Starting phenix.real_space_refine on Fri Dec 27 12:05:45 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7we6_32440/12_2024/7we6_32440.cif Found real_map, /net/cci-nas-00/data/ceres_data/7we6_32440/12_2024/7we6_32440.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7we6_32440/12_2024/7we6_32440.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7we6_32440/12_2024/7we6_32440.map" model { file = "/net/cci-nas-00/data/ceres_data/7we6_32440/12_2024/7we6_32440.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7we6_32440/12_2024/7we6_32440.cif" } resolution = 3.2 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= 0.000 sd= 0.002 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 162 5.49 5 S 46 5.16 5 C 29651 2.51 5 N 8814 2.21 5 O 9651 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 130 residue(s): 0.10s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5532/modules/chem_data/mon_lib" Total number of atoms: 48324 Number of models: 1 Model: "" Number of chains: 26 Chain: "B" Number of atoms: 2198 Number of conformers: 1 Conformer: "" Number of residues, atoms: 305, 2198 Classifications: {'peptide': 305} Incomplete info: {'truncation_to_alanine': 51} Link IDs: {'PTRANS': 23, 'TRANS': 281} Chain breaks: 1 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 215 Unresolved non-hydrogen angles: 275 Unresolved non-hydrogen dihedrals: 179 Unresolved non-hydrogen chiralities: 19 Planarities with less than four sites: {'GLN:plan1': 1, 'TYR:plan': 1, 'ASN:plan1': 3, 'TRP:plan': 2, 'HIS:plan': 2, 'PHE:plan': 1, 'GLU:plan': 6, 'ARG:plan': 11} Unresolved non-hydrogen planarities: 133 Chain: "C" Number of atoms: 2144 Number of conformers: 1 Conformer: "" Number of residues, atoms: 293, 2144 Classifications: {'peptide': 293} Incomplete info: {'truncation_to_alanine': 29} Link IDs: {'PTRANS': 10, 'TRANS': 282} Chain breaks: 2 Unresolved non-hydrogen bonds: 136 Unresolved non-hydrogen angles: 170 Unresolved non-hydrogen dihedrals: 113 Unresolved non-hydrogen chiralities: 5 Planarities with less than four sites: {'GLN:plan1': 4, 'ASP:plan': 3, 'TYR:plan': 1, 'HIS:plan': 2, 'PHE:plan': 2, 'GLU:plan': 4, 'ARG:plan': 7} Unresolved non-hydrogen planarities: 105 Chain: "D" Number of atoms: 2531 Number of conformers: 1 Conformer: "" Number of residues, atoms: 334, 2531 Classifications: {'peptide': 334} Incomplete info: {'truncation_to_alanine': 14} Link IDs: {'PTRANS': 12, 'TRANS': 321} Unresolved non-hydrogen bonds: 59 Unresolved non-hydrogen angles: 69 Unresolved non-hydrogen dihedrals: 49 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLU:plan': 1, 'ARG:plan': 4, 'ASP:plan': 3} Unresolved non-hydrogen planarities: 33 Chain: "E" Number of atoms: 2587 Number of conformers: 1 Conformer: "" Number of residues, atoms: 337, 2587 Classifications: {'peptide': 337} Incomplete info: {'truncation_to_alanine': 7} Link IDs: {'PTRANS': 12, 'TRANS': 324} Unresolved non-hydrogen bonds: 26 Unresolved non-hydrogen angles: 32 Unresolved non-hydrogen dihedrals: 20 Planarities with less than four sites: {'GLU:plan': 1, 'ARG:plan': 1, 'ASP:plan': 4} Unresolved non-hydrogen planarities: 21 Chain: "F" Number of atoms: 2577 Number of conformers: 1 Conformer: "" Number of residues, atoms: 335, 2577 Classifications: {'peptide': 335} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PTRANS': 12, 'TRANS': 322} Unresolved non-hydrogen bonds: 18 Unresolved non-hydrogen angles: 22 Unresolved non-hydrogen dihedrals: 14 Planarities with less than four sites: {'GLU:plan': 2, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 14 Chain: "G" Number of atoms: 2523 Number of conformers: 1 Conformer: "" Number of residues, atoms: 329, 2523 Classifications: {'peptide': 329} Incomplete info: {'truncation_to_alanine': 8} Link IDs: {'PTRANS': 12, 'TRANS': 316} Chain breaks: 1 Unresolved non-hydrogen bonds: 29 Unresolved non-hydrogen angles: 36 Unresolved non-hydrogen dihedrals: 22 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 1, 'ARG:plan': 1, 'ASP:plan': 4} Unresolved non-hydrogen planarities: 21 Chain: "H" Number of atoms: 2487 Number of conformers: 1 Conformer: "" Number of residues, atoms: 332, 2487 Classifications: {'peptide': 332} Incomplete info: {'truncation_to_alanine': 21} Link IDs: {'PTRANS': 12, 'TRANS': 319} Unresolved non-hydrogen bonds: 91 Unresolved non-hydrogen angles: 114 Unresolved non-hydrogen dihedrals: 78 Unresolved non-hydrogen chiralities: 5 Planarities with less than four sites: {'GLN:plan1': 1, 'ASP:plan': 2, 'TYR:plan': 2, 'ASN:plan1': 1, 'HIS:plan': 2, 'GLU:plan': 2, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 55 Chain: "I" Number of atoms: 1445 Number of conformers: 1 Conformer: "" Number of residues, atoms: 187, 1445 Classifications: {'peptide': 187} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 9} Link IDs: {'PCIS': 1, 'PTRANS': 14, 'TRANS': 171} Unresolved non-hydrogen bonds: 67 Unresolved non-hydrogen angles: 80 Unresolved non-hydrogen dihedrals: 54 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 3, 'ARG:plan': 8} Unresolved non-hydrogen planarities: 54 Chain: "L" Number of atoms: 2321 Number of conformers: 1 Conformer: "" Number of residues, atoms: 305, 2321 Classifications: {'peptide': 305} Incomplete info: {'truncation_to_alanine': 22} Link IDs: {'PTRANS': 23, 'TRANS': 281} Chain breaks: 1 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 85 Unresolved non-hydrogen angles: 106 Unresolved non-hydrogen dihedrals: 67 Unresolved non-hydrogen chiralities: 7 Planarities with less than four sites: {'PHE:plan': 1, 'GLU:plan': 6, 'ARG:plan': 3, 'ASN:plan1': 1, 'GLN:plan1': 1} Unresolved non-hydrogen planarities: 52 Chain: "M" Number of atoms: 2227 Number of conformers: 1 Conformer: "" Number of residues, atoms: 293, 2227 Classifications: {'peptide': 293} Incomplete info: {'truncation_to_alanine': 10} Link IDs: {'PTRANS': 10, 'TRANS': 282} Chain breaks: 2 Unresolved non-hydrogen bonds: 49 Unresolved non-hydrogen angles: 60 Unresolved non-hydrogen dihedrals: 40 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 2, 'ARG:plan': 4, 'PHE:plan': 1, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 44 Chain: "N" Number of atoms: 2571 Number of conformers: 1 Conformer: "" Number of residues, atoms: 335, 2571 Classifications: {'peptide': 335} Incomplete info: {'truncation_to_alanine': 7} Link IDs: {'PTRANS': 12, 'TRANS': 322} Unresolved non-hydrogen bonds: 25 Unresolved non-hydrogen angles: 29 Unresolved non-hydrogen dihedrals: 21 Planarities with less than four sites: {'GLU:plan': 1, 'ASP:plan': 3} Unresolved non-hydrogen planarities: 13 Chain: "O" Number of atoms: 2562 Number of conformers: 1 Conformer: "" Number of residues, atoms: 334, 2562 Classifications: {'peptide': 334} Incomplete info: {'truncation_to_alanine': 8} Link IDs: {'PTRANS': 12, 'TRANS': 321} Unresolved non-hydrogen bonds: 28 Unresolved non-hydrogen angles: 34 Unresolved non-hydrogen dihedrals: 22 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 1, 'ASP:plan': 4} Unresolved non-hydrogen planarities: 20 Chain: "P" Number of atoms: 2581 Number of conformers: 1 Conformer: "" Number of residues, atoms: 335, 2581 Classifications: {'peptide': 335} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 12, 'TRANS': 322} Unresolved non-hydrogen bonds: 14 Unresolved non-hydrogen angles: 18 Unresolved non-hydrogen dihedrals: 10 Planarities with less than four sites: {'GLU:plan': 2, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 14 Chain: "Q" Number of atoms: 2552 Number of conformers: 1 Conformer: "" Number of residues, atoms: 333, 2552 Classifications: {'peptide': 333} Incomplete info: {'truncation_to_alanine': 8} Link IDs: {'PTRANS': 12, 'TRANS': 320} Unresolved non-hydrogen bonds: 30 Unresolved non-hydrogen angles: 37 Unresolved non-hydrogen dihedrals: 23 Planarities with less than four sites: {'GLU:plan': 2, 'ARG:plan': 1, 'ASP:plan': 4} Unresolved non-hydrogen planarities: 25 Chain: "R" Number of atoms: 2529 Number of conformers: 1 Conformer: "" Number of residues, atoms: 333, 2529 Classifications: {'peptide': 333} Incomplete info: {'truncation_to_alanine': 15} Link IDs: {'PTRANS': 12, 'TRANS': 320} Unresolved non-hydrogen bonds: 53 Unresolved non-hydrogen angles: 63 Unresolved non-hydrogen dihedrals: 43 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLU:plan': 3, 'ASN:plan1': 1, 'ASP:plan': 3, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 29 Chain: "S" Number of atoms: 1445 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 187, 1442 Classifications: {'peptide': 187} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 10} Link IDs: {'PCIS': 1, 'PTRANS': 14, 'TRANS': 171} Unresolved non-hydrogen bonds: 70 Unresolved non-hydrogen angles: 84 Unresolved non-hydrogen dihedrals: 56 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 3, 'ARG:plan': 8} Unresolved non-hydrogen planarities: 54 Conformer: "B" Number of residues, atoms: 187, 1442 Classifications: {'peptide': 187} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 10} Link IDs: {'PCIS': 1, 'PTRANS': 14, 'TRANS': 171} Unresolved non-hydrogen bonds: 70 Unresolved non-hydrogen angles: 84 Unresolved non-hydrogen dihedrals: 56 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 3, 'ARG:plan': 8} Unresolved non-hydrogen planarities: 54 bond proxies already assigned to first conformer: 1477 Chain: "U" Number of atoms: 1758 Number of conformers: 1 Conformer: "" Number of residues, atoms: 227, 1758 Classifications: {'peptide': 227} Link IDs: {'PTRANS': 16, 'TRANS': 210} Chain: "V" Number of atoms: 1758 Number of conformers: 1 Conformer: "" Number of residues, atoms: 227, 1758 Classifications: {'peptide': 227} Link IDs: {'PTRANS': 16, 'TRANS': 210} Chain: "J" Number of atoms: 1271 Number of conformers: 1 Conformer: "" Number of residues, atoms: 60, 1271 Classifications: {'RNA': 60} Modifications used: {'5*END': 1, 'rna2p_pur': 11, 'rna2p_pyr': 17, 'rna3p_pur': 17, 'rna3p_pyr': 14} Link IDs: {'rna2p': 27, 'rna3p': 32} Unresolved chain link angles: 2 Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 2 Unresolved non-hydrogen chiralities: 1 Chain: "T" Number of atoms: 1271 Number of conformers: 1 Conformer: "" Number of residues, atoms: 60, 1271 Classifications: {'RNA': 60} Modifications used: {'5*END': 1, 'rna2p_pur': 11, 'rna2p_pyr': 17, 'rna3p_pur': 17, 'rna3p_pyr': 14} Link IDs: {'rna2p': 27, 'rna3p': 32} Unresolved chain link angles: 2 Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 2 Unresolved non-hydrogen chiralities: 1 Chain: "A" Number of atoms: 2251 Number of conformers: 1 Conformer: "" Number of residues, atoms: 424, 2251 Classifications: {'peptide': 424} Incomplete info: {'backbone_only': 266, 'truncation_to_alanine': 2} Link IDs: {'PTRANS': 24, 'TRANS': 399} Unresolved chain link angles: 9 Unresolved non-hydrogen bonds: 1200 Unresolved non-hydrogen angles: 1728 Unresolved non-hydrogen dihedrals: 778 Unresolved non-hydrogen chiralities: 330 Planarities with less than four sites: {'GLN:plan1': 25, 'ASP:plan': 21, 'TYR:plan': 3, 'ASN:plan1': 9, 'TRP:plan': 8, 'HIS:plan': 6, 'PHE:plan': 10, 'GLU:plan': 24, 'ARG:plan': 29} Unresolved non-hydrogen planarities: 670 Chain: "X" Number of atoms: 2251 Number of conformers: 1 Conformer: "" Number of residues, atoms: 424, 2251 Classifications: {'peptide': 424} Incomplete info: {'backbone_only': 266, 'truncation_to_alanine': 2} Link IDs: {'PTRANS': 24, 'TRANS': 399} Unresolved chain link angles: 9 Unresolved non-hydrogen bonds: 1200 Unresolved non-hydrogen angles: 1728 Unresolved non-hydrogen dihedrals: 778 Unresolved non-hydrogen chiralities: 330 Planarities with less than four sites: {'GLN:plan1': 25, 'ASP:plan': 21, 'TYR:plan': 3, 'ASN:plan1': 9, 'TRP:plan': 8, 'HIS:plan': 6, 'PHE:plan': 10, 'GLU:plan': 24, 'ARG:plan': 29} Unresolved non-hydrogen planarities: 670 Chain: "Y" Number of atoms: 121 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 121 Classifications: {'DNA': 11} Link IDs: {'rna3p': 10} Unresolved non-hydrogen bonds: 121 Unresolved non-hydrogen angles: 193 Unresolved non-hydrogen dihedrals: 89 Unresolved non-hydrogen chiralities: 11 Planarities with less than four sites: {' DG:plan': 4, ' DG:plan2': 4, ' DC:plan2': 3, ' DA:plan2': 1, ' DC:plan': 3, ' DT:plan': 3, ' DA:plan': 1} Unresolved non-hydrogen planarities: 121 Chain: "Z" Number of atoms: 121 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 121 Classifications: {'DNA': 11} Link IDs: {'rna3p': 10} Unresolved non-hydrogen bonds: 121 Unresolved non-hydrogen angles: 192 Unresolved non-hydrogen dihedrals: 108 Unresolved non-hydrogen chiralities: 11 Planarities with less than four sites: {' DG:plan': 3, ' DG:plan2': 3, ' DC:plan2': 4, ' DA:plan2': 3, ' DC:plan': 4, ' DT:plan': 1, ' DA:plan': 3} Unresolved non-hydrogen planarities: 124 Chain: "K" Number of atoms: 121 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 121 Classifications: {'DNA': 11} Link IDs: {'rna3p': 10} Unresolved non-hydrogen bonds: 121 Unresolved non-hydrogen angles: 193 Unresolved non-hydrogen dihedrals: 89 Unresolved non-hydrogen chiralities: 11 Planarities with less than four sites: {' DG:plan': 4, ' DG:plan2': 4, ' DC:plan2': 3, ' DA:plan2': 1, ' DC:plan': 3, ' DT:plan': 3, ' DA:plan': 1} Unresolved non-hydrogen planarities: 121 Chain: "W" Number of atoms: 121 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 121 Classifications: {'DNA': 11} Link IDs: {'rna3p': 10} Unresolved non-hydrogen bonds: 121 Unresolved non-hydrogen angles: 192 Unresolved non-hydrogen dihedrals: 108 Unresolved non-hydrogen chiralities: 11 Planarities with less than four sites: {' DG:plan': 3, ' DG:plan2': 3, ' DC:plan2': 4, ' DA:plan2': 3, ' DC:plan': 4, ' DT:plan': 1, ' DA:plan': 3} Unresolved non-hydrogen planarities: 124 Time building chain proxies: 21.11, per 1000 atoms: 0.44 Number of scatterers: 48324 At special positions: 0 Unit cell: (168.3, 165, 235.4, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 46 16.00 P 162 15.00 O 9651 8.00 N 8814 7.00 C 29651 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 8.61 Conformation dependent library (CDL) restraints added in 4.9 seconds 12312 Ramachandran restraints generated. 6156 Oldfield, 0 Emsley, 6156 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 10474 Finding SS restraints... Secondary structure from input PDB file: 171 helices and 92 sheets defined 34.3% alpha, 19.6% beta 12 base pairs and 48 stacking pairs defined. Time for finding SS restraints: 11.85 Creating SS restraints... Processing helix chain 'B' and resid 33 through 48 removed outlier: 3.786A pdb=" N PHE B 37 " --> pdb=" O SER B 33 " (cutoff:3.500A) Processing helix chain 'B' and resid 116 through 121 removed outlier: 3.813A pdb=" N ASP B 120 " --> pdb=" O ASP B 116 " (cutoff:3.500A) removed outlier: 4.205A pdb=" N HIS B 121 " --> pdb=" O GLY B 117 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 116 through 121' Processing helix chain 'B' and resid 122 through 135 removed outlier: 3.564A pdb=" N ILE B 126 " --> pdb=" O PRO B 122 " (cutoff:3.500A) Processing helix chain 'B' and resid 165 through 178 Processing helix chain 'B' and resid 189 through 201 removed outlier: 3.598A pdb=" N LEU B 193 " --> pdb=" O ARG B 189 " (cutoff:3.500A) Processing helix chain 'B' and resid 207 through 214 removed outlier: 4.125A pdb=" N ASP B 211 " --> pdb=" O ALA B 207 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N LEU B 214 " --> pdb=" O LEU B 210 " (cutoff:3.500A) Processing helix chain 'B' and resid 291 through 295 removed outlier: 3.949A pdb=" N VAL B 295 " --> pdb=" O PRO B 292 " (cutoff:3.500A) Processing helix chain 'B' and resid 297 through 301 removed outlier: 3.607A pdb=" N ASP B 300 " --> pdb=" O ALA B 297 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N LEU B 301 " --> pdb=" O LEU B 298 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 297 through 301' Processing helix chain 'C' and resid 111 through 129 removed outlier: 3.624A pdb=" N ARG C 115 " --> pdb=" O ASP C 111 " (cutoff:3.500A) Processing helix chain 'C' and resid 131 through 144 removed outlier: 3.594A pdb=" N ASN C 144 " --> pdb=" O HIS C 140 " (cutoff:3.500A) Processing helix chain 'C' and resid 189 through 204 Processing helix chain 'C' and resid 256 through 265 removed outlier: 3.550A pdb=" N ILE C 260 " --> pdb=" O HIS C 256 " (cutoff:3.500A) Processing helix chain 'C' and resid 303 through 312 Processing helix chain 'C' and resid 319 through 333 Processing helix chain 'D' and resid 63 through 72 removed outlier: 3.886A pdb=" N LEU D 67 " --> pdb=" O ASP D 63 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N GLN D 72 " --> pdb=" O ASP D 68 " (cutoff:3.500A) Processing helix chain 'D' and resid 112 through 129 Processing helix chain 'D' and resid 131 through 144 Processing helix chain 'D' and resid 189 through 204 Processing helix chain 'D' and resid 256 through 265 removed outlier: 3.510A pdb=" N ILE D 260 " --> pdb=" O HIS D 256 " (cutoff:3.500A) Processing helix chain 'D' and resid 303 through 313 removed outlier: 3.524A pdb=" N LEU D 307 " --> pdb=" O ASP D 303 " (cutoff:3.500A) Processing helix chain 'D' and resid 319 through 333 Processing helix chain 'E' and resid 63 through 73 removed outlier: 3.528A pdb=" N SER E 73 " --> pdb=" O ALA E 69 " (cutoff:3.500A) Processing helix chain 'E' and resid 111 through 129 Processing helix chain 'E' and resid 131 through 144 Processing helix chain 'E' and resid 189 through 204 Processing helix chain 'E' and resid 256 through 265 removed outlier: 3.555A pdb=" N ILE E 260 " --> pdb=" O HIS E 256 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N ARG E 265 " --> pdb=" O GLY E 261 " (cutoff:3.500A) Processing helix chain 'E' and resid 303 through 313 removed outlier: 3.553A pdb=" N LEU E 307 " --> pdb=" O ASP E 303 " (cutoff:3.500A) Processing helix chain 'E' and resid 319 through 333 Processing helix chain 'F' and resid 32 through 36 removed outlier: 3.753A pdb=" N SER F 36 " --> pdb=" O ARG F 33 " (cutoff:3.500A) Processing helix chain 'F' and resid 63 through 73 removed outlier: 3.911A pdb=" N LEU F 67 " --> pdb=" O ASP F 63 " (cutoff:3.500A) Processing helix chain 'F' and resid 111 through 129 Processing helix chain 'F' and resid 131 through 144 Processing helix chain 'F' and resid 189 through 204 Processing helix chain 'F' and resid 256 through 265 removed outlier: 3.748A pdb=" N ILE F 260 " --> pdb=" O HIS F 256 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N ARG F 265 " --> pdb=" O GLY F 261 " (cutoff:3.500A) Processing helix chain 'F' and resid 303 through 313 removed outlier: 3.610A pdb=" N LEU F 307 " --> pdb=" O ASP F 303 " (cutoff:3.500A) Processing helix chain 'F' and resid 319 through 333 Processing helix chain 'G' and resid 32 through 36 removed outlier: 3.558A pdb=" N SER G 36 " --> pdb=" O ARG G 33 " (cutoff:3.500A) Processing helix chain 'G' and resid 63 through 73 removed outlier: 3.750A pdb=" N SER G 73 " --> pdb=" O ALA G 69 " (cutoff:3.500A) Processing helix chain 'G' and resid 111 through 129 Processing helix chain 'G' and resid 131 through 144 Processing helix chain 'G' and resid 189 through 204 Processing helix chain 'G' and resid 256 through 265 Processing helix chain 'G' and resid 303 through 313 Processing helix chain 'G' and resid 319 through 333 Processing helix chain 'H' and resid 32 through 36 Processing helix chain 'H' and resid 63 through 72 Processing helix chain 'H' and resid 111 through 129 removed outlier: 3.559A pdb=" N ARG H 115 " --> pdb=" O ASP H 111 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N GLN H 129 " --> pdb=" O TYR H 125 " (cutoff:3.500A) Processing helix chain 'H' and resid 131 through 144 Processing helix chain 'H' and resid 189 through 204 Processing helix chain 'H' and resid 256 through 265 removed outlier: 3.577A pdb=" N ILE H 260 " --> pdb=" O HIS H 256 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N ARG H 265 " --> pdb=" O GLY H 261 " (cutoff:3.500A) Processing helix chain 'H' and resid 303 through 313 Processing helix chain 'H' and resid 319 through 333 removed outlier: 3.583A pdb=" N GLY H 333 " --> pdb=" O ASN H 329 " (cutoff:3.500A) Processing helix chain 'I' and resid 16 through 36 removed outlier: 3.617A pdb=" N LEU I 20 " --> pdb=" O PRO I 16 " (cutoff:3.500A) Processing helix chain 'I' and resid 63 through 71 Processing helix chain 'I' and resid 73 through 77 removed outlier: 3.588A pdb=" N LEU I 76 " --> pdb=" O ARG I 73 " (cutoff:3.500A) Processing helix chain 'I' and resid 109 through 121 Processing helix chain 'I' and resid 123 through 131 removed outlier: 3.863A pdb=" N ILE I 131 " --> pdb=" O ALA I 127 " (cutoff:3.500A) Processing helix chain 'I' and resid 132 through 136 removed outlier: 3.725A pdb=" N VAL I 135 " --> pdb=" O PRO I 132 " (cutoff:3.500A) Processing helix chain 'L' and resid 33 through 49 removed outlier: 4.210A pdb=" N PHE L 37 " --> pdb=" O SER L 33 " (cutoff:3.500A) Processing helix chain 'L' and resid 116 through 121 removed outlier: 4.143A pdb=" N ASP L 120 " --> pdb=" O ASP L 116 " (cutoff:3.500A) removed outlier: 4.043A pdb=" N HIS L 121 " --> pdb=" O GLY L 117 " (cutoff:3.500A) No H-bonds generated for 'chain 'L' and resid 116 through 121' Processing helix chain 'L' and resid 122 through 135 removed outlier: 3.507A pdb=" N ILE L 126 " --> pdb=" O PRO L 122 " (cutoff:3.500A) Processing helix chain 'L' and resid 165 through 178 Processing helix chain 'L' and resid 189 through 202 Processing helix chain 'L' and resid 207 through 214 removed outlier: 4.051A pdb=" N ASP L 211 " --> pdb=" O ALA L 207 " (cutoff:3.500A) Processing helix chain 'L' and resid 291 through 295 removed outlier: 3.532A pdb=" N VAL L 295 " --> pdb=" O PRO L 292 " (cutoff:3.500A) Processing helix chain 'L' and resid 297 through 301 removed outlier: 3.886A pdb=" N LEU L 301 " --> pdb=" O LEU L 298 " (cutoff:3.500A) Processing helix chain 'M' and resid 112 through 129 Processing helix chain 'M' and resid 131 through 144 Processing helix chain 'M' and resid 189 through 204 Processing helix chain 'M' and resid 256 through 265 removed outlier: 3.630A pdb=" N ILE M 260 " --> pdb=" O HIS M 256 " (cutoff:3.500A) Processing helix chain 'M' and resid 303 through 313 removed outlier: 3.505A pdb=" N LEU M 313 " --> pdb=" O ASP M 309 " (cutoff:3.500A) Processing helix chain 'M' and resid 319 through 333 Processing helix chain 'N' and resid 63 through 72 Processing helix chain 'N' and resid 111 through 129 removed outlier: 3.537A pdb=" N ARG N 115 " --> pdb=" O ASP N 111 " (cutoff:3.500A) Processing helix chain 'N' and resid 131 through 144 Processing helix chain 'N' and resid 189 through 204 Processing helix chain 'N' and resid 256 through 265 removed outlier: 3.515A pdb=" N ILE N 260 " --> pdb=" O HIS N 256 " (cutoff:3.500A) Processing helix chain 'N' and resid 303 through 313 Processing helix chain 'N' and resid 319 through 333 Processing helix chain 'O' and resid 32 through 36 removed outlier: 3.847A pdb=" N SER O 36 " --> pdb=" O ARG O 33 " (cutoff:3.500A) Processing helix chain 'O' and resid 58 through 62 removed outlier: 3.514A pdb=" N ARG O 62 " --> pdb=" O THR O 59 " (cutoff:3.500A) Processing helix chain 'O' and resid 63 through 73 removed outlier: 3.519A pdb=" N SER O 73 " --> pdb=" O ALA O 69 " (cutoff:3.500A) Processing helix chain 'O' and resid 111 through 129 removed outlier: 3.520A pdb=" N ARG O 115 " --> pdb=" O ASP O 111 " (cutoff:3.500A) Processing helix chain 'O' and resid 131 through 144 Processing helix chain 'O' and resid 190 through 204 Processing helix chain 'O' and resid 256 through 265 removed outlier: 3.557A pdb=" N ILE O 260 " --> pdb=" O HIS O 256 " (cutoff:3.500A) Processing helix chain 'O' and resid 303 through 314 removed outlier: 3.589A pdb=" N LEU O 307 " --> pdb=" O ASP O 303 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N ARG O 314 " --> pdb=" O ASN O 310 " (cutoff:3.500A) Processing helix chain 'O' and resid 319 through 333 Processing helix chain 'P' and resid 32 through 36 removed outlier: 3.515A pdb=" N SER P 36 " --> pdb=" O ARG P 33 " (cutoff:3.500A) Processing helix chain 'P' and resid 64 through 72 removed outlier: 3.618A pdb=" N ASP P 68 " --> pdb=" O PRO P 64 " (cutoff:3.500A) Processing helix chain 'P' and resid 111 through 129 removed outlier: 3.614A pdb=" N ARG P 115 " --> pdb=" O ASP P 111 " (cutoff:3.500A) Processing helix chain 'P' and resid 131 through 144 Processing helix chain 'P' and resid 189 through 204 Processing helix chain 'P' and resid 256 through 265 removed outlier: 3.637A pdb=" N ILE P 260 " --> pdb=" O HIS P 256 " (cutoff:3.500A) Processing helix chain 'P' and resid 303 through 313 removed outlier: 3.560A pdb=" N LEU P 307 " --> pdb=" O ASP P 303 " (cutoff:3.500A) Processing helix chain 'P' and resid 319 through 333 Processing helix chain 'Q' and resid 32 through 36 removed outlier: 3.627A pdb=" N SER Q 36 " --> pdb=" O ARG Q 33 " (cutoff:3.500A) Processing helix chain 'Q' and resid 63 through 73 removed outlier: 3.542A pdb=" N SER Q 73 " --> pdb=" O ALA Q 69 " (cutoff:3.500A) Processing helix chain 'Q' and resid 111 through 129 Processing helix chain 'Q' and resid 131 through 144 Processing helix chain 'Q' and resid 189 through 204 Processing helix chain 'Q' and resid 256 through 265 Processing helix chain 'Q' and resid 303 through 313 Processing helix chain 'Q' and resid 319 through 333 Processing helix chain 'R' and resid 58 through 62 removed outlier: 4.017A pdb=" N ARG R 62 " --> pdb=" O THR R 59 " (cutoff:3.500A) Processing helix chain 'R' and resid 63 through 72 Processing helix chain 'R' and resid 112 through 129 Processing helix chain 'R' and resid 131 through 144 Processing helix chain 'R' and resid 189 through 204 Processing helix chain 'R' and resid 256 through 265 removed outlier: 3.628A pdb=" N ILE R 260 " --> pdb=" O HIS R 256 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N ARG R 265 " --> pdb=" O GLY R 261 " (cutoff:3.500A) Processing helix chain 'R' and resid 303 through 312 removed outlier: 3.610A pdb=" N LEU R 307 " --> pdb=" O ASP R 303 " (cutoff:3.500A) Processing helix chain 'R' and resid 319 through 333 removed outlier: 3.609A pdb=" N GLY R 333 " --> pdb=" O ASN R 329 " (cutoff:3.500A) Processing helix chain 'S' and resid 16 through 36 removed outlier: 3.561A pdb=" N LEU S 20 " --> pdb=" O PRO S 16 " (cutoff:3.500A) Processing helix chain 'S' and resid 63 through 71 Processing helix chain 'S' and resid 109 through 121 Processing helix chain 'S' and resid 123 through 131 removed outlier: 3.736A pdb=" N ILE S 131 " --> pdb=" O ALA S 127 " (cutoff:3.500A) Processing helix chain 'S' and resid 132 through 136 removed outlier: 3.876A pdb=" N VAL S 135 " --> pdb=" O PRO S 132 " (cutoff:3.500A) removed outlier: 4.050A pdb=" N ALA S 136 " --> pdb=" O ASP S 133 " (cutoff:3.500A) No H-bonds generated for 'chain 'S' and resid 132 through 136' Processing helix chain 'U' and resid 47 through 70 removed outlier: 3.900A pdb=" N PHE U 55 " --> pdb=" O VAL U 51 " (cutoff:3.500A) removed outlier: 5.088A pdb=" N ASP U 57 " --> pdb=" O ASP U 53 " (cutoff:3.500A) removed outlier: 5.680A pdb=" N ILE U 58 " --> pdb=" O GLU U 54 " (cutoff:3.500A) Processing helix chain 'U' and resid 126 through 136 removed outlier: 3.679A pdb=" N SER U 136 " --> pdb=" O ALA U 132 " (cutoff:3.500A) Processing helix chain 'U' and resid 140 through 147 removed outlier: 3.520A pdb=" N ILE U 143 " --> pdb=" O LEU U 140 " (cutoff:3.500A) Processing helix chain 'U' and resid 163 through 168 Processing helix chain 'U' and resid 180 through 188 Processing helix chain 'U' and resid 191 through 197 Processing helix chain 'U' and resid 202 through 206 removed outlier: 3.680A pdb=" N ASN U 206 " --> pdb=" O SER U 203 " (cutoff:3.500A) Processing helix chain 'U' and resid 211 through 222 Processing helix chain 'V' and resid 47 through 70 removed outlier: 3.901A pdb=" N PHE V 55 " --> pdb=" O VAL V 51 " (cutoff:3.500A) removed outlier: 5.088A pdb=" N ASP V 57 " --> pdb=" O ASP V 53 " (cutoff:3.500A) removed outlier: 5.681A pdb=" N ILE V 58 " --> pdb=" O GLU V 54 " (cutoff:3.500A) Processing helix chain 'V' and resid 126 through 136 removed outlier: 3.679A pdb=" N SER V 136 " --> pdb=" O ALA V 132 " (cutoff:3.500A) Processing helix chain 'V' and resid 140 through 147 removed outlier: 3.520A pdb=" N ILE V 143 " --> pdb=" O LEU V 140 " (cutoff:3.500A) Processing helix chain 'V' and resid 163 through 168 Processing helix chain 'V' and resid 180 through 188 Processing helix chain 'V' and resid 191 through 197 Processing helix chain 'V' and resid 202 through 206 removed outlier: 3.679A pdb=" N ASN V 206 " --> pdb=" O SER V 203 " (cutoff:3.500A) Processing helix chain 'V' and resid 211 through 222 Processing helix chain 'A' and resid 12 through 29 Processing helix chain 'A' and resid 36 through 61 removed outlier: 3.706A pdb=" N ARG A 40 " --> pdb=" O GLU A 36 " (cutoff:3.500A) removed outlier: 7.350A pdb=" N LEU A 53 " --> pdb=" O ARG A 49 " (cutoff:3.500A) removed outlier: 6.286A pdb=" N ALA A 54 " --> pdb=" O GLU A 50 " (cutoff:3.500A) removed outlier: 4.305A pdb=" N ARG A 58 " --> pdb=" O ALA A 54 " (cutoff:3.500A) removed outlier: 3.861A pdb=" N ARG A 59 " --> pdb=" O ASP A 55 " (cutoff:3.500A) Processing helix chain 'A' and resid 96 through 100 removed outlier: 3.659A pdb=" N GLU A 99 " --> pdb=" O GLY A 96 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N LEU A 100 " --> pdb=" O SER A 97 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 96 through 100' Processing helix chain 'A' and resid 111 through 126 Processing helix chain 'A' and resid 129 through 134 Processing helix chain 'A' and resid 138 through 146 removed outlier: 3.501A pdb=" N SER A 146 " --> pdb=" O VAL A 142 " (cutoff:3.500A) Processing helix chain 'A' and resid 148 through 164 Processing helix chain 'A' and resid 196 through 211 Processing helix chain 'A' and resid 212 through 225 Processing helix chain 'A' and resid 247 through 251 removed outlier: 4.318A pdb=" N ASN A 250 " --> pdb=" O LYS A 247 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N ILE A 251 " --> pdb=" O PRO A 248 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 247 through 251' Processing helix chain 'A' and resid 252 through 258 Processing helix chain 'A' and resid 282 through 292 Processing helix chain 'A' and resid 294 through 307 Processing helix chain 'A' and resid 314 through 344 Processing helix chain 'A' and resid 355 through 361 Processing helix chain 'A' and resid 372 through 382 Processing helix chain 'A' and resid 384 through 399 Processing helix chain 'A' and resid 402 through 408 Processing helix chain 'A' and resid 408 through 433 removed outlier: 3.626A pdb=" N ALA A 412 " --> pdb=" O SER A 408 " (cutoff:3.500A) Processing helix chain 'X' and resid 12 through 29 Processing helix chain 'X' and resid 36 through 61 removed outlier: 3.707A pdb=" N ARG X 40 " --> pdb=" O GLU X 36 " (cutoff:3.500A) removed outlier: 7.349A pdb=" N LEU X 53 " --> pdb=" O ARG X 49 " (cutoff:3.500A) removed outlier: 6.286A pdb=" N ALA X 54 " --> pdb=" O GLU X 50 " (cutoff:3.500A) removed outlier: 4.304A pdb=" N ARG X 58 " --> pdb=" O ALA X 54 " (cutoff:3.500A) removed outlier: 3.860A pdb=" N ARG X 59 " --> pdb=" O ASP X 55 " (cutoff:3.500A) Processing helix chain 'X' and resid 96 through 100 removed outlier: 3.659A pdb=" N GLU X 99 " --> pdb=" O GLY X 96 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N LEU X 100 " --> pdb=" O SER X 97 " (cutoff:3.500A) No H-bonds generated for 'chain 'X' and resid 96 through 100' Processing helix chain 'X' and resid 111 through 126 Processing helix chain 'X' and resid 129 through 134 Processing helix chain 'X' and resid 138 through 146 removed outlier: 3.501A pdb=" N SER X 146 " --> pdb=" O VAL X 142 " (cutoff:3.500A) Processing helix chain 'X' and resid 148 through 164 Processing helix chain 'X' and resid 196 through 211 Processing helix chain 'X' and resid 212 through 225 Processing helix chain 'X' and resid 247 through 251 removed outlier: 4.317A pdb=" N ASN X 250 " --> pdb=" O LYS X 247 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N ILE X 251 " --> pdb=" O PRO X 248 " (cutoff:3.500A) No H-bonds generated for 'chain 'X' and resid 247 through 251' Processing helix chain 'X' and resid 252 through 258 Processing helix chain 'X' and resid 282 through 292 Processing helix chain 'X' and resid 294 through 307 Processing helix chain 'X' and resid 314 through 344 Processing helix chain 'X' and resid 355 through 361 Processing helix chain 'X' and resid 372 through 382 Processing helix chain 'X' and resid 384 through 399 Processing helix chain 'X' and resid 402 through 408 Processing helix chain 'X' and resid 408 through 433 removed outlier: 3.627A pdb=" N ALA X 412 " --> pdb=" O SER X 408 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'B' and resid 59 through 60 removed outlier: 3.562A pdb=" N ARG B 65 " --> pdb=" O GLU B 106 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 59 through 60 removed outlier: 6.298A pdb=" N ALA B 103 " --> pdb=" O GLN B 18 " (cutoff:3.500A) removed outlier: 4.998A pdb=" N GLN B 18 " --> pdb=" O ALA B 103 " (cutoff:3.500A) removed outlier: 6.876A pdb=" N LEU B 105 " --> pdb=" O SER B 16 " (cutoff:3.500A) removed outlier: 4.817A pdb=" N SER B 16 " --> pdb=" O LEU B 105 " (cutoff:3.500A) removed outlier: 6.344A pdb=" N VAL B 107 " --> pdb=" O ARG B 14 " (cutoff:3.500A) removed outlier: 4.496A pdb=" N ARG B 14 " --> pdb=" O VAL B 107 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 70 through 71 Processing sheet with id=AA4, first strand: chain 'B' and resid 185 through 188 removed outlier: 7.116A pdb=" N PHE B 279 " --> pdb=" O ALA B 257 " (cutoff:3.500A) removed outlier: 4.712A pdb=" N ALA B 257 " --> pdb=" O PHE B 279 " (cutoff:3.500A) removed outlier: 6.315A pdb=" N GLU B 281 " --> pdb=" O TYR B 255 " (cutoff:3.500A) removed outlier: 4.472A pdb=" N TYR B 255 " --> pdb=" O GLU B 281 " (cutoff:3.500A) removed outlier: 6.419A pdb=" N LEU B 283 " --> pdb=" O ALA B 253 " (cutoff:3.500A) removed outlier: 6.310A pdb=" N ALA B 253 " --> pdb=" O TRP B 316 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N TRP B 316 " --> pdb=" O ALA B 253 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N LEU B 313 " --> pdb=" O GLU B 308 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 185 through 188 removed outlier: 6.416A pdb=" N ARG B 278 " --> pdb=" O ALA A 191 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 219 through 220 Processing sheet with id=AA7, first strand: chain 'C' and resid 108 through 109 removed outlier: 3.564A pdb=" N PHE C 14 " --> pdb=" O GLY C 334 " (cutoff:3.500A) removed outlier: 3.782A pdb=" N GLY C 334 " --> pdb=" O PHE C 14 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'C' and resid 170 through 177 removed outlier: 6.785A pdb=" N HIS C 164 " --> pdb=" O ALA C 171 " (cutoff:3.500A) removed outlier: 4.503A pdb=" N THR C 173 " --> pdb=" O ILE C 162 " (cutoff:3.500A) removed outlier: 6.824A pdb=" N ILE C 162 " --> pdb=" O THR C 173 " (cutoff:3.500A) removed outlier: 5.169A pdb=" N ARG C 175 " --> pdb=" O VAL C 160 " (cutoff:3.500A) removed outlier: 7.222A pdb=" N VAL C 160 " --> pdb=" O ARG C 175 " (cutoff:3.500A) removed outlier: 5.456A pdb=" N ASP C 177 " --> pdb=" O VAL C 158 " (cutoff:3.500A) removed outlier: 7.821A pdb=" N VAL C 158 " --> pdb=" O ASP C 177 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N ALA C 157 " --> pdb=" O ARG C 218 " (cutoff:3.500A) removed outlier: 4.831A pdb=" N LEU C 210 " --> pdb=" O ILE C 165 " (cutoff:3.500A) removed outlier: 3.997A pdb=" N VAL C 209 " --> pdb=" O VAL C 99 " (cutoff:3.500A) removed outlier: 3.858A pdb=" N ALA C 217 " --> pdb=" O LEU C 91 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N LEU C 91 " --> pdb=" O ALA C 217 " (cutoff:3.500A) removed outlier: 5.223A pdb=" N ALA C 253 " --> pdb=" O MET C 25 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'C' and resid 45 through 47 Processing sheet with id=AB1, first strand: chain 'C' and resid 266 through 268 Processing sheet with id=AB2, first strand: chain 'D' and resid 108 through 109 removed outlier: 3.566A pdb=" N ALA D 108 " --> pdb=" O ALA D 13 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'D' and resid 19 through 20 removed outlier: 4.058A pdb=" N VAL D 209 " --> pdb=" O VAL D 99 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'D' and resid 19 through 20 removed outlier: 5.132A pdb=" N ALA D 253 " --> pdb=" O MET D 25 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'D' and resid 45 through 50 Processing sheet with id=AB6, first strand: chain 'D' and resid 266 through 268 Processing sheet with id=AB7, first strand: chain 'D' and resid 287 through 288 removed outlier: 3.577A pdb=" N LYS D 293 " --> pdb=" O VAL D 288 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'E' and resid 11 through 14 Processing sheet with id=AB9, first strand: chain 'E' and resid 19 through 20 removed outlier: 3.521A pdb=" N LEU E 24 " --> pdb=" O ARG E 94 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'E' and resid 19 through 20 removed outlier: 4.106A pdb=" N VAL E 99 " --> pdb=" O VAL E 209 " (cutoff:3.500A) removed outlier: 4.772A pdb=" N VAL E 209 " --> pdb=" O VAL E 99 " (cutoff:3.500A) removed outlier: 4.384A pdb=" N LEU E 210 " --> pdb=" O ILE E 165 " (cutoff:3.500A) removed outlier: 7.354A pdb=" N VAL E 158 " --> pdb=" O ASP E 177 " (cutoff:3.500A) removed outlier: 4.792A pdb=" N ASP E 177 " --> pdb=" O VAL E 158 " (cutoff:3.500A) removed outlier: 6.759A pdb=" N VAL E 160 " --> pdb=" O ARG E 175 " (cutoff:3.500A) removed outlier: 4.412A pdb=" N ARG E 175 " --> pdb=" O VAL E 160 " (cutoff:3.500A) removed outlier: 6.557A pdb=" N ILE E 162 " --> pdb=" O THR E 173 " (cutoff:3.500A) removed outlier: 4.434A pdb=" N THR E 173 " --> pdb=" O ILE E 162 " (cutoff:3.500A) removed outlier: 6.668A pdb=" N HIS E 164 " --> pdb=" O ALA E 171 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'E' and resid 45 through 51 removed outlier: 3.594A pdb=" N GLY E 51 " --> pdb=" O ASN E 75 " (cutoff:3.500A) removed outlier: 4.498A pdb=" N ASN E 75 " --> pdb=" O GLY E 51 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'E' and resid 287 through 288 removed outlier: 3.669A pdb=" N VAL E 288 " --> pdb=" O LYS E 293 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N LYS E 293 " --> pdb=" O VAL E 288 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC3 Processing sheet with id=AC4, first strand: chain 'F' and resid 13 through 14 Processing sheet with id=AC5, first strand: chain 'F' and resid 19 through 20 removed outlier: 3.752A pdb=" N VAL F 99 " --> pdb=" O VAL F 209 " (cutoff:3.500A) removed outlier: 4.413A pdb=" N VAL F 209 " --> pdb=" O VAL F 99 " (cutoff:3.500A) removed outlier: 4.149A pdb=" N LEU F 210 " --> pdb=" O ILE F 165 " (cutoff:3.500A) removed outlier: 6.987A pdb=" N VAL F 160 " --> pdb=" O ARG F 175 " (cutoff:3.500A) removed outlier: 4.820A pdb=" N ARG F 175 " --> pdb=" O VAL F 160 " (cutoff:3.500A) removed outlier: 6.657A pdb=" N ILE F 162 " --> pdb=" O THR F 173 " (cutoff:3.500A) removed outlier: 4.496A pdb=" N THR F 173 " --> pdb=" O ILE F 162 " (cutoff:3.500A) removed outlier: 6.404A pdb=" N HIS F 164 " --> pdb=" O ALA F 171 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'F' and resid 19 through 20 Processing sheet with id=AC7, first strand: chain 'F' and resid 44 through 51 Processing sheet with id=AC8, first strand: chain 'F' and resid 266 through 268 Processing sheet with id=AC9, first strand: chain 'F' and resid 287 through 288 removed outlier: 3.514A pdb=" N LYS F 293 " --> pdb=" O VAL F 288 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'G' and resid 11 through 13 Processing sheet with id=AD2, first strand: chain 'G' and resid 19 through 20 removed outlier: 3.926A pdb=" N VAL G 209 " --> pdb=" O VAL G 99 " (cutoff:3.500A) removed outlier: 3.998A pdb=" N LEU G 210 " --> pdb=" O ILE G 165 " (cutoff:3.500A) removed outlier: 4.029A pdb=" N ALA G 157 " --> pdb=" O ARG G 218 " (cutoff:3.500A) removed outlier: 7.325A pdb=" N VAL G 158 " --> pdb=" O ASP G 177 " (cutoff:3.500A) removed outlier: 5.060A pdb=" N ASP G 177 " --> pdb=" O VAL G 158 " (cutoff:3.500A) removed outlier: 6.818A pdb=" N VAL G 160 " --> pdb=" O ARG G 175 " (cutoff:3.500A) removed outlier: 4.397A pdb=" N ARG G 175 " --> pdb=" O VAL G 160 " (cutoff:3.500A) removed outlier: 6.640A pdb=" N ILE G 162 " --> pdb=" O THR G 173 " (cutoff:3.500A) removed outlier: 4.604A pdb=" N THR G 173 " --> pdb=" O ILE G 162 " (cutoff:3.500A) removed outlier: 6.709A pdb=" N HIS G 164 " --> pdb=" O ALA G 171 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'G' and resid 19 through 20 removed outlier: 3.643A pdb=" N LEU G 24 " --> pdb=" O ARG G 94 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N ALA G 23 " --> pdb=" O ILE G 255 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'G' and resid 45 through 50 Processing sheet with id=AD5, first strand: chain 'G' and resid 266 through 268 Processing sheet with id=AD6, first strand: chain 'G' and resid 287 through 288 removed outlier: 3.634A pdb=" N LYS G 293 " --> pdb=" O VAL G 288 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'H' and resid 108 through 109 removed outlier: 3.719A pdb=" N ALA H 108 " --> pdb=" O ALA H 13 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N ALA H 13 " --> pdb=" O ALA H 108 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'H' and resid 19 through 20 removed outlier: 3.882A pdb=" N LEU H 210 " --> pdb=" O ILE H 165 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N VAL H 160 " --> pdb=" O PHE H 176 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'H' and resid 19 through 20 removed outlier: 3.537A pdb=" N ALA H 23 " --> pdb=" O ILE H 255 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'H' and resid 45 through 51 removed outlier: 4.042A pdb=" N ASN H 75 " --> pdb=" O GLY H 51 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'H' and resid 45 through 51 removed outlier: 4.042A pdb=" N ASN H 75 " --> pdb=" O GLY H 51 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N ALA U 38 " --> pdb=" O LEU U 30 " (cutoff:3.500A) removed outlier: 6.490A pdb=" N TYR U 32 " --> pdb=" O GLU U 36 " (cutoff:3.500A) removed outlier: 5.448A pdb=" N GLU U 36 " --> pdb=" O TYR U 32 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'H' and resid 266 through 268 Processing sheet with id=AE4, first strand: chain 'I' and resid 41 through 43 removed outlier: 3.967A pdb=" N LEU I 58 " --> pdb=" O ILE I 7 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N ILE I 7 " --> pdb=" O LEU I 58 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'I' and resid 41 through 43 removed outlier: 3.967A pdb=" N LEU I 58 " --> pdb=" O ILE I 7 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N ILE I 7 " --> pdb=" O LEU I 58 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N TYR I 4 " --> pdb=" O ALA I 89 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N ALA I 89 " --> pdb=" O TYR I 4 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'I' and resid 97 through 98 Processing sheet with id=AE7, first strand: chain 'I' and resid 143 through 146 Processing sheet with id=AE8, first strand: chain 'I' and resid 172 through 173 removed outlier: 4.065A pdb=" N GLY I 172 " --> pdb=" O LYS I 180 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'L' and resid 56 through 60 removed outlier: 5.038A pdb=" N GLY L 58 " --> pdb=" O GLY L 112 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N GLY L 112 " --> pdb=" O GLY L 58 " (cutoff:3.500A) removed outlier: 6.516A pdb=" N ALA L 103 " --> pdb=" O GLN L 18 " (cutoff:3.500A) removed outlier: 4.849A pdb=" N GLN L 18 " --> pdb=" O ALA L 103 " (cutoff:3.500A) removed outlier: 6.630A pdb=" N LEU L 105 " --> pdb=" O SER L 16 " (cutoff:3.500A) removed outlier: 4.565A pdb=" N SER L 16 " --> pdb=" O LEU L 105 " (cutoff:3.500A) removed outlier: 6.340A pdb=" N VAL L 107 " --> pdb=" O ARG L 14 " (cutoff:3.500A) removed outlier: 4.422A pdb=" N ARG L 14 " --> pdb=" O VAL L 107 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N GLN L 18 " --> pdb=" O SER L 143 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N SER L 143 " --> pdb=" O GLN L 18 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'L' and resid 65 through 68 removed outlier: 6.516A pdb=" N ALA L 103 " --> pdb=" O GLN L 18 " (cutoff:3.500A) removed outlier: 4.849A pdb=" N GLN L 18 " --> pdb=" O ALA L 103 " (cutoff:3.500A) removed outlier: 6.630A pdb=" N LEU L 105 " --> pdb=" O SER L 16 " (cutoff:3.500A) removed outlier: 4.565A pdb=" N SER L 16 " --> pdb=" O LEU L 105 " (cutoff:3.500A) removed outlier: 6.340A pdb=" N VAL L 107 " --> pdb=" O ARG L 14 " (cutoff:3.500A) removed outlier: 4.422A pdb=" N ARG L 14 " --> pdb=" O VAL L 107 " (cutoff:3.500A) removed outlier: 4.039A pdb=" N ALA L 157 " --> pdb=" O LEU L 11 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'L' and resid 70 through 71 removed outlier: 6.462A pdb=" N LYS L 79 " --> pdb=" O ILE X 240 " (cutoff:3.500A) removed outlier: 8.445A pdb=" N LYS X 242 " --> pdb=" O LYS L 79 " (cutoff:3.500A) removed outlier: 9.582A pdb=" N PHE L 81 " --> pdb=" O LYS X 242 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'L' and resid 185 through 188 removed outlier: 3.554A pdb=" N GLU L 288 " --> pdb=" O VAL L 187 " (cutoff:3.500A) removed outlier: 7.275A pdb=" N PHE L 279 " --> pdb=" O ALA L 257 " (cutoff:3.500A) removed outlier: 4.885A pdb=" N ALA L 257 " --> pdb=" O PHE L 279 " (cutoff:3.500A) removed outlier: 6.346A pdb=" N GLU L 281 " --> pdb=" O TYR L 255 " (cutoff:3.500A) removed outlier: 4.478A pdb=" N TYR L 255 " --> pdb=" O GLU L 281 " (cutoff:3.500A) removed outlier: 6.405A pdb=" N LEU L 283 " --> pdb=" O ALA L 253 " (cutoff:3.500A) removed outlier: 6.218A pdb=" N ALA L 253 " --> pdb=" O TRP L 316 " (cutoff:3.500A) Processing sheet with id=AF4, first strand: chain 'L' and resid 185 through 188 removed outlier: 3.554A pdb=" N GLU L 288 " --> pdb=" O VAL L 187 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N ALA X 191 " --> pdb=" O ARG L 278 " (cutoff:3.500A) Processing sheet with id=AF5, first strand: chain 'L' and resid 217 through 218 Processing sheet with id=AF6, first strand: chain 'M' and resid 108 through 109 removed outlier: 3.760A pdb=" N GLY M 334 " --> pdb=" O PHE M 14 " (cutoff:3.500A) Processing sheet with id=AF7, first strand: chain 'M' and resid 173 through 176 removed outlier: 3.813A pdb=" N ILE M 162 " --> pdb=" O TRP M 174 " (cutoff:3.500A) removed outlier: 3.907A pdb=" N VAL M 209 " --> pdb=" O VAL M 99 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N ALA M 217 " --> pdb=" O LEU M 91 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N MET M 25 " --> pdb=" O ALA M 253 " (cutoff:3.500A) removed outlier: 4.984A pdb=" N ALA M 253 " --> pdb=" O MET M 25 " (cutoff:3.500A) Processing sheet with id=AF8, first strand: chain 'M' and resid 45 through 47 removed outlier: 3.931A pdb=" N VAL M 79 " --> pdb=" O LYS M 47 " (cutoff:3.500A) Processing sheet with id=AF9, first strand: chain 'M' and resid 266 through 268 Processing sheet with id=AG1, first strand: chain 'M' and resid 287 through 288 removed outlier: 4.015A pdb=" N LYS M 293 " --> pdb=" O VAL M 288 " (cutoff:3.500A) Processing sheet with id=AG2, first strand: chain 'N' and resid 108 through 109 removed outlier: 3.721A pdb=" N ALA N 108 " --> pdb=" O ALA N 13 " (cutoff:3.500A) Processing sheet with id=AG3, first strand: chain 'N' and resid 19 through 20 removed outlier: 4.151A pdb=" N VAL N 209 " --> pdb=" O VAL N 99 " (cutoff:3.500A) removed outlier: 4.921A pdb=" N LEU N 210 " --> pdb=" O ILE N 165 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N ILE N 162 " --> pdb=" O TRP N 174 " (cutoff:3.500A) removed outlier: 3.853A pdb=" N ARG N 172 " --> pdb=" O HIS N 164 " (cutoff:3.500A) Processing sheet with id=AG4, first strand: chain 'N' and resid 19 through 20 Processing sheet with id=AG5, first strand: chain 'N' and resid 45 through 50 Processing sheet with id=AG6, first strand: chain 'N' and resid 287 through 288 removed outlier: 3.511A pdb=" N VAL N 288 " --> pdb=" O LYS N 293 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N LYS N 293 " --> pdb=" O VAL N 288 " (cutoff:3.500A) No H-bonds generated for sheet with id=AG6 Processing sheet with id=AG7, first strand: chain 'O' and resid 13 through 14 Processing sheet with id=AG8, first strand: chain 'O' and resid 19 through 20 removed outlier: 3.782A pdb=" N VAL O 99 " --> pdb=" O VAL O 209 " (cutoff:3.500A) removed outlier: 4.751A pdb=" N VAL O 209 " --> pdb=" O VAL O 99 " (cutoff:3.500A) removed outlier: 4.821A pdb=" N LEU O 210 " --> pdb=" O ILE O 165 " (cutoff:3.500A) removed outlier: 7.415A pdb=" N VAL O 158 " --> pdb=" O ASP O 177 " (cutoff:3.500A) removed outlier: 4.820A pdb=" N ASP O 177 " --> pdb=" O VAL O 158 " (cutoff:3.500A) removed outlier: 6.800A pdb=" N VAL O 160 " --> pdb=" O ARG O 175 " (cutoff:3.500A) removed outlier: 4.394A pdb=" N ARG O 175 " --> pdb=" O VAL O 160 " (cutoff:3.500A) removed outlier: 6.431A pdb=" N ILE O 162 " --> pdb=" O THR O 173 " (cutoff:3.500A) removed outlier: 4.498A pdb=" N THR O 173 " --> pdb=" O ILE O 162 " (cutoff:3.500A) removed outlier: 6.688A pdb=" N HIS O 164 " --> pdb=" O ALA O 171 " (cutoff:3.500A) Processing sheet with id=AG9, first strand: chain 'O' and resid 19 through 20 removed outlier: 3.604A pdb=" N ALA O 23 " --> pdb=" O ILE O 255 " (cutoff:3.500A) Processing sheet with id=AH1, first strand: chain 'O' and resid 45 through 50 Processing sheet with id=AH2, first strand: chain 'O' and resid 287 through 288 removed outlier: 3.694A pdb=" N LYS O 293 " --> pdb=" O VAL O 288 " (cutoff:3.500A) Processing sheet with id=AH3, first strand: chain 'P' and resid 13 through 14 Processing sheet with id=AH4, first strand: chain 'P' and resid 19 through 20 removed outlier: 3.510A pdb=" N LEU P 24 " --> pdb=" O ARG P 94 " (cutoff:3.500A) Processing sheet with id=AH5, first strand: chain 'P' and resid 19 through 20 removed outlier: 3.914A pdb=" N VAL P 99 " --> pdb=" O VAL P 209 " (cutoff:3.500A) removed outlier: 4.445A pdb=" N VAL P 209 " --> pdb=" O VAL P 99 " (cutoff:3.500A) removed outlier: 4.515A pdb=" N LEU P 210 " --> pdb=" O ILE P 165 " (cutoff:3.500A) removed outlier: 6.684A pdb=" N VAL P 160 " --> pdb=" O ARG P 175 " (cutoff:3.500A) removed outlier: 4.446A pdb=" N ARG P 175 " --> pdb=" O VAL P 160 " (cutoff:3.500A) removed outlier: 6.582A pdb=" N ILE P 162 " --> pdb=" O THR P 173 " (cutoff:3.500A) removed outlier: 4.538A pdb=" N THR P 173 " --> pdb=" O ILE P 162 " (cutoff:3.500A) removed outlier: 6.513A pdb=" N HIS P 164 " --> pdb=" O ALA P 171 " (cutoff:3.500A) Processing sheet with id=AH6, first strand: chain 'P' and resid 45 through 51 Processing sheet with id=AH7, first strand: chain 'P' and resid 287 through 288 Processing sheet with id=AH8, first strand: chain 'Q' and resid 19 through 20 removed outlier: 3.592A pdb=" N VAL Q 99 " --> pdb=" O VAL Q 209 " (cutoff:3.500A) removed outlier: 4.143A pdb=" N VAL Q 209 " --> pdb=" O VAL Q 99 " (cutoff:3.500A) removed outlier: 3.962A pdb=" N LEU Q 210 " --> pdb=" O ILE Q 165 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N GLU Q 212 " --> pdb=" O ASN Q 163 " (cutoff:3.500A) removed outlier: 7.415A pdb=" N VAL Q 158 " --> pdb=" O ASP Q 177 " (cutoff:3.500A) removed outlier: 4.924A pdb=" N ASP Q 177 " --> pdb=" O VAL Q 158 " (cutoff:3.500A) removed outlier: 6.652A pdb=" N VAL Q 160 " --> pdb=" O ARG Q 175 " (cutoff:3.500A) removed outlier: 4.245A pdb=" N ARG Q 175 " --> pdb=" O VAL Q 160 " (cutoff:3.500A) removed outlier: 6.635A pdb=" N ILE Q 162 " --> pdb=" O THR Q 173 " (cutoff:3.500A) removed outlier: 4.410A pdb=" N THR Q 173 " --> pdb=" O ILE Q 162 " (cutoff:3.500A) removed outlier: 6.344A pdb=" N HIS Q 164 " --> pdb=" O ALA Q 171 " (cutoff:3.500A) Processing sheet with id=AH9, first strand: chain 'Q' and resid 19 through 20 removed outlier: 3.558A pdb=" N LEU Q 24 " --> pdb=" O ARG Q 94 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N ALA Q 23 " --> pdb=" O ILE Q 255 " (cutoff:3.500A) Processing sheet with id=AI1, first strand: chain 'Q' and resid 45 through 51 removed outlier: 3.942A pdb=" N ASN Q 75 " --> pdb=" O GLY Q 51 " (cutoff:3.500A) Processing sheet with id=AI2, first strand: chain 'Q' and resid 266 through 268 Processing sheet with id=AI3, first strand: chain 'Q' and resid 287 through 288 removed outlier: 3.548A pdb=" N LYS Q 293 " --> pdb=" O VAL Q 288 " (cutoff:3.500A) Processing sheet with id=AI4, first strand: chain 'R' and resid 108 through 109 removed outlier: 3.575A pdb=" N ALA R 108 " --> pdb=" O ALA R 13 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N LEU R 12 " --> pdb=" O PHE R 336 " (cutoff:3.500A) Processing sheet with id=AI5, first strand: chain 'R' and resid 19 through 20 removed outlier: 3.546A pdb=" N LEU R 91 " --> pdb=" O ALA R 217 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N ALA R 217 " --> pdb=" O LEU R 91 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N LEU R 210 " --> pdb=" O ILE R 165 " (cutoff:3.500A) Processing sheet with id=AI6, first strand: chain 'R' and resid 19 through 20 removed outlier: 3.676A pdb=" N ALA R 23 " --> pdb=" O ILE R 255 " (cutoff:3.500A) Processing sheet with id=AI7, first strand: chain 'R' and resid 44 through 51 removed outlier: 4.214A pdb=" N ASN R 75 " --> pdb=" O GLY R 51 " (cutoff:3.500A) Processing sheet with id=AI8, first strand: chain 'R' and resid 44 through 51 removed outlier: 4.214A pdb=" N ASN R 75 " --> pdb=" O GLY R 51 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N ALA V 38 " --> pdb=" O LEU V 30 " (cutoff:3.500A) removed outlier: 6.491A pdb=" N TYR V 32 " --> pdb=" O GLU V 36 " (cutoff:3.500A) removed outlier: 5.448A pdb=" N GLU V 36 " --> pdb=" O TYR V 32 " (cutoff:3.500A) Processing sheet with id=AI9, first strand: chain 'R' and resid 266 through 268 Processing sheet with id=AJ1, first strand: chain 'S' and resid 41 through 43 removed outlier: 3.535A pdb=" N LEU S 58 " --> pdb=" O ILE S 7 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N HIS S 3 " --> pdb=" O ALA S 62 " (cutoff:3.500A) Processing sheet with id=AJ2, first strand: chain 'S' and resid 41 through 43 removed outlier: 3.535A pdb=" N LEU S 58 " --> pdb=" O ILE S 7 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N HIS S 3 " --> pdb=" O ALA S 62 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N TYR S 4 " --> pdb=" O ALA S 89 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N ALA S 89 " --> pdb=" O TYR S 4 " (cutoff:3.500A) Processing sheet with id=AJ3, first strand: chain 'S' and resid 97 through 98 removed outlier: 3.867A pdb=" N ARG S 98 " --> pdb=" O VAL S 184 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N VAL S 184 " --> pdb=" O ARG S 98 " (cutoff:3.500A) No H-bonds generated for sheet with id=AJ3 Processing sheet with id=AJ4, first strand: chain 'S' and resid 100 through 103 removed outlier: 4.380A pdb=" N PHE S 158 " --> pdb=" O VAL S 103 " (cutoff:3.500A) Processing sheet with id=AJ5, first strand: chain 'U' and resid 87 through 91 removed outlier: 3.773A pdb=" N ALA U 87 " --> pdb=" O LEU U 77 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N ASP U 73 " --> pdb=" O VAL U 91 " (cutoff:3.500A) Processing sheet with id=AJ6, first strand: chain 'V' and resid 87 through 91 removed outlier: 3.773A pdb=" N ALA V 87 " --> pdb=" O LEU V 77 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N ASP V 73 " --> pdb=" O VAL V 91 " (cutoff:3.500A) Processing sheet with id=AJ7, first strand: chain 'A' and resid 64 through 66 removed outlier: 3.967A pdb=" N GLN A 64 " --> pdb=" O VAL A 109 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N VAL A 109 " --> pdb=" O GLN A 64 " (cutoff:3.500A) Processing sheet with id=AJ8, first strand: chain 'A' and resid 68 through 69 Processing sheet with id=AJ9, first strand: chain 'A' and resid 239 through 242 Processing sheet with id=AK1, first strand: chain 'X' and resid 64 through 66 removed outlier: 3.967A pdb=" N GLN X 64 " --> pdb=" O VAL X 109 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N VAL X 109 " --> pdb=" O GLN X 64 " (cutoff:3.500A) Processing sheet with id=AK2, first strand: chain 'X' and resid 68 through 69 2072 hydrogen bonds defined for protein. 5784 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 32 hydrogen bonds 56 hydrogen bond angles 0 basepair planarities 12 basepair parallelities 48 stacking parallelities Total time for adding SS restraints: 16.56 Time building geometry restraints manager: 10.18 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.33: 12200 1.33 - 1.45: 11476 1.45 - 1.58: 25507 1.58 - 1.70: 321 1.70 - 1.83: 71 Bond restraints: 49575 Sorted by residual: bond pdb=" CA THR I 151 " pdb=" CB THR I 151 " ideal model delta sigma weight residual 1.526 1.593 -0.067 1.76e-02 3.23e+03 1.45e+01 bond pdb=" CB GLU U 61 " pdb=" CG GLU U 61 " ideal model delta sigma weight residual 1.520 1.598 -0.078 3.00e-02 1.11e+03 6.75e+00 bond pdb=" O4' DC W 11 " pdb=" C1' DC W 11 " ideal model delta sigma weight residual 1.414 1.362 0.052 2.00e-02 2.50e+03 6.73e+00 bond pdb=" CB GLU V 61 " pdb=" CG GLU V 61 " ideal model delta sigma weight residual 1.520 1.597 -0.077 3.00e-02 1.11e+03 6.67e+00 bond pdb=" CB GLU X 226 " pdb=" CG GLU X 226 " ideal model delta sigma weight residual 1.520 1.597 -0.077 3.00e-02 1.11e+03 6.59e+00 ... (remaining 49570 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.39: 67196 3.39 - 6.78: 550 6.78 - 10.16: 66 10.16 - 13.55: 12 13.55 - 16.94: 5 Bond angle restraints: 67829 Sorted by residual: angle pdb=" CA GLU V 61 " pdb=" CB GLU V 61 " pdb=" CG GLU V 61 " ideal model delta sigma weight residual 114.10 128.49 -14.39 2.00e+00 2.50e-01 5.18e+01 angle pdb=" CA GLU U 61 " pdb=" CB GLU U 61 " pdb=" CG GLU U 61 " ideal model delta sigma weight residual 114.10 128.35 -14.25 2.00e+00 2.50e-01 5.08e+01 angle pdb=" CA GLU V 96 " pdb=" CB GLU V 96 " pdb=" CG GLU V 96 " ideal model delta sigma weight residual 114.10 126.92 -12.82 2.00e+00 2.50e-01 4.11e+01 angle pdb=" CA GLU U 96 " pdb=" CB GLU U 96 " pdb=" CG GLU U 96 " ideal model delta sigma weight residual 114.10 126.88 -12.78 2.00e+00 2.50e-01 4.09e+01 angle pdb=" CA GLU A 226 " pdb=" CB GLU A 226 " pdb=" CG GLU A 226 " ideal model delta sigma weight residual 114.10 126.80 -12.70 2.00e+00 2.50e-01 4.03e+01 ... (remaining 67824 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.86: 27849 35.86 - 71.72: 1190 71.72 - 107.58: 85 107.58 - 143.44: 4 143.44 - 179.31: 10 Dihedral angle restraints: 29138 sinusoidal: 12336 harmonic: 16802 Sorted by residual: dihedral pdb=" O4' U J 21 " pdb=" C1' U J 21 " pdb=" N1 U J 21 " pdb=" C2 U J 21 " ideal model delta sinusoidal sigma weight residual 200.00 55.22 144.78 1 1.50e+01 4.44e-03 7.75e+01 dihedral pdb=" O4' U T 21 " pdb=" C1' U T 21 " pdb=" N1 U T 21 " pdb=" C2 U T 21 " ideal model delta sinusoidal sigma weight residual 200.00 55.22 144.78 1 1.50e+01 4.44e-03 7.75e+01 dihedral pdb=" O4' U T 33 " pdb=" C1' U T 33 " pdb=" N1 U T 33 " pdb=" C2 U T 33 " ideal model delta sinusoidal sigma weight residual 200.00 70.11 129.89 1 1.50e+01 4.44e-03 7.00e+01 ... (remaining 29135 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.112: 7081 0.112 - 0.223: 344 0.223 - 0.335: 9 0.335 - 0.446: 0 0.446 - 0.558: 1 Chirality restraints: 7435 Sorted by residual: chirality pdb=" CB ILE O 165 " pdb=" CA ILE O 165 " pdb=" CG1 ILE O 165 " pdb=" CG2 ILE O 165 " both_signs ideal model delta sigma weight residual False 2.64 2.09 0.56 2.00e-01 2.50e+01 7.77e+00 chirality pdb=" CG LEU L 210 " pdb=" CB LEU L 210 " pdb=" CD1 LEU L 210 " pdb=" CD2 LEU L 210 " both_signs ideal model delta sigma weight residual False -2.59 -2.28 -0.31 2.00e-01 2.50e+01 2.42e+00 chirality pdb=" CB THR P 266 " pdb=" CA THR P 266 " pdb=" OG1 THR P 266 " pdb=" CG2 THR P 266 " both_signs ideal model delta sigma weight residual False 2.55 2.27 0.28 2.00e-01 2.50e+01 2.01e+00 ... (remaining 7432 not shown) Planarity restraints: 8566 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LYS X 71 " 0.052 5.00e-02 4.00e+02 7.69e-02 9.47e+00 pdb=" N PRO X 72 " -0.133 5.00e-02 4.00e+02 pdb=" CA PRO X 72 " 0.038 5.00e-02 4.00e+02 pdb=" CD PRO X 72 " 0.043 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LYS A 71 " 0.051 5.00e-02 4.00e+02 7.66e-02 9.40e+00 pdb=" N PRO A 72 " -0.133 5.00e-02 4.00e+02 pdb=" CA PRO A 72 " 0.038 5.00e-02 4.00e+02 pdb=" CD PRO A 72 " 0.043 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CG GLU A 226 " -0.015 2.00e-02 2.50e+03 3.05e-02 9.32e+00 pdb=" CD GLU A 226 " 0.053 2.00e-02 2.50e+03 pdb=" OE1 GLU A 226 " -0.019 2.00e-02 2.50e+03 pdb=" OE2 GLU A 226 " -0.019 2.00e-02 2.50e+03 ... (remaining 8563 not shown) Histogram of nonbonded interaction distances: 2.15 - 2.70: 2405 2.70 - 3.25: 44756 3.25 - 3.80: 80472 3.80 - 4.35: 93451 4.35 - 4.90: 156883 Nonbonded interactions: 377967 Sorted by model distance: nonbonded pdb=" N THR X 246 " pdb=" OP2 DG K 33 " model vdw 2.152 3.120 nonbonded pdb=" N THR A 246 " pdb=" OP2 DG Y 33 " model vdw 2.153 3.120 nonbonded pdb=" CA GLY X 245 " pdb=" OP2 DG K 33 " model vdw 2.208 3.440 nonbonded pdb=" CA GLY A 245 " pdb=" OP2 DG Y 33 " model vdw 2.210 3.440 nonbonded pdb=" O LYS G 117 " pdb=" OG1 THR G 121 " model vdw 2.255 3.040 ... (remaining 377962 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 'X' } ncs_group { reference = (chain 'B' and (resid 3 through 6 or (resid 7 through 8 and (name N or name CA o \ r name C or name O or name CB )) or resid 9 through 75 or (resid 76 through 77 a \ nd (name N or name CA or name C or name O or name CB )) or resid 78 through 149 \ or (resid 150 through 151 and (name N or name CA or name C or name O or name CB \ )) or resid 152 through 166 or (resid 167 and (name N or name CA or name C or na \ me O or name CB )) or resid 168 through 188 or (resid 189 through 192 and (name \ N or name CA or name C or name O or name CB )) or resid 193 through 239 or (resi \ d 240 and (name N or name CA or name C or name O or name CB )) or resid 241 thro \ ugh 285 or (resid 286 and (name N or name CA or name C or name O or name CB )) o \ r resid 287 through 322)) selection = (chain 'L' and ((resid 3 and (name N or name CA or name C or name O or name CB ) \ ) or resid 4 through 11 or (resid 12 and (name N or name CA or name C or name O \ or name CB )) or resid 13 or (resid 14 and (name N or name CA or name C or name \ O or name CB )) or resid 15 through 43 or (resid 44 and (name N or name CA or na \ me C or name O or name CB )) or resid 45 through 51 or (resid 52 and (name N or \ name CA or name C or name O or name CB )) or resid 53 through 62 or (resid 63 an \ d (name N or name CA or name C or name O or name CB )) or resid 64 through 66 or \ (resid 67 through 68 and (name N or name CA or name C or name O or name CB )) o \ r resid 69 through 76 or (resid 77 and (name N or name CA or name C or name O or \ name CB )) or resid 78 through 93 or (resid 94 through 96 and (name N or name C \ A or name C or name O or name CB )) or resid 97 through 107 or (resid 108 and (n \ ame N or name CA or name C or name O or name CB )) or resid 109 through 112 or ( \ resid 113 and (name N or name CA or name C or name O or name CB )) or resid 114 \ through 120 or (resid 121 and (name N or name CA or name C or name O or name CB \ )) or resid 122 through 127 or (resid 128 and (name N or name CA or name C or na \ me O or name CB )) or resid 129 through 146 or (resid 147 and (name N or name CA \ or name C or name O or name CB )) or resid 148 through 157 or (resid 158 and (n \ ame N or name CA or name C or name O or name CB )) or resid 159 through 160 or ( \ resid 161 through 162 and (name N or name CA or name C or name O or name CB )) o \ r resid 163 through 168 or (resid 169 through 170 and (name N or name CA or name \ C or name O or name CB )) or resid 171 or (resid 172 through 173 and (name N or \ name CA or name C or name O or name CB )) or resid 174 or (resid 175 and (name \ N or name CA or name C or name O or name CB )) or resid 176 through 177 or (resi \ d 178 and (name N or name CA or name C or name O or name CB )) or resid 179 thro \ ugh 191 or (resid 192 and (name N or name CA or name C or name O or name CB )) o \ r resid 193 through 197 or (resid 198 and (name N or name CA or name C or name O \ or name CB )) or resid 199 through 209 or (resid 210 and (name N or name CA or \ name C or name O or name CB )) or resid 211 through 213 or (resid 214 and (name \ N or name CA or name C or name O or name CB )) or resid 215 through 217 or (resi \ d 218 and (name N or name CA or name C or name O or name CB )) or resid 219 thro \ ugh 223 or (resid 239 through 240 and (name N or name CA or name C or name O or \ name CB )) or resid 241 through 265 or (resid 266 and (name N or name CA or name \ C or name O or name CB )) or resid 267 through 276 or (resid 277 and (name N or \ name CA or name C or name O or name CB )) or resid 278 through 281 or (resid 28 \ 2 and (name N or name CA or name C or name O or name CB )) or resid 283 through \ 289 or (resid 290 and (name N or name CA or name C or name O or name CB )) or re \ sid 291 through 300 or (resid 301 and (name N or name CA or name C or name O or \ name CB )) or resid 302 through 304 or (resid 305 and (name N or name CA or name \ C or name O or name CB )) or resid 306 through 313 or (resid 314 and (name N or \ name CA or name C or name O or name CB )) or resid 315 through 319 or (resid 32 \ 0 and (name N or name CA or name C or name O or name CB )) or resid 321 through \ 322)) } ncs_group { reference = (chain 'C' and (resid 7 or (resid 8 through 9 and (name N or name CA or name C o \ r name O or name CB )) or resid 10 through 14 or (resid 15 and (name N or name C \ A or name C or name O or name CB )) or resid 16 or (resid 17 and (name N or name \ CA or name C or name O or name CB )) or resid 18 through 48 or (resid 77 and (n \ ame N or name CA or name C or name O or name CB )) or resid 78 through 79 or (re \ sid 80 and (name N or name CA or name C or name O or name CB )) or resid 81 thro \ ugh 97 or (resid 98 and (name N or name CA or name C or name O or name CB )) or \ resid 99 through 108 or (resid 109 through 110 and (name N or name CA or name C \ or name O or name CB )) or resid 111 through 113 or (resid 114 through 115 and ( \ name N or name CA or name C or name O or name CB )) or resid 116 or (resid 117 t \ hrough 118 and (name N or name CA or name C or name O or name CB )) or resid 119 \ through 132 or (resid 133 and (name N or name CA or name C or name O or name CB \ )) or resid 134 through 149 or (resid 150 and (name N or name CA or name C or n \ ame O or name CB )) or resid 151 through 161 or (resid 162 and (name N or name C \ A or name C or name O or name CB )) or resid 163 or (resid 164 and (name N or na \ me CA or name C or name O or name CB )) or resid 165 through 207 or (resid 208 a \ nd (name N or name CA or name C or name O or name CB )) or resid 209 through 217 \ or (resid 218 and (name N or name CA or name C or name O or name CB )) or resid \ 219 through 249 or (resid 250 and (name N or name CA or name C or name O or nam \ e CB )) or resid 251 through 273 or (resid 274 through 275 and (name N or name C \ A or name C or name O or name CB )) or resid 276 or (resid 277 and (name N or na \ me CA or name C or name O or name CB )) or resid 278 through 282 or (resid 283 a \ nd (name N or name CA or name C or name O or name CB )) or resid 284 or (resid 2 \ 85 and (name N or name CA or name C or name O or name CB )) or resid 286 through \ 306 or (resid 307 and (name N or name CA or name C or name O or name CB )) or r \ esid 308 through 320 or (resid 321 and (name N or name CA or name C or name O or \ name CB )) or resid 322 through 326 or (resid 327 through 328 and (name N or na \ me CA or name C or name O or name CB )) or resid 329 or (resid 330 and (name N o \ r name CA or name C or name O or name CB )) or resid 331 through 337 or (resid 3 \ 38 and (name N or name CA or name C or name O or name CB )))) selection = (chain 'D' and (resid 7 or (resid 8 through 9 and (name N or name CA or name C o \ r name O or name CB )) or resid 10 through 14 or (resid 15 and (name N or name C \ A or name C or name O or name CB )) or resid 16 or (resid 17 and (name N or name \ CA or name C or name O or name CB )) or resid 18 or (resid 19 and (name N or na \ me CA or name C or name O or name CB )) or resid 20 through 32 or (resid 33 and \ (name N or name CA or name C or name O or name CB )) or resid 34 through 36 or ( \ resid 37 and (name N or name CA or name C or name O or name CB )) or resid 38 th \ rough 44 or (resid 45 and (name N or name CA or name C or name O or name CB )) o \ r resid 46 through 48 or (resid 77 and (name N or name CA or name C or name O or \ name CB )) or resid 78 through 79 or (resid 80 and (name N or name CA or name C \ or name O or name CB )) or resid 81 through 83 or (resid 84 and (name N or name \ CA or name C or name O or name CB )) or resid 85 through 97 or (resid 98 and (n \ ame N or name CA or name C or name O or name CB )) or resid 99 through 108 or (r \ esid 109 through 110 and (name N or name CA or name C or name O or name CB )) or \ resid 111 through 113 or (resid 114 through 115 and (name N or name CA or name \ C or name O or name CB )) or resid 116 or (resid 117 through 118 and (name N or \ name CA or name C or name O or name CB )) or resid 119 through 130 or (resid 131 \ through 133 and (name N or name CA or name C or name O or name CB )) or resid 1 \ 34 through 135 or (resid 136 and (name N or name CA or name C or name O or name \ CB )) or resid 137 through 139 or (resid 140 and (name N or name CA or name C or \ name O or name CB )) or resid 141 through 149 or (resid 150 and (name N or name \ CA or name C or name O or name CB )) or resid 151 through 155 or (resid 156 thr \ ough 157 and (name N or name CA or name C or name O or name CB )) or resid 158 o \ r (resid 159 and (name N or name CA or name C or name O or name CB )) or resid 1 \ 60 through 161 or (resid 162 and (name N or name CA or name C or name O or name \ CB )) or resid 163 or (resid 164 and (name N or name CA or name C or name O or n \ ame CB )) or resid 165 through 168 or (resid 169 and (name N or name CA or name \ C or name O or name CB )) or resid 170 through 183 or (resid 184 and (name N or \ name CA or name C or name O or name CB )) or resid 185 or (resid 186 and (name N \ or name CA or name C or name O or name CB )) or resid 187 through 207 or (resid \ 208 and (name N or name CA or name C or name O or name CB )) or resid 209 or (r \ esid 210 and (name N or name CA or name C or name O or name CB )) or resid 211 o \ r (resid 212 and (name N or name CA or name C or name O or name CB )) or resid 2 \ 13 through 228 or (resid 229 and (name N or name CA or name C or name O or name \ CB )) or resid 230 or (resid 231 and (name N or name CA or name C or name O or n \ ame CB )) or resid 244 through 245 or (resid 246 and (name N or name CA or name \ C or name O or name CB )) or resid 247 through 249 or (resid 250 and (name N or \ name CA or name C or name O or name CB )) or resid 251 through 270 or (resid 271 \ and (name N or name CA or name C or name O or name CB )) or resid 272 through 2 \ 76 or (resid 277 and (name N or name CA or name C or name O or name CB )) or res \ id 278 through 282 or (resid 283 and (name N or name CA or name C or name O or n \ ame CB )) or resid 284 or (resid 285 and (name N or name CA or name C or name O \ or name CB )) or resid 286 through 290 or (resid 291 and (name N or name CA or n \ ame C or name O or name CB )) or resid 292 through 295 or (resid 296 through 297 \ and (name N or name CA or name C or name O or name CB )) or resid 298 or (resid \ 299 and (name N or name CA or name C or name O or name CB )) or resid 300 throu \ gh 301 or (resid 302 through 303 and (name N or name CA or name C or name O or n \ ame CB )) or resid 304 through 306 or (resid 307 and (name N or name CA or name \ C or name O or name CB )) or resid 308 through 313 or (resid 314 and (name N or \ name CA or name C or name O or name CB )) or resid 315 through 320 or (resid 321 \ and (name N or name CA or name C or name O or name CB )) or resid 322 through 3 \ 23 or (resid 324 and (name N or name CA or name C or name O or name CB )) or res \ id 325 through 326 or (resid 327 through 328 and (name N or name CA or name C or \ name O or name CB )) or resid 329 or (resid 330 and (name N or name CA or name \ C or name O or name CB )) or resid 331 through 337 or (resid 338 and (name N or \ name CA or name C or name O or name CB )))) selection = (chain 'E' and (resid 7 or (resid 8 through 9 and (name N or name CA or name C o \ r name O or name CB )) or resid 10 through 14 or (resid 15 and (name N or name C \ A or name C or name O or name CB )) or resid 16 or (resid 17 and (name N or name \ CA or name C or name O or name CB )) or resid 18 or (resid 19 and (name N or na \ me CA or name C or name O or name CB )) or resid 20 through 36 or (resid 37 and \ (name N or name CA or name C or name O or name CB )) or resid 38 through 44 or ( \ resid 45 and (name N or name CA or name C or name O or name CB )) or resid 46 th \ rough 48 or (resid 77 and (name N or name CA or name C or name O or name CB )) o \ r resid 78 through 79 or (resid 80 and (name N or name CA or name C or name O or \ name CB )) or resid 81 through 83 or (resid 84 and (name N or name CA or name C \ or name O or name CB )) or resid 85 through 97 or (resid 98 and (name N or name \ CA or name C or name O or name CB )) or resid 99 through 108 or (resid 109 thro \ ugh 110 and (name N or name CA or name C or name O or name CB )) or resid 111 th \ rough 113 or (resid 114 through 115 and (name N or name CA or name C or name O o \ r name CB )) or resid 116 or (resid 117 through 118 and (name N or name CA or na \ me C or name O or name CB )) or resid 119 through 130 or (resid 131 through 133 \ and (name N or name CA or name C or name O or name CB )) or resid 134 through 13 \ 5 or (resid 136 and (name N or name CA or name C or name O or name CB )) or resi \ d 137 through 139 or (resid 140 and (name N or name CA or name C or name O or na \ me CB )) or resid 141 through 149 or (resid 150 and (name N or name CA or name C \ or name O or name CB )) or resid 151 through 155 or (resid 156 through 157 and \ (name N or name CA or name C or name O or name CB )) or resid 158 or (resid 159 \ and (name N or name CA or name C or name O or name CB )) or resid 160 or (resid \ 161 through 162 and (name N or name CA or name C or name O or name CB )) or resi \ d 163 or (resid 164 and (name N or name CA or name C or name O or name CB )) or \ resid 165 through 168 or (resid 169 and (name N or name CA or name C or name O o \ r name CB )) or resid 170 through 183 or (resid 184 and (name N or name CA or na \ me C or name O or name CB )) or resid 185 or (resid 186 and (name N or name CA o \ r name C or name O or name CB )) or resid 187 through 207 or (resid 208 and (nam \ e N or name CA or name C or name O or name CB )) or resid 209 or (resid 210 and \ (name N or name CA or name C or name O or name CB )) or resid 211 or (resid 212 \ and (name N or name CA or name C or name O or name CB )) or resid 213 through 21 \ 7 or (resid 218 and (name N or name CA or name C or name O or name CB )) or resi \ d 219 through 228 or (resid 229 and (name N or name CA or name C or name O or na \ me CB )) or resid 230 or (resid 231 and (name N or name CA or name C or name O o \ r name CB )) or resid 244 through 245 or (resid 246 and (name N or name CA or na \ me C or name O or name CB )) or resid 247 through 249 or (resid 250 and (name N \ or name CA or name C or name O or name CB )) or resid 251 through 270 or (resid \ 271 and (name N or name CA or name C or name O or name CB )) or resid 272 throug \ h 276 or (resid 277 and (name N or name CA or name C or name O or name CB )) or \ resid 278 through 282 or (resid 283 and (name N or name CA or name C or name O o \ r name CB )) or resid 284 or (resid 285 and (name N or name CA or name C or name \ O or name CB )) or resid 286 through 290 or (resid 291 and (name N or name CA o \ r name C or name O or name CB )) or resid 292 through 295 or (resid 296 through \ 297 and (name N or name CA or name C or name O or name CB )) or resid 298 or (re \ sid 299 and (name N or name CA or name C or name O or name CB )) or resid 300 th \ rough 301 or (resid 302 through 303 and (name N or name CA or name C or name O o \ r name CB )) or resid 304 through 306 or (resid 307 and (name N or name CA or na \ me C or name O or name CB )) or resid 308 through 313 or (resid 314 and (name N \ or name CA or name C or name O or name CB )) or resid 315 through 320 or (resid \ 321 and (name N or name CA or name C or name O or name CB )) or resid 322 throug \ h 323 or (resid 324 and (name N or name CA or name C or name O or name CB )) or \ resid 325 through 326 or (resid 327 through 328 and (name N or name CA or name C \ or name O or name CB )) or resid 329 or (resid 330 and (name N or name CA or na \ me C or name O or name CB )) or resid 331 through 337 or (resid 338 and (name N \ or name CA or name C or name O or name CB )))) selection = (chain 'F' and (resid 7 or (resid 8 through 9 and (name N or name CA or name C o \ r name O or name CB )) or resid 10 through 14 or (resid 15 and (name N or name C \ A or name C or name O or name CB )) or resid 16 or (resid 17 and (name N or name \ CA or name C or name O or name CB )) or resid 18 or (resid 19 and (name N or na \ me CA or name C or name O or name CB )) or resid 20 through 32 or (resid 33 and \ (name N or name CA or name C or name O or name CB )) or resid 34 through 36 or ( \ resid 37 and (name N or name CA or name C or name O or name CB )) or resid 38 th \ rough 44 or (resid 45 and (name N or name CA or name C or name O or name CB )) o \ r resid 46 through 48 or (resid 77 and (name N or name CA or name C or name O or \ name CB )) or resid 78 through 79 or (resid 80 and (name N or name CA or name C \ or name O or name CB )) or resid 81 through 83 or (resid 84 and (name N or name \ CA or name C or name O or name CB )) or resid 85 through 97 or (resid 98 and (n \ ame N or name CA or name C or name O or name CB )) or resid 99 through 108 or (r \ esid 109 through 110 and (name N or name CA or name C or name O or name CB )) or \ resid 111 through 113 or (resid 114 through 115 and (name N or name CA or name \ C or name O or name CB )) or resid 116 or (resid 117 through 118 and (name N or \ name CA or name C or name O or name CB )) or resid 119 through 130 or (resid 131 \ through 133 and (name N or name CA or name C or name O or name CB )) or resid 1 \ 34 through 135 or (resid 136 and (name N or name CA or name C or name O or name \ CB )) or resid 137 through 139 or (resid 140 and (name N or name CA or name C or \ name O or name CB )) or resid 141 through 149 or (resid 150 and (name N or name \ CA or name C or name O or name CB )) or resid 151 through 155 or (resid 156 thr \ ough 157 and (name N or name CA or name C or name O or name CB )) or resid 158 o \ r (resid 159 and (name N or name CA or name C or name O or name CB )) or resid 1 \ 60 or (resid 161 through 162 and (name N or name CA or name C or name O or name \ CB )) or resid 163 or (resid 164 and (name N or name CA or name C or name O or n \ ame CB )) or resid 165 through 168 or (resid 169 and (name N or name CA or name \ C or name O or name CB )) or resid 170 through 183 or (resid 184 and (name N or \ name CA or name C or name O or name CB )) or resid 185 or (resid 186 and (name N \ or name CA or name C or name O or name CB )) or resid 187 through 207 or (resid \ 208 and (name N or name CA or name C or name O or name CB )) or resid 209 or (r \ esid 210 and (name N or name CA or name C or name O or name CB )) or resid 211 o \ r (resid 212 and (name N or name CA or name C or name O or name CB )) or resid 2 \ 13 through 217 or (resid 218 and (name N or name CA or name C or name O or name \ CB )) or resid 219 through 228 or (resid 229 and (name N or name CA or name C or \ name O or name CB )) or resid 230 or (resid 231 and (name N or name CA or name \ C or name O or name CB )) or resid 244 through 245 or (resid 246 and (name N or \ name CA or name C or name O or name CB )) or resid 247 through 249 or (resid 250 \ and (name N or name CA or name C or name O or name CB )) or resid 251 through 2 \ 70 or (resid 271 and (name N or name CA or name C or name O or name CB )) or res \ id 272 through 276 or (resid 277 and (name N or name CA or name C or name O or n \ ame CB )) or resid 278 through 284 or (resid 285 and (name N or name CA or name \ C or name O or name CB )) or resid 286 through 290 or (resid 291 and (name N or \ name CA or name C or name O or name CB )) or resid 292 through 295 or (resid 296 \ through 297 and (name N or name CA or name C or name O or name CB )) or resid 2 \ 98 or (resid 299 and (name N or name CA or name C or name O or name CB )) or res \ id 300 through 301 or (resid 302 through 303 and (name N or name CA or name C or \ name O or name CB )) or resid 304 through 306 or (resid 307 and (name N or name \ CA or name C or name O or name CB )) or resid 308 through 313 or (resid 314 and \ (name N or name CA or name C or name O or name CB )) or resid 315 through 320 o \ r (resid 321 and (name N or name CA or name C or name O or name CB )) or resid 3 \ 22 through 323 or (resid 324 and (name N or name CA or name C or name O or name \ CB )) or resid 325 through 326 or (resid 327 through 328 and (name N or name CA \ or name C or name O or name CB )) or resid 329 or (resid 330 and (name N or name \ CA or name C or name O or name CB )) or resid 331 through 337 or (resid 338 and \ (name N or name CA or name C or name O or name CB )))) selection = (chain 'G' and (resid 7 or (resid 8 through 9 and (name N or name CA or name C o \ r name O or name CB )) or resid 10 through 14 or (resid 15 and (name N or name C \ A or name C or name O or name CB )) or resid 16 through 18 or (resid 19 and (nam \ e N or name CA or name C or name O or name CB )) or resid 20 through 32 or (resi \ d 33 and (name N or name CA or name C or name O or name CB )) or resid 34 throug \ h 36 or (resid 37 and (name N or name CA or name C or name O or name CB )) or re \ sid 38 through 44 or (resid 45 and (name N or name CA or name C or name O or nam \ e CB )) or resid 46 through 48 or (resid 77 and (name N or name CA or name C or \ name O or name CB )) or resid 78 through 79 or (resid 80 and (name N or name CA \ or name C or name O or name CB )) or resid 81 through 83 or (resid 84 and (name \ N or name CA or name C or name O or name CB )) or resid 85 through 97 or (resid \ 98 and (name N or name CA or name C or name O or name CB )) or resid 99 through \ 108 or (resid 109 through 110 and (name N or name CA or name C or name O or name \ CB )) or resid 111 through 113 or (resid 114 through 115 and (name N or name CA \ or name C or name O or name CB )) or resid 116 or (resid 117 through 118 and (n \ ame N or name CA or name C or name O or name CB )) or resid 119 through 130 or ( \ resid 131 through 133 and (name N or name CA or name C or name O or name CB )) o \ r resid 134 through 135 or (resid 136 and (name N or name CA or name C or name O \ or name CB )) or resid 137 through 139 or (resid 140 and (name N or name CA or \ name C or name O or name CB )) or resid 141 through 149 or (resid 150 and (name \ N or name CA or name C or name O or name CB )) or resid 151 through 155 or (resi \ d 156 through 157 and (name N or name CA or name C or name O or name CB )) or re \ sid 158 or (resid 159 and (name N or name CA or name C or name O or name CB )) o \ r resid 160 or (resid 161 through 162 and (name N or name CA or name C or name O \ or name CB )) or resid 163 or (resid 164 and (name N or name CA or name C or na \ me O or name CB )) or resid 165 through 168 or (resid 169 and (name N or name CA \ or name C or name O or name CB )) or resid 170 through 183 or (resid 184 and (n \ ame N or name CA or name C or name O or name CB )) or resid 185 or (resid 186 an \ d (name N or name CA or name C or name O or name CB )) or resid 187 through 207 \ or (resid 208 and (name N or name CA or name C or name O or name CB )) or resid \ 209 or (resid 210 and (name N or name CA or name C or name O or name CB )) or re \ sid 211 or (resid 212 and (name N or name CA or name C or name O or name CB )) o \ r resid 213 through 217 or (resid 218 and (name N or name CA or name C or name O \ or name CB )) or resid 219 through 228 or (resid 229 and (name N or name CA or \ name C or name O or name CB )) or resid 230 or (resid 231 and (name N or name CA \ or name C or name O or name CB )) or resid 244 through 245 or (resid 246 and (n \ ame N or name CA or name C or name O or name CB )) or resid 247 through 249 or ( \ resid 250 and (name N or name CA or name C or name O or name CB )) or resid 251 \ through 270 or (resid 271 and (name N or name CA or name C or name O or name CB \ )) or resid 272 through 282 or (resid 283 and (name N or name CA or name C or na \ me O or name CB )) or resid 284 or (resid 285 and (name N or name CA or name C o \ r name O or name CB )) or resid 286 through 290 or (resid 291 and (name N or nam \ e CA or name C or name O or name CB )) or resid 292 through 295 or (resid 296 th \ rough 297 and (name N or name CA or name C or name O or name CB )) or resid 298 \ or (resid 299 and (name N or name CA or name C or name O or name CB )) or resid \ 300 through 301 or (resid 302 through 303 and (name N or name CA or name C or na \ me O or name CB )) or resid 304 through 306 or (resid 307 and (name N or name CA \ or name C or name O or name CB )) or resid 308 through 320 or (resid 321 and (n \ ame N or name CA or name C or name O or name CB )) or resid 322 through 323 or ( \ resid 324 and (name N or name CA or name C or name O or name CB )) or resid 325 \ through 326 or (resid 327 through 328 and (name N or name CA or name C or name O \ or name CB )) or resid 329 or (resid 330 and (name N or name CA or name C or na \ me O or name CB )) or resid 331 through 337 or (resid 338 and (name N or name CA \ or name C or name O or name CB )))) selection = (chain 'H' and (resid 7 through 18 or (resid 19 and (name N or name CA or name C \ or name O or name CB )) or resid 20 through 32 or (resid 33 and (name N or name \ CA or name C or name O or name CB )) or resid 34 through 44 or (resid 45 and (n \ ame N or name CA or name C or name O or name CB )) or resid 46 through 48 or (re \ sid 77 and (name N or name CA or name C or name O or name CB )) or resid 78 thro \ ugh 79 or (resid 80 and (name N or name CA or name C or name O or name CB )) or \ resid 81 through 83 or (resid 84 and (name N or name CA or name C or name O or n \ ame CB )) or resid 85 through 108 or (resid 109 through 110 and (name N or name \ CA or name C or name O or name CB )) or resid 111 through 130 or (resid 131 thro \ ugh 133 and (name N or name CA or name C or name O or name CB )) or resid 134 th \ rough 135 or (resid 136 and (name N or name CA or name C or name O or name CB )) \ or resid 137 through 139 or (resid 140 and (name N or name CA or name C or name \ O or name CB )) or resid 141 through 149 or (resid 150 and (name N or name CA o \ r name C or name O or name CB )) or resid 151 through 155 or (resid 156 through \ 157 and (name N or name CA or name C or name O or name CB )) or resid 158 or (re \ sid 159 and (name N or name CA or name C or name O or name CB )) or resid 160 or \ (resid 161 through 162 and (name N or name CA or name C or name O or name CB )) \ or resid 163 through 168 or (resid 169 and (name N or name CA or name C or name \ O or name CB )) or resid 170 through 183 or (resid 184 and (name N or name CA o \ r name C or name O or name CB )) or resid 185 or (resid 186 and (name N or name \ CA or name C or name O or name CB )) or resid 187 through 209 or (resid 210 and \ (name N or name CA or name C or name O or name CB )) or resid 211 or (resid 212 \ and (name N or name CA or name C or name O or name CB )) or resid 213 through 21 \ 7 or (resid 218 and (name N or name CA or name C or name O or name CB )) or resi \ d 219 through 228 or (resid 229 and (name N or name CA or name C or name O or na \ me CB )) or resid 230 or (resid 231 and (name N or name CA or name C or name O o \ r name CB )) or resid 244 through 245 or (resid 246 and (name N or name CA or na \ me C or name O or name CB )) or resid 247 through 249 or (resid 250 and (name N \ or name CA or name C or name O or name CB )) or resid 251 through 270 or (resid \ 271 and (name N or name CA or name C or name O or name CB )) or resid 272 throug \ h 276 or (resid 277 and (name N or name CA or name C or name O or name CB )) or \ resid 278 through 282 or (resid 283 and (name N or name CA or name C or name O o \ r name CB )) or resid 284 through 290 or (resid 291 and (name N or name CA or na \ me C or name O or name CB )) or resid 292 through 295 or (resid 296 through 297 \ and (name N or name CA or name C or name O or name CB )) or resid 298 or (resid \ 299 and (name N or name CA or name 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and (name N or name CA or name C \ or name O or name CB )) or resid 81 through 83 or (resid 84 and (name N or name \ CA or name C or name O or name CB )) or resid 85 through 97 or (resid 98 and (n \ ame N or name CA or name C or name O or name CB )) or resid 99 through 113 or (r \ esid 114 through 115 and (name N or name CA or name C or name O or name CB )) or \ resid 116 or (resid 117 through 118 and (name N or name CA or name C or name O \ or name CB )) or resid 119 through 130 or (resid 131 through 133 and (name N or \ name CA or name C or name O or name CB )) or resid 134 through 135 or (resid 136 \ and (name N or name CA or name C or name O or name CB )) or resid 137 through 1 \ 39 or (resid 140 and (name N or name CA or name C or name O or name CB )) or res \ id 141 through 149 or (resid 150 and (name N or name CA or name C or name O or n \ ame CB )) or resid 151 through 155 or (resid 156 through 157 and (name N or name \ CA or name C or name O or name CB )) or resid 158 or (resid 159 and (name N or \ name CA or name C or name O or name CB )) or resid 160 or (resid 161 through 162 \ and (name N or name CA or name C or name O or name CB )) or resid 163 or (resid \ 164 and (name N or name CA or name C or name O or name CB )) or resid 165 throu \ gh 168 or (resid 169 and (name N or name CA or name C or name O or name CB )) or \ resid 170 through 185 or (resid 186 and (name N or name CA or name C or name O \ or name CB )) or resid 187 through 207 or (resid 208 and (name N or name CA or n \ ame C or name O or name CB )) or resid 209 or (resid 210 and (name N or name CA \ or name C or name O or name CB )) or resid 211 through 217 or (resid 218 and (na \ me N or name CA or name C or name O or name CB )) or resid 219 through 228 or (r \ esid 229 and (name N or name CA or name C or name O or name CB )) or resid 230 o \ r (resid 231 and (name N or name CA or name C or name O or name CB )) or resid 2 \ 44 through 245 or (resid 246 and (name N or name CA or name C or name O or name \ CB )) or resid 247 through 249 or (resid 250 and (name N or name CA or name C or \ name O or name CB )) or resid 251 through 270 or (resid 271 and (name N or name \ CA or name C or name O or name CB )) or resid 272 through 276 or (resid 277 and \ (name N or name CA or name C or name O or name CB )) or resid 278 through 282 o \ r (resid 283 and (name N or name CA or name C or name O or name CB )) or resid 2 \ 84 or (resid 285 and (name N or name CA or name C or name O or name CB )) or res \ id 286 through 290 or (resid 291 and (name N or name CA or name C or name O or n \ ame CB )) or resid 292 through 295 or (resid 296 through 297 and (name N or name \ CA or name C or name O or name CB )) or resid 298 or (resid 299 and (name N or \ name CA or name C or name O or name CB )) or resid 300 through 301 or (resid 302 \ through 303 and (name N or name CA or name C or name O or name CB )) or resid 3 \ 04 through 306 or (resid 307 and (name N or name CA or name C or name O or name \ CB )) or resid 308 through 313 or (resid 314 and (name N or name CA or name C or \ name O or name CB )) or resid 315 through 320 or (resid 321 and (name N or name \ CA or name C or name O or name CB )) or resid 322 through 323 or (resid 324 and \ (name N or name CA or name C or name O or name CB )) or resid 325 through 329 o \ r (resid 330 and (name N or name CA or name C or name O or name CB )) or resid 3 \ 31 through 337 or (resid 338 and (name N or name CA or name C or name O or name \ CB )))) } ncs_group { reference = (chain 'I' and (resid 1 through 174 or resid 176 through 177 or (resid 178 and ( \ name N or name CA or name C or name O or name CB )) or resid 179 through 187)) selection = (chain 'S' and (resid 1 through 174 or resid 176 through 187)) } ncs_group { reference = chain 'J' selection = chain 'T' } ncs_group { reference = chain 'K' selection = chain 'Y' } ncs_group { reference = chain 'U' selection = chain 'V' } ncs_group { reference = chain 'W' selection = chain 'Z' } 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=0.37 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: 0.820 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.030 Extract box with map and model: 1.330 Check model and map are aligned: 0.260 Set scattering table: 0.340 Process input model: 87.100 Find NCS groups from input model: 1.970 Set up NCS constraints: 0.230 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.380 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 94.470 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8408 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 : 0.007 0.078 49575 Z= 0.465 Angle : 0.908 16.939 67829 Z= 0.503 Chirality : 0.052 0.558 7435 Planarity : 0.006 0.077 8566 Dihedral : 18.663 179.305 18664 Min Nonbonded Distance : 2.152 Molprobity Statistics. All-atom Clashscore : 6.70 Ramachandran Plot: Outliers : 0.02 % Allowed : 6.82 % Favored : 93.16 % Rotamer: Outliers : 5.96 % Allowed : 17.72 % Favored : 76.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.68 % 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: -3.43 (0.09), residues: 6156 helix: -2.15 (0.08), residues: 1945 sheet: -1.33 (0.15), residues: 1070 loop : -2.74 (0.09), residues: 3141 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP F 174 HIS 0.015 0.002 HIS I 29 PHE 0.021 0.002 PHE S 143 TYR 0.020 0.002 TYR E 285 ARG 0.016 0.001 ARG B 271 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12312 Ramachandran restraints generated. 6156 Oldfield, 0 Emsley, 6156 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12312 Ramachandran restraints generated. 6156 Oldfield, 0 Emsley, 6156 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 534 residues out of total 5025 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 257 poor density : 277 time to evaluate : 3.965 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 79 LYS cc_start: 0.8759 (OUTLIER) cc_final: 0.7914 (ttmm) REVERT: C 127 ASN cc_start: 0.8582 (m110) cc_final: 0.8172 (p0) REVERT: C 293 LYS cc_start: 0.9254 (ttmt) cc_final: 0.8955 (ttpp) REVERT: D 241 GLN cc_start: 0.8520 (mp10) cc_final: 0.8053 (mp10) REVERT: I 12 ASP cc_start: 0.7061 (t0) cc_final: 0.6765 (t0) REVERT: L 171 LYS cc_start: 0.8969 (tmtt) cc_final: 0.8767 (tptt) REVERT: L 247 TRP cc_start: 0.8124 (m100) cc_final: 0.7758 (m-10) REVERT: L 321 PHE cc_start: 0.7266 (p90) cc_final: 0.7006 (t80) REVERT: M 301 LYS cc_start: 0.9529 (mppt) cc_final: 0.9195 (mmmt) REVERT: N 241 GLN cc_start: 0.7566 (mm-40) cc_final: 0.7342 (mm110) REVERT: P 185 ASP cc_start: 0.8655 (OUTLIER) cc_final: 0.8332 (p0) REVERT: R 195 LEU cc_start: 0.9144 (mt) cc_final: 0.8916 (mt) REVERT: S 173 PHE cc_start: 0.6562 (m-80) cc_final: 0.6132 (m-10) REVERT: V 155 ASP cc_start: 0.8842 (OUTLIER) cc_final: 0.7164 (t0) REVERT: V 187 LEU cc_start: 0.9525 (OUTLIER) cc_final: 0.9131 (mp) REVERT: A 173 SER cc_start: 0.4346 (OUTLIER) cc_final: 0.4052 (t) REVERT: A 182 LEU cc_start: 0.7303 (OUTLIER) cc_final: 0.7040 (mm) REVERT: A 234 GLU cc_start: 0.8844 (tp30) cc_final: 0.7945 (tm-30) REVERT: A 242 LYS cc_start: 0.7970 (mmmm) cc_final: 0.7750 (mmmm) REVERT: A 251 ILE cc_start: 0.7845 (mm) cc_final: 0.7164 (mm) REVERT: A 261 GLU cc_start: 0.8100 (mt-10) cc_final: 0.7876 (mm-30) REVERT: X 173 SER cc_start: 0.5781 (OUTLIER) cc_final: 0.5264 (p) REVERT: X 182 LEU cc_start: 0.7932 (OUTLIER) cc_final: 0.7647 (mp) REVERT: X 210 ARG cc_start: 0.8539 (mtm-85) cc_final: 0.8159 (mtm180) REVERT: X 213 ASP cc_start: 0.8399 (OUTLIER) cc_final: 0.8144 (p0) REVERT: X 216 LYS cc_start: 0.9381 (mptt) cc_final: 0.9148 (mmtp) REVERT: X 222 ARG cc_start: 0.6847 (tpp-160) cc_final: 0.6367 (mmm160) REVERT: X 230 HIS cc_start: 0.8461 (t-90) cc_final: 0.8101 (t-90) REVERT: X 242 LYS cc_start: 0.8967 (mmmm) cc_final: 0.8743 (mmmm) outliers start: 257 outliers final: 135 residues processed: 517 average time/residue: 0.4641 time to fit residues: 401.0579 Evaluate side-chains 338 residues out of total 5025 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 144 poor density : 194 time to evaluate : 3.924 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 4 THR Chi-restraints excluded: chain B residue 15 LEU Chi-restraints excluded: chain B residue 59 VAL Chi-restraints excluded: chain B residue 79 LYS Chi-restraints excluded: chain B residue 300 ASP Chi-restraints excluded: chain B residue 322 VAL Chi-restraints excluded: chain C residue 133 GLU Chi-restraints excluded: chain C residue 165 ILE Chi-restraints excluded: chain C residue 206 SER Chi-restraints excluded: chain C residue 225 VAL Chi-restraints excluded: chain C residue 282 VAL Chi-restraints excluded: chain C residue 288 VAL Chi-restraints excluded: chain C residue 326 VAL Chi-restraints excluded: chain D residue 87 ASP Chi-restraints excluded: chain D residue 99 VAL Chi-restraints excluded: chain D residue 105 THR Chi-restraints excluded: chain D residue 251 ASP Chi-restraints excluded: chain D residue 282 VAL Chi-restraints excluded: chain D residue 299 LYS Chi-restraints excluded: chain E residue 24 LEU Chi-restraints excluded: chain E residue 79 VAL Chi-restraints excluded: chain E residue 99 VAL Chi-restraints excluded: chain E residue 158 VAL Chi-restraints excluded: chain E residue 160 VAL Chi-restraints excluded: chain E residue 165 ILE Chi-restraints excluded: chain E residue 201 SER Chi-restraints excluded: chain E residue 245 THR Chi-restraints excluded: chain E residue 251 ASP Chi-restraints excluded: chain E residue 285 TYR Chi-restraints excluded: chain F residue 44 VAL Chi-restraints excluded: chain F residue 59 THR Chi-restraints excluded: chain F residue 158 VAL Chi-restraints excluded: chain F residue 208 HIS Chi-restraints excluded: chain F residue 237 ASP Chi-restraints excluded: chain F residue 243 SER Chi-restraints excluded: chain F residue 282 VAL Chi-restraints excluded: chain F residue 290 SER Chi-restraints excluded: chain F residue 331 ILE Chi-restraints excluded: chain G residue 24 LEU Chi-restraints excluded: chain G residue 42 VAL Chi-restraints excluded: chain G residue 105 THR Chi-restraints excluded: chain G residue 140 HIS Chi-restraints excluded: chain G residue 158 VAL Chi-restraints excluded: chain G residue 160 VAL Chi-restraints excluded: chain G residue 208 HIS Chi-restraints excluded: chain G residue 213 VAL Chi-restraints excluded: chain G residue 245 THR Chi-restraints excluded: chain G residue 251 ASP Chi-restraints excluded: chain G residue 285 TYR Chi-restraints excluded: chain G residue 290 SER Chi-restraints excluded: chain H residue 34 ASP Chi-restraints excluded: chain H residue 105 THR Chi-restraints excluded: chain H residue 170 VAL Chi-restraints excluded: chain H residue 189 ASP Chi-restraints excluded: chain H residue 231 LEU Chi-restraints excluded: chain H residue 245 THR Chi-restraints excluded: chain H residue 251 ASP Chi-restraints excluded: chain L residue 4 THR Chi-restraints excluded: chain L residue 17 ILE Chi-restraints excluded: chain L residue 25 SER Chi-restraints excluded: chain L residue 143 SER Chi-restraints excluded: chain L residue 277 LEU Chi-restraints excluded: chain L residue 280 VAL Chi-restraints excluded: chain M residue 10 SER Chi-restraints excluded: chain M residue 21 SER Chi-restraints excluded: chain M residue 81 VAL Chi-restraints excluded: chain M residue 93 VAL Chi-restraints excluded: chain M residue 225 VAL Chi-restraints excluded: chain M residue 282 VAL Chi-restraints excluded: chain M residue 288 VAL Chi-restraints excluded: chain N residue 21 SER Chi-restraints excluded: chain N residue 81 VAL Chi-restraints excluded: chain N residue 232 ILE Chi-restraints excluded: chain N residue 251 ASP Chi-restraints excluded: chain N residue 264 LEU Chi-restraints excluded: chain N residue 266 THR Chi-restraints excluded: chain N residue 315 ASP Chi-restraints excluded: chain N residue 320 VAL Chi-restraints excluded: chain O residue 21 SER Chi-restraints excluded: chain O residue 49 VAL Chi-restraints excluded: chain O residue 78 THR Chi-restraints excluded: chain O residue 158 VAL Chi-restraints excluded: chain O residue 160 VAL Chi-restraints excluded: chain O residue 181 ILE Chi-restraints excluded: chain O residue 201 SER Chi-restraints excluded: chain O residue 251 ASP Chi-restraints excluded: chain O residue 285 TYR Chi-restraints excluded: chain P residue 59 THR Chi-restraints excluded: chain P residue 158 VAL Chi-restraints excluded: chain P residue 185 ASP Chi-restraints excluded: chain P residue 208 HIS Chi-restraints excluded: chain P residue 251 ASP Chi-restraints excluded: chain P residue 285 TYR Chi-restraints excluded: chain P residue 289 THR Chi-restraints excluded: chain P residue 314 ARG Chi-restraints excluded: chain Q residue 24 LEU Chi-restraints excluded: chain Q residue 53 ILE Chi-restraints excluded: chain Q residue 78 THR Chi-restraints excluded: chain Q residue 105 THR Chi-restraints excluded: chain Q residue 158 VAL Chi-restraints excluded: chain Q residue 173 THR Chi-restraints excluded: chain Q residue 221 ASP Chi-restraints excluded: chain Q residue 285 TYR Chi-restraints excluded: chain Q residue 315 ASP Chi-restraints excluded: chain R residue 52 THR Chi-restraints excluded: chain R residue 63 ASP Chi-restraints excluded: chain R residue 91 LEU Chi-restraints excluded: chain R residue 160 VAL Chi-restraints excluded: chain R residue 170 VAL Chi-restraints excluded: chain R residue 234 ASP Chi-restraints excluded: chain R residue 245 THR Chi-restraints excluded: chain R residue 285 TYR Chi-restraints excluded: chain R residue 290 SER Chi-restraints excluded: chain R residue 320 VAL Chi-restraints excluded: chain S residue 100 VAL Chi-restraints excluded: chain S residue 103 VAL Chi-restraints excluded: chain U residue 12 THR Chi-restraints excluded: chain U residue 61 GLU Chi-restraints excluded: chain U residue 73 ASP Chi-restraints excluded: chain U residue 113 THR Chi-restraints excluded: chain U residue 171 VAL Chi-restraints excluded: chain U residue 187 LEU Chi-restraints excluded: chain V residue 12 THR Chi-restraints excluded: chain V residue 61 GLU Chi-restraints excluded: chain V residue 113 THR Chi-restraints excluded: chain V residue 155 ASP Chi-restraints excluded: chain V residue 187 LEU Chi-restraints excluded: chain A residue 63 LEU Chi-restraints excluded: chain A residue 108 VAL Chi-restraints excluded: chain A residue 173 SER Chi-restraints excluded: chain A residue 182 LEU Chi-restraints excluded: chain A residue 197 SER Chi-restraints excluded: chain A residue 199 VAL Chi-restraints excluded: chain A residue 213 ASP Chi-restraints excluded: chain A residue 226 GLU Chi-restraints excluded: chain X residue 63 LEU Chi-restraints excluded: chain X residue 108 VAL Chi-restraints excluded: chain X residue 173 SER Chi-restraints excluded: chain X residue 182 LEU Chi-restraints excluded: chain X residue 197 SER Chi-restraints excluded: chain X residue 199 VAL Chi-restraints excluded: chain X residue 213 ASP Chi-restraints excluded: chain X residue 226 GLU Chi-restraints excluded: chain X residue 268 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 627 random chunks: chunk 529 optimal weight: 5.9990 chunk 475 optimal weight: 5.9990 chunk 263 optimal weight: 30.0000 chunk 162 optimal weight: 3.9990 chunk 320 optimal weight: 5.9990 chunk 253 optimal weight: 50.0000 chunk 491 optimal weight: 5.9990 chunk 190 optimal weight: 20.0000 chunk 298 optimal weight: 9.9990 chunk 365 optimal weight: 0.9980 chunk 569 optimal weight: 8.9990 overall best weight: 4.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 19 ASN B 42 HIS B 69 GLN B 82 ASN B 86 ASN ** B 131 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 194 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 110 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 120 GLN C 127 ASN ** D 110 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 110 ASN ** G 120 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 262 ASN ** I 3 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 30 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 99 GLN I 120 HIS L 19 ASN L 129 GLN ** L 131 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 156 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 195 GLN L 256 ASN M 144 ASN M 229 GLN N 151 ASN N 297 GLN O 110 ASN P 120 GLN Q 208 HIS Q 223 GLN Q 300 GLN R 75 ASN R 310 ASN R 329 ASN ** S 35 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** U 26 HIS V 26 HIS V 194 ASN A 249 GLN ** X 188 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** X 237 ASN X 249 GLN Total number of N/Q/H flips: 33 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8413 moved from start: 0.1433 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.073 49575 Z= 0.338 Angle : 0.632 12.352 67829 Z= 0.336 Chirality : 0.043 0.219 7435 Planarity : 0.005 0.058 8566 Dihedral : 16.252 179.699 9246 Min Nonbonded Distance : 2.496 Molprobity Statistics. All-atom Clashscore : 6.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.34 % Favored : 93.66 % Rotamer: Outliers : 4.01 % Allowed : 19.37 % Favored : 76.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.68 % 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: -1.87 (0.10), residues: 6156 helix: 0.17 (0.11), residues: 1974 sheet: -0.79 (0.15), residues: 1070 loop : -2.44 (0.10), residues: 3112 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP D 174 HIS 0.010 0.001 HIS M 208 PHE 0.018 0.002 PHE I 143 TYR 0.018 0.002 TYR E 285 ARG 0.010 0.000 ARG B 271 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12312 Ramachandran restraints generated. 6156 Oldfield, 0 Emsley, 6156 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12312 Ramachandran restraints generated. 6156 Oldfield, 0 Emsley, 6156 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 415 residues out of total 5025 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 173 poor density : 242 time to evaluate : 4.019 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 79 LYS cc_start: 0.8814 (OUTLIER) cc_final: 0.7783 (ttmm) REVERT: C 97 LEU cc_start: 0.8852 (OUTLIER) cc_final: 0.8485 (mm) REVERT: C 127 ASN cc_start: 0.8641 (m-40) cc_final: 0.8159 (p0) REVERT: C 128 GLU cc_start: 0.7618 (OUTLIER) cc_final: 0.7255 (tm-30) REVERT: C 293 LYS cc_start: 0.9228 (ttmt) cc_final: 0.8869 (ttpp) REVERT: C 309 ASP cc_start: 0.8695 (OUTLIER) cc_final: 0.8097 (p0) REVERT: D 241 GLN cc_start: 0.8669 (mp10) cc_final: 0.8336 (mt0) REVERT: E 285 TYR cc_start: 0.9339 (OUTLIER) cc_final: 0.9121 (m-80) REVERT: G 24 LEU cc_start: 0.9063 (OUTLIER) cc_final: 0.8718 (pp) REVERT: I 12 ASP cc_start: 0.6938 (t0) cc_final: 0.6667 (t0) REVERT: I 44 PHE cc_start: 0.8402 (m-80) cc_final: 0.8114 (m-10) REVERT: I 143 PHE cc_start: 0.5737 (p90) cc_final: 0.5521 (p90) REVERT: L 137 MET cc_start: 0.8210 (mtm) cc_final: 0.7626 (mtm) REVERT: M 283 GLU cc_start: 0.8834 (OUTLIER) cc_final: 0.8319 (mp0) REVERT: N 19 ASP cc_start: 0.8015 (m-30) cc_final: 0.7773 (p0) REVERT: N 129 GLN cc_start: 0.8433 (OUTLIER) cc_final: 0.7993 (mp10) REVERT: N 224 GLU cc_start: 0.7241 (mm-30) cc_final: 0.6971 (mm-30) REVERT: N 241 GLN cc_start: 0.7769 (mm-40) cc_final: 0.7216 (mm-40) REVERT: R 50 ARG cc_start: 0.8859 (OUTLIER) cc_final: 0.7964 (ttt180) REVERT: R 195 LEU cc_start: 0.9213 (mt) cc_final: 0.8936 (mt) REVERT: S 173 PHE cc_start: 0.6035 (m-80) cc_final: 0.5475 (m-80) REVERT: V 158 GLU cc_start: 0.8604 (mp0) cc_final: 0.7835 (mp0) REVERT: V 187 LEU cc_start: 0.9481 (OUTLIER) cc_final: 0.9100 (mp) REVERT: V 197 LYS cc_start: 0.9320 (OUTLIER) cc_final: 0.9108 (ttmm) REVERT: V 198 TYR cc_start: 0.9355 (m-80) cc_final: 0.8876 (m-80) REVERT: A 216 LYS cc_start: 0.8951 (mptt) cc_final: 0.8466 (mmtt) REVERT: X 78 ARG cc_start: 0.7233 (mtm-85) cc_final: 0.6911 (mtm-85) REVERT: X 173 SER cc_start: 0.6309 (OUTLIER) cc_final: 0.5837 (p) REVERT: X 176 LYS cc_start: 0.7169 (mmtt) cc_final: 0.5841 (mmtp) REVERT: X 200 HIS cc_start: 0.8869 (t70) cc_final: 0.8541 (t-90) REVERT: X 210 ARG cc_start: 0.8700 (mtm-85) cc_final: 0.8414 (mtm180) REVERT: X 216 LYS cc_start: 0.9303 (mptt) cc_final: 0.9019 (mmtp) REVERT: X 222 ARG cc_start: 0.6455 (tpp-160) cc_final: 0.6092 (mmm160) outliers start: 173 outliers final: 97 residues processed: 400 average time/residue: 0.4766 time to fit residues: 316.5319 Evaluate side-chains 307 residues out of total 5025 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 109 poor density : 198 time to evaluate : 3.892 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 28 THR Chi-restraints excluded: chain B residue 48 VAL Chi-restraints excluded: chain B residue 59 VAL Chi-restraints excluded: chain B residue 79 LYS Chi-restraints excluded: chain B residue 150 GLU Chi-restraints excluded: chain B residue 216 LEU Chi-restraints excluded: chain C residue 97 LEU Chi-restraints excluded: chain C residue 128 GLU Chi-restraints excluded: chain C residue 225 VAL Chi-restraints excluded: chain C residue 248 SER Chi-restraints excluded: chain C residue 282 VAL Chi-restraints excluded: chain C residue 288 VAL Chi-restraints excluded: chain C residue 308 LEU Chi-restraints excluded: chain C residue 309 ASP Chi-restraints excluded: chain D residue 11 VAL Chi-restraints excluded: chain D residue 99 VAL Chi-restraints excluded: chain D residue 105 THR Chi-restraints excluded: chain D residue 208 HIS Chi-restraints excluded: chain D residue 282 VAL Chi-restraints excluded: chain D residue 299 LYS Chi-restraints excluded: chain E residue 24 LEU Chi-restraints excluded: chain E residue 118 LEU Chi-restraints excluded: chain E residue 158 VAL Chi-restraints excluded: chain E residue 160 VAL Chi-restraints excluded: chain E residue 285 TYR Chi-restraints excluded: chain F residue 44 VAL Chi-restraints excluded: chain F residue 54 SER Chi-restraints excluded: chain F residue 59 THR Chi-restraints excluded: chain F residue 158 VAL Chi-restraints excluded: chain F residue 160 VAL Chi-restraints excluded: chain F residue 208 HIS Chi-restraints excluded: chain F residue 237 ASP Chi-restraints excluded: chain G residue 11 VAL Chi-restraints excluded: chain G residue 24 LEU Chi-restraints excluded: chain G residue 42 VAL Chi-restraints excluded: chain G residue 105 THR Chi-restraints excluded: chain G residue 158 VAL Chi-restraints excluded: chain G residue 160 VAL Chi-restraints excluded: chain G residue 213 VAL Chi-restraints excluded: chain G residue 245 THR Chi-restraints excluded: chain G residue 285 TYR Chi-restraints excluded: chain H residue 53 ILE Chi-restraints excluded: chain H residue 170 VAL Chi-restraints excluded: chain H residue 231 LEU Chi-restraints excluded: chain H residue 245 THR Chi-restraints excluded: chain H residue 308 LEU Chi-restraints excluded: chain I residue 134 THR Chi-restraints excluded: chain I residue 138 THR Chi-restraints excluded: chain L residue 17 ILE Chi-restraints excluded: chain L residue 28 THR Chi-restraints excluded: chain L residue 51 SER Chi-restraints excluded: chain M residue 11 VAL Chi-restraints excluded: chain M residue 93 VAL Chi-restraints excluded: chain M residue 225 VAL Chi-restraints excluded: chain M residue 246 LEU Chi-restraints excluded: chain M residue 282 VAL Chi-restraints excluded: chain M residue 283 GLU Chi-restraints excluded: chain M residue 288 VAL Chi-restraints excluded: chain N residue 129 GLN Chi-restraints excluded: chain N residue 264 LEU Chi-restraints excluded: chain O residue 78 THR Chi-restraints excluded: chain O residue 158 VAL Chi-restraints excluded: chain O residue 160 VAL Chi-restraints excluded: chain O residue 285 TYR Chi-restraints excluded: chain P residue 59 THR Chi-restraints excluded: chain P residue 105 THR Chi-restraints excluded: chain P residue 158 VAL Chi-restraints excluded: chain P residue 208 HIS Chi-restraints excluded: chain P residue 285 TYR Chi-restraints excluded: chain P residue 289 THR Chi-restraints excluded: chain Q residue 24 LEU Chi-restraints excluded: chain Q residue 100 LEU Chi-restraints excluded: chain Q residue 105 THR Chi-restraints excluded: chain Q residue 158 VAL Chi-restraints excluded: chain Q residue 170 VAL Chi-restraints excluded: chain Q residue 173 THR Chi-restraints excluded: chain R residue 50 ARG Chi-restraints excluded: chain R residue 52 THR Chi-restraints excluded: chain R residue 91 LEU Chi-restraints excluded: chain R residue 170 VAL Chi-restraints excluded: chain R residue 192 LEU Chi-restraints excluded: chain R residue 213 VAL Chi-restraints excluded: chain R residue 245 THR Chi-restraints excluded: chain R residue 264 LEU Chi-restraints excluded: chain R residue 285 TYR Chi-restraints excluded: chain S residue 100 VAL Chi-restraints excluded: chain S residue 103 VAL Chi-restraints excluded: chain U residue 167 LEU Chi-restraints excluded: chain U residue 177 THR Chi-restraints excluded: chain U residue 180 SER Chi-restraints excluded: chain U residue 187 LEU Chi-restraints excluded: chain U residue 190 MET Chi-restraints excluded: chain V residue 12 THR Chi-restraints excluded: chain V residue 113 THR Chi-restraints excluded: chain V residue 177 THR Chi-restraints excluded: chain V residue 180 SER Chi-restraints excluded: chain V residue 187 LEU Chi-restraints excluded: chain V residue 197 LYS Chi-restraints excluded: chain A residue 66 VAL Chi-restraints excluded: chain A residue 108 VAL Chi-restraints excluded: chain A residue 199 VAL Chi-restraints excluded: chain A residue 227 SER Chi-restraints excluded: chain A residue 256 SER Chi-restraints excluded: chain X residue 63 LEU Chi-restraints excluded: chain X residue 66 VAL Chi-restraints excluded: chain X residue 173 SER Chi-restraints excluded: chain X residue 227 SER Chi-restraints excluded: chain X residue 246 THR Chi-restraints excluded: chain X residue 268 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 627 random chunks: chunk 316 optimal weight: 6.9990 chunk 176 optimal weight: 10.0000 chunk 473 optimal weight: 20.0000 chunk 387 optimal weight: 6.9990 chunk 157 optimal weight: 3.9990 chunk 570 optimal weight: 40.0000 chunk 616 optimal weight: 30.0000 chunk 508 optimal weight: 0.6980 chunk 565 optimal weight: 0.3980 chunk 194 optimal weight: 7.9990 chunk 457 optimal weight: 9.9990 overall best weight: 3.8186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 131 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 194 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 110 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 110 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 110 ASN G 83 ASN ** G 120 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 3 HIS I 30 GLN L 131 GLN L 156 ASN P 291 GLN ** S 35 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** U 26 HIS V 206 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8409 moved from start: 0.1849 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.065 49575 Z= 0.281 Angle : 0.577 10.109 67829 Z= 0.303 Chirality : 0.041 0.251 7435 Planarity : 0.004 0.057 8566 Dihedral : 15.833 179.397 9118 Min Nonbonded Distance : 2.471 Molprobity Statistics. All-atom Clashscore : 6.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.39 % Favored : 93.61 % Rotamer: Outliers : 3.85 % Allowed : 20.34 % Favored : 75.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.68 % 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: -1.17 (0.10), residues: 6156 helix: 1.04 (0.12), residues: 1989 sheet: -0.41 (0.16), residues: 1043 loop : -2.22 (0.10), residues: 3124 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP D 174 HIS 0.009 0.001 HIS M 208 PHE 0.021 0.001 PHE S 158 TYR 0.017 0.001 TYR E 285 ARG 0.010 0.000 ARG B 271 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12312 Ramachandran restraints generated. 6156 Oldfield, 0 Emsley, 6156 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12312 Ramachandran restraints generated. 6156 Oldfield, 0 Emsley, 6156 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 397 residues out of total 5025 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 166 poor density : 231 time to evaluate : 3.937 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 79 LYS cc_start: 0.8970 (OUTLIER) cc_final: 0.8250 (mtmm) REVERT: B 322 VAL cc_start: 0.6434 (OUTLIER) cc_final: 0.6009 (p) REVERT: C 97 LEU cc_start: 0.8908 (OUTLIER) cc_final: 0.8560 (mm) REVERT: C 128 GLU cc_start: 0.7677 (OUTLIER) cc_final: 0.7296 (tm-30) REVERT: C 293 LYS cc_start: 0.9244 (ttmt) cc_final: 0.8879 (ttpp) REVERT: C 309 ASP cc_start: 0.8731 (OUTLIER) cc_final: 0.8103 (p0) REVERT: D 241 GLN cc_start: 0.8702 (mp10) cc_final: 0.8385 (mt0) REVERT: F 193 ASP cc_start: 0.8450 (m-30) cc_final: 0.8146 (m-30) REVERT: G 24 LEU cc_start: 0.9165 (OUTLIER) cc_final: 0.8823 (pp) REVERT: I 12 ASP cc_start: 0.7172 (t0) cc_final: 0.6930 (t0) REVERT: I 143 PHE cc_start: 0.5738 (p90) cc_final: 0.5512 (p90) REVERT: L 137 MET cc_start: 0.8492 (mtm) cc_final: 0.8183 (mtm) REVERT: L 144 ILE cc_start: 0.8723 (OUTLIER) cc_final: 0.8425 (mp) REVERT: L 311 LYS cc_start: 0.8060 (mmmt) cc_final: 0.7465 (pttm) REVERT: M 283 GLU cc_start: 0.8827 (OUTLIER) cc_final: 0.8342 (mp0) REVERT: N 129 GLN cc_start: 0.8329 (OUTLIER) cc_final: 0.7995 (mp10) REVERT: N 224 GLU cc_start: 0.7163 (mm-30) cc_final: 0.6910 (mm-30) REVERT: N 241 GLN cc_start: 0.7695 (mm-40) cc_final: 0.7194 (mm-40) REVERT: R 98 ARG cc_start: 0.7759 (OUTLIER) cc_final: 0.7538 (ptt180) REVERT: S 114 ARG cc_start: 0.6405 (OUTLIER) cc_final: 0.5965 (tmm160) REVERT: S 173 PHE cc_start: 0.6342 (m-80) cc_final: 0.5760 (m-80) REVERT: V 158 GLU cc_start: 0.8477 (mp0) cc_final: 0.8215 (mp0) REVERT: V 187 LEU cc_start: 0.9509 (OUTLIER) cc_final: 0.9162 (mp) REVERT: V 197 LYS cc_start: 0.9297 (OUTLIER) cc_final: 0.9004 (ttmm) REVERT: V 198 TYR cc_start: 0.9356 (m-80) cc_final: 0.8757 (m-80) REVERT: V 208 GLN cc_start: 0.8171 (mp10) cc_final: 0.7968 (pm20) REVERT: A 234 GLU cc_start: 0.8948 (tp30) cc_final: 0.7960 (tm-30) REVERT: X 78 ARG cc_start: 0.7208 (mtm-85) cc_final: 0.6885 (mtm-85) REVERT: X 176 LYS cc_start: 0.7243 (mmtt) cc_final: 0.5871 (mmtp) REVERT: X 200 HIS cc_start: 0.8925 (t70) cc_final: 0.8557 (t-90) REVERT: X 210 ARG cc_start: 0.8808 (mtm-85) cc_final: 0.8573 (mtm-85) REVERT: X 216 LYS cc_start: 0.9343 (mptt) cc_final: 0.9047 (mmtp) outliers start: 166 outliers final: 107 residues processed: 384 average time/residue: 0.4724 time to fit residues: 302.4657 Evaluate side-chains 306 residues out of total 5025 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 120 poor density : 186 time to evaluate : 3.981 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 23 ILE Chi-restraints excluded: chain B residue 28 THR Chi-restraints excluded: chain B residue 48 VAL Chi-restraints excluded: chain B residue 59 VAL Chi-restraints excluded: chain B residue 79 LYS Chi-restraints excluded: chain B residue 80 VAL Chi-restraints excluded: chain B residue 150 GLU Chi-restraints excluded: chain B residue 216 LEU Chi-restraints excluded: chain B residue 322 VAL Chi-restraints excluded: chain C residue 97 LEU Chi-restraints excluded: chain C residue 128 GLU Chi-restraints excluded: chain C residue 225 VAL Chi-restraints excluded: chain C residue 282 VAL Chi-restraints excluded: chain C residue 288 VAL Chi-restraints excluded: chain C residue 308 LEU Chi-restraints excluded: chain C residue 309 ASP Chi-restraints excluded: chain D residue 105 THR Chi-restraints excluded: chain D residue 208 HIS Chi-restraints excluded: chain D residue 243 SER Chi-restraints excluded: chain D residue 282 VAL Chi-restraints excluded: chain D residue 299 LYS Chi-restraints excluded: chain E residue 24 LEU Chi-restraints excluded: chain E residue 99 VAL Chi-restraints excluded: chain E residue 118 LEU Chi-restraints excluded: chain E residue 158 VAL Chi-restraints excluded: chain E residue 160 VAL Chi-restraints excluded: chain E residue 170 VAL Chi-restraints excluded: chain E residue 245 THR Chi-restraints excluded: chain E residue 285 TYR Chi-restraints excluded: chain F residue 24 LEU Chi-restraints excluded: chain F residue 44 VAL Chi-restraints excluded: chain F residue 54 SER Chi-restraints excluded: chain F residue 59 THR Chi-restraints excluded: chain F residue 158 VAL Chi-restraints excluded: chain F residue 160 VAL Chi-restraints excluded: chain F residue 208 HIS Chi-restraints excluded: chain F residue 237 ASP Chi-restraints excluded: chain F residue 282 VAL Chi-restraints excluded: chain G residue 11 VAL Chi-restraints excluded: chain G residue 24 LEU Chi-restraints excluded: chain G residue 42 VAL Chi-restraints excluded: chain G residue 158 VAL Chi-restraints excluded: chain G residue 160 VAL Chi-restraints excluded: chain G residue 208 HIS Chi-restraints excluded: chain G residue 213 VAL Chi-restraints excluded: chain G residue 285 TYR Chi-restraints excluded: chain H residue 53 ILE Chi-restraints excluded: chain H residue 170 VAL Chi-restraints excluded: chain H residue 172 ARG Chi-restraints excluded: chain H residue 231 LEU Chi-restraints excluded: chain H residue 245 THR Chi-restraints excluded: chain H residue 308 LEU Chi-restraints excluded: chain I residue 134 THR Chi-restraints excluded: chain I residue 145 THR Chi-restraints excluded: chain L residue 17 ILE Chi-restraints excluded: chain L residue 28 THR Chi-restraints excluded: chain L residue 41 VAL Chi-restraints excluded: chain L residue 51 SER Chi-restraints excluded: chain L residue 144 ILE Chi-restraints excluded: chain L residue 152 PHE Chi-restraints excluded: chain M residue 93 VAL Chi-restraints excluded: chain M residue 134 LEU Chi-restraints excluded: chain M residue 225 VAL Chi-restraints excluded: chain M residue 246 LEU Chi-restraints excluded: chain M residue 282 VAL Chi-restraints excluded: chain M residue 283 GLU Chi-restraints excluded: chain M residue 285 TYR Chi-restraints excluded: chain M residue 288 VAL Chi-restraints excluded: chain N residue 129 GLN Chi-restraints excluded: chain N residue 179 LEU Chi-restraints excluded: chain O residue 78 THR Chi-restraints excluded: chain O residue 107 SER Chi-restraints excluded: chain O residue 158 VAL Chi-restraints excluded: chain O residue 160 VAL Chi-restraints excluded: chain O residue 201 SER Chi-restraints excluded: chain O residue 285 TYR Chi-restraints excluded: chain P residue 59 THR Chi-restraints excluded: chain P residue 105 THR Chi-restraints excluded: chain P residue 158 VAL Chi-restraints excluded: chain P residue 173 THR Chi-restraints excluded: chain P residue 208 HIS Chi-restraints excluded: chain P residue 232 ILE Chi-restraints excluded: chain P residue 285 TYR Chi-restraints excluded: chain Q residue 24 LEU Chi-restraints excluded: chain Q residue 43 THR Chi-restraints excluded: chain Q residue 105 THR Chi-restraints excluded: chain Q residue 158 VAL Chi-restraints excluded: chain R residue 52 THR Chi-restraints excluded: chain R residue 53 ILE Chi-restraints excluded: chain R residue 71 ILE Chi-restraints excluded: chain R residue 86 SER Chi-restraints excluded: chain R residue 91 LEU Chi-restraints excluded: chain R residue 98 ARG Chi-restraints excluded: chain R residue 170 VAL Chi-restraints excluded: chain R residue 192 LEU Chi-restraints excluded: chain R residue 245 THR Chi-restraints excluded: chain R residue 285 TYR Chi-restraints excluded: chain S residue 100 VAL Chi-restraints excluded: chain S residue 103 VAL Chi-restraints excluded: chain S residue 114 ARG Chi-restraints excluded: chain U residue 73 ASP Chi-restraints excluded: chain U residue 127 GLU Chi-restraints excluded: chain U residue 167 LEU Chi-restraints excluded: chain U residue 177 THR Chi-restraints excluded: chain U residue 180 SER Chi-restraints excluded: chain U residue 187 LEU Chi-restraints excluded: chain U residue 197 LYS Chi-restraints excluded: chain V residue 85 VAL Chi-restraints excluded: chain V residue 177 THR Chi-restraints excluded: chain V residue 180 SER Chi-restraints excluded: chain V residue 187 LEU Chi-restraints excluded: chain V residue 197 LYS Chi-restraints excluded: chain A residue 66 VAL Chi-restraints excluded: chain A residue 108 VAL Chi-restraints excluded: chain A residue 173 SER Chi-restraints excluded: chain A residue 227 SER Chi-restraints excluded: chain A residue 256 SER Chi-restraints excluded: chain X residue 63 LEU Chi-restraints excluded: chain X residue 66 VAL Chi-restraints excluded: chain X residue 227 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 627 random chunks: chunk 563 optimal weight: 0.3980 chunk 428 optimal weight: 3.9990 chunk 296 optimal weight: 9.9990 chunk 63 optimal weight: 9.9990 chunk 272 optimal weight: 6.9990 chunk 383 optimal weight: 0.0870 chunk 572 optimal weight: 20.0000 chunk 606 optimal weight: 8.9990 chunk 299 optimal weight: 9.9990 chunk 542 optimal weight: 10.0000 chunk 163 optimal weight: 10.0000 overall best weight: 4.0964 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 131 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 194 GLN B 306 HIS ** C 110 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 110 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 140 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 120 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 35 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** U 26 HIS U 206 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8415 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 : 0.005 0.066 49575 Z= 0.297 Angle : 0.574 10.430 67829 Z= 0.300 Chirality : 0.041 0.196 7435 Planarity : 0.004 0.055 8566 Dihedral : 15.681 179.630 9105 Min Nonbonded Distance : 2.507 Molprobity Statistics. All-atom Clashscore : 6.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.34 % Favored : 93.66 % Rotamer: Outliers : 4.55 % Allowed : 20.83 % Favored : 74.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.68 % 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: -0.86 (0.11), residues: 6156 helix: 1.40 (0.12), residues: 1988 sheet: -0.29 (0.16), residues: 1077 loop : -2.10 (0.10), residues: 3091 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP D 174 HIS 0.008 0.001 HIS M 208 PHE 0.029 0.001 PHE S 158 TYR 0.018 0.001 TYR E 285 ARG 0.013 0.000 ARG B 271 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12312 Ramachandran restraints generated. 6156 Oldfield, 0 Emsley, 6156 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12312 Ramachandran restraints generated. 6156 Oldfield, 0 Emsley, 6156 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 401 residues out of total 5025 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 196 poor density : 205 time to evaluate : 3.940 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 79 LYS cc_start: 0.8971 (OUTLIER) cc_final: 0.8101 (mtmm) REVERT: B 262 TYR cc_start: 0.7803 (m-10) cc_final: 0.7523 (m-10) REVERT: B 322 VAL cc_start: 0.6635 (OUTLIER) cc_final: 0.6260 (p) REVERT: C 97 LEU cc_start: 0.8937 (OUTLIER) cc_final: 0.8603 (mm) REVERT: C 128 GLU cc_start: 0.7671 (OUTLIER) cc_final: 0.7293 (tm-30) REVERT: C 293 LYS cc_start: 0.9258 (OUTLIER) cc_final: 0.8876 (ttpp) REVERT: C 309 ASP cc_start: 0.8720 (OUTLIER) cc_final: 0.8092 (p0) REVERT: C 330 LEU cc_start: 0.8793 (OUTLIER) cc_final: 0.8477 (mp) REVERT: D 241 GLN cc_start: 0.8721 (mp10) cc_final: 0.8421 (mt0) REVERT: F 193 ASP cc_start: 0.8485 (m-30) cc_final: 0.8185 (m-30) REVERT: G 24 LEU cc_start: 0.9200 (OUTLIER) cc_final: 0.8832 (pp) REVERT: I 12 ASP cc_start: 0.7019 (t0) cc_final: 0.6777 (t0) REVERT: I 143 PHE cc_start: 0.5607 (p90) cc_final: 0.5214 (p90) REVERT: M 283 GLU cc_start: 0.8804 (OUTLIER) cc_final: 0.8355 (mp0) REVERT: N 129 GLN cc_start: 0.8286 (OUTLIER) cc_final: 0.7816 (mp10) REVERT: N 224 GLU cc_start: 0.7181 (mm-30) cc_final: 0.6969 (mm-30) REVERT: N 241 GLN cc_start: 0.7560 (mm-40) cc_final: 0.7020 (mm-40) REVERT: R 50 ARG cc_start: 0.8901 (OUTLIER) cc_final: 0.7993 (ttt-90) REVERT: R 98 ARG cc_start: 0.7739 (OUTLIER) cc_final: 0.7539 (ptt180) REVERT: S 114 ARG cc_start: 0.6245 (OUTLIER) cc_final: 0.5765 (tmm160) REVERT: S 173 PHE cc_start: 0.6483 (m-80) cc_final: 0.5875 (m-80) REVERT: V 158 GLU cc_start: 0.8433 (mp0) cc_final: 0.8129 (mp0) REVERT: V 197 LYS cc_start: 0.9306 (OUTLIER) cc_final: 0.9011 (ttmm) REVERT: A 216 LYS cc_start: 0.9166 (mptt) cc_final: 0.8697 (mmtt) REVERT: A 234 GLU cc_start: 0.8997 (tp30) cc_final: 0.8511 (tp30) REVERT: X 78 ARG cc_start: 0.7270 (mtm-85) cc_final: 0.6895 (mtm-85) REVERT: X 176 LYS cc_start: 0.7154 (mmtt) cc_final: 0.5772 (mmtp) REVERT: X 200 HIS cc_start: 0.8939 (t70) cc_final: 0.8592 (t-90) REVERT: X 210 ARG cc_start: 0.8891 (mtm-85) cc_final: 0.8541 (mmm-85) REVERT: X 211 PHE cc_start: 0.9041 (m-80) cc_final: 0.8837 (m-80) REVERT: X 216 LYS cc_start: 0.9372 (mptt) cc_final: 0.9062 (mmtp) REVERT: X 222 ARG cc_start: 0.6440 (tpp-160) cc_final: 0.6090 (mmm160) REVERT: X 242 LYS cc_start: 0.8713 (mmmm) cc_final: 0.8435 (mmmm) outliers start: 196 outliers final: 133 residues processed: 383 average time/residue: 0.4830 time to fit residues: 305.4395 Evaluate side-chains 338 residues out of total 5025 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 147 poor density : 191 time to evaluate : 3.880 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 23 ILE Chi-restraints excluded: chain B residue 28 THR Chi-restraints excluded: chain B residue 48 VAL Chi-restraints excluded: chain B residue 59 VAL Chi-restraints excluded: chain B residue 79 LYS Chi-restraints excluded: chain B residue 80 VAL Chi-restraints excluded: chain B residue 150 GLU Chi-restraints excluded: chain B residue 216 LEU Chi-restraints excluded: chain B residue 313 LEU Chi-restraints excluded: chain B residue 322 VAL Chi-restraints excluded: chain C residue 97 LEU Chi-restraints excluded: chain C residue 128 GLU Chi-restraints excluded: chain C residue 225 VAL Chi-restraints excluded: chain C residue 282 VAL Chi-restraints excluded: chain C residue 288 VAL Chi-restraints excluded: chain C residue 293 LYS Chi-restraints excluded: chain C residue 308 LEU Chi-restraints excluded: chain C residue 309 ASP Chi-restraints excluded: chain C residue 326 VAL Chi-restraints excluded: chain C residue 330 LEU Chi-restraints excluded: chain D residue 11 VAL Chi-restraints excluded: chain D residue 77 GLN Chi-restraints excluded: chain D residue 97 LEU Chi-restraints excluded: chain D residue 105 THR Chi-restraints excluded: chain D residue 208 HIS Chi-restraints excluded: chain D residue 243 SER Chi-restraints excluded: chain D residue 282 VAL Chi-restraints excluded: chain D residue 289 THR Chi-restraints excluded: chain D residue 299 LYS Chi-restraints excluded: chain E residue 24 LEU Chi-restraints excluded: chain E residue 100 LEU Chi-restraints excluded: chain E residue 118 LEU Chi-restraints excluded: chain E residue 158 VAL Chi-restraints excluded: chain E residue 160 VAL Chi-restraints excluded: chain E residue 170 VAL Chi-restraints excluded: chain E residue 285 TYR Chi-restraints excluded: chain F residue 24 LEU Chi-restraints excluded: chain F residue 44 VAL Chi-restraints excluded: chain F residue 54 SER Chi-restraints excluded: chain F residue 59 THR Chi-restraints excluded: chain F residue 158 VAL Chi-restraints excluded: chain F residue 160 VAL Chi-restraints excluded: chain F residue 173 THR Chi-restraints excluded: chain F residue 208 HIS Chi-restraints excluded: chain F residue 237 ASP Chi-restraints excluded: chain F residue 285 TYR Chi-restraints excluded: chain G residue 11 VAL Chi-restraints excluded: chain G residue 24 LEU Chi-restraints excluded: chain G residue 42 VAL Chi-restraints excluded: chain G residue 105 THR Chi-restraints excluded: chain G residue 158 VAL Chi-restraints excluded: chain G residue 160 VAL Chi-restraints excluded: chain G residue 208 HIS Chi-restraints excluded: chain G residue 213 VAL Chi-restraints excluded: chain G residue 245 THR Chi-restraints excluded: chain G residue 285 TYR Chi-restraints excluded: chain H residue 53 ILE Chi-restraints excluded: chain H residue 170 VAL Chi-restraints excluded: chain H residue 231 LEU Chi-restraints excluded: chain H residue 245 THR Chi-restraints excluded: chain H residue 308 LEU Chi-restraints excluded: chain I residue 35 GLN Chi-restraints excluded: chain I residue 134 THR Chi-restraints excluded: chain I residue 138 THR Chi-restraints excluded: chain L residue 17 ILE Chi-restraints excluded: chain L residue 28 THR Chi-restraints excluded: chain L residue 41 VAL Chi-restraints excluded: chain L residue 51 SER Chi-restraints excluded: chain L residue 94 THR Chi-restraints excluded: chain L residue 152 PHE Chi-restraints excluded: chain L residue 210 LEU Chi-restraints excluded: chain L residue 280 VAL Chi-restraints excluded: chain M residue 10 SER Chi-restraints excluded: chain M residue 25 MET Chi-restraints excluded: chain M residue 93 VAL Chi-restraints excluded: chain M residue 225 VAL Chi-restraints excluded: chain M residue 246 LEU Chi-restraints excluded: chain M residue 264 LEU Chi-restraints excluded: chain M residue 282 VAL Chi-restraints excluded: chain M residue 283 GLU Chi-restraints excluded: chain M residue 285 TYR Chi-restraints excluded: chain M residue 288 VAL Chi-restraints excluded: chain N residue 97 LEU Chi-restraints excluded: chain N residue 129 GLN Chi-restraints excluded: chain N residue 179 LEU Chi-restraints excluded: chain N residue 264 LEU Chi-restraints excluded: chain N residue 331 ILE Chi-restraints excluded: chain O residue 78 THR Chi-restraints excluded: chain O residue 107 SER Chi-restraints excluded: chain O residue 158 VAL Chi-restraints excluded: chain O residue 160 VAL Chi-restraints excluded: chain O residue 201 SER Chi-restraints excluded: chain O residue 285 TYR Chi-restraints excluded: chain P residue 24 LEU Chi-restraints excluded: chain P residue 25 MET Chi-restraints excluded: chain P residue 59 THR Chi-restraints excluded: chain P residue 105 THR Chi-restraints excluded: chain P residue 158 VAL Chi-restraints excluded: chain P residue 173 THR Chi-restraints excluded: chain P residue 199 ILE Chi-restraints excluded: chain P residue 208 HIS Chi-restraints excluded: chain P residue 285 TYR Chi-restraints excluded: chain Q residue 24 LEU Chi-restraints excluded: chain Q residue 43 THR Chi-restraints excluded: chain Q residue 53 ILE Chi-restraints excluded: chain Q residue 100 LEU Chi-restraints excluded: chain Q residue 105 THR Chi-restraints excluded: chain Q residue 158 VAL Chi-restraints excluded: chain Q residue 170 VAL Chi-restraints excluded: chain Q residue 173 THR Chi-restraints excluded: chain Q residue 208 HIS Chi-restraints excluded: chain R residue 50 ARG Chi-restraints excluded: chain R residue 52 THR Chi-restraints excluded: chain R residue 71 ILE Chi-restraints excluded: chain R residue 86 SER Chi-restraints excluded: chain R residue 91 LEU Chi-restraints excluded: chain R residue 98 ARG Chi-restraints excluded: chain R residue 170 VAL Chi-restraints excluded: chain R residue 192 LEU Chi-restraints excluded: chain R residue 203 LEU Chi-restraints excluded: chain R residue 213 VAL Chi-restraints excluded: chain R residue 245 THR Chi-restraints excluded: chain R residue 285 TYR Chi-restraints excluded: chain S residue 100 VAL Chi-restraints excluded: chain S residue 114 ARG Chi-restraints excluded: chain U residue 73 ASP Chi-restraints excluded: chain U residue 127 GLU Chi-restraints excluded: chain U residue 167 LEU Chi-restraints excluded: chain U residue 177 THR Chi-restraints excluded: chain U residue 180 SER Chi-restraints excluded: chain U residue 187 LEU Chi-restraints excluded: chain U residue 197 LYS Chi-restraints excluded: chain V residue 12 THR Chi-restraints excluded: chain V residue 63 VAL Chi-restraints excluded: chain V residue 113 THR Chi-restraints excluded: chain V residue 127 GLU Chi-restraints excluded: chain V residue 177 THR Chi-restraints excluded: chain V residue 180 SER Chi-restraints excluded: chain V residue 197 LYS Chi-restraints excluded: chain V residue 209 LYS Chi-restraints excluded: chain A residue 66 VAL Chi-restraints excluded: chain A residue 108 VAL Chi-restraints excluded: chain A residue 178 LEU Chi-restraints excluded: chain A residue 227 SER Chi-restraints excluded: chain A residue 256 SER Chi-restraints excluded: chain X residue 63 LEU Chi-restraints excluded: chain X residue 66 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 627 random chunks: chunk 504 optimal weight: 0.7980 chunk 344 optimal weight: 4.9990 chunk 8 optimal weight: 20.0000 chunk 451 optimal weight: 9.9990 chunk 250 optimal weight: 4.9990 chunk 517 optimal weight: 0.6980 chunk 418 optimal weight: 5.9990 chunk 0 optimal weight: 40.0000 chunk 309 optimal weight: 8.9990 chunk 543 optimal weight: 10.0000 chunk 152 optimal weight: 9.9990 overall best weight: 3.4986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 131 GLN ** C 110 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 110 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 140 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 120 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 61 HIS U 26 HIS ** A 241 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8408 moved from start: 0.2362 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.061 49575 Z= 0.259 Angle : 0.554 12.484 67829 Z= 0.288 Chirality : 0.041 0.185 7435 Planarity : 0.004 0.053 8566 Dihedral : 15.577 179.757 9102 Min Nonbonded Distance : 2.427 Molprobity Statistics. All-atom Clashscore : 6.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.27 % Favored : 93.73 % Rotamer: Outliers : 4.15 % Allowed : 21.97 % Favored : 73.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.68 % 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: -0.69 (0.11), residues: 6156 helix: 1.55 (0.12), residues: 2007 sheet: -0.15 (0.16), residues: 1061 loop : -2.04 (0.10), residues: 3088 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP H 174 HIS 0.007 0.001 HIS M 208 PHE 0.022 0.001 PHE S 158 TYR 0.018 0.001 TYR U 46 ARG 0.013 0.000 ARG B 271 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12312 Ramachandran restraints generated. 6156 Oldfield, 0 Emsley, 6156 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12312 Ramachandran restraints generated. 6156 Oldfield, 0 Emsley, 6156 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 391 residues out of total 5025 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 179 poor density : 212 time to evaluate : 3.960 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 79 LYS cc_start: 0.9020 (OUTLIER) cc_final: 0.8049 (mtmm) REVERT: B 322 VAL cc_start: 0.6720 (OUTLIER) cc_final: 0.6370 (p) REVERT: C 97 LEU cc_start: 0.8828 (OUTLIER) cc_final: 0.8536 (mm) REVERT: C 127 ASN cc_start: 0.8426 (m-40) cc_final: 0.8015 (p0) REVERT: C 293 LYS cc_start: 0.9259 (tmmt) cc_final: 0.9022 (ttpp) REVERT: C 309 ASP cc_start: 0.8720 (OUTLIER) cc_final: 0.8085 (p0) REVERT: C 330 LEU cc_start: 0.8776 (OUTLIER) cc_final: 0.8462 (mp) REVERT: D 241 GLN cc_start: 0.8728 (mp10) cc_final: 0.8387 (mt0) REVERT: H 50 ARG cc_start: 0.8949 (OUTLIER) cc_final: 0.7804 (ttm-80) REVERT: I 143 PHE cc_start: 0.5829 (p90) cc_final: 0.5411 (p90) REVERT: L 144 ILE cc_start: 0.8692 (OUTLIER) cc_final: 0.8394 (mp) REVERT: L 311 LYS cc_start: 0.8008 (mmmt) cc_final: 0.7372 (pttm) REVERT: M 283 GLU cc_start: 0.8788 (OUTLIER) cc_final: 0.8381 (mp0) REVERT: N 129 GLN cc_start: 0.8315 (OUTLIER) cc_final: 0.7807 (mp10) REVERT: N 224 GLU cc_start: 0.7167 (mm-30) cc_final: 0.6506 (mm-30) REVERT: N 231 LEU cc_start: 0.9451 (OUTLIER) cc_final: 0.9066 (tt) REVERT: N 241 GLN cc_start: 0.7577 (mm-40) cc_final: 0.7050 (mm-40) REVERT: R 50 ARG cc_start: 0.8869 (OUTLIER) cc_final: 0.7977 (ttt-90) REVERT: R 98 ARG cc_start: 0.7672 (OUTLIER) cc_final: 0.7467 (ptt180) REVERT: S 114 ARG cc_start: 0.6207 (OUTLIER) cc_final: 0.5732 (tmm160) REVERT: S 173 PHE cc_start: 0.6602 (m-80) cc_final: 0.6163 (m-80) REVERT: V 158 GLU cc_start: 0.8450 (mp0) cc_final: 0.8147 (mp0) REVERT: V 197 LYS cc_start: 0.9342 (OUTLIER) cc_final: 0.9060 (mtmm) REVERT: A 234 GLU cc_start: 0.8982 (tp30) cc_final: 0.8016 (tm-30) REVERT: X 78 ARG cc_start: 0.7325 (mtm-85) cc_final: 0.6942 (mtm-85) REVERT: X 176 LYS cc_start: 0.7116 (mmtt) cc_final: 0.5792 (mmtp) REVERT: X 210 ARG cc_start: 0.8918 (mtm-85) cc_final: 0.8697 (mmm-85) REVERT: X 216 LYS cc_start: 0.9386 (mptt) cc_final: 0.9057 (mmtp) outliers start: 179 outliers final: 130 residues processed: 375 average time/residue: 0.4789 time to fit residues: 297.7728 Evaluate side-chains 329 residues out of total 5025 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 144 poor density : 185 time to evaluate : 3.930 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 23 ILE Chi-restraints excluded: chain B residue 28 THR Chi-restraints excluded: chain B residue 48 VAL Chi-restraints excluded: chain B residue 59 VAL Chi-restraints excluded: chain B residue 79 LYS Chi-restraints excluded: chain B residue 80 VAL Chi-restraints excluded: chain B residue 150 GLU Chi-restraints excluded: chain B residue 216 LEU Chi-restraints excluded: chain B residue 259 SER Chi-restraints excluded: chain B residue 322 VAL Chi-restraints excluded: chain C residue 97 LEU Chi-restraints excluded: chain C residue 225 VAL Chi-restraints excluded: chain C residue 248 SER Chi-restraints excluded: chain C residue 282 VAL Chi-restraints excluded: chain C residue 288 VAL Chi-restraints excluded: chain C residue 309 ASP Chi-restraints excluded: chain C residue 326 VAL Chi-restraints excluded: chain C residue 330 LEU Chi-restraints excluded: chain D residue 11 VAL Chi-restraints excluded: chain D residue 77 GLN Chi-restraints excluded: chain D residue 78 THR Chi-restraints excluded: chain D residue 105 THR Chi-restraints excluded: chain D residue 208 HIS Chi-restraints excluded: chain D residue 243 SER Chi-restraints excluded: chain D residue 264 LEU Chi-restraints excluded: chain D residue 282 VAL Chi-restraints excluded: chain D residue 289 THR Chi-restraints excluded: chain D residue 299 LYS Chi-restraints excluded: chain E residue 24 LEU Chi-restraints excluded: chain E residue 99 VAL Chi-restraints excluded: chain E residue 100 LEU Chi-restraints excluded: chain E residue 118 LEU Chi-restraints excluded: chain E residue 158 VAL Chi-restraints excluded: chain E residue 160 VAL Chi-restraints excluded: chain E residue 170 VAL Chi-restraints excluded: chain E residue 245 THR Chi-restraints excluded: chain E residue 285 TYR Chi-restraints excluded: chain F residue 158 VAL Chi-restraints excluded: chain F residue 160 VAL Chi-restraints excluded: chain F residue 208 HIS Chi-restraints excluded: chain F residue 237 ASP Chi-restraints excluded: chain F residue 282 VAL Chi-restraints excluded: chain G residue 11 VAL Chi-restraints excluded: chain G residue 24 LEU Chi-restraints excluded: chain G residue 42 VAL Chi-restraints excluded: chain G residue 158 VAL Chi-restraints excluded: chain G residue 160 VAL Chi-restraints excluded: chain G residue 183 LEU Chi-restraints excluded: chain G residue 208 HIS Chi-restraints excluded: chain G residue 213 VAL Chi-restraints excluded: chain G residue 245 THR Chi-restraints excluded: chain G residue 285 TYR Chi-restraints excluded: chain H residue 50 ARG Chi-restraints excluded: chain H residue 53 ILE Chi-restraints excluded: chain H residue 170 VAL Chi-restraints excluded: chain H residue 231 LEU Chi-restraints excluded: chain H residue 245 THR Chi-restraints excluded: chain H residue 308 LEU Chi-restraints excluded: chain I residue 42 VAL Chi-restraints excluded: chain I residue 134 THR Chi-restraints excluded: chain I residue 138 THR Chi-restraints excluded: chain L residue 17 ILE Chi-restraints excluded: chain L residue 28 THR Chi-restraints excluded: chain L residue 41 VAL Chi-restraints excluded: chain L residue 51 SER Chi-restraints excluded: chain L residue 79 LYS Chi-restraints excluded: chain L residue 94 THR Chi-restraints excluded: chain L residue 98 VAL Chi-restraints excluded: chain L residue 137 MET Chi-restraints excluded: chain L residue 144 ILE Chi-restraints excluded: chain L residue 152 PHE Chi-restraints excluded: chain L residue 210 LEU Chi-restraints excluded: chain M residue 10 SER Chi-restraints excluded: chain M residue 11 VAL Chi-restraints excluded: chain M residue 25 MET Chi-restraints excluded: chain M residue 93 VAL Chi-restraints excluded: chain M residue 192 LEU Chi-restraints excluded: chain M residue 225 VAL Chi-restraints excluded: chain M residue 246 LEU Chi-restraints excluded: chain M residue 282 VAL Chi-restraints excluded: chain M residue 283 GLU Chi-restraints excluded: chain M residue 288 VAL Chi-restraints excluded: chain N residue 129 GLN Chi-restraints excluded: chain N residue 179 LEU Chi-restraints excluded: chain N residue 206 SER Chi-restraints excluded: chain N residue 231 LEU Chi-restraints excluded: chain N residue 264 LEU Chi-restraints excluded: chain N residue 331 ILE Chi-restraints excluded: chain O residue 78 THR Chi-restraints excluded: chain O residue 107 SER Chi-restraints excluded: chain O residue 158 VAL Chi-restraints excluded: chain O residue 160 VAL Chi-restraints excluded: chain O residue 201 SER Chi-restraints excluded: chain O residue 285 TYR Chi-restraints excluded: chain P residue 25 MET Chi-restraints excluded: chain P residue 59 THR Chi-restraints excluded: chain P residue 158 VAL Chi-restraints excluded: chain P residue 173 THR Chi-restraints excluded: chain P residue 192 LEU Chi-restraints excluded: chain P residue 208 HIS Chi-restraints excluded: chain P residue 232 ILE Chi-restraints excluded: chain P residue 285 TYR Chi-restraints excluded: chain Q residue 24 LEU Chi-restraints excluded: chain Q residue 25 MET Chi-restraints excluded: chain Q residue 43 THR Chi-restraints excluded: chain Q residue 105 THR Chi-restraints excluded: chain Q residue 158 VAL Chi-restraints excluded: chain Q residue 208 HIS Chi-restraints excluded: chain R residue 50 ARG Chi-restraints excluded: chain R residue 52 THR Chi-restraints excluded: chain R residue 71 ILE Chi-restraints excluded: chain R residue 86 SER Chi-restraints excluded: chain R residue 91 LEU Chi-restraints excluded: chain R residue 98 ARG Chi-restraints excluded: chain R residue 160 VAL Chi-restraints excluded: chain R residue 170 VAL Chi-restraints excluded: chain R residue 192 LEU Chi-restraints excluded: chain R residue 203 LEU Chi-restraints excluded: chain R residue 245 THR Chi-restraints excluded: chain R residue 285 TYR Chi-restraints excluded: chain S residue 100 VAL Chi-restraints excluded: chain S residue 114 ARG Chi-restraints excluded: chain U residue 46 TYR Chi-restraints excluded: chain U residue 73 ASP Chi-restraints excluded: chain U residue 127 GLU Chi-restraints excluded: chain U residue 167 LEU Chi-restraints excluded: chain U residue 177 THR Chi-restraints excluded: chain U residue 180 SER Chi-restraints excluded: chain U residue 197 LYS Chi-restraints excluded: chain V residue 63 VAL Chi-restraints excluded: chain V residue 85 VAL Chi-restraints excluded: chain V residue 113 THR Chi-restraints excluded: chain V residue 127 GLU Chi-restraints excluded: chain V residue 177 THR Chi-restraints excluded: chain V residue 180 SER Chi-restraints excluded: chain V residue 197 LYS Chi-restraints excluded: chain V residue 209 LYS Chi-restraints excluded: chain A residue 66 VAL Chi-restraints excluded: chain A residue 108 VAL Chi-restraints excluded: chain A residue 182 LEU Chi-restraints excluded: chain A residue 227 SER Chi-restraints excluded: chain A residue 256 SER Chi-restraints excluded: chain X residue 63 LEU Chi-restraints excluded: chain X residue 66 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 627 random chunks: chunk 203 optimal weight: 6.9990 chunk 545 optimal weight: 20.0000 chunk 119 optimal weight: 10.0000 chunk 355 optimal weight: 6.9990 chunk 149 optimal weight: 0.9980 chunk 606 optimal weight: 40.0000 chunk 503 optimal weight: 7.9990 chunk 280 optimal weight: 30.0000 chunk 50 optimal weight: 3.9990 chunk 200 optimal weight: 0.6980 chunk 318 optimal weight: 9.9990 overall best weight: 3.9386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 104 HIS ** C 110 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 110 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 140 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** U 26 HIS V 194 ASN A 64 GLN ** A 241 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8416 moved from start: 0.2539 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.062 49575 Z= 0.286 Angle : 0.563 13.296 67829 Z= 0.294 Chirality : 0.041 0.236 7435 Planarity : 0.004 0.050 8566 Dihedral : 15.510 179.952 9098 Min Nonbonded Distance : 2.380 Molprobity Statistics. All-atom Clashscore : 6.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.65 % Favored : 93.35 % Rotamer: Outliers : 4.64 % Allowed : 21.85 % Favored : 73.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.68 % 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: -0.60 (0.11), residues: 6156 helix: 1.65 (0.12), residues: 2000 sheet: -0.16 (0.16), residues: 1069 loop : -1.98 (0.11), residues: 3087 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP H 174 HIS 0.010 0.001 HIS C 208 PHE 0.016 0.001 PHE S 158 TYR 0.017 0.001 TYR E 285 ARG 0.013 0.000 ARG B 271 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12312 Ramachandran restraints generated. 6156 Oldfield, 0 Emsley, 6156 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12312 Ramachandran restraints generated. 6156 Oldfield, 0 Emsley, 6156 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 398 residues out of total 5025 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 200 poor density : 198 time to evaluate : 3.935 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 79 LYS cc_start: 0.9019 (OUTLIER) cc_final: 0.7987 (mtmm) REVERT: B 322 VAL cc_start: 0.6747 (OUTLIER) cc_final: 0.6416 (p) REVERT: C 97 LEU cc_start: 0.8922 (OUTLIER) cc_final: 0.8574 (mm) REVERT: C 128 GLU cc_start: 0.7664 (OUTLIER) cc_final: 0.7449 (tm-30) REVERT: C 293 LYS cc_start: 0.9239 (OUTLIER) cc_final: 0.8958 (ttpp) REVERT: C 309 ASP cc_start: 0.8699 (OUTLIER) cc_final: 0.8125 (p0) REVERT: C 330 LEU cc_start: 0.8770 (OUTLIER) cc_final: 0.8458 (mp) REVERT: D 241 GLN cc_start: 0.8696 (mp10) cc_final: 0.8401 (mt0) REVERT: H 50 ARG cc_start: 0.8968 (OUTLIER) cc_final: 0.7786 (ttm-80) REVERT: I 35 GLN cc_start: 0.2705 (OUTLIER) cc_final: 0.2313 (mp10) REVERT: I 117 MET cc_start: 0.5811 (mmp) cc_final: 0.5579 (ptt) REVERT: I 143 PHE cc_start: 0.5799 (p90) cc_final: 0.5311 (p90) REVERT: L 311 LYS cc_start: 0.8127 (mmmt) cc_final: 0.7484 (pttm) REVERT: M 283 GLU cc_start: 0.8722 (OUTLIER) cc_final: 0.8343 (mp0) REVERT: N 129 GLN cc_start: 0.8260 (OUTLIER) cc_final: 0.7748 (mp10) REVERT: N 224 GLU cc_start: 0.7138 (mm-30) cc_final: 0.6491 (mm-30) REVERT: N 231 LEU cc_start: 0.9497 (OUTLIER) cc_final: 0.9125 (tt) REVERT: N 241 GLN cc_start: 0.7537 (mm-40) cc_final: 0.7009 (mm-40) REVERT: O 136 ARG cc_start: 0.8905 (OUTLIER) cc_final: 0.8701 (ttp80) REVERT: R 50 ARG cc_start: 0.8884 (OUTLIER) cc_final: 0.7977 (ttt-90) REVERT: S 173 PHE cc_start: 0.6491 (m-80) cc_final: 0.6128 (m-80) REVERT: V 158 GLU cc_start: 0.8445 (mp0) cc_final: 0.8130 (mp0) REVERT: A 216 LYS cc_start: 0.8913 (mmtt) cc_final: 0.8567 (mmtt) REVERT: A 222 ARG cc_start: 0.5106 (mmp-170) cc_final: 0.4834 (mmp-170) REVERT: A 228 TRP cc_start: 0.6428 (OUTLIER) cc_final: 0.6041 (p90) REVERT: A 234 GLU cc_start: 0.8981 (tp30) cc_final: 0.8521 (tp30) REVERT: X 78 ARG cc_start: 0.7320 (mtm-85) cc_final: 0.6943 (mtm-85) REVERT: X 176 LYS cc_start: 0.7171 (mmtt) cc_final: 0.5862 (mmtp) REVERT: X 210 ARG cc_start: 0.8940 (mtm-85) cc_final: 0.8616 (mtm-85) REVERT: X 213 ASP cc_start: 0.8647 (OUTLIER) cc_final: 0.8435 (p0) REVERT: X 216 LYS cc_start: 0.9412 (mptt) cc_final: 0.9082 (mmtp) outliers start: 200 outliers final: 149 residues processed: 385 average time/residue: 0.4753 time to fit residues: 305.0412 Evaluate side-chains 356 residues out of total 5025 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 165 poor density : 191 time to evaluate : 3.962 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 23 ILE Chi-restraints excluded: chain B residue 28 THR Chi-restraints excluded: chain B residue 48 VAL Chi-restraints excluded: chain B residue 59 VAL Chi-restraints excluded: chain B residue 79 LYS Chi-restraints excluded: chain B residue 80 VAL Chi-restraints excluded: chain B residue 150 GLU Chi-restraints excluded: chain B residue 216 LEU Chi-restraints excluded: chain B residue 259 SER Chi-restraints excluded: chain B residue 322 VAL Chi-restraints excluded: chain C residue 36 SER Chi-restraints excluded: chain C residue 97 LEU Chi-restraints excluded: chain C residue 128 GLU Chi-restraints excluded: chain C residue 225 VAL Chi-restraints excluded: chain C residue 248 SER Chi-restraints excluded: chain C residue 282 VAL Chi-restraints excluded: chain C residue 288 VAL Chi-restraints excluded: chain C residue 293 LYS Chi-restraints excluded: chain C residue 308 LEU Chi-restraints excluded: chain C residue 309 ASP Chi-restraints excluded: chain C residue 326 VAL Chi-restraints excluded: chain C residue 330 LEU Chi-restraints excluded: chain D residue 11 VAL Chi-restraints excluded: chain D residue 77 GLN Chi-restraints excluded: chain D residue 97 LEU Chi-restraints excluded: chain D residue 99 VAL Chi-restraints excluded: chain D residue 105 THR Chi-restraints excluded: chain D residue 208 HIS Chi-restraints excluded: chain D residue 264 LEU Chi-restraints excluded: chain D residue 282 VAL Chi-restraints excluded: chain D residue 289 THR Chi-restraints excluded: chain D residue 299 LYS Chi-restraints excluded: chain E residue 24 LEU Chi-restraints excluded: chain E residue 99 VAL Chi-restraints excluded: chain E residue 100 LEU Chi-restraints excluded: chain E residue 118 LEU Chi-restraints excluded: chain E residue 158 VAL Chi-restraints excluded: chain E residue 160 VAL Chi-restraints excluded: chain E residue 245 THR Chi-restraints excluded: chain E residue 285 TYR Chi-restraints excluded: chain F residue 24 LEU Chi-restraints excluded: chain F residue 54 SER Chi-restraints excluded: chain F residue 158 VAL Chi-restraints excluded: chain F residue 160 VAL Chi-restraints excluded: chain F residue 173 THR Chi-restraints excluded: chain F residue 208 HIS Chi-restraints excluded: chain F residue 237 ASP Chi-restraints excluded: chain F residue 282 VAL Chi-restraints excluded: chain F residue 285 TYR Chi-restraints excluded: chain F residue 315 ASP Chi-restraints excluded: chain G residue 11 VAL Chi-restraints excluded: chain G residue 24 LEU Chi-restraints excluded: chain G residue 42 VAL Chi-restraints excluded: chain G residue 105 THR Chi-restraints excluded: chain G residue 140 HIS Chi-restraints excluded: chain G residue 158 VAL Chi-restraints excluded: chain G residue 160 VAL Chi-restraints excluded: chain G residue 208 HIS Chi-restraints excluded: chain G residue 213 VAL Chi-restraints excluded: chain G residue 245 THR Chi-restraints excluded: chain G residue 285 TYR Chi-restraints excluded: chain H residue 50 ARG Chi-restraints excluded: chain H residue 53 ILE Chi-restraints excluded: chain H residue 170 VAL Chi-restraints excluded: chain H residue 231 LEU Chi-restraints excluded: chain H residue 245 THR Chi-restraints excluded: chain H residue 308 LEU Chi-restraints excluded: chain I residue 35 GLN Chi-restraints excluded: chain I residue 42 VAL Chi-restraints excluded: chain I residue 134 THR Chi-restraints excluded: chain I residue 138 THR Chi-restraints excluded: chain I residue 145 THR Chi-restraints excluded: chain L residue 17 ILE Chi-restraints excluded: chain L residue 28 THR Chi-restraints excluded: chain L residue 41 VAL Chi-restraints excluded: chain L residue 51 SER Chi-restraints excluded: chain L residue 79 LYS Chi-restraints excluded: chain L residue 94 THR Chi-restraints excluded: chain L residue 137 MET Chi-restraints excluded: chain L residue 152 PHE Chi-restraints excluded: chain L residue 162 LEU Chi-restraints excluded: chain L residue 210 LEU Chi-restraints excluded: chain L residue 280 VAL Chi-restraints excluded: chain M residue 10 SER Chi-restraints excluded: chain M residue 11 VAL Chi-restraints excluded: chain M residue 25 MET Chi-restraints excluded: chain M residue 93 VAL Chi-restraints excluded: chain M residue 192 LEU Chi-restraints excluded: chain M residue 225 VAL Chi-restraints excluded: chain M residue 246 LEU Chi-restraints excluded: chain M residue 264 LEU Chi-restraints excluded: chain M residue 282 VAL Chi-restraints excluded: chain M residue 283 GLU Chi-restraints excluded: chain M residue 288 VAL Chi-restraints excluded: chain N residue 8 THR Chi-restraints excluded: chain N residue 67 LEU Chi-restraints excluded: chain N residue 97 LEU Chi-restraints excluded: chain N residue 129 GLN Chi-restraints excluded: chain N residue 179 LEU Chi-restraints excluded: chain N residue 206 SER Chi-restraints excluded: chain N residue 231 LEU Chi-restraints excluded: chain N residue 264 LEU Chi-restraints excluded: chain O residue 78 THR Chi-restraints excluded: chain O residue 107 SER Chi-restraints excluded: chain O residue 136 ARG Chi-restraints excluded: chain O residue 158 VAL Chi-restraints excluded: chain O residue 160 VAL Chi-restraints excluded: chain O residue 201 SER Chi-restraints excluded: chain O residue 245 THR Chi-restraints excluded: chain O residue 285 TYR Chi-restraints excluded: chain P residue 24 LEU Chi-restraints excluded: chain P residue 25 MET Chi-restraints excluded: chain P residue 158 VAL Chi-restraints excluded: chain P residue 173 THR Chi-restraints excluded: chain P residue 192 LEU Chi-restraints excluded: chain P residue 208 HIS Chi-restraints excluded: chain P residue 232 ILE Chi-restraints excluded: chain P residue 285 TYR Chi-restraints excluded: chain Q residue 24 LEU Chi-restraints excluded: chain Q residue 25 MET Chi-restraints excluded: chain Q residue 43 THR Chi-restraints excluded: chain Q residue 100 LEU Chi-restraints excluded: chain Q residue 105 THR Chi-restraints excluded: chain Q residue 158 VAL Chi-restraints excluded: chain Q residue 173 THR Chi-restraints excluded: chain Q residue 208 HIS Chi-restraints excluded: chain Q residue 290 SER Chi-restraints excluded: chain R residue 34 ASP Chi-restraints excluded: chain R residue 50 ARG Chi-restraints excluded: chain R residue 52 THR Chi-restraints excluded: chain R residue 71 ILE Chi-restraints excluded: chain R residue 86 SER Chi-restraints excluded: chain R residue 91 LEU Chi-restraints excluded: chain R residue 160 VAL Chi-restraints excluded: chain R residue 170 VAL Chi-restraints excluded: chain R residue 192 LEU Chi-restraints excluded: chain R residue 203 LEU Chi-restraints excluded: chain R residue 213 VAL Chi-restraints excluded: chain R residue 245 THR Chi-restraints excluded: chain R residue 264 LEU Chi-restraints excluded: chain R residue 285 TYR Chi-restraints excluded: chain R residue 320 VAL Chi-restraints excluded: chain S residue 100 VAL Chi-restraints excluded: chain U residue 46 TYR Chi-restraints excluded: chain U residue 73 ASP Chi-restraints excluded: chain U residue 127 GLU Chi-restraints excluded: chain U residue 167 LEU Chi-restraints excluded: chain U residue 177 THR Chi-restraints excluded: chain U residue 180 SER Chi-restraints excluded: chain U residue 197 LYS Chi-restraints excluded: chain V residue 63 VAL Chi-restraints excluded: chain V residue 85 VAL Chi-restraints excluded: chain V residue 113 THR Chi-restraints excluded: chain V residue 127 GLU Chi-restraints excluded: chain V residue 177 THR Chi-restraints excluded: chain V residue 179 VAL Chi-restraints excluded: chain V residue 180 SER Chi-restraints excluded: chain A residue 64 GLN Chi-restraints excluded: chain A residue 66 VAL Chi-restraints excluded: chain A residue 178 LEU Chi-restraints excluded: chain A residue 182 LEU Chi-restraints excluded: chain A residue 228 TRP Chi-restraints excluded: chain A residue 256 SER Chi-restraints excluded: chain X residue 66 VAL Chi-restraints excluded: chain X residue 213 ASP Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 627 random chunks: chunk 584 optimal weight: 8.9990 chunk 68 optimal weight: 4.9990 chunk 345 optimal weight: 5.9990 chunk 443 optimal weight: 8.9990 chunk 343 optimal weight: 9.9990 chunk 510 optimal weight: 2.9990 chunk 338 optimal weight: 0.3980 chunk 604 optimal weight: 9.9990 chunk 378 optimal weight: 4.9990 chunk 368 optimal weight: 2.9990 chunk 279 optimal weight: 10.0000 overall best weight: 3.2788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 110 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 110 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 140 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** S 19 GLN U 26 HIS ** A 241 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8407 moved from start: 0.2663 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.056 49575 Z= 0.247 Angle : 0.554 13.985 67829 Z= 0.286 Chirality : 0.040 0.241 7435 Planarity : 0.004 0.051 8566 Dihedral : 15.444 179.968 9094 Min Nonbonded Distance : 2.370 Molprobity Statistics. All-atom Clashscore : 6.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.37 % Favored : 93.63 % Rotamer: Outliers : 4.36 % Allowed : 22.22 % Favored : 73.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.68 % 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: -0.50 (0.11), residues: 6156 helix: 1.73 (0.12), residues: 2001 sheet: -0.03 (0.16), residues: 1058 loop : -1.94 (0.11), residues: 3097 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP H 174 HIS 0.010 0.001 HIS C 208 PHE 0.013 0.001 PHE X 211 TYR 0.016 0.001 TYR E 285 ARG 0.013 0.000 ARG B 271 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12312 Ramachandran restraints generated. 6156 Oldfield, 0 Emsley, 6156 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12312 Ramachandran restraints generated. 6156 Oldfield, 0 Emsley, 6156 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 395 residues out of total 5025 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 188 poor density : 207 time to evaluate : 4.017 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 79 LYS cc_start: 0.9012 (OUTLIER) cc_final: 0.7955 (mtmm) REVERT: B 80 VAL cc_start: 0.9050 (OUTLIER) cc_final: 0.8817 (m) REVERT: B 322 VAL cc_start: 0.6878 (OUTLIER) cc_final: 0.6505 (p) REVERT: C 97 LEU cc_start: 0.8806 (OUTLIER) cc_final: 0.8487 (mm) REVERT: C 128 GLU cc_start: 0.7833 (OUTLIER) cc_final: 0.7476 (tm-30) REVERT: C 248 SER cc_start: 0.8706 (OUTLIER) cc_final: 0.8204 (p) REVERT: C 293 LYS cc_start: 0.9236 (OUTLIER) cc_final: 0.8863 (ttpp) REVERT: C 309 ASP cc_start: 0.8681 (OUTLIER) cc_final: 0.8086 (p0) REVERT: C 330 LEU cc_start: 0.8760 (OUTLIER) cc_final: 0.8463 (mp) REVERT: D 241 GLN cc_start: 0.8670 (mp10) cc_final: 0.8375 (mt0) REVERT: H 50 ARG cc_start: 0.8944 (OUTLIER) cc_final: 0.7780 (ttm-80) REVERT: I 35 GLN cc_start: 0.2703 (OUTLIER) cc_final: 0.2300 (mp10) REVERT: I 143 PHE cc_start: 0.5867 (p90) cc_final: 0.5529 (p90) REVERT: L 242 ARG cc_start: 0.8534 (ptt90) cc_final: 0.8235 (ptt-90) REVERT: L 311 LYS cc_start: 0.8115 (mmmt) cc_final: 0.7467 (pttm) REVERT: N 129 GLN cc_start: 0.8264 (OUTLIER) cc_final: 0.7754 (mp10) REVERT: N 224 GLU cc_start: 0.7103 (mm-30) cc_final: 0.6472 (mm-30) REVERT: N 231 LEU cc_start: 0.9485 (OUTLIER) cc_final: 0.9137 (tt) REVERT: N 241 GLN cc_start: 0.7539 (mm-40) cc_final: 0.7002 (mm-40) REVERT: R 50 ARG cc_start: 0.8856 (OUTLIER) cc_final: 0.7952 (ttt-90) REVERT: R 91 LEU cc_start: 0.9413 (OUTLIER) cc_final: 0.9161 (tp) REVERT: S 173 PHE cc_start: 0.6458 (m-80) cc_final: 0.6103 (m-80) REVERT: V 158 GLU cc_start: 0.8438 (mp0) cc_final: 0.8137 (mp0) REVERT: V 198 TYR cc_start: 0.9233 (m-80) cc_final: 0.8655 (m-80) REVERT: A 211 PHE cc_start: 0.8224 (m-80) cc_final: 0.7944 (m-80) REVERT: A 222 ARG cc_start: 0.5170 (mmp-170) cc_final: 0.4926 (mmp-170) REVERT: A 234 GLU cc_start: 0.8977 (tp30) cc_final: 0.8459 (tp30) REVERT: X 78 ARG cc_start: 0.7343 (mtm-85) cc_final: 0.6977 (mtm-85) REVERT: X 176 LYS cc_start: 0.7127 (mmtt) cc_final: 0.5761 (mmtp) REVERT: X 210 ARG cc_start: 0.8941 (mtm-85) cc_final: 0.8715 (mtm-85) REVERT: X 213 ASP cc_start: 0.8668 (OUTLIER) cc_final: 0.8447 (p0) REVERT: X 216 LYS cc_start: 0.9443 (mptt) cc_final: 0.9104 (mmtp) outliers start: 188 outliers final: 149 residues processed: 382 average time/residue: 0.4739 time to fit residues: 303.0145 Evaluate side-chains 363 residues out of total 5025 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 165 poor density : 198 time to evaluate : 3.915 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 23 ILE Chi-restraints excluded: chain B residue 28 THR Chi-restraints excluded: chain B residue 48 VAL Chi-restraints excluded: chain B residue 59 VAL Chi-restraints excluded: chain B residue 79 LYS Chi-restraints excluded: chain B residue 80 VAL Chi-restraints excluded: chain B residue 150 GLU Chi-restraints excluded: chain B residue 213 LEU Chi-restraints excluded: chain B residue 216 LEU Chi-restraints excluded: chain B residue 259 SER Chi-restraints excluded: chain B residue 322 VAL Chi-restraints excluded: chain C residue 97 LEU Chi-restraints excluded: chain C residue 128 GLU Chi-restraints excluded: chain C residue 165 ILE Chi-restraints excluded: chain C residue 225 VAL Chi-restraints excluded: chain C residue 248 SER Chi-restraints excluded: chain C residue 282 VAL Chi-restraints excluded: chain C residue 288 VAL Chi-restraints excluded: chain C residue 293 LYS Chi-restraints excluded: chain C residue 308 LEU Chi-restraints excluded: chain C residue 309 ASP Chi-restraints excluded: chain C residue 326 VAL Chi-restraints excluded: chain C residue 330 LEU Chi-restraints excluded: chain D residue 11 VAL Chi-restraints excluded: chain D residue 77 GLN Chi-restraints excluded: chain D residue 78 THR Chi-restraints excluded: chain D residue 97 LEU Chi-restraints excluded: chain D residue 99 VAL Chi-restraints excluded: chain D residue 105 THR Chi-restraints excluded: chain D residue 208 HIS Chi-restraints excluded: chain D residue 264 LEU Chi-restraints excluded: chain D residue 282 VAL Chi-restraints excluded: chain D residue 288 VAL Chi-restraints excluded: chain D residue 289 THR Chi-restraints excluded: chain D residue 299 LYS Chi-restraints excluded: chain E residue 24 LEU Chi-restraints excluded: chain E residue 99 VAL Chi-restraints excluded: chain E residue 100 LEU Chi-restraints excluded: chain E residue 118 LEU Chi-restraints excluded: chain E residue 158 VAL Chi-restraints excluded: chain E residue 160 VAL Chi-restraints excluded: chain E residue 245 THR Chi-restraints excluded: chain E residue 285 TYR Chi-restraints excluded: chain F residue 24 LEU Chi-restraints excluded: chain F residue 44 VAL Chi-restraints excluded: chain F residue 54 SER Chi-restraints excluded: chain F residue 158 VAL Chi-restraints excluded: chain F residue 173 THR Chi-restraints excluded: chain F residue 208 HIS Chi-restraints excluded: chain F residue 237 ASP Chi-restraints excluded: chain F residue 282 VAL Chi-restraints excluded: chain F residue 331 ILE Chi-restraints excluded: chain G residue 11 VAL Chi-restraints excluded: chain G residue 24 LEU Chi-restraints excluded: chain G residue 42 VAL Chi-restraints excluded: chain G residue 140 HIS Chi-restraints excluded: chain G residue 158 VAL Chi-restraints excluded: chain G residue 160 VAL Chi-restraints excluded: chain G residue 208 HIS Chi-restraints excluded: chain G residue 213 VAL Chi-restraints excluded: chain G residue 243 SER Chi-restraints excluded: chain G residue 245 THR Chi-restraints excluded: chain G residue 285 TYR Chi-restraints excluded: chain H residue 50 ARG Chi-restraints excluded: chain H residue 53 ILE Chi-restraints excluded: chain H residue 170 VAL Chi-restraints excluded: chain H residue 231 LEU Chi-restraints excluded: chain H residue 245 THR Chi-restraints excluded: chain H residue 308 LEU Chi-restraints excluded: chain I residue 35 GLN Chi-restraints excluded: chain I residue 42 VAL Chi-restraints excluded: chain I residue 134 THR Chi-restraints excluded: chain I residue 138 THR Chi-restraints excluded: chain I residue 145 THR Chi-restraints excluded: chain L residue 17 ILE Chi-restraints excluded: chain L residue 28 THR Chi-restraints excluded: chain L residue 41 VAL Chi-restraints excluded: chain L residue 51 SER Chi-restraints excluded: chain L residue 94 THR Chi-restraints excluded: chain L residue 98 VAL Chi-restraints excluded: chain L residue 152 PHE Chi-restraints excluded: chain L residue 210 LEU Chi-restraints excluded: chain L residue 280 VAL Chi-restraints excluded: chain M residue 10 SER Chi-restraints excluded: chain M residue 11 VAL Chi-restraints excluded: chain M residue 192 LEU Chi-restraints excluded: chain M residue 225 VAL Chi-restraints excluded: chain M residue 246 LEU Chi-restraints excluded: chain M residue 282 VAL Chi-restraints excluded: chain M residue 283 GLU Chi-restraints excluded: chain M residue 288 VAL Chi-restraints excluded: chain M residue 302 LEU Chi-restraints excluded: chain N residue 8 THR Chi-restraints excluded: chain N residue 67 LEU Chi-restraints excluded: chain N residue 97 LEU Chi-restraints excluded: chain N residue 129 GLN Chi-restraints excluded: chain N residue 179 LEU Chi-restraints excluded: chain N residue 206 SER Chi-restraints excluded: chain N residue 231 LEU Chi-restraints excluded: chain N residue 264 LEU Chi-restraints excluded: chain O residue 78 THR Chi-restraints excluded: chain O residue 107 SER Chi-restraints excluded: chain O residue 158 VAL Chi-restraints excluded: chain O residue 160 VAL Chi-restraints excluded: chain O residue 201 SER Chi-restraints excluded: chain O residue 209 VAL Chi-restraints excluded: chain O residue 238 LYS Chi-restraints excluded: chain O residue 285 TYR Chi-restraints excluded: chain P residue 25 MET Chi-restraints excluded: chain P residue 158 VAL Chi-restraints excluded: chain P residue 173 THR Chi-restraints excluded: chain P residue 192 LEU Chi-restraints excluded: chain P residue 208 HIS Chi-restraints excluded: chain P residue 232 ILE Chi-restraints excluded: chain P residue 285 TYR Chi-restraints excluded: chain Q residue 24 LEU Chi-restraints excluded: chain Q residue 25 MET Chi-restraints excluded: chain Q residue 43 THR Chi-restraints excluded: chain Q residue 105 THR Chi-restraints excluded: chain Q residue 158 VAL Chi-restraints excluded: chain Q residue 170 VAL Chi-restraints excluded: chain Q residue 173 THR Chi-restraints excluded: chain Q residue 208 HIS Chi-restraints excluded: chain Q residue 285 TYR Chi-restraints excluded: chain Q residue 290 SER Chi-restraints excluded: chain R residue 34 ASP Chi-restraints excluded: chain R residue 50 ARG Chi-restraints excluded: chain R residue 52 THR Chi-restraints excluded: chain R residue 71 ILE Chi-restraints excluded: chain R residue 86 SER Chi-restraints excluded: chain R residue 91 LEU Chi-restraints excluded: chain R residue 160 VAL Chi-restraints excluded: chain R residue 170 VAL Chi-restraints excluded: chain R residue 192 LEU Chi-restraints excluded: chain R residue 203 LEU Chi-restraints excluded: chain R residue 213 VAL Chi-restraints excluded: chain R residue 231 LEU Chi-restraints excluded: chain R residue 245 THR Chi-restraints excluded: chain R residue 285 TYR Chi-restraints excluded: chain R residue 320 VAL Chi-restraints excluded: chain S residue 100 VAL Chi-restraints excluded: chain U residue 12 THR Chi-restraints excluded: chain U residue 46 TYR Chi-restraints excluded: chain U residue 73 ASP Chi-restraints excluded: chain U residue 127 GLU Chi-restraints excluded: chain U residue 167 LEU Chi-restraints excluded: chain U residue 177 THR Chi-restraints excluded: chain U residue 191 SER Chi-restraints excluded: chain U residue 197 LYS Chi-restraints excluded: chain V residue 12 THR Chi-restraints excluded: chain V residue 63 VAL Chi-restraints excluded: chain V residue 85 VAL Chi-restraints excluded: chain V residue 113 THR Chi-restraints excluded: chain V residue 127 GLU Chi-restraints excluded: chain V residue 177 THR Chi-restraints excluded: chain V residue 179 VAL Chi-restraints excluded: chain V residue 180 SER Chi-restraints excluded: chain A residue 66 VAL Chi-restraints excluded: chain A residue 173 SER Chi-restraints excluded: chain A residue 178 LEU Chi-restraints excluded: chain A residue 182 LEU Chi-restraints excluded: chain A residue 227 SER Chi-restraints excluded: chain A residue 256 SER Chi-restraints excluded: chain X residue 66 VAL Chi-restraints excluded: chain X residue 213 ASP Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 627 random chunks: chunk 373 optimal weight: 8.9990 chunk 241 optimal weight: 20.0000 chunk 360 optimal weight: 8.9990 chunk 182 optimal weight: 4.9990 chunk 118 optimal weight: 6.9990 chunk 117 optimal weight: 2.9990 chunk 384 optimal weight: 9.9990 chunk 411 optimal weight: 10.0000 chunk 298 optimal weight: 7.9990 chunk 56 optimal weight: 0.0770 chunk 475 optimal weight: 5.9990 overall best weight: 4.2146 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 110 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 110 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 140 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 297 GLN ** S 19 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** U 26 HIS A 225 GLN ** A 241 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8421 moved from start: 0.2778 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.064 49575 Z= 0.302 Angle : 0.578 13.908 67829 Z= 0.300 Chirality : 0.041 0.256 7435 Planarity : 0.004 0.053 8566 Dihedral : 15.409 179.988 9093 Min Nonbonded Distance : 2.357 Molprobity Statistics. All-atom Clashscore : 6.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.79 % Favored : 93.21 % Rotamer: Outliers : 4.48 % Allowed : 22.66 % Favored : 72.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.68 % 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: -0.51 (0.11), residues: 6156 helix: 1.71 (0.12), residues: 2007 sheet: -0.03 (0.16), residues: 1053 loop : -1.95 (0.11), residues: 3096 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.034 0.001 TRP A 228 HIS 0.009 0.001 HIS C 208 PHE 0.012 0.001 PHE C 95 TYR 0.018 0.001 TYR E 285 ARG 0.013 0.000 ARG B 271 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12312 Ramachandran restraints generated. 6156 Oldfield, 0 Emsley, 6156 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12312 Ramachandran restraints generated. 6156 Oldfield, 0 Emsley, 6156 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 396 residues out of total 5025 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 193 poor density : 203 time to evaluate : 3.936 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 79 LYS cc_start: 0.9029 (OUTLIER) cc_final: 0.7989 (mtmm) REVERT: B 80 VAL cc_start: 0.9063 (OUTLIER) cc_final: 0.8846 (m) REVERT: B 322 VAL cc_start: 0.6956 (OUTLIER) cc_final: 0.6595 (p) REVERT: C 97 LEU cc_start: 0.8918 (OUTLIER) cc_final: 0.8545 (mm) REVERT: C 128 GLU cc_start: 0.7807 (OUTLIER) cc_final: 0.7506 (tm-30) REVERT: C 293 LYS cc_start: 0.9258 (OUTLIER) cc_final: 0.8956 (ttpp) REVERT: C 309 ASP cc_start: 0.8649 (OUTLIER) cc_final: 0.8096 (p0) REVERT: C 330 LEU cc_start: 0.8801 (OUTLIER) cc_final: 0.8502 (mp) REVERT: D 241 GLN cc_start: 0.8714 (mp10) cc_final: 0.8430 (mt0) REVERT: I 35 GLN cc_start: 0.2698 (OUTLIER) cc_final: 0.2298 (mp10) REVERT: I 143 PHE cc_start: 0.5935 (p90) cc_final: 0.5628 (p90) REVERT: L 242 ARG cc_start: 0.8523 (ptt90) cc_final: 0.8158 (ptt-90) REVERT: N 129 GLN cc_start: 0.8287 (OUTLIER) cc_final: 0.7768 (mp10) REVERT: N 224 GLU cc_start: 0.7137 (mm-30) cc_final: 0.6534 (mm-30) REVERT: N 231 LEU cc_start: 0.9475 (OUTLIER) cc_final: 0.9105 (tt) REVERT: N 241 GLN cc_start: 0.7551 (mm-40) cc_final: 0.7008 (mm-40) REVERT: O 195 LEU cc_start: 0.9363 (OUTLIER) cc_final: 0.9142 (tp) REVERT: R 50 ARG cc_start: 0.8875 (OUTLIER) cc_final: 0.7955 (ttt-90) REVERT: R 208 HIS cc_start: 0.6831 (OUTLIER) cc_final: 0.6385 (m-70) REVERT: S 173 PHE cc_start: 0.6497 (m-80) cc_final: 0.6146 (m-80) REVERT: V 198 TYR cc_start: 0.9254 (m-80) cc_final: 0.8655 (m-80) REVERT: A 222 ARG cc_start: 0.5518 (mmp-170) cc_final: 0.5317 (mmp-170) REVERT: A 234 GLU cc_start: 0.8989 (tp30) cc_final: 0.8535 (tp30) REVERT: A 257 GLU cc_start: 0.8644 (pp20) cc_final: 0.8383 (pp20) REVERT: A 261 GLU cc_start: 0.8844 (mt-10) cc_final: 0.8358 (mm-30) REVERT: X 78 ARG cc_start: 0.7349 (mtm-85) cc_final: 0.6983 (mtm-85) REVERT: X 176 LYS cc_start: 0.7133 (mmtt) cc_final: 0.5810 (mmtp) REVERT: X 210 ARG cc_start: 0.9012 (mtm-85) cc_final: 0.8718 (mtm180) REVERT: X 213 ASP cc_start: 0.8700 (OUTLIER) cc_final: 0.8486 (p0) REVERT: X 216 LYS cc_start: 0.9421 (mptt) cc_final: 0.9089 (mmtp) outliers start: 193 outliers final: 157 residues processed: 384 average time/residue: 0.4722 time to fit residues: 303.2445 Evaluate side-chains 369 residues out of total 5025 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 172 poor density : 197 time to evaluate : 3.926 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 23 ILE Chi-restraints excluded: chain B residue 28 THR Chi-restraints excluded: chain B residue 48 VAL Chi-restraints excluded: chain B residue 59 VAL Chi-restraints excluded: chain B residue 79 LYS Chi-restraints excluded: chain B residue 80 VAL Chi-restraints excluded: chain B residue 150 GLU Chi-restraints excluded: chain B residue 213 LEU Chi-restraints excluded: chain B residue 216 LEU Chi-restraints excluded: chain B residue 259 SER Chi-restraints excluded: chain B residue 322 VAL Chi-restraints excluded: chain C residue 36 SER Chi-restraints excluded: chain C residue 97 LEU Chi-restraints excluded: chain C residue 128 GLU Chi-restraints excluded: chain C residue 225 VAL Chi-restraints excluded: chain C residue 248 SER Chi-restraints excluded: chain C residue 282 VAL Chi-restraints excluded: chain C residue 288 VAL Chi-restraints excluded: chain C residue 293 LYS Chi-restraints excluded: chain C residue 308 LEU Chi-restraints excluded: chain C residue 309 ASP Chi-restraints excluded: chain C residue 326 VAL Chi-restraints excluded: chain C residue 330 LEU Chi-restraints excluded: chain D residue 11 VAL Chi-restraints excluded: chain D residue 77 GLN Chi-restraints excluded: chain D residue 97 LEU Chi-restraints excluded: chain D residue 99 VAL Chi-restraints excluded: chain D residue 105 THR Chi-restraints excluded: chain D residue 208 HIS Chi-restraints excluded: chain D residue 264 LEU Chi-restraints excluded: chain D residue 282 VAL Chi-restraints excluded: chain D residue 289 THR Chi-restraints excluded: chain D residue 299 LYS Chi-restraints excluded: chain E residue 24 LEU Chi-restraints excluded: chain E residue 79 VAL Chi-restraints excluded: chain E residue 86 SER Chi-restraints excluded: chain E residue 99 VAL Chi-restraints excluded: chain E residue 100 LEU Chi-restraints excluded: chain E residue 118 LEU Chi-restraints excluded: chain E residue 158 VAL Chi-restraints excluded: chain E residue 160 VAL Chi-restraints excluded: chain E residue 245 THR Chi-restraints excluded: chain E residue 285 TYR Chi-restraints excluded: chain F residue 24 LEU Chi-restraints excluded: chain F residue 44 VAL Chi-restraints excluded: chain F residue 54 SER Chi-restraints excluded: chain F residue 158 VAL Chi-restraints excluded: chain F residue 173 THR Chi-restraints excluded: chain F residue 208 HIS Chi-restraints excluded: chain F residue 237 ASP Chi-restraints excluded: chain F residue 282 VAL Chi-restraints excluded: chain F residue 331 ILE Chi-restraints excluded: chain G residue 11 VAL Chi-restraints excluded: chain G residue 24 LEU Chi-restraints excluded: chain G residue 42 VAL Chi-restraints excluded: chain G residue 105 THR Chi-restraints excluded: chain G residue 140 HIS Chi-restraints excluded: chain G residue 158 VAL Chi-restraints excluded: chain G residue 160 VAL Chi-restraints excluded: chain G residue 183 LEU Chi-restraints excluded: chain G residue 208 HIS Chi-restraints excluded: chain G residue 213 VAL Chi-restraints excluded: chain G residue 243 SER Chi-restraints excluded: chain G residue 245 THR Chi-restraints excluded: chain G residue 285 TYR Chi-restraints excluded: chain H residue 53 ILE Chi-restraints excluded: chain H residue 170 VAL Chi-restraints excluded: chain H residue 231 LEU Chi-restraints excluded: chain H residue 243 SER Chi-restraints excluded: chain H residue 245 THR Chi-restraints excluded: chain H residue 289 THR Chi-restraints excluded: chain H residue 308 LEU Chi-restraints excluded: chain I residue 35 GLN Chi-restraints excluded: chain I residue 42 VAL Chi-restraints excluded: chain I residue 134 THR Chi-restraints excluded: chain I residue 138 THR Chi-restraints excluded: chain I residue 145 THR Chi-restraints excluded: chain L residue 17 ILE Chi-restraints excluded: chain L residue 28 THR Chi-restraints excluded: chain L residue 41 VAL Chi-restraints excluded: chain L residue 51 SER Chi-restraints excluded: chain L residue 94 THR Chi-restraints excluded: chain L residue 98 VAL Chi-restraints excluded: chain L residue 152 PHE Chi-restraints excluded: chain L residue 188 SER Chi-restraints excluded: chain L residue 210 LEU Chi-restraints excluded: chain L residue 280 VAL Chi-restraints excluded: chain M residue 10 SER Chi-restraints excluded: chain M residue 11 VAL Chi-restraints excluded: chain M residue 192 LEU Chi-restraints excluded: chain M residue 225 VAL Chi-restraints excluded: chain M residue 246 LEU Chi-restraints excluded: chain M residue 282 VAL Chi-restraints excluded: chain M residue 283 GLU Chi-restraints excluded: chain M residue 288 VAL Chi-restraints excluded: chain M residue 302 LEU Chi-restraints excluded: chain N residue 8 THR Chi-restraints excluded: chain N residue 67 LEU Chi-restraints excluded: chain N residue 97 LEU Chi-restraints excluded: chain N residue 129 GLN Chi-restraints excluded: chain N residue 179 LEU Chi-restraints excluded: chain N residue 206 SER Chi-restraints excluded: chain N residue 231 LEU Chi-restraints excluded: chain N residue 264 LEU Chi-restraints excluded: chain O residue 78 THR Chi-restraints excluded: chain O residue 107 SER Chi-restraints excluded: chain O residue 158 VAL Chi-restraints excluded: chain O residue 160 VAL Chi-restraints excluded: chain O residue 195 LEU Chi-restraints excluded: chain O residue 201 SER Chi-restraints excluded: chain O residue 238 LYS Chi-restraints excluded: chain O residue 285 TYR Chi-restraints excluded: chain P residue 24 LEU Chi-restraints excluded: chain P residue 25 MET Chi-restraints excluded: chain P residue 158 VAL Chi-restraints excluded: chain P residue 173 THR Chi-restraints excluded: chain P residue 192 LEU Chi-restraints excluded: chain P residue 199 ILE Chi-restraints excluded: chain P residue 208 HIS Chi-restraints excluded: chain P residue 232 ILE Chi-restraints excluded: chain P residue 285 TYR Chi-restraints excluded: chain Q residue 24 LEU Chi-restraints excluded: chain Q residue 25 MET Chi-restraints excluded: chain Q residue 43 THR Chi-restraints excluded: chain Q residue 105 THR Chi-restraints excluded: chain Q residue 158 VAL Chi-restraints excluded: chain Q residue 170 VAL Chi-restraints excluded: chain Q residue 173 THR Chi-restraints excluded: chain Q residue 208 HIS Chi-restraints excluded: chain Q residue 285 TYR Chi-restraints excluded: chain Q residue 290 SER Chi-restraints excluded: chain R residue 34 ASP Chi-restraints excluded: chain R residue 50 ARG Chi-restraints excluded: chain R residue 52 THR Chi-restraints excluded: chain R residue 71 ILE Chi-restraints excluded: chain R residue 86 SER Chi-restraints excluded: chain R residue 105 THR Chi-restraints excluded: chain R residue 160 VAL Chi-restraints excluded: chain R residue 170 VAL Chi-restraints excluded: chain R residue 192 LEU Chi-restraints excluded: chain R residue 203 LEU Chi-restraints excluded: chain R residue 208 HIS Chi-restraints excluded: chain R residue 213 VAL Chi-restraints excluded: chain R residue 231 LEU Chi-restraints excluded: chain R residue 245 THR Chi-restraints excluded: chain R residue 264 LEU Chi-restraints excluded: chain R residue 285 TYR Chi-restraints excluded: chain R residue 320 VAL Chi-restraints excluded: chain S residue 100 VAL Chi-restraints excluded: chain U residue 12 THR Chi-restraints excluded: chain U residue 46 TYR Chi-restraints excluded: chain U residue 73 ASP Chi-restraints excluded: chain U residue 127 GLU Chi-restraints excluded: chain U residue 167 LEU Chi-restraints excluded: chain U residue 177 THR Chi-restraints excluded: chain U residue 197 LYS Chi-restraints excluded: chain V residue 12 THR Chi-restraints excluded: chain V residue 63 VAL Chi-restraints excluded: chain V residue 85 VAL Chi-restraints excluded: chain V residue 113 THR Chi-restraints excluded: chain V residue 127 GLU Chi-restraints excluded: chain V residue 177 THR Chi-restraints excluded: chain V residue 179 VAL Chi-restraints excluded: chain V residue 180 SER Chi-restraints excluded: chain A residue 66 VAL Chi-restraints excluded: chain A residue 173 SER Chi-restraints excluded: chain A residue 178 LEU Chi-restraints excluded: chain A residue 182 LEU Chi-restraints excluded: chain A residue 227 SER Chi-restraints excluded: chain A residue 256 SER Chi-restraints excluded: chain X residue 66 VAL Chi-restraints excluded: chain X residue 213 ASP Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 627 random chunks: chunk 549 optimal weight: 40.0000 chunk 578 optimal weight: 50.0000 chunk 528 optimal weight: 8.9990 chunk 563 optimal weight: 3.9990 chunk 338 optimal weight: 0.7980 chunk 245 optimal weight: 20.0000 chunk 442 optimal weight: 7.9990 chunk 172 optimal weight: 3.9990 chunk 508 optimal weight: 6.9990 chunk 532 optimal weight: 50.0000 chunk 561 optimal weight: 20.0000 overall best weight: 4.7588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 110 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 110 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 140 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 37 GLN M 262 ASN ** S 19 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** U 26 HIS ** A 241 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8429 moved from start: 0.2890 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.068 49575 Z= 0.334 Angle : 0.597 14.929 67829 Z= 0.309 Chirality : 0.042 0.241 7435 Planarity : 0.004 0.056 8566 Dihedral : 15.382 179.942 9091 Min Nonbonded Distance : 2.353 Molprobity Statistics. All-atom Clashscore : 6.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.84 % Favored : 93.16 % Rotamer: Outliers : 4.43 % Allowed : 22.78 % Favored : 72.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.68 % 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: -0.52 (0.11), residues: 6156 helix: 1.71 (0.12), residues: 2006 sheet: -0.03 (0.16), residues: 1047 loop : -1.95 (0.11), residues: 3103 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.001 TRP A 228 HIS 0.010 0.001 HIS C 208 PHE 0.017 0.001 PHE I 158 TYR 0.019 0.002 TYR E 285 ARG 0.012 0.000 ARG B 271 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12312 Ramachandran restraints generated. 6156 Oldfield, 0 Emsley, 6156 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12312 Ramachandran restraints generated. 6156 Oldfield, 0 Emsley, 6156 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 390 residues out of total 5025 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 191 poor density : 199 time to evaluate : 5.102 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 79 LYS cc_start: 0.9053 (OUTLIER) cc_final: 0.7979 (mtmm) REVERT: B 80 VAL cc_start: 0.9047 (OUTLIER) cc_final: 0.8831 (m) REVERT: B 322 VAL cc_start: 0.7020 (OUTLIER) cc_final: 0.6667 (p) REVERT: C 97 LEU cc_start: 0.8772 (OUTLIER) cc_final: 0.8431 (mm) REVERT: C 128 GLU cc_start: 0.7759 (OUTLIER) cc_final: 0.7485 (tm-30) REVERT: C 293 LYS cc_start: 0.9264 (OUTLIER) cc_final: 0.8997 (ttpp) REVERT: C 309 ASP cc_start: 0.8630 (OUTLIER) cc_final: 0.8071 (p0) REVERT: C 330 LEU cc_start: 0.8803 (OUTLIER) cc_final: 0.8508 (mp) REVERT: D 241 GLN cc_start: 0.8714 (mp10) cc_final: 0.8422 (mt0) REVERT: H 50 ARG cc_start: 0.8976 (OUTLIER) cc_final: 0.7779 (ttm-80) REVERT: I 35 GLN cc_start: 0.2706 (OUTLIER) cc_final: 0.2322 (mp10) REVERT: I 143 PHE cc_start: 0.6327 (p90) cc_final: 0.5964 (p90) REVERT: L 200 LEU cc_start: 0.9560 (OUTLIER) cc_final: 0.9323 (pp) REVERT: L 311 LYS cc_start: 0.7859 (mmmt) cc_final: 0.7137 (pttm) REVERT: N 129 GLN cc_start: 0.8280 (OUTLIER) cc_final: 0.7746 (mp10) REVERT: N 224 GLU cc_start: 0.7139 (mm-30) cc_final: 0.6523 (mm-30) REVERT: N 231 LEU cc_start: 0.9478 (OUTLIER) cc_final: 0.9135 (tt) REVERT: N 241 GLN cc_start: 0.7576 (mm-40) cc_final: 0.7045 (mm-40) REVERT: O 195 LEU cc_start: 0.9370 (OUTLIER) cc_final: 0.9145 (tp) REVERT: R 50 ARG cc_start: 0.8885 (OUTLIER) cc_final: 0.7948 (ttt-90) REVERT: S 1 MET cc_start: 0.3557 (mtm) cc_final: 0.3018 (mpp) REVERT: S 173 PHE cc_start: 0.6511 (m-80) cc_final: 0.6058 (m-80) REVERT: V 198 TYR cc_start: 0.9317 (m-80) cc_final: 0.8813 (m-80) REVERT: A 234 GLU cc_start: 0.8996 (tp30) cc_final: 0.8534 (tp30) REVERT: A 257 GLU cc_start: 0.8678 (pp20) cc_final: 0.8440 (pp20) REVERT: A 261 GLU cc_start: 0.8889 (mt-10) cc_final: 0.8357 (mm-30) REVERT: X 176 LYS cc_start: 0.7143 (mmtt) cc_final: 0.5813 (mmtp) REVERT: X 210 ARG cc_start: 0.9006 (mtm-85) cc_final: 0.8723 (mtm180) REVERT: X 216 LYS cc_start: 0.9428 (mptt) cc_final: 0.9103 (mmtp) outliers start: 191 outliers final: 161 residues processed: 374 average time/residue: 0.4686 time to fit residues: 294.1588 Evaluate side-chains 365 residues out of total 5025 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 176 poor density : 189 time to evaluate : 3.929 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 28 THR Chi-restraints excluded: chain B residue 48 VAL Chi-restraints excluded: chain B residue 59 VAL Chi-restraints excluded: chain B residue 79 LYS Chi-restraints excluded: chain B residue 80 VAL Chi-restraints excluded: chain B residue 150 GLU Chi-restraints excluded: chain B residue 213 LEU Chi-restraints excluded: chain B residue 216 LEU Chi-restraints excluded: chain B residue 259 SER Chi-restraints excluded: chain B residue 322 VAL Chi-restraints excluded: chain C residue 25 MET Chi-restraints excluded: chain C residue 36 SER Chi-restraints excluded: chain C residue 97 LEU Chi-restraints excluded: chain C residue 128 GLU Chi-restraints excluded: chain C residue 165 ILE Chi-restraints excluded: chain C residue 225 VAL Chi-restraints excluded: chain C residue 248 SER Chi-restraints excluded: chain C residue 282 VAL Chi-restraints excluded: chain C residue 288 VAL Chi-restraints excluded: chain C residue 293 LYS Chi-restraints excluded: chain C residue 309 ASP Chi-restraints excluded: chain C residue 326 VAL Chi-restraints excluded: chain C residue 330 LEU Chi-restraints excluded: chain D residue 11 VAL Chi-restraints excluded: chain D residue 77 GLN Chi-restraints excluded: chain D residue 78 THR Chi-restraints excluded: chain D residue 97 LEU Chi-restraints excluded: chain D residue 99 VAL Chi-restraints excluded: chain D residue 105 THR Chi-restraints excluded: chain D residue 208 HIS Chi-restraints excluded: chain D residue 264 LEU Chi-restraints excluded: chain D residue 282 VAL Chi-restraints excluded: chain D residue 289 THR Chi-restraints excluded: chain D residue 299 LYS Chi-restraints excluded: chain E residue 24 LEU Chi-restraints excluded: chain E residue 79 VAL Chi-restraints excluded: chain E residue 86 SER Chi-restraints excluded: chain E residue 99 VAL Chi-restraints excluded: chain E residue 100 LEU Chi-restraints excluded: chain E residue 118 LEU Chi-restraints excluded: chain E residue 158 VAL Chi-restraints excluded: chain E residue 160 VAL Chi-restraints excluded: chain E residue 245 THR Chi-restraints excluded: chain E residue 285 TYR Chi-restraints excluded: chain F residue 24 LEU Chi-restraints excluded: chain F residue 44 VAL Chi-restraints excluded: chain F residue 54 SER Chi-restraints excluded: chain F residue 158 VAL Chi-restraints excluded: chain F residue 173 THR Chi-restraints excluded: chain F residue 208 HIS Chi-restraints excluded: chain F residue 237 ASP Chi-restraints excluded: chain F residue 282 VAL Chi-restraints excluded: chain F residue 331 ILE Chi-restraints excluded: chain G residue 11 VAL Chi-restraints excluded: chain G residue 24 LEU Chi-restraints excluded: chain G residue 42 VAL Chi-restraints excluded: chain G residue 105 THR Chi-restraints excluded: chain G residue 140 HIS Chi-restraints excluded: chain G residue 158 VAL Chi-restraints excluded: chain G residue 160 VAL Chi-restraints excluded: chain G residue 183 LEU Chi-restraints excluded: chain G residue 208 HIS Chi-restraints excluded: chain G residue 213 VAL Chi-restraints excluded: chain G residue 243 SER Chi-restraints excluded: chain G residue 245 THR Chi-restraints excluded: chain G residue 285 TYR Chi-restraints excluded: chain H residue 34 ASP Chi-restraints excluded: chain H residue 50 ARG Chi-restraints excluded: chain H residue 53 ILE Chi-restraints excluded: chain H residue 170 VAL Chi-restraints excluded: chain H residue 231 LEU Chi-restraints excluded: chain H residue 243 SER Chi-restraints excluded: chain H residue 245 THR Chi-restraints excluded: chain H residue 289 THR Chi-restraints excluded: chain H residue 308 LEU Chi-restraints excluded: chain I residue 35 GLN Chi-restraints excluded: chain I residue 42 VAL Chi-restraints excluded: chain I residue 134 THR Chi-restraints excluded: chain I residue 138 THR Chi-restraints excluded: chain I residue 145 THR Chi-restraints excluded: chain L residue 17 ILE Chi-restraints excluded: chain L residue 28 THR Chi-restraints excluded: chain L residue 41 VAL Chi-restraints excluded: chain L residue 51 SER Chi-restraints excluded: chain L residue 94 THR Chi-restraints excluded: chain L residue 152 PHE Chi-restraints excluded: chain L residue 188 SER Chi-restraints excluded: chain L residue 200 LEU Chi-restraints excluded: chain L residue 210 LEU Chi-restraints excluded: chain L residue 280 VAL Chi-restraints excluded: chain M residue 11 VAL Chi-restraints excluded: chain M residue 192 LEU Chi-restraints excluded: chain M residue 225 VAL Chi-restraints excluded: chain M residue 246 LEU Chi-restraints excluded: chain M residue 264 LEU Chi-restraints excluded: chain M residue 282 VAL Chi-restraints excluded: chain M residue 283 GLU Chi-restraints excluded: chain M residue 288 VAL Chi-restraints excluded: chain M residue 302 LEU Chi-restraints excluded: chain N residue 8 THR Chi-restraints excluded: chain N residue 67 LEU Chi-restraints excluded: chain N residue 97 LEU Chi-restraints excluded: chain N residue 129 GLN Chi-restraints excluded: chain N residue 179 LEU Chi-restraints excluded: chain N residue 206 SER Chi-restraints excluded: chain N residue 231 LEU Chi-restraints excluded: chain N residue 264 LEU Chi-restraints excluded: chain O residue 78 THR Chi-restraints excluded: chain O residue 107 SER Chi-restraints excluded: chain O residue 158 VAL Chi-restraints excluded: chain O residue 160 VAL Chi-restraints excluded: chain O residue 195 LEU Chi-restraints excluded: chain O residue 201 SER Chi-restraints excluded: chain O residue 238 LYS Chi-restraints excluded: chain O residue 285 TYR Chi-restraints excluded: chain P residue 24 LEU Chi-restraints excluded: chain P residue 25 MET Chi-restraints excluded: chain P residue 158 VAL Chi-restraints excluded: chain P residue 173 THR Chi-restraints excluded: chain P residue 192 LEU Chi-restraints excluded: chain P residue 199 ILE Chi-restraints excluded: chain P residue 208 HIS Chi-restraints excluded: chain P residue 232 ILE Chi-restraints excluded: chain P residue 285 TYR Chi-restraints excluded: chain P residue 289 THR Chi-restraints excluded: chain Q residue 24 LEU Chi-restraints excluded: chain Q residue 25 MET Chi-restraints excluded: chain Q residue 42 VAL Chi-restraints excluded: chain Q residue 43 THR Chi-restraints excluded: chain Q residue 105 THR Chi-restraints excluded: chain Q residue 158 VAL Chi-restraints excluded: chain Q residue 170 VAL Chi-restraints excluded: chain Q residue 173 THR Chi-restraints excluded: chain Q residue 208 HIS Chi-restraints excluded: chain Q residue 285 TYR Chi-restraints excluded: chain Q residue 290 SER Chi-restraints excluded: chain R residue 34 ASP Chi-restraints excluded: chain R residue 50 ARG Chi-restraints excluded: chain R residue 52 THR Chi-restraints excluded: chain R residue 71 ILE Chi-restraints excluded: chain R residue 86 SER Chi-restraints excluded: chain R residue 105 THR Chi-restraints excluded: chain R residue 160 VAL Chi-restraints excluded: chain R residue 170 VAL Chi-restraints excluded: chain R residue 192 LEU Chi-restraints excluded: chain R residue 203 LEU Chi-restraints excluded: chain R residue 213 VAL Chi-restraints excluded: chain R residue 231 LEU Chi-restraints excluded: chain R residue 245 THR Chi-restraints excluded: chain R residue 264 LEU Chi-restraints excluded: chain R residue 285 TYR Chi-restraints excluded: chain R residue 320 VAL Chi-restraints excluded: chain S residue 100 VAL Chi-restraints excluded: chain U residue 12 THR Chi-restraints excluded: chain U residue 46 TYR Chi-restraints excluded: chain U residue 73 ASP Chi-restraints excluded: chain U residue 127 GLU Chi-restraints excluded: chain U residue 167 LEU Chi-restraints excluded: chain U residue 177 THR Chi-restraints excluded: chain U residue 191 SER Chi-restraints excluded: chain U residue 197 LYS Chi-restraints excluded: chain V residue 12 THR Chi-restraints excluded: chain V residue 63 VAL Chi-restraints excluded: chain V residue 85 VAL Chi-restraints excluded: chain V residue 113 THR Chi-restraints excluded: chain V residue 127 GLU Chi-restraints excluded: chain V residue 177 THR Chi-restraints excluded: chain V residue 179 VAL Chi-restraints excluded: chain V residue 180 SER Chi-restraints excluded: chain A residue 66 VAL Chi-restraints excluded: chain A residue 173 SER Chi-restraints excluded: chain A residue 178 LEU Chi-restraints excluded: chain A residue 182 LEU Chi-restraints excluded: chain A residue 227 SER Chi-restraints excluded: chain A residue 256 SER Chi-restraints excluded: chain X residue 66 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 627 random chunks: chunk 369 optimal weight: 7.9990 chunk 595 optimal weight: 8.9990 chunk 363 optimal weight: 3.9990 chunk 282 optimal weight: 8.9990 chunk 413 optimal weight: 4.9990 chunk 624 optimal weight: 80.0000 chunk 574 optimal weight: 20.0000 chunk 497 optimal weight: 0.9990 chunk 51 optimal weight: 8.9990 chunk 384 optimal weight: 3.9990 chunk 305 optimal weight: 6.9990 overall best weight: 4.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 110 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 110 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 140 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 19 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** U 26 HIS ** A 241 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8424 moved from start: 0.2996 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.065 49575 Z= 0.301 Angle : 0.589 15.227 67829 Z= 0.305 Chirality : 0.041 0.244 7435 Planarity : 0.004 0.065 8566 Dihedral : 15.287 179.925 9091 Min Nonbonded Distance : 2.369 Molprobity Statistics. All-atom Clashscore : 6.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.63 % Favored : 93.37 % Rotamer: Outliers : 4.20 % Allowed : 23.01 % Favored : 72.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.68 % 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: -0.49 (0.11), residues: 6156 helix: 1.73 (0.12), residues: 2006 sheet: -0.00 (0.16), residues: 1045 loop : -1.94 (0.11), residues: 3105 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.001 TRP A 272 HIS 0.009 0.001 HIS C 208 PHE 0.014 0.001 PHE I 158 TYR 0.018 0.002 TYR G 285 ARG 0.012 0.000 ARG B 271 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12312 Ramachandran restraints generated. 6156 Oldfield, 0 Emsley, 6156 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12312 Ramachandran restraints generated. 6156 Oldfield, 0 Emsley, 6156 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 374 residues out of total 5025 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 181 poor density : 193 time to evaluate : 4.003 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 79 LYS cc_start: 0.9004 (OUTLIER) cc_final: 0.7819 (mtmm) REVERT: B 80 VAL cc_start: 0.9049 (OUTLIER) cc_final: 0.8845 (m) REVERT: B 322 VAL cc_start: 0.7060 (OUTLIER) cc_final: 0.6704 (p) REVERT: C 128 GLU cc_start: 0.7819 (OUTLIER) cc_final: 0.7453 (tm-30) REVERT: C 293 LYS cc_start: 0.9262 (OUTLIER) cc_final: 0.8980 (ttpp) REVERT: C 309 ASP cc_start: 0.8628 (OUTLIER) cc_final: 0.8067 (p0) REVERT: C 330 LEU cc_start: 0.8828 (OUTLIER) cc_final: 0.8526 (mp) REVERT: D 241 GLN cc_start: 0.8898 (mp10) cc_final: 0.8065 (mp10) REVERT: H 50 ARG cc_start: 0.8969 (OUTLIER) cc_final: 0.7781 (ttm-80) REVERT: I 21 MET cc_start: 0.6585 (mtt) cc_final: 0.6196 (ppp) REVERT: I 35 GLN cc_start: 0.2701 (OUTLIER) cc_final: 0.2336 (mp10) REVERT: I 143 PHE cc_start: 0.6366 (p90) cc_final: 0.5925 (p90) REVERT: L 311 LYS cc_start: 0.7849 (mmmt) cc_final: 0.7036 (pttm) REVERT: M 283 GLU cc_start: 0.8707 (OUTLIER) cc_final: 0.8364 (mp0) REVERT: N 129 GLN cc_start: 0.8330 (OUTLIER) cc_final: 0.7786 (mp10) REVERT: N 224 GLU cc_start: 0.7122 (mm-30) cc_final: 0.6517 (mm-30) REVERT: N 231 LEU cc_start: 0.9418 (OUTLIER) cc_final: 0.9113 (tt) REVERT: N 241 GLN cc_start: 0.7599 (mm-40) cc_final: 0.7068 (mm-40) REVERT: O 195 LEU cc_start: 0.9361 (OUTLIER) cc_final: 0.9139 (tp) REVERT: R 50 ARG cc_start: 0.8865 (OUTLIER) cc_final: 0.7928 (ttt-90) REVERT: S 1 MET cc_start: 0.3566 (mtm) cc_final: 0.3065 (mpp) REVERT: S 173 PHE cc_start: 0.6547 (m-80) cc_final: 0.6047 (m-80) REVERT: V 198 TYR cc_start: 0.9305 (m-80) cc_final: 0.8804 (m-80) REVERT: A 222 ARG cc_start: 0.5087 (mmp-170) cc_final: 0.4288 (mmm160) REVERT: A 234 GLU cc_start: 0.8999 (tp30) cc_final: 0.8559 (tp30) REVERT: A 257 GLU cc_start: 0.8717 (pp20) cc_final: 0.8481 (pp20) REVERT: A 261 GLU cc_start: 0.8988 (mt-10) cc_final: 0.8491 (mm-30) REVERT: X 71 LYS cc_start: 0.8051 (tmtt) cc_final: 0.7403 (tmtt) REVERT: X 176 LYS cc_start: 0.7110 (mmtt) cc_final: 0.5763 (mmtp) REVERT: X 210 ARG cc_start: 0.8997 (mtm-85) cc_final: 0.8683 (mtm-85) REVERT: X 216 LYS cc_start: 0.9439 (mptt) cc_final: 0.9132 (mmtp) outliers start: 181 outliers final: 156 residues processed: 361 average time/residue: 0.4777 time to fit residues: 287.7994 Evaluate side-chains 364 residues out of total 5025 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 170 poor density : 194 time to evaluate : 3.931 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 28 THR Chi-restraints excluded: chain B residue 48 VAL Chi-restraints excluded: chain B residue 59 VAL Chi-restraints excluded: chain B residue 79 LYS Chi-restraints excluded: chain B residue 80 VAL Chi-restraints excluded: chain B residue 150 GLU Chi-restraints excluded: chain B residue 213 LEU Chi-restraints excluded: chain B residue 216 LEU Chi-restraints excluded: chain B residue 259 SER Chi-restraints excluded: chain B residue 322 VAL Chi-restraints excluded: chain C residue 25 MET Chi-restraints excluded: chain C residue 36 SER Chi-restraints excluded: chain C residue 128 GLU Chi-restraints excluded: chain C residue 165 ILE Chi-restraints excluded: chain C residue 225 VAL Chi-restraints excluded: chain C residue 248 SER Chi-restraints excluded: chain C residue 282 VAL Chi-restraints excluded: chain C residue 288 VAL Chi-restraints excluded: chain C residue 293 LYS Chi-restraints excluded: chain C residue 308 LEU Chi-restraints excluded: chain C residue 309 ASP Chi-restraints excluded: chain C residue 326 VAL Chi-restraints excluded: chain C residue 330 LEU Chi-restraints excluded: chain D residue 11 VAL Chi-restraints excluded: chain D residue 77 GLN Chi-restraints excluded: chain D residue 97 LEU Chi-restraints excluded: chain D residue 99 VAL Chi-restraints excluded: chain D residue 105 THR Chi-restraints excluded: chain D residue 208 HIS Chi-restraints excluded: chain D residue 264 LEU Chi-restraints excluded: chain D residue 282 VAL Chi-restraints excluded: chain D residue 288 VAL Chi-restraints excluded: chain D residue 289 THR Chi-restraints excluded: chain D residue 299 LYS Chi-restraints excluded: chain E residue 24 LEU Chi-restraints excluded: chain E residue 79 VAL Chi-restraints excluded: chain E residue 86 SER Chi-restraints excluded: chain E residue 99 VAL Chi-restraints excluded: chain E residue 100 LEU Chi-restraints excluded: chain E residue 118 LEU Chi-restraints excluded: chain E residue 158 VAL Chi-restraints excluded: chain E residue 160 VAL Chi-restraints excluded: chain E residue 245 THR Chi-restraints excluded: chain E residue 285 TYR Chi-restraints excluded: chain F residue 24 LEU Chi-restraints excluded: chain F residue 44 VAL Chi-restraints excluded: chain F residue 54 SER Chi-restraints excluded: chain F residue 158 VAL Chi-restraints excluded: chain F residue 173 THR Chi-restraints excluded: chain F residue 237 ASP Chi-restraints excluded: chain F residue 282 VAL Chi-restraints excluded: chain F residue 331 ILE Chi-restraints excluded: chain G residue 11 VAL Chi-restraints excluded: chain G residue 24 LEU Chi-restraints excluded: chain G residue 42 VAL Chi-restraints excluded: chain G residue 105 THR Chi-restraints excluded: chain G residue 140 HIS Chi-restraints excluded: chain G residue 158 VAL Chi-restraints excluded: chain G residue 160 VAL Chi-restraints excluded: chain G residue 183 LEU Chi-restraints excluded: chain G residue 208 HIS Chi-restraints excluded: chain G residue 213 VAL Chi-restraints excluded: chain G residue 243 SER Chi-restraints excluded: chain G residue 245 THR Chi-restraints excluded: chain G residue 285 TYR Chi-restraints excluded: chain H residue 34 ASP Chi-restraints excluded: chain H residue 50 ARG Chi-restraints excluded: chain H residue 53 ILE Chi-restraints excluded: chain H residue 170 VAL Chi-restraints excluded: chain H residue 231 LEU Chi-restraints excluded: chain H residue 243 SER Chi-restraints excluded: chain H residue 245 THR Chi-restraints excluded: chain H residue 289 THR Chi-restraints excluded: chain H residue 308 LEU Chi-restraints excluded: chain I residue 35 GLN Chi-restraints excluded: chain I residue 42 VAL Chi-restraints excluded: chain I residue 134 THR Chi-restraints excluded: chain I residue 138 THR Chi-restraints excluded: chain I residue 145 THR Chi-restraints excluded: chain L residue 17 ILE Chi-restraints excluded: chain L residue 28 THR Chi-restraints excluded: chain L residue 41 VAL Chi-restraints excluded: chain L residue 51 SER Chi-restraints excluded: chain L residue 137 MET Chi-restraints excluded: chain L residue 152 PHE Chi-restraints excluded: chain L residue 188 SER Chi-restraints excluded: chain L residue 210 LEU Chi-restraints excluded: chain L residue 280 VAL Chi-restraints excluded: chain M residue 11 VAL Chi-restraints excluded: chain M residue 192 LEU Chi-restraints excluded: chain M residue 225 VAL Chi-restraints excluded: chain M residue 246 LEU Chi-restraints excluded: chain M residue 264 LEU Chi-restraints excluded: chain M residue 282 VAL Chi-restraints excluded: chain M residue 283 GLU Chi-restraints excluded: chain M residue 288 VAL Chi-restraints excluded: chain N residue 8 THR Chi-restraints excluded: chain N residue 67 LEU Chi-restraints excluded: chain N residue 97 LEU Chi-restraints excluded: chain N residue 129 GLN Chi-restraints excluded: chain N residue 179 LEU Chi-restraints excluded: chain N residue 206 SER Chi-restraints excluded: chain N residue 231 LEU Chi-restraints excluded: chain N residue 264 LEU Chi-restraints excluded: chain O residue 78 THR Chi-restraints excluded: chain O residue 107 SER Chi-restraints excluded: chain O residue 158 VAL Chi-restraints excluded: chain O residue 160 VAL Chi-restraints excluded: chain O residue 195 LEU Chi-restraints excluded: chain O residue 201 SER Chi-restraints excluded: chain O residue 238 LYS Chi-restraints excluded: chain O residue 285 TYR Chi-restraints excluded: chain P residue 24 LEU Chi-restraints excluded: chain P residue 25 MET Chi-restraints excluded: chain P residue 158 VAL Chi-restraints excluded: chain P residue 173 THR Chi-restraints excluded: chain P residue 192 LEU Chi-restraints excluded: chain P residue 199 ILE Chi-restraints excluded: chain P residue 232 ILE Chi-restraints excluded: chain P residue 285 TYR Chi-restraints excluded: chain P residue 289 THR Chi-restraints excluded: chain Q residue 24 LEU Chi-restraints excluded: chain Q residue 25 MET Chi-restraints excluded: chain Q residue 43 THR Chi-restraints excluded: chain Q residue 105 THR Chi-restraints excluded: chain Q residue 158 VAL Chi-restraints excluded: chain Q residue 170 VAL Chi-restraints excluded: chain Q residue 173 THR Chi-restraints excluded: chain Q residue 208 HIS Chi-restraints excluded: chain Q residue 285 TYR Chi-restraints excluded: chain Q residue 290 SER Chi-restraints excluded: chain R residue 34 ASP Chi-restraints excluded: chain R residue 50 ARG Chi-restraints excluded: chain R residue 52 THR Chi-restraints excluded: chain R residue 71 ILE Chi-restraints excluded: chain R residue 86 SER Chi-restraints excluded: chain R residue 105 THR Chi-restraints excluded: chain R residue 160 VAL Chi-restraints excluded: chain R residue 170 VAL Chi-restraints excluded: chain R residue 192 LEU Chi-restraints excluded: chain R residue 203 LEU Chi-restraints excluded: chain R residue 213 VAL Chi-restraints excluded: chain R residue 231 LEU Chi-restraints excluded: chain R residue 245 THR Chi-restraints excluded: chain R residue 264 LEU Chi-restraints excluded: chain R residue 285 TYR Chi-restraints excluded: chain R residue 320 VAL Chi-restraints excluded: chain S residue 100 VAL Chi-restraints excluded: chain U residue 12 THR Chi-restraints excluded: chain U residue 46 TYR Chi-restraints excluded: chain U residue 73 ASP Chi-restraints excluded: chain U residue 127 GLU Chi-restraints excluded: chain U residue 167 LEU Chi-restraints excluded: chain U residue 177 THR Chi-restraints excluded: chain U residue 191 SER Chi-restraints excluded: chain U residue 197 LYS Chi-restraints excluded: chain V residue 12 THR Chi-restraints excluded: chain V residue 63 VAL Chi-restraints excluded: chain V residue 85 VAL Chi-restraints excluded: chain V residue 113 THR Chi-restraints excluded: chain V residue 127 GLU Chi-restraints excluded: chain V residue 177 THR Chi-restraints excluded: chain V residue 179 VAL Chi-restraints excluded: chain V residue 180 SER Chi-restraints excluded: chain A residue 66 VAL Chi-restraints excluded: chain A residue 173 SER Chi-restraints excluded: chain A residue 178 LEU Chi-restraints excluded: chain A residue 182 LEU Chi-restraints excluded: chain A residue 256 SER Chi-restraints excluded: chain X residue 66 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 627 random chunks: chunk 395 optimal weight: 6.9990 chunk 529 optimal weight: 8.9990 chunk 152 optimal weight: 4.9990 chunk 458 optimal weight: 20.0000 chunk 73 optimal weight: 8.9990 chunk 138 optimal weight: 3.9990 chunk 498 optimal weight: 0.0980 chunk 208 optimal weight: 6.9990 chunk 511 optimal weight: 2.9990 chunk 63 optimal weight: 5.9990 chunk 91 optimal weight: 0.9980 overall best weight: 2.6186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 110 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 110 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 140 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 84 GLN N 77 GLN ** S 19 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** U 26 HIS ** A 241 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3789 r_free = 0.3789 target = 0.093634 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3006 r_free = 0.3006 target = 0.057989 restraints weight = 189864.043| |-----------------------------------------------------------------------------| r_work (start): 0.2913 rms_B_bonded: 3.85 r_work: 0.2770 rms_B_bonded: 4.20 restraints_weight: 0.5000 r_work (final): 0.2770 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2764 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2764 r_free = 0.2764 target_work(ls_wunit_k1) = 0.049 | | occupancies: max = 1.00 min = 0.37 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2764 r_free = 0.2764 target_work(ls_wunit_k1) = 0.049 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 11 | |-----------------------------------------------------------------------------| r_final: 0.2764 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8666 moved from start: 0.3081 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 49575 Z= 0.215 Angle : 0.558 15.154 67829 Z= 0.287 Chirality : 0.040 0.235 7435 Planarity : 0.004 0.058 8566 Dihedral : 15.159 179.870 9087 Min Nonbonded Distance : 2.374 Molprobity Statistics. All-atom Clashscore : 6.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.13 % Favored : 93.87 % Rotamer: Outliers : 3.60 % Allowed : 23.59 % Favored : 72.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.68 % 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: -0.40 (0.11), residues: 6156 helix: 1.79 (0.12), residues: 2004 sheet: 0.10 (0.16), residues: 1052 loop : -1.90 (0.11), residues: 3100 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.045 0.001 TRP A 272 HIS 0.007 0.001 HIS C 208 PHE 0.016 0.001 PHE A 211 TYR 0.017 0.001 TYR X 259 ARG 0.017 0.000 ARG R 175 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7608.93 seconds wall clock time: 135 minutes 12.41 seconds (8112.41 seconds total)