 (mp0) REVERT: C 375 GLU cc_start: 0.7127 (pt0) cc_final: 0.6742 (pm20) REVERT: C 399 LYS cc_start: 0.8149 (ttmm) cc_final: 0.7404 (tmmt) REVERT: C 461 MET cc_start: 0.2408 (OUTLIER) cc_final: 0.1766 (mmm) REVERT: E 61 LYS cc_start: 0.8201 (mtmm) cc_final: 0.7545 (mmtm) REVERT: E 100 GLU cc_start: 0.8065 (tp30) cc_final: 0.7324 (mp0) REVERT: E 158 GLU cc_start: 0.8199 (mm-30) cc_final: 0.7587 (tm-30) REVERT: E 197 MET cc_start: 0.8924 (mmp) cc_final: 0.8150 (mtp) REVERT: E 285 MET cc_start: 0.7551 (mtp) cc_final: 0.7235 (mtp) REVERT: E 335 GLU cc_start: 0.6746 (mp0) cc_final: 0.6234 (tm-30) REVERT: E 338 GLU cc_start: 0.7073 (mt-10) cc_final: 0.6094 (mm-30) REVERT: E 375 GLU cc_start: 0.7100 (pt0) cc_final: 0.6755 (pm20) REVERT: E 399 LYS cc_start: 0.8145 (ttmm) cc_final: 0.7615 (tmmt) REVERT: E 461 MET cc_start: 0.2448 (OUTLIER) cc_final: 0.1973 (mpp) REVERT: F 42 LYS cc_start: 0.8439 (ttpp) cc_final: 0.8193 (tmtm) REVERT: F 61 LYS cc_start: 0.8286 (mtmm) cc_final: 0.7540 (mmtm) REVERT: F 100 GLU cc_start: 0.8042 (tp30) cc_final: 0.7288 (mp0) REVERT: F 133 THR cc_start: 0.6540 (OUTLIER) cc_final: 0.6314 (t) REVERT: F 150 ARG cc_start: 0.7377 (mtm110) cc_final: 0.7063 (mtm110) REVERT: F 197 MET cc_start: 0.9040 (mmp) cc_final: 0.8272 (mtp) REVERT: F 283 LYS cc_start: 0.7360 (mmtm) cc_final: 0.7007 (mppt) REVERT: F 335 GLU cc_start: 0.6783 (mp0) cc_final: 0.6110 (tm-30) REVERT: F 338 GLU cc_start: 0.6933 (mt-10) cc_final: 0.6151 (mm-30) REVERT: F 343 GLN cc_start: 0.7547 (mt0) cc_final: 0.7108 (mt0) REVERT: F 365 GLU cc_start: 0.6894 (mp0) cc_final: 0.6139 (mp0) REVERT: F 375 GLU cc_start: 0.7126 (pt0) cc_final: 0.6745 (pm20) REVERT: F 399 LYS cc_start: 0.8155 (ttmm) cc_final: 0.7411 (tmmt) REVERT: F 461 MET cc_start: 0.2362 (OUTLIER) cc_final: 0.1750 (mmm) outliers start: 41 outliers final: 35 residues processed: 338 average time/residue: 1.5406 time to fit residues: 597.9645 Evaluate side-chains 340 residues out of total 2790 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 300 time to evaluate : 2.892 ------------------------------------------------------------------------------- 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 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 133 THR 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 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 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 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 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 318 random chunks: chunk 263 optimal weight: 20.0000 chunk 244 optimal weight: 6.9990 chunk 256 optimal weight: 8.9990 chunk 236 optimal weight: 5.9990 chunk 23 optimal weight: 1.9990 chunk 315 optimal weight: 7.9990 chunk 200 optimal weight: 0.7980 chunk 173 optimal weight: 8.9990 chunk 1 optimal weight: 1.9990 chunk 240 optimal weight: 5.9990 chunk 103 optimal weight: 20.0000 overall best weight: 3.3588 ------------------------------------------------------------------------------- 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 448 HIS C 154 GLN C 160 ASN E 154 GLN E 343 GLN F 154 GLN F 206 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4073 r_free = 0.4073 target = 0.192751 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3240 r_free = 0.3240 target = 0.117316 restraints weight = 16818.956| |-----------------------------------------------------------------------------| r_work (start): 0.3215 rms_B_bonded: 1.64 r_work: 0.3017 rms_B_bonded: 2.21 restraints_weight: 0.5000 r_work: 0.2898 rms_B_bonded: 3.27 restraints_weight: 0.2500 r_work (final): 0.2898 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7965 moved from start: 0.2375 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= 0.234 Angle : 0.754 9.789 35424 Z= 0.386 Chirality : 0.052 0.236 4002 Planarity : 0.005 0.041 4494 Dihedral : 7.404 59.074 3534 Min Nonbonded Distance : 2.313 Molprobity Statistics. All-atom Clashscore : 6.82 Ramachandran Plot: Outliers : 0.19 % Allowed : 4.55 % Favored : 95.27 % Rotamer: Outliers : 1.66 % Allowed : 10.21 % Favored : 88.13 % 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: -0.29 (0.14), residues: 3168 helix: 0.61 (0.15), residues: 1104 sheet: -0.64 (0.21), residues: 546 loop : -0.52 (0.15), residues: 1518 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP A 402 HIS 0.006 0.002 HIS C 39 PHE 0.025 0.003 PHE F 81 TYR 0.026 0.003 TYR A 245 ARG 0.005 0.001 ARG B 47 Details of bonding type rmsd hydrogen bonds : bond 0.06588 ( 948) hydrogen bonds : angle 6.23360 ( 2682) covalent geometry : bond 0.00492 (26118) covalent geometry : angle 0.75417 (35424) Misc. bond : bond 0.00510 ( 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 347 residues out of total 2790 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 301 time to evaluate : 2.748 Fit side-chains REVERT: A 61 LYS cc_start: 0.8105 (mtmm) cc_final: 0.7305 (mmtm) REVERT: A 197 MET cc_start: 0.8874 (mmp) cc_final: 0.8045 (mtp) REVERT: A 283 LYS cc_start: 0.7616 (mptt) cc_final: 0.7296 (mptt) REVERT: A 335 GLU cc_start: 0.6659 (mp0) cc_final: 0.5915 (tm-30) REVERT: A 343 GLN cc_start: 0.7670 (mt0) cc_final: 0.7358 (mt0) REVERT: A 375 GLU cc_start: 0.7046 (OUTLIER) cc_final: 0.6438 (pm20) REVERT: A 399 LYS cc_start: 0.8163 (ttmm) cc_final: 0.7336 (tmmt) REVERT: D 61 LYS cc_start: 0.8045 (mtmm) cc_final: 0.7321 (mmtm) REVERT: D 89 LYS cc_start: 0.8776 (mtpt) cc_final: 0.8532 (mttt) REVERT: D 100 GLU cc_start: 0.7915 (tp30) cc_final: 0.7084 (mp0) REVERT: D 158 GLU cc_start: 0.8073 (mm-30) cc_final: 0.7410 (tm-30) REVERT: D 197 MET cc_start: 0.8820 (mmp) cc_final: 0.8037 (mtp) REVERT: D 285 MET cc_start: 0.7499 (mtp) cc_final: 0.7138 (mtp) REVERT: D 338 GLU cc_start: 0.6870 (mt-10) cc_final: 0.5879 (mm-30) REVERT: D 375 GLU cc_start: 0.7040 (pt0) cc_final: 0.6667 (pm20) REVERT: D 399 LYS cc_start: 0.8074 (ttmm) cc_final: 0.7394 (tmmt) REVERT: B 61 LYS cc_start: 0.8107 (mtmm) cc_final: 0.7307 (mmtm) REVERT: B 197 MET cc_start: 0.8875 (mmp) cc_final: 0.8043 (mtp) REVERT: B 283 LYS cc_start: 0.7601 (mptt) cc_final: 0.7272 (mptt) REVERT: B 335 GLU cc_start: 0.6672 (mp0) cc_final: 0.5932 (tm-30) REVERT: B 343 GLN cc_start: 0.7677 (mt0) cc_final: 0.7372 (mt0) REVERT: B 375 GLU cc_start: 0.7033 (OUTLIER) cc_final: 0.6426 (pm20) REVERT: B 399 LYS cc_start: 0.8154 (ttmm) cc_final: 0.7336 (tmmt) REVERT: C 42 LYS cc_start: 0.8216 (tmtp) cc_final: 0.7811 (ttpp) REVERT: C 61 LYS cc_start: 0.8145 (mtmm) cc_final: 0.7323 (mmtm) REVERT: C 100 GLU cc_start: 0.7882 (tp30) cc_final: 0.7033 (mp0) REVERT: C 133 THR cc_start: 0.6605 (OUTLIER) cc_final: 0.6305 (t) REVERT: C 150 ARG cc_start: 0.7195 (mtm110) cc_final: 0.6745 (mtm110) REVERT: C 197 MET cc_start: 0.8974 (mmp) cc_final: 0.8143 (mtp) REVERT: C 283 LYS cc_start: 0.7334 (mmtm) cc_final: 0.6968 (mppt) REVERT: C 335 GLU cc_start: 0.6628 (mp0) cc_final: 0.5936 (tm-30) REVERT: C 338 GLU cc_start: 0.6870 (mt-10) cc_final: 0.6022 (mm-30) REVERT: C 343 GLN cc_start: 0.7415 (mt0) cc_final: 0.7042 (mt0) REVERT: C 375 GLU cc_start: 0.6936 (pt0) cc_final: 0.6533 (pm20) REVERT: C 399 LYS cc_start: 0.8055 (ttmm) cc_final: 0.7191 (tmmt) REVERT: C 461 MET cc_start: 0.2621 (OUTLIER) cc_final: 0.1854 (mmm) REVERT: E 61 LYS cc_start: 0.8066 (mtmm) cc_final: 0.7324 (mmtt) REVERT: E 100 GLU cc_start: 0.7920 (tp30) cc_final: 0.7098 (mp0) REVERT: E 158 GLU cc_start: 0.8065 (mm-30) cc_final: 0.7412 (tm-30) REVERT: E 197 MET cc_start: 0.8825 (mmp) cc_final: 0.8040 (mtp) REVERT: E 285 MET cc_start: 0.7492 (mtp) cc_final: 0.7129 (mtp) REVERT: E 335 GLU cc_start: 0.6617 (mp0) cc_final: 0.6028 (tm-30) REVERT: E 338 GLU cc_start: 0.6880 (mt-10) cc_final: 0.5875 (mm-30) REVERT: E 375 GLU cc_start: 0.7026 (pt0) cc_final: 0.6650 (pm20) REVERT: E 399 LYS cc_start: 0.8073 (ttmm) cc_final: 0.7398 (tmmt) REVERT: F 61 LYS cc_start: 0.8140 (mtmm) cc_final: 0.7300 (mmtm) REVERT: F 100 GLU cc_start: 0.7876 (tp30) cc_final: 0.7024 (mp0) REVERT: F 133 THR cc_start: 0.6625 (OUTLIER) cc_final: 0.6333 (t) REVERT: F 150 ARG cc_start: 0.7203 (mtm110) cc_final: 0.6747 (mtm110) REVERT: F 197 MET cc_start: 0.8975 (mmp) cc_final: 0.8143 (mtp) REVERT: F 283 LYS cc_start: 0.7323 (mmtm) cc_final: 0.6959 (mppt) REVERT: F 335 GLU cc_start: 0.6630 (mp0) cc_final: 0.5955 (tm-30) REVERT: F 338 GLU cc_start: 0.6789 (mt-10) cc_final: 0.5931 (mm-30) REVERT: F 343 GLN cc_start: 0.7439 (mt0) cc_final: 0.6994 (mt0) REVERT: F 375 GLU cc_start: 0.6951 (pt0) cc_final: 0.6549 (pm20) REVERT: F 399 LYS cc_start: 0.8066 (ttmm) cc_final: 0.7202 (tmmt) REVERT: F 461 MET cc_start: 0.2654 (OUTLIER) cc_final: 0.1882 (mmm) outliers start: 46 outliers final: 32 residues processed: 337 average time/residue: 1.4861 time to fit residues: 572.2848 Evaluate side-chains 338 residues out of total 2790 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 300 time to evaluate : 2.893 ------------------------------------------------------------------------------- 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 375 GLU 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 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 375 GLU 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 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 221 ILE Chi-restraints excluded: chain E residue 227 VAL 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 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 269 optimal weight: 0.9990 chunk 133 optimal weight: 8.9990 chunk 62 optimal weight: 1.9990 chunk 260 optimal weight: 0.3980 chunk 107 optimal weight: 4.9990 chunk 44 optimal weight: 5.9990 chunk 41 optimal weight: 0.9980 chunk 127 optimal weight: 0.0030 chunk 173 optimal weight: 7.9990 chunk 225 optimal weight: 9.9990 chunk 38 optimal weight: 0.5980 overall best weight: 0.5992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 154 GLN D 126 GLN 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: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4095 r_free = 0.4095 target = 0.196298 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3301 r_free = 0.3301 target = 0.122421 restraints weight = 17036.765| |-----------------------------------------------------------------------------| r_work (start): 0.3299 rms_B_bonded: 1.33 r_work: 0.3127 rms_B_bonded: 2.00 restraints_weight: 0.5000 r_work: 0.3011 rms_B_bonded: 2.93 restraints_weight: 0.2500 r_work (final): 0.3011 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7907 moved from start: 0.2265 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 26124 Z= 0.113 Angle : 0.596 8.253 35424 Z= 0.307 Chirality : 0.045 0.179 4002 Planarity : 0.004 0.036 4494 Dihedral : 6.644 58.712 3534 Min Nonbonded Distance : 2.446 Molprobity Statistics. All-atom Clashscore : 6.49 Ramachandran Plot: Outliers : 0.19 % Allowed : 3.91 % Favored : 95.90 % Rotamer: Outliers : 1.26 % Allowed : 10.79 % Favored : 87.95 % 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: 0.93 (0.16), residues: 1116 sheet: -0.43 (0.21), residues: 546 loop : -0.50 (0.16), residues: 1506 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP E 402 HIS 0.003 0.001 HIS D 195 PHE 0.017 0.001 PHE B 81 TYR 0.012 0.001 TYR A 245 ARG 0.002 0.000 ARG B 47 Details of bonding type rmsd hydrogen bonds : bond 0.04469 ( 948) hydrogen bonds : angle 5.64445 ( 2682) covalent geometry : bond 0.00226 (26118) covalent geometry : angle 0.59609 (35424) Misc. bond : bond 0.00115 ( 6) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 32131.28 seconds wall clock time: 559 minutes 37.36 seconds (33577.36 seconds total)