Starting phenix.real_space_refine on Fri Aug 9 07:49:37 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8jyu_36731/08_2024/8jyu_36731.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8jyu_36731/08_2024/8jyu_36731.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.19 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8jyu_36731/08_2024/8jyu_36731.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8jyu_36731/08_2024/8jyu_36731.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8jyu_36731/08_2024/8jyu_36731.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8jyu_36731/08_2024/8jyu_36731.cif" } resolution = 2.19 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.002 sd= 0.176 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians P 6 5.49 5 Mg 6 5.21 5 S 108 5.16 5 C 16374 2.51 5 N 4266 2.21 5 O 4782 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A TYR 11": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 76": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 80": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 104": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 111": "OD1" <-> "OD2" Residue "A ASP 252": "OD1" <-> "OD2" Residue "A GLU 365": "OE1" <-> "OE2" Residue "A ASP 417": "OD1" <-> "OD2" Residue "D TYR 11": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 76": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 80": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 104": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 111": "OD1" <-> "OD2" Residue "D ASP 252": "OD1" <-> "OD2" Residue "D GLU 365": "OE1" <-> "OE2" Residue "D ASP 417": "OD1" <-> "OD2" Residue "B TYR 11": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 76": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 80": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 104": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 111": "OD1" <-> "OD2" Residue "B ASP 252": "OD1" <-> "OD2" Residue "B GLU 365": "OE1" <-> "OE2" Residue "B ASP 417": "OD1" <-> "OD2" Residue "C TYR 11": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 76": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 80": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 104": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 111": "OD1" <-> "OD2" Residue "C ASP 252": "OD1" <-> "OD2" Residue "C GLU 365": "OE1" <-> "OE2" Residue "C ASP 417": "OD1" <-> "OD2" Residue "E TYR 11": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 76": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 80": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 104": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ASP 111": "OD1" <-> "OD2" Residue "E ASP 252": "OD1" <-> "OD2" Residue "E GLU 365": "OE1" <-> "OE2" Residue "E ASP 417": "OD1" <-> "OD2" Residue "F TYR 11": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F TYR 76": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F TYR 80": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F TYR 104": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ASP 111": "OD1" <-> "OD2" Residue "F ASP 252": "OD1" <-> "OD2" Residue "F GLU 365": "OE1" <-> "OE2" Residue "F ASP 417": "OD1" <-> "OD2" Time to flip residues: 0.08s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/chem_data/mon_lib" Total number of atoms: 25542 Number of models: 1 Model: "" Number of chains: 12 Chain: "A" Number of atoms: 4222 Number of conformers: 1 Conformer: "" Number of residues, atoms: 530, 4222 Classifications: {'peptide': 530} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PCIS': 1, 'PTRANS': 22, 'TRANS': 506} Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 8 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ASN:plan1': 1} Unresolved non-hydrogen planarities: 3 Chain: "D" Number of atoms: 4222 Number of conformers: 1 Conformer: "" Number of residues, atoms: 530, 4222 Classifications: {'peptide': 530} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PCIS': 1, 'PTRANS': 22, 'TRANS': 506} Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 8 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ASN:plan1': 1} Unresolved non-hydrogen planarities: 3 Chain: "B" Number of atoms: 4222 Number of conformers: 1 Conformer: "" Number of residues, atoms: 530, 4222 Classifications: {'peptide': 530} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PCIS': 1, 'PTRANS': 22, 'TRANS': 506} Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 8 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ASN:plan1': 1} Unresolved non-hydrogen planarities: 3 Chain: "C" Number of atoms: 4222 Number of conformers: 1 Conformer: "" Number of residues, atoms: 530, 4222 Classifications: {'peptide': 530} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PCIS': 1, 'PTRANS': 22, 'TRANS': 506} Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 8 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ASN:plan1': 1} Unresolved non-hydrogen planarities: 3 Chain: "E" Number of atoms: 4222 Number of conformers: 1 Conformer: "" Number of residues, atoms: 530, 4222 Classifications: {'peptide': 530} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PCIS': 1, 'PTRANS': 22, 'TRANS': 506} Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 8 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ASN:plan1': 1} Unresolved non-hydrogen planarities: 3 Chain: "F" Number of atoms: 4222 Number of conformers: 1 Conformer: "" Number of residues, atoms: 530, 4222 Classifications: {'peptide': 530} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PCIS': 1, 'PTRANS': 22, 'TRANS': 506} Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 8 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ASN:plan1': 1} Unresolved non-hydrogen planarities: 3 Chain: "A" Number of atoms: 35 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 35 Unusual residues: {' MG': 1, 'DKA': 1} Classifications: {'RNA': 1, 'undetermined': 2} Modifications used: {'rna3p': 1} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 1 Chain: "D" Number of atoms: 35 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 35 Unusual residues: {' MG': 1, 'DKA': 1} Classifications: {'RNA': 1, 'undetermined': 2} Modifications used: {'rna3p': 1} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 1 Chain: "B" Number of atoms: 35 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 35 Unusual residues: {' MG': 1, 'DKA': 1} Classifications: {'RNA': 1, 'undetermined': 2} Modifications used: {'rna3p': 1} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 1 Chain: "C" Number of atoms: 35 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 35 Unusual residues: {' MG': 1, 'DKA': 1} Classifications: {'RNA': 1, 'undetermined': 2} Modifications used: {'rna3p': 1} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 1 Chain: "E" Number of atoms: 35 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 35 Unusual residues: {' MG': 1, 'DKA': 1} Classifications: {'RNA': 1, 'undetermined': 2} Modifications used: {'rna3p': 1} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 1 Chain: "F" Number of atoms: 35 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 35 Unusual residues: {' MG': 1, 'DKA': 1} Classifications: {'RNA': 1, 'undetermined': 2} Modifications used: {'rna3p': 1} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 1 Time building chain proxies: 12.79, per 1000 atoms: 0.50 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 - 3.50 Amino acid : False - 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: 10.27 Conformation dependent library (CDL) restraints added in 4.7 seconds 6336 Ramachandran restraints generated. 3168 Oldfield, 0 Emsley, 3168 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5964 Finding SS restraints... Secondary structure from input PDB file: 138 helices and 36 sheets defined 39.4% alpha, 17.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 3.39 Creating SS restraints... Processing helix chain 'A' and resid 14 through 21 Processing helix chain 'A' and resid 41 through 58 Processing helix chain 'A' and resid 73 through 86 Proline residue: A 84 - end of helix Processing helix chain 'A' and resid 98 through 110 Processing helix chain 'A' and resid 120 through 128 removed outlier: 3.628A pdb=" N GLN A 126 " --> pdb=" O PRO A 122 " (cutoff:3.500A) removed outlier: 3.805A pdb=" N ILE A 127 " --> pdb=" O ILE A 123 " (cutoff:3.500A) Processing helix chain 'A' and resid 129 through 131 No H-bonds generated for 'chain 'A' and resid 129 through 131' Processing helix chain 'A' and resid 146 through 154 Processing helix chain 'A' and resid 189 through 203 Processing helix chain 'A' and resid 226 through 231 Processing helix chain 'A' and resid 231 through 240 Processing helix chain 'A' and resid 250 through 262 Processing helix chain 'A' and resid 269 through 279 Processing helix chain 'A' and resid 280 through 283 removed outlier: 3.515A pdb=" N LYS A 283 " --> pdb=" O PRO A 280 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 280 through 283' Processing helix chain 'A' and resid 300 through 309 Processing helix chain 'A' and resid 321 through 324 removed outlier: 4.327A pdb=" N GLY A 324 " --> pdb=" O SER A 321 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 321 through 324' Processing helix chain 'A' and resid 333 through 338 removed outlier: 3.508A pdb=" N GLU A 338 " --> pdb=" O PRO A 334 " (cutoff:3.500A) Processing helix chain 'A' and resid 340 through 349 Processing helix chain 'A' and resid 395 through 402 Processing helix chain 'A' and resid 403 through 406 removed outlier: 3.690A pdb=" N TYR A 406 " --> pdb=" O ARG A 403 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 403 through 406' Processing helix chain 'A' and resid 439 through 448 removed outlier: 3.879A pdb=" N LEU A 443 " --> pdb=" O SER A 439 " (cutoff:3.500A) Processing helix chain 'A' and resid 483 through 492 Processing helix chain 'A' and resid 503 through 508 removed outlier: 4.700A pdb=" N LYS A 508 " --> pdb=" O ALA A 504 " (cutoff:3.500A) Processing helix chain 'A' and resid 524 through 531 removed outlier: 3.639A pdb=" N LEU A 531 " --> pdb=" O GLU A 527 " (cutoff:3.500A) Processing helix chain 'D' and resid 14 through 21 Processing helix chain 'D' and resid 41 through 58 Processing helix chain 'D' and resid 73 through 86 Proline residue: D 84 - end of helix Processing helix chain 'D' and resid 98 through 110 Processing helix chain 'D' and resid 120 through 128 removed outlier: 3.628A pdb=" N GLN D 126 " --> pdb=" O PRO D 122 " (cutoff:3.500A) removed outlier: 3.805A pdb=" N ILE D 127 " --> pdb=" O ILE D 123 " (cutoff:3.500A) Processing helix chain 'D' and resid 129 through 131 No H-bonds generated for 'chain 'D' and resid 129 through 131' Processing helix chain 'D' and resid 146 through 154 Processing helix chain 'D' and resid 189 through 203 Processing helix chain 'D' and resid 226 through 231 Processing helix chain 'D' and resid 231 through 240 Processing helix chain 'D' and resid 250 through 262 Processing helix chain 'D' and resid 269 through 279 Processing helix chain 'D' and resid 280 through 283 removed outlier: 3.515A pdb=" N LYS D 283 " --> pdb=" O PRO D 280 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 280 through 283' Processing helix chain 'D' and resid 300 through 309 Processing helix chain 'D' and resid 321 through 324 removed outlier: 4.327A pdb=" N GLY D 324 " --> pdb=" O SER D 321 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 321 through 324' Processing helix chain 'D' and resid 333 through 338 removed outlier: 3.507A pdb=" N GLU D 338 " --> pdb=" O PRO D 334 " (cutoff:3.500A) Processing helix chain 'D' and resid 340 through 349 Processing helix chain 'D' and resid 395 through 402 Processing helix chain 'D' and resid 403 through 406 removed outlier: 3.690A pdb=" N TYR D 406 " --> pdb=" O ARG D 403 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 403 through 406' Processing helix chain 'D' and resid 439 through 448 removed outlier: 3.879A pdb=" N LEU D 443 " --> pdb=" O SER D 439 " (cutoff:3.500A) Processing helix chain 'D' and resid 483 through 492 Processing helix chain 'D' and resid 503 through 508 removed outlier: 4.700A pdb=" N LYS D 508 " --> pdb=" O ALA D 504 " (cutoff:3.500A) Processing helix chain 'D' and resid 524 through 531 removed outlier: 3.640A pdb=" N LEU D 531 " --> pdb=" O GLU D 527 " (cutoff:3.500A) Processing helix chain 'B' and resid 14 through 21 Processing helix chain 'B' and resid 41 through 58 Processing helix chain 'B' and resid 73 through 86 Proline residue: B 84 - end of helix Processing helix chain 'B' and resid 98 through 110 Processing helix chain 'B' and resid 120 through 128 removed outlier: 3.628A pdb=" N GLN B 126 " --> pdb=" O PRO B 122 " (cutoff:3.500A) removed outlier: 3.805A pdb=" N ILE B 127 " --> pdb=" O ILE B 123 " (cutoff:3.500A) Processing helix chain 'B' and resid 129 through 131 No H-bonds generated for 'chain 'B' and resid 129 through 131' Processing helix chain 'B' and resid 146 through 154 Processing helix chain 'B' and resid 189 through 203 Processing helix chain 'B' and resid 226 through 231 Processing helix chain 'B' and resid 231 through 240 Processing helix chain 'B' and resid 250 through 262 Processing helix chain 'B' and resid 269 through 279 Processing helix chain 'B' and resid 280 through 283 removed outlier: 3.515A pdb=" N LYS B 283 " --> pdb=" O PRO B 280 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 280 through 283' Processing helix chain 'B' and resid 300 through 309 Processing helix chain 'B' and resid 321 through 324 removed outlier: 4.327A pdb=" N GLY B 324 " --> pdb=" O SER B 321 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 321 through 324' Processing helix chain 'B' and resid 333 through 338 removed outlier: 3.508A pdb=" N GLU B 338 " --> pdb=" O PRO B 334 " (cutoff:3.500A) Processing helix chain 'B' and resid 340 through 349 Processing helix chain 'B' and resid 395 through 402 Processing helix chain 'B' and resid 403 through 406 removed outlier: 3.690A pdb=" N TYR B 406 " --> pdb=" O ARG B 403 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 403 through 406' Processing helix chain 'B' and resid 439 through 448 removed outlier: 3.878A pdb=" N LEU B 443 " --> pdb=" O SER B 439 " (cutoff:3.500A) Processing helix chain 'B' and resid 483 through 492 Processing helix chain 'B' and resid 503 through 508 removed outlier: 4.700A pdb=" N LYS B 508 " --> pdb=" O ALA B 504 " (cutoff:3.500A) Processing helix chain 'B' and resid 524 through 531 removed outlier: 3.639A pdb=" N LEU B 531 " --> pdb=" O GLU B 527 " (cutoff:3.500A) Processing helix chain 'C' and resid 14 through 21 Processing helix chain 'C' and resid 41 through 58 Processing helix chain 'C' and resid 73 through 86 Proline residue: C 84 - end of helix Processing helix chain 'C' and resid 98 through 110 Processing helix chain 'C' and resid 120 through 128 removed outlier: 3.628A pdb=" N GLN C 126 " --> pdb=" O PRO C 122 " (cutoff:3.500A) removed outlier: 3.805A pdb=" N ILE C 127 " --> pdb=" O ILE C 123 " (cutoff:3.500A) Processing helix chain 'C' and resid 129 through 131 No H-bonds generated for 'chain 'C' and resid 129 through 131' Processing helix chain 'C' and resid 146 through 154 Processing helix chain 'C' and resid 189 through 203 Processing helix chain 'C' and resid 226 through 231 Processing helix chain 'C' and resid 231 through 240 Processing helix chain 'C' and resid 250 through 262 Processing helix chain 'C' and resid 269 through 279 Processing helix chain 'C' and resid 280 through 283 removed outlier: 3.515A pdb=" N LYS C 283 " --> pdb=" O PRO C 280 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 280 through 283' Processing helix chain 'C' and resid 300 through 309 Processing helix chain 'C' and resid 321 through 324 removed outlier: 4.327A pdb=" N GLY C 324 " --> pdb=" O SER C 321 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 321 through 324' Processing helix chain 'C' and resid 333 through 338 removed outlier: 3.508A pdb=" N GLU C 338 " --> pdb=" O PRO C 334 " (cutoff:3.500A) Processing helix chain 'C' and resid 340 through 349 Processing helix chain 'C' and resid 395 through 402 Processing helix chain 'C' and resid 403 through 406 removed outlier: 3.690A pdb=" N TYR C 406 " --> pdb=" O ARG C 403 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 403 through 406' Processing helix chain 'C' and resid 439 through 448 removed outlier: 3.879A pdb=" N LEU C 443 " --> pdb=" O SER C 439 " (cutoff:3.500A) Processing helix chain 'C' and resid 483 through 492 Processing helix chain 'C' and resid 503 through 508 removed outlier: 4.699A pdb=" N LYS C 508 " --> pdb=" O ALA C 504 " (cutoff:3.500A) Processing helix chain 'C' and resid 524 through 531 removed outlier: 3.638A pdb=" N LEU C 531 " --> pdb=" O GLU C 527 " (cutoff:3.500A) Processing helix chain 'E' and resid 14 through 21 Processing helix chain 'E' and resid 41 through 58 Processing helix chain 'E' and resid 73 through 86 Proline residue: E 84 - end of helix Processing helix chain 'E' and resid 98 through 110 Processing helix chain 'E' and resid 120 through 128 removed outlier: 3.629A pdb=" N GLN E 126 " --> pdb=" O PRO E 122 " (cutoff:3.500A) removed outlier: 3.805A pdb=" N ILE E 127 " --> pdb=" O ILE E 123 " (cutoff:3.500A) Processing helix chain 'E' and resid 129 through 131 No H-bonds generated for 'chain 'E' and resid 129 through 131' Processing helix chain 'E' and resid 146 through 154 Processing helix chain 'E' and resid 189 through 203 Processing helix chain 'E' and resid 226 through 231 Processing helix chain 'E' and resid 231 through 240 Processing helix chain 'E' and resid 250 through 262 Processing helix chain 'E' and resid 269 through 279 Processing helix chain 'E' and resid 280 through 283 removed outlier: 3.515A pdb=" N LYS E 283 " --> pdb=" O PRO E 280 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 280 through 283' Processing helix chain 'E' and resid 300 through 309 Processing helix chain 'E' and resid 321 through 324 removed outlier: 4.328A pdb=" N GLY E 324 " --> pdb=" O SER E 321 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 321 through 324' Processing helix chain 'E' and resid 333 through 338 removed outlier: 3.507A pdb=" N GLU E 338 " --> pdb=" O PRO E 334 " (cutoff:3.500A) Processing helix chain 'E' and resid 340 through 349 Processing helix chain 'E' and resid 395 through 402 Processing helix chain 'E' and resid 403 through 406 removed outlier: 3.690A pdb=" N TYR E 406 " --> pdb=" O ARG E 403 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 403 through 406' Processing helix chain 'E' and resid 439 through 448 removed outlier: 3.879A pdb=" N LEU E 443 " --> pdb=" O SER E 439 " (cutoff:3.500A) Processing helix chain 'E' and resid 483 through 492 Processing helix chain 'E' and resid 503 through 508 removed outlier: 4.700A pdb=" N LYS E 508 " --> pdb=" O ALA E 504 " (cutoff:3.500A) Processing helix chain 'E' and resid 524 through 531 removed outlier: 3.638A pdb=" N LEU E 531 " --> pdb=" O GLU E 527 " (cutoff:3.500A) Processing helix chain 'F' and resid 14 through 21 Processing helix chain 'F' and resid 41 through 58 Processing helix chain 'F' and resid 73 through 86 Proline residue: F 84 - end of helix Processing helix chain 'F' and resid 98 through 110 Processing helix chain 'F' and resid 120 through 128 removed outlier: 3.628A pdb=" N GLN F 126 " --> pdb=" O PRO F 122 " (cutoff:3.500A) removed outlier: 3.806A pdb=" N ILE F 127 " --> pdb=" O ILE F 123 " (cutoff:3.500A) Processing helix chain 'F' and resid 129 through 131 No H-bonds generated for 'chain 'F' and resid 129 through 131' Processing helix chain 'F' and resid 146 through 154 Processing helix chain 'F' and resid 189 through 203 Processing helix chain 'F' and resid 226 through 231 Processing helix chain 'F' and resid 231 through 240 Processing helix chain 'F' and resid 250 through 262 Processing helix chain 'F' and resid 269 through 279 Processing helix chain 'F' and resid 280 through 283 removed outlier: 3.515A pdb=" N LYS F 283 " --> pdb=" O PRO F 280 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 280 through 283' Processing helix chain 'F' and resid 300 through 309 Processing helix chain 'F' and resid 321 through 324 removed outlier: 4.327A pdb=" N GLY F 324 " --> pdb=" O SER F 321 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 321 through 324' Processing helix chain 'F' and resid 333 through 338 removed outlier: 3.508A pdb=" N GLU F 338 " --> pdb=" O PRO F 334 " (cutoff:3.500A) Processing helix chain 'F' and resid 340 through 349 Processing helix chain 'F' and resid 395 through 402 Processing helix chain 'F' and resid 403 through 406 removed outlier: 3.690A pdb=" N TYR F 406 " --> pdb=" O ARG F 403 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 403 through 406' Processing helix chain 'F' and resid 439 through 448 removed outlier: 3.879A pdb=" N LEU F 443 " --> pdb=" O SER F 439 " (cutoff:3.500A) Processing helix chain 'F' and resid 483 through 492 Processing helix chain 'F' and resid 503 through 508 removed outlier: 4.700A pdb=" N LYS F 508 " --> pdb=" O ALA F 504 " (cutoff:3.500A) Processing helix chain 'F' and resid 524 through 531 removed outlier: 3.639A pdb=" N LEU F 531 " --> pdb=" O GLU F 527 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 37 through 40 removed outlier: 6.615A pdb=" N GLU A 30 " --> pdb=" O GLN A 243 " (cutoff:3.500A) removed outlier: 8.056A pdb=" N TYR A 245 " --> pdb=" O GLU A 30 " (cutoff:3.500A) removed outlier: 6.599A pdb=" N VAL A 32 " --> pdb=" O TYR A 245 " (cutoff:3.500A) removed outlier: 6.335A pdb=" N TYR A 218 " --> pdb=" O VAL A 244 " (cutoff:3.500A) removed outlier: 5.995A pdb=" N ILE A 217 " --> pdb=" O PHE A 265 " (cutoff:3.500A) removed outlier: 8.458A pdb=" N HIS A 267 " --> pdb=" O ILE A 217 " (cutoff:3.500A) removed outlier: 7.811A pdb=" N MET A 219 " --> pdb=" O HIS A 267 " (cutoff:3.500A) removed outlier: 7.062A pdb=" N ALA A 316 " --> pdb=" O ILE A 329 " (cutoff:3.500A) removed outlier: 4.849A pdb=" N ILE A 329 " --> pdb=" O ALA A 316 " (cutoff:3.500A) removed outlier: 6.770A pdb=" N TYR A 318 " --> pdb=" O LEU A 327 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 136 through 140 removed outlier: 6.479A pdb=" N ILE A 114 " --> pdb=" O VAL A 138 " (cutoff:3.500A) removed outlier: 7.172A pdb=" N LEU A 140 " --> pdb=" O ILE A 114 " (cutoff:3.500A) removed outlier: 6.676A pdb=" N ILE A 116 " --> pdb=" O LEU A 140 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N ILE A 113 " --> pdb=" O THR A 65 " (cutoff:3.500A) removed outlier: 4.695A pdb=" N TYR A 174 " --> pdb=" O MET A 92 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 359 through 363 removed outlier: 5.108A pdb=" N ASP A 411 " --> pdb=" O ILE A 380 " (cutoff:3.500A) removed outlier: 8.841A pdb=" N VAL A 382 " --> pdb=" O THR A 409 " (cutoff:3.500A) removed outlier: 7.166A pdb=" N THR A 409 " --> pdb=" O VAL A 382 " (cutoff:3.500A) removed outlier: 6.553A pdb=" N HIS A 414 " --> pdb=" O ILE A 423 " (cutoff:3.500A) removed outlier: 5.353A pdb=" N ILE A 423 " --> pdb=" O HIS A 414 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 431 through 433 removed outlier: 3.779A pdb=" N ILE A 433 " --> pdb=" O GLU A 436 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 453 through 458 removed outlier: 6.464A pdb=" N THR A 475 " --> pdb=" O SER A 454 " (cutoff:3.500A) removed outlier: 4.264A pdb=" N VAL A 456 " --> pdb=" O LEU A 473 " (cutoff:3.500A) removed outlier: 6.638A pdb=" N LEU A 473 " --> pdb=" O VAL A 456 " (cutoff:3.500A) removed outlier: 6.222A pdb=" N ALA A 472 " --> pdb=" O LYS A 510 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 461 through 463 Processing sheet with id=AA7, first strand: chain 'D' and resid 37 through 40 removed outlier: 6.616A pdb=" N GLU D 30 " --> pdb=" O GLN D 243 " (cutoff:3.500A) removed outlier: 8.056A pdb=" N TYR D 245 " --> pdb=" O GLU D 30 " (cutoff:3.500A) removed outlier: 6.599A pdb=" N VAL D 32 " --> pdb=" O TYR D 245 " (cutoff:3.500A) removed outlier: 6.335A pdb=" N TYR D 218 " --> pdb=" O VAL D 244 " (cutoff:3.500A) removed outlier: 5.995A pdb=" N ILE D 217 " --> pdb=" O PHE D 265 " (cutoff:3.500A) removed outlier: 8.459A pdb=" N HIS D 267 " --> pdb=" O ILE D 217 " (cutoff:3.500A) removed outlier: 7.811A pdb=" N MET D 219 " --> pdb=" O HIS D 267 " (cutoff:3.500A) removed outlier: 7.062A pdb=" N ALA D 316 " --> pdb=" O ILE D 329 " (cutoff:3.500A) removed outlier: 4.849A pdb=" N ILE D 329 " --> pdb=" O ALA D 316 " (cutoff:3.500A) removed outlier: 6.770A pdb=" N TYR D 318 " --> pdb=" O LEU D 327 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'D' and resid 136 through 140 removed outlier: 6.478A pdb=" N ILE D 114 " --> pdb=" O VAL D 138 " (cutoff:3.500A) removed outlier: 7.173A pdb=" N LEU D 140 " --> pdb=" O ILE D 114 " (cutoff:3.500A) removed outlier: 6.675A pdb=" N ILE D 116 " --> pdb=" O LEU D 140 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N ILE D 113 " --> pdb=" O THR D 65 " (cutoff:3.500A) removed outlier: 4.696A pdb=" N TYR D 174 " --> pdb=" O MET D 92 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'D' and resid 359 through 363 removed outlier: 5.109A pdb=" N ASP D 411 " --> pdb=" O ILE D 380 " (cutoff:3.500A) removed outlier: 8.841A pdb=" N VAL D 382 " --> pdb=" O THR D 409 " (cutoff:3.500A) removed outlier: 7.166A pdb=" N THR D 409 " --> pdb=" O VAL D 382 " (cutoff:3.500A) removed outlier: 6.553A pdb=" N HIS D 414 " --> pdb=" O ILE D 423 " (cutoff:3.500A) removed outlier: 5.352A pdb=" N ILE D 423 " --> pdb=" O HIS D 414 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'D' and resid 431 through 433 removed outlier: 3.778A pdb=" N ILE D 433 " --> pdb=" O GLU D 436 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'D' and resid 453 through 458 removed outlier: 6.463A pdb=" N THR D 475 " --> pdb=" O SER D 454 " (cutoff:3.500A) removed outlier: 4.264A pdb=" N VAL D 456 " --> pdb=" O LEU D 473 " (cutoff:3.500A) removed outlier: 6.638A pdb=" N LEU D 473 " --> pdb=" O VAL D 456 " (cutoff:3.500A) removed outlier: 6.223A pdb=" N ALA D 472 " --> pdb=" O LYS D 510 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'D' and resid 461 through 463 Processing sheet with id=AB4, first strand: chain 'B' and resid 37 through 40 removed outlier: 6.615A pdb=" N GLU B 30 " --> pdb=" O GLN B 243 " (cutoff:3.500A) removed outlier: 8.055A pdb=" N TYR B 245 " --> pdb=" O GLU B 30 " (cutoff:3.500A) removed outlier: 6.598A pdb=" N VAL B 32 " --> pdb=" O TYR B 245 " (cutoff:3.500A) removed outlier: 6.335A pdb=" N TYR B 218 " --> pdb=" O VAL B 244 " (cutoff:3.500A) removed outlier: 5.995A pdb=" N ILE B 217 " --> pdb=" O PHE B 265 " (cutoff:3.500A) removed outlier: 8.458A pdb=" N HIS B 267 " --> pdb=" O ILE B 217 " (cutoff:3.500A) removed outlier: 7.811A pdb=" N MET B 219 " --> pdb=" O HIS B 267 " (cutoff:3.500A) removed outlier: 7.062A pdb=" N ALA B 316 " --> pdb=" O ILE B 329 " (cutoff:3.500A) removed outlier: 4.849A pdb=" N ILE B 329 " --> pdb=" O ALA B 316 " (cutoff:3.500A) removed outlier: 6.770A pdb=" N TYR B 318 " --> pdb=" O LEU B 327 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'B' and resid 136 through 140 removed outlier: 6.479A pdb=" N ILE B 114 " --> pdb=" O VAL B 138 " (cutoff:3.500A) removed outlier: 7.172A pdb=" N LEU B 140 " --> pdb=" O ILE B 114 " (cutoff:3.500A) removed outlier: 6.675A pdb=" N ILE B 116 " --> pdb=" O LEU B 140 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N ILE B 113 " --> pdb=" O THR B 65 " (cutoff:3.500A) removed outlier: 4.695A pdb=" N TYR B 174 " --> pdb=" O MET B 92 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'B' and resid 359 through 363 removed outlier: 5.109A pdb=" N ASP B 411 " --> pdb=" O ILE B 380 " (cutoff:3.500A) removed outlier: 8.841A pdb=" N VAL B 382 " --> pdb=" O THR B 409 " (cutoff:3.500A) removed outlier: 7.166A pdb=" N THR B 409 " --> pdb=" O VAL B 382 " (cutoff:3.500A) removed outlier: 6.553A pdb=" N HIS B 414 " --> pdb=" O ILE B 423 " (cutoff:3.500A) removed outlier: 5.353A pdb=" N ILE B 423 " --> pdb=" O HIS B 414 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'B' and resid 431 through 433 removed outlier: 3.779A pdb=" N ILE B 433 " --> pdb=" O GLU B 436 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'B' and resid 453 through 458 removed outlier: 6.463A pdb=" N THR B 475 " --> pdb=" O SER B 454 " (cutoff:3.500A) removed outlier: 4.264A pdb=" N VAL B 456 " --> pdb=" O LEU B 473 " (cutoff:3.500A) removed outlier: 6.638A pdb=" N LEU B 473 " --> pdb=" O VAL B 456 " (cutoff:3.500A) removed outlier: 6.222A pdb=" N ALA B 472 " --> pdb=" O LYS B 510 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'B' and resid 461 through 463 Processing sheet with id=AC1, first strand: chain 'C' and resid 37 through 40 removed outlier: 6.617A pdb=" N GLU C 30 " --> pdb=" O GLN C 243 " (cutoff:3.500A) removed outlier: 8.056A pdb=" N TYR C 245 " --> pdb=" O GLU C 30 " (cutoff:3.500A) removed outlier: 6.599A pdb=" N VAL C 32 " --> pdb=" O TYR C 245 " (cutoff:3.500A) removed outlier: 6.335A pdb=" N TYR C 218 " --> pdb=" O VAL C 244 " (cutoff:3.500A) removed outlier: 5.995A pdb=" N ILE C 217 " --> pdb=" O PHE C 265 " (cutoff:3.500A) removed outlier: 8.458A pdb=" N HIS C 267 " --> pdb=" O ILE C 217 " (cutoff:3.500A) removed outlier: 7.811A pdb=" N MET C 219 " --> pdb=" O HIS C 267 " (cutoff:3.500A) removed outlier: 7.062A pdb=" N ALA C 316 " --> pdb=" O ILE C 329 " (cutoff:3.500A) removed outlier: 4.849A pdb=" N ILE C 329 " --> pdb=" O ALA C 316 " (cutoff:3.500A) removed outlier: 6.770A pdb=" N TYR C 318 " --> pdb=" O LEU C 327 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'C' and resid 136 through 140 removed outlier: 6.479A pdb=" N ILE C 114 " --> pdb=" O VAL C 138 " (cutoff:3.500A) removed outlier: 7.173A pdb=" N LEU C 140 " --> pdb=" O ILE C 114 " (cutoff:3.500A) removed outlier: 6.675A pdb=" N ILE C 116 " --> pdb=" O LEU C 140 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N ILE C 113 " --> pdb=" O THR C 65 " (cutoff:3.500A) removed outlier: 4.695A pdb=" N TYR C 174 " --> pdb=" O MET C 92 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'C' and resid 359 through 363 removed outlier: 5.108A pdb=" N ASP C 411 " --> pdb=" O ILE C 380 " (cutoff:3.500A) removed outlier: 8.842A pdb=" N VAL C 382 " --> pdb=" O THR C 409 " (cutoff:3.500A) removed outlier: 7.166A pdb=" N THR C 409 " --> pdb=" O VAL C 382 " (cutoff:3.500A) removed outlier: 6.553A pdb=" N HIS C 414 " --> pdb=" O ILE C 423 " (cutoff:3.500A) removed outlier: 5.352A pdb=" N ILE C 423 " --> pdb=" O HIS C 414 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'C' and resid 431 through 433 removed outlier: 3.779A pdb=" N ILE C 433 " --> pdb=" O GLU C 436 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'C' and resid 453 through 458 removed outlier: 6.464A pdb=" N THR C 475 " --> pdb=" O SER C 454 " (cutoff:3.500A) removed outlier: 4.264A pdb=" N VAL C 456 " --> pdb=" O LEU C 473 " (cutoff:3.500A) removed outlier: 6.638A pdb=" N LEU C 473 " --> pdb=" O VAL C 456 " (cutoff:3.500A) removed outlier: 6.223A pdb=" N ALA C 472 " --> pdb=" O LYS C 510 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'C' and resid 461 through 463 Processing sheet with id=AC7, first strand: chain 'E' and resid 37 through 40 removed outlier: 6.615A pdb=" N GLU E 30 " --> pdb=" O GLN E 243 " (cutoff:3.500A) removed outlier: 8.056A pdb=" N TYR E 245 " --> pdb=" O GLU E 30 " (cutoff:3.500A) removed outlier: 6.598A pdb=" N VAL E 32 " --> pdb=" O TYR E 245 " (cutoff:3.500A) removed outlier: 6.336A pdb=" N TYR E 218 " --> pdb=" O VAL E 244 " (cutoff:3.500A) removed outlier: 5.995A pdb=" N ILE E 217 " --> pdb=" O PHE E 265 " (cutoff:3.500A) removed outlier: 8.458A pdb=" N HIS E 267 " --> pdb=" O ILE E 217 " (cutoff:3.500A) removed outlier: 7.811A pdb=" N MET E 219 " --> pdb=" O HIS E 267 " (cutoff:3.500A) removed outlier: 7.061A pdb=" N ALA E 316 " --> pdb=" O ILE E 329 " (cutoff:3.500A) removed outlier: 4.848A pdb=" N ILE E 329 " --> pdb=" O ALA E 316 " (cutoff:3.500A) removed outlier: 6.769A pdb=" N TYR E 318 " --> pdb=" O LEU E 327 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'E' and resid 136 through 140 removed outlier: 6.479A pdb=" N ILE E 114 " --> pdb=" O VAL E 138 " (cutoff:3.500A) removed outlier: 7.173A pdb=" N LEU E 140 " --> pdb=" O ILE E 114 " (cutoff:3.500A) removed outlier: 6.676A pdb=" N ILE E 116 " --> pdb=" O LEU E 140 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N ILE E 113 " --> pdb=" O THR E 65 " (cutoff:3.500A) removed outlier: 4.695A pdb=" N TYR E 174 " --> pdb=" O MET E 92 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'E' and resid 359 through 363 removed outlier: 5.108A pdb=" N ASP E 411 " --> pdb=" O ILE E 380 " (cutoff:3.500A) removed outlier: 8.841A pdb=" N VAL E 382 " --> pdb=" O THR E 409 " (cutoff:3.500A) removed outlier: 7.166A pdb=" N THR E 409 " --> pdb=" O VAL E 382 " (cutoff:3.500A) removed outlier: 6.553A pdb=" N HIS E 414 " --> pdb=" O ILE E 423 " (cutoff:3.500A) removed outlier: 5.353A pdb=" N ILE E 423 " --> pdb=" O HIS E 414 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'E' and resid 431 through 433 removed outlier: 3.779A pdb=" N ILE E 433 " --> pdb=" O GLU E 436 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'E' and resid 453 through 458 removed outlier: 6.464A pdb=" N THR E 475 " --> pdb=" O SER E 454 " (cutoff:3.500A) removed outlier: 4.264A pdb=" N VAL E 456 " --> pdb=" O LEU E 473 " (cutoff:3.500A) removed outlier: 6.638A pdb=" N LEU E 473 " --> pdb=" O VAL E 456 " (cutoff:3.500A) removed outlier: 6.222A pdb=" N ALA E 472 " --> pdb=" O LYS E 510 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'E' and resid 461 through 463 Processing sheet with id=AD4, first strand: chain 'F' and resid 37 through 40 removed outlier: 6.615A pdb=" N GLU F 30 " --> pdb=" O GLN F 243 " (cutoff:3.500A) removed outlier: 8.056A pdb=" N TYR F 245 " --> pdb=" O GLU F 30 " (cutoff:3.500A) removed outlier: 6.599A pdb=" N VAL F 32 " --> pdb=" O TYR F 245 " (cutoff:3.500A) removed outlier: 6.336A pdb=" N TYR F 218 " --> pdb=" O VAL F 244 " (cutoff:3.500A) removed outlier: 5.996A pdb=" N ILE F 217 " --> pdb=" O PHE F 265 " (cutoff:3.500A) removed outlier: 8.458A pdb=" N HIS F 267 " --> pdb=" O ILE F 217 " (cutoff:3.500A) removed outlier: 7.811A pdb=" N MET F 219 " --> pdb=" O HIS F 267 " (cutoff:3.500A) removed outlier: 7.061A pdb=" N ALA F 316 " --> pdb=" O ILE F 329 " (cutoff:3.500A) removed outlier: 4.849A pdb=" N ILE F 329 " --> pdb=" O ALA F 316 " (cutoff:3.500A) removed outlier: 6.769A pdb=" N TYR F 318 " --> pdb=" O LEU F 327 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'F' and resid 136 through 140 removed outlier: 6.479A pdb=" N ILE F 114 " --> pdb=" O VAL F 138 " (cutoff:3.500A) removed outlier: 7.172A pdb=" N LEU F 140 " --> pdb=" O ILE F 114 " (cutoff:3.500A) removed outlier: 6.675A pdb=" N ILE F 116 " --> pdb=" O LEU F 140 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N ILE F 113 " --> pdb=" O THR F 65 " (cutoff:3.500A) removed outlier: 4.696A pdb=" N TYR F 174 " --> pdb=" O MET F 92 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'F' and resid 359 through 363 removed outlier: 5.108A pdb=" N ASP F 411 " --> pdb=" O ILE F 380 " (cutoff:3.500A) removed outlier: 8.841A pdb=" N VAL F 382 " --> pdb=" O THR F 409 " (cutoff:3.500A) removed outlier: 7.166A pdb=" N THR F 409 " --> pdb=" O VAL F 382 " (cutoff:3.500A) removed outlier: 6.554A pdb=" N HIS F 414 " --> pdb=" O ILE F 423 " (cutoff:3.500A) removed outlier: 5.353A pdb=" N ILE F 423 " --> pdb=" O HIS F 414 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'F' and resid 431 through 433 removed outlier: 3.778A pdb=" N ILE F 433 " --> pdb=" O GLU F 436 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'F' and resid 453 through 458 removed outlier: 6.464A pdb=" N THR F 475 " --> pdb=" O SER F 454 " (cutoff:3.500A) removed outlier: 4.264A pdb=" N VAL F 456 " --> pdb=" O LEU F 473 " (cutoff:3.500A) removed outlier: 6.637A pdb=" N LEU F 473 " --> pdb=" O VAL F 456 " (cutoff:3.500A) removed outlier: 6.222A pdb=" N ALA F 472 " --> pdb=" O LYS F 510 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'F' and resid 461 through 463 948 hydrogen bonds defined for protein. 2682 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 10.55 Time building geometry restraints manager: 10.81 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: 99.06 - 106.49: 822 106.49 - 113.91: 15022 113.91 - 121.34: 13005 121.34 - 128.76: 6341 128.76 - 136.19: 234 Bond angle restraints: 35424 Sorted by residual: angle pdb=" N TYR B 249 " pdb=" CA TYR B 249 " pdb=" C TYR B 249 " ideal model delta sigma weight residual 109.15 119.93 -10.78 1.44e+00 4.82e-01 5.61e+01 angle pdb=" N TYR C 249 " pdb=" CA TYR C 249 " pdb=" C TYR C 249 " ideal model delta sigma weight residual 109.15 119.92 -10.77 1.44e+00 4.82e-01 5.60e+01 angle pdb=" N TYR E 249 " pdb=" CA TYR E 249 " pdb=" C TYR E 249 " ideal model delta sigma weight residual 109.15 119.91 -10.76 1.44e+00 4.82e-01 5.59e+01 angle pdb=" N TYR D 249 " pdb=" CA TYR D 249 " pdb=" C TYR D 249 " ideal model delta sigma weight residual 109.15 119.91 -10.76 1.44e+00 4.82e-01 5.58e+01 angle pdb=" N TYR A 249 " pdb=" CA TYR A 249 " pdb=" C TYR A 249 " ideal model delta sigma weight residual 109.15 119.91 -10.76 1.44e+00 4.82e-01 5.58e+01 ... (remaining 35419 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.94: 14324 17.94 - 35.89: 949 35.89 - 53.83: 267 53.83 - 71.78: 60 71.78 - 89.72: 36 Dihedral angle restraints: 15636 sinusoidal: 6366 harmonic: 9270 Sorted by residual: dihedral pdb=" CA PRO F 325 " pdb=" C PRO F 325 " pdb=" N ILE F 326 " pdb=" CA ILE F 326 " ideal model delta harmonic sigma weight residual -180.00 -160.71 -19.29 0 5.00e+00 4.00e-02 1.49e+01 dihedral pdb=" CA PRO D 325 " pdb=" C PRO D 325 " pdb=" N ILE D 326 " pdb=" CA ILE D 326 " ideal model delta harmonic sigma weight residual 180.00 -160.74 -19.26 0 5.00e+00 4.00e-02 1.48e+01 dihedral pdb=" CA PRO A 325 " pdb=" C PRO A 325 " pdb=" N ILE A 326 " pdb=" CA ILE A 326 " ideal model delta harmonic sigma weight residual -180.00 -160.75 -19.25 0 5.00e+00 4.00e-02 1.48e+01 ... (remaining 15633 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.079: 3530 0.079 - 0.159: 454 0.159 - 0.238: 0 0.238 - 0.317: 0 0.317 - 0.396: 18 Chirality restraints: 4002 Sorted by residual: chirality pdb=" CA PHE C 81 " pdb=" N PHE C 81 " pdb=" C PHE C 81 " pdb=" CB PHE C 81 " both_signs ideal model delta sigma weight residual False 2.51 2.11 0.40 2.00e-01 2.50e+01 3.93e+00 chirality pdb=" CA PHE E 81 " pdb=" N PHE E 81 " pdb=" C PHE E 81 " pdb=" CB PHE E 81 " both_signs ideal model delta sigma weight residual False 2.51 2.12 0.40 2.00e-01 2.50e+01 3.90e+00 chirality pdb=" CA PHE D 81 " pdb=" N PHE D 81 " pdb=" C PHE D 81 " pdb=" CB PHE D 81 " both_signs ideal model delta sigma weight residual False 2.51 2.12 0.39 2.00e-01 2.50e+01 3.90e+00 ... (remaining 3999 not shown) Planarity restraints: 4494 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA GLU C 78 " -0.015 2.00e-02 2.50e+03 3.06e-02 9.36e+00 pdb=" C GLU C 78 " 0.053 2.00e-02 2.50e+03 pdb=" O GLU C 78 " -0.020 2.00e-02 2.50e+03 pdb=" N CYS C 79 " -0.018 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLU B 78 " 0.015 2.00e-02 2.50e+03 3.06e-02 9.36e+00 pdb=" C GLU B 78 " -0.053 2.00e-02 2.50e+03 pdb=" O GLU B 78 " 0.020 2.00e-02 2.50e+03 pdb=" N CYS B 79 " 0.018 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLU D 78 " 0.015 2.00e-02 2.50e+03 3.06e-02 9.34e+00 pdb=" C GLU D 78 " -0.053 2.00e-02 2.50e+03 pdb=" O GLU D 78 " 0.020 2.00e-02 2.50e+03 pdb=" N CYS D 79 " 0.018 2.00e-02 2.50e+03 ... (remaining 4491 not shown) Histogram of nonbonded interaction distances: 2.23 - 2.76: 4101 2.76 - 3.30: 24752 3.30 - 3.83: 45681 3.83 - 4.37: 57715 4.37 - 4.90: 93277 Nonbonded interactions: 225526 Sorted by model distance: nonbonded pdb="MG MG F 601 " pdb=" O2P AMP F 602 " model vdw 2.229 2.170 nonbonded pdb="MG MG B 601 " pdb=" O2P AMP B 602 " model vdw 2.229 2.170 nonbonded pdb="MG MG D 601 " pdb=" O2P AMP D 602 " model vdw 2.229 2.170 nonbonded pdb="MG MG A 601 " pdb=" O1P AMP A 602 " model vdw 2.230 2.170 nonbonded pdb="MG MG C 601 " pdb=" O1P AMP C 602 " model vdw 2.230 2.170 ... (remaining 225521 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' 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: 1.230 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: 0.880 Check model and map are aligned: 0.160 Set scattering table: 0.220 Process input model: 69.320 Find NCS groups from input model: 1.480 Set up NCS constraints: 0.240 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: 0.020 Load rotamer database and sin/cos tables:14.530 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 88.100 ------------------------------------------------------------------------------- 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 26118 Z= 0.250 Angle : 0.658 10.784 35424 Z= 0.394 Chirality : 0.050 0.396 4002 Planarity : 0.004 0.039 4494 Dihedral : 14.446 89.722 9672 Min Nonbonded Distance : 2.229 Molprobity Statistics. All-atom Clashscore : 6.37 Ramachandran Plot: Outliers : 0.19 % Allowed : 4.32 % Favored : 95.49 % Rotamer: Outliers : 0.14 % Allowed : 7.22 % Favored : 92.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.35 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.10 (0.15), residues: 3168 helix: 1.25 (0.17), residues: 1050 sheet: 0.03 (0.21), residues: 576 loop : -0.72 (0.16), residues: 1542 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP C 386 HIS 0.002 0.001 HIS B 408 PHE 0.011 0.001 PHE C 161 TYR 0.012 0.001 TYR B 80 ARG 0.002 0.000 ARG B 529 *********************** 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 fitting. rotamer outliers: 4 poor density : 406 time to evaluate : 2.655 Fit side-chains REVERT: A 28 GLU cc_start: 0.6917 (mm-30) cc_final: 0.6695 (mp0) REVERT: A 42 LYS cc_start: 0.7118 (ttpp) cc_final: 0.6734 (ttpp) REVERT: A 61 LYS cc_start: 0.6927 (mtmm) cc_final: 0.5971 (mmtm) REVERT: A 100 GLU cc_start: 0.6435 (tp30) cc_final: 0.5923 (tp30) REVERT: A 112 ASP cc_start: 0.7812 (m-30) cc_final: 0.7608 (m-30) REVERT: A 145 GLU cc_start: 0.5641 (mm-30) cc_final: 0.5259 (mp0) REVERT: A 150 ARG cc_start: 0.6339 (mtm110) cc_final: 0.6127 (mtm-85) REVERT: A 158 GLU cc_start: 0.7531 (mm-30) cc_final: 0.7080 (mp0) REVERT: A 160 ASN cc_start: 0.7479 (m-40) cc_final: 0.7261 (m-40) REVERT: A 197 MET cc_start: 0.7883 (mmp) cc_final: 0.6507 (mtp) REVERT: A 256 ASN cc_start: 0.7290 (t0) cc_final: 0.6905 (t0) REVERT: A 285 MET cc_start: 0.7144 (mtp) cc_final: 0.6935 (mtp) REVERT: A 309 GLU cc_start: 0.7012 (mt-10) cc_final: 0.6704 (mt-10) REVERT: A 343 GLN cc_start: 0.7059 (mt0) cc_final: 0.6560 (mt0) REVERT: A 366 ASP cc_start: 0.5427 (m-30) cc_final: 0.5180 (m-30) REVERT: A 399 LYS cc_start: 0.6883 (ttmm) cc_final: 0.5926 (tmmt) REVERT: A 461 MET cc_start: 0.3195 (OUTLIER) cc_final: 0.2213 (mpp) REVERT: D 42 LYS cc_start: 0.6930 (ttpp) cc_final: 0.6608 (ttpp) REVERT: D 61 LYS cc_start: 0.7030 (mtmm) cc_final: 0.6003 (mmtt) REVERT: D 100 GLU cc_start: 0.6353 (tp30) cc_final: 0.5283 (mp0) REVERT: D 118 GLU cc_start: 0.7106 (pt0) cc_final: 0.6493 (pp20) REVERT: D 145 GLU cc_start: 0.5585 (mm-30) cc_final: 0.5200 (mp0) REVERT: D 150 ARG cc_start: 0.6432 (mtm110) cc_final: 0.6204 (mtm-85) REVERT: D 158 GLU cc_start: 0.7540 (mm-30) cc_final: 0.6308 (tm-30) REVERT: D 160 ASN cc_start: 0.7300 (m-40) cc_final: 0.7023 (m-40) REVERT: D 197 MET cc_start: 0.7804 (mmp) cc_final: 0.6427 (mtm) REVERT: D 248 LYS cc_start: 0.7494 (tttp) cc_final: 0.7211 (tttm) REVERT: D 262 LYS cc_start: 0.7306 (mmtm) cc_final: 0.6858 (mptt) REVERT: D 285 MET cc_start: 0.6924 (mtp) cc_final: 0.6617 (mtp) REVERT: D 344 GLN cc_start: 0.7851 (mt0) cc_final: 0.7486 (mt0) REVERT: D 346 GLU cc_start: 0.6990 (tp30) cc_final: 0.6757 (tp30) REVERT: D 399 LYS cc_start: 0.6912 (ttmm) cc_final: 0.6095 (tmmt) REVERT: D 403 ARG cc_start: 0.7464 (ttp-110) cc_final: 0.7219 (ttp80) REVERT: D 461 MET cc_start: 0.2999 (ppp) cc_final: 0.2436 (mpp) REVERT: B 42 LYS cc_start: 0.7130 (ttpp) cc_final: 0.6730 (ttpp) REVERT: B 61 LYS cc_start: 0.6927 (mtmm) cc_final: 0.5969 (mmtm) REVERT: B 100 GLU cc_start: 0.6359 (tp30) cc_final: 0.6112 (tp30) REVERT: B 112 ASP cc_start: 0.7769 (m-30) cc_final: 0.7569 (m-30) REVERT: B 145 GLU cc_start: 0.5645 (mm-30) cc_final: 0.5290 (mp0) REVERT: B 150 ARG cc_start: 0.6339 (mtm110) cc_final: 0.6131 (mtm-85) REVERT: B 158 GLU cc_start: 0.7531 (mm-30) cc_final: 0.7079 (mp0) REVERT: B 160 ASN cc_start: 0.7481 (m-40) cc_final: 0.7265 (m-40) REVERT: B 197 MET cc_start: 0.7840 (mmp) cc_final: 0.6488 (mtp) REVERT: B 248 LYS cc_start: 0.7512 (tttp) cc_final: 0.7214 (tttm) REVERT: B 256 ASN cc_start: 0.7278 (t0) cc_final: 0.6860 (t0) REVERT: B 285 MET cc_start: 0.7151 (mtp) cc_final: 0.6932 (mtp) REVERT: B 309 GLU cc_start: 0.7022 (mt-10) cc_final: 0.6712 (mt-10) REVERT: B 343 GLN cc_start: 0.7052 (mt0) cc_final: 0.6566 (mt0) REVERT: B 366 ASP cc_start: 0.5447 (m-30) cc_final: 0.5196 (m-30) REVERT: B 399 LYS cc_start: 0.6900 (ttmm) cc_final: 0.5952 (tmmt) REVERT: B 461 MET cc_start: 0.3037 (OUTLIER) cc_final: 0.2095 (mpp) REVERT: C 28 GLU cc_start: 0.6768 (mm-30) cc_final: 0.6489 (mp0) REVERT: C 42 LYS cc_start: 0.7042 (ttpp) cc_final: 0.6740 (tmtp) REVERT: C 61 LYS cc_start: 0.7144 (mtmm) cc_final: 0.6153 (mmtm) REVERT: C 100 GLU cc_start: 0.6519 (tp30) cc_final: 0.5294 (mp0) REVERT: C 118 GLU cc_start: 0.7061 (pt0) cc_final: 0.6409 (pp20) REVERT: C 136 ARG cc_start: 0.7739 (ttt180) cc_final: 0.7352 (tpt-90) REVERT: C 145 GLU cc_start: 0.5648 (mm-30) cc_final: 0.5208 (mp0) REVERT: C 150 ARG cc_start: 0.6272 (mtm110) cc_final: 0.5894 (mtm110) REVERT: C 151 LEU cc_start: 0.7668 (mt) cc_final: 0.7410 (mt) REVERT: C 158 GLU cc_start: 0.7438 (mm-30) cc_final: 0.7035 (mp0) REVERT: C 165 ASP cc_start: 0.7933 (t0) cc_final: 0.7681 (t0) REVERT: C 197 MET cc_start: 0.7712 (mmp) cc_final: 0.6705 (mtp) REVERT: C 248 LYS cc_start: 0.7605 (tttp) cc_final: 0.7339 (tttm) REVERT: C 274 HIS cc_start: 0.7553 (t70) cc_final: 0.7296 (t70) REVERT: C 309 GLU cc_start: 0.7174 (mt-10) cc_final: 0.6834 (mt-10) REVERT: C 335 GLU cc_start: 0.5675 (mp0) cc_final: 0.5393 (tm-30) REVERT: C 343 GLN cc_start: 0.6730 (mt0) cc_final: 0.6127 (mt0) REVERT: C 344 GLN cc_start: 0.7892 (mt0) cc_final: 0.7431 (mt0) REVERT: C 366 ASP cc_start: 0.5334 (m-30) cc_final: 0.5116 (m-30) REVERT: C 399 LYS cc_start: 0.6771 (ttmm) cc_final: 0.5792 (tmmt) REVERT: C 403 ARG cc_start: 0.7570 (ttp-110) cc_final: 0.7274 (tmm160) REVERT: C 461 MET cc_start: 0.2941 (OUTLIER) cc_final: 0.2014 (mmt) REVERT: E 42 LYS cc_start: 0.6934 (ttpp) cc_final: 0.6603 (ttpp) REVERT: E 61 LYS cc_start: 0.7067 (mtmm) cc_final: 0.6050 (mmtt) REVERT: E 100 GLU cc_start: 0.6358 (tp30) cc_final: 0.5289 (mp0) REVERT: E 118 GLU cc_start: 0.7093 (pt0) cc_final: 0.6482 (pp20) REVERT: E 145 GLU cc_start: 0.5587 (mm-30) cc_final: 0.5167 (mp0) REVERT: E 150 ARG cc_start: 0.6404 (mtm110) cc_final: 0.6175 (mtm-85) REVERT: E 158 GLU cc_start: 0.7487 (mm-30) cc_final: 0.6310 (tm-30) REVERT: E 160 ASN cc_start: 0.7306 (m-40) cc_final: 0.7040 (m-40) REVERT: E 197 MET cc_start: 0.7827 (mmp) cc_final: 0.6436 (mtm) REVERT: E 248 LYS cc_start: 0.7485 (tttp) cc_final: 0.7198 (tttm) REVERT: E 285 MET cc_start: 0.6889 (mtp) cc_final: 0.6588 (mtp) REVERT: E 344 GLN cc_start: 0.7851 (mt0) cc_final: 0.7493 (mt0) REVERT: E 346 GLU cc_start: 0.6992 (tp30) cc_final: 0.6756 (tp30) REVERT: E 399 LYS cc_start: 0.6994 (ttmm) cc_final: 0.6160 (tmmt) REVERT: E 403 ARG cc_start: 0.7418 (ttp-110) cc_final: 0.7173 (ttp80) REVERT: E 461 MET cc_start: 0.3019 (ppp) cc_final: 0.2427 (mpp) REVERT: F 28 GLU cc_start: 0.6768 (mm-30) cc_final: 0.6490 (mp0) REVERT: F 42 LYS cc_start: 0.7039 (ttpp) cc_final: 0.6737 (tmtp) REVERT: F 61 LYS cc_start: 0.7146 (mtmm) cc_final: 0.6156 (mmtm) REVERT: F 100 GLU cc_start: 0.6517 (tp30) cc_final: 0.5292 (mp0) REVERT: F 118 GLU cc_start: 0.7066 (pt0) cc_final: 0.6411 (pp20) REVERT: F 136 ARG cc_start: 0.7749 (ttt180) cc_final: 0.7375 (tpt-90) REVERT: F 145 GLU cc_start: 0.5565 (mm-30) cc_final: 0.5147 (mp0) REVERT: F 150 ARG cc_start: 0.6271 (mtm110) cc_final: 0.5890 (mtm110) REVERT: F 151 LEU cc_start: 0.7669 (mt) cc_final: 0.7418 (mt) REVERT: F 158 GLU cc_start: 0.7436 (mm-30) cc_final: 0.7035 (mp0) REVERT: F 165 ASP cc_start: 0.7930 (t0) cc_final: 0.7689 (t0) REVERT: F 197 MET cc_start: 0.7697 (mmp) cc_final: 0.6681 (mtp) REVERT: F 248 LYS cc_start: 0.7599 (tttp) cc_final: 0.7330 (tttm) REVERT: F 274 HIS cc_start: 0.7545 (t70) cc_final: 0.7314 (t70) REVERT: F 309 GLU cc_start: 0.7163 (mt-10) cc_final: 0.6840 (mt-10) REVERT: F 335 GLU cc_start: 0.5703 (mp0) cc_final: 0.5401 (tm-30) REVERT: F 343 GLN cc_start: 0.6659 (mt0) cc_final: 0.6056 (mt0) REVERT: F 344 GLN cc_start: 0.7877 (mt0) cc_final: 0.7424 (mt0) REVERT: F 366 ASP cc_start: 0.5399 (m-30) cc_final: 0.5174 (m-30) REVERT: F 399 LYS cc_start: 0.6767 (ttmm) cc_final: 0.5787 (tmmt) REVERT: F 403 ARG cc_start: 0.7569 (ttp-110) cc_final: 0.7271 (tmm160) REVERT: F 461 MET cc_start: 0.2939 (OUTLIER) cc_final: 0.2014 (mmt) outliers start: 4 outliers final: 0 residues processed: 406 average time/residue: 1.6565 time to fit residues: 758.8458 Evaluate side-chains 351 residues out of total 2790 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 347 time to evaluate : 2.872 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 461 MET Chi-restraints excluded: chain B residue 461 MET Chi-restraints excluded: chain C residue 461 MET Chi-restraints excluded: chain F residue 461 MET Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 318 random chunks: chunk 268 optimal weight: 6.9990 chunk 241 optimal weight: 8.9990 chunk 133 optimal weight: 0.1980 chunk 82 optimal weight: 8.9990 chunk 162 optimal weight: 6.9990 chunk 128 optimal weight: 2.9990 chunk 249 optimal weight: 10.0000 chunk 96 optimal weight: 6.9990 chunk 151 optimal weight: 6.9990 chunk 185 optimal weight: 6.9990 chunk 288 optimal weight: 0.0770 overall best weight: 3.4544 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 206 ASN A 226 HIS A 344 GLN A 532 HIS D 226 HIS D 395 ASN D 532 HIS B 206 ASN B 226 HIS B 344 GLN B 532 HIS C 206 ASN C 226 HIS C 532 HIS E 226 HIS E 395 ASN E 532 HIS F 206 ASN F 226 HIS F 532 HIS Total number of N/Q/H flips: 20 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7082 moved from start: 0.1678 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.043 26118 Z= 0.335 Angle : 0.749 9.417 35424 Z= 0.392 Chirality : 0.052 0.224 4002 Planarity : 0.005 0.038 4494 Dihedral : 7.450 59.194 3534 Min Nonbonded Distance : 2.169 Molprobity Statistics. All-atom Clashscore : 5.61 Ramachandran Plot: Outliers : 0.19 % Allowed : 4.23 % Favored : 95.58 % Rotamer: Outliers : 1.30 % Allowed : 8.01 % Favored : 90.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.35 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.23 (0.14), residues: 3168 helix: 0.63 (0.15), residues: 1104 sheet: -0.47 (0.21), residues: 576 loop : -0.51 (0.16), residues: 1488 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP F 402 HIS 0.007 0.002 HIS E 74 PHE 0.023 0.003 PHE A 187 TYR 0.031 0.003 TYR A 245 ARG 0.005 0.001 ARG A 190 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6336 Ramachandran restraints generated. 3168 Oldfield, 0 Emsley, 3168 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6336 Ramachandran restraints generated. 3168 Oldfield, 0 Emsley, 3168 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 368 residues out of total 2790 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 332 time to evaluate : 2.584 Fit side-chains REVERT: A 28 GLU cc_start: 0.7054 (mm-30) cc_final: 0.6846 (mp0) REVERT: A 42 LYS cc_start: 0.7212 (ttpp) cc_final: 0.6801 (tmmt) REVERT: A 61 LYS cc_start: 0.7192 (mtmm) cc_final: 0.6178 (mmtm) REVERT: A 112 ASP cc_start: 0.7908 (m-30) cc_final: 0.7668 (m-30) REVERT: A 144 GLU cc_start: 0.6110 (pm20) cc_final: 0.5674 (pm20) REVERT: A 150 ARG cc_start: 0.5909 (mtm110) cc_final: 0.5709 (mtm-85) REVERT: A 158 GLU cc_start: 0.7560 (mm-30) cc_final: 0.7031 (mp0) REVERT: A 197 MET cc_start: 0.8271 (mmp) cc_final: 0.7165 (mtp) REVERT: A 256 ASN cc_start: 0.7263 (t0) cc_final: 0.6887 (t0) REVERT: A 283 LYS cc_start: 0.6856 (mmtm) cc_final: 0.6568 (mptt) REVERT: A 309 GLU cc_start: 0.6908 (mt-10) cc_final: 0.6631 (mt-10) REVERT: A 335 GLU cc_start: 0.5902 (mp0) cc_final: 0.5282 (tm-30) REVERT: A 343 GLN cc_start: 0.7101 (mt0) cc_final: 0.6746 (mt0) REVERT: A 366 ASP cc_start: 0.5868 (m-30) cc_final: 0.5633 (m-30) REVERT: A 375 GLU cc_start: 0.6114 (pt0) cc_final: 0.5623 (pm20) REVERT: A 399 LYS cc_start: 0.6904 (ttmm) cc_final: 0.5952 (tmmt) REVERT: D 42 LYS cc_start: 0.7049 (ttpp) cc_final: 0.6663 (ttpp) REVERT: D 61 LYS cc_start: 0.7237 (mtmm) cc_final: 0.6209 (mmtt) REVERT: D 100 GLU cc_start: 0.6459 (tp30) cc_final: 0.5451 (mp0) REVERT: D 158 GLU cc_start: 0.7547 (mm-30) cc_final: 0.6359 (tm-30) REVERT: D 197 MET cc_start: 0.8190 (mmp) cc_final: 0.7146 (mtp) REVERT: D 262 LYS cc_start: 0.7341 (mmtm) cc_final: 0.7092 (mmtp) REVERT: D 285 MET cc_start: 0.7135 (mtp) cc_final: 0.6788 (mtp) REVERT: D 338 GLU cc_start: 0.6562 (mt-10) cc_final: 0.5519 (mm-30) REVERT: D 346 GLU cc_start: 0.6916 (tp30) cc_final: 0.6591 (tp30) REVERT: D 375 GLU cc_start: 0.6025 (pt0) cc_final: 0.5492 (pm20) REVERT: D 399 LYS cc_start: 0.6893 (ttmm) cc_final: 0.6061 (tmmt) REVERT: B 42 LYS cc_start: 0.7210 (ttpp) cc_final: 0.6801 (tmmt) REVERT: B 61 LYS cc_start: 0.7191 (mtmm) cc_final: 0.6178 (mmtm) REVERT: B 112 ASP cc_start: 0.7910 (m-30) cc_final: 0.7671 (m-30) REVERT: B 144 GLU cc_start: 0.6112 (pm20) cc_final: 0.5699 (pm20) REVERT: B 158 GLU cc_start: 0.7563 (mm-30) cc_final: 0.7029 (mp0) REVERT: B 197 MET cc_start: 0.8268 (mmp) cc_final: 0.7160 (mtp) REVERT: B 256 ASN cc_start: 0.7264 (t0) cc_final: 0.6891 (t0) REVERT: B 283 LYS cc_start: 0.6858 (mmtm) cc_final: 0.6643 (mptt) REVERT: B 309 GLU cc_start: 0.6913 (mt-10) cc_final: 0.6636 (mt-10) REVERT: B 335 GLU cc_start: 0.5954 (mp0) cc_final: 0.5335 (tm-30) REVERT: B 343 GLN cc_start: 0.7097 (mt0) cc_final: 0.6727 (mt0) REVERT: B 366 ASP cc_start: 0.5875 (m-30) cc_final: 0.5645 (m-30) REVERT: B 375 GLU cc_start: 0.6098 (pt0) cc_final: 0.5607 (pm20) REVERT: B 399 LYS cc_start: 0.6904 (ttmm) cc_final: 0.5951 (tmmt) REVERT: C 42 LYS cc_start: 0.7059 (ttpp) cc_final: 0.6811 (tmtp) REVERT: C 61 LYS cc_start: 0.7369 (mtmm) cc_final: 0.6319 (mmtm) REVERT: C 89 LYS cc_start: 0.8138 (mtpt) cc_final: 0.7786 (mttt) REVERT: C 100 GLU cc_start: 0.6627 (tp30) cc_final: 0.5405 (mp0) REVERT: C 133 THR cc_start: 0.5679 (OUTLIER) cc_final: 0.5383 (t) REVERT: C 136 ARG cc_start: 0.7854 (ttt180) cc_final: 0.7604 (tpt-90) REVERT: C 145 GLU cc_start: 0.5802 (mm-30) cc_final: 0.5351 (mp0) REVERT: C 150 ARG cc_start: 0.6024 (mtm110) cc_final: 0.5532 (mtm110) REVERT: C 158 GLU cc_start: 0.7485 (mm-30) cc_final: 0.6927 (mp0) REVERT: C 165 ASP cc_start: 0.8033 (t0) cc_final: 0.7814 (t0) REVERT: C 197 MET cc_start: 0.8372 (mmp) cc_final: 0.7217 (mtp) REVERT: C 248 LYS cc_start: 0.7481 (tttp) cc_final: 0.7252 (tttm) REVERT: C 262 LYS cc_start: 0.7255 (mmtm) cc_final: 0.7041 (mmtp) REVERT: C 274 HIS cc_start: 0.7497 (t70) cc_final: 0.7240 (t70) REVERT: C 283 LYS cc_start: 0.6848 (mmtm) cc_final: 0.6580 (mppt) REVERT: C 338 GLU cc_start: 0.6593 (mt-10) cc_final: 0.5616 (mm-30) REVERT: C 343 GLN cc_start: 0.6757 (mt0) cc_final: 0.6283 (mt0) REVERT: C 375 GLU cc_start: 0.6104 (pt0) cc_final: 0.5575 (pm20) REVERT: C 399 LYS cc_start: 0.6804 (ttmm) cc_final: 0.5741 (tmmt) REVERT: E 42 LYS cc_start: 0.7024 (ttpp) cc_final: 0.6659 (ttpp) REVERT: E 61 LYS cc_start: 0.7236 (mtmm) cc_final: 0.6207 (mmtt) REVERT: E 100 GLU cc_start: 0.6458 (tp30) cc_final: 0.5435 (mp0) REVERT: E 150 ARG cc_start: 0.6252 (mtm110) cc_final: 0.6039 (mtm-85) REVERT: E 158 GLU cc_start: 0.7535 (mm-30) cc_final: 0.6369 (tm-30) REVERT: E 197 MET cc_start: 0.8190 (mmp) cc_final: 0.7146 (mtp) REVERT: E 285 MET cc_start: 0.7132 (mtp) cc_final: 0.6837 (mtp) REVERT: E 338 GLU cc_start: 0.6564 (mt-10) cc_final: 0.5522 (mm-30) REVERT: E 346 GLU cc_start: 0.6916 (tp30) cc_final: 0.6590 (tp30) REVERT: E 375 GLU cc_start: 0.6028 (pt0) cc_final: 0.5491 (pm20) REVERT: E 399 LYS cc_start: 0.6892 (ttmm) cc_final: 0.6060 (tmmt) REVERT: F 42 LYS cc_start: 0.7061 (ttpp) cc_final: 0.6803 (tmtp) REVERT: F 61 LYS cc_start: 0.7389 (mtmm) cc_final: 0.6320 (mmtm) REVERT: F 89 LYS cc_start: 0.8137 (mtpt) cc_final: 0.7786 (mttt) REVERT: F 100 GLU cc_start: 0.6625 (tp30) cc_final: 0.5401 (mp0) REVERT: F 118 GLU cc_start: 0.7185 (pt0) cc_final: 0.6476 (pp20) REVERT: F 133 THR cc_start: 0.5681 (OUTLIER) cc_final: 0.5385 (t) REVERT: F 136 ARG cc_start: 0.7852 (ttt180) cc_final: 0.7603 (tpt-90) REVERT: F 145 GLU cc_start: 0.5778 (mm-30) cc_final: 0.5327 (mp0) REVERT: F 150 ARG cc_start: 0.6034 (mtm110) cc_final: 0.5543 (mtm110) REVERT: F 158 GLU cc_start: 0.7491 (mm-30) cc_final: 0.7018 (mp0) REVERT: F 165 ASP cc_start: 0.8034 (t0) cc_final: 0.7815 (t0) REVERT: F 197 MET cc_start: 0.8372 (mmp) cc_final: 0.7224 (mtp) REVERT: F 248 LYS cc_start: 0.7478 (tttp) cc_final: 0.7251 (tttm) REVERT: F 262 LYS cc_start: 0.7253 (mmtm) cc_final: 0.7038 (mmtp) REVERT: F 274 HIS cc_start: 0.7497 (t70) cc_final: 0.7237 (t70) REVERT: F 283 LYS cc_start: 0.6858 (mmtm) cc_final: 0.6589 (mppt) REVERT: F 335 GLU cc_start: 0.6012 (mp0) cc_final: 0.5450 (tm-30) REVERT: F 338 GLU cc_start: 0.6607 (mt-10) cc_final: 0.5632 (mm-30) REVERT: F 343 GLN cc_start: 0.6762 (mt0) cc_final: 0.6294 (mt0) REVERT: F 375 GLU cc_start: 0.6105 (pt0) cc_final: 0.5578 (pm20) REVERT: F 399 LYS cc_start: 0.6799 (ttmm) cc_final: 0.5741 (tmmt) outliers start: 36 outliers final: 22 residues processed: 360 average time/residue: 1.5789 time to fit residues: 644.9417 Evaluate side-chains 345 residues out of total 2790 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 321 time to evaluate : 2.847 ------------------------------------------------------------------------------- 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 160 optimal weight: 3.9990 chunk 89 optimal weight: 5.9990 chunk 240 optimal weight: 9.9990 chunk 196 optimal weight: 2.9990 chunk 79 optimal weight: 7.9990 chunk 289 optimal weight: 5.9990 chunk 312 optimal weight: 0.7980 chunk 257 optimal weight: 9.9990 chunk 286 optimal weight: 2.9990 chunk 98 optimal weight: 30.0000 chunk 232 optimal weight: 0.9990 overall best weight: 2.3588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 126 GLN A 154 GLN D 343 GLN B 126 GLN C 154 GLN C 160 ASN C 368 ASN E 343 GLN F 154 GLN F 368 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7069 moved from start: 0.1858 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 26118 Z= 0.252 Angle : 0.671 8.671 35424 Z= 0.351 Chirality : 0.049 0.206 4002 Planarity : 0.004 0.038 4494 Dihedral : 7.303 59.313 3534 Min Nonbonded Distance : 2.366 Molprobity Statistics. All-atom Clashscore : 5.90 Ramachandran Plot: Outliers : 0.19 % Allowed : 3.69 % Favored : 96.12 % Rotamer: Outliers : 1.73 % Allowed : 8.30 % Favored : 89.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.35 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.21 (0.15), residues: 3168 helix: 0.69 (0.15), residues: 1104 sheet: -0.54 (0.21), residues: 576 loop : -0.51 (0.16), residues: 1488 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP F 402 HIS 0.005 0.001 HIS D 39 PHE 0.021 0.002 PHE F 81 TYR 0.026 0.002 TYR B 245 ARG 0.004 0.001 ARG A 47 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6336 Ramachandran restraints generated. 3168 Oldfield, 0 Emsley, 3168 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6336 Ramachandran restraints generated. 3168 Oldfield, 0 Emsley, 3168 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 366 residues out of total 2790 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 318 time to evaluate : 2.855 Fit side-chains REVERT: A 42 LYS cc_start: 0.7234 (ttpp) cc_final: 0.6792 (tmmt) REVERT: A 61 LYS cc_start: 0.7209 (mtmm) cc_final: 0.6182 (mmtm) REVERT: A 112 ASP cc_start: 0.7879 (m-30) cc_final: 0.7602 (m-30) REVERT: A 158 GLU cc_start: 0.7504 (mm-30) cc_final: 0.6969 (mp0) REVERT: A 197 MET cc_start: 0.8308 (mmp) cc_final: 0.7165 (mtp) REVERT: A 256 ASN cc_start: 0.7166 (t0) cc_final: 0.6854 (t0) REVERT: A 309 GLU cc_start: 0.6886 (mt-10) cc_final: 0.6666 (mt-10) REVERT: A 335 GLU cc_start: 0.5977 (mp0) cc_final: 0.5222 (tm-30) REVERT: A 343 GLN cc_start: 0.7062 (mt0) cc_final: 0.6702 (mt0) REVERT: A 366 ASP cc_start: 0.5841 (m-30) cc_final: 0.5593 (m-30) REVERT: A 375 GLU cc_start: 0.6153 (pt0) cc_final: 0.5655 (pm20) REVERT: A 399 LYS cc_start: 0.6922 (ttmm) cc_final: 0.5935 (tmmt) REVERT: D 42 LYS cc_start: 0.7065 (ttpp) cc_final: 0.6683 (ttpp) REVERT: D 61 LYS cc_start: 0.7218 (mtmm) cc_final: 0.6166 (mmtt) REVERT: D 100 GLU cc_start: 0.6490 (tp30) cc_final: 0.5458 (mp0) REVERT: D 136 ARG cc_start: 0.8034 (ttt180) cc_final: 0.7712 (tpt-90) REVERT: D 158 GLU cc_start: 0.7465 (mm-30) cc_final: 0.6376 (tm-30) REVERT: D 197 MET cc_start: 0.8197 (mmp) cc_final: 0.7086 (mtp) REVERT: D 285 MET cc_start: 0.7073 (mtp) cc_final: 0.6759 (mtp) REVERT: D 335 GLU cc_start: 0.6198 (mp0) cc_final: 0.5444 (tm-30) REVERT: D 338 GLU cc_start: 0.6460 (mt-10) cc_final: 0.5374 (mm-30) REVERT: D 346 GLU cc_start: 0.6929 (tp30) cc_final: 0.6576 (tp30) REVERT: D 375 GLU cc_start: 0.6148 (pt0) cc_final: 0.5657 (pm20) REVERT: D 399 LYS cc_start: 0.6932 (ttmm) cc_final: 0.6109 (tmmt) REVERT: B 42 LYS cc_start: 0.7235 (ttpp) cc_final: 0.6795 (tmmt) REVERT: B 61 LYS cc_start: 0.7209 (mtmm) cc_final: 0.6183 (mmtm) REVERT: B 112 ASP cc_start: 0.7879 (m-30) cc_final: 0.7603 (m-30) REVERT: B 158 GLU cc_start: 0.7502 (mm-30) cc_final: 0.6967 (mp0) REVERT: B 197 MET cc_start: 0.8307 (mmp) cc_final: 0.7161 (mtp) REVERT: B 256 ASN cc_start: 0.7169 (t0) cc_final: 0.6853 (t0) REVERT: B 309 GLU cc_start: 0.6885 (mt-10) cc_final: 0.6666 (mt-10) REVERT: B 335 GLU cc_start: 0.5957 (mp0) cc_final: 0.5216 (tm-30) REVERT: B 343 GLN cc_start: 0.7058 (mt0) cc_final: 0.6683 (mt0) REVERT: B 366 ASP cc_start: 0.5849 (m-30) cc_final: 0.5607 (m-30) REVERT: B 375 GLU cc_start: 0.6155 (pt0) cc_final: 0.5657 (pm20) REVERT: B 399 LYS cc_start: 0.6922 (ttmm) cc_final: 0.5935 (tmmt) REVERT: C 42 LYS cc_start: 0.6991 (ttpp) cc_final: 0.6730 (tmtp) REVERT: C 61 LYS cc_start: 0.7377 (mtmm) cc_final: 0.6311 (mmtm) REVERT: C 100 GLU cc_start: 0.6501 (tp30) cc_final: 0.5345 (mp0) REVERT: C 133 THR cc_start: 0.5626 (OUTLIER) cc_final: 0.5328 (t) REVERT: C 136 ARG cc_start: 0.7873 (ttt180) cc_final: 0.7633 (tpt-90) REVERT: C 145 GLU cc_start: 0.5852 (mm-30) cc_final: 0.5344 (mp0) REVERT: C 150 ARG cc_start: 0.5826 (mtm110) cc_final: 0.5351 (mtm110) REVERT: C 158 GLU cc_start: 0.7407 (mm-30) cc_final: 0.7010 (mp0) REVERT: C 165 ASP cc_start: 0.8022 (t0) cc_final: 0.7784 (t0) REVERT: C 197 MET cc_start: 0.8356 (mmp) cc_final: 0.7212 (mtp) REVERT: C 248 LYS cc_start: 0.7489 (tttp) cc_final: 0.7202 (tttm) REVERT: C 274 HIS cc_start: 0.7539 (t70) cc_final: 0.7264 (t70) REVERT: C 335 GLU cc_start: 0.6146 (mp0) cc_final: 0.5413 (tm-30) REVERT: C 338 GLU cc_start: 0.6431 (mt-10) cc_final: 0.5544 (mm-30) REVERT: C 343 GLN cc_start: 0.6732 (mt0) cc_final: 0.6272 (mt0) REVERT: C 375 GLU cc_start: 0.6144 (pt0) cc_final: 0.5657 (pm20) REVERT: C 399 LYS cc_start: 0.6874 (ttmm) cc_final: 0.5816 (tmmt) REVERT: E 42 LYS cc_start: 0.7026 (ttpp) cc_final: 0.6672 (ttpp) REVERT: E 61 LYS cc_start: 0.7220 (mtmm) cc_final: 0.6167 (mmtt) REVERT: E 100 GLU cc_start: 0.6491 (tp30) cc_final: 0.5458 (mp0) REVERT: E 158 GLU cc_start: 0.7463 (mm-30) cc_final: 0.6376 (tm-30) REVERT: E 197 MET cc_start: 0.8200 (mmp) cc_final: 0.7013 (mtp) REVERT: E 262 LYS cc_start: 0.7381 (mmtm) cc_final: 0.7022 (mmmt) REVERT: E 285 MET cc_start: 0.7070 (mtp) cc_final: 0.6755 (mtp) REVERT: E 335 GLU cc_start: 0.6216 (mp0) cc_final: 0.5475 (tm-30) REVERT: E 338 GLU cc_start: 0.6462 (mt-10) cc_final: 0.5377 (mm-30) REVERT: E 346 GLU cc_start: 0.6955 (tp30) cc_final: 0.6608 (tp30) REVERT: E 375 GLU cc_start: 0.6148 (pt0) cc_final: 0.5658 (pm20) REVERT: E 399 LYS cc_start: 0.6937 (ttmm) cc_final: 0.6112 (tmmt) REVERT: F 42 LYS cc_start: 0.6990 (ttpp) cc_final: 0.6728 (tmtp) REVERT: F 61 LYS cc_start: 0.7378 (mtmm) cc_final: 0.6311 (mmtm) REVERT: F 100 GLU cc_start: 0.6497 (tp30) cc_final: 0.5340 (mp0) REVERT: F 118 GLU cc_start: 0.7141 (pt0) cc_final: 0.6453 (pp20) REVERT: F 133 THR cc_start: 0.5628 (OUTLIER) cc_final: 0.5329 (t) REVERT: F 136 ARG cc_start: 0.7871 (ttt180) cc_final: 0.7633 (tpt-90) REVERT: F 145 GLU cc_start: 0.5839 (mm-30) cc_final: 0.5371 (mp0) REVERT: F 150 ARG cc_start: 0.5814 (mtm110) cc_final: 0.5342 (mtm110) REVERT: F 158 GLU cc_start: 0.7430 (mm-30) cc_final: 0.7020 (mp0) REVERT: F 165 ASP cc_start: 0.8021 (t0) cc_final: 0.7784 (t0) REVERT: F 197 MET cc_start: 0.8354 (mmp) cc_final: 0.7208 (mtp) REVERT: F 248 LYS cc_start: 0.7466 (tttp) cc_final: 0.7183 (tttm) REVERT: F 262 LYS cc_start: 0.7346 (mmtm) cc_final: 0.7142 (mmtp) REVERT: F 274 HIS cc_start: 0.7542 (t70) cc_final: 0.7261 (t70) REVERT: F 335 GLU cc_start: 0.6151 (mp0) cc_final: 0.5415 (tm-30) REVERT: F 338 GLU cc_start: 0.6432 (mt-10) cc_final: 0.5482 (mm-30) REVERT: F 343 GLN cc_start: 0.6736 (mt0) cc_final: 0.6273 (mt0) REVERT: F 375 GLU cc_start: 0.6140 (pt0) cc_final: 0.5658 (pm20) REVERT: F 399 LYS cc_start: 0.6873 (ttmm) cc_final: 0.5819 (tmmt) outliers start: 48 outliers final: 34 residues processed: 356 average time/residue: 1.5324 time to fit residues: 620.9890 Evaluate side-chains 351 residues out of total 2790 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 315 time to evaluate : 2.783 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 111 ASP Chi-restraints excluded: chain A residue 118 GLU Chi-restraints excluded: chain A residue 221 ILE Chi-restraints excluded: chain A residue 227 VAL Chi-restraints excluded: chain A residue 459 ILE Chi-restraints excluded: chain A residue 461 MET Chi-restraints excluded: chain D residue 111 ASP Chi-restraints excluded: chain D residue 118 GLU Chi-restraints excluded: chain D residue 221 ILE Chi-restraints excluded: chain D residue 227 VAL Chi-restraints excluded: chain D residue 272 ILE Chi-restraints excluded: chain D residue 459 ILE Chi-restraints excluded: chain D residue 461 MET Chi-restraints excluded: chain B residue 111 ASP Chi-restraints excluded: chain B residue 118 GLU Chi-restraints excluded: chain B residue 221 ILE Chi-restraints excluded: chain B residue 227 VAL Chi-restraints excluded: chain B residue 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 459 ILE Chi-restraints excluded: chain E residue 461 MET Chi-restraints excluded: chain F residue 133 THR Chi-restraints excluded: chain F residue 221 ILE Chi-restraints excluded: chain F residue 227 VAL Chi-restraints excluded: chain F residue 459 ILE Chi-restraints excluded: chain F residue 461 MET Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 318 random chunks: chunk 285 optimal weight: 0.2980 chunk 217 optimal weight: 6.9990 chunk 150 optimal weight: 0.9990 chunk 32 optimal weight: 0.7980 chunk 138 optimal weight: 0.0670 chunk 194 optimal weight: 2.9990 chunk 290 optimal weight: 7.9990 chunk 307 optimal weight: 10.0000 chunk 151 optimal weight: 5.9990 chunk 275 optimal weight: 5.9990 chunk 82 optimal weight: 6.9990 overall best weight: 1.0322 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 343 GLN C 154 GLN C 160 ASN E 343 GLN F 154 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7037 moved from start: 0.1855 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 26118 Z= 0.167 Angle : 0.595 8.470 35424 Z= 0.312 Chirality : 0.046 0.192 4002 Planarity : 0.004 0.036 4494 Dihedral : 7.058 59.772 3534 Min Nonbonded Distance : 2.427 Molprobity Statistics. All-atom Clashscore : 6.10 Ramachandran Plot: Outliers : 0.19 % Allowed : 3.85 % Favored : 95.96 % Rotamer: Outliers : 1.33 % Allowed : 8.69 % Favored : 89.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.35 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.08 (0.15), residues: 3168 helix: 0.93 (0.16), residues: 1104 sheet: -0.44 (0.21), residues: 576 loop : -0.56 (0.16), residues: 1488 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP F 402 HIS 0.003 0.001 HIS E 39 PHE 0.018 0.002 PHE C 81 TYR 0.018 0.001 TYR B 245 ARG 0.002 0.000 ARG A 47 *********************** 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 366 residues out of total 2790 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 329 time to evaluate : 3.074 Fit side-chains REVERT: A 42 LYS cc_start: 0.7212 (ttpp) cc_final: 0.6827 (ttpp) REVERT: A 61 LYS cc_start: 0.7181 (mtmm) cc_final: 0.6183 (mmtm) REVERT: A 112 ASP cc_start: 0.7833 (m-30) cc_final: 0.7558 (m-30) REVERT: A 158 GLU cc_start: 0.7480 (mm-30) cc_final: 0.6962 (mp0) REVERT: A 197 MET cc_start: 0.8264 (mmp) cc_final: 0.7044 (mtp) REVERT: A 256 ASN cc_start: 0.7271 (t0) cc_final: 0.6916 (t0) REVERT: A 309 GLU cc_start: 0.6959 (mt-10) cc_final: 0.6698 (mt-10) REVERT: A 335 GLU cc_start: 0.5974 (mp0) cc_final: 0.5218 (tm-30) REVERT: A 343 GLN cc_start: 0.7041 (mt0) cc_final: 0.6648 (mt0) REVERT: A 366 ASP cc_start: 0.5763 (m-30) cc_final: 0.5513 (m-30) REVERT: A 375 GLU cc_start: 0.6221 (pt0) cc_final: 0.5729 (pm20) REVERT: A 399 LYS cc_start: 0.6979 (ttmm) cc_final: 0.5994 (tmmt) REVERT: D 42 LYS cc_start: 0.7033 (ttpp) cc_final: 0.6672 (ttpp) REVERT: D 61 LYS cc_start: 0.7245 (mtmm) cc_final: 0.6227 (mmtm) REVERT: D 100 GLU cc_start: 0.6437 (tp30) cc_final: 0.5397 (mp0) REVERT: D 136 ARG cc_start: 0.7972 (ttt180) cc_final: 0.7748 (tpt-90) REVERT: D 158 GLU cc_start: 0.7420 (mm-30) cc_final: 0.6417 (tm-30) REVERT: D 197 MET cc_start: 0.8228 (mmp) cc_final: 0.7005 (mtp) REVERT: D 248 LYS cc_start: 0.7574 (tttm) cc_final: 0.7273 (tttm) REVERT: D 278 SER cc_start: 0.7777 (m) cc_final: 0.7451 (p) REVERT: D 285 MET cc_start: 0.7041 (mtp) cc_final: 0.6736 (mtp) REVERT: D 335 GLU cc_start: 0.6283 (mp0) cc_final: 0.5534 (tm-30) REVERT: D 338 GLU cc_start: 0.6532 (mt-10) cc_final: 0.5442 (mm-30) REVERT: D 346 GLU cc_start: 0.7047 (tp30) cc_final: 0.6699 (tp30) REVERT: D 375 GLU cc_start: 0.6158 (pt0) cc_final: 0.5667 (pm20) REVERT: D 399 LYS cc_start: 0.6914 (ttmm) cc_final: 0.6110 (tmmt) REVERT: B 42 LYS cc_start: 0.7171 (ttpp) cc_final: 0.6799 (ttpp) REVERT: B 61 LYS cc_start: 0.7180 (mtmm) cc_final: 0.6183 (mmtm) REVERT: B 112 ASP cc_start: 0.7833 (m-30) cc_final: 0.7559 (m-30) REVERT: B 158 GLU cc_start: 0.7489 (mm-30) cc_final: 0.6974 (mp0) REVERT: B 197 MET cc_start: 0.8260 (mmp) cc_final: 0.7040 (mtp) REVERT: B 256 ASN cc_start: 0.7250 (t0) cc_final: 0.6888 (t0) REVERT: B 309 GLU cc_start: 0.6959 (mt-10) cc_final: 0.6698 (mt-10) REVERT: B 335 GLU cc_start: 0.5988 (mp0) cc_final: 0.5217 (tm-30) REVERT: B 343 GLN cc_start: 0.7055 (mt0) cc_final: 0.6660 (mt0) REVERT: B 366 ASP cc_start: 0.5770 (m-30) cc_final: 0.5519 (m-30) REVERT: B 375 GLU cc_start: 0.6221 (pt0) cc_final: 0.5730 (pm20) REVERT: B 399 LYS cc_start: 0.7028 (ttmm) cc_final: 0.6026 (tmmt) REVERT: C 42 LYS cc_start: 0.6965 (ttpp) cc_final: 0.6489 (ttpp) REVERT: C 61 LYS cc_start: 0.7376 (mtmm) cc_final: 0.6337 (mmtm) REVERT: C 100 GLU cc_start: 0.6492 (tp30) cc_final: 0.5344 (mp0) REVERT: C 133 THR cc_start: 0.5362 (OUTLIER) cc_final: 0.5096 (t) REVERT: C 136 ARG cc_start: 0.7834 (ttt180) cc_final: 0.7575 (tpt-90) REVERT: C 145 GLU cc_start: 0.5891 (mm-30) cc_final: 0.5429 (mp0) REVERT: C 150 ARG cc_start: 0.5776 (mtm110) cc_final: 0.5440 (mtm110) REVERT: C 151 LEU cc_start: 0.7394 (mt) cc_final: 0.7150 (mt) REVERT: C 158 GLU cc_start: 0.7378 (mm-30) cc_final: 0.6981 (mp0) REVERT: C 165 ASP cc_start: 0.8000 (t0) cc_final: 0.7750 (t0) REVERT: C 197 MET cc_start: 0.8280 (mmp) cc_final: 0.7126 (mtp) REVERT: C 248 LYS cc_start: 0.7509 (tttp) cc_final: 0.7216 (tttm) REVERT: C 274 HIS cc_start: 0.7558 (t70) cc_final: 0.7290 (t70) REVERT: C 335 GLU cc_start: 0.6043 (mp0) cc_final: 0.5341 (tm-30) REVERT: C 338 GLU cc_start: 0.6448 (mt-10) cc_final: 0.5585 (mm-30) REVERT: C 343 GLN cc_start: 0.6730 (mt0) cc_final: 0.6256 (mt0) REVERT: C 375 GLU cc_start: 0.6106 (pt0) cc_final: 0.5609 (pm20) REVERT: C 399 LYS cc_start: 0.6796 (ttmm) cc_final: 0.5747 (tmmt) REVERT: C 403 ARG cc_start: 0.7225 (ttp-110) cc_final: 0.6845 (ttp80) REVERT: E 42 LYS cc_start: 0.7024 (ttpp) cc_final: 0.6686 (ttpp) REVERT: E 61 LYS cc_start: 0.7246 (mtmm) cc_final: 0.6227 (mmtm) REVERT: E 100 GLU cc_start: 0.6439 (tp30) cc_final: 0.5401 (mp0) REVERT: E 136 ARG cc_start: 0.7966 (ttt180) cc_final: 0.7739 (tpt-90) REVERT: E 158 GLU cc_start: 0.7417 (mm-30) cc_final: 0.6416 (tm-30) REVERT: E 197 MET cc_start: 0.8229 (mmp) cc_final: 0.7009 (mtp) REVERT: E 278 SER cc_start: 0.7777 (m) cc_final: 0.7446 (p) REVERT: E 285 MET cc_start: 0.7049 (mtp) cc_final: 0.6742 (mtp) REVERT: E 335 GLU cc_start: 0.6284 (mp0) cc_final: 0.5536 (tm-30) REVERT: E 338 GLU cc_start: 0.6530 (mt-10) cc_final: 0.5439 (mm-30) REVERT: E 346 GLU cc_start: 0.7045 (tp30) cc_final: 0.6698 (tp30) REVERT: E 375 GLU cc_start: 0.6158 (pt0) cc_final: 0.5667 (pm20) REVERT: E 399 LYS cc_start: 0.6917 (ttmm) cc_final: 0.6111 (tmmt) REVERT: F 42 LYS cc_start: 0.6967 (ttpp) cc_final: 0.6490 (ttpp) REVERT: F 61 LYS cc_start: 0.7376 (mtmm) cc_final: 0.6336 (mmtm) REVERT: F 100 GLU cc_start: 0.6465 (tp30) cc_final: 0.5331 (mp0) REVERT: F 118 GLU cc_start: 0.7073 (pt0) cc_final: 0.6389 (pp20) REVERT: F 133 THR cc_start: 0.5363 (OUTLIER) cc_final: 0.5096 (t) REVERT: F 136 ARG cc_start: 0.7835 (ttt180) cc_final: 0.7574 (tpt-90) REVERT: F 145 GLU cc_start: 0.5851 (mm-30) cc_final: 0.5380 (mp0) REVERT: F 150 ARG cc_start: 0.5775 (mtm110) cc_final: 0.5438 (mtm110) REVERT: F 151 LEU cc_start: 0.7392 (mt) cc_final: 0.7149 (mt) REVERT: F 158 GLU cc_start: 0.7395 (mm-30) cc_final: 0.6924 (mp0) REVERT: F 165 ASP cc_start: 0.7999 (t0) cc_final: 0.7748 (t0) REVERT: F 197 MET cc_start: 0.8336 (mmp) cc_final: 0.7186 (mtp) REVERT: F 248 LYS cc_start: 0.7509 (tttp) cc_final: 0.7247 (tttm) REVERT: F 274 HIS cc_start: 0.7559 (t70) cc_final: 0.7284 (t70) REVERT: F 283 LYS cc_start: 0.6938 (mmtm) cc_final: 0.6530 (mppt) REVERT: F 335 GLU cc_start: 0.6048 (mp0) cc_final: 0.5343 (tm-30) REVERT: F 338 GLU cc_start: 0.6449 (mt-10) cc_final: 0.5500 (mm-30) REVERT: F 343 GLN cc_start: 0.6713 (mt0) cc_final: 0.6239 (mt0) REVERT: F 375 GLU cc_start: 0.6111 (pt0) cc_final: 0.5624 (pm20) REVERT: F 399 LYS cc_start: 0.6795 (ttmm) cc_final: 0.5750 (tmmt) REVERT: F 403 ARG cc_start: 0.7225 (ttp-110) cc_final: 0.6844 (ttp80) outliers start: 37 outliers final: 28 residues processed: 358 average time/residue: 1.6472 time to fit residues: 667.3544 Evaluate side-chains 355 residues out of total 2790 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 325 time to evaluate : 3.083 ------------------------------------------------------------------------------- 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 461 MET Chi-restraints excluded: chain D residue 111 ASP Chi-restraints excluded: chain D residue 118 GLU Chi-restraints excluded: chain D residue 221 ILE Chi-restraints excluded: chain D residue 227 VAL Chi-restraints excluded: chain D residue 272 ILE Chi-restraints excluded: chain D residue 461 MET Chi-restraints excluded: chain B residue 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 C residue 118 GLU Chi-restraints excluded: chain C residue 133 THR Chi-restraints excluded: chain C residue 221 ILE Chi-restraints excluded: chain C residue 227 VAL Chi-restraints excluded: chain C residue 272 ILE Chi-restraints excluded: chain C residue 461 MET Chi-restraints excluded: chain E residue 111 ASP Chi-restraints excluded: chain E residue 118 GLU Chi-restraints excluded: chain E residue 221 ILE Chi-restraints excluded: chain E residue 227 VAL Chi-restraints excluded: chain E residue 272 ILE Chi-restraints excluded: chain E residue 461 MET Chi-restraints excluded: chain F residue 133 THR Chi-restraints excluded: chain F residue 221 ILE Chi-restraints excluded: chain F residue 227 VAL Chi-restraints excluded: chain F residue 272 ILE Chi-restraints excluded: chain F residue 461 MET Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 318 random chunks: chunk 255 optimal weight: 6.9990 chunk 174 optimal weight: 5.9990 chunk 4 optimal weight: 4.9990 chunk 228 optimal weight: 1.9990 chunk 126 optimal weight: 0.0870 chunk 262 optimal weight: 20.0000 chunk 212 optimal weight: 6.9990 chunk 0 optimal weight: 10.0000 chunk 156 optimal weight: 30.0000 chunk 275 optimal weight: 4.9990 chunk 77 optimal weight: 0.6980 overall best weight: 2.5564 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 343 GLN C 154 GLN C 160 ASN E 343 GLN F 154 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7071 moved from start: 0.2042 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 26118 Z= 0.266 Angle : 0.682 8.679 35424 Z= 0.357 Chirality : 0.049 0.213 4002 Planarity : 0.004 0.037 4494 Dihedral : 7.411 59.153 3534 Min Nonbonded Distance : 2.328 Molprobity Statistics. All-atom Clashscore : 6.25 Ramachandran Plot: Outliers : 0.19 % Allowed : 4.39 % Favored : 95.42 % Rotamer: Outliers : 1.73 % Allowed : 8.77 % Favored : 89.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.35 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.21 (0.15), residues: 3168 helix: 0.73 (0.15), residues: 1104 sheet: -0.54 (0.21), residues: 576 loop : -0.54 (0.16), residues: 1488 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP F 402 HIS 0.006 0.001 HIS E 39 PHE 0.024 0.002 PHE F 81 TYR 0.025 0.002 TYR A 245 ARG 0.004 0.001 ARG B 47 *********************** 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 367 residues out of total 2790 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 319 time to evaluate : 3.097 Fit side-chains REVERT: A 42 LYS cc_start: 0.7178 (ttpp) cc_final: 0.6849 (ttpp) REVERT: A 61 LYS cc_start: 0.7221 (mtmm) cc_final: 0.6190 (mmtm) REVERT: A 158 GLU cc_start: 0.7512 (mm-30) cc_final: 0.7097 (mp0) REVERT: A 197 MET cc_start: 0.8265 (mmp) cc_final: 0.7112 (mtp) REVERT: A 256 ASN cc_start: 0.7177 (t0) cc_final: 0.6846 (t0) REVERT: A 309 GLU cc_start: 0.6916 (mt-10) cc_final: 0.6673 (mt-10) REVERT: A 335 GLU cc_start: 0.6005 (mp0) cc_final: 0.5239 (tm-30) REVERT: A 343 GLN cc_start: 0.7102 (mt0) cc_final: 0.6686 (mt0) REVERT: A 366 ASP cc_start: 0.5923 (m-30) cc_final: 0.5675 (m-30) REVERT: A 375 GLU cc_start: 0.6172 (pt0) cc_final: 0.5696 (pm20) REVERT: A 399 LYS cc_start: 0.7069 (ttmm) cc_final: 0.6014 (tmmt) REVERT: D 42 LYS cc_start: 0.7045 (ttpp) cc_final: 0.6659 (ttpp) REVERT: D 61 LYS cc_start: 0.7165 (mtmm) cc_final: 0.6172 (mmtm) REVERT: D 100 GLU cc_start: 0.6503 (tp30) cc_final: 0.5440 (mp0) REVERT: D 158 GLU cc_start: 0.7479 (mm-30) cc_final: 0.6394 (tm-30) REVERT: D 197 MET cc_start: 0.8249 (mmp) cc_final: 0.7125 (mtp) REVERT: D 248 LYS cc_start: 0.7563 (tttm) cc_final: 0.7305 (tttm) REVERT: D 262 LYS cc_start: 0.7461 (mmtm) cc_final: 0.7177 (mmmt) REVERT: D 285 MET cc_start: 0.7067 (mtp) cc_final: 0.6732 (mtp) REVERT: D 335 GLU cc_start: 0.6174 (mp0) cc_final: 0.5433 (tm-30) REVERT: D 338 GLU cc_start: 0.6440 (mt-10) cc_final: 0.5343 (mm-30) REVERT: D 346 GLU cc_start: 0.6939 (tp30) cc_final: 0.6624 (tp30) REVERT: D 375 GLU cc_start: 0.6022 (pt0) cc_final: 0.5504 (pm20) REVERT: D 399 LYS cc_start: 0.6939 (ttmm) cc_final: 0.6131 (tmmt) REVERT: B 42 LYS cc_start: 0.7179 (ttpp) cc_final: 0.6848 (ttpp) REVERT: B 61 LYS cc_start: 0.7221 (mtmm) cc_final: 0.6190 (mmtm) REVERT: B 158 GLU cc_start: 0.7512 (mm-30) cc_final: 0.7095 (mp0) REVERT: B 197 MET cc_start: 0.8263 (mmp) cc_final: 0.7107 (mtp) REVERT: B 248 LYS cc_start: 0.7476 (tttm) cc_final: 0.7190 (tttm) REVERT: B 256 ASN cc_start: 0.7175 (t0) cc_final: 0.6843 (t0) REVERT: B 309 GLU cc_start: 0.6917 (mt-10) cc_final: 0.6673 (mt-10) REVERT: B 335 GLU cc_start: 0.6025 (mp0) cc_final: 0.5245 (tm-30) REVERT: B 343 GLN cc_start: 0.7102 (mt0) cc_final: 0.6731 (mt0) REVERT: B 366 ASP cc_start: 0.5926 (m-30) cc_final: 0.5677 (m-30) REVERT: B 375 GLU cc_start: 0.6172 (pt0) cc_final: 0.5696 (pm20) REVERT: B 399 LYS cc_start: 0.7069 (ttmm) cc_final: 0.6012 (tmmt) REVERT: C 42 LYS cc_start: 0.6985 (ttpp) cc_final: 0.6719 (tmtp) REVERT: C 61 LYS cc_start: 0.7348 (mtmm) cc_final: 0.6271 (mmtm) REVERT: C 89 LYS cc_start: 0.8150 (mtpt) cc_final: 0.7800 (mttt) REVERT: C 100 GLU cc_start: 0.6526 (tp30) cc_final: 0.5362 (mp0) REVERT: C 133 THR cc_start: 0.5747 (OUTLIER) cc_final: 0.5445 (t) REVERT: C 136 ARG cc_start: 0.7903 (ttt180) cc_final: 0.7616 (tpt-90) REVERT: C 150 ARG cc_start: 0.5847 (mtm110) cc_final: 0.5380 (mtm110) REVERT: C 158 GLU cc_start: 0.7382 (mm-30) cc_final: 0.6957 (mp0) REVERT: C 165 ASP cc_start: 0.8018 (t0) cc_final: 0.7781 (t0) REVERT: C 197 MET cc_start: 0.8397 (mmp) cc_final: 0.7243 (mtp) REVERT: C 248 LYS cc_start: 0.7521 (tttp) cc_final: 0.7239 (tttm) REVERT: C 274 HIS cc_start: 0.7563 (t70) cc_final: 0.7301 (t70) REVERT: C 335 GLU cc_start: 0.6168 (mp0) cc_final: 0.5380 (tm-30) REVERT: C 338 GLU cc_start: 0.6323 (mt-10) cc_final: 0.5412 (mm-30) REVERT: C 343 GLN cc_start: 0.6749 (mt0) cc_final: 0.6217 (mt0) REVERT: C 375 GLU cc_start: 0.6072 (pt0) cc_final: 0.5565 (pm20) REVERT: C 399 LYS cc_start: 0.6869 (ttmm) cc_final: 0.5832 (tmmt) REVERT: E 42 LYS cc_start: 0.7028 (ttpp) cc_final: 0.6667 (ttpp) REVERT: E 61 LYS cc_start: 0.7164 (mtmm) cc_final: 0.6113 (mmtt) REVERT: E 100 GLU cc_start: 0.6505 (tp30) cc_final: 0.5444 (mp0) REVERT: E 158 GLU cc_start: 0.7477 (mm-30) cc_final: 0.6393 (tm-30) REVERT: E 197 MET cc_start: 0.8250 (mmp) cc_final: 0.7126 (mtp) REVERT: E 248 LYS cc_start: 0.7562 (tttm) cc_final: 0.7330 (tttm) REVERT: E 262 LYS cc_start: 0.7453 (mmtm) cc_final: 0.7071 (mmmt) REVERT: E 285 MET cc_start: 0.7065 (mtp) cc_final: 0.6729 (mtp) REVERT: E 335 GLU cc_start: 0.6173 (mp0) cc_final: 0.5433 (tm-30) REVERT: E 338 GLU cc_start: 0.6440 (mt-10) cc_final: 0.5341 (mm-30) REVERT: E 346 GLU cc_start: 0.6935 (tp30) cc_final: 0.6622 (tp30) REVERT: E 375 GLU cc_start: 0.6024 (pt0) cc_final: 0.5504 (pm20) REVERT: E 399 LYS cc_start: 0.6945 (ttmm) cc_final: 0.6134 (tmmt) REVERT: F 42 LYS cc_start: 0.6983 (ttpp) cc_final: 0.6716 (tmtp) REVERT: F 61 LYS cc_start: 0.7349 (mtmm) cc_final: 0.6272 (mmtm) REVERT: F 89 LYS cc_start: 0.8125 (mtpt) cc_final: 0.7775 (mttt) REVERT: F 100 GLU cc_start: 0.6524 (tp30) cc_final: 0.5360 (mp0) REVERT: F 118 GLU cc_start: 0.7112 (pt0) cc_final: 0.6493 (pp20) REVERT: F 133 THR cc_start: 0.5750 (OUTLIER) cc_final: 0.5449 (t) REVERT: F 136 ARG cc_start: 0.7901 (ttt180) cc_final: 0.7615 (tpt-90) REVERT: F 150 ARG cc_start: 0.5849 (mtm110) cc_final: 0.5380 (mtm110) REVERT: F 158 GLU cc_start: 0.7418 (mm-30) cc_final: 0.6975 (mp0) REVERT: F 165 ASP cc_start: 0.8020 (t0) cc_final: 0.7783 (t0) REVERT: F 197 MET cc_start: 0.8375 (mmp) cc_final: 0.7203 (mtp) REVERT: F 248 LYS cc_start: 0.7502 (tttp) cc_final: 0.7222 (tttm) REVERT: F 274 HIS cc_start: 0.7514 (t70) cc_final: 0.7245 (t70) REVERT: F 283 LYS cc_start: 0.6878 (mmtm) cc_final: 0.6475 (mppt) REVERT: F 335 GLU cc_start: 0.6173 (mp0) cc_final: 0.5381 (tm-30) REVERT: F 338 GLU cc_start: 0.6335 (mt-10) cc_final: 0.5418 (mm-30) REVERT: F 343 GLN cc_start: 0.6752 (mt0) cc_final: 0.6220 (mt0) REVERT: F 375 GLU cc_start: 0.6068 (pt0) cc_final: 0.5565 (pm20) REVERT: F 399 LYS cc_start: 0.6868 (ttmm) cc_final: 0.5832 (tmmt) outliers start: 48 outliers final: 38 residues processed: 355 average time/residue: 1.5353 time to fit residues: 620.3577 Evaluate side-chains 357 residues out of total 2790 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 317 time to evaluate : 2.543 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 111 ASP Chi-restraints excluded: chain A residue 118 GLU Chi-restraints excluded: chain A residue 221 ILE Chi-restraints excluded: chain A residue 227 VAL Chi-restraints excluded: chain A residue 459 ILE Chi-restraints excluded: chain A residue 461 MET Chi-restraints excluded: chain D residue 111 ASP Chi-restraints excluded: chain D residue 118 GLU Chi-restraints excluded: chain D residue 221 ILE Chi-restraints excluded: chain D residue 227 VAL Chi-restraints excluded: chain D residue 272 ILE Chi-restraints excluded: chain D residue 459 ILE Chi-restraints excluded: chain D residue 461 MET Chi-restraints excluded: chain B residue 111 ASP Chi-restraints excluded: chain B residue 118 GLU Chi-restraints excluded: chain B residue 221 ILE Chi-restraints excluded: chain B residue 227 VAL Chi-restraints excluded: chain B residue 459 ILE Chi-restraints excluded: chain B residue 461 MET Chi-restraints excluded: chain C residue 118 GLU Chi-restraints excluded: chain C residue 133 THR Chi-restraints excluded: chain C residue 221 ILE Chi-restraints excluded: chain C residue 227 VAL Chi-restraints excluded: chain C residue 272 ILE Chi-restraints excluded: chain C residue 459 ILE Chi-restraints excluded: chain C residue 461 MET Chi-restraints excluded: chain E residue 111 ASP Chi-restraints excluded: chain E residue 118 GLU Chi-restraints excluded: chain E residue 133 THR Chi-restraints excluded: chain E residue 221 ILE Chi-restraints excluded: chain E residue 227 VAL Chi-restraints excluded: chain E residue 272 ILE Chi-restraints excluded: chain E residue 459 ILE Chi-restraints excluded: chain E residue 461 MET Chi-restraints excluded: chain F residue 133 THR Chi-restraints excluded: chain F residue 221 ILE Chi-restraints excluded: chain F residue 227 VAL Chi-restraints excluded: chain F residue 272 ILE Chi-restraints excluded: chain F residue 459 ILE Chi-restraints excluded: chain F residue 461 MET Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 318 random chunks: chunk 103 optimal weight: 0.9990 chunk 276 optimal weight: 8.9990 chunk 60 optimal weight: 1.9990 chunk 180 optimal weight: 5.9990 chunk 75 optimal weight: 6.9990 chunk 307 optimal weight: 0.0010 chunk 255 optimal weight: 5.9990 chunk 142 optimal weight: 5.9990 chunk 25 optimal weight: 5.9990 chunk 101 optimal weight: 5.9990 chunk 161 optimal weight: 10.0000 overall best weight: 2.9994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 154 GLN A 448 HIS D 154 GLN D 343 GLN D 448 HIS C 154 GLN C 160 ASN E 343 GLN F 126 GLN F 154 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7077 moved from start: 0.2161 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 26118 Z= 0.297 Angle : 0.710 8.946 35424 Z= 0.371 Chirality : 0.050 0.227 4002 Planarity : 0.005 0.040 4494 Dihedral : 7.469 59.253 3534 Min Nonbonded Distance : 2.348 Molprobity Statistics. All-atom Clashscore : 6.35 Ramachandran Plot: Outliers : 0.19 % Allowed : 4.51 % Favored : 95.30 % Rotamer: Outliers : 1.62 % Allowed : 8.66 % Favored : 89.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.35 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.25 (0.14), residues: 3168 helix: 0.68 (0.15), residues: 1098 sheet: -0.55 (0.21), residues: 546 loop : -0.55 (0.15), residues: 1524 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP B 402 HIS 0.006 0.001 HIS E 39 PHE 0.025 0.002 PHE C 81 TYR 0.027 0.003 TYR B 245 ARG 0.004 0.001 ARG A 190 *********************** 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 363 residues out of total 2790 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 318 time to evaluate : 3.180 Fit side-chains REVERT: A 42 LYS cc_start: 0.7204 (ttpp) cc_final: 0.6760 (tmmt) REVERT: A 61 LYS cc_start: 0.7217 (mtmm) cc_final: 0.6185 (mmtm) REVERT: A 158 GLU cc_start: 0.7529 (mm-30) cc_final: 0.6993 (mp0) REVERT: A 197 MET cc_start: 0.8321 (mmp) cc_final: 0.7141 (mtp) REVERT: A 256 ASN cc_start: 0.7170 (t0) cc_final: 0.6835 (t0) REVERT: A 309 GLU cc_start: 0.6876 (mt-10) cc_final: 0.6622 (mt-10) REVERT: A 335 GLU cc_start: 0.6037 (mp0) cc_final: 0.5205 (tm-30) REVERT: A 343 GLN cc_start: 0.7106 (mt0) cc_final: 0.6730 (mt0) REVERT: A 366 ASP cc_start: 0.5977 (m-30) cc_final: 0.5695 (m-30) REVERT: A 375 GLU cc_start: 0.6168 (pt0) cc_final: 0.5698 (pm20) REVERT: A 399 LYS cc_start: 0.7130 (ttmm) cc_final: 0.6046 (tmmt) REVERT: D 42 LYS cc_start: 0.7104 (ttpp) cc_final: 0.6685 (ttpp) REVERT: D 61 LYS cc_start: 0.7140 (mtmm) cc_final: 0.6113 (mmtt) REVERT: D 100 GLU cc_start: 0.6465 (tp30) cc_final: 0.5413 (mp0) REVERT: D 158 GLU cc_start: 0.7480 (mm-30) cc_final: 0.6413 (tm-30) REVERT: D 197 MET cc_start: 0.8253 (mmp) cc_final: 0.7157 (mtp) REVERT: D 248 LYS cc_start: 0.7559 (tttm) cc_final: 0.7310 (tttm) REVERT: D 262 LYS cc_start: 0.7444 (mmtm) cc_final: 0.7143 (mmmt) REVERT: D 285 MET cc_start: 0.7066 (mtp) cc_final: 0.6725 (mtp) REVERT: D 335 GLU cc_start: 0.6199 (mp0) cc_final: 0.5439 (tm-30) REVERT: D 338 GLU cc_start: 0.6445 (mt-10) cc_final: 0.5325 (mm-30) REVERT: D 346 GLU cc_start: 0.6905 (tp30) cc_final: 0.6631 (tp30) REVERT: D 375 GLU cc_start: 0.5992 (pt0) cc_final: 0.5507 (pm20) REVERT: D 399 LYS cc_start: 0.6944 (ttmm) cc_final: 0.6122 (tmmt) REVERT: B 42 LYS cc_start: 0.7204 (ttpp) cc_final: 0.6762 (tmmt) REVERT: B 61 LYS cc_start: 0.7219 (mtmm) cc_final: 0.6187 (mmtm) REVERT: B 158 GLU cc_start: 0.7527 (mm-30) cc_final: 0.6990 (mp0) REVERT: B 197 MET cc_start: 0.8318 (mmp) cc_final: 0.7137 (mtp) REVERT: B 248 LYS cc_start: 0.7532 (tttm) cc_final: 0.7252 (tttm) REVERT: B 256 ASN cc_start: 0.7172 (t0) cc_final: 0.6831 (t0) REVERT: B 309 GLU cc_start: 0.6900 (mt-10) cc_final: 0.6647 (mt-10) REVERT: B 335 GLU cc_start: 0.6037 (mp0) cc_final: 0.5206 (tm-30) REVERT: B 343 GLN cc_start: 0.7082 (mt0) cc_final: 0.6711 (mt0) REVERT: B 366 ASP cc_start: 0.5985 (m-30) cc_final: 0.5698 (m-30) REVERT: B 375 GLU cc_start: 0.6168 (pt0) cc_final: 0.5700 (pm20) REVERT: B 399 LYS cc_start: 0.7130 (ttmm) cc_final: 0.6045 (tmmt) REVERT: C 42 LYS cc_start: 0.6939 (ttpp) cc_final: 0.6689 (tmtp) REVERT: C 61 LYS cc_start: 0.7341 (mtmm) cc_final: 0.6262 (mmtm) REVERT: C 100 GLU cc_start: 0.6517 (tp30) cc_final: 0.5355 (mp0) REVERT: C 133 THR cc_start: 0.5825 (OUTLIER) cc_final: 0.5534 (t) REVERT: C 136 ARG cc_start: 0.7927 (ttt180) cc_final: 0.7630 (tpt-90) REVERT: C 150 ARG cc_start: 0.5895 (mtm110) cc_final: 0.5397 (mtm110) REVERT: C 158 GLU cc_start: 0.7366 (mm-30) cc_final: 0.6995 (mp0) REVERT: C 165 ASP cc_start: 0.8028 (t0) cc_final: 0.7808 (t0) REVERT: C 197 MET cc_start: 0.8398 (mmp) cc_final: 0.7245 (mtp) REVERT: C 248 LYS cc_start: 0.7479 (tttp) cc_final: 0.7194 (tttm) REVERT: C 274 HIS cc_start: 0.7545 (t70) cc_final: 0.7266 (t70) REVERT: C 283 LYS cc_start: 0.6867 (mmtm) cc_final: 0.6472 (mppt) REVERT: C 335 GLU cc_start: 0.6182 (mp0) cc_final: 0.5339 (tm-30) REVERT: C 338 GLU cc_start: 0.6302 (mt-10) cc_final: 0.5376 (mm-30) REVERT: C 343 GLN cc_start: 0.6721 (mt0) cc_final: 0.6204 (mt0) REVERT: C 375 GLU cc_start: 0.6056 (pt0) cc_final: 0.5533 (pm20) REVERT: C 399 LYS cc_start: 0.7043 (ttmm) cc_final: 0.5922 (tmmt) REVERT: E 42 LYS cc_start: 0.7068 (ttpp) cc_final: 0.6677 (ttpp) REVERT: E 61 LYS cc_start: 0.7140 (mtmm) cc_final: 0.6112 (mmtt) REVERT: E 100 GLU cc_start: 0.6467 (tp30) cc_final: 0.5419 (mp0) REVERT: E 158 GLU cc_start: 0.7478 (mm-30) cc_final: 0.6413 (tm-30) REVERT: E 197 MET cc_start: 0.8253 (mmp) cc_final: 0.7159 (mtp) REVERT: E 248 LYS cc_start: 0.7571 (tttm) cc_final: 0.7325 (tttm) REVERT: E 262 LYS cc_start: 0.7404 (mmtm) cc_final: 0.7031 (mmmt) REVERT: E 285 MET cc_start: 0.7067 (mtp) cc_final: 0.6725 (mtp) REVERT: E 335 GLU cc_start: 0.6201 (mp0) cc_final: 0.5441 (tm-30) REVERT: E 338 GLU cc_start: 0.6444 (mt-10) cc_final: 0.5324 (mm-30) REVERT: E 346 GLU cc_start: 0.6900 (tp30) cc_final: 0.6630 (tp30) REVERT: E 375 GLU cc_start: 0.5995 (pt0) cc_final: 0.5507 (pm20) REVERT: E 399 LYS cc_start: 0.6948 (ttmm) cc_final: 0.6124 (tmmt) REVERT: F 42 LYS cc_start: 0.6939 (ttpp) cc_final: 0.6688 (tmtp) REVERT: F 61 LYS cc_start: 0.7342 (mtmm) cc_final: 0.6264 (mmtm) REVERT: F 89 LYS cc_start: 0.8121 (mtpt) cc_final: 0.7765 (mttt) REVERT: F 100 GLU cc_start: 0.6512 (tp30) cc_final: 0.5351 (mp0) REVERT: F 118 GLU cc_start: 0.7150 (pt0) cc_final: 0.6541 (pp20) REVERT: F 133 THR cc_start: 0.5827 (OUTLIER) cc_final: 0.5538 (t) REVERT: F 136 ARG cc_start: 0.7926 (ttt180) cc_final: 0.7631 (tpt-90) REVERT: F 150 ARG cc_start: 0.5857 (mtm110) cc_final: 0.5388 (mtm110) REVERT: F 158 GLU cc_start: 0.7384 (mm-30) cc_final: 0.6988 (mp0) REVERT: F 165 ASP cc_start: 0.8030 (t0) cc_final: 0.7808 (t0) REVERT: F 197 MET cc_start: 0.8398 (mmp) cc_final: 0.7245 (mtp) REVERT: F 248 LYS cc_start: 0.7478 (tttp) cc_final: 0.7195 (tttm) REVERT: F 274 HIS cc_start: 0.7547 (t70) cc_final: 0.7298 (t70) REVERT: F 283 LYS cc_start: 0.6866 (mmtm) cc_final: 0.6474 (mppt) REVERT: F 335 GLU cc_start: 0.6186 (mp0) cc_final: 0.5340 (tm-30) REVERT: F 338 GLU cc_start: 0.6301 (mt-10) cc_final: 0.5375 (mm-30) REVERT: F 343 GLN cc_start: 0.6722 (mt0) cc_final: 0.6204 (mt0) REVERT: F 375 GLU cc_start: 0.6051 (pt0) cc_final: 0.5533 (pm20) REVERT: F 399 LYS cc_start: 0.7041 (ttmm) cc_final: 0.5921 (tmmt) REVERT: F 461 MET cc_start: 0.2665 (OUTLIER) cc_final: 0.1951 (mtt) outliers start: 45 outliers final: 42 residues processed: 355 average time/residue: 1.6575 time to fit residues: 668.0239 Evaluate side-chains 363 residues out of total 2790 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 318 time to evaluate : 2.929 ------------------------------------------------------------------------------- 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 272 ILE 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 272 ILE Chi-restraints excluded: chain C residue 459 ILE Chi-restraints excluded: chain C residue 461 MET Chi-restraints excluded: chain C residue 469 VAL Chi-restraints excluded: chain E residue 111 ASP Chi-restraints excluded: chain E residue 118 GLU Chi-restraints excluded: chain E residue 133 THR Chi-restraints excluded: chain E residue 221 ILE Chi-restraints excluded: chain E residue 227 VAL Chi-restraints excluded: chain E residue 272 ILE Chi-restraints excluded: chain E residue 459 ILE Chi-restraints excluded: chain E residue 461 MET Chi-restraints excluded: chain F residue 133 THR Chi-restraints excluded: chain F residue 221 ILE Chi-restraints excluded: chain F residue 227 VAL Chi-restraints excluded: chain F residue 272 ILE Chi-restraints excluded: chain F residue 459 ILE Chi-restraints excluded: chain F residue 461 MET Chi-restraints excluded: chain F residue 469 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 318 random chunks: chunk 296 optimal weight: 4.9990 chunk 34 optimal weight: 1.9990 chunk 175 optimal weight: 0.9980 chunk 224 optimal weight: 5.9990 chunk 174 optimal weight: 0.6980 chunk 259 optimal weight: 5.9990 chunk 171 optimal weight: 5.9990 chunk 306 optimal weight: 0.7980 chunk 191 optimal weight: 4.9990 chunk 186 optimal weight: 8.9990 chunk 141 optimal weight: 0.8980 overall best weight: 1.0782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 126 GLN D 343 GLN B 154 GLN C 126 GLN C 154 GLN C 160 ASN E 343 GLN F 154 GLN F 206 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7038 moved from start: 0.2092 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 26118 Z= 0.170 Angle : 0.598 7.999 35424 Z= 0.313 Chirality : 0.046 0.195 4002 Planarity : 0.004 0.036 4494 Dihedral : 7.094 59.675 3534 Min Nonbonded Distance : 2.437 Molprobity Statistics. All-atom Clashscore : 6.21 Ramachandran Plot: Outliers : 0.19 % Allowed : 3.85 % Favored : 95.96 % Rotamer: Outliers : 1.52 % Allowed : 9.24 % Favored : 89.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.35 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.07 (0.15), residues: 3168 helix: 0.85 (0.16), residues: 1116 sheet: -0.42 (0.21), residues: 546 loop : -0.50 (0.16), residues: 1506 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP D 402 HIS 0.003 0.001 HIS D 39 PHE 0.019 0.002 PHE B 81 TYR 0.017 0.002 TYR A 245 ARG 0.002 0.000 ARG C 130 *********************** 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 364 residues out of total 2790 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 322 time to evaluate : 3.023 Fit side-chains REVERT: A 42 LYS cc_start: 0.7172 (ttpp) cc_final: 0.6784 (ttpp) REVERT: A 61 LYS cc_start: 0.7204 (mtmm) cc_final: 0.6182 (mmtm) REVERT: A 112 ASP cc_start: 0.7827 (m-30) cc_final: 0.7549 (m-30) REVERT: A 158 GLU cc_start: 0.7444 (mm-30) cc_final: 0.6924 (mp0) REVERT: A 197 MET cc_start: 0.8262 (mmp) cc_final: 0.7035 (mtp) REVERT: A 256 ASN cc_start: 0.7133 (t0) cc_final: 0.6837 (t0) REVERT: A 309 GLU cc_start: 0.6929 (mt-10) cc_final: 0.6668 (mt-10) REVERT: A 335 GLU cc_start: 0.6199 (mp0) cc_final: 0.5385 (tm-30) REVERT: A 343 GLN cc_start: 0.7036 (mt0) cc_final: 0.6639 (mt0) REVERT: A 366 ASP cc_start: 0.5797 (m-30) cc_final: 0.5571 (m-30) REVERT: A 399 LYS cc_start: 0.7189 (ttmm) cc_final: 0.6062 (tmmt) REVERT: D 42 LYS cc_start: 0.7094 (ttpp) cc_final: 0.6713 (ttpp) REVERT: D 61 LYS cc_start: 0.7142 (mtmm) cc_final: 0.6147 (mmtm) REVERT: D 100 GLU cc_start: 0.6434 (tp30) cc_final: 0.5395 (mp0) REVERT: D 136 ARG cc_start: 0.7972 (ttt180) cc_final: 0.7719 (tpt-90) REVERT: D 158 GLU cc_start: 0.7494 (mm-30) cc_final: 0.6447 (tm-30) REVERT: D 197 MET cc_start: 0.8231 (mmp) cc_final: 0.7024 (mtp) REVERT: D 248 LYS cc_start: 0.7534 (tttm) cc_final: 0.7285 (tttm) REVERT: D 262 LYS cc_start: 0.7423 (mmtm) cc_final: 0.7136 (mmmt) REVERT: D 278 SER cc_start: 0.7785 (m) cc_final: 0.7469 (p) REVERT: D 285 MET cc_start: 0.7058 (mtp) cc_final: 0.6764 (mtp) REVERT: D 335 GLU cc_start: 0.6252 (mp0) cc_final: 0.5523 (tm-30) REVERT: D 338 GLU cc_start: 0.6444 (mt-10) cc_final: 0.5338 (mm-30) REVERT: D 346 GLU cc_start: 0.6928 (tp30) cc_final: 0.6671 (tp30) REVERT: D 375 GLU cc_start: 0.6139 (pt0) cc_final: 0.5658 (pm20) REVERT: D 399 LYS cc_start: 0.6973 (ttmm) cc_final: 0.6162 (tmmt) REVERT: B 42 LYS cc_start: 0.7171 (ttpp) cc_final: 0.6784 (ttpp) REVERT: B 61 LYS cc_start: 0.7200 (mtmm) cc_final: 0.6184 (mmtm) REVERT: B 112 ASP cc_start: 0.7826 (m-30) cc_final: 0.7549 (m-30) REVERT: B 158 GLU cc_start: 0.7443 (mm-30) cc_final: 0.6925 (mp0) REVERT: B 197 MET cc_start: 0.8259 (mmp) cc_final: 0.7031 (mtp) REVERT: B 248 LYS cc_start: 0.7449 (tttm) cc_final: 0.7153 (tttm) REVERT: B 256 ASN cc_start: 0.7133 (t0) cc_final: 0.6837 (t0) REVERT: B 309 GLU cc_start: 0.6931 (mt-10) cc_final: 0.6669 (mt-10) REVERT: B 335 GLU cc_start: 0.6198 (mp0) cc_final: 0.5385 (tm-30) REVERT: B 343 GLN cc_start: 0.7051 (mt0) cc_final: 0.6647 (mt0) REVERT: B 366 ASP cc_start: 0.5803 (m-30) cc_final: 0.5572 (m-30) REVERT: B 399 LYS cc_start: 0.7189 (ttmm) cc_final: 0.6061 (tmmt) REVERT: C 42 LYS cc_start: 0.6997 (ttpp) cc_final: 0.6524 (ttpp) REVERT: C 61 LYS cc_start: 0.7320 (mtmm) cc_final: 0.6247 (mmtm) REVERT: C 100 GLU cc_start: 0.6509 (tp30) cc_final: 0.5348 (mp0) REVERT: C 133 THR cc_start: 0.5511 (OUTLIER) cc_final: 0.5258 (t) REVERT: C 136 ARG cc_start: 0.7853 (ttt180) cc_final: 0.7571 (tpt-90) REVERT: C 150 ARG cc_start: 0.5805 (mtm110) cc_final: 0.5461 (mtm110) REVERT: C 158 GLU cc_start: 0.7381 (mm-30) cc_final: 0.6985 (mp0) REVERT: C 165 ASP cc_start: 0.7995 (t0) cc_final: 0.7746 (t0) REVERT: C 197 MET cc_start: 0.8343 (mmp) cc_final: 0.7170 (mtp) REVERT: C 248 LYS cc_start: 0.7532 (tttp) cc_final: 0.7231 (tttm) REVERT: C 274 HIS cc_start: 0.7561 (t70) cc_final: 0.7280 (t70) REVERT: C 283 LYS cc_start: 0.6800 (mmtm) cc_final: 0.6421 (mppt) REVERT: C 335 GLU cc_start: 0.6248 (mp0) cc_final: 0.5431 (tm-30) REVERT: C 338 GLU cc_start: 0.6331 (mt-10) cc_final: 0.5423 (mm-30) REVERT: C 343 GLN cc_start: 0.6703 (mt0) cc_final: 0.6259 (mt0) REVERT: C 365 GLU cc_start: 0.5825 (mp0) cc_final: 0.5037 (mp0) REVERT: C 375 GLU cc_start: 0.6112 (pt0) cc_final: 0.5608 (pm20) REVERT: C 399 LYS cc_start: 0.6966 (ttmm) cc_final: 0.5917 (tmmt) REVERT: C 403 ARG cc_start: 0.7230 (ttp-110) cc_final: 0.6837 (ttp80) REVERT: E 42 LYS cc_start: 0.7095 (ttpp) cc_final: 0.6713 (ttpp) REVERT: E 61 LYS cc_start: 0.7143 (mtmm) cc_final: 0.6147 (mmtm) REVERT: E 100 GLU cc_start: 0.6436 (tp30) cc_final: 0.5393 (mp0) REVERT: E 136 ARG cc_start: 0.7967 (ttt180) cc_final: 0.7717 (tpt-90) REVERT: E 158 GLU cc_start: 0.7490 (mm-30) cc_final: 0.6446 (tm-30) REVERT: E 197 MET cc_start: 0.8233 (mmp) cc_final: 0.7025 (mtp) REVERT: E 248 LYS cc_start: 0.7534 (tttm) cc_final: 0.7287 (tttm) REVERT: E 262 LYS cc_start: 0.7383 (mmtm) cc_final: 0.7016 (mmmt) REVERT: E 278 SER cc_start: 0.7785 (m) cc_final: 0.7468 (p) REVERT: E 285 MET cc_start: 0.7063 (mtp) cc_final: 0.6767 (mtp) REVERT: E 335 GLU cc_start: 0.6253 (mp0) cc_final: 0.5524 (tm-30) REVERT: E 338 GLU cc_start: 0.6443 (mt-10) cc_final: 0.5336 (mm-30) REVERT: E 346 GLU cc_start: 0.6925 (tp30) cc_final: 0.6671 (tp30) REVERT: E 375 GLU cc_start: 0.6139 (pt0) cc_final: 0.5659 (pm20) REVERT: E 399 LYS cc_start: 0.6978 (ttmm) cc_final: 0.6163 (tmmt) REVERT: F 42 LYS cc_start: 0.6995 (ttpp) cc_final: 0.6522 (ttpp) REVERT: F 61 LYS cc_start: 0.7322 (mtmm) cc_final: 0.6250 (mmtm) REVERT: F 100 GLU cc_start: 0.6504 (tp30) cc_final: 0.5344 (mp0) REVERT: F 118 GLU cc_start: 0.7086 (pt0) cc_final: 0.6455 (pp20) REVERT: F 133 THR cc_start: 0.5511 (OUTLIER) cc_final: 0.5257 (t) REVERT: F 136 ARG cc_start: 0.7852 (ttt180) cc_final: 0.7570 (tpt-90) REVERT: F 150 ARG cc_start: 0.5812 (mtm110) cc_final: 0.5474 (mtm110) REVERT: F 158 GLU cc_start: 0.7408 (mm-30) cc_final: 0.6933 (mp0) REVERT: F 165 ASP cc_start: 0.7995 (t0) cc_final: 0.7746 (t0) REVERT: F 197 MET cc_start: 0.8341 (mmp) cc_final: 0.7170 (mtp) REVERT: F 248 LYS cc_start: 0.7534 (tttp) cc_final: 0.7263 (tttm) REVERT: F 274 HIS cc_start: 0.7562 (t70) cc_final: 0.7311 (t70) REVERT: F 283 LYS cc_start: 0.6803 (mmtm) cc_final: 0.6416 (mppt) REVERT: F 335 GLU cc_start: 0.6261 (mp0) cc_final: 0.5406 (tm-30) REVERT: F 338 GLU cc_start: 0.6332 (mt-10) cc_final: 0.5422 (mm-30) REVERT: F 343 GLN cc_start: 0.6687 (mt0) cc_final: 0.6235 (mt0) REVERT: F 365 GLU cc_start: 0.5827 (mp0) cc_final: 0.5038 (mp0) REVERT: F 375 GLU cc_start: 0.6111 (pt0) cc_final: 0.5609 (pm20) REVERT: F 399 LYS cc_start: 0.6964 (ttmm) cc_final: 0.5916 (tmmt) REVERT: F 403 ARG cc_start: 0.7229 (ttp-110) cc_final: 0.6835 (ttp80) outliers start: 42 outliers final: 37 residues processed: 356 average time/residue: 1.5958 time to fit residues: 644.8888 Evaluate side-chains 368 residues out of total 2790 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 329 time to evaluate : 2.583 ------------------------------------------------------------------------------- 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 111 ASP Chi-restraints excluded: chain D residue 118 GLU Chi-restraints excluded: chain D residue 221 ILE Chi-restraints excluded: chain D residue 227 VAL Chi-restraints excluded: chain D residue 272 ILE Chi-restraints excluded: chain D residue 459 ILE Chi-restraints excluded: chain D residue 461 MET Chi-restraints excluded: chain B residue 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 111 ASP Chi-restraints excluded: chain E residue 118 GLU Chi-restraints excluded: chain E residue 133 THR Chi-restraints excluded: chain E residue 221 ILE Chi-restraints excluded: chain E residue 227 VAL Chi-restraints excluded: chain E residue 272 ILE Chi-restraints excluded: chain E residue 459 ILE Chi-restraints excluded: chain E residue 461 MET Chi-restraints excluded: chain F residue 133 THR Chi-restraints excluded: chain F residue 221 ILE Chi-restraints excluded: chain F residue 227 VAL Chi-restraints excluded: chain F residue 272 ILE Chi-restraints excluded: chain F residue 459 ILE Chi-restraints excluded: chain F residue 461 MET Chi-restraints excluded: chain F residue 469 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 318 random chunks: chunk 189 optimal weight: 8.9990 chunk 122 optimal weight: 5.9990 chunk 183 optimal weight: 0.9980 chunk 92 optimal weight: 0.9990 chunk 60 optimal weight: 8.9990 chunk 59 optimal weight: 10.0000 chunk 194 optimal weight: 0.6980 chunk 208 optimal weight: 0.9990 chunk 151 optimal weight: 20.0000 chunk 28 optimal weight: 7.9990 chunk 240 optimal weight: 5.9990 overall best weight: 1.9386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 154 GLN D 343 GLN B 154 GLN C 154 GLN C 160 ASN E 154 GLN E 343 GLN F 154 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7060 moved from start: 0.2160 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 26118 Z= 0.225 Angle : 0.645 8.198 35424 Z= 0.337 Chirality : 0.048 0.221 4002 Planarity : 0.004 0.037 4494 Dihedral : 7.282 59.207 3534 Min Nonbonded Distance : 2.371 Molprobity Statistics. All-atom Clashscore : 6.25 Ramachandran Plot: Outliers : 0.19 % Allowed : 4.23 % Favored : 95.58 % Rotamer: Outliers : 1.62 % Allowed : 9.31 % Favored : 89.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.35 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.10 (0.15), residues: 3168 helix: 0.87 (0.16), residues: 1098 sheet: -0.46 (0.21), residues: 546 loop : -0.52 (0.16), residues: 1524 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP F 402 HIS 0.005 0.001 HIS E 39 PHE 0.022 0.002 PHE C 81 TYR 0.022 0.002 TYR B 245 ARG 0.003 0.000 ARG B 47 *********************** 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 369 residues out of total 2790 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 324 time to evaluate : 2.735 Fit side-chains REVERT: A 42 LYS cc_start: 0.7170 (ttpp) cc_final: 0.6836 (ttpp) REVERT: A 61 LYS cc_start: 0.7190 (mtmm) cc_final: 0.6175 (mmtm) REVERT: A 158 GLU cc_start: 0.7443 (mm-30) cc_final: 0.7034 (mp0) REVERT: A 197 MET cc_start: 0.8276 (mmp) cc_final: 0.7094 (mtp) REVERT: A 256 ASN cc_start: 0.7161 (t0) cc_final: 0.6821 (t0) REVERT: A 309 GLU cc_start: 0.6915 (mt-10) cc_final: 0.6655 (mt-10) REVERT: A 335 GLU cc_start: 0.6085 (mp0) cc_final: 0.5239 (tm-30) REVERT: A 343 GLN cc_start: 0.7066 (mt0) cc_final: 0.6660 (mt0) REVERT: A 366 ASP cc_start: 0.5983 (m-30) cc_final: 0.5704 (m-30) REVERT: A 375 GLU cc_start: 0.6193 (pt0) cc_final: 0.5728 (pm20) REVERT: A 399 LYS cc_start: 0.7204 (ttmm) cc_final: 0.6064 (tmmt) REVERT: D 42 LYS cc_start: 0.7084 (ttpp) cc_final: 0.6679 (ttpp) REVERT: D 61 LYS cc_start: 0.7145 (mtmm) cc_final: 0.6143 (mmtm) REVERT: D 100 GLU cc_start: 0.6529 (tp30) cc_final: 0.5461 (mp0) REVERT: D 158 GLU cc_start: 0.7467 (mm-30) cc_final: 0.6482 (tm-30) REVERT: D 197 MET cc_start: 0.8256 (mmp) cc_final: 0.7088 (mtp) REVERT: D 248 LYS cc_start: 0.7568 (tttm) cc_final: 0.7325 (tttm) REVERT: D 262 LYS cc_start: 0.7399 (mmtm) cc_final: 0.7108 (mmmt) REVERT: D 278 SER cc_start: 0.7782 (m) cc_final: 0.7462 (p) REVERT: D 285 MET cc_start: 0.7023 (mtp) cc_final: 0.6705 (mtp) REVERT: D 335 GLU cc_start: 0.6182 (mp0) cc_final: 0.5413 (tm-30) REVERT: D 338 GLU cc_start: 0.6441 (mt-10) cc_final: 0.5332 (mm-30) REVERT: D 346 GLU cc_start: 0.6963 (tp30) cc_final: 0.6731 (tp30) REVERT: D 399 LYS cc_start: 0.6983 (ttmm) cc_final: 0.6154 (tmmt) REVERT: B 42 LYS cc_start: 0.7170 (ttpp) cc_final: 0.6836 (ttpp) REVERT: B 61 LYS cc_start: 0.7193 (mtmm) cc_final: 0.6178 (mmtm) REVERT: B 158 GLU cc_start: 0.7443 (mm-30) cc_final: 0.7033 (mp0) REVERT: B 197 MET cc_start: 0.8273 (mmp) cc_final: 0.7089 (mtp) REVERT: B 248 LYS cc_start: 0.7454 (tttm) cc_final: 0.7144 (tttm) REVERT: B 256 ASN cc_start: 0.7160 (t0) cc_final: 0.6822 (t0) REVERT: B 309 GLU cc_start: 0.6916 (mt-10) cc_final: 0.6656 (mt-10) REVERT: B 335 GLU cc_start: 0.6087 (mp0) cc_final: 0.5241 (tm-30) REVERT: B 343 GLN cc_start: 0.7060 (mt0) cc_final: 0.6657 (mt0) REVERT: B 366 ASP cc_start: 0.5939 (m-30) cc_final: 0.5687 (m-30) REVERT: B 375 GLU cc_start: 0.6173 (pt0) cc_final: 0.5704 (pm20) REVERT: B 399 LYS cc_start: 0.7189 (ttmm) cc_final: 0.6058 (tmmt) REVERT: C 42 LYS cc_start: 0.7006 (ttpp) cc_final: 0.6493 (ttpp) REVERT: C 61 LYS cc_start: 0.7314 (mtmm) cc_final: 0.6240 (mmtm) REVERT: C 89 LYS cc_start: 0.8156 (mtpt) cc_final: 0.7795 (mttt) REVERT: C 100 GLU cc_start: 0.6517 (tp30) cc_final: 0.5369 (mp0) REVERT: C 133 THR cc_start: 0.5649 (OUTLIER) cc_final: 0.5369 (t) REVERT: C 136 ARG cc_start: 0.7876 (ttt180) cc_final: 0.7622 (tpt-90) REVERT: C 150 ARG cc_start: 0.5881 (mtm110) cc_final: 0.5370 (mtm110) REVERT: C 158 GLU cc_start: 0.7382 (mm-30) cc_final: 0.7010 (mp0) REVERT: C 165 ASP cc_start: 0.8008 (t0) cc_final: 0.7758 (t0) REVERT: C 197 MET cc_start: 0.8374 (mmp) cc_final: 0.7203 (mtp) REVERT: C 248 LYS cc_start: 0.7533 (tttp) cc_final: 0.7247 (tttm) REVERT: C 274 HIS cc_start: 0.7547 (t70) cc_final: 0.7303 (t70) REVERT: C 283 LYS cc_start: 0.6778 (mmtm) cc_final: 0.6383 (mppt) REVERT: C 335 GLU cc_start: 0.6232 (mp0) cc_final: 0.5423 (tm-30) REVERT: C 338 GLU cc_start: 0.6319 (mt-10) cc_final: 0.5395 (mm-30) REVERT: C 343 GLN cc_start: 0.6753 (mt0) cc_final: 0.6304 (mt0) REVERT: C 375 GLU cc_start: 0.6102 (pt0) cc_final: 0.5601 (pm20) REVERT: C 399 LYS cc_start: 0.7011 (ttmm) cc_final: 0.5902 (tmmt) REVERT: E 42 LYS cc_start: 0.7061 (ttpp) cc_final: 0.6681 (ttpp) REVERT: E 61 LYS cc_start: 0.7145 (mtmm) cc_final: 0.6143 (mmtm) REVERT: E 100 GLU cc_start: 0.6459 (tp30) cc_final: 0.5419 (mp0) REVERT: E 158 GLU cc_start: 0.7486 (mm-30) cc_final: 0.6447 (tm-30) REVERT: E 197 MET cc_start: 0.8259 (mmp) cc_final: 0.7091 (mtp) REVERT: E 248 LYS cc_start: 0.7567 (tttm) cc_final: 0.7320 (tttm) REVERT: E 262 LYS cc_start: 0.7352 (mmtm) cc_final: 0.7029 (mmmt) REVERT: E 278 SER cc_start: 0.7781 (m) cc_final: 0.7461 (p) REVERT: E 285 MET cc_start: 0.7021 (mtp) cc_final: 0.6705 (mtp) REVERT: E 335 GLU cc_start: 0.6185 (mp0) cc_final: 0.5415 (tm-30) REVERT: E 338 GLU cc_start: 0.6439 (mt-10) cc_final: 0.5330 (mm-30) REVERT: E 346 GLU cc_start: 0.6957 (tp30) cc_final: 0.6729 (tp30) REVERT: E 399 LYS cc_start: 0.6982 (ttmm) cc_final: 0.6157 (tmmt) REVERT: F 42 LYS cc_start: 0.7006 (ttpp) cc_final: 0.6493 (ttpp) REVERT: F 61 LYS cc_start: 0.7342 (mtmm) cc_final: 0.6259 (mmtm) REVERT: F 89 LYS cc_start: 0.8156 (mtpt) cc_final: 0.7795 (mttt) REVERT: F 100 GLU cc_start: 0.6512 (tp30) cc_final: 0.5364 (mp0) REVERT: F 118 GLU cc_start: 0.7094 (pt0) cc_final: 0.6471 (pp20) REVERT: F 133 THR cc_start: 0.5651 (OUTLIER) cc_final: 0.5371 (t) REVERT: F 136 ARG cc_start: 0.7874 (ttt180) cc_final: 0.7620 (tpt-90) REVERT: F 150 ARG cc_start: 0.5846 (mtm110) cc_final: 0.5355 (mtm110) REVERT: F 158 GLU cc_start: 0.7395 (mm-30) cc_final: 0.7006 (mp0) REVERT: F 165 ASP cc_start: 0.8009 (t0) cc_final: 0.7759 (t0) REVERT: F 197 MET cc_start: 0.8377 (mmp) cc_final: 0.7204 (mtp) REVERT: F 248 LYS cc_start: 0.7533 (tttp) cc_final: 0.7248 (tttm) REVERT: F 274 HIS cc_start: 0.7549 (t70) cc_final: 0.7297 (t70) REVERT: F 283 LYS cc_start: 0.6785 (mmtm) cc_final: 0.6389 (mppt) REVERT: F 335 GLU cc_start: 0.6236 (mp0) cc_final: 0.5424 (tm-30) REVERT: F 338 GLU cc_start: 0.6318 (mt-10) cc_final: 0.5393 (mm-30) REVERT: F 343 GLN cc_start: 0.6756 (mt0) cc_final: 0.6229 (mt0) REVERT: F 375 GLU cc_start: 0.6099 (pt0) cc_final: 0.5601 (pm20) REVERT: F 399 LYS cc_start: 0.7030 (ttmm) cc_final: 0.5911 (tmmt) outliers start: 45 outliers final: 41 residues processed: 358 average time/residue: 1.5921 time to fit residues: 648.7978 Evaluate side-chains 366 residues out of total 2790 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 323 time to evaluate : 2.709 ------------------------------------------------------------------------------- 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 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 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 459 ILE Chi-restraints excluded: chain B residue 461 MET Chi-restraints excluded: chain B residue 469 VAL Chi-restraints excluded: chain C residue 133 THR Chi-restraints excluded: chain C residue 221 ILE Chi-restraints excluded: chain C residue 227 VAL Chi-restraints excluded: chain C residue 272 ILE Chi-restraints excluded: chain C residue 459 ILE Chi-restraints excluded: chain C residue 461 MET Chi-restraints excluded: chain C residue 469 VAL Chi-restraints excluded: chain E residue 111 ASP Chi-restraints excluded: chain E residue 118 GLU Chi-restraints excluded: chain E residue 133 THR Chi-restraints excluded: chain E residue 221 ILE Chi-restraints excluded: chain E residue 227 VAL Chi-restraints excluded: chain E residue 272 ILE Chi-restraints excluded: chain E residue 459 ILE Chi-restraints excluded: chain E residue 461 MET Chi-restraints excluded: chain F residue 133 THR Chi-restraints excluded: chain F residue 221 ILE Chi-restraints excluded: chain F residue 227 VAL Chi-restraints excluded: chain F residue 272 ILE Chi-restraints excluded: chain F residue 459 ILE Chi-restraints excluded: chain F residue 461 MET Chi-restraints excluded: chain F residue 469 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 318 random chunks: chunk 278 optimal weight: 4.9990 chunk 293 optimal weight: 8.9990 chunk 267 optimal weight: 9.9990 chunk 285 optimal weight: 0.9980 chunk 171 optimal weight: 5.9990 chunk 124 optimal weight: 8.9990 chunk 224 optimal weight: 5.9990 chunk 87 optimal weight: 10.0000 chunk 258 optimal weight: 5.9990 chunk 270 optimal weight: 5.9990 chunk 284 optimal weight: 3.9990 overall best weight: 4.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 154 GLN D 154 GLN D 343 GLN B 154 GLN B 448 HIS C 154 GLN C 160 ASN E 343 GLN E 448 HIS F 154 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7087 moved from start: 0.2354 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.054 26118 Z= 0.399 Angle : 0.793 9.676 35424 Z= 0.414 Chirality : 0.054 0.239 4002 Planarity : 0.006 0.047 4494 Dihedral : 7.684 59.448 3534 Min Nonbonded Distance : 2.297 Molprobity Statistics. All-atom Clashscore : 6.94 Ramachandran Plot: Outliers : 0.19 % Allowed : 4.77 % Favored : 95.04 % Rotamer: Outliers : 1.73 % Allowed : 9.24 % Favored : 89.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.35 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.38 (0.14), residues: 3168 helix: 0.48 (0.15), residues: 1104 sheet: -0.69 (0.20), residues: 546 loop : -0.52 (0.15), residues: 1518 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP A 402 HIS 0.007 0.002 HIS E 39 PHE 0.027 0.003 PHE C 81 TYR 0.030 0.004 TYR B 245 ARG 0.006 0.001 ARG A 49 *********************** 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 370 residues out of total 2790 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 322 time to evaluate : 2.843 Fit side-chains REVERT: A 42 LYS cc_start: 0.7240 (ttpp) cc_final: 0.6805 (ttpp) REVERT: A 61 LYS cc_start: 0.7217 (mtmm) cc_final: 0.6183 (mmtm) REVERT: A 158 GLU cc_start: 0.7557 (mm-30) cc_final: 0.7089 (mp0) REVERT: A 197 MET cc_start: 0.8274 (mmp) cc_final: 0.7110 (mtp) REVERT: A 256 ASN cc_start: 0.7146 (t0) cc_final: 0.6826 (t0) REVERT: A 283 LYS cc_start: 0.6854 (mmtm) cc_final: 0.6522 (mptt) REVERT: A 309 GLU cc_start: 0.6825 (mt-10) cc_final: 0.6567 (mt-10) REVERT: A 335 GLU cc_start: 0.6070 (mp0) cc_final: 0.5140 (tm-30) REVERT: A 343 GLN cc_start: 0.7120 (mt0) cc_final: 0.6753 (mt0) REVERT: A 366 ASP cc_start: 0.5971 (m-30) cc_final: 0.5716 (m-30) REVERT: A 375 GLU cc_start: 0.6133 (pt0) cc_final: 0.5658 (pm20) REVERT: A 399 LYS cc_start: 0.7224 (ttmm) cc_final: 0.6126 (tmmt) REVERT: A 461 MET cc_start: 0.2567 (OUTLIER) cc_final: 0.1651 (mmm) REVERT: D 42 LYS cc_start: 0.7151 (ttpp) cc_final: 0.6791 (ttpp) REVERT: D 61 LYS cc_start: 0.7153 (mtmm) cc_final: 0.6145 (mmtt) REVERT: D 100 GLU cc_start: 0.6452 (tp30) cc_final: 0.5435 (mp0) REVERT: D 158 GLU cc_start: 0.7496 (mm-30) cc_final: 0.6400 (tm-30) REVERT: D 197 MET cc_start: 0.8217 (mmp) cc_final: 0.7142 (mtp) REVERT: D 248 LYS cc_start: 0.7567 (tttm) cc_final: 0.7274 (tttm) REVERT: D 262 LYS cc_start: 0.7412 (mmtm) cc_final: 0.7098 (mmmt) REVERT: D 285 MET cc_start: 0.7100 (mtp) cc_final: 0.6856 (mtp) REVERT: D 335 GLU cc_start: 0.6090 (mp0) cc_final: 0.5413 (tm-30) REVERT: D 346 GLU cc_start: 0.6959 (tp30) cc_final: 0.6750 (tp30) REVERT: D 375 GLU cc_start: 0.6082 (pt0) cc_final: 0.5610 (pm20) REVERT: D 399 LYS cc_start: 0.7130 (ttmm) cc_final: 0.6271 (tmmt) REVERT: B 42 LYS cc_start: 0.7240 (ttpp) cc_final: 0.6807 (ttpp) REVERT: B 61 LYS cc_start: 0.7218 (mtmm) cc_final: 0.6185 (mmtm) REVERT: B 144 GLU cc_start: 0.6020 (pm20) cc_final: 0.5600 (pm20) REVERT: B 158 GLU cc_start: 0.7559 (mm-30) cc_final: 0.7089 (mp0) REVERT: B 197 MET cc_start: 0.8271 (mmp) cc_final: 0.7105 (mtp) REVERT: B 248 LYS cc_start: 0.7548 (tttm) cc_final: 0.7250 (tttm) REVERT: B 256 ASN cc_start: 0.7148 (t0) cc_final: 0.6827 (t0) REVERT: B 283 LYS cc_start: 0.6857 (mmtm) cc_final: 0.6526 (mptt) REVERT: B 309 GLU cc_start: 0.6826 (mt-10) cc_final: 0.6567 (mt-10) REVERT: B 335 GLU cc_start: 0.6073 (mp0) cc_final: 0.5143 (tm-30) REVERT: B 343 GLN cc_start: 0.7119 (mt0) cc_final: 0.6758 (mt0) REVERT: B 366 ASP cc_start: 0.5972 (m-30) cc_final: 0.5714 (m-30) REVERT: B 375 GLU cc_start: 0.6135 (pt0) cc_final: 0.5660 (pm20) REVERT: B 399 LYS cc_start: 0.7174 (ttmm) cc_final: 0.6090 (tmmt) REVERT: B 461 MET cc_start: 0.2485 (OUTLIER) cc_final: 0.1592 (mmm) REVERT: C 42 LYS cc_start: 0.7019 (ttpp) cc_final: 0.6078 (tptp) REVERT: C 61 LYS cc_start: 0.7332 (mtmm) cc_final: 0.6251 (mmtm) REVERT: C 89 LYS cc_start: 0.8139 (mtpt) cc_final: 0.7786 (mttt) REVERT: C 100 GLU cc_start: 0.6518 (tp30) cc_final: 0.5370 (mp0) REVERT: C 133 THR cc_start: 0.5881 (OUTLIER) cc_final: 0.5582 (t) REVERT: C 150 ARG cc_start: 0.6050 (mtm110) cc_final: 0.5544 (mtm110) REVERT: C 158 GLU cc_start: 0.7345 (mm-30) cc_final: 0.7008 (mp0) REVERT: C 165 ASP cc_start: 0.8063 (t0) cc_final: 0.7854 (t0) REVERT: C 197 MET cc_start: 0.8381 (mmp) cc_final: 0.7255 (mtp) REVERT: C 248 LYS cc_start: 0.7498 (tttp) cc_final: 0.7268 (tttm) REVERT: C 274 HIS cc_start: 0.7479 (t70) cc_final: 0.7251 (t70) REVERT: C 283 LYS cc_start: 0.6857 (mmtm) cc_final: 0.6473 (mppt) REVERT: C 335 GLU cc_start: 0.6106 (mp0) cc_final: 0.5226 (tm-30) REVERT: C 338 GLU cc_start: 0.6321 (mt-10) cc_final: 0.5365 (mm-30) REVERT: C 343 GLN cc_start: 0.6721 (mt0) cc_final: 0.6210 (mt0) REVERT: C 375 GLU cc_start: 0.5888 (pt0) cc_final: 0.5354 (pm20) REVERT: C 399 LYS cc_start: 0.7091 (ttmm) cc_final: 0.5941 (tmmt) REVERT: C 461 MET cc_start: 0.2673 (OUTLIER) cc_final: 0.1901 (mmm) REVERT: E 42 LYS cc_start: 0.7066 (ttpp) cc_final: 0.6779 (ttpp) REVERT: E 61 LYS cc_start: 0.7155 (mtmm) cc_final: 0.6147 (mmtt) REVERT: E 100 GLU cc_start: 0.6462 (tp30) cc_final: 0.5452 (mp0) REVERT: E 158 GLU cc_start: 0.7468 (mm-30) cc_final: 0.6388 (tm-30) REVERT: E 197 MET cc_start: 0.8218 (mmp) cc_final: 0.7145 (mtp) REVERT: E 248 LYS cc_start: 0.7579 (tttm) cc_final: 0.7300 (tttm) REVERT: E 262 LYS cc_start: 0.7396 (mmtm) cc_final: 0.7027 (mmmt) REVERT: E 285 MET cc_start: 0.7097 (mtp) cc_final: 0.6856 (mtp) REVERT: E 335 GLU cc_start: 0.6090 (mp0) cc_final: 0.5373 (tm-30) REVERT: E 346 GLU cc_start: 0.6954 (tp30) cc_final: 0.6747 (tp30) REVERT: E 375 GLU cc_start: 0.6083 (pt0) cc_final: 0.5611 (pm20) REVERT: E 399 LYS cc_start: 0.7130 (ttmm) cc_final: 0.6233 (tmmt) REVERT: F 42 LYS cc_start: 0.7019 (ttpp) cc_final: 0.6078 (tptp) REVERT: F 61 LYS cc_start: 0.7336 (mtmm) cc_final: 0.6255 (mmtm) REVERT: F 89 LYS cc_start: 0.8138 (mtpt) cc_final: 0.7786 (mttt) REVERT: F 100 GLU cc_start: 0.6517 (tp30) cc_final: 0.5366 (mp0) REVERT: F 118 GLU cc_start: 0.7115 (pt0) cc_final: 0.6493 (pp20) REVERT: F 133 THR cc_start: 0.5884 (OUTLIER) cc_final: 0.5584 (t) REVERT: F 150 ARG cc_start: 0.6023 (mtm110) cc_final: 0.5537 (mtm110) REVERT: F 158 GLU cc_start: 0.7436 (mm-30) cc_final: 0.7081 (mp0) REVERT: F 165 ASP cc_start: 0.8065 (t0) cc_final: 0.7856 (t0) REVERT: F 197 MET cc_start: 0.8381 (mmp) cc_final: 0.7256 (mtp) REVERT: F 248 LYS cc_start: 0.7495 (tttp) cc_final: 0.7267 (tttm) REVERT: F 274 HIS cc_start: 0.7481 (t70) cc_final: 0.7245 (t70) REVERT: F 283 LYS cc_start: 0.6877 (mmtm) cc_final: 0.6493 (mppt) REVERT: F 335 GLU cc_start: 0.6108 (mp0) cc_final: 0.5226 (tm-30) REVERT: F 338 GLU cc_start: 0.6442 (mt-10) cc_final: 0.5493 (mm-30) REVERT: F 343 GLN cc_start: 0.6734 (mt0) cc_final: 0.6280 (mt0) REVERT: F 375 GLU cc_start: 0.5884 (pt0) cc_final: 0.5355 (pm20) REVERT: F 399 LYS cc_start: 0.7089 (ttmm) cc_final: 0.5941 (tmmt) REVERT: F 461 MET cc_start: 0.2670 (OUTLIER) cc_final: 0.1898 (mmm) outliers start: 48 outliers final: 33 residues processed: 360 average time/residue: 1.3075 time to fit residues: 535.6694 Evaluate side-chains 360 residues out of total 2790 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 321 time to evaluate : 1.854 ------------------------------------------------------------------------------- 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 272 ILE 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 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 221 ILE Chi-restraints excluded: chain E residue 227 VAL Chi-restraints excluded: chain E residue 272 ILE Chi-restraints excluded: chain E residue 459 ILE Chi-restraints excluded: chain E residue 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 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 187 optimal weight: 10.0000 chunk 302 optimal weight: 0.8980 chunk 184 optimal weight: 4.9990 chunk 143 optimal weight: 6.9990 chunk 209 optimal weight: 8.9990 chunk 316 optimal weight: 6.9990 chunk 291 optimal weight: 0.9990 chunk 252 optimal weight: 3.9990 chunk 26 optimal weight: 1.9990 chunk 194 optimal weight: 1.9990 chunk 154 optimal weight: 1.9990 overall best weight: 1.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 154 GLN D 154 GLN D 343 GLN B 154 GLN C 160 ASN E 343 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7054 moved from start: 0.2262 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 26118 Z= 0.206 Angle : 0.642 9.830 35424 Z= 0.335 Chirality : 0.047 0.213 4002 Planarity : 0.004 0.036 4494 Dihedral : 7.298 59.383 3534 Min Nonbonded Distance : 2.417 Molprobity Statistics. All-atom Clashscore : 6.67 Ramachandran Plot: Outliers : 0.19 % Allowed : 3.76 % Favored : 96.05 % Rotamer: Outliers : 1.55 % Allowed : 9.38 % Favored : 89.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.35 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.17 (0.14), residues: 3168 helix: 0.81 (0.16), residues: 1098 sheet: -0.59 (0.21), residues: 546 loop : -0.52 (0.16), residues: 1524 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP D 402 HIS 0.004 0.001 HIS E 39 PHE 0.021 0.002 PHE C 81 TYR 0.021 0.002 TYR B 245 ARG 0.003 0.000 ARG A 47 ********************** 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 364 residues out of total 2790 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 321 time to evaluate : 3.235 Fit side-chains revert: symmetry clash REVERT: A 42 LYS cc_start: 0.7172 (ttpp) cc_final: 0.6838 (ttpp) REVERT: A 61 LYS cc_start: 0.7198 (mtmm) cc_final: 0.6176 (mmtm) REVERT: A 158 GLU cc_start: 0.7444 (mm-30) cc_final: 0.6922 (mp0) REVERT: A 197 MET cc_start: 0.8272 (mmp) cc_final: 0.7089 (mtp) REVERT: A 256 ASN cc_start: 0.7117 (t0) cc_final: 0.6833 (t0) REVERT: A 309 GLU cc_start: 0.6885 (mt-10) cc_final: 0.6616 (mt-10) REVERT: A 335 GLU cc_start: 0.6148 (mp0) cc_final: 0.5285 (tm-30) REVERT: A 343 GLN cc_start: 0.7047 (mt0) cc_final: 0.6666 (mt0) REVERT: A 366 ASP cc_start: 0.5892 (m-30) cc_final: 0.5643 (m-30) REVERT: A 399 LYS cc_start: 0.7158 (ttmm) cc_final: 0.6054 (tmmt) REVERT: D 42 LYS cc_start: 0.7113 (ttpp) cc_final: 0.6706 (ttpp) REVERT: D 61 LYS cc_start: 0.7146 (mtmm) cc_final: 0.6137 (mmtm) REVERT: D 100 GLU cc_start: 0.6524 (tp30) cc_final: 0.5462 (mp0) REVERT: D 136 ARG cc_start: 0.8015 (ttt180) cc_final: 0.7699 (tpt-90) REVERT: D 158 GLU cc_start: 0.7482 (mm-30) cc_final: 0.6440 (tm-30) REVERT: D 197 MET cc_start: 0.8229 (mmp) cc_final: 0.7147 (mtp) REVERT: D 248 LYS cc_start: 0.7545 (tttm) cc_final: 0.7315 (tttm) REVERT: D 262 LYS cc_start: 0.7481 (mmtm) cc_final: 0.7183 (mmmt) REVERT: D 278 SER cc_start: 0.7789 (m) cc_final: 0.7475 (p) REVERT: D 285 MET cc_start: 0.7048 (mtp) cc_final: 0.6690 (mtp) REVERT: D 335 GLU cc_start: 0.6201 (mp0) cc_final: 0.5428 (tm-30) REVERT: D 338 GLU cc_start: 0.6434 (mt-10) cc_final: 0.5322 (mm-30) REVERT: D 346 GLU cc_start: 0.6965 (tp30) cc_final: 0.6722 (tp30) REVERT: D 375 GLU cc_start: 0.6122 (pt0) cc_final: 0.5663 (pm20) REVERT: D 399 LYS cc_start: 0.7112 (ttmm) cc_final: 0.6264 (tmmt) REVERT: B 42 LYS cc_start: 0.7169 (ttpp) cc_final: 0.6839 (ttpp) REVERT: B 61 LYS cc_start: 0.7198 (mtmm) cc_final: 0.6177 (mmtm) REVERT: B 158 GLU cc_start: 0.7443 (mm-30) cc_final: 0.6919 (mp0) REVERT: B 197 MET cc_start: 0.8269 (mmp) cc_final: 0.7085 (mtp) REVERT: B 248 LYS cc_start: 0.7494 (tttm) cc_final: 0.7211 (tttm) REVERT: B 256 ASN cc_start: 0.7130 (t0) cc_final: 0.6844 (t0) REVERT: B 309 GLU cc_start: 0.6911 (mt-10) cc_final: 0.6644 (mt-10) REVERT: B 335 GLU cc_start: 0.6151 (mp0) cc_final: 0.5287 (tm-30) REVERT: B 343 GLN cc_start: 0.7048 (mt0) cc_final: 0.6651 (mt0) REVERT: B 366 ASP cc_start: 0.5893 (m-30) cc_final: 0.5623 (m-30) REVERT: B 399 LYS cc_start: 0.7157 (ttmm) cc_final: 0.6053 (tmmt) REVERT: C 42 LYS cc_start: 0.7008 (ttpp) cc_final: 0.6754 (tmtp) REVERT: C 61 LYS cc_start: 0.7302 (mtmm) cc_final: 0.6228 (mmtm) REVERT: C 100 GLU cc_start: 0.6505 (tp30) cc_final: 0.5363 (mp0) REVERT: C 133 THR cc_start: 0.5659 (OUTLIER) cc_final: 0.5378 (t) REVERT: C 136 ARG cc_start: 0.7892 (ttt180) cc_final: 0.7661 (tpt-90) REVERT: C 150 ARG cc_start: 0.5871 (mtm110) cc_final: 0.5353 (mtm110) REVERT: C 158 GLU cc_start: 0.7332 (mm-30) cc_final: 0.6908 (mp0) REVERT: C 165 ASP cc_start: 0.7999 (t0) cc_final: 0.7749 (t0) REVERT: C 197 MET cc_start: 0.8372 (mmp) cc_final: 0.7222 (mtp) REVERT: C 248 LYS cc_start: 0.7537 (tttp) cc_final: 0.7241 (tttm) REVERT: C 274 HIS cc_start: 0.7542 (t70) cc_final: 0.7287 (t70) REVERT: C 283 LYS cc_start: 0.6856 (mmtm) cc_final: 0.6463 (mppt) REVERT: C 335 GLU cc_start: 0.6194 (mp0) cc_final: 0.5306 (tm-30) REVERT: C 338 GLU cc_start: 0.6299 (mt-10) cc_final: 0.5371 (mm-30) REVERT: C 343 GLN cc_start: 0.6733 (mt0) cc_final: 0.6216 (mt0) REVERT: C 365 GLU cc_start: 0.5819 (mp0) cc_final: 0.5105 (mp0) REVERT: C 375 GLU cc_start: 0.6121 (pt0) cc_final: 0.5617 (pm20) REVERT: C 399 LYS cc_start: 0.7057 (ttmm) cc_final: 0.5934 (tmmt) REVERT: E 42 LYS cc_start: 0.7098 (ttpp) cc_final: 0.6704 (ttpp) REVERT: E 61 LYS cc_start: 0.7145 (mtmm) cc_final: 0.6135 (mmtm) REVERT: E 100 GLU cc_start: 0.6525 (tp30) cc_final: 0.5467 (mp0) REVERT: E 136 ARG cc_start: 0.7996 (ttt180) cc_final: 0.7694 (tpt-90) REVERT: E 158 GLU cc_start: 0.7481 (mm-30) cc_final: 0.6447 (tm-30) REVERT: E 197 MET cc_start: 0.8232 (mmp) cc_final: 0.7148 (mtp) REVERT: E 248 LYS cc_start: 0.7553 (tttm) cc_final: 0.7333 (tttm) REVERT: E 262 LYS cc_start: 0.7447 (mmtm) cc_final: 0.7072 (mmmt) REVERT: E 278 SER cc_start: 0.7788 (m) cc_final: 0.7473 (p) REVERT: E 285 MET cc_start: 0.7037 (mtp) cc_final: 0.6724 (mtp) REVERT: E 335 GLU cc_start: 0.6211 (mp0) cc_final: 0.5450 (tm-30) REVERT: E 338 GLU cc_start: 0.6434 (mt-10) cc_final: 0.5323 (mm-30) REVERT: E 346 GLU cc_start: 0.6970 (tp30) cc_final: 0.6733 (tp30) REVERT: E 366 ASP cc_start: 0.5703 (m-30) cc_final: 0.5495 (m-30) REVERT: E 375 GLU cc_start: 0.6123 (pt0) cc_final: 0.5663 (pm20) REVERT: E 399 LYS cc_start: 0.7118 (ttmm) cc_final: 0.6264 (tmmt) REVERT: F 42 LYS cc_start: 0.7008 (ttpp) cc_final: 0.6751 (tmtp) REVERT: F 61 LYS cc_start: 0.7306 (mtmm) cc_final: 0.6247 (mmtm) REVERT: F 100 GLU cc_start: 0.6500 (tp30) cc_final: 0.5358 (mp0) REVERT: F 118 GLU cc_start: 0.7120 (pt0) cc_final: 0.6498 (pp20) REVERT: F 133 THR cc_start: 0.5659 (OUTLIER) cc_final: 0.5379 (t) REVERT: F 136 ARG cc_start: 0.7890 (ttt180) cc_final: 0.7659 (tpt-90) REVERT: F 150 ARG cc_start: 0.5873 (mtm110) cc_final: 0.5356 (mtm110) REVERT: F 158 GLU cc_start: 0.7348 (mm-30) cc_final: 0.7007 (mp0) REVERT: F 165 ASP cc_start: 0.7999 (t0) cc_final: 0.7749 (t0) REVERT: F 197 MET cc_start: 0.8372 (mmp) cc_final: 0.7221 (mtp) REVERT: F 248 LYS cc_start: 0.7534 (tttp) cc_final: 0.7240 (tttm) REVERT: F 274 HIS cc_start: 0.7544 (t70) cc_final: 0.7282 (t70) REVERT: F 283 LYS cc_start: 0.6769 (mmtm) cc_final: 0.6381 (mppt) REVERT: F 335 GLU cc_start: 0.6196 (mp0) cc_final: 0.5307 (tm-30) REVERT: F 338 GLU cc_start: 0.6323 (mt-10) cc_final: 0.5384 (mm-30) REVERT: F 343 GLN cc_start: 0.6738 (mt0) cc_final: 0.6215 (mt0) REVERT: F 365 GLU cc_start: 0.5816 (mp0) cc_final: 0.5105 (mp0) REVERT: F 375 GLU cc_start: 0.6120 (pt0) cc_final: 0.5618 (pm20) REVERT: F 399 LYS cc_start: 0.7055 (ttmm) cc_final: 0.5932 (tmmt) REVERT: F 461 MET cc_start: 0.2652 (OUTLIER) cc_final: 0.1946 (mtt) outliers start: 43 outliers final: 36 residues processed: 354 average time/residue: 1.6255 time to fit residues: 655.2564 Evaluate side-chains 360 residues out of total 2790 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 321 time to evaluate : 3.270 ------------------------------------------------------------------------------- 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 272 ILE Chi-restraints excluded: chain D residue 306 SER Chi-restraints excluded: chain D residue 459 ILE Chi-restraints excluded: chain B residue 118 GLU Chi-restraints excluded: chain B residue 221 ILE Chi-restraints excluded: chain B residue 227 VAL Chi-restraints excluded: chain B residue 459 ILE Chi-restraints excluded: chain B residue 461 MET Chi-restraints excluded: chain B residue 469 VAL Chi-restraints excluded: chain C residue 133 THR Chi-restraints excluded: chain C residue 221 ILE Chi-restraints excluded: chain C residue 227 VAL Chi-restraints excluded: chain C residue 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 272 ILE Chi-restraints excluded: chain E residue 459 ILE Chi-restraints excluded: chain E residue 461 MET Chi-restraints excluded: chain F residue 133 THR Chi-restraints excluded: chain F residue 221 ILE Chi-restraints excluded: chain F residue 227 VAL Chi-restraints excluded: chain F residue 459 ILE Chi-restraints excluded: chain F residue 461 MET 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 200 optimal weight: 0.8980 chunk 268 optimal weight: 3.9990 chunk 77 optimal weight: 5.9990 chunk 232 optimal weight: 0.9990 chunk 37 optimal weight: 9.9990 chunk 70 optimal weight: 0.0020 chunk 252 optimal weight: 0.1980 chunk 105 optimal weight: 8.9990 chunk 259 optimal weight: 0.2980 chunk 31 optimal weight: 8.9990 chunk 46 optimal weight: 8.9990 overall best weight: 0.4790 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Sorry: Reduce crashed with command 'molprobity.reduce -quiet -trim -'. Dumping stdin to file 'reduce_failure.pdb'. Return code: -15 Dumping stderr: