Starting phenix.real_space_refine on Mon Aug 25 04:58:26 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8jyu_36731/08_2025/8jyu_36731.cif Found real_map, /net/cci-nas-00/data/ceres_data/8jyu_36731/08_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 { model { file = "/net/cci-nas-00/data/ceres_data/8jyu_36731/08_2025/8jyu_36731.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8jyu_36731/08_2025/8jyu_36731.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8jyu_36731/08_2025/8jyu_36731.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8jyu_36731/08_2025/8jyu_36731.map" } resolution = 2.19 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.002 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): 0.03s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/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: 6.12, per 1000 atoms: 0.24 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: 2.10 Conformation dependent library (CDL) restraints added in 1.2 seconds Enol-peptide restraints added in 953.7 nanoseconds 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: 1.12 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: 6.04 Time building geometry restraints manager: 2.78 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: 0.08 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'D' selection = chain 'B' selection = chain 'C' selection = chain 'E' selection = chain 'F' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.820 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: 0.380 Check model and map are aligned: 0.090 Set scattering table: 0.070 Process input model: 25.920 Find NCS groups from input model: 0.230 Set up NCS constraints: 0.060 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:7.280 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 35.880 ------------------------------------------------------------------------------- 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 : 6.35 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. 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 ARG 0.002 0.000 ARG B 529 TYR 0.012 0.001 TYR B 80 PHE 0.011 0.001 PHE C 161 TRP 0.008 0.001 TRP C 386 HIS 0.002 0.001 HIS B 408 Details of bonding type rmsd covalent geometry : bond 0.00396 (26118) covalent geometry : angle 0.69018 (35424) hydrogen bonds : bond 0.19172 ( 948) hydrogen bonds : angle 7.51129 ( 2682) 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 : 1.026 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: 0.8869 time to fit residues: 403.6715 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 : 1.017 ------------------------------------------------------------------------------- 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 197 optimal weight: 0.8980 chunk 215 optimal weight: 7.9990 chunk 20 optimal weight: 5.9990 chunk 132 optimal weight: 1.9990 chunk 261 optimal weight: 2.9990 chunk 248 optimal weight: 7.9990 chunk 207 optimal weight: 3.9990 chunk 155 optimal weight: 20.0000 chunk 244 optimal weight: 4.9990 chunk 183 optimal weight: 9.9990 chunk 298 optimal weight: 4.9990 overall best weight: 2.9788 ------------------------------------------------------------------------------- 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 = 0.4149 r_free = 0.4149 target = 0.198461 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3363 r_free = 0.3363 target = 0.126486 restraints weight = 17104.483| |-----------------------------------------------------------------------------| r_work (start): 0.3325 rms_B_bonded: 1.57 r_work: 0.3146 rms_B_bonded: 2.06 restraints_weight: 0.5000 r_work: 0.3026 rms_B_bonded: 3.09 restraints_weight: 0.2500 r_work (final): 0.3026 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8016 moved from start: 0.1579 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.040 26124 Z= 0.219 Angle : 0.739 9.230 35424 Z= 0.381 Chirality : 0.051 0.221 4002 Planarity : 0.005 0.037 4494 Dihedral : 7.244 59.359 3534 Min Nonbonded Distance : 2.163 Molprobity Statistics. All-atom Clashscore : 5.55 Ramachandran Plot: Outliers : 0.19 % Allowed : 4.23 % Favored : 95.58 % Rotamer: Outliers : 1.23 % Allowed : 8.19 % Favored : 90.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.35 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.16 (0.15), residues: 3168 helix: 0.72 (0.15), residues: 1104 sheet: -0.42 (0.21), residues: 576 loop : -0.50 (0.16), residues: 1488 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG F 211 TYR 0.029 0.003 TYR A 245 PHE 0.021 0.003 PHE A 187 TRP 0.016 0.002 TRP F 402 HIS 0.006 0.002 HIS E 74 Details of bonding type rmsd covalent geometry : bond 0.00457 (26118) covalent geometry : angle 0.73928 (35424) hydrogen bonds : bond 0.06770 ( 948) hydrogen bonds : angle 6.48900 ( 2682) Misc. bond : bond 0.00301 ( 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 365 residues out of total 2790 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 331 time to evaluate : 1.190 Fit side-chains REVERT: A 61 LYS cc_start: 0.8120 (mtmm) cc_final: 0.7432 (mmtm) REVERT: A 112 ASP cc_start: 0.8490 (m-30) cc_final: 0.8234 (m-30) REVERT: A 145 GLU cc_start: 0.6901 (mm-30) cc_final: 0.6540 (mp0) REVERT: A 158 GLU cc_start: 0.8197 (mm-30) cc_final: 0.7946 (mp0) REVERT: A 197 MET cc_start: 0.8913 (mmp) cc_final: 0.8134 (mtp) REVERT: A 256 ASN cc_start: 0.8106 (t0) cc_final: 0.7806 (t0) REVERT: A 309 GLU cc_start: 0.7754 (mt-10) cc_final: 0.7517 (mt-10) REVERT: A 335 GLU cc_start: 0.6567 (mp0) cc_final: 0.6159 (tm-30) REVERT: A 343 GLN cc_start: 0.7777 (mt0) cc_final: 0.7491 (mt0) REVERT: A 366 ASP cc_start: 0.6956 (m-30) cc_final: 0.6740 (m-30) REVERT: A 375 GLU cc_start: 0.7053 (pt0) cc_final: 0.6729 (pm20) REVERT: A 399 LYS cc_start: 0.8000 (ttmm) cc_final: 0.7366 (tmmt) REVERT: D 42 LYS cc_start: 0.8234 (ttpp) cc_final: 0.8031 (ttpp) REVERT: D 61 LYS cc_start: 0.8161 (mtmm) cc_final: 0.7480 (mmtt) REVERT: D 100 GLU cc_start: 0.7946 (tp30) cc_final: 0.7188 (mp0) REVERT: D 158 GLU cc_start: 0.8211 (mm-30) cc_final: 0.7453 (tm-30) REVERT: D 197 MET cc_start: 0.8869 (mmp) cc_final: 0.8117 (mtp) REVERT: D 285 MET cc_start: 0.7504 (mtp) cc_final: 0.7161 (mtp) REVERT: D 338 GLU cc_start: 0.7139 (mt-10) cc_final: 0.6275 (mm-30) REVERT: D 346 GLU cc_start: 0.7813 (tp30) cc_final: 0.7520 (tp30) REVERT: D 375 GLU cc_start: 0.7070 (pt0) cc_final: 0.6688 (pm20) REVERT: D 399 LYS cc_start: 0.7937 (ttmm) cc_final: 0.7357 (tmmt) REVERT: B 61 LYS cc_start: 0.8120 (mtmm) cc_final: 0.7429 (mmtm) REVERT: B 112 ASP cc_start: 0.8498 (m-30) cc_final: 0.8242 (m-30) REVERT: B 144 GLU cc_start: 0.6678 (pm20) cc_final: 0.6361 (pm20) REVERT: B 158 GLU cc_start: 0.8193 (mm-30) cc_final: 0.7940 (mp0) REVERT: B 197 MET cc_start: 0.8914 (mmp) cc_final: 0.8134 (mtp) REVERT: B 256 ASN cc_start: 0.8066 (t0) cc_final: 0.7759 (t0) REVERT: B 309 GLU cc_start: 0.7752 (mt-10) cc_final: 0.7515 (mt-10) REVERT: B 335 GLU cc_start: 0.6580 (mp0) cc_final: 0.6174 (tm-30) REVERT: B 343 GLN cc_start: 0.7770 (mt0) cc_final: 0.7475 (mt0) REVERT: B 366 ASP cc_start: 0.6969 (m-30) cc_final: 0.6761 (m-30) REVERT: B 375 GLU cc_start: 0.7028 (pt0) cc_final: 0.6690 (pm20) REVERT: B 399 LYS cc_start: 0.8019 (ttmm) cc_final: 0.7382 (tmmt) REVERT: C 28 GLU cc_start: 0.7645 (mm-30) cc_final: 0.7430 (mp0) REVERT: C 61 LYS cc_start: 0.8261 (mtmm) cc_final: 0.7541 (mmtm) REVERT: C 100 GLU cc_start: 0.8013 (tp30) cc_final: 0.7223 (mp0) REVERT: C 133 THR cc_start: 0.6353 (OUTLIER) cc_final: 0.6075 (t) REVERT: C 136 ARG cc_start: 0.8449 (ttt180) cc_final: 0.8156 (tpt-90) REVERT: C 145 GLU cc_start: 0.6748 (mm-30) cc_final: 0.6413 (mp0) REVERT: C 150 ARG cc_start: 0.7382 (mtm110) cc_final: 0.7014 (mtm110) REVERT: C 158 GLU cc_start: 0.8199 (mm-30) cc_final: 0.7892 (mp0) REVERT: C 197 MET cc_start: 0.8961 (mmp) cc_final: 0.8153 (mtp) REVERT: C 248 LYS cc_start: 0.8407 (tttp) cc_final: 0.8199 (tttm) REVERT: C 274 HIS cc_start: 0.8092 (t70) cc_final: 0.7865 (t70) REVERT: C 338 GLU cc_start: 0.7087 (mt-10) cc_final: 0.6319 (mm-30) REVERT: C 343 GLN cc_start: 0.7541 (mt0) cc_final: 0.7141 (mt0) REVERT: C 375 GLU cc_start: 0.6976 (pt0) cc_final: 0.6583 (pm20) REVERT: C 399 LYS cc_start: 0.7962 (ttmm) cc_final: 0.7209 (tmmt) REVERT: C 403 ARG cc_start: 0.7987 (ttp-110) cc_final: 0.7677 (ttp80) REVERT: E 61 LYS cc_start: 0.8166 (mtmm) cc_final: 0.7487 (mmtt) REVERT: E 100 GLU cc_start: 0.7918 (tp30) cc_final: 0.7175 (mp0) REVERT: E 158 GLU cc_start: 0.8211 (mm-30) cc_final: 0.7528 (tm-30) REVERT: E 197 MET cc_start: 0.8879 (mmp) cc_final: 0.8124 (mtp) REVERT: E 285 MET cc_start: 0.7492 (mtp) cc_final: 0.7190 (mtp) REVERT: E 338 GLU cc_start: 0.7157 (mt-10) cc_final: 0.6297 (mm-30) REVERT: E 346 GLU cc_start: 0.7813 (tp30) cc_final: 0.7520 (tp30) REVERT: E 375 GLU cc_start: 0.7045 (pt0) cc_final: 0.6676 (pm20) REVERT: E 399 LYS cc_start: 0.7959 (ttmm) cc_final: 0.7408 (tmmt) REVERT: F 28 GLU cc_start: 0.7652 (mm-30) cc_final: 0.7437 (mp0) REVERT: F 61 LYS cc_start: 0.8250 (mtmm) cc_final: 0.7532 (mmtm) REVERT: F 100 GLU cc_start: 0.8012 (tp30) cc_final: 0.7220 (mp0) REVERT: F 133 THR cc_start: 0.6355 (OUTLIER) cc_final: 0.6076 (t) REVERT: F 145 GLU cc_start: 0.6752 (mm-30) cc_final: 0.6428 (mp0) REVERT: F 150 ARG cc_start: 0.7373 (mtm110) cc_final: 0.7007 (mtm110) REVERT: F 158 GLU cc_start: 0.8216 (mm-30) cc_final: 0.7906 (mp0) REVERT: F 197 MET cc_start: 0.8962 (mmp) cc_final: 0.8150 (mtp) REVERT: F 248 LYS cc_start: 0.8407 (tttp) cc_final: 0.8196 (tttm) REVERT: F 274 HIS cc_start: 0.8095 (t70) cc_final: 0.7867 (t70) REVERT: F 338 GLU cc_start: 0.7089 (mt-10) cc_final: 0.6317 (mm-30) REVERT: F 343 GLN cc_start: 0.7539 (mt0) cc_final: 0.7120 (mt0) REVERT: F 375 GLU cc_start: 0.6962 (pt0) cc_final: 0.6585 (pm20) REVERT: F 399 LYS cc_start: 0.7960 (ttmm) cc_final: 0.7203 (tmmt) outliers start: 34 outliers final: 22 residues processed: 357 average time/residue: 0.8576 time to fit residues: 344.4763 Evaluate side-chains 335 residues out of total 2790 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 311 time to evaluate : 1.068 ------------------------------------------------------------------------------- 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 118 optimal weight: 0.1980 chunk 149 optimal weight: 2.9990 chunk 215 optimal weight: 0.9990 chunk 221 optimal weight: 0.6980 chunk 191 optimal weight: 0.7980 chunk 279 optimal weight: 6.9990 chunk 16 optimal weight: 2.9990 chunk 244 optimal weight: 7.9990 chunk 15 optimal weight: 0.9980 chunk 42 optimal weight: 5.9990 chunk 100 optimal weight: 6.9990 overall best weight: 0.7382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 154 GLN D 343 GLN D 344 GLN D 368 ASN C 154 GLN C 160 ASN C 368 ASN E 343 GLN E 344 GLN E 368 ASN F 154 GLN F 368 ASN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4242 r_free = 0.4242 target = 0.206735 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 66)----------------| | r_work = 0.3828 r_free = 0.3828 target = 0.163845 restraints weight = 17509.773| |-----------------------------------------------------------------------------| r_work (start): 0.3810 rms_B_bonded: 0.80 r_work: 0.3450 rms_B_bonded: 1.92 restraints_weight: 0.5000 r_work: 0.3266 rms_B_bonded: 4.29 restraints_weight: 0.2500 r_work (final): 0.3266 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8128 moved from start: 0.1615 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.025 26124 Z= 0.117 Angle : 0.593 7.655 35424 Z= 0.306 Chirality : 0.046 0.185 4002 Planarity : 0.004 0.036 4494 Dihedral : 6.616 57.249 3534 Min Nonbonded Distance : 2.276 Molprobity Statistics. All-atom Clashscore : 6.16 Ramachandran Plot: Outliers : 0.19 % Allowed : 3.76 % Favored : 96.05 % Rotamer: Outliers : 1.59 % Allowed : 9.13 % Favored : 89.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.35 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.00 (0.15), residues: 3168 helix: 0.99 (0.16), residues: 1104 sheet: -0.37 (0.21), residues: 576 loop : -0.53 (0.16), residues: 1488 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 130 TYR 0.015 0.001 TYR A 245 PHE 0.017 0.001 PHE C 81 TRP 0.010 0.001 TRP D 402 HIS 0.003 0.001 HIS D 39 Details of bonding type rmsd covalent geometry : bond 0.00230 (26118) covalent geometry : angle 0.59336 (35424) hydrogen bonds : bond 0.04785 ( 948) hydrogen bonds : angle 5.87778 ( 2682) Misc. bond : bond 0.00101 ( 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 369 residues out of total 2790 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 325 time to evaluate : 1.056 Fit side-chains REVERT: A 61 LYS cc_start: 0.8457 (mtmm) cc_final: 0.8009 (mmtm) REVERT: A 112 ASP cc_start: 0.8713 (m-30) cc_final: 0.8447 (m-30) REVERT: A 145 GLU cc_start: 0.7522 (mm-30) cc_final: 0.7277 (mp0) REVERT: A 197 MET cc_start: 0.9027 (mmp) cc_final: 0.8413 (mtp) REVERT: A 309 GLU cc_start: 0.8200 (mt-10) cc_final: 0.7968 (mt-10) REVERT: A 343 GLN cc_start: 0.8198 (mt0) cc_final: 0.7978 (mt0) REVERT: A 399 LYS cc_start: 0.8327 (ttmm) cc_final: 0.7915 (tmmt) REVERT: D 61 LYS cc_start: 0.8534 (mtmm) cc_final: 0.8073 (mmtm) REVERT: D 100 GLU cc_start: 0.8509 (tp30) cc_final: 0.7935 (mp0) REVERT: D 158 GLU cc_start: 0.8486 (mm-30) cc_final: 0.8051 (tm-30) REVERT: D 197 MET cc_start: 0.8996 (mmp) cc_final: 0.8326 (mtp) REVERT: D 285 MET cc_start: 0.7807 (mtp) cc_final: 0.7581 (mtp) REVERT: D 338 GLU cc_start: 0.7516 (mt-10) cc_final: 0.6856 (mm-30) REVERT: D 399 LYS cc_start: 0.8302 (ttmm) cc_final: 0.8003 (tmmt) REVERT: B 61 LYS cc_start: 0.8449 (mtmm) cc_final: 0.8003 (mmtm) REVERT: B 112 ASP cc_start: 0.8718 (m-30) cc_final: 0.8450 (m-30) REVERT: B 197 MET cc_start: 0.9022 (mmp) cc_final: 0.8408 (mtp) REVERT: B 309 GLU cc_start: 0.8205 (mt-10) cc_final: 0.7975 (mt-10) REVERT: B 343 GLN cc_start: 0.8192 (mt0) cc_final: 0.7982 (mt0) REVERT: B 399 LYS cc_start: 0.8335 (ttmm) cc_final: 0.7923 (tmmt) REVERT: C 61 LYS cc_start: 0.8507 (mtmm) cc_final: 0.8057 (mmtm) REVERT: C 100 GLU cc_start: 0.8382 (tp30) cc_final: 0.7907 (mp0) REVERT: C 145 GLU cc_start: 0.7363 (mm-30) cc_final: 0.7148 (mp0) REVERT: C 150 ARG cc_start: 0.7796 (mtm110) cc_final: 0.7521 (mtm110) REVERT: C 197 MET cc_start: 0.9056 (mmp) cc_final: 0.8441 (mtp) REVERT: C 338 GLU cc_start: 0.7483 (mt-10) cc_final: 0.6914 (mm-30) REVERT: C 343 GLN cc_start: 0.8024 (mt0) cc_final: 0.7712 (mt0) REVERT: C 344 GLN cc_start: 0.8624 (mt0) cc_final: 0.8300 (mt0) REVERT: C 365 GLU cc_start: 0.7217 (mp0) cc_final: 0.6604 (pm20) REVERT: C 375 GLU cc_start: 0.7164 (pt0) cc_final: 0.6886 (pm20) REVERT: C 399 LYS cc_start: 0.8280 (ttmm) cc_final: 0.7855 (tmmt) REVERT: E 61 LYS cc_start: 0.8506 (mtmm) cc_final: 0.8064 (mmtm) REVERT: E 100 GLU cc_start: 0.8503 (tp30) cc_final: 0.7927 (mp0) REVERT: E 158 GLU cc_start: 0.8487 (mm-30) cc_final: 0.8049 (tm-30) REVERT: E 197 MET cc_start: 0.9007 (mmp) cc_final: 0.8335 (mtp) REVERT: E 285 MET cc_start: 0.7804 (mtp) cc_final: 0.7575 (mtp) REVERT: E 338 GLU cc_start: 0.7525 (mt-10) cc_final: 0.6877 (mm-30) REVERT: E 399 LYS cc_start: 0.8299 (ttmm) cc_final: 0.7988 (tmmt) REVERT: F 61 LYS cc_start: 0.8530 (mtmm) cc_final: 0.8077 (mmtm) REVERT: F 100 GLU cc_start: 0.8393 (tp30) cc_final: 0.7909 (mp0) REVERT: F 145 GLU cc_start: 0.7363 (mm-30) cc_final: 0.7148 (mp0) REVERT: F 150 ARG cc_start: 0.7778 (mtm110) cc_final: 0.7559 (mtm110) REVERT: F 197 MET cc_start: 0.9060 (mmp) cc_final: 0.8447 (mtp) REVERT: F 338 GLU cc_start: 0.7513 (mt-10) cc_final: 0.6945 (mm-30) REVERT: F 343 GLN cc_start: 0.8039 (mt0) cc_final: 0.7769 (mt0) REVERT: F 344 GLN cc_start: 0.8611 (mt0) cc_final: 0.8295 (mt0) REVERT: F 365 GLU cc_start: 0.7185 (mp0) cc_final: 0.6597 (pm20) REVERT: F 375 GLU cc_start: 0.7192 (pt0) cc_final: 0.6911 (pm20) REVERT: F 399 LYS cc_start: 0.8272 (ttmm) cc_final: 0.7847 (tmmt) outliers start: 44 outliers final: 20 residues processed: 361 average time/residue: 0.8192 time to fit residues: 334.5605 Evaluate side-chains 313 residues out of total 2790 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 293 time to evaluate : 1.053 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 227 VAL Chi-restraints excluded: chain A residue 461 MET 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 461 MET Chi-restraints excluded: chain B residue 227 VAL Chi-restraints excluded: chain B residue 461 MET Chi-restraints excluded: chain B residue 499 ILE Chi-restraints excluded: chain C residue 118 GLU Chi-restraints excluded: chain C residue 227 VAL Chi-restraints excluded: chain C residue 461 MET 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 461 MET Chi-restraints excluded: chain F residue 118 GLU 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 313 optimal weight: 10.0000 chunk 126 optimal weight: 7.9990 chunk 22 optimal weight: 9.9990 chunk 100 optimal weight: 0.9990 chunk 162 optimal weight: 7.9990 chunk 265 optimal weight: 2.9990 chunk 3 optimal weight: 7.9990 chunk 9 optimal weight: 0.8980 chunk 211 optimal weight: 9.9990 chunk 20 optimal weight: 0.4980 chunk 263 optimal weight: 1.9990 overall best weight: 1.4786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 343 GLN B 126 GLN C 154 GLN 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 = 0.4164 r_free = 0.4164 target = 0.200255 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 73)----------------| | r_work = 0.3378 r_free = 0.3378 target = 0.127599 restraints weight = 17230.816| |-----------------------------------------------------------------------------| r_work (start): 0.3346 rms_B_bonded: 1.49 r_work: 0.3143 rms_B_bonded: 2.40 restraints_weight: 0.5000 r_work: 0.3037 rms_B_bonded: 3.49 restraints_weight: 0.2500 r_work (final): 0.3037 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8073 moved from start: 0.1835 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= 0.145 Angle : 0.635 8.481 35424 Z= 0.327 Chirality : 0.047 0.204 4002 Planarity : 0.004 0.037 4494 Dihedral : 6.866 59.953 3534 Min Nonbonded Distance : 2.271 Molprobity Statistics. All-atom Clashscore : 5.90 Ramachandran Plot: Outliers : 0.19 % Allowed : 4.26 % Favored : 95.55 % Rotamer: Outliers : 1.73 % Allowed : 9.34 % Favored : 88.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.35 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.06 (0.15), residues: 3168 helix: 0.94 (0.16), residues: 1104 sheet: -0.41 (0.21), residues: 576 loop : -0.55 (0.16), residues: 1488 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 47 TYR 0.020 0.002 TYR A 245 PHE 0.019 0.002 PHE C 81 TRP 0.010 0.001 TRP A 402 HIS 0.004 0.001 HIS D 39 Details of bonding type rmsd covalent geometry : bond 0.00294 (26118) covalent geometry : angle 0.63491 (35424) hydrogen bonds : bond 0.05379 ( 948) hydrogen bonds : angle 5.96849 ( 2682) Misc. bond : bond 0.00219 ( 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 348 residues out of total 2790 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 300 time to evaluate : 1.039 Fit side-chains REVERT: A 61 LYS cc_start: 0.8178 (mtmm) cc_final: 0.7482 (mmtm) REVERT: A 112 ASP cc_start: 0.8528 (m-30) cc_final: 0.8255 (m-30) REVERT: A 197 MET cc_start: 0.8997 (mmp) cc_final: 0.8249 (mtp) REVERT: A 309 GLU cc_start: 0.7890 (mt-10) cc_final: 0.7682 (mt-10) REVERT: A 343 GLN cc_start: 0.7842 (mt0) cc_final: 0.7541 (mt0) REVERT: A 366 ASP cc_start: 0.6768 (OUTLIER) cc_final: 0.6451 (m-30) REVERT: A 375 GLU cc_start: 0.7190 (pt0) cc_final: 0.6855 (pm20) REVERT: A 399 LYS cc_start: 0.8091 (ttmm) cc_final: 0.7463 (tmmt) REVERT: D 42 LYS cc_start: 0.8499 (ttpp) cc_final: 0.8295 (ttpp) REVERT: D 61 LYS cc_start: 0.8251 (mtmm) cc_final: 0.7581 (mmtm) REVERT: D 100 GLU cc_start: 0.8101 (tp30) cc_final: 0.7361 (mp0) REVERT: D 158 GLU cc_start: 0.8250 (mm-30) cc_final: 0.7629 (tm-30) REVERT: D 197 MET cc_start: 0.8935 (mmp) cc_final: 0.8094 (mtp) REVERT: D 285 MET cc_start: 0.7555 (mtp) cc_final: 0.7296 (mtp) REVERT: D 338 GLU cc_start: 0.7150 (mt-10) cc_final: 0.6298 (mm-30) REVERT: D 399 LYS cc_start: 0.8120 (ttmm) cc_final: 0.7572 (tmmt) REVERT: B 61 LYS cc_start: 0.8178 (mtmm) cc_final: 0.7481 (mmtm) REVERT: B 112 ASP cc_start: 0.8536 (m-30) cc_final: 0.8262 (m-30) REVERT: B 197 MET cc_start: 0.8996 (mmp) cc_final: 0.8245 (mtp) REVERT: B 343 GLN cc_start: 0.7843 (mt0) cc_final: 0.7530 (mt0) REVERT: B 366 ASP cc_start: 0.6854 (OUTLIER) cc_final: 0.6534 (m-30) REVERT: B 375 GLU cc_start: 0.7189 (pt0) cc_final: 0.6858 (pm20) REVERT: B 399 LYS cc_start: 0.8109 (ttmm) cc_final: 0.7476 (tmmt) REVERT: C 42 LYS cc_start: 0.8378 (tmtp) cc_final: 0.8037 (ttpp) REVERT: C 61 LYS cc_start: 0.8340 (mtmm) cc_final: 0.7602 (mmtm) REVERT: C 100 GLU cc_start: 0.8027 (tp30) cc_final: 0.7307 (mp0) REVERT: C 145 GLU cc_start: 0.6849 (mm-30) cc_final: 0.6516 (mp0) REVERT: C 150 ARG cc_start: 0.7389 (mtm110) cc_final: 0.7102 (mtm110) REVERT: C 165 ASP cc_start: 0.9013 (t0) cc_final: 0.8798 (t0) REVERT: C 197 MET cc_start: 0.9028 (mmp) cc_final: 0.8273 (mtp) REVERT: C 338 GLU cc_start: 0.7122 (mt-10) cc_final: 0.6321 (mm-30) REVERT: C 343 GLN cc_start: 0.7599 (mt0) cc_final: 0.7188 (mt0) REVERT: C 375 GLU cc_start: 0.7133 (pt0) cc_final: 0.6745 (pm20) REVERT: C 399 LYS cc_start: 0.8097 (ttmm) cc_final: 0.7431 (tmmt) REVERT: E 61 LYS cc_start: 0.8254 (mtmm) cc_final: 0.7581 (mmtm) REVERT: E 100 GLU cc_start: 0.8101 (tp30) cc_final: 0.7358 (mp0) REVERT: E 158 GLU cc_start: 0.8246 (mm-30) cc_final: 0.7627 (tm-30) REVERT: E 197 MET cc_start: 0.8948 (mmp) cc_final: 0.8152 (mtp) REVERT: E 285 MET cc_start: 0.7560 (mtp) cc_final: 0.7307 (mtp) REVERT: E 338 GLU cc_start: 0.7152 (mt-10) cc_final: 0.6269 (mm-30) REVERT: E 366 ASP cc_start: 0.6800 (OUTLIER) cc_final: 0.6547 (m-30) REVERT: E 399 LYS cc_start: 0.8104 (ttmm) cc_final: 0.7568 (tmmt) REVERT: F 42 LYS cc_start: 0.8384 (tmtp) cc_final: 0.8042 (ttpp) REVERT: F 61 LYS cc_start: 0.8336 (mtmm) cc_final: 0.7603 (mmtm) REVERT: F 100 GLU cc_start: 0.8036 (tp30) cc_final: 0.7324 (mp0) REVERT: F 145 GLU cc_start: 0.6849 (mm-30) cc_final: 0.6523 (mp0) REVERT: F 150 ARG cc_start: 0.7394 (mtm110) cc_final: 0.7112 (mtm110) REVERT: F 165 ASP cc_start: 0.9013 (t0) cc_final: 0.8800 (t0) REVERT: F 197 MET cc_start: 0.9031 (mmp) cc_final: 0.8272 (mtp) REVERT: F 338 GLU cc_start: 0.7115 (mt-10) cc_final: 0.6317 (mm-30) REVERT: F 343 GLN cc_start: 0.7598 (mt0) cc_final: 0.7191 (mt0) REVERT: F 375 GLU cc_start: 0.7088 (pt0) cc_final: 0.6741 (pm20) REVERT: F 399 LYS cc_start: 0.8088 (ttmm) cc_final: 0.7421 (tmmt) outliers start: 48 outliers final: 40 residues processed: 337 average time/residue: 0.7714 time to fit residues: 296.6682 Evaluate side-chains 337 residues out of total 2790 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 294 time to evaluate : 1.061 ------------------------------------------------------------------------------- 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 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 366 ASP 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 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 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 Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 318 random chunks: chunk 267 optimal weight: 5.9990 chunk 308 optimal weight: 9.9990 chunk 183 optimal weight: 0.0970 chunk 279 optimal weight: 10.0000 chunk 55 optimal weight: 0.0770 chunk 89 optimal weight: 7.9990 chunk 234 optimal weight: 0.9980 chunk 202 optimal weight: 20.0000 chunk 70 optimal weight: 9.9990 chunk 270 optimal weight: 9.9990 chunk 237 optimal weight: 4.9990 overall best weight: 2.4340 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 126 GLN A 154 GLN D 343 GLN C 154 GLN 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 = 0.4145 r_free = 0.4145 target = 0.198262 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3381 r_free = 0.3381 target = 0.128118 restraints weight = 17077.793| |-----------------------------------------------------------------------------| r_work (start): 0.3348 rms_B_bonded: 1.60 r_work: 0.3150 rms_B_bonded: 2.08 restraints_weight: 0.5000 r_work: 0.3037 rms_B_bonded: 3.06 restraints_weight: 0.2500 r_work (final): 0.3037 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7987 moved from start: 0.2061 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 26124 Z= 0.190 Angle : 0.700 9.061 35424 Z= 0.359 Chirality : 0.049 0.207 4002 Planarity : 0.004 0.037 4494 Dihedral : 7.251 59.573 3534 Min Nonbonded Distance : 2.283 Molprobity Statistics. All-atom Clashscore : 5.98 Ramachandran Plot: Outliers : 0.19 % Allowed : 4.23 % Favored : 95.58 % Rotamer: Outliers : 1.98 % Allowed : 9.16 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.19 (0.15), residues: 3168 helix: 0.77 (0.16), residues: 1104 sheet: -0.54 (0.21), residues: 576 loop : -0.54 (0.16), residues: 1488 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG A 190 TYR 0.024 0.002 TYR A 245 PHE 0.024 0.002 PHE C 81 TRP 0.012 0.001 TRP B 402 HIS 0.005 0.001 HIS F 39 Details of bonding type rmsd covalent geometry : bond 0.00392 (26118) covalent geometry : angle 0.69959 (35424) hydrogen bonds : bond 0.06083 ( 948) hydrogen bonds : angle 6.16789 ( 2682) Misc. bond : bond 0.00368 ( 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 356 residues out of total 2790 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 301 time to evaluate : 1.031 Fit side-chains REVERT: A 61 LYS cc_start: 0.8143 (mtmm) cc_final: 0.7398 (mmtm) REVERT: A 197 MET cc_start: 0.8937 (mmp) cc_final: 0.8147 (mtp) REVERT: A 309 GLU cc_start: 0.7747 (mt-10) cc_final: 0.7541 (mt-10) REVERT: A 343 GLN cc_start: 0.7744 (mt0) cc_final: 0.7455 (mt0) REVERT: A 366 ASP cc_start: 0.6852 (OUTLIER) cc_final: 0.6530 (m-30) REVERT: A 375 GLU cc_start: 0.7140 (pt0) cc_final: 0.6806 (pm20) REVERT: A 399 LYS cc_start: 0.8053 (ttmm) cc_final: 0.7364 (tmmt) REVERT: D 61 LYS cc_start: 0.8147 (mtmm) cc_final: 0.7443 (mmtt) REVERT: D 100 GLU cc_start: 0.7922 (tp30) cc_final: 0.7170 (mp0) REVERT: D 158 GLU cc_start: 0.8078 (mm-30) cc_final: 0.7432 (tm-30) REVERT: D 197 MET cc_start: 0.8877 (mmp) cc_final: 0.8072 (mtp) REVERT: D 262 LYS cc_start: 0.8136 (mmtm) cc_final: 0.7894 (mmmt) REVERT: D 285 MET cc_start: 0.7508 (mtp) cc_final: 0.7182 (mtp) REVERT: D 335 GLU cc_start: 0.6680 (mp0) cc_final: 0.6190 (tm-30) REVERT: D 338 GLU cc_start: 0.6984 (mt-10) cc_final: 0.6007 (mm-30) REVERT: D 366 ASP cc_start: 0.6713 (OUTLIER) cc_final: 0.6456 (m-30) REVERT: D 375 GLU cc_start: 0.7059 (pt0) cc_final: 0.6665 (pm20) REVERT: D 399 LYS cc_start: 0.7987 (ttmm) cc_final: 0.7429 (tmmt) REVERT: B 61 LYS cc_start: 0.8146 (mtmm) cc_final: 0.7398 (mmtm) REVERT: B 144 GLU cc_start: 0.6579 (pm20) cc_final: 0.6247 (pm20) REVERT: B 197 MET cc_start: 0.8933 (mmp) cc_final: 0.8139 (mtp) REVERT: B 248 LYS cc_start: 0.8324 (tttm) cc_final: 0.8075 (tttm) REVERT: B 343 GLN cc_start: 0.7737 (mt0) cc_final: 0.7443 (mt0) REVERT: B 366 ASP cc_start: 0.6853 (OUTLIER) cc_final: 0.6527 (m-30) REVERT: B 375 GLU cc_start: 0.7137 (pt0) cc_final: 0.6776 (pm20) REVERT: B 399 LYS cc_start: 0.8057 (ttmm) cc_final: 0.7366 (tmmt) REVERT: C 42 LYS cc_start: 0.8296 (tmtp) cc_final: 0.7921 (ttpp) REVERT: C 61 LYS cc_start: 0.8231 (mtmm) cc_final: 0.7476 (mmtm) REVERT: C 100 GLU cc_start: 0.7910 (tp30) cc_final: 0.7157 (mp0) REVERT: C 150 ARG cc_start: 0.7244 (mtm110) cc_final: 0.6827 (mtm110) REVERT: C 165 ASP cc_start: 0.8936 (t0) cc_final: 0.8725 (t0) REVERT: C 197 MET cc_start: 0.8957 (mmp) cc_final: 0.8161 (mtp) REVERT: C 335 GLU cc_start: 0.6683 (mp0) cc_final: 0.6100 (tm-30) REVERT: C 338 GLU cc_start: 0.6931 (mt-10) cc_final: 0.6179 (mm-30) REVERT: C 343 GLN cc_start: 0.7489 (mt0) cc_final: 0.7090 (mt0) REVERT: C 375 GLU cc_start: 0.7062 (pt0) cc_final: 0.6692 (pm20) REVERT: C 399 LYS cc_start: 0.7997 (ttmm) cc_final: 0.7257 (tmmt) REVERT: E 61 LYS cc_start: 0.8148 (mtmm) cc_final: 0.7439 (mmtt) REVERT: E 100 GLU cc_start: 0.7888 (tp30) cc_final: 0.7143 (mp0) REVERT: E 158 GLU cc_start: 0.8071 (mm-30) cc_final: 0.7436 (tm-30) REVERT: E 197 MET cc_start: 0.8881 (mmp) cc_final: 0.8095 (mtp) REVERT: E 262 LYS cc_start: 0.8139 (mmtm) cc_final: 0.7899 (mmmt) REVERT: E 285 MET cc_start: 0.7533 (mtp) cc_final: 0.7211 (mtp) REVERT: E 335 GLU cc_start: 0.6682 (mp0) cc_final: 0.6185 (tm-30) REVERT: E 338 GLU cc_start: 0.6984 (mt-10) cc_final: 0.6014 (mm-30) REVERT: E 366 ASP cc_start: 0.6672 (OUTLIER) cc_final: 0.6418 (m-30) REVERT: E 375 GLU cc_start: 0.7036 (pt0) cc_final: 0.6661 (pm20) REVERT: E 399 LYS cc_start: 0.7995 (ttmm) cc_final: 0.7428 (tmmt) REVERT: F 42 LYS cc_start: 0.8299 (tmtp) cc_final: 0.7918 (ttpp) REVERT: F 61 LYS cc_start: 0.8229 (mtmm) cc_final: 0.7479 (mmtm) REVERT: F 100 GLU cc_start: 0.7907 (tp30) cc_final: 0.7151 (mp0) REVERT: F 150 ARG cc_start: 0.7242 (mtm110) cc_final: 0.6826 (mtm110) REVERT: F 165 ASP cc_start: 0.8940 (t0) cc_final: 0.8738 (t0) REVERT: F 197 MET cc_start: 0.8960 (mmp) cc_final: 0.8160 (mtp) REVERT: F 335 GLU cc_start: 0.6682 (mp0) cc_final: 0.6101 (tm-30) REVERT: F 338 GLU cc_start: 0.6925 (mt-10) cc_final: 0.6175 (mm-30) REVERT: F 343 GLN cc_start: 0.7484 (mt0) cc_final: 0.7080 (mt0) REVERT: F 375 GLU cc_start: 0.7074 (pt0) cc_final: 0.6703 (pm20) REVERT: F 399 LYS cc_start: 0.7993 (ttmm) cc_final: 0.7255 (tmmt) outliers start: 55 outliers final: 39 residues processed: 340 average time/residue: 0.7843 time to fit residues: 303.6327 Evaluate side-chains 340 residues out of total 2790 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 297 time to evaluate : 1.028 ------------------------------------------------------------------------------- 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 D residue 111 ASP Chi-restraints excluded: chain D residue 118 GLU Chi-restraints excluded: chain D residue 221 ILE Chi-restraints excluded: chain D residue 227 VAL Chi-restraints excluded: chain D residue 306 SER Chi-restraints excluded: chain D residue 366 ASP Chi-restraints excluded: chain D residue 459 ILE Chi-restraints excluded: chain D residue 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 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 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 Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 318 random chunks: chunk 72 optimal weight: 1.9990 chunk 172 optimal weight: 0.4980 chunk 287 optimal weight: 7.9990 chunk 35 optimal weight: 1.9990 chunk 155 optimal weight: 0.0770 chunk 135 optimal weight: 6.9990 chunk 166 optimal weight: 6.9990 chunk 115 optimal weight: 0.9980 chunk 144 optimal weight: 2.9990 chunk 184 optimal weight: 4.9990 chunk 118 optimal weight: 0.9980 overall best weight: 0.9140 ------------------------------------------------------------------------------- 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 E 343 GLN F 154 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4236 r_free = 0.4236 target = 0.206069 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 67)----------------| | r_work = 0.3809 r_free = 0.3809 target = 0.161899 restraints weight = 17355.778| |-----------------------------------------------------------------------------| r_work (start): 0.3790 rms_B_bonded: 0.80 r_work: 0.3419 rms_B_bonded: 1.98 restraints_weight: 0.5000 r_work: 0.3199 rms_B_bonded: 4.87 restraints_weight: 0.2500 r_work (final): 0.3199 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8175 moved from start: 0.2022 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 26124 Z= 0.121 Angle : 0.598 7.844 35424 Z= 0.308 Chirality : 0.046 0.191 4002 Planarity : 0.004 0.037 4494 Dihedral : 6.676 59.302 3534 Min Nonbonded Distance : 2.368 Molprobity Statistics. All-atom Clashscore : 6.00 Ramachandran Plot: Outliers : 0.19 % Allowed : 3.91 % Favored : 95.90 % Rotamer: Outliers : 1.62 % Allowed : 9.92 % Favored : 88.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.35 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.02 (0.15), residues: 3168 helix: 0.94 (0.16), residues: 1116 sheet: -0.31 (0.22), residues: 546 loop : -0.49 (0.16), residues: 1506 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 47 TYR 0.016 0.001 TYR A 245 PHE 0.018 0.001 PHE A 81 TRP 0.009 0.001 TRP D 402 HIS 0.003 0.001 HIS E 39 Details of bonding type rmsd covalent geometry : bond 0.00241 (26118) covalent geometry : angle 0.59811 (35424) hydrogen bonds : bond 0.04721 ( 948) hydrogen bonds : angle 5.73347 ( 2682) Misc. bond : bond 0.00155 ( 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 347 residues out of total 2790 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 302 time to evaluate : 1.053 Fit side-chains REVERT: A 61 LYS cc_start: 0.8381 (mtmm) cc_final: 0.7767 (mmtm) REVERT: A 112 ASP cc_start: 0.8705 (m-30) cc_final: 0.8436 (m-30) REVERT: A 197 MET cc_start: 0.9080 (mmp) cc_final: 0.8414 (mtp) REVERT: A 343 GLN cc_start: 0.8162 (mt0) cc_final: 0.7894 (mt0) REVERT: A 399 LYS cc_start: 0.8406 (ttmm) cc_final: 0.7849 (tmmt) REVERT: D 61 LYS cc_start: 0.8513 (mtmm) cc_final: 0.7900 (mmtm) REVERT: D 100 GLU cc_start: 0.8499 (tp30) cc_final: 0.7809 (mp0) REVERT: D 158 GLU cc_start: 0.8428 (mm-30) cc_final: 0.7868 (tm-30) REVERT: D 197 MET cc_start: 0.9021 (mmp) cc_final: 0.8340 (mtp) REVERT: D 285 MET cc_start: 0.7668 (mtp) cc_final: 0.7394 (mtp) REVERT: D 335 GLU cc_start: 0.7149 (mp0) cc_final: 0.6665 (tm-30) REVERT: D 338 GLU cc_start: 0.7424 (mt-10) cc_final: 0.6530 (mm-30) REVERT: D 375 GLU cc_start: 0.7350 (pt0) cc_final: 0.6957 (pm20) REVERT: D 399 LYS cc_start: 0.8301 (ttmm) cc_final: 0.7875 (tmmt) REVERT: D 461 MET cc_start: 0.2232 (OUTLIER) cc_final: 0.1840 (mpp) REVERT: B 61 LYS cc_start: 0.8378 (mtmm) cc_final: 0.7778 (mmtm) REVERT: B 112 ASP cc_start: 0.8704 (m-30) cc_final: 0.8439 (m-30) REVERT: B 197 MET cc_start: 0.9075 (mmp) cc_final: 0.8406 (mtp) REVERT: B 343 GLN cc_start: 0.8160 (mt0) cc_final: 0.7912 (mt0) REVERT: B 399 LYS cc_start: 0.8430 (ttmm) cc_final: 0.7872 (tmmt) REVERT: C 61 LYS cc_start: 0.8487 (mtmm) cc_final: 0.7851 (mmtm) REVERT: C 100 GLU cc_start: 0.8467 (tp30) cc_final: 0.7801 (mp0) REVERT: C 150 ARG cc_start: 0.7814 (mtm110) cc_final: 0.7562 (mtm110) REVERT: C 197 MET cc_start: 0.9106 (mmp) cc_final: 0.8440 (mtp) REVERT: C 335 GLU cc_start: 0.6931 (mp0) cc_final: 0.6413 (tm-30) REVERT: C 338 GLU cc_start: 0.7346 (mt-10) cc_final: 0.6617 (mm-30) REVERT: C 343 GLN cc_start: 0.7912 (mt0) cc_final: 0.7522 (mt0) REVERT: C 365 GLU cc_start: 0.7175 (mp0) cc_final: 0.6526 (mp0) REVERT: C 375 GLU cc_start: 0.7268 (pt0) cc_final: 0.6920 (pm20) REVERT: C 399 LYS cc_start: 0.8329 (ttmm) cc_final: 0.7763 (tmmt) REVERT: C 461 MET cc_start: 0.2493 (OUTLIER) cc_final: 0.1684 (mtt) REVERT: E 61 LYS cc_start: 0.8504 (mtmm) cc_final: 0.7903 (mmtm) REVERT: E 100 GLU cc_start: 0.8515 (tp30) cc_final: 0.7817 (mp0) REVERT: E 158 GLU cc_start: 0.8415 (mm-30) cc_final: 0.7859 (tm-30) REVERT: E 197 MET cc_start: 0.9023 (mmp) cc_final: 0.8396 (mtp) REVERT: E 285 MET cc_start: 0.7668 (mtp) cc_final: 0.7397 (mtp) REVERT: E 335 GLU cc_start: 0.7137 (mp0) cc_final: 0.6653 (tm-30) REVERT: E 338 GLU cc_start: 0.7424 (mt-10) cc_final: 0.6533 (mm-30) REVERT: E 375 GLU cc_start: 0.7329 (pt0) cc_final: 0.6930 (pm20) REVERT: E 399 LYS cc_start: 0.8299 (ttmm) cc_final: 0.7859 (tmmt) REVERT: F 61 LYS cc_start: 0.8491 (mtmm) cc_final: 0.7870 (mmtm) REVERT: F 100 GLU cc_start: 0.8463 (tp30) cc_final: 0.7809 (mp0) REVERT: F 150 ARG cc_start: 0.7804 (mtm110) cc_final: 0.7554 (mtm110) REVERT: F 197 MET cc_start: 0.9106 (mmp) cc_final: 0.8441 (mtp) REVERT: F 335 GLU cc_start: 0.6912 (mp0) cc_final: 0.6397 (tm-30) REVERT: F 338 GLU cc_start: 0.7353 (mt-10) cc_final: 0.6617 (mm-30) REVERT: F 343 GLN cc_start: 0.7911 (mt0) cc_final: 0.7510 (mt0) REVERT: F 365 GLU cc_start: 0.7212 (mp0) cc_final: 0.6510 (mp0) REVERT: F 375 GLU cc_start: 0.7276 (pt0) cc_final: 0.6927 (pm20) REVERT: F 399 LYS cc_start: 0.8324 (ttmm) cc_final: 0.7761 (tmmt) REVERT: F 461 MET cc_start: 0.2521 (OUTLIER) cc_final: 0.1691 (mtt) outliers start: 45 outliers final: 33 residues processed: 339 average time/residue: 0.7725 time to fit residues: 298.2207 Evaluate side-chains 328 residues out of total 2790 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 292 time to evaluate : 1.079 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 118 GLU 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 221 ILE 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 D residue 469 VAL Chi-restraints excluded: chain B residue 118 GLU 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 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 221 ILE 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 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 318 random chunks: chunk 147 optimal weight: 0.7980 chunk 252 optimal weight: 7.9990 chunk 45 optimal weight: 20.0000 chunk 242 optimal weight: 9.9990 chunk 230 optimal weight: 7.9990 chunk 1 optimal weight: 0.8980 chunk 16 optimal weight: 3.9990 chunk 175 optimal weight: 0.9980 chunk 76 optimal weight: 5.9990 chunk 297 optimal weight: 5.9990 chunk 137 optimal weight: 10.0000 overall best weight: 2.5384 ------------------------------------------------------------------------------- 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 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 = 0.198180 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3369 r_free = 0.3369 target = 0.126983 restraints weight = 17065.238| |-----------------------------------------------------------------------------| r_work (start): 0.3335 rms_B_bonded: 1.53 r_work: 0.3149 rms_B_bonded: 2.10 restraints_weight: 0.5000 r_work: 0.3029 rms_B_bonded: 3.16 restraints_weight: 0.2500 r_work (final): 0.3029 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8007 moved from start: 0.2179 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 26124 Z= 0.194 Angle : 0.700 8.727 35424 Z= 0.359 Chirality : 0.050 0.237 4002 Planarity : 0.004 0.038 4494 Dihedral : 7.154 59.343 3534 Min Nonbonded Distance : 2.284 Molprobity Statistics. All-atom Clashscore : 6.14 Ramachandran Plot: Outliers : 0.19 % Allowed : 4.45 % Favored : 95.36 % Rotamer: Outliers : 1.88 % Allowed : 9.99 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.12 (0.15), residues: 3168 helix: 0.80 (0.16), residues: 1104 sheet: -0.43 (0.21), residues: 546 loop : -0.51 (0.16), residues: 1518 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG A 47 TYR 0.024 0.002 TYR A 245 PHE 0.024 0.002 PHE C 81 TRP 0.011 0.001 TRP F 402 HIS 0.006 0.001 HIS C 39 Details of bonding type rmsd covalent geometry : bond 0.00404 (26118) covalent geometry : angle 0.69994 (35424) hydrogen bonds : bond 0.06074 ( 948) hydrogen bonds : angle 6.09312 ( 2682) Misc. bond : bond 0.00396 ( 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 350 residues out of total 2790 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 298 time to evaluate : 1.102 Fit side-chains REVERT: A 61 LYS cc_start: 0.8171 (mtmm) cc_final: 0.7421 (mmtm) REVERT: A 197 MET cc_start: 0.8896 (mmp) cc_final: 0.8110 (mtp) REVERT: A 343 GLN cc_start: 0.7746 (mt0) cc_final: 0.7445 (mt0) REVERT: A 375 GLU cc_start: 0.7170 (pt0) cc_final: 0.6797 (pm20) REVERT: A 399 LYS cc_start: 0.8149 (ttmm) cc_final: 0.7420 (tmmt) REVERT: D 61 LYS cc_start: 0.8140 (mtmm) cc_final: 0.7499 (mmtm) REVERT: D 100 GLU cc_start: 0.7920 (tp30) cc_final: 0.7170 (mp0) REVERT: D 158 GLU cc_start: 0.8135 (mm-30) cc_final: 0.7472 (tm-30) REVERT: D 197 MET cc_start: 0.8887 (mmp) cc_final: 0.8126 (mtp) REVERT: D 262 LYS cc_start: 0.8192 (mmtm) cc_final: 0.7948 (mmmt) REVERT: D 285 MET cc_start: 0.7486 (mtp) cc_final: 0.7141 (mtp) REVERT: D 335 GLU cc_start: 0.6637 (mp0) cc_final: 0.6089 (tm-30) REVERT: D 338 GLU cc_start: 0.6967 (mt-10) cc_final: 0.5965 (mm-30) REVERT: D 366 ASP cc_start: 0.6561 (OUTLIER) cc_final: 0.6312 (m-30) REVERT: D 375 GLU cc_start: 0.7058 (pt0) cc_final: 0.6693 (pm20) REVERT: D 399 LYS cc_start: 0.7987 (ttmm) cc_final: 0.7432 (tmmt) REVERT: B 61 LYS cc_start: 0.8166 (mtmm) cc_final: 0.7414 (mmtm) REVERT: B 144 GLU cc_start: 0.6605 (pm20) cc_final: 0.6286 (pm20) REVERT: B 197 MET cc_start: 0.8892 (mmp) cc_final: 0.8105 (mtp) REVERT: B 248 LYS cc_start: 0.8306 (tttm) cc_final: 0.8099 (tttp) REVERT: B 343 GLN cc_start: 0.7742 (mt0) cc_final: 0.7441 (mt0) REVERT: B 366 ASP cc_start: 0.6882 (OUTLIER) cc_final: 0.6556 (m-30) REVERT: B 375 GLU cc_start: 0.7171 (pt0) cc_final: 0.6821 (pm20) REVERT: B 399 LYS cc_start: 0.8159 (ttmm) cc_final: 0.7422 (tmmt) REVERT: C 42 LYS cc_start: 0.8314 (tmtp) cc_final: 0.7933 (ttpp) REVERT: C 61 LYS cc_start: 0.8251 (mtmm) cc_final: 0.7491 (mmtm) REVERT: C 100 GLU cc_start: 0.7940 (tp30) cc_final: 0.7170 (mp0) REVERT: C 150 ARG cc_start: 0.7277 (mtm110) cc_final: 0.6860 (mtm110) REVERT: C 197 MET cc_start: 0.8975 (mmp) cc_final: 0.8186 (mtp) REVERT: C 335 GLU cc_start: 0.6667 (mp0) cc_final: 0.6060 (tm-30) REVERT: C 338 GLU cc_start: 0.6839 (mt-10) cc_final: 0.6040 (mm-30) REVERT: C 343 GLN cc_start: 0.7498 (mt0) cc_final: 0.7046 (mt0) REVERT: C 375 GLU cc_start: 0.7103 (pt0) cc_final: 0.6704 (pm20) REVERT: C 399 LYS cc_start: 0.8017 (ttmm) cc_final: 0.7279 (tmmt) REVERT: C 461 MET cc_start: 0.2419 (OUTLIER) cc_final: 0.1639 (mtt) REVERT: E 61 LYS cc_start: 0.8138 (mtmm) cc_final: 0.7429 (mmtt) REVERT: E 100 GLU cc_start: 0.7909 (tp30) cc_final: 0.7160 (mp0) REVERT: E 158 GLU cc_start: 0.8122 (mm-30) cc_final: 0.7474 (tm-30) REVERT: E 197 MET cc_start: 0.8891 (mmp) cc_final: 0.8127 (mtp) REVERT: E 262 LYS cc_start: 0.8196 (mmtm) cc_final: 0.7953 (mmmt) REVERT: E 285 MET cc_start: 0.7494 (mtp) cc_final: 0.7150 (mtp) REVERT: E 335 GLU cc_start: 0.6635 (mp0) cc_final: 0.6072 (tm-30) REVERT: E 338 GLU cc_start: 0.6967 (mt-10) cc_final: 0.5961 (mm-30) REVERT: E 366 ASP cc_start: 0.6595 (OUTLIER) cc_final: 0.6323 (m-30) REVERT: E 375 GLU cc_start: 0.7058 (pt0) cc_final: 0.6692 (pm20) REVERT: E 399 LYS cc_start: 0.7995 (ttmm) cc_final: 0.7442 (tmmt) REVERT: F 42 LYS cc_start: 0.8313 (tmtp) cc_final: 0.7934 (ttpp) REVERT: F 61 LYS cc_start: 0.8250 (mtmm) cc_final: 0.7494 (mmtm) REVERT: F 100 GLU cc_start: 0.7942 (tp30) cc_final: 0.7171 (mp0) REVERT: F 150 ARG cc_start: 0.7277 (mtm110) cc_final: 0.6862 (mtm110) REVERT: F 197 MET cc_start: 0.8973 (mmp) cc_final: 0.8180 (mtp) REVERT: F 335 GLU cc_start: 0.6672 (mp0) cc_final: 0.6056 (tm-30) REVERT: F 338 GLU cc_start: 0.6825 (mt-10) cc_final: 0.6029 (mm-30) REVERT: F 343 GLN cc_start: 0.7488 (mt0) cc_final: 0.7029 (mt0) REVERT: F 375 GLU cc_start: 0.7045 (pt0) cc_final: 0.6643 (pm20) REVERT: F 399 LYS cc_start: 0.8012 (ttmm) cc_final: 0.7273 (tmmt) outliers start: 52 outliers final: 42 residues processed: 335 average time/residue: 0.7584 time to fit residues: 289.4093 Evaluate side-chains 343 residues out of total 2790 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 297 time to evaluate : 0.882 ------------------------------------------------------------------------------- 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 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 D residue 469 VAL Chi-restraints excluded: chain B residue 118 GLU Chi-restraints excluded: chain B residue 221 ILE Chi-restraints excluded: chain B residue 227 VAL Chi-restraints excluded: chain B residue 366 ASP Chi-restraints excluded: chain B residue 459 ILE Chi-restraints excluded: chain B residue 461 MET Chi-restraints excluded: chain B residue 469 VAL Chi-restraints excluded: chain C residue 118 GLU Chi-restraints excluded: chain C residue 133 THR Chi-restraints excluded: chain C residue 221 ILE Chi-restraints excluded: chain C residue 227 VAL Chi-restraints excluded: chain C residue 459 ILE Chi-restraints excluded: chain C residue 461 MET Chi-restraints excluded: chain C residue 469 VAL Chi-restraints excluded: chain E residue 111 ASP Chi-restraints excluded: chain E residue 118 GLU Chi-restraints excluded: chain E residue 133 THR Chi-restraints excluded: chain E residue 221 ILE Chi-restraints excluded: chain E residue 227 VAL Chi-restraints excluded: chain E residue 306 SER Chi-restraints excluded: chain E residue 366 ASP Chi-restraints excluded: chain E residue 459 ILE Chi-restraints excluded: chain E residue 461 MET Chi-restraints excluded: chain E residue 469 VAL Chi-restraints excluded: chain F residue 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 318 random chunks: chunk 146 optimal weight: 7.9990 chunk 47 optimal weight: 9.9990 chunk 56 optimal weight: 5.9990 chunk 110 optimal weight: 5.9990 chunk 251 optimal weight: 1.9990 chunk 6 optimal weight: 9.9990 chunk 229 optimal weight: 0.9990 chunk 306 optimal weight: 0.6980 chunk 18 optimal weight: 1.9990 chunk 137 optimal weight: 6.9990 chunk 51 optimal weight: 8.9990 overall best weight: 2.3388 ------------------------------------------------------------------------------- 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 E 154 GLN 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 = 0.4151 r_free = 0.4151 target = 0.198669 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3408 r_free = 0.3408 target = 0.130033 restraints weight = 17155.674| |-----------------------------------------------------------------------------| r_work (start): 0.3381 rms_B_bonded: 1.32 r_work: 0.3147 rms_B_bonded: 2.18 restraints_weight: 0.5000 r_work: 0.3037 rms_B_bonded: 3.17 restraints_weight: 0.2500 r_work (final): 0.3037 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8045 moved from start: 0.2204 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 26124 Z= 0.183 Angle : 0.685 8.609 35424 Z= 0.351 Chirality : 0.049 0.231 4002 Planarity : 0.004 0.038 4494 Dihedral : 7.155 59.093 3534 Min Nonbonded Distance : 2.325 Molprobity Statistics. All-atom Clashscore : 6.18 Ramachandran Plot: Outliers : 0.19 % Allowed : 4.04 % Favored : 95.77 % Rotamer: Outliers : 1.77 % Allowed : 10.03 % Favored : 88.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.35 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.15 (0.15), residues: 3168 helix: 0.77 (0.16), residues: 1104 sheet: -0.48 (0.21), residues: 546 loop : -0.51 (0.16), residues: 1518 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 190 TYR 0.023 0.002 TYR A 245 PHE 0.023 0.002 PHE F 81 TRP 0.011 0.001 TRP A 402 HIS 0.005 0.001 HIS D 39 Details of bonding type rmsd covalent geometry : bond 0.00381 (26118) covalent geometry : angle 0.68460 (35424) hydrogen bonds : bond 0.05902 ( 948) hydrogen bonds : angle 6.04745 ( 2682) Misc. bond : bond 0.00348 ( 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 346 residues out of total 2790 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 297 time to evaluate : 0.864 Fit side-chains REVERT: A 61 LYS cc_start: 0.8197 (mtmm) cc_final: 0.7484 (mmtm) REVERT: A 197 MET cc_start: 0.8927 (mmp) cc_final: 0.8169 (mtp) REVERT: A 343 GLN cc_start: 0.7774 (mt0) cc_final: 0.7446 (mt0) REVERT: A 375 GLU cc_start: 0.7207 (pt0) cc_final: 0.6867 (pm20) REVERT: A 399 LYS cc_start: 0.8225 (ttmm) cc_final: 0.7537 (tmmt) REVERT: D 61 LYS cc_start: 0.8174 (mtmm) cc_final: 0.7532 (mmtm) REVERT: D 100 GLU cc_start: 0.7983 (tp30) cc_final: 0.7266 (mp0) REVERT: D 158 GLU cc_start: 0.8158 (mm-30) cc_final: 0.7548 (tm-30) REVERT: D 197 MET cc_start: 0.8887 (mmp) cc_final: 0.8152 (mtp) REVERT: D 262 LYS cc_start: 0.8257 (mmtm) cc_final: 0.8018 (mmmt) REVERT: D 285 MET cc_start: 0.7526 (mtp) cc_final: 0.7188 (mtp) REVERT: D 335 GLU cc_start: 0.6706 (mp0) cc_final: 0.6225 (tm-30) REVERT: D 338 GLU cc_start: 0.7000 (mt-10) cc_final: 0.6029 (mm-30) REVERT: D 399 LYS cc_start: 0.8054 (ttmm) cc_final: 0.7538 (tmmt) REVERT: B 61 LYS cc_start: 0.8198 (mtmm) cc_final: 0.7480 (mmtm) REVERT: B 197 MET cc_start: 0.8923 (mmp) cc_final: 0.8161 (mtp) REVERT: B 343 GLN cc_start: 0.7778 (mt0) cc_final: 0.7455 (mt0) REVERT: B 375 GLU cc_start: 0.7208 (pt0) cc_final: 0.6872 (pm20) REVERT: B 399 LYS cc_start: 0.8236 (ttmm) cc_final: 0.7542 (tmmt) REVERT: C 61 LYS cc_start: 0.8278 (mtmm) cc_final: 0.7554 (mmtm) REVERT: C 100 GLU cc_start: 0.7998 (tp30) cc_final: 0.7269 (mp0) REVERT: C 150 ARG cc_start: 0.7354 (mtm110) cc_final: 0.6934 (mtm110) REVERT: C 197 MET cc_start: 0.9019 (mmp) cc_final: 0.8242 (mtp) REVERT: C 335 GLU cc_start: 0.6737 (mp0) cc_final: 0.6141 (tm-30) REVERT: C 338 GLU cc_start: 0.6891 (mt-10) cc_final: 0.6135 (mm-30) REVERT: C 343 GLN cc_start: 0.7546 (mt0) cc_final: 0.7158 (mt0) REVERT: C 375 GLU cc_start: 0.7120 (pt0) cc_final: 0.6734 (pm20) REVERT: C 399 LYS cc_start: 0.8069 (ttmm) cc_final: 0.7366 (tmmt) REVERT: C 461 MET cc_start: 0.2459 (OUTLIER) cc_final: 0.1816 (mmm) REVERT: E 61 LYS cc_start: 0.8173 (mtmm) cc_final: 0.7502 (mmtt) REVERT: E 100 GLU cc_start: 0.7960 (tp30) cc_final: 0.7249 (mp0) REVERT: E 158 GLU cc_start: 0.8142 (mm-30) cc_final: 0.7545 (tm-30) REVERT: E 197 MET cc_start: 0.8889 (mmp) cc_final: 0.8155 (mtp) REVERT: E 262 LYS cc_start: 0.8249 (mmtm) cc_final: 0.8016 (mmmt) REVERT: E 285 MET cc_start: 0.7527 (mtp) cc_final: 0.7192 (mtp) REVERT: E 335 GLU cc_start: 0.6703 (mp0) cc_final: 0.6219 (tm-30) REVERT: E 338 GLU cc_start: 0.6992 (mt-10) cc_final: 0.6022 (mm-30) REVERT: E 399 LYS cc_start: 0.8060 (ttmm) cc_final: 0.7547 (tmmt) REVERT: F 42 LYS cc_start: 0.8355 (tmtp) cc_final: 0.8001 (ttpp) REVERT: F 61 LYS cc_start: 0.8277 (mtmm) cc_final: 0.7557 (mmtm) REVERT: F 100 GLU cc_start: 0.8004 (tp30) cc_final: 0.7269 (mp0) REVERT: F 150 ARG cc_start: 0.7351 (mtm110) cc_final: 0.6933 (mtm110) REVERT: F 197 MET cc_start: 0.9016 (mmp) cc_final: 0.8237 (mtp) REVERT: F 335 GLU cc_start: 0.6741 (mp0) cc_final: 0.6143 (tm-30) REVERT: F 338 GLU cc_start: 0.6863 (mt-10) cc_final: 0.6102 (mm-30) REVERT: F 343 GLN cc_start: 0.7524 (mt0) cc_final: 0.7141 (mt0) REVERT: F 365 GLU cc_start: 0.6902 (mp0) cc_final: 0.6115 (mp0) REVERT: F 375 GLU cc_start: 0.7126 (pt0) cc_final: 0.6739 (pm20) REVERT: F 399 LYS cc_start: 0.8060 (ttmm) cc_final: 0.7361 (tmmt) REVERT: F 461 MET cc_start: 0.2435 (OUTLIER) cc_final: 0.1802 (mmm) outliers start: 49 outliers final: 42 residues processed: 335 average time/residue: 0.6548 time to fit residues: 250.6653 Evaluate side-chains 338 residues out of total 2790 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 294 time to evaluate : 0.862 ------------------------------------------------------------------------------- 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 A residue 469 VAL Chi-restraints excluded: chain D residue 111 ASP Chi-restraints excluded: chain D residue 118 GLU Chi-restraints excluded: chain D residue 221 ILE Chi-restraints excluded: chain D residue 227 VAL Chi-restraints excluded: chain D residue 306 SER Chi-restraints excluded: chain D residue 459 ILE Chi-restraints excluded: chain D residue 461 MET Chi-restraints excluded: chain D residue 469 VAL Chi-restraints excluded: chain B residue 111 ASP Chi-restraints excluded: chain B residue 118 GLU Chi-restraints excluded: chain B residue 221 ILE Chi-restraints excluded: chain B residue 227 VAL Chi-restraints excluded: chain B residue 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 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 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 84 optimal weight: 0.7980 chunk 266 optimal weight: 0.8980 chunk 64 optimal weight: 4.9990 chunk 7 optimal weight: 2.9990 chunk 206 optimal weight: 30.0000 chunk 193 optimal weight: 7.9990 chunk 303 optimal weight: 0.9990 chunk 139 optimal weight: 5.9990 chunk 278 optimal weight: 8.9990 chunk 128 optimal weight: 5.9990 chunk 261 optimal weight: 0.0370 overall best weight: 1.1462 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 154 GLN D 343 GLN C 154 GLN E 154 GLN 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 = 0.4226 r_free = 0.4226 target = 0.205067 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.3794 r_free = 0.3794 target = 0.160508 restraints weight = 17200.404| |-----------------------------------------------------------------------------| r_work (start): 0.3778 rms_B_bonded: 0.78 r_work: 0.3395 rms_B_bonded: 2.09 restraints_weight: 0.5000 r_work: 0.3190 rms_B_bonded: 4.54 restraints_weight: 0.2500 r_work (final): 0.3190 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8187 moved from start: 0.2170 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 26124 Z= 0.131 Angle : 0.615 7.893 35424 Z= 0.317 Chirality : 0.046 0.202 4002 Planarity : 0.004 0.037 4494 Dihedral : 6.820 59.947 3534 Min Nonbonded Distance : 2.364 Molprobity Statistics. All-atom Clashscore : 6.12 Ramachandran Plot: Outliers : 0.06 % Allowed : 4.10 % Favored : 95.83 % Rotamer: Outliers : 1.62 % Allowed : 10.35 % Favored : 88.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.35 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.02 (0.15), residues: 3168 helix: 0.96 (0.16), residues: 1104 sheet: -0.40 (0.21), residues: 546 loop : -0.51 (0.16), residues: 1518 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 47 TYR 0.017 0.002 TYR B 245 PHE 0.019 0.002 PHE A 81 TRP 0.010 0.001 TRP D 402 HIS 0.004 0.001 HIS E 39 Details of bonding type rmsd covalent geometry : bond 0.00264 (26118) covalent geometry : angle 0.61536 (35424) hydrogen bonds : bond 0.04984 ( 948) hydrogen bonds : angle 5.76932 ( 2682) Misc. bond : bond 0.00193 ( 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 346 residues out of total 2790 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 301 time to evaluate : 0.741 Fit side-chains REVERT: A 61 LYS cc_start: 0.8403 (mtmm) cc_final: 0.7785 (mmtm) REVERT: A 112 ASP cc_start: 0.8695 (m-30) cc_final: 0.8426 (m-30) REVERT: A 197 MET cc_start: 0.9038 (mmp) cc_final: 0.8404 (mtp) REVERT: A 343 GLN cc_start: 0.8134 (mt0) cc_final: 0.7867 (mt0) REVERT: A 399 LYS cc_start: 0.8463 (ttmm) cc_final: 0.7912 (tmmt) REVERT: D 61 LYS cc_start: 0.8456 (mtmm) cc_final: 0.7868 (mmtm) REVERT: D 100 GLU cc_start: 0.8477 (tp30) cc_final: 0.7798 (mp0) REVERT: D 158 GLU cc_start: 0.8436 (mm-30) cc_final: 0.7860 (tm-30) REVERT: D 197 MET cc_start: 0.8987 (mmp) cc_final: 0.8366 (mtp) REVERT: D 285 MET cc_start: 0.7632 (mtp) cc_final: 0.7334 (mtp) REVERT: D 335 GLU cc_start: 0.7108 (mp0) cc_final: 0.6686 (tm-30) REVERT: D 338 GLU cc_start: 0.7395 (mt-10) cc_final: 0.6489 (mm-30) REVERT: D 367 MET cc_start: 0.7846 (mtp) cc_final: 0.7617 (mtp) REVERT: D 375 GLU cc_start: 0.7381 (pt0) cc_final: 0.7057 (pm20) REVERT: D 399 LYS cc_start: 0.8284 (ttmm) cc_final: 0.7890 (tmmt) REVERT: D 461 MET cc_start: 0.2339 (OUTLIER) cc_final: 0.1894 (mpp) REVERT: B 61 LYS cc_start: 0.8407 (mtmm) cc_final: 0.7794 (mmtm) REVERT: B 112 ASP cc_start: 0.8704 (m-30) cc_final: 0.8438 (m-30) REVERT: B 197 MET cc_start: 0.9032 (mmp) cc_final: 0.8396 (mtp) REVERT: B 343 GLN cc_start: 0.8150 (mt0) cc_final: 0.7879 (mt0) REVERT: B 399 LYS cc_start: 0.8492 (ttmm) cc_final: 0.7940 (tmmt) REVERT: C 61 LYS cc_start: 0.8484 (mtmm) cc_final: 0.7857 (mmtm) REVERT: C 100 GLU cc_start: 0.8459 (tp30) cc_final: 0.7805 (mp0) REVERT: C 150 ARG cc_start: 0.7816 (mtm110) cc_final: 0.7564 (mtm110) REVERT: C 197 MET cc_start: 0.9104 (mmp) cc_final: 0.8448 (mtp) REVERT: C 335 GLU cc_start: 0.7056 (mp0) cc_final: 0.6481 (tm-30) REVERT: C 338 GLU cc_start: 0.7268 (mt-10) cc_final: 0.6536 (mm-30) REVERT: C 343 GLN cc_start: 0.7841 (mt0) cc_final: 0.7451 (mt0) REVERT: C 365 GLU cc_start: 0.7166 (mp0) cc_final: 0.6495 (mp0) REVERT: C 375 GLU cc_start: 0.7346 (pt0) cc_final: 0.7007 (pm20) REVERT: C 399 LYS cc_start: 0.8382 (ttmm) cc_final: 0.7822 (tmmt) REVERT: C 461 MET cc_start: 0.2355 (OUTLIER) cc_final: 0.1773 (mmm) REVERT: E 61 LYS cc_start: 0.8442 (mtmm) cc_final: 0.7861 (mmtm) REVERT: E 100 GLU cc_start: 0.8490 (tp30) cc_final: 0.7800 (mp0) REVERT: E 158 GLU cc_start: 0.8429 (mm-30) cc_final: 0.7846 (tm-30) REVERT: E 197 MET cc_start: 0.8988 (mmp) cc_final: 0.8371 (mtp) REVERT: E 285 MET cc_start: 0.7655 (mtp) cc_final: 0.7362 (mtp) REVERT: E 335 GLU cc_start: 0.7111 (mp0) cc_final: 0.6687 (tm-30) REVERT: E 338 GLU cc_start: 0.7394 (mt-10) cc_final: 0.6496 (mm-30) REVERT: E 375 GLU cc_start: 0.7369 (pt0) cc_final: 0.7043 (pm20) REVERT: E 399 LYS cc_start: 0.8310 (ttmm) cc_final: 0.7899 (tmmt) REVERT: E 461 MET cc_start: 0.2289 (OUTLIER) cc_final: 0.1855 (mpp) REVERT: F 61 LYS cc_start: 0.8479 (mtmm) cc_final: 0.7869 (mmtm) REVERT: F 100 GLU cc_start: 0.8459 (tp30) cc_final: 0.7807 (mp0) REVERT: F 150 ARG cc_start: 0.7797 (mtm110) cc_final: 0.7544 (mtm110) REVERT: F 197 MET cc_start: 0.9109 (mmp) cc_final: 0.8452 (mtp) REVERT: F 335 GLU cc_start: 0.7039 (mp0) cc_final: 0.6472 (tm-30) REVERT: F 338 GLU cc_start: 0.7270 (mt-10) cc_final: 0.6547 (mm-30) REVERT: F 343 GLN cc_start: 0.7837 (mt0) cc_final: 0.7501 (mt0) REVERT: F 365 GLU cc_start: 0.7128 (mp0) cc_final: 0.6455 (mp0) REVERT: F 375 GLU cc_start: 0.7341 (pt0) cc_final: 0.7004 (pm20) REVERT: F 399 LYS cc_start: 0.8381 (ttmm) cc_final: 0.7822 (tmmt) REVERT: F 461 MET cc_start: 0.2379 (OUTLIER) cc_final: 0.1796 (mmm) outliers start: 45 outliers final: 37 residues processed: 336 average time/residue: 0.7297 time to fit residues: 279.8791 Evaluate side-chains 329 residues out of total 2790 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 288 time to evaluate : 0.667 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 118 GLU 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 221 ILE 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 D residue 469 VAL Chi-restraints excluded: chain B residue 118 GLU 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 118 GLU Chi-restraints excluded: chain C residue 133 THR Chi-restraints excluded: chain C residue 221 ILE Chi-restraints excluded: chain C residue 227 VAL Chi-restraints excluded: chain C residue 272 ILE Chi-restraints excluded: chain C residue 459 ILE Chi-restraints excluded: chain C residue 461 MET Chi-restraints excluded: chain 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 221 ILE 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 E residue 469 VAL 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 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 38 optimal weight: 0.2980 chunk 154 optimal weight: 0.8980 chunk 270 optimal weight: 9.9990 chunk 292 optimal weight: 5.9990 chunk 220 optimal weight: 0.0980 chunk 226 optimal weight: 9.9990 chunk 269 optimal weight: 1.9990 chunk 277 optimal weight: 6.9990 chunk 80 optimal weight: 3.9990 chunk 4 optimal weight: 5.9990 chunk 265 optimal weight: 0.9980 overall best weight: 0.8582 ------------------------------------------------------------------------------- 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 E 343 GLN F 154 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4238 r_free = 0.4238 target = 0.206324 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3577 r_free = 0.3577 target = 0.144995 restraints weight = 17303.658| |-----------------------------------------------------------------------------| r_work (start): 0.3507 rms_B_bonded: 2.68 r_work: 0.3274 rms_B_bonded: 2.30 restraints_weight: 0.5000 r_work: 0.3166 rms_B_bonded: 3.42 restraints_weight: 0.2500 r_work (final): 0.3166 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8034 moved from start: 0.2175 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 26124 Z= 0.119 Angle : 0.595 7.675 35424 Z= 0.307 Chirality : 0.046 0.204 4002 Planarity : 0.004 0.036 4494 Dihedral : 6.568 58.634 3534 Min Nonbonded Distance : 2.373 Molprobity Statistics. All-atom Clashscore : 6.00 Ramachandran Plot: Outliers : 0.06 % Allowed : 4.29 % Favored : 95.64 % Rotamer: Outliers : 1.48 % Allowed : 10.71 % Favored : 87.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.35 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.01 (0.15), residues: 3168 helix: 0.95 (0.16), residues: 1122 sheet: -0.33 (0.22), residues: 546 loop : -0.50 (0.16), residues: 1500 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 47 TYR 0.015 0.001 TYR A 245 PHE 0.018 0.001 PHE C 81 TRP 0.009 0.001 TRP D 402 HIS 0.003 0.001 HIS E 39 Details of bonding type rmsd covalent geometry : bond 0.00238 (26118) covalent geometry : angle 0.59474 (35424) hydrogen bonds : bond 0.04633 ( 948) hydrogen bonds : angle 5.61926 ( 2682) Misc. bond : bond 0.00153 ( 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 332 residues out of total 2790 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 291 time to evaluate : 0.683 Fit side-chains REVERT: A 61 LYS cc_start: 0.8174 (mtmm) cc_final: 0.7501 (mmtm) REVERT: A 112 ASP cc_start: 0.8522 (m-30) cc_final: 0.8258 (m-30) REVERT: A 197 MET cc_start: 0.8961 (mmp) cc_final: 0.8218 (mtp) REVERT: A 343 GLN cc_start: 0.7841 (mt0) cc_final: 0.7530 (mt0) REVERT: A 365 GLU cc_start: 0.7016 (mp0) cc_final: 0.6530 (mp0) REVERT: A 399 LYS cc_start: 0.8275 (ttmm) cc_final: 0.7626 (tmmt) REVERT: D 61 LYS cc_start: 0.8268 (mtmm) cc_final: 0.7607 (mmtm) REVERT: D 100 GLU cc_start: 0.8079 (tp30) cc_final: 0.7357 (mp0) REVERT: D 158 GLU cc_start: 0.8179 (mm-30) cc_final: 0.7668 (tm-30) REVERT: D 285 MET cc_start: 0.7412 (mtp) cc_final: 0.7167 (mtp) REVERT: D 335 GLU cc_start: 0.6819 (mp0) cc_final: 0.6328 (tm-30) REVERT: D 338 GLU cc_start: 0.7053 (mt-10) cc_final: 0.6084 (mm-30) REVERT: D 367 MET cc_start: 0.7593 (mtp) cc_final: 0.7392 (mtp) REVERT: D 399 LYS cc_start: 0.8085 (ttmm) cc_final: 0.7591 (tmmt) REVERT: B 61 LYS cc_start: 0.8171 (mtmm) cc_final: 0.7499 (mmtm) REVERT: B 112 ASP cc_start: 0.8529 (m-30) cc_final: 0.8267 (m-30) REVERT: B 197 MET cc_start: 0.8954 (mmp) cc_final: 0.8208 (mtp) REVERT: B 343 GLN cc_start: 0.7847 (mt0) cc_final: 0.7535 (mt0) REVERT: B 365 GLU cc_start: 0.6956 (mp0) cc_final: 0.6474 (mp0) REVERT: B 399 LYS cc_start: 0.8293 (ttmm) cc_final: 0.7636 (tmmt) REVERT: C 61 LYS cc_start: 0.8270 (mtmm) cc_final: 0.7566 (mmtm) REVERT: C 100 GLU cc_start: 0.8028 (tp30) cc_final: 0.7323 (mp0) REVERT: C 150 ARG cc_start: 0.7326 (mtm110) cc_final: 0.7024 (mtm110) REVERT: C 197 MET cc_start: 0.9012 (mmp) cc_final: 0.8217 (mtp) REVERT: C 335 GLU cc_start: 0.6685 (mp0) cc_final: 0.6110 (tm-30) REVERT: C 338 GLU cc_start: 0.6985 (mt-10) cc_final: 0.6201 (mm-30) REVERT: C 343 GLN cc_start: 0.7451 (mt0) cc_final: 0.7028 (mt0) REVERT: C 365 GLU cc_start: 0.6850 (mp0) cc_final: 0.6143 (mp0) REVERT: C 399 LYS cc_start: 0.8162 (ttmm) cc_final: 0.7521 (tmmt) REVERT: C 461 MET cc_start: 0.2494 (OUTLIER) cc_final: 0.1745 (mmm) REVERT: E 61 LYS cc_start: 0.8259 (mtmm) cc_final: 0.7592 (mmtm) REVERT: E 100 GLU cc_start: 0.8079 (tp30) cc_final: 0.7348 (mp0) REVERT: E 158 GLU cc_start: 0.8156 (mm-30) cc_final: 0.7659 (tm-30) REVERT: E 285 MET cc_start: 0.7421 (mtp) cc_final: 0.7068 (mtp) REVERT: E 335 GLU cc_start: 0.6825 (mp0) cc_final: 0.6337 (tm-30) REVERT: E 338 GLU cc_start: 0.7061 (mt-10) cc_final: 0.6096 (mm-30) REVERT: E 399 LYS cc_start: 0.8097 (ttmm) cc_final: 0.7601 (tmmt) REVERT: F 61 LYS cc_start: 0.8274 (mtmm) cc_final: 0.7586 (mmtm) REVERT: F 100 GLU cc_start: 0.8041 (tp30) cc_final: 0.7340 (mp0) REVERT: F 150 ARG cc_start: 0.7315 (mtm110) cc_final: 0.7014 (mtm110) REVERT: F 197 MET cc_start: 0.9011 (mmp) cc_final: 0.8210 (mtp) REVERT: F 335 GLU cc_start: 0.6683 (mp0) cc_final: 0.6105 (tm-30) REVERT: F 338 GLU cc_start: 0.6980 (mt-10) cc_final: 0.6233 (mm-30) REVERT: F 343 GLN cc_start: 0.7440 (mt0) cc_final: 0.7018 (mt0) REVERT: F 365 GLU cc_start: 0.6784 (mp0) cc_final: 0.6140 (mp0) REVERT: F 399 LYS cc_start: 0.8160 (ttmm) cc_final: 0.7516 (tmmt) REVERT: F 430 MET cc_start: 0.6160 (mmm) cc_final: 0.5864 (mmm) REVERT: F 461 MET cc_start: 0.2385 (OUTLIER) cc_final: 0.1692 (mmm) outliers start: 41 outliers final: 34 residues processed: 326 average time/residue: 0.6684 time to fit residues: 249.5540 Evaluate side-chains 320 residues out of total 2790 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 284 time to evaluate : 0.845 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 118 GLU 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 469 VAL Chi-restraints excluded: chain B residue 118 GLU 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 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 E residue 469 VAL Chi-restraints excluded: chain F residue 133 THR Chi-restraints excluded: chain F residue 221 ILE Chi-restraints excluded: chain F residue 227 VAL Chi-restraints excluded: chain F residue 272 ILE Chi-restraints excluded: chain F residue 459 ILE Chi-restraints excluded: chain F residue 461 MET Chi-restraints excluded: chain F residue 469 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 318 random chunks: chunk 127 optimal weight: 7.9990 chunk 16 optimal weight: 2.9990 chunk 120 optimal weight: 8.9990 chunk 112 optimal weight: 7.9990 chunk 18 optimal weight: 8.9990 chunk 181 optimal weight: 0.0050 chunk 214 optimal weight: 4.9990 chunk 174 optimal weight: 4.9990 chunk 132 optimal weight: 6.9990 chunk 158 optimal weight: 0.0470 chunk 59 optimal weight: 9.9990 overall best weight: 2.6098 ------------------------------------------------------------------------------- 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 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 = 0.4056 r_free = 0.4056 target = 0.192226 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3290 r_free = 0.3290 target = 0.122090 restraints weight = 16721.424| |-----------------------------------------------------------------------------| r_work (start): 0.3265 rms_B_bonded: 1.71 r_work: 0.3040 rms_B_bonded: 2.02 restraints_weight: 0.5000 r_work: 0.2921 rms_B_bonded: 2.97 restraints_weight: 0.2500 r_work (final): 0.2921 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7910 moved from start: 0.2330 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 26124 Z= 0.198 Angle : 0.713 10.122 35424 Z= 0.364 Chirality : 0.050 0.236 4002 Planarity : 0.005 0.038 4494 Dihedral : 7.137 59.313 3534 Min Nonbonded Distance : 2.305 Molprobity Statistics. All-atom Clashscore : 6.55 Ramachandran Plot: Outliers : 0.16 % Allowed : 4.61 % Favored : 95.23 % Rotamer: Outliers : 1.48 % Allowed : 10.97 % Favored : 87.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.35 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.11 (0.15), residues: 3168 helix: 0.84 (0.16), residues: 1098 sheet: -0.45 (0.21), residues: 546 loop : -0.52 (0.16), residues: 1524 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG A 190 TYR 0.024 0.003 TYR A 245 PHE 0.024 0.002 PHE F 81 TRP 0.011 0.002 TRP B 402 HIS 0.006 0.001 HIS F 39 Details of bonding type rmsd covalent geometry : bond 0.00413 (26118) covalent geometry : angle 0.71293 (35424) hydrogen bonds : bond 0.06105 ( 948) hydrogen bonds : angle 6.05899 ( 2682) Misc. bond : bond 0.00405 ( 6) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 12442.98 seconds wall clock time: 212 minutes 27.25 seconds (12747.25 seconds total)