Starting phenix.real_space_refine on Sat Feb 7 00:30:49 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9v2m_64733/02_2026/9v2m_64733.cif Found real_map, /net/cci-nas-00/data/ceres_data/9v2m_64733/02_2026/9v2m_64733.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.67 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9v2m_64733/02_2026/9v2m_64733.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9v2m_64733/02_2026/9v2m_64733.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9v2m_64733/02_2026/9v2m_64733.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9v2m_64733/02_2026/9v2m_64733.map" } resolution = 3.67 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.003 sd= 0.043 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: 4 Type Number sf(0) Gaussians S 96 5.16 5 C 18296 2.51 5 N 5088 2.21 5 O 5312 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 72 residue(s): 0.03s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 28792 Number of models: 1 Model: "" Number of chains: 16 Chain: "A" Number of atoms: 1396 Number of conformers: 1 Conformer: "" Number of residues, atoms: 180, 1396 Classifications: {'peptide': 180} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 1, 'PTRANS': 8, 'TRANS': 170} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Unresolved non-hydrogen chiralities: 1 Chain: "B" Number of atoms: 1396 Number of conformers: 1 Conformer: "" Number of residues, atoms: 180, 1396 Classifications: {'peptide': 180} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 1, 'PTRANS': 8, 'TRANS': 170} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Unresolved non-hydrogen chiralities: 1 Chain: "C" Number of atoms: 1396 Number of conformers: 1 Conformer: "" Number of residues, atoms: 180, 1396 Classifications: {'peptide': 180} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 1, 'PTRANS': 8, 'TRANS': 170} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Unresolved non-hydrogen chiralities: 1 Chain: "D" Number of atoms: 1396 Number of conformers: 1 Conformer: "" Number of residues, atoms: 180, 1396 Classifications: {'peptide': 180} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 1, 'PTRANS': 8, 'TRANS': 170} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Unresolved non-hydrogen chiralities: 1 Chain: "E" Number of atoms: 2203 Number of conformers: 1 Conformer: "" Number of residues, atoms: 277, 2203 Classifications: {'peptide': 277} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 13, 'TRANS': 263} Chain: "F" Number of atoms: 2203 Number of conformers: 1 Conformer: "" Number of residues, atoms: 277, 2203 Classifications: {'peptide': 277} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 13, 'TRANS': 263} Chain: "G" Number of atoms: 2203 Number of conformers: 1 Conformer: "" Number of residues, atoms: 277, 2203 Classifications: {'peptide': 277} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 13, 'TRANS': 263} Chain: "H" Number of atoms: 2203 Number of conformers: 1 Conformer: "" Number of residues, atoms: 277, 2203 Classifications: {'peptide': 277} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 13, 'TRANS': 263} Chain: "Q" Number of atoms: 1396 Number of conformers: 1 Conformer: "" Number of residues, atoms: 180, 1396 Classifications: {'peptide': 180} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 1, 'PTRANS': 8, 'TRANS': 170} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Unresolved non-hydrogen chiralities: 1 Chain: "R" Number of atoms: 1396 Number of conformers: 1 Conformer: "" Number of residues, atoms: 180, 1396 Classifications: {'peptide': 180} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 1, 'PTRANS': 8, 'TRANS': 170} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Unresolved non-hydrogen chiralities: 1 Chain: "S" Number of atoms: 1396 Number of conformers: 1 Conformer: "" Number of residues, atoms: 180, 1396 Classifications: {'peptide': 180} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 1, 'PTRANS': 8, 'TRANS': 170} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Unresolved non-hydrogen chiralities: 1 Chain: "T" Number of atoms: 1396 Number of conformers: 1 Conformer: "" Number of residues, atoms: 180, 1396 Classifications: {'peptide': 180} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 1, 'PTRANS': 8, 'TRANS': 170} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Unresolved non-hydrogen chiralities: 1 Chain: "U" Number of atoms: 2203 Number of conformers: 1 Conformer: "" Number of residues, atoms: 277, 2203 Classifications: {'peptide': 277} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 13, 'TRANS': 263} Chain: "V" Number of atoms: 2203 Number of conformers: 1 Conformer: "" Number of residues, atoms: 277, 2203 Classifications: {'peptide': 277} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 13, 'TRANS': 263} Chain: "W" Number of atoms: 2203 Number of conformers: 1 Conformer: "" Number of residues, atoms: 277, 2203 Classifications: {'peptide': 277} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 13, 'TRANS': 263} Chain: "X" Number of atoms: 2203 Number of conformers: 1 Conformer: "" Number of residues, atoms: 277, 2203 Classifications: {'peptide': 277} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 13, 'TRANS': 263} Time building chain proxies: 6.07, per 1000 atoms: 0.21 Number of scatterers: 28792 At special positions: 0 Unit cell: (136.15, 169.604, 150.154, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 96 16.00 O 5312 8.00 N 5088 7.00 C 18296 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: 2.46 Conformation dependent library (CDL) restraints added in 1.3 seconds 7248 Ramachandran restraints generated. 3624 Oldfield, 0 Emsley, 3624 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6832 Finding SS restraints... Secondary structure from input PDB file: 192 helices and 24 sheets defined 51.4% alpha, 17.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.32 Creating SS restraints... Processing helix chain 'A' and resid 11 through 22 removed outlier: 3.693A pdb=" N ARG A 16 " --> pdb=" O SER A 12 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N VAL A 21 " --> pdb=" O GLU A 17 " (cutoff:3.500A) Processing helix chain 'A' and resid 42 through 59 removed outlier: 3.585A pdb=" N ALA A 51 " --> pdb=" O ILE A 47 " (cutoff:3.500A) removed outlier: 4.087A pdb=" N ILE A 52 " --> pdb=" O ARG A 48 " (cutoff:3.500A) removed outlier: 3.745A pdb=" N ALA A 57 " --> pdb=" O ALA A 53 " (cutoff:3.500A) Processing helix chain 'A' and resid 81 through 87 removed outlier: 3.913A pdb=" N PHE A 85 " --> pdb=" O LEU A 81 " (cutoff:3.500A) Processing helix chain 'A' and resid 91 through 95 Processing helix chain 'A' and resid 158 through 163 Processing helix chain 'A' and resid 166 through 180 removed outlier: 3.749A pdb=" N ARG A 170 " --> pdb=" O SER A 166 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N HIS A 172 " --> pdb=" O LEU A 168 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N THR A 173 " --> pdb=" O GLY A 169 " (cutoff:3.500A) Processing helix chain 'B' and resid 11 through 22 removed outlier: 3.693A pdb=" N ARG B 16 " --> pdb=" O SER B 12 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N VAL B 21 " --> pdb=" O GLU B 17 " (cutoff:3.500A) Processing helix chain 'B' and resid 42 through 59 removed outlier: 3.586A pdb=" N ALA B 51 " --> pdb=" O ILE B 47 " (cutoff:3.500A) removed outlier: 4.087A pdb=" N ILE B 52 " --> pdb=" O ARG B 48 " (cutoff:3.500A) removed outlier: 3.745A pdb=" N ALA B 57 " --> pdb=" O ALA B 53 " (cutoff:3.500A) Processing helix chain 'B' and resid 81 through 87 removed outlier: 3.915A pdb=" N PHE B 85 " --> pdb=" O LEU B 81 " (cutoff:3.500A) Processing helix chain 'B' and resid 91 through 95 Processing helix chain 'B' and resid 158 through 163 Processing helix chain 'B' and resid 166 through 180 removed outlier: 3.750A pdb=" N ARG B 170 " --> pdb=" O SER B 166 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N HIS B 172 " --> pdb=" O LEU B 168 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N THR B 173 " --> pdb=" O GLY B 169 " (cutoff:3.500A) Processing helix chain 'C' and resid 11 through 22 removed outlier: 3.692A pdb=" N ARG C 16 " --> pdb=" O SER C 12 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N VAL C 21 " --> pdb=" O GLU C 17 " (cutoff:3.500A) Processing helix chain 'C' and resid 42 through 59 removed outlier: 3.587A pdb=" N ALA C 51 " --> pdb=" O ILE C 47 " (cutoff:3.500A) removed outlier: 4.087A pdb=" N ILE C 52 " --> pdb=" O ARG C 48 " (cutoff:3.500A) removed outlier: 3.742A pdb=" N ALA C 57 " --> pdb=" O ALA C 53 " (cutoff:3.500A) Processing helix chain 'C' and resid 81 through 87 removed outlier: 3.803A pdb=" N PHE C 85 " --> pdb=" O LEU C 81 " (cutoff:3.500A) Processing helix chain 'C' and resid 91 through 95 Processing helix chain 'C' and resid 158 through 163 Processing helix chain 'C' and resid 166 through 180 removed outlier: 3.748A pdb=" N ARG C 170 " --> pdb=" O SER C 166 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N HIS C 172 " --> pdb=" O LEU C 168 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N THR C 173 " --> pdb=" O GLY C 169 " (cutoff:3.500A) Processing helix chain 'D' and resid 11 through 22 removed outlier: 3.692A pdb=" N ARG D 16 " --> pdb=" O SER D 12 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N VAL D 21 " --> pdb=" O GLU D 17 " (cutoff:3.500A) Processing helix chain 'D' and resid 42 through 59 removed outlier: 3.587A pdb=" N ALA D 51 " --> pdb=" O ILE D 47 " (cutoff:3.500A) removed outlier: 4.086A pdb=" N ILE D 52 " --> pdb=" O ARG D 48 " (cutoff:3.500A) removed outlier: 3.744A pdb=" N ALA D 57 " --> pdb=" O ALA D 53 " (cutoff:3.500A) Processing helix chain 'D' and resid 81 through 87 removed outlier: 3.802A pdb=" N PHE D 85 " --> pdb=" O LEU D 81 " (cutoff:3.500A) Processing helix chain 'D' and resid 91 through 95 Processing helix chain 'D' and resid 158 through 163 Processing helix chain 'D' and resid 166 through 180 removed outlier: 3.748A pdb=" N ARG D 170 " --> pdb=" O SER D 166 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N HIS D 172 " --> pdb=" O LEU D 168 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N THR D 173 " --> pdb=" O GLY D 169 " (cutoff:3.500A) Processing helix chain 'E' and resid 5 through 19 Proline residue: E 11 - end of helix removed outlier: 3.539A pdb=" N GLU E 16 " --> pdb=" O LEU E 12 " (cutoff:3.500A) removed outlier: 3.902A pdb=" N GLU E 19 " --> pdb=" O LYS E 15 " (cutoff:3.500A) Processing helix chain 'E' and resid 28 through 35 Proline residue: E 33 - end of helix Processing helix chain 'E' and resid 39 through 47 Processing helix chain 'E' and resid 48 through 51 Processing helix chain 'E' and resid 53 through 58 Processing helix chain 'E' and resid 59 through 61 No H-bonds generated for 'chain 'E' and resid 59 through 61' Processing helix chain 'E' and resid 62 through 74 Processing helix chain 'E' and resid 74 through 90 removed outlier: 3.688A pdb=" N LEU E 78 " --> pdb=" O ALA E 74 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N ASP E 90 " --> pdb=" O SER E 86 " (cutoff:3.500A) Processing helix chain 'E' and resid 91 through 101 removed outlier: 3.789A pdb=" N LYS E 100 " --> pdb=" O ALA E 96 " (cutoff:3.500A) Processing helix chain 'E' and resid 101 through 109 Processing helix chain 'E' and resid 124 through 131 removed outlier: 3.680A pdb=" N LEU E 128 " --> pdb=" O VAL E 124 " (cutoff:3.500A) Processing helix chain 'E' and resid 140 through 146 Processing helix chain 'E' and resid 164 through 168 removed outlier: 3.522A pdb=" N ILE E 168 " --> pdb=" O PRO E 165 " (cutoff:3.500A) Processing helix chain 'E' and resid 171 through 178 Processing helix chain 'E' and resid 183 through 193 removed outlier: 3.681A pdb=" N ALA E 191 " --> pdb=" O GLN E 187 " (cutoff:3.500A) Processing helix chain 'E' and resid 209 through 224 removed outlier: 3.511A pdb=" N ASN E 218 " --> pdb=" O TRP E 214 " (cutoff:3.500A) Processing helix chain 'E' and resid 246 through 253 removed outlier: 3.520A pdb=" N ILE E 250 " --> pdb=" O VAL E 246 " (cutoff:3.500A) removed outlier: 3.960A pdb=" N GLN E 253 " --> pdb=" O ASP E 249 " (cutoff:3.500A) Processing helix chain 'E' and resid 265 through 278 removed outlier: 3.565A pdb=" N ILE E 277 " --> pdb=" O LEU E 273 " (cutoff:3.500A) removed outlier: 3.974A pdb=" N ALA E 278 " --> pdb=" O LEU E 274 " (cutoff:3.500A) Processing helix chain 'F' and resid 5 through 19 Proline residue: F 11 - end of helix removed outlier: 3.538A pdb=" N GLU F 16 " --> pdb=" O LEU F 12 " (cutoff:3.500A) removed outlier: 3.903A pdb=" N GLU F 19 " --> pdb=" O LYS F 15 " (cutoff:3.500A) Processing helix chain 'F' and resid 28 through 35 Proline residue: F 33 - end of helix Processing helix chain 'F' and resid 39 through 47 Processing helix chain 'F' and resid 48 through 51 Processing helix chain 'F' and resid 53 through 58 Processing helix chain 'F' and resid 59 through 61 No H-bonds generated for 'chain 'F' and resid 59 through 61' Processing helix chain 'F' and resid 62 through 74 Processing helix chain 'F' and resid 74 through 90 removed outlier: 3.687A pdb=" N LEU F 78 " --> pdb=" O ALA F 74 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N ASP F 90 " --> pdb=" O SER F 86 " (cutoff:3.500A) Processing helix chain 'F' and resid 91 through 101 removed outlier: 3.790A pdb=" N LYS F 100 " --> pdb=" O ALA F 96 " (cutoff:3.500A) Processing helix chain 'F' and resid 101 through 109 Processing helix chain 'F' and resid 124 through 131 removed outlier: 3.680A pdb=" N LEU F 128 " --> pdb=" O VAL F 124 " (cutoff:3.500A) Processing helix chain 'F' and resid 140 through 146 Processing helix chain 'F' and resid 164 through 168 removed outlier: 3.523A pdb=" N ILE F 168 " --> pdb=" O PRO F 165 " (cutoff:3.500A) Processing helix chain 'F' and resid 171 through 178 Processing helix chain 'F' and resid 183 through 193 removed outlier: 3.680A pdb=" N ALA F 191 " --> pdb=" O GLN F 187 " (cutoff:3.500A) Processing helix chain 'F' and resid 209 through 224 removed outlier: 3.512A pdb=" N ASN F 218 " --> pdb=" O TRP F 214 " (cutoff:3.500A) Processing helix chain 'F' and resid 246 through 253 removed outlier: 3.520A pdb=" N ILE F 250 " --> pdb=" O VAL F 246 " (cutoff:3.500A) removed outlier: 3.958A pdb=" N GLN F 253 " --> pdb=" O ASP F 249 " (cutoff:3.500A) Processing helix chain 'F' and resid 265 through 278 removed outlier: 3.565A pdb=" N ILE F 277 " --> pdb=" O LEU F 273 " (cutoff:3.500A) removed outlier: 3.975A pdb=" N ALA F 278 " --> pdb=" O LEU F 274 " (cutoff:3.500A) Processing helix chain 'G' and resid 5 through 19 Proline residue: G 11 - end of helix removed outlier: 3.539A pdb=" N GLU G 16 " --> pdb=" O LEU G 12 " (cutoff:3.500A) removed outlier: 3.903A pdb=" N GLU G 19 " --> pdb=" O LYS G 15 " (cutoff:3.500A) Processing helix chain 'G' and resid 28 through 35 Proline residue: G 33 - end of helix Processing helix chain 'G' and resid 39 through 47 Processing helix chain 'G' and resid 48 through 51 Processing helix chain 'G' and resid 53 through 58 Processing helix chain 'G' and resid 59 through 61 No H-bonds generated for 'chain 'G' and resid 59 through 61' Processing helix chain 'G' and resid 62 through 74 Processing helix chain 'G' and resid 74 through 90 removed outlier: 3.688A pdb=" N LEU G 78 " --> pdb=" O ALA G 74 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N ASP G 90 " --> pdb=" O SER G 86 " (cutoff:3.500A) Processing helix chain 'G' and resid 91 through 101 removed outlier: 3.789A pdb=" N LYS G 100 " --> pdb=" O ALA G 96 " (cutoff:3.500A) Processing helix chain 'G' and resid 101 through 109 Processing helix chain 'G' and resid 124 through 131 removed outlier: 3.681A pdb=" N LEU G 128 " --> pdb=" O VAL G 124 " (cutoff:3.500A) Processing helix chain 'G' and resid 140 through 146 Processing helix chain 'G' and resid 164 through 168 removed outlier: 3.523A pdb=" N ILE G 168 " --> pdb=" O PRO G 165 " (cutoff:3.500A) Processing helix chain 'G' and resid 171 through 178 Processing helix chain 'G' and resid 183 through 193 removed outlier: 3.680A pdb=" N ALA G 191 " --> pdb=" O GLN G 187 " (cutoff:3.500A) Processing helix chain 'G' and resid 209 through 224 removed outlier: 3.512A pdb=" N ASN G 218 " --> pdb=" O TRP G 214 " (cutoff:3.500A) Processing helix chain 'G' and resid 246 through 253 removed outlier: 3.521A pdb=" N ILE G 250 " --> pdb=" O VAL G 246 " (cutoff:3.500A) removed outlier: 3.961A pdb=" N GLN G 253 " --> pdb=" O ASP G 249 " (cutoff:3.500A) Processing helix chain 'G' and resid 265 through 278 removed outlier: 3.566A pdb=" N ILE G 277 " --> pdb=" O LEU G 273 " (cutoff:3.500A) removed outlier: 3.975A pdb=" N ALA G 278 " --> pdb=" O LEU G 274 " (cutoff:3.500A) Processing helix chain 'H' and resid 5 through 19 Proline residue: H 11 - end of helix removed outlier: 3.538A pdb=" N GLU H 16 " --> pdb=" O LEU H 12 " (cutoff:3.500A) removed outlier: 3.902A pdb=" N GLU H 19 " --> pdb=" O LYS H 15 " (cutoff:3.500A) Processing helix chain 'H' and resid 28 through 35 Proline residue: H 33 - end of helix Processing helix chain 'H' and resid 39 through 47 Processing helix chain 'H' and resid 48 through 51 Processing helix chain 'H' and resid 53 through 58 Processing helix chain 'H' and resid 59 through 61 No H-bonds generated for 'chain 'H' and resid 59 through 61' Processing helix chain 'H' and resid 62 through 74 Processing helix chain 'H' and resid 74 through 90 removed outlier: 3.687A pdb=" N LEU H 78 " --> pdb=" O ALA H 74 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N ASP H 90 " --> pdb=" O SER H 86 " (cutoff:3.500A) Processing helix chain 'H' and resid 91 through 101 removed outlier: 3.789A pdb=" N LYS H 100 " --> pdb=" O ALA H 96 " (cutoff:3.500A) Processing helix chain 'H' and resid 101 through 109 Processing helix chain 'H' and resid 124 through 131 removed outlier: 3.681A pdb=" N LEU H 128 " --> pdb=" O VAL H 124 " (cutoff:3.500A) Processing helix chain 'H' and resid 140 through 146 Processing helix chain 'H' and resid 164 through 168 removed outlier: 3.524A pdb=" N ILE H 168 " --> pdb=" O PRO H 165 " (cutoff:3.500A) Processing helix chain 'H' and resid 171 through 178 Processing helix chain 'H' and resid 183 through 193 removed outlier: 3.681A pdb=" N ALA H 191 " --> pdb=" O GLN H 187 " (cutoff:3.500A) Processing helix chain 'H' and resid 209 through 224 removed outlier: 3.511A pdb=" N ASN H 218 " --> pdb=" O TRP H 214 " (cutoff:3.500A) Processing helix chain 'H' and resid 246 through 253 removed outlier: 3.520A pdb=" N ILE H 250 " --> pdb=" O VAL H 246 " (cutoff:3.500A) removed outlier: 3.959A pdb=" N GLN H 253 " --> pdb=" O ASP H 249 " (cutoff:3.500A) Processing helix chain 'H' and resid 265 through 278 removed outlier: 3.566A pdb=" N ILE H 277 " --> pdb=" O LEU H 273 " (cutoff:3.500A) removed outlier: 3.975A pdb=" N ALA H 278 " --> pdb=" O LEU H 274 " (cutoff:3.500A) Processing helix chain 'Q' and resid 11 through 22 removed outlier: 3.693A pdb=" N ARG Q 16 " --> pdb=" O SER Q 12 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N VAL Q 21 " --> pdb=" O GLU Q 17 " (cutoff:3.500A) Processing helix chain 'Q' and resid 42 through 59 removed outlier: 3.586A pdb=" N ALA Q 51 " --> pdb=" O ILE Q 47 " (cutoff:3.500A) removed outlier: 4.087A pdb=" N ILE Q 52 " --> pdb=" O ARG Q 48 " (cutoff:3.500A) removed outlier: 3.745A pdb=" N ALA Q 57 " --> pdb=" O ALA Q 53 " (cutoff:3.500A) Processing helix chain 'Q' and resid 81 through 87 removed outlier: 3.913A pdb=" N PHE Q 85 " --> pdb=" O LEU Q 81 " (cutoff:3.500A) Processing helix chain 'Q' and resid 91 through 95 Processing helix chain 'Q' and resid 158 through 163 Processing helix chain 'Q' and resid 166 through 180 removed outlier: 3.750A pdb=" N ARG Q 170 " --> pdb=" O SER Q 166 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N HIS Q 172 " --> pdb=" O LEU Q 168 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N THR Q 173 " --> pdb=" O GLY Q 169 " (cutoff:3.500A) Processing helix chain 'R' and resid 11 through 22 removed outlier: 3.692A pdb=" N ARG R 16 " --> pdb=" O SER R 12 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N VAL R 21 " --> pdb=" O GLU R 17 " (cutoff:3.500A) Processing helix chain 'R' and resid 42 through 59 removed outlier: 3.585A pdb=" N ALA R 51 " --> pdb=" O ILE R 47 " (cutoff:3.500A) removed outlier: 4.087A pdb=" N ILE R 52 " --> pdb=" O ARG R 48 " (cutoff:3.500A) removed outlier: 3.744A pdb=" N ALA R 57 " --> pdb=" O ALA R 53 " (cutoff:3.500A) Processing helix chain 'R' and resid 81 through 87 removed outlier: 3.914A pdb=" N PHE R 85 " --> pdb=" O LEU R 81 " (cutoff:3.500A) Processing helix chain 'R' and resid 91 through 95 Processing helix chain 'R' and resid 158 through 163 Processing helix chain 'R' and resid 166 through 180 removed outlier: 3.749A pdb=" N ARG R 170 " --> pdb=" O SER R 166 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N HIS R 172 " --> pdb=" O LEU R 168 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N THR R 173 " --> pdb=" O GLY R 169 " (cutoff:3.500A) Processing helix chain 'S' and resid 11 through 22 removed outlier: 3.692A pdb=" N ARG S 16 " --> pdb=" O SER S 12 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N VAL S 21 " --> pdb=" O GLU S 17 " (cutoff:3.500A) Processing helix chain 'S' and resid 42 through 59 removed outlier: 3.587A pdb=" N ALA S 51 " --> pdb=" O ILE S 47 " (cutoff:3.500A) removed outlier: 4.087A pdb=" N ILE S 52 " --> pdb=" O ARG S 48 " (cutoff:3.500A) removed outlier: 3.743A pdb=" N ALA S 57 " --> pdb=" O ALA S 53 " (cutoff:3.500A) Processing helix chain 'S' and resid 81 through 87 removed outlier: 3.802A pdb=" N PHE S 85 " --> pdb=" O LEU S 81 " (cutoff:3.500A) Processing helix chain 'S' and resid 91 through 95 Processing helix chain 'S' and resid 158 through 163 Processing helix chain 'S' and resid 166 through 180 removed outlier: 3.748A pdb=" N ARG S 170 " --> pdb=" O SER S 166 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N HIS S 172 " --> pdb=" O LEU S 168 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N THR S 173 " --> pdb=" O GLY S 169 " (cutoff:3.500A) Processing helix chain 'T' and resid 11 through 22 removed outlier: 3.692A pdb=" N ARG T 16 " --> pdb=" O SER T 12 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N VAL T 21 " --> pdb=" O GLU T 17 " (cutoff:3.500A) Processing helix chain 'T' and resid 42 through 59 removed outlier: 3.589A pdb=" N ALA T 51 " --> pdb=" O ILE T 47 " (cutoff:3.500A) removed outlier: 4.086A pdb=" N ILE T 52 " --> pdb=" O ARG T 48 " (cutoff:3.500A) removed outlier: 3.743A pdb=" N ALA T 57 " --> pdb=" O ALA T 53 " (cutoff:3.500A) Processing helix chain 'T' and resid 81 through 87 removed outlier: 3.802A pdb=" N PHE T 85 " --> pdb=" O LEU T 81 " (cutoff:3.500A) Processing helix chain 'T' and resid 91 through 95 Processing helix chain 'T' and resid 158 through 163 Processing helix chain 'T' and resid 166 through 180 removed outlier: 3.749A pdb=" N ARG T 170 " --> pdb=" O SER T 166 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N HIS T 172 " --> pdb=" O LEU T 168 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N THR T 173 " --> pdb=" O GLY T 169 " (cutoff:3.500A) Processing helix chain 'U' and resid 5 through 19 Proline residue: U 11 - end of helix removed outlier: 3.539A pdb=" N GLU U 16 " --> pdb=" O LEU U 12 " (cutoff:3.500A) removed outlier: 3.902A pdb=" N GLU U 19 " --> pdb=" O LYS U 15 " (cutoff:3.500A) Processing helix chain 'U' and resid 28 through 35 Proline residue: U 33 - end of helix Processing helix chain 'U' and resid 39 through 47 Processing helix chain 'U' and resid 48 through 51 Processing helix chain 'U' and resid 53 through 58 Processing helix chain 'U' and resid 59 through 61 No H-bonds generated for 'chain 'U' and resid 59 through 61' Processing helix chain 'U' and resid 62 through 74 Processing helix chain 'U' and resid 74 through 90 removed outlier: 3.687A pdb=" N LEU U 78 " --> pdb=" O ALA U 74 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N ASP U 90 " --> pdb=" O SER U 86 " (cutoff:3.500A) Processing helix chain 'U' and resid 91 through 101 removed outlier: 3.788A pdb=" N LYS U 100 " --> pdb=" O ALA U 96 " (cutoff:3.500A) Processing helix chain 'U' and resid 101 through 109 Processing helix chain 'U' and resid 124 through 131 removed outlier: 3.680A pdb=" N LEU U 128 " --> pdb=" O VAL U 124 " (cutoff:3.500A) Processing helix chain 'U' and resid 140 through 146 Processing helix chain 'U' and resid 164 through 168 removed outlier: 3.523A pdb=" N ILE U 168 " --> pdb=" O PRO U 165 " (cutoff:3.500A) Processing helix chain 'U' and resid 171 through 178 Processing helix chain 'U' and resid 183 through 193 removed outlier: 3.681A pdb=" N ALA U 191 " --> pdb=" O GLN U 187 " (cutoff:3.500A) Processing helix chain 'U' and resid 209 through 224 removed outlier: 3.512A pdb=" N ASN U 218 " --> pdb=" O TRP U 214 " (cutoff:3.500A) Processing helix chain 'U' and resid 246 through 253 removed outlier: 3.520A pdb=" N ILE U 250 " --> pdb=" O VAL U 246 " (cutoff:3.500A) removed outlier: 3.959A pdb=" N GLN U 253 " --> pdb=" O ASP U 249 " (cutoff:3.500A) Processing helix chain 'U' and resid 265 through 278 removed outlier: 3.566A pdb=" N ILE U 277 " --> pdb=" O LEU U 273 " (cutoff:3.500A) removed outlier: 3.974A pdb=" N ALA U 278 " --> pdb=" O LEU U 274 " (cutoff:3.500A) Processing helix chain 'V' and resid 5 through 19 Proline residue: V 11 - end of helix removed outlier: 3.540A pdb=" N GLU V 16 " --> pdb=" O LEU V 12 " (cutoff:3.500A) removed outlier: 3.902A pdb=" N GLU V 19 " --> pdb=" O LYS V 15 " (cutoff:3.500A) Processing helix chain 'V' and resid 28 through 35 Proline residue: V 33 - end of helix Processing helix chain 'V' and resid 39 through 47 Processing helix chain 'V' and resid 48 through 51 Processing helix chain 'V' and resid 53 through 58 Processing helix chain 'V' and resid 59 through 61 No H-bonds generated for 'chain 'V' and resid 59 through 61' Processing helix chain 'V' and resid 62 through 74 Processing helix chain 'V' and resid 74 through 90 removed outlier: 3.688A pdb=" N LEU V 78 " --> pdb=" O ALA V 74 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N ASP V 90 " --> pdb=" O SER V 86 " (cutoff:3.500A) Processing helix chain 'V' and resid 91 through 101 removed outlier: 3.788A pdb=" N LYS V 100 " --> pdb=" O ALA V 96 " (cutoff:3.500A) Processing helix chain 'V' and resid 101 through 109 Processing helix chain 'V' and resid 124 through 131 removed outlier: 3.681A pdb=" N LEU V 128 " --> pdb=" O VAL V 124 " (cutoff:3.500A) Processing helix chain 'V' and resid 140 through 146 Processing helix chain 'V' and resid 164 through 168 removed outlier: 3.524A pdb=" N ILE V 168 " --> pdb=" O PRO V 165 " (cutoff:3.500A) Processing helix chain 'V' and resid 171 through 178 Processing helix chain 'V' and resid 183 through 193 removed outlier: 3.680A pdb=" N ALA V 191 " --> pdb=" O GLN V 187 " (cutoff:3.500A) Processing helix chain 'V' and resid 209 through 224 removed outlier: 3.512A pdb=" N ASN V 218 " --> pdb=" O TRP V 214 " (cutoff:3.500A) Processing helix chain 'V' and resid 246 through 253 removed outlier: 3.521A pdb=" N ILE V 250 " --> pdb=" O VAL V 246 " (cutoff:3.500A) removed outlier: 3.959A pdb=" N GLN V 253 " --> pdb=" O ASP V 249 " (cutoff:3.500A) Processing helix chain 'V' and resid 265 through 278 removed outlier: 3.565A pdb=" N ILE V 277 " --> pdb=" O LEU V 273 " (cutoff:3.500A) removed outlier: 3.976A pdb=" N ALA V 278 " --> pdb=" O LEU V 274 " (cutoff:3.500A) Processing helix chain 'W' and resid 5 through 19 Proline residue: W 11 - end of helix removed outlier: 3.539A pdb=" N GLU W 16 " --> pdb=" O LEU W 12 " (cutoff:3.500A) removed outlier: 3.902A pdb=" N GLU W 19 " --> pdb=" O LYS W 15 " (cutoff:3.500A) Processing helix chain 'W' and resid 28 through 35 Proline residue: W 33 - end of helix Processing helix chain 'W' and resid 39 through 47 Processing helix chain 'W' and resid 48 through 51 Processing helix chain 'W' and resid 53 through 58 Processing helix chain 'W' and resid 59 through 61 No H-bonds generated for 'chain 'W' and resid 59 through 61' Processing helix chain 'W' and resid 62 through 74 Processing helix chain 'W' and resid 74 through 90 removed outlier: 3.687A pdb=" N LEU W 78 " --> pdb=" O ALA W 74 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N ASP W 90 " --> pdb=" O SER W 86 " (cutoff:3.500A) Processing helix chain 'W' and resid 91 through 101 removed outlier: 3.789A pdb=" N LYS W 100 " --> pdb=" O ALA W 96 " (cutoff:3.500A) Processing helix chain 'W' and resid 101 through 109 Processing helix chain 'W' and resid 124 through 131 removed outlier: 3.680A pdb=" N LEU W 128 " --> pdb=" O VAL W 124 " (cutoff:3.500A) Processing helix chain 'W' and resid 140 through 146 Processing helix chain 'W' and resid 164 through 168 removed outlier: 3.523A pdb=" N ILE W 168 " --> pdb=" O PRO W 165 " (cutoff:3.500A) Processing helix chain 'W' and resid 171 through 178 Processing helix chain 'W' and resid 183 through 193 removed outlier: 3.681A pdb=" N ALA W 191 " --> pdb=" O GLN W 187 " (cutoff:3.500A) Processing helix chain 'W' and resid 209 through 224 removed outlier: 3.512A pdb=" N ASN W 218 " --> pdb=" O TRP W 214 " (cutoff:3.500A) Processing helix chain 'W' and resid 246 through 253 removed outlier: 3.519A pdb=" N ILE W 250 " --> pdb=" O VAL W 246 " (cutoff:3.500A) removed outlier: 3.959A pdb=" N GLN W 253 " --> pdb=" O ASP W 249 " (cutoff:3.500A) Processing helix chain 'W' and resid 265 through 278 removed outlier: 3.565A pdb=" N ILE W 277 " --> pdb=" O LEU W 273 " (cutoff:3.500A) removed outlier: 3.975A pdb=" N ALA W 278 " --> pdb=" O LEU W 274 " (cutoff:3.500A) Processing helix chain 'X' and resid 5 through 19 Proline residue: X 11 - end of helix removed outlier: 3.539A pdb=" N GLU X 16 " --> pdb=" O LEU X 12 " (cutoff:3.500A) removed outlier: 3.902A pdb=" N GLU X 19 " --> pdb=" O LYS X 15 " (cutoff:3.500A) Processing helix chain 'X' and resid 28 through 35 Proline residue: X 33 - end of helix Processing helix chain 'X' and resid 39 through 47 Processing helix chain 'X' and resid 48 through 51 Processing helix chain 'X' and resid 53 through 58 Processing helix chain 'X' and resid 59 through 61 No H-bonds generated for 'chain 'X' and resid 59 through 61' Processing helix chain 'X' and resid 62 through 74 Processing helix chain 'X' and resid 74 through 90 removed outlier: 3.687A pdb=" N LEU X 78 " --> pdb=" O ALA X 74 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N ASP X 90 " --> pdb=" O SER X 86 " (cutoff:3.500A) Processing helix chain 'X' and resid 91 through 101 removed outlier: 3.788A pdb=" N LYS X 100 " --> pdb=" O ALA X 96 " (cutoff:3.500A) Processing helix chain 'X' and resid 101 through 109 Processing helix chain 'X' and resid 124 through 131 removed outlier: 3.680A pdb=" N LEU X 128 " --> pdb=" O VAL X 124 " (cutoff:3.500A) Processing helix chain 'X' and resid 140 through 146 Processing helix chain 'X' and resid 164 through 168 removed outlier: 3.524A pdb=" N ILE X 168 " --> pdb=" O PRO X 165 " (cutoff:3.500A) Processing helix chain 'X' and resid 171 through 178 Processing helix chain 'X' and resid 183 through 193 removed outlier: 3.681A pdb=" N ALA X 191 " --> pdb=" O GLN X 187 " (cutoff:3.500A) Processing helix chain 'X' and resid 209 through 224 removed outlier: 3.512A pdb=" N ASN X 218 " --> pdb=" O TRP X 214 " (cutoff:3.500A) Processing helix chain 'X' and resid 246 through 253 removed outlier: 3.519A pdb=" N ILE X 250 " --> pdb=" O VAL X 246 " (cutoff:3.500A) removed outlier: 3.960A pdb=" N GLN X 253 " --> pdb=" O ASP X 249 " (cutoff:3.500A) Processing helix chain 'X' and resid 265 through 278 removed outlier: 3.565A pdb=" N ILE X 277 " --> pdb=" O LEU X 273 " (cutoff:3.500A) removed outlier: 3.974A pdb=" N ALA X 278 " --> pdb=" O LEU X 274 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 28 through 31 removed outlier: 6.635A pdb=" N TRP A 5 " --> pdb=" O GLY A 29 " (cutoff:3.500A) removed outlier: 7.502A pdb=" N LEU A 31 " --> pdb=" O TRP A 5 " (cutoff:3.500A) removed outlier: 5.924A pdb=" N TYR A 7 " --> pdb=" O LEU A 31 " (cutoff:3.500A) removed outlier: 4.850A pdb=" N GLU A 65 " --> pdb=" O ASN A 8 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N LEU A 77 " --> pdb=" O ILE A 71 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 28 through 31 removed outlier: 6.635A pdb=" N TRP A 5 " --> pdb=" O GLY A 29 " (cutoff:3.500A) removed outlier: 7.502A pdb=" N LEU A 31 " --> pdb=" O TRP A 5 " (cutoff:3.500A) removed outlier: 5.924A pdb=" N TYR A 7 " --> pdb=" O LEU A 31 " (cutoff:3.500A) removed outlier: 4.850A pdb=" N GLU A 65 " --> pdb=" O ASN A 8 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 28 through 31 removed outlier: 6.634A pdb=" N TRP B 5 " --> pdb=" O GLY B 29 " (cutoff:3.500A) removed outlier: 7.502A pdb=" N LEU B 31 " --> pdb=" O TRP B 5 " (cutoff:3.500A) removed outlier: 5.924A pdb=" N TYR B 7 " --> pdb=" O LEU B 31 " (cutoff:3.500A) removed outlier: 4.850A pdb=" N GLU B 65 " --> pdb=" O ASN B 8 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N LEU B 77 " --> pdb=" O ILE B 71 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 28 through 31 removed outlier: 6.634A pdb=" N TRP B 5 " --> pdb=" O GLY B 29 " (cutoff:3.500A) removed outlier: 7.502A pdb=" N LEU B 31 " --> pdb=" O TRP B 5 " (cutoff:3.500A) removed outlier: 5.924A pdb=" N TYR B 7 " --> pdb=" O LEU B 31 " (cutoff:3.500A) removed outlier: 4.850A pdb=" N GLU B 65 " --> pdb=" O ASN B 8 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'C' and resid 28 through 31 removed outlier: 6.631A pdb=" N TRP C 5 " --> pdb=" O GLY C 29 " (cutoff:3.500A) removed outlier: 7.503A pdb=" N LEU C 31 " --> pdb=" O TRP C 5 " (cutoff:3.500A) removed outlier: 5.923A pdb=" N TYR C 7 " --> pdb=" O LEU C 31 " (cutoff:3.500A) removed outlier: 4.852A pdb=" N GLU C 65 " --> pdb=" O ASN C 8 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'C' and resid 28 through 31 removed outlier: 6.631A pdb=" N TRP C 5 " --> pdb=" O GLY C 29 " (cutoff:3.500A) removed outlier: 7.503A pdb=" N LEU C 31 " --> pdb=" O TRP C 5 " (cutoff:3.500A) removed outlier: 5.923A pdb=" N TYR C 7 " --> pdb=" O LEU C 31 " (cutoff:3.500A) removed outlier: 4.852A pdb=" N GLU C 65 " --> pdb=" O ASN C 8 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'D' and resid 28 through 31 removed outlier: 6.632A pdb=" N TRP D 5 " --> pdb=" O GLY D 29 " (cutoff:3.500A) removed outlier: 7.502A pdb=" N LEU D 31 " --> pdb=" O TRP D 5 " (cutoff:3.500A) removed outlier: 5.922A pdb=" N TYR D 7 " --> pdb=" O LEU D 31 " (cutoff:3.500A) removed outlier: 4.852A pdb=" N GLU D 65 " --> pdb=" O ASN D 8 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'D' and resid 28 through 31 removed outlier: 6.632A pdb=" N TRP D 5 " --> pdb=" O GLY D 29 " (cutoff:3.500A) removed outlier: 7.502A pdb=" N LEU D 31 " --> pdb=" O TRP D 5 " (cutoff:3.500A) removed outlier: 5.922A pdb=" N TYR D 7 " --> pdb=" O LEU D 31 " (cutoff:3.500A) removed outlier: 4.852A pdb=" N GLU D 65 " --> pdb=" O ASN D 8 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'E' and resid 135 through 138 removed outlier: 5.896A pdb=" N ALA E 136 " --> pdb=" O VAL E 155 " (cutoff:3.500A) removed outlier: 6.772A pdb=" N LYS E 157 " --> pdb=" O ALA E 136 " (cutoff:3.500A) removed outlier: 6.570A pdb=" N LEU E 138 " --> pdb=" O LYS E 157 " (cutoff:3.500A) removed outlier: 7.111A pdb=" N LEU E 22 " --> pdb=" O THR E 114 " (cutoff:3.500A) removed outlier: 8.156A pdb=" N TYR E 116 " --> pdb=" O LEU E 22 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'F' and resid 135 through 138 removed outlier: 5.896A pdb=" N ALA F 136 " --> pdb=" O VAL F 155 " (cutoff:3.500A) removed outlier: 6.773A pdb=" N LYS F 157 " --> pdb=" O ALA F 136 " (cutoff:3.500A) removed outlier: 6.570A pdb=" N LEU F 138 " --> pdb=" O LYS F 157 " (cutoff:3.500A) removed outlier: 7.111A pdb=" N LEU F 22 " --> pdb=" O THR F 114 " (cutoff:3.500A) removed outlier: 8.155A pdb=" N TYR F 116 " --> pdb=" O LEU F 22 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'G' and resid 135 through 138 removed outlier: 5.896A pdb=" N ALA G 136 " --> pdb=" O VAL G 155 " (cutoff:3.500A) removed outlier: 6.773A pdb=" N LYS G 157 " --> pdb=" O ALA G 136 " (cutoff:3.500A) removed outlier: 6.568A pdb=" N LEU G 138 " --> pdb=" O LYS G 157 " (cutoff:3.500A) removed outlier: 7.111A pdb=" N LEU G 22 " --> pdb=" O THR G 114 " (cutoff:3.500A) removed outlier: 8.155A pdb=" N TYR G 116 " --> pdb=" O LEU G 22 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'H' and resid 135 through 138 removed outlier: 5.896A pdb=" N ALA H 136 " --> pdb=" O VAL H 155 " (cutoff:3.500A) removed outlier: 6.773A pdb=" N LYS H 157 " --> pdb=" O ALA H 136 " (cutoff:3.500A) removed outlier: 6.569A pdb=" N LEU H 138 " --> pdb=" O LYS H 157 " (cutoff:3.500A) removed outlier: 7.112A pdb=" N LEU H 22 " --> pdb=" O THR H 114 " (cutoff:3.500A) removed outlier: 8.156A pdb=" N TYR H 116 " --> pdb=" O LEU H 22 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'Q' and resid 28 through 31 removed outlier: 6.635A pdb=" N TRP Q 5 " --> pdb=" O GLY Q 29 " (cutoff:3.500A) removed outlier: 7.502A pdb=" N LEU Q 31 " --> pdb=" O TRP Q 5 " (cutoff:3.500A) removed outlier: 5.923A pdb=" N TYR Q 7 " --> pdb=" O LEU Q 31 " (cutoff:3.500A) removed outlier: 4.852A pdb=" N GLU Q 65 " --> pdb=" O ASN Q 8 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N LEU Q 77 " --> pdb=" O ILE Q 71 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'Q' and resid 28 through 31 removed outlier: 6.635A pdb=" N TRP Q 5 " --> pdb=" O GLY Q 29 " (cutoff:3.500A) removed outlier: 7.502A pdb=" N LEU Q 31 " --> pdb=" O TRP Q 5 " (cutoff:3.500A) removed outlier: 5.923A pdb=" N TYR Q 7 " --> pdb=" O LEU Q 31 " (cutoff:3.500A) removed outlier: 4.852A pdb=" N GLU Q 65 " --> pdb=" O ASN Q 8 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'R' and resid 28 through 31 removed outlier: 6.634A pdb=" N TRP R 5 " --> pdb=" O GLY R 29 " (cutoff:3.500A) removed outlier: 7.501A pdb=" N LEU R 31 " --> pdb=" O TRP R 5 " (cutoff:3.500A) removed outlier: 5.924A pdb=" N TYR R 7 " --> pdb=" O LEU R 31 " (cutoff:3.500A) removed outlier: 4.850A pdb=" N GLU R 65 " --> pdb=" O ASN R 8 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N LEU R 77 " --> pdb=" O ILE R 71 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'R' and resid 28 through 31 removed outlier: 6.634A pdb=" N TRP R 5 " --> pdb=" O GLY R 29 " (cutoff:3.500A) removed outlier: 7.501A pdb=" N LEU R 31 " --> pdb=" O TRP R 5 " (cutoff:3.500A) removed outlier: 5.924A pdb=" N TYR R 7 " --> pdb=" O LEU R 31 " (cutoff:3.500A) removed outlier: 4.850A pdb=" N GLU R 65 " --> pdb=" O ASN R 8 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'S' and resid 28 through 31 removed outlier: 6.632A pdb=" N TRP S 5 " --> pdb=" O GLY S 29 " (cutoff:3.500A) removed outlier: 7.502A pdb=" N LEU S 31 " --> pdb=" O TRP S 5 " (cutoff:3.500A) removed outlier: 5.922A pdb=" N TYR S 7 " --> pdb=" O LEU S 31 " (cutoff:3.500A) removed outlier: 4.850A pdb=" N GLU S 65 " --> pdb=" O ASN S 8 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'S' and resid 28 through 31 removed outlier: 6.632A pdb=" N TRP S 5 " --> pdb=" O GLY S 29 " (cutoff:3.500A) removed outlier: 7.502A pdb=" N LEU S 31 " --> pdb=" O TRP S 5 " (cutoff:3.500A) removed outlier: 5.922A pdb=" N TYR S 7 " --> pdb=" O LEU S 31 " (cutoff:3.500A) removed outlier: 4.850A pdb=" N GLU S 65 " --> pdb=" O ASN S 8 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'T' and resid 28 through 31 removed outlier: 6.633A pdb=" N TRP T 5 " --> pdb=" O GLY T 29 " (cutoff:3.500A) removed outlier: 7.503A pdb=" N LEU T 31 " --> pdb=" O TRP T 5 " (cutoff:3.500A) removed outlier: 5.923A pdb=" N TYR T 7 " --> pdb=" O LEU T 31 " (cutoff:3.500A) removed outlier: 4.852A pdb=" N GLU T 65 " --> pdb=" O ASN T 8 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'T' and resid 28 through 31 removed outlier: 6.633A pdb=" N TRP T 5 " --> pdb=" O GLY T 29 " (cutoff:3.500A) removed outlier: 7.503A pdb=" N LEU T 31 " --> pdb=" O TRP T 5 " (cutoff:3.500A) removed outlier: 5.923A pdb=" N TYR T 7 " --> pdb=" O LEU T 31 " (cutoff:3.500A) removed outlier: 4.852A pdb=" N GLU T 65 " --> pdb=" O ASN T 8 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'U' and resid 135 through 138 removed outlier: 5.895A pdb=" N ALA U 136 " --> pdb=" O VAL U 155 " (cutoff:3.500A) removed outlier: 6.771A pdb=" N LYS U 157 " --> pdb=" O ALA U 136 " (cutoff:3.500A) removed outlier: 6.569A pdb=" N LEU U 138 " --> pdb=" O LYS U 157 " (cutoff:3.500A) removed outlier: 7.111A pdb=" N LEU U 22 " --> pdb=" O THR U 114 " (cutoff:3.500A) removed outlier: 8.155A pdb=" N TYR U 116 " --> pdb=" O LEU U 22 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'V' and resid 135 through 138 removed outlier: 5.897A pdb=" N ALA V 136 " --> pdb=" O VAL V 155 " (cutoff:3.500A) removed outlier: 6.773A pdb=" N LYS V 157 " --> pdb=" O ALA V 136 " (cutoff:3.500A) removed outlier: 6.570A pdb=" N LEU V 138 " --> pdb=" O LYS V 157 " (cutoff:3.500A) removed outlier: 7.111A pdb=" N LEU V 22 " --> pdb=" O THR V 114 " (cutoff:3.500A) removed outlier: 8.156A pdb=" N TYR V 116 " --> pdb=" O LEU V 22 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'W' and resid 135 through 138 removed outlier: 5.896A pdb=" N ALA W 136 " --> pdb=" O VAL W 155 " (cutoff:3.500A) removed outlier: 6.771A pdb=" N LYS W 157 " --> pdb=" O ALA W 136 " (cutoff:3.500A) removed outlier: 6.569A pdb=" N LEU W 138 " --> pdb=" O LYS W 157 " (cutoff:3.500A) removed outlier: 7.112A pdb=" N LEU W 22 " --> pdb=" O THR W 114 " (cutoff:3.500A) removed outlier: 8.156A pdb=" N TYR W 116 " --> pdb=" O LEU W 22 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'X' and resid 135 through 138 removed outlier: 5.897A pdb=" N ALA X 136 " --> pdb=" O VAL X 155 " (cutoff:3.500A) removed outlier: 6.772A pdb=" N LYS X 157 " --> pdb=" O ALA X 136 " (cutoff:3.500A) removed outlier: 6.568A pdb=" N LEU X 138 " --> pdb=" O LYS X 157 " (cutoff:3.500A) removed outlier: 7.112A pdb=" N LEU X 22 " --> pdb=" O THR X 114 " (cutoff:3.500A) removed outlier: 8.155A pdb=" N TYR X 116 " --> pdb=" O LEU X 22 " (cutoff:3.500A) 1268 hydrogen bonds defined for protein. 3636 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 5.30 Time building geometry restraints manager: 3.24 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 9028 1.33 - 1.45: 4828 1.45 - 1.57: 15416 1.57 - 1.69: 0 1.69 - 1.81: 144 Bond restraints: 29416 Sorted by residual: bond pdb=" N ILE Q 71 " pdb=" CA ILE Q 71 " ideal model delta sigma weight residual 1.459 1.494 -0.035 1.27e-02 6.20e+03 7.56e+00 bond pdb=" N ILE C 71 " pdb=" CA ILE C 71 " ideal model delta sigma weight residual 1.459 1.494 -0.035 1.27e-02 6.20e+03 7.50e+00 bond pdb=" N ILE T 71 " pdb=" CA ILE T 71 " ideal model delta sigma weight residual 1.459 1.494 -0.035 1.27e-02 6.20e+03 7.50e+00 bond pdb=" N ILE S 71 " pdb=" CA ILE S 71 " ideal model delta sigma weight residual 1.459 1.494 -0.035 1.27e-02 6.20e+03 7.48e+00 bond pdb=" N ILE R 71 " pdb=" CA ILE R 71 " ideal model delta sigma weight residual 1.459 1.494 -0.035 1.27e-02 6.20e+03 7.44e+00 ... (remaining 29411 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.16: 38430 2.16 - 4.33: 1259 4.33 - 6.49: 99 6.49 - 8.65: 60 8.65 - 10.81: 8 Bond angle restraints: 39856 Sorted by residual: angle pdb=" C PHE T 139 " pdb=" N HIS T 140 " pdb=" CA HIS T 140 " ideal model delta sigma weight residual 121.54 132.35 -10.81 1.91e+00 2.74e-01 3.21e+01 angle pdb=" C PHE B 139 " pdb=" N HIS B 140 " pdb=" CA HIS B 140 " ideal model delta sigma weight residual 121.54 132.33 -10.79 1.91e+00 2.74e-01 3.19e+01 angle pdb=" C PHE R 139 " pdb=" N HIS R 140 " pdb=" CA HIS R 140 " ideal model delta sigma weight residual 121.54 132.33 -10.79 1.91e+00 2.74e-01 3.19e+01 angle pdb=" C PHE D 139 " pdb=" N HIS D 140 " pdb=" CA HIS D 140 " ideal model delta sigma weight residual 121.54 132.31 -10.77 1.91e+00 2.74e-01 3.18e+01 angle pdb=" C PHE A 139 " pdb=" N HIS A 140 " pdb=" CA HIS A 140 " ideal model delta sigma weight residual 121.54 132.30 -10.76 1.91e+00 2.74e-01 3.17e+01 ... (remaining 39851 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 13.61: 16614 13.61 - 27.21: 750 27.21 - 40.82: 276 40.82 - 54.42: 56 54.42 - 68.03: 16 Dihedral angle restraints: 17712 sinusoidal: 7152 harmonic: 10560 Sorted by residual: dihedral pdb=" CA PHE E 52 " pdb=" C PHE E 52 " pdb=" N GLU E 53 " pdb=" CA GLU E 53 " ideal model delta harmonic sigma weight residual 180.00 161.30 18.70 0 5.00e+00 4.00e-02 1.40e+01 dihedral pdb=" CA PHE V 52 " pdb=" C PHE V 52 " pdb=" N GLU V 53 " pdb=" CA GLU V 53 " ideal model delta harmonic sigma weight residual 180.00 161.33 18.67 0 5.00e+00 4.00e-02 1.39e+01 dihedral pdb=" CA PHE F 52 " pdb=" C PHE F 52 " pdb=" N GLU F 53 " pdb=" CA GLU F 53 " ideal model delta harmonic sigma weight residual 180.00 161.35 18.65 0 5.00e+00 4.00e-02 1.39e+01 ... (remaining 17709 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.040: 2454 0.040 - 0.080: 1308 0.080 - 0.119: 461 0.119 - 0.159: 146 0.159 - 0.199: 63 Chirality restraints: 4432 Sorted by residual: chirality pdb=" CB VAL B 62 " pdb=" CA VAL B 62 " pdb=" CG1 VAL B 62 " pdb=" CG2 VAL B 62 " both_signs ideal model delta sigma weight residual False -2.63 -2.43 -0.20 2.00e-01 2.50e+01 9.91e-01 chirality pdb=" CB VAL D 62 " pdb=" CA VAL D 62 " pdb=" CG1 VAL D 62 " pdb=" CG2 VAL D 62 " both_signs ideal model delta sigma weight residual False -2.63 -2.43 -0.20 2.00e-01 2.50e+01 9.79e-01 chirality pdb=" CB VAL C 62 " pdb=" CA VAL C 62 " pdb=" CG1 VAL C 62 " pdb=" CG2 VAL C 62 " both_signs ideal model delta sigma weight residual False -2.63 -2.43 -0.20 2.00e-01 2.50e+01 9.69e-01 ... (remaining 4429 not shown) Planarity restraints: 5200 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB PHE B 154 " 0.022 2.00e-02 2.50e+03 2.28e-02 9.13e+00 pdb=" CG PHE B 154 " -0.053 2.00e-02 2.50e+03 pdb=" CD1 PHE B 154 " 0.016 2.00e-02 2.50e+03 pdb=" CD2 PHE B 154 " 0.005 2.00e-02 2.50e+03 pdb=" CE1 PHE B 154 " -0.000 2.00e-02 2.50e+03 pdb=" CE2 PHE B 154 " 0.010 2.00e-02 2.50e+03 pdb=" CZ PHE B 154 " -0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE C 154 " -0.022 2.00e-02 2.50e+03 2.28e-02 9.07e+00 pdb=" CG PHE C 154 " 0.053 2.00e-02 2.50e+03 pdb=" CD1 PHE C 154 " -0.015 2.00e-02 2.50e+03 pdb=" CD2 PHE C 154 " -0.006 2.00e-02 2.50e+03 pdb=" CE1 PHE C 154 " 0.000 2.00e-02 2.50e+03 pdb=" CE2 PHE C 154 " -0.010 2.00e-02 2.50e+03 pdb=" CZ PHE C 154 " 0.000 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE D 154 " -0.022 2.00e-02 2.50e+03 2.27e-02 8.99e+00 pdb=" CG PHE D 154 " 0.052 2.00e-02 2.50e+03 pdb=" CD1 PHE D 154 " -0.016 2.00e-02 2.50e+03 pdb=" CD2 PHE D 154 " -0.005 2.00e-02 2.50e+03 pdb=" CE1 PHE D 154 " 0.000 2.00e-02 2.50e+03 pdb=" CE2 PHE D 154 " -0.010 2.00e-02 2.50e+03 pdb=" CZ PHE D 154 " 0.001 2.00e-02 2.50e+03 ... (remaining 5197 not shown) Histogram of nonbonded interaction distances: 2.26 - 2.79: 7456 2.79 - 3.32: 24894 3.32 - 3.85: 47195 3.85 - 4.37: 59466 4.37 - 4.90: 99533 Nonbonded interactions: 238544 Sorted by model distance: nonbonded pdb=" OH TYR H 116 " pdb=" OD2 ASP H 192 " model vdw 2.263 3.040 nonbonded pdb=" OH TYR F 116 " pdb=" OD2 ASP F 192 " model vdw 2.263 3.040 nonbonded pdb=" OH TYR V 116 " pdb=" OD2 ASP V 192 " model vdw 2.263 3.040 nonbonded pdb=" OH TYR E 116 " pdb=" OD2 ASP E 192 " model vdw 2.263 3.040 nonbonded pdb=" OH TYR X 116 " pdb=" OD2 ASP X 192 " model vdw 2.263 3.040 ... (remaining 238539 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: 0.10 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'Q' selection = chain 'R' selection = chain 'S' selection = chain 'T' } ncs_group { reference = chain 'E' selection = chain 'F' selection = chain 'G' selection = chain 'H' selection = chain 'U' selection = chain 'V' selection = chain 'W' selection = chain 'X' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue 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: 3.660 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.480 Check model and map are aligned: 0.080 Set scattering table: 0.080 Process input model: 25.670 Find NCS groups from input model: 0.270 Set up NCS constraints: 0.080 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: 0.000 Load rotamer database and sin/cos tables:1.310 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 31.650 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5875 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 : 0.008 0.064 29416 Z= 0.349 Angle : 0.914 10.815 39856 Z= 0.518 Chirality : 0.057 0.199 4432 Planarity : 0.008 0.071 5200 Dihedral : 9.641 68.029 10880 Min Nonbonded Distance : 2.263 Molprobity Statistics. All-atom Clashscore : 4.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.42 % Favored : 96.58 % Rotamer: Outliers : 0.00 % Allowed : 2.52 % Favored : 97.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.55 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -4.58 (0.10), residues: 3624 helix: -3.99 (0.06), residues: 1640 sheet: -1.16 (0.19), residues: 624 loop : -2.39 (0.13), residues: 1360 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG R 102 TYR 0.020 0.004 TYR D 112 PHE 0.053 0.004 PHE B 154 TRP 0.017 0.003 TRP W 214 HIS 0.018 0.003 HIS C 140 Details of bonding type rmsd covalent geometry : bond 0.00790 (29416) covalent geometry : angle 0.91412 (39856) hydrogen bonds : bond 0.29725 ( 1252) hydrogen bonds : angle 8.96718 ( 3636) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7248 Ramachandran restraints generated. 3624 Oldfield, 0 Emsley, 3624 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7248 Ramachandran restraints generated. 3624 Oldfield, 0 Emsley, 3624 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1060 residues out of total 3024 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 1060 time to evaluate : 1.108 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: symmetry clash 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: symmetry clash 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: symmetry clash 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: symmetry clash 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: symmetry clash 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: A 5 TRP cc_start: 0.6495 (m100) cc_final: 0.5676 (m100) REVERT: A 173 THR cc_start: 0.7035 (m) cc_final: 0.6717 (p) REVERT: B 32 THR cc_start: 0.8127 (p) cc_final: 0.7857 (p) REVERT: C 17 GLU cc_start: 0.6761 (mt-10) cc_final: 0.5983 (mt-10) REVERT: C 129 ILE cc_start: 0.8057 (tt) cc_final: 0.7626 (tt) REVERT: D 121 LEU cc_start: 0.6789 (mt) cc_final: 0.6366 (mt) REVERT: E 143 ASP cc_start: 0.6679 (m-30) cc_final: 0.6328 (m-30) REVERT: E 155 VAL cc_start: 0.7466 (t) cc_final: 0.7234 (p) REVERT: E 171 THR cc_start: 0.6125 (m) cc_final: 0.5891 (t) REVERT: E 177 GLN cc_start: 0.6987 (pp30) cc_final: 0.6642 (pp30) REVERT: E 251 LEU cc_start: 0.7179 (mm) cc_final: 0.6699 (mp) REVERT: F 73 SER cc_start: 0.6948 (p) cc_final: 0.6587 (t) REVERT: F 84 GLU cc_start: 0.6845 (pt0) cc_final: 0.5819 (pt0) REVERT: F 110 LEU cc_start: 0.7184 (mt) cc_final: 0.6981 (mt) REVERT: F 119 ASN cc_start: 0.6984 (p0) cc_final: 0.6736 (p0) REVERT: F 156 ILE cc_start: 0.8167 (mp) cc_final: 0.7957 (mp) REVERT: F 173 SER cc_start: 0.7958 (m) cc_final: 0.7754 (p) REVERT: F 177 GLN cc_start: 0.7014 (pp30) cc_final: 0.6600 (pp30) REVERT: F 222 GLU cc_start: 0.6212 (mm-30) cc_final: 0.5726 (mm-30) REVERT: G 15 LYS cc_start: 0.8104 (tmtp) cc_final: 0.7556 (tmtp) REVERT: G 220 LEU cc_start: 0.7774 (mt) cc_final: 0.7492 (mp) REVERT: H 95 GLU cc_start: 0.5446 (mt-10) cc_final: 0.5226 (mt-10) REVERT: H 164 GLN cc_start: 0.4921 (mt0) cc_final: 0.4156 (mt0) REVERT: H 167 THR cc_start: 0.5978 (p) cc_final: 0.5088 (m) REVERT: H 210 ILE cc_start: 0.7855 (tp) cc_final: 0.7518 (tp) REVERT: H 218 ASN cc_start: 0.7585 (t0) cc_final: 0.7365 (t0) REVERT: H 223 GLN cc_start: 0.7445 (tt0) cc_final: 0.7118 (tt0) REVERT: H 235 ARG cc_start: 0.6884 (tpp-160) cc_final: 0.5996 (tpp80) REVERT: H 257 ASP cc_start: 0.5885 (m-30) cc_final: 0.5535 (m-30) REVERT: Q 17 GLU cc_start: 0.6368 (mt-10) cc_final: 0.5400 (mt-10) REVERT: Q 30 TYR cc_start: 0.8205 (m-80) cc_final: 0.7797 (m-80) REVERT: R 173 THR cc_start: 0.6919 (m) cc_final: 0.6655 (p) REVERT: S 121 LEU cc_start: 0.6554 (mt) cc_final: 0.6060 (mt) REVERT: T 11 ASN cc_start: 0.6553 (t0) cc_final: 0.6253 (t0) REVERT: T 13 GLU cc_start: 0.6412 (tp30) cc_final: 0.5748 (tp30) REVERT: T 17 GLU cc_start: 0.6806 (mt-10) cc_final: 0.6010 (mt-10) REVERT: T 85 PHE cc_start: 0.6758 (m-10) cc_final: 0.6541 (m-10) REVERT: T 129 ILE cc_start: 0.8232 (tt) cc_final: 0.7846 (tt) REVERT: T 175 LEU cc_start: 0.6686 (tp) cc_final: 0.6380 (tp) REVERT: U 18 ARG cc_start: 0.6413 (mmt-90) cc_final: 0.6179 (mmt-90) REVERT: U 164 GLN cc_start: 0.4875 (mt0) cc_final: 0.4223 (mt0) REVERT: U 167 THR cc_start: 0.6408 (p) cc_final: 0.5620 (m) REVERT: U 210 ILE cc_start: 0.7988 (tp) cc_final: 0.7700 (tp) REVERT: U 223 GLN cc_start: 0.7429 (tt0) cc_final: 0.7223 (tt0) REVERT: U 235 ARG cc_start: 0.6819 (tpp-160) cc_final: 0.6468 (ttm-80) REVERT: V 15 LYS cc_start: 0.8132 (tmtp) cc_final: 0.7786 (tmtp) REVERT: V 105 ARG cc_start: 0.6300 (mtt180) cc_final: 0.6093 (mtt90) REVERT: V 200 PHE cc_start: 0.6071 (m-80) cc_final: 0.5863 (m-80) REVERT: V 213 ILE cc_start: 0.7686 (mm) cc_final: 0.7429 (mm) REVERT: W 78 LEU cc_start: 0.8445 (tp) cc_final: 0.8138 (tp) REVERT: W 88 SER cc_start: 0.7211 (m) cc_final: 0.6892 (t) REVERT: W 93 GLU cc_start: 0.6526 (mp0) cc_final: 0.6309 (mp0) REVERT: W 128 LEU cc_start: 0.7718 (mt) cc_final: 0.7500 (mp) REVERT: W 137 VAL cc_start: 0.8182 (t) cc_final: 0.7951 (m) REVERT: W 158 PHE cc_start: 0.7703 (t80) cc_final: 0.7270 (t80) REVERT: W 178 ARG cc_start: 0.6107 (mmm-85) cc_final: 0.5656 (mmm-85) REVERT: W 182 ASP cc_start: 0.5596 (m-30) cc_final: 0.5228 (m-30) REVERT: W 187 GLN cc_start: 0.6590 (mm-40) cc_final: 0.6320 (mp10) REVERT: W 222 GLU cc_start: 0.6374 (mm-30) cc_final: 0.6024 (mm-30) REVERT: X 65 GLN cc_start: 0.7372 (mt0) cc_final: 0.7130 (mt0) REVERT: X 76 ASN cc_start: 0.7442 (p0) cc_final: 0.7139 (p0) REVERT: X 78 LEU cc_start: 0.8406 (tp) cc_final: 0.8000 (tt) REVERT: X 81 LEU cc_start: 0.8290 (tp) cc_final: 0.7956 (tt) REVERT: X 85 MET cc_start: 0.6724 (mtm) cc_final: 0.6441 (mtm) REVERT: X 155 VAL cc_start: 0.7514 (t) cc_final: 0.7212 (p) REVERT: X 168 ILE cc_start: 0.7848 (mm) cc_final: 0.7555 (mm) REVERT: X 208 THR cc_start: 0.8150 (p) cc_final: 0.7795 (m) REVERT: X 251 LEU cc_start: 0.7166 (mm) cc_final: 0.6848 (mt) outliers start: 0 outliers final: 0 residues processed: 1060 average time/residue: 0.2304 time to fit residues: 360.7768 Evaluate side-chains 945 residues out of total 3024 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 945 time to evaluate : 0.734 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 360 random chunks: chunk 197 optimal weight: 2.9990 chunk 215 optimal weight: 1.9990 chunk 20 optimal weight: 0.8980 chunk 132 optimal weight: 1.9990 chunk 261 optimal weight: 4.9990 chunk 248 optimal weight: 3.9990 chunk 207 optimal weight: 5.9990 chunk 155 optimal weight: 0.5980 chunk 244 optimal weight: 0.9990 chunk 183 optimal weight: 2.9990 chunk 298 optimal weight: 3.9990 overall best weight: 1.2986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 150 GLN C 11 ASN D 150 GLN E 65 GLN E 159 HIS G 41 GLN G 60 HIS G 252 GLN H 41 GLN Q 150 GLN R 101 GLN ** R 172 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** S 150 GLN S 172 HIS T 140 HIS U 60 HIS U 230 HIS W 196 ASN W 218 ASN X 41 GLN Total number of N/Q/H flips: 19 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4068 r_free = 0.4068 target = 0.142698 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3767 r_free = 0.3767 target = 0.121939 restraints weight = 63008.844| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3825 r_free = 0.3825 target = 0.126069 restraints weight = 34780.187| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3863 r_free = 0.3863 target = 0.128810 restraints weight = 21629.976| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3889 r_free = 0.3889 target = 0.130684 restraints weight = 14751.797| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3905 r_free = 0.3905 target = 0.131865 restraints weight = 10799.694| |-----------------------------------------------------------------------------| r_work (final): 0.3925 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6905 moved from start: 0.4467 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.058 29416 Z= 0.195 Angle : 0.748 12.288 39856 Z= 0.387 Chirality : 0.048 0.240 4432 Planarity : 0.007 0.072 5200 Dihedral : 5.105 28.954 4024 Min Nonbonded Distance : 2.502 Molprobity Statistics. All-atom Clashscore : 11.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.35 % Favored : 97.65 % Rotamer: Outliers : 2.85 % Allowed : 10.64 % Favored : 86.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.55 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.74 (0.12), residues: 3624 helix: -1.67 (0.11), residues: 1688 sheet: -1.07 (0.18), residues: 648 loop : -2.17 (0.14), residues: 1288 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG T 152 TYR 0.024 0.002 TYR X 83 PHE 0.024 0.002 PHE F 205 TRP 0.039 0.002 TRP Q 141 HIS 0.011 0.002 HIS A 20 Details of bonding type rmsd covalent geometry : bond 0.00416 (29416) covalent geometry : angle 0.74783 (39856) hydrogen bonds : bond 0.04061 ( 1252) hydrogen bonds : angle 5.53243 ( 3636) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7248 Ramachandran restraints generated. 3624 Oldfield, 0 Emsley, 3624 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7248 Ramachandran restraints generated. 3624 Oldfield, 0 Emsley, 3624 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1172 residues out of total 3024 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 86 poor density : 1086 time to evaluate : 1.119 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: symmetry clash 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: symmetry clash 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: symmetry clash 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 118 ARG cc_start: 0.6821 (OUTLIER) cc_final: 0.6509 (ttp-170) REVERT: A 123 GLU cc_start: 0.6643 (mm-30) cc_final: 0.5651 (mm-30) REVERT: B 16 ARG cc_start: 0.7405 (ttp80) cc_final: 0.7019 (ttp80) REVERT: B 34 LYS cc_start: 0.8099 (tttm) cc_final: 0.7885 (tttm) REVERT: B 59 ARG cc_start: 0.7746 (mmt180) cc_final: 0.7392 (mmt180) REVERT: B 101 GLN cc_start: 0.8240 (pm20) cc_final: 0.8016 (pm20) REVERT: B 140 HIS cc_start: 0.7159 (m-70) cc_final: 0.6945 (m-70) REVERT: C 4 THR cc_start: 0.7879 (p) cc_final: 0.7487 (t) REVERT: C 12 SER cc_start: 0.8481 (OUTLIER) cc_final: 0.8220 (p) REVERT: C 14 LYS cc_start: 0.8209 (mttm) cc_final: 0.7975 (mttm) REVERT: C 19 GLN cc_start: 0.7777 (mm-40) cc_final: 0.7445 (mm-40) REVERT: C 55 TYR cc_start: 0.8210 (t80) cc_final: 0.7971 (t80) REVERT: C 105 ARG cc_start: 0.7377 (mtm180) cc_final: 0.6477 (mtm110) REVERT: C 107 ARG cc_start: 0.6012 (mmm-85) cc_final: 0.5583 (mmm-85) REVERT: C 124 GLU cc_start: 0.7042 (pp20) cc_final: 0.6365 (tp30) REVERT: C 148 LYS cc_start: 0.8159 (pttm) cc_final: 0.7914 (pttm) REVERT: C 160 ASP cc_start: 0.8437 (p0) cc_final: 0.8031 (p0) REVERT: C 170 ARG cc_start: 0.7441 (mtm-85) cc_final: 0.7089 (mpp80) REVERT: D 32 THR cc_start: 0.7462 (p) cc_final: 0.7138 (t) REVERT: D 56 ARG cc_start: 0.7811 (ttm170) cc_final: 0.7447 (mtt-85) REVERT: E 15 LYS cc_start: 0.8253 (tmtp) cc_final: 0.7472 (tmtp) REVERT: E 16 GLU cc_start: 0.7596 (mm-30) cc_final: 0.6928 (mm-30) REVERT: E 46 LEU cc_start: 0.8119 (mt) cc_final: 0.7887 (mm) REVERT: E 48 LYS cc_start: 0.8711 (ttmm) cc_final: 0.8508 (tppp) REVERT: E 76 ASN cc_start: 0.8410 (p0) cc_final: 0.7953 (p0) REVERT: E 80 ARG cc_start: 0.7920 (tpt170) cc_final: 0.7103 (tpt170) REVERT: E 85 MET cc_start: 0.7846 (mtt) cc_final: 0.7604 (mtm) REVERT: E 143 ASP cc_start: 0.7206 (m-30) cc_final: 0.6260 (m-30) REVERT: E 145 GLN cc_start: 0.8122 (tp40) cc_final: 0.7600 (mm-40) REVERT: E 179 MET cc_start: 0.7303 (OUTLIER) cc_final: 0.6841 (mmt) REVERT: E 182 ASP cc_start: 0.7282 (m-30) cc_final: 0.7009 (m-30) REVERT: E 200 PHE cc_start: 0.7745 (m-80) cc_final: 0.7337 (m-80) REVERT: E 217 MET cc_start: 0.7588 (mtt) cc_final: 0.7290 (mtt) REVERT: E 262 ASP cc_start: 0.7749 (t0) cc_final: 0.7451 (t70) REVERT: E 275 GLU cc_start: 0.7003 (mt-10) cc_final: 0.6605 (mt-10) REVERT: F 35 LYS cc_start: 0.8840 (OUTLIER) cc_final: 0.8531 (mtmm) REVERT: F 36 LEU cc_start: 0.8552 (mt) cc_final: 0.8164 (tp) REVERT: F 63 PHE cc_start: 0.7852 (t80) cc_final: 0.7564 (t80) REVERT: F 64 GLU cc_start: 0.7477 (pm20) cc_final: 0.7233 (pm20) REVERT: F 77 ARG cc_start: 0.8086 (mpt90) cc_final: 0.7744 (mpt90) REVERT: F 105 ARG cc_start: 0.7692 (mtt180) cc_final: 0.7304 (mtt-85) REVERT: F 110 LEU cc_start: 0.7862 (mt) cc_final: 0.7636 (mt) REVERT: F 118 THR cc_start: 0.8416 (t) cc_final: 0.8116 (t) REVERT: F 119 ASN cc_start: 0.7605 (p0) cc_final: 0.7363 (p0) REVERT: F 166 ASP cc_start: 0.6518 (p0) cc_final: 0.6235 (p0) REVERT: F 177 GLN cc_start: 0.7854 (pp30) cc_final: 0.7641 (pp30) REVERT: F 178 ARG cc_start: 0.7560 (tpp80) cc_final: 0.7342 (tpp80) REVERT: F 188 ARG cc_start: 0.8542 (mmm-85) cc_final: 0.8261 (mmm-85) REVERT: F 192 ASP cc_start: 0.7558 (m-30) cc_final: 0.7217 (m-30) REVERT: F 205 PHE cc_start: 0.6817 (m-80) cc_final: 0.6483 (m-80) REVERT: F 212 TYR cc_start: 0.6773 (t80) cc_final: 0.6324 (t80) REVERT: F 216 ARG cc_start: 0.7680 (ttt90) cc_final: 0.7206 (mtp85) REVERT: F 238 PHE cc_start: 0.6295 (t80) cc_final: 0.5560 (t80) REVERT: F 247 GLN cc_start: 0.7136 (mt0) cc_final: 0.6902 (mt0) REVERT: G 13 LEU cc_start: 0.8134 (mt) cc_final: 0.7900 (mt) REVERT: G 14 LYS cc_start: 0.8238 (ttmm) cc_final: 0.7725 (ttmm) REVERT: G 15 LYS cc_start: 0.8449 (tmtp) cc_final: 0.7901 (tmtp) REVERT: G 68 GLU cc_start: 0.7241 (tp30) cc_final: 0.6287 (tp30) REVERT: G 69 PHE cc_start: 0.6993 (t80) cc_final: 0.6576 (t80) REVERT: G 81 LEU cc_start: 0.8550 (tp) cc_final: 0.8197 (tt) REVERT: G 84 GLU cc_start: 0.8010 (pt0) cc_final: 0.7594 (pm20) REVERT: G 93 GLU cc_start: 0.7955 (tp30) cc_final: 0.7726 (tp30) REVERT: G 177 GLN cc_start: 0.7344 (pp30) cc_final: 0.6959 (pp30) REVERT: G 209 ASN cc_start: 0.6747 (t0) cc_final: 0.6428 (t0) REVERT: G 222 GLU cc_start: 0.7665 (mm-30) cc_final: 0.7343 (mm-30) REVERT: G 235 ARG cc_start: 0.7264 (mmm160) cc_final: 0.6752 (mmm160) REVERT: H 16 GLU cc_start: 0.6818 (mm-30) cc_final: 0.6573 (mm-30) REVERT: H 84 GLU cc_start: 0.8070 (pt0) cc_final: 0.7761 (pt0) REVERT: H 113 ARG cc_start: 0.6782 (mtt180) cc_final: 0.6513 (mtt180) REVERT: H 143 ASP cc_start: 0.8294 (m-30) cc_final: 0.8037 (m-30) REVERT: H 154 GLU cc_start: 0.7331 (mt-10) cc_final: 0.6891 (mt-10) REVERT: H 194 LEU cc_start: 0.8100 (mt) cc_final: 0.7857 (mt) REVERT: H 210 ILE cc_start: 0.8201 (tp) cc_final: 0.7715 (tp) REVERT: H 221 ARG cc_start: 0.7738 (ttm-80) cc_final: 0.7206 (ttp-110) REVERT: H 223 GLN cc_start: 0.8094 (tt0) cc_final: 0.7583 (tt0) REVERT: H 235 ARG cc_start: 0.7271 (tpp-160) cc_final: 0.6890 (mmm160) REVERT: H 237 PHE cc_start: 0.7798 (m-80) cc_final: 0.7453 (m-80) REVERT: H 249 ASP cc_start: 0.7188 (m-30) cc_final: 0.6881 (m-30) REVERT: H 253 GLN cc_start: 0.8266 (mm-40) cc_final: 0.7654 (mm-40) REVERT: Q 13 GLU cc_start: 0.7346 (tp30) cc_final: 0.6633 (tp30) REVERT: Q 58 VAL cc_start: 0.8979 (p) cc_final: 0.8770 (t) REVERT: Q 101 GLN cc_start: 0.8320 (pm20) cc_final: 0.8068 (pm20) REVERT: Q 141 TRP cc_start: 0.6361 (m-90) cc_final: 0.6106 (m100) REVERT: Q 174 ARG cc_start: 0.7328 (mtp180) cc_final: 0.6871 (mtp180) REVERT: R 5 TRP cc_start: 0.7039 (m100) cc_final: 0.5855 (m100) REVERT: R 126 GLU cc_start: 0.7875 (tp30) cc_final: 0.7399 (tp30) REVERT: R 174 ARG cc_start: 0.8101 (mmm-85) cc_final: 0.7873 (mtp85) REVERT: S 60 VAL cc_start: 0.6442 (m) cc_final: 0.6123 (p) REVERT: S 63 ILE cc_start: 0.5611 (mt) cc_final: 0.5276 (mp) REVERT: S 111 CYS cc_start: 0.5811 (t) cc_final: 0.5346 (m) REVERT: T 6 PHE cc_start: 0.7802 (m-80) cc_final: 0.7584 (m-10) REVERT: T 14 LYS cc_start: 0.8289 (mttm) cc_final: 0.7929 (mttm) REVERT: T 19 GLN cc_start: 0.7738 (mm-40) cc_final: 0.7363 (mm-40) REVERT: T 55 TYR cc_start: 0.8056 (t80) cc_final: 0.7826 (t80) REVERT: T 89 LEU cc_start: 0.6689 (tp) cc_final: 0.6156 (tp) REVERT: T 102 ARG cc_start: 0.6426 (mmm160) cc_final: 0.5979 (mmm-85) REVERT: T 105 ARG cc_start: 0.7294 (OUTLIER) cc_final: 0.6645 (mtm110) REVERT: T 129 ILE cc_start: 0.8040 (tt) cc_final: 0.7773 (tt) REVERT: T 175 LEU cc_start: 0.7852 (tp) cc_final: 0.7647 (tp) REVERT: U 32 LYS cc_start: 0.8176 (ttpp) cc_final: 0.7957 (ttpp) REVERT: U 35 LYS cc_start: 0.8245 (mmtm) cc_final: 0.7921 (mmtm) REVERT: U 123 HIS cc_start: 0.7218 (m170) cc_final: 0.7005 (m-70) REVERT: U 143 ASP cc_start: 0.8002 (m-30) cc_final: 0.7662 (m-30) REVERT: U 148 ARG cc_start: 0.6689 (ptp90) cc_final: 0.6487 (ptp90) REVERT: U 197 SER cc_start: 0.7335 (p) cc_final: 0.6845 (m) REVERT: U 210 ILE cc_start: 0.8472 (tp) cc_final: 0.8090 (tp) REVERT: U 223 GLN cc_start: 0.8022 (tt0) cc_final: 0.7775 (tt0) REVERT: U 225 GLN cc_start: 0.7459 (pt0) cc_final: 0.7252 (pt0) REVERT: U 235 ARG cc_start: 0.7436 (tpp-160) cc_final: 0.6888 (ttm-80) REVERT: U 237 PHE cc_start: 0.7543 (m-80) cc_final: 0.7237 (m-80) REVERT: U 238 PHE cc_start: 0.7388 (t80) cc_final: 0.7107 (t80) REVERT: U 252 GLN cc_start: 0.7618 (OUTLIER) cc_final: 0.7344 (tm-30) REVERT: U 253 GLN cc_start: 0.8131 (mm-40) cc_final: 0.7603 (mm-40) REVERT: U 257 ASP cc_start: 0.6596 (m-30) cc_final: 0.6011 (m-30) REVERT: U 275 GLU cc_start: 0.7392 (pp20) cc_final: 0.7069 (pp20) REVERT: V 15 LYS cc_start: 0.8414 (tmtp) cc_final: 0.7871 (tmtp) REVERT: V 105 ARG cc_start: 0.7190 (mtt180) cc_final: 0.6604 (ttm-80) REVERT: V 177 GLN cc_start: 0.7218 (pp30) cc_final: 0.6709 (pp30) REVERT: V 178 ARG cc_start: 0.7620 (mmm-85) cc_final: 0.7372 (mmm-85) REVERT: V 179 MET cc_start: 0.7833 (mtt) cc_final: 0.7354 (mtt) REVERT: V 198 PHE cc_start: 0.6539 (m-10) cc_final: 0.6315 (m-10) REVERT: V 235 ARG cc_start: 0.7008 (tpp-160) cc_final: 0.6709 (tpp80) REVERT: W 59 MET cc_start: 0.7456 (ttp) cc_final: 0.7232 (tmm) REVERT: W 62 ARG cc_start: 0.6941 (mtp85) cc_final: 0.6631 (mtp85) REVERT: W 64 GLU cc_start: 0.7506 (pm20) cc_final: 0.7201 (pm20) REVERT: W 78 LEU cc_start: 0.8619 (tp) cc_final: 0.8314 (tt) REVERT: W 88 SER cc_start: 0.7986 (m) cc_final: 0.7611 (t) REVERT: W 93 GLU cc_start: 0.7672 (mp0) cc_final: 0.7437 (mp0) REVERT: W 105 ARG cc_start: 0.8057 (ttm-80) cc_final: 0.7827 (ttm-80) REVERT: W 122 LYS cc_start: 0.7267 (OUTLIER) cc_final: 0.6822 (ptpp) REVERT: W 129 ARG cc_start: 0.6590 (ttm110) cc_final: 0.6068 (mmt-90) REVERT: W 141 PHE cc_start: 0.7970 (t80) cc_final: 0.7733 (t80) REVERT: W 145 GLN cc_start: 0.7936 (mm-40) cc_final: 0.7728 (mm-40) REVERT: W 154 GLU cc_start: 0.6993 (mt-10) cc_final: 0.6628 (mt-10) REVERT: W 158 PHE cc_start: 0.7852 (t80) cc_final: 0.7443 (t80) REVERT: W 166 ASP cc_start: 0.6769 (p0) cc_final: 0.6419 (p0) REVERT: W 172 GLU cc_start: 0.7438 (tt0) cc_final: 0.7203 (tt0) REVERT: W 177 GLN cc_start: 0.7855 (pp30) cc_final: 0.7470 (pp30) REVERT: W 178 ARG cc_start: 0.7406 (mmm-85) cc_final: 0.6517 (mmm-85) REVERT: W 187 GLN cc_start: 0.8168 (mm-40) cc_final: 0.7436 (mp10) REVERT: W 188 ARG cc_start: 0.7808 (tpp80) cc_final: 0.7348 (tpp80) REVERT: W 192 ASP cc_start: 0.7544 (m-30) cc_final: 0.7139 (m-30) REVERT: W 200 PHE cc_start: 0.7074 (m-80) cc_final: 0.6729 (m-80) REVERT: W 222 GLU cc_start: 0.7626 (mm-30) cc_final: 0.7401 (mm-30) REVERT: W 225 GLN cc_start: 0.7481 (pt0) cc_final: 0.7064 (mt0) REVERT: X 15 LYS cc_start: 0.8057 (tmtp) cc_final: 0.7421 (tmtp) REVERT: X 53 GLU cc_start: 0.7438 (tm-30) cc_final: 0.7033 (tm-30) REVERT: X 55 GLU cc_start: 0.7554 (mp0) cc_final: 0.7328 (mp0) REVERT: X 68 GLU cc_start: 0.7134 (tp30) cc_final: 0.6909 (tp30) REVERT: X 80 ARG cc_start: 0.7981 (tpt170) cc_final: 0.7552 (tpt90) REVERT: X 141 PHE cc_start: 0.8167 (t80) cc_final: 0.7848 (t80) REVERT: X 145 GLN cc_start: 0.8108 (mm-40) cc_final: 0.7541 (mm-40) REVERT: X 155 VAL cc_start: 0.8119 (t) cc_final: 0.7830 (p) REVERT: X 158 PHE cc_start: 0.7755 (t80) cc_final: 0.7469 (t80) REVERT: X 168 ILE cc_start: 0.8210 (mm) cc_final: 0.7910 (mm) REVERT: X 221 ARG cc_start: 0.7673 (mtt-85) cc_final: 0.7386 (mpt-90) REVERT: X 275 GLU cc_start: 0.7197 (mt-10) cc_final: 0.6875 (mt-10) outliers start: 86 outliers final: 30 residues processed: 1126 average time/residue: 0.2258 time to fit residues: 377.1965 Evaluate side-chains 1059 residues out of total 3024 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 1022 time to evaluate : 1.089 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 118 ARG Chi-restraints excluded: chain C residue 12 SER Chi-restraints excluded: chain C residue 41 VAL Chi-restraints excluded: chain C residue 60 VAL Chi-restraints excluded: chain C residue 64 VAL Chi-restraints excluded: chain C residue 120 VAL Chi-restraints excluded: chain D residue 45 THR Chi-restraints excluded: chain D residue 166 SER Chi-restraints excluded: chain E residue 179 MET Chi-restraints excluded: chain F residue 3 THR Chi-restraints excluded: chain F residue 35 LYS Chi-restraints excluded: chain G residue 3 THR Chi-restraints excluded: chain G residue 101 SER Chi-restraints excluded: chain G residue 189 LEU Chi-restraints excluded: chain G residue 252 GLN Chi-restraints excluded: chain H residue 193 LEU Chi-restraints excluded: chain Q residue 21 VAL Chi-restraints excluded: chain Q residue 43 LEU Chi-restraints excluded: chain R residue 120 VAL Chi-restraints excluded: chain S residue 43 LEU Chi-restraints excluded: chain S residue 173 THR Chi-restraints excluded: chain T residue 21 VAL Chi-restraints excluded: chain T residue 41 VAL Chi-restraints excluded: chain T residue 64 VAL Chi-restraints excluded: chain T residue 105 ARG Chi-restraints excluded: chain T residue 120 VAL Chi-restraints excluded: chain T residue 144 ILE Chi-restraints excluded: chain U residue 193 LEU Chi-restraints excluded: chain U residue 240 THR Chi-restraints excluded: chain U residue 252 GLN Chi-restraints excluded: chain V residue 84 GLU Chi-restraints excluded: chain V residue 272 ARG Chi-restraints excluded: chain W residue 77 ARG Chi-restraints excluded: chain W residue 118 THR Chi-restraints excluded: chain W residue 122 LYS Chi-restraints excluded: chain W residue 155 VAL Chi-restraints excluded: chain W residue 170 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 360 random chunks: chunk 101 optimal weight: 0.9990 chunk 242 optimal weight: 4.9990 chunk 202 optimal weight: 2.9990 chunk 204 optimal weight: 6.9990 chunk 198 optimal weight: 2.9990 chunk 291 optimal weight: 0.8980 chunk 116 optimal weight: 3.9990 chunk 54 optimal weight: 5.9990 chunk 338 optimal weight: 3.9990 chunk 178 optimal weight: 2.9990 chunk 201 optimal weight: 0.9980 overall best weight: 1.7786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 11 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 20 HIS A 119 HIS C 119 HIS E 41 GLN E 65 GLN ** E 123 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 159 HIS ** G 65 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 159 HIS R 19 GLN R 119 HIS ** R 172 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 140 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** U 159 HIS V 60 HIS V 65 GLN V 159 HIS V 164 GLN W 218 ASN X 79 GLN ** X 123 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3921 r_free = 0.3921 target = 0.131133 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3611 r_free = 0.3611 target = 0.111100 restraints weight = 62880.818| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.3669 r_free = 0.3669 target = 0.115015 restraints weight = 33524.410| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 45)----------------| | r_work = 0.3707 r_free = 0.3707 target = 0.117587 restraints weight = 20573.542| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3732 r_free = 0.3732 target = 0.119307 restraints weight = 13920.988| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 35)----------------| | r_work = 0.3750 r_free = 0.3750 target = 0.120526 restraints weight = 10224.527| |-----------------------------------------------------------------------------| r_work (final): 0.3770 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7147 moved from start: 0.6515 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.077 29416 Z= 0.221 Angle : 0.742 9.359 39856 Z= 0.386 Chirality : 0.048 0.255 4432 Planarity : 0.006 0.061 5200 Dihedral : 5.083 28.277 4024 Min Nonbonded Distance : 2.472 Molprobity Statistics. All-atom Clashscore : 13.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.23 % Favored : 96.77 % Rotamer: Outliers : 3.58 % Allowed : 15.65 % Favored : 80.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.55 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.91 (0.13), residues: 3624 helix: -0.65 (0.12), residues: 1672 sheet: -1.01 (0.18), residues: 656 loop : -2.06 (0.15), residues: 1296 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG U 113 TYR 0.051 0.003 TYR E 203 PHE 0.020 0.002 PHE X 25 TRP 0.033 0.002 TRP T 141 HIS 0.011 0.001 HIS A 20 Details of bonding type rmsd covalent geometry : bond 0.00466 (29416) covalent geometry : angle 0.74244 (39856) hydrogen bonds : bond 0.04887 ( 1252) hydrogen bonds : angle 5.31228 ( 3636) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7248 Ramachandran restraints generated. 3624 Oldfield, 0 Emsley, 3624 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7248 Ramachandran restraints generated. 3624 Oldfield, 0 Emsley, 3624 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1255 residues out of total 3024 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 108 poor density : 1147 time to evaluate : 0.969 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: symmetry clash 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: symmetry clash 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 30 TYR cc_start: 0.6732 (m-80) cc_final: 0.6483 (m-80) REVERT: A 59 ARG cc_start: 0.7426 (mmt180) cc_final: 0.7128 (tpp80) REVERT: A 111 CYS cc_start: 0.5972 (t) cc_final: 0.5670 (t) REVERT: A 123 GLU cc_start: 0.6813 (mm-30) cc_final: 0.6607 (mm-30) REVERT: A 174 ARG cc_start: 0.8291 (OUTLIER) cc_final: 0.7919 (mtm-85) REVERT: B 16 ARG cc_start: 0.7671 (ttp80) cc_final: 0.7281 (ttp80) REVERT: B 27 LYS cc_start: 0.7395 (ptmt) cc_final: 0.6965 (ptmt) REVERT: B 117 GLU cc_start: 0.7338 (pt0) cc_final: 0.6863 (pt0) REVERT: B 140 HIS cc_start: 0.6985 (m-70) cc_final: 0.6755 (m-70) REVERT: C 11 ASN cc_start: 0.7329 (t0) cc_final: 0.6585 (t0) REVERT: C 12 SER cc_start: 0.8566 (OUTLIER) cc_final: 0.8289 (p) REVERT: C 14 LYS cc_start: 0.8535 (mttm) cc_final: 0.8267 (mttm) REVERT: C 17 GLU cc_start: 0.7882 (mt-10) cc_final: 0.7569 (mt-10) REVERT: C 19 GLN cc_start: 0.7796 (mm-40) cc_final: 0.7400 (mm-40) REVERT: C 27 LYS cc_start: 0.8146 (OUTLIER) cc_final: 0.7841 (ptpp) REVERT: C 30 TYR cc_start: 0.7311 (m-80) cc_final: 0.6603 (m-80) REVERT: C 59 ARG cc_start: 0.7484 (mmt180) cc_final: 0.7171 (mmt180) REVERT: C 66 HIS cc_start: 0.6492 (t70) cc_final: 0.6246 (t70) REVERT: C 89 LEU cc_start: 0.7269 (tp) cc_final: 0.6185 (tt) REVERT: C 139 PHE cc_start: 0.6929 (p90) cc_final: 0.6401 (p90) REVERT: C 148 LYS cc_start: 0.8083 (pttm) cc_final: 0.7723 (pttm) REVERT: C 168 LEU cc_start: 0.8010 (tp) cc_final: 0.7624 (tp) REVERT: C 170 ARG cc_start: 0.7680 (mtm-85) cc_final: 0.7326 (ptp-170) REVERT: C 174 ARG cc_start: 0.7832 (mtp180) cc_final: 0.7597 (mtp180) REVERT: D 27 LYS cc_start: 0.8182 (ptmt) cc_final: 0.7653 (ptmt) REVERT: D 38 ILE cc_start: 0.8330 (tt) cc_final: 0.8104 (tt) REVERT: D 56 ARG cc_start: 0.7889 (ttm170) cc_final: 0.7523 (mtt-85) REVERT: D 69 LEU cc_start: 0.7418 (tp) cc_final: 0.7216 (tp) REVERT: D 157 MET cc_start: 0.5807 (mtt) cc_final: 0.4911 (mtt) REVERT: D 176 ARG cc_start: 0.8744 (mtp180) cc_final: 0.8434 (mtp85) REVERT: E 15 LYS cc_start: 0.8565 (tmtp) cc_final: 0.7879 (tmtp) REVERT: E 16 GLU cc_start: 0.7871 (mm-30) cc_final: 0.7190 (mm-30) REVERT: E 36 LEU cc_start: 0.8503 (mt) cc_final: 0.8259 (mt) REVERT: E 46 LEU cc_start: 0.8429 (mt) cc_final: 0.8216 (mm) REVERT: E 53 GLU cc_start: 0.7853 (tm-30) cc_final: 0.7385 (tm-30) REVERT: E 55 GLU cc_start: 0.7229 (mt-10) cc_final: 0.6984 (mt-10) REVERT: E 80 ARG cc_start: 0.8030 (tpt170) cc_final: 0.7227 (tpt90) REVERT: E 89 PHE cc_start: 0.7831 (m-80) cc_final: 0.7600 (m-80) REVERT: E 133 LYS cc_start: 0.6991 (mtmm) cc_final: 0.6593 (mtmm) REVERT: E 141 PHE cc_start: 0.8150 (t80) cc_final: 0.7935 (t80) REVERT: E 179 MET cc_start: 0.7144 (OUTLIER) cc_final: 0.6571 (mmt) REVERT: E 181 LEU cc_start: 0.7783 (mt) cc_final: 0.7453 (mp) REVERT: E 182 ASP cc_start: 0.7459 (m-30) cc_final: 0.7214 (m-30) REVERT: E 196 ASN cc_start: 0.7407 (m-40) cc_final: 0.7114 (m-40) REVERT: E 225 GLN cc_start: 0.7549 (OUTLIER) cc_final: 0.7271 (mt0) REVERT: E 245 LEU cc_start: 0.7609 (mp) cc_final: 0.7333 (mp) REVERT: E 275 GLU cc_start: 0.7322 (mt-10) cc_final: 0.6875 (mt-10) REVERT: F 15 LYS cc_start: 0.8339 (tmtp) cc_final: 0.8039 (tttp) REVERT: F 26 LEU cc_start: 0.7856 (mt) cc_final: 0.7545 (mt) REVERT: F 35 LYS cc_start: 0.8918 (OUTLIER) cc_final: 0.8644 (mtmm) REVERT: F 38 ASP cc_start: 0.8491 (p0) cc_final: 0.8254 (p0) REVERT: F 63 PHE cc_start: 0.8291 (t80) cc_final: 0.7917 (t80) REVERT: F 77 ARG cc_start: 0.8086 (mpt90) cc_final: 0.7533 (mpt90) REVERT: F 171 THR cc_start: 0.8027 (m) cc_final: 0.7289 (p) REVERT: F 188 ARG cc_start: 0.8576 (mmm-85) cc_final: 0.7951 (tpt90) REVERT: F 192 ASP cc_start: 0.7963 (m-30) cc_final: 0.7638 (m-30) REVERT: G 14 LYS cc_start: 0.8349 (ttmm) cc_final: 0.7819 (ttmm) REVERT: G 88 SER cc_start: 0.8731 (OUTLIER) cc_final: 0.8363 (t) REVERT: G 105 ARG cc_start: 0.7241 (mtt180) cc_final: 0.6510 (ttm-80) REVERT: G 113 ARG cc_start: 0.7464 (mtt180) cc_final: 0.7246 (mtt180) REVERT: G 118 THR cc_start: 0.7681 (t) cc_final: 0.7389 (m) REVERT: G 158 PHE cc_start: 0.7651 (t80) cc_final: 0.7417 (t80) REVERT: G 175 TYR cc_start: 0.7182 (OUTLIER) cc_final: 0.6586 (t80) REVERT: G 178 ARG cc_start: 0.7777 (tpp80) cc_final: 0.7371 (tpp80) REVERT: G 211 ARG cc_start: 0.7969 (mtp85) cc_final: 0.7591 (ttm-80) REVERT: G 222 GLU cc_start: 0.7655 (mm-30) cc_final: 0.7280 (mm-30) REVERT: G 235 ARG cc_start: 0.7346 (mmm160) cc_final: 0.6675 (mmm160) REVERT: G 274 LEU cc_start: 0.8164 (mt) cc_final: 0.7895 (tt) REVERT: G 275 GLU cc_start: 0.7161 (pp20) cc_final: 0.6896 (pp20) REVERT: H 25 PHE cc_start: 0.7023 (t80) cc_final: 0.6753 (t80) REVERT: H 65 GLN cc_start: 0.7677 (mp10) cc_final: 0.6986 (mp10) REVERT: H 70 PHE cc_start: 0.7039 (OUTLIER) cc_final: 0.6763 (m-10) REVERT: H 84 GLU cc_start: 0.8047 (pt0) cc_final: 0.7722 (pt0) REVERT: H 89 PHE cc_start: 0.6455 (m-10) cc_final: 0.6158 (m-10) REVERT: H 122 LYS cc_start: 0.8058 (pttt) cc_final: 0.7651 (pttt) REVERT: H 175 TYR cc_start: 0.6999 (m-80) cc_final: 0.6572 (m-80) REVERT: H 188 ARG cc_start: 0.7589 (tpp80) cc_final: 0.6910 (tpp80) REVERT: H 210 ILE cc_start: 0.8280 (tp) cc_final: 0.7809 (tp) REVERT: H 212 TYR cc_start: 0.7279 (t80) cc_final: 0.6978 (t80) REVERT: H 215 TYR cc_start: 0.8005 (t80) cc_final: 0.7636 (t80) REVERT: H 217 MET cc_start: 0.6843 (mtp) cc_final: 0.6613 (tpp) REVERT: H 221 ARG cc_start: 0.7765 (ttm-80) cc_final: 0.7156 (ttm-80) REVERT: H 223 GLN cc_start: 0.8064 (tt0) cc_final: 0.7616 (tt0) REVERT: H 235 ARG cc_start: 0.7471 (tpp-160) cc_final: 0.7025 (mmm160) REVERT: H 249 ASP cc_start: 0.7234 (m-30) cc_final: 0.6897 (m-30) REVERT: H 252 GLN cc_start: 0.7532 (tm-30) cc_final: 0.6849 (tm-30) REVERT: H 253 GLN cc_start: 0.8079 (mm-40) cc_final: 0.7654 (mm-40) REVERT: H 275 GLU cc_start: 0.7371 (pt0) cc_final: 0.7115 (pt0) REVERT: Q 19 GLN cc_start: 0.8118 (mt0) cc_final: 0.7893 (mt0) REVERT: Q 56 ARG cc_start: 0.7587 (mtt-85) cc_final: 0.7245 (mtt-85) REVERT: Q 101 GLN cc_start: 0.8405 (pm20) cc_final: 0.8061 (pm20) REVERT: Q 162 LYS cc_start: 0.7993 (OUTLIER) cc_final: 0.7712 (tttm) REVERT: R 44 GLU cc_start: 0.7038 (tm-30) cc_final: 0.6812 (tm-30) REVERT: R 59 ARG cc_start: 0.7351 (mmt180) cc_final: 0.7071 (mmt180) REVERT: R 61 PRO cc_start: 0.8016 (Cg_exo) cc_final: 0.7714 (Cg_endo) REVERT: R 77 LEU cc_start: 0.5717 (mt) cc_final: 0.5497 (mt) REVERT: R 126 GLU cc_start: 0.7646 (tp30) cc_final: 0.7394 (tp30) REVERT: S 27 LYS cc_start: 0.8503 (ptmt) cc_final: 0.7846 (ptmt) REVERT: S 55 TYR cc_start: 0.7968 (t80) cc_final: 0.7741 (t80) REVERT: S 56 ARG cc_start: 0.7780 (tmm160) cc_final: 0.7032 (tmm160) REVERT: S 65 GLU cc_start: 0.5692 (tm-30) cc_final: 0.5430 (tm-30) REVERT: S 176 ARG cc_start: 0.8703 (mtm-85) cc_final: 0.8494 (mtm-85) REVERT: T 13 GLU cc_start: 0.8255 (pm20) cc_final: 0.7827 (pm20) REVERT: T 17 GLU cc_start: 0.7780 (mt-10) cc_final: 0.6696 (mt-10) REVERT: T 19 GLN cc_start: 0.7945 (mm-40) cc_final: 0.7527 (tp40) REVERT: T 27 LYS cc_start: 0.8054 (ptmt) cc_final: 0.7812 (ptpp) REVERT: T 89 LEU cc_start: 0.6571 (tp) cc_final: 0.6213 (tp) REVERT: T 128 GLU cc_start: 0.7087 (OUTLIER) cc_final: 0.6881 (mp0) REVERT: T 139 PHE cc_start: 0.6747 (p90) cc_final: 0.6403 (p90) REVERT: T 160 ASP cc_start: 0.8296 (p0) cc_final: 0.7945 (p0) REVERT: T 165 PHE cc_start: 0.8579 (m-80) cc_final: 0.8276 (m-80) REVERT: T 176 ARG cc_start: 0.8450 (ptp-110) cc_final: 0.8151 (ptp-110) REVERT: U 35 LYS cc_start: 0.8569 (mmtm) cc_final: 0.8173 (mmtm) REVERT: U 68 GLU cc_start: 0.7175 (tp30) cc_final: 0.6635 (tp30) REVERT: U 70 PHE cc_start: 0.7141 (OUTLIER) cc_final: 0.6909 (m-10) REVERT: U 103 MET cc_start: 0.7080 (mtp) cc_final: 0.6566 (mtt) REVERT: U 143 ASP cc_start: 0.8158 (m-30) cc_final: 0.7873 (m-30) REVERT: U 148 ARG cc_start: 0.7012 (ptp90) cc_final: 0.6732 (ptp90) REVERT: U 155 VAL cc_start: 0.8479 (t) cc_final: 0.8266 (m) REVERT: U 157 LYS cc_start: 0.7704 (mmtt) cc_final: 0.7354 (mmtp) REVERT: U 210 ILE cc_start: 0.8497 (tp) cc_final: 0.8132 (tp) REVERT: U 223 GLN cc_start: 0.8027 (tt0) cc_final: 0.7557 (tt0) REVERT: U 253 GLN cc_start: 0.8111 (mm-40) cc_final: 0.7842 (mm-40) REVERT: U 275 GLU cc_start: 0.7139 (pp20) cc_final: 0.6758 (pp20) REVERT: V 14 LYS cc_start: 0.8271 (tttp) cc_final: 0.7919 (ttmm) REVERT: V 15 LYS cc_start: 0.8334 (tmtp) cc_final: 0.7944 (tmtp) REVERT: V 68 GLU cc_start: 0.7564 (tp30) cc_final: 0.6774 (tp30) REVERT: V 69 PHE cc_start: 0.8158 (t80) cc_final: 0.7756 (t80) REVERT: V 105 ARG cc_start: 0.7422 (mtt180) cc_final: 0.6737 (ttm-80) REVERT: V 143 ASP cc_start: 0.7387 (m-30) cc_final: 0.7132 (m-30) REVERT: V 148 ARG cc_start: 0.7490 (ptp90) cc_final: 0.7138 (ptp90) REVERT: V 150 ARG cc_start: 0.6747 (mtm180) cc_final: 0.6318 (mmm160) REVERT: V 177 GLN cc_start: 0.7532 (pp30) cc_final: 0.7300 (pp30) REVERT: V 192 ASP cc_start: 0.7289 (m-30) cc_final: 0.6684 (m-30) REVERT: V 265 ASP cc_start: 0.7730 (t0) cc_final: 0.7482 (t0) REVERT: V 273 LEU cc_start: 0.8309 (tp) cc_final: 0.8097 (tp) REVERT: V 275 GLU cc_start: 0.6998 (pp20) cc_final: 0.6674 (pp20) REVERT: W 15 LYS cc_start: 0.8284 (tmtp) cc_final: 0.7858 (tmtp) REVERT: W 19 GLU cc_start: 0.7853 (pt0) cc_final: 0.7597 (pt0) REVERT: W 59 MET cc_start: 0.7754 (ttp) cc_final: 0.7466 (ttp) REVERT: W 62 ARG cc_start: 0.6994 (mtp85) cc_final: 0.6664 (mtp85) REVERT: W 63 PHE cc_start: 0.8346 (t80) cc_final: 0.8136 (t80) REVERT: W 64 GLU cc_start: 0.7559 (pm20) cc_final: 0.7205 (pm20) REVERT: W 85 MET cc_start: 0.8043 (mtm) cc_final: 0.7720 (mtp) REVERT: W 99 GLU cc_start: 0.6783 (mm-30) cc_final: 0.6512 (mm-30) REVERT: W 105 ARG cc_start: 0.7914 (ttm-80) cc_final: 0.7663 (ttm-80) REVERT: W 125 GLU cc_start: 0.6995 (mp0) cc_final: 0.6282 (mp0) REVERT: W 129 ARG cc_start: 0.6836 (ttm110) cc_final: 0.6492 (ttm170) REVERT: W 166 ASP cc_start: 0.7479 (p0) cc_final: 0.7205 (p0) REVERT: W 188 ARG cc_start: 0.8227 (tpp80) cc_final: 0.7942 (tpp80) REVERT: W 210 ILE cc_start: 0.7891 (tp) cc_final: 0.7691 (mm) REVERT: W 218 ASN cc_start: 0.7953 (t0) cc_final: 0.6804 (m110) REVERT: W 221 ARG cc_start: 0.7809 (mtt90) cc_final: 0.7371 (mtt90) REVERT: W 222 GLU cc_start: 0.7786 (mm-30) cc_final: 0.7211 (mm-30) REVERT: X 15 LYS cc_start: 0.8460 (tmtp) cc_final: 0.7795 (tppt) REVERT: X 16 GLU cc_start: 0.7913 (mm-30) cc_final: 0.7409 (mm-30) REVERT: X 23 ILE cc_start: 0.7301 (mt) cc_final: 0.6730 (tt) REVERT: X 42 LEU cc_start: 0.8610 (OUTLIER) cc_final: 0.8248 (mt) REVERT: X 46 LEU cc_start: 0.8229 (mt) cc_final: 0.7980 (mp) REVERT: X 53 GLU cc_start: 0.7613 (tm-30) cc_final: 0.6565 (tm-30) REVERT: X 55 GLU cc_start: 0.7546 (mp0) cc_final: 0.7157 (mp0) REVERT: X 88 SER cc_start: 0.7980 (m) cc_final: 0.7721 (t) REVERT: X 103 MET cc_start: 0.7006 (mmm) cc_final: 0.6780 (mmm) REVERT: X 141 PHE cc_start: 0.8025 (t80) cc_final: 0.7717 (t80) REVERT: X 155 VAL cc_start: 0.8144 (t) cc_final: 0.7806 (p) REVERT: X 158 PHE cc_start: 0.7874 (t80) cc_final: 0.7585 (t80) REVERT: X 168 ILE cc_start: 0.8281 (mm) cc_final: 0.8009 (mm) REVERT: X 171 THR cc_start: 0.7725 (m) cc_final: 0.7425 (t) REVERT: X 176 PHE cc_start: 0.8501 (m-10) cc_final: 0.8260 (m-80) REVERT: X 181 LEU cc_start: 0.7679 (mt) cc_final: 0.7264 (mt) REVERT: X 182 ASP cc_start: 0.7299 (m-30) cc_final: 0.6938 (m-30) REVERT: X 225 GLN cc_start: 0.7534 (pt0) cc_final: 0.7156 (pt0) REVERT: X 247 GLN cc_start: 0.7152 (mm-40) cc_final: 0.6479 (mt0) outliers start: 108 outliers final: 52 residues processed: 1183 average time/residue: 0.2296 time to fit residues: 400.8433 Evaluate side-chains 1160 residues out of total 3024 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 1095 time to evaluate : 1.106 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 174 ARG Chi-restraints excluded: chain C residue 12 SER Chi-restraints excluded: chain C residue 21 VAL Chi-restraints excluded: chain C residue 27 LYS Chi-restraints excluded: chain C residue 41 VAL Chi-restraints excluded: chain C residue 60 VAL Chi-restraints excluded: chain C residue 120 VAL Chi-restraints excluded: chain D residue 60 VAL Chi-restraints excluded: chain D residue 117 GLU Chi-restraints excluded: chain E residue 49 THR Chi-restraints excluded: chain E residue 179 MET Chi-restraints excluded: chain E residue 201 ILE Chi-restraints excluded: chain E residue 218 ASN Chi-restraints excluded: chain E residue 225 GLN Chi-restraints excluded: chain E residue 264 THR Chi-restraints excluded: chain E residue 276 SER Chi-restraints excluded: chain F residue 3 THR Chi-restraints excluded: chain F residue 35 LYS Chi-restraints excluded: chain F residue 159 HIS Chi-restraints excluded: chain F residue 270 VAL Chi-restraints excluded: chain G residue 3 THR Chi-restraints excluded: chain G residue 88 SER Chi-restraints excluded: chain G residue 101 SER Chi-restraints excluded: chain G residue 175 TYR Chi-restraints excluded: chain G residue 249 ASP Chi-restraints excluded: chain H residue 6 LEU Chi-restraints excluded: chain H residue 70 PHE Chi-restraints excluded: chain H residue 193 LEU Chi-restraints excluded: chain Q residue 21 VAL Chi-restraints excluded: chain Q residue 43 LEU Chi-restraints excluded: chain Q residue 162 LYS Chi-restraints excluded: chain R residue 120 VAL Chi-restraints excluded: chain S residue 12 SER Chi-restraints excluded: chain S residue 173 THR Chi-restraints excluded: chain T residue 10 THR Chi-restraints excluded: chain T residue 21 VAL Chi-restraints excluded: chain T residue 41 VAL Chi-restraints excluded: chain T residue 120 VAL Chi-restraints excluded: chain T residue 128 GLU Chi-restraints excluded: chain T residue 144 ILE Chi-restraints excluded: chain U residue 18 ARG Chi-restraints excluded: chain U residue 38 ASP Chi-restraints excluded: chain U residue 70 PHE Chi-restraints excluded: chain U residue 111 ASP Chi-restraints excluded: chain U residue 120 TYR Chi-restraints excluded: chain U residue 252 GLN Chi-restraints excluded: chain V residue 4 LEU Chi-restraints excluded: chain V residue 65 GLN Chi-restraints excluded: chain V residue 77 ARG Chi-restraints excluded: chain V residue 164 GLN Chi-restraints excluded: chain V residue 193 LEU Chi-restraints excluded: chain V residue 201 ILE Chi-restraints excluded: chain V residue 252 GLN Chi-restraints excluded: chain V residue 276 SER Chi-restraints excluded: chain W residue 77 ARG Chi-restraints excluded: chain W residue 81 LEU Chi-restraints excluded: chain W residue 91 SER Chi-restraints excluded: chain W residue 120 TYR Chi-restraints excluded: chain W residue 159 HIS Chi-restraints excluded: chain W residue 170 LEU Chi-restraints excluded: chain W residue 246 VAL Chi-restraints excluded: chain X residue 42 LEU Chi-restraints excluded: chain X residue 79 GLN Chi-restraints excluded: chain X residue 210 ILE Chi-restraints excluded: chain X residue 264 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 360 random chunks: chunk 30 optimal weight: 0.2980 chunk 45 optimal weight: 5.9990 chunk 162 optimal weight: 6.9990 chunk 12 optimal weight: 3.9990 chunk 138 optimal weight: 0.8980 chunk 67 optimal weight: 7.9990 chunk 108 optimal weight: 0.9990 chunk 66 optimal weight: 50.0000 chunk 145 optimal weight: 1.9990 chunk 306 optimal weight: 7.9990 chunk 331 optimal weight: 1.9990 overall best weight: 1.2386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 119 HIS ** A 172 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 145 GLN ** F 123 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 65 GLN ** G 225 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 230 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 232 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 252 GLN H 60 HIS H 209 ASN ** H 225 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 119 HIS ** R 172 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** T 119 HIS ** W 123 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** W 241 HIS Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3903 r_free = 0.3903 target = 0.129841 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3597 r_free = 0.3597 target = 0.110020 restraints weight = 62268.961| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3654 r_free = 0.3654 target = 0.113883 restraints weight = 32795.381| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3691 r_free = 0.3691 target = 0.116414 restraints weight = 20010.616| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 38)----------------| | r_work = 0.3716 r_free = 0.3716 target = 0.118108 restraints weight = 13499.994| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 37)----------------| | r_work = 0.3733 r_free = 0.3733 target = 0.119271 restraints weight = 9928.288| |-----------------------------------------------------------------------------| r_work (final): 0.3732 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7168 moved from start: 0.7208 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 29416 Z= 0.162 Angle : 0.668 9.079 39856 Z= 0.342 Chirality : 0.046 0.197 4432 Planarity : 0.005 0.066 5200 Dihedral : 4.762 25.702 4024 Min Nonbonded Distance : 2.489 Molprobity Statistics. All-atom Clashscore : 13.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.31 % Favored : 96.69 % Rotamer: Outliers : 3.61 % Allowed : 19.83 % Favored : 76.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.55 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.45 (0.13), residues: 3624 helix: -0.20 (0.12), residues: 1672 sheet: -0.88 (0.19), residues: 608 loop : -1.86 (0.15), residues: 1344 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG A 176 TYR 0.028 0.002 TYR W 212 PHE 0.023 0.002 PHE T 139 TRP 0.043 0.002 TRP C 141 HIS 0.010 0.001 HIS F 159 Details of bonding type rmsd covalent geometry : bond 0.00350 (29416) covalent geometry : angle 0.66809 (39856) hydrogen bonds : bond 0.03854 ( 1252) hydrogen bonds : angle 5.04558 ( 3636) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7248 Ramachandran restraints generated. 3624 Oldfield, 0 Emsley, 3624 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7248 Ramachandran restraints generated. 3624 Oldfield, 0 Emsley, 3624 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1277 residues out of total 3024 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 109 poor density : 1168 time to evaluate : 1.045 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: symmetry clash 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: symmetry clash 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: symmetry clash 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: symmetry clash revert: symmetry clash REVERT: A 5 TRP cc_start: 0.7326 (m100) cc_final: 0.5967 (m100) REVERT: A 19 GLN cc_start: 0.7723 (tm-30) cc_final: 0.7437 (tp-100) REVERT: A 30 TYR cc_start: 0.7039 (m-80) cc_final: 0.6646 (m-80) REVERT: A 32 THR cc_start: 0.8158 (p) cc_final: 0.7924 (m) REVERT: A 59 ARG cc_start: 0.7341 (mmt180) cc_final: 0.7071 (tpp80) REVERT: B 16 ARG cc_start: 0.7744 (ttp80) cc_final: 0.7277 (ttp80) REVERT: B 27 LYS cc_start: 0.7404 (ptmt) cc_final: 0.7004 (ptmt) REVERT: B 117 GLU cc_start: 0.7428 (pt0) cc_final: 0.6971 (pt0) REVERT: B 140 HIS cc_start: 0.6897 (m-70) cc_final: 0.6610 (m-70) REVERT: C 11 ASN cc_start: 0.7268 (t0) cc_final: 0.6517 (t0) REVERT: C 12 SER cc_start: 0.8605 (OUTLIER) cc_final: 0.8391 (p) REVERT: C 14 LYS cc_start: 0.8620 (mttm) cc_final: 0.8260 (mttm) REVERT: C 17 GLU cc_start: 0.7852 (mt-10) cc_final: 0.7524 (mt-10) REVERT: C 19 GLN cc_start: 0.7889 (mm-40) cc_final: 0.7651 (mm-40) REVERT: C 27 LYS cc_start: 0.8155 (OUTLIER) cc_final: 0.7833 (ptpp) REVERT: C 30 TYR cc_start: 0.7391 (m-80) cc_final: 0.6729 (m-80) REVERT: C 89 LEU cc_start: 0.7260 (tp) cc_final: 0.6128 (tt) REVERT: C 139 PHE cc_start: 0.6790 (p90) cc_final: 0.6343 (p90) REVERT: C 148 LYS cc_start: 0.8200 (pttm) cc_final: 0.7840 (pttm) REVERT: C 168 LEU cc_start: 0.8015 (tp) cc_final: 0.7726 (tp) REVERT: C 170 ARG cc_start: 0.7769 (mtm-85) cc_final: 0.7465 (ptp-170) REVERT: C 172 HIS cc_start: 0.7888 (m90) cc_final: 0.7586 (m-70) REVERT: C 174 ARG cc_start: 0.7799 (mtp180) cc_final: 0.7548 (mtp180) REVERT: D 9 THR cc_start: 0.8426 (t) cc_final: 0.7655 (t) REVERT: D 38 ILE cc_start: 0.8296 (tt) cc_final: 0.7670 (tt) REVERT: D 50 LYS cc_start: 0.8147 (mmpt) cc_final: 0.7764 (mmpt) REVERT: D 69 LEU cc_start: 0.7572 (tp) cc_final: 0.7270 (tp) REVERT: D 162 LYS cc_start: 0.7667 (mmmt) cc_final: 0.7419 (mmmt) REVERT: D 176 ARG cc_start: 0.8659 (mtp180) cc_final: 0.8384 (mtp85) REVERT: E 15 LYS cc_start: 0.8581 (tmtp) cc_final: 0.7889 (tmtp) REVERT: E 16 GLU cc_start: 0.7834 (mm-30) cc_final: 0.7022 (mm-30) REVERT: E 46 LEU cc_start: 0.8435 (mt) cc_final: 0.8204 (mm) REVERT: E 53 GLU cc_start: 0.7742 (tm-30) cc_final: 0.7409 (tm-30) REVERT: E 62 ARG cc_start: 0.6610 (mmp80) cc_final: 0.6242 (mmp80) REVERT: E 80 ARG cc_start: 0.8002 (tpt170) cc_final: 0.7338 (tpt90) REVERT: E 89 PHE cc_start: 0.8061 (m-10) cc_final: 0.7411 (m-80) REVERT: E 133 LYS cc_start: 0.6871 (mtmm) cc_final: 0.6331 (mtmm) REVERT: E 141 PHE cc_start: 0.8050 (t80) cc_final: 0.7844 (t80) REVERT: E 179 MET cc_start: 0.7035 (OUTLIER) cc_final: 0.6451 (mmt) REVERT: E 181 LEU cc_start: 0.7840 (mt) cc_final: 0.7518 (mp) REVERT: E 182 ASP cc_start: 0.7491 (m-30) cc_final: 0.7255 (m-30) REVERT: E 196 ASN cc_start: 0.7446 (m-40) cc_final: 0.7213 (m-40) REVERT: E 217 MET cc_start: 0.7388 (mtt) cc_final: 0.7113 (mmm) REVERT: E 225 GLN cc_start: 0.7564 (OUTLIER) cc_final: 0.7286 (mt0) REVERT: E 245 LEU cc_start: 0.7922 (mp) cc_final: 0.7703 (mp) REVERT: E 272 ARG cc_start: 0.7801 (mmp80) cc_final: 0.6393 (mmp80) REVERT: E 275 GLU cc_start: 0.7479 (mt-10) cc_final: 0.6721 (mt-10) REVERT: F 15 LYS cc_start: 0.8333 (tmtp) cc_final: 0.8105 (tttp) REVERT: F 19 GLU cc_start: 0.7895 (pt0) cc_final: 0.7567 (pt0) REVERT: F 35 LYS cc_start: 0.8885 (OUTLIER) cc_final: 0.8598 (mtmm) REVERT: F 38 ASP cc_start: 0.8553 (p0) cc_final: 0.8316 (p0) REVERT: F 41 GLN cc_start: 0.8265 (tm-30) cc_final: 0.8042 (tm-30) REVERT: F 63 PHE cc_start: 0.8264 (t80) cc_final: 0.7979 (t80) REVERT: F 66 LEU cc_start: 0.8925 (mt) cc_final: 0.8572 (mp) REVERT: F 68 GLU cc_start: 0.7193 (tp30) cc_final: 0.6653 (tp30) REVERT: F 70 PHE cc_start: 0.8675 (m-80) cc_final: 0.8425 (m-80) REVERT: F 77 ARG cc_start: 0.8024 (mpt90) cc_final: 0.7453 (mpt90) REVERT: F 80 ARG cc_start: 0.7740 (tpt90) cc_final: 0.7098 (tpt90) REVERT: F 95 GLU cc_start: 0.7923 (mt-10) cc_final: 0.7514 (mt-10) REVERT: F 187 GLN cc_start: 0.8390 (mm-40) cc_final: 0.7747 (mm110) REVERT: F 188 ARG cc_start: 0.8525 (mmm-85) cc_final: 0.8111 (tpt90) REVERT: F 217 MET cc_start: 0.7169 (OUTLIER) cc_final: 0.6939 (mtt) REVERT: F 218 ASN cc_start: 0.7692 (t0) cc_final: 0.7427 (t0) REVERT: F 247 GLN cc_start: 0.7603 (mt0) cc_final: 0.7353 (mt0) REVERT: G 13 LEU cc_start: 0.8520 (mt) cc_final: 0.8067 (mt) REVERT: G 31 SER cc_start: 0.8539 (m) cc_final: 0.8232 (p) REVERT: G 65 GLN cc_start: 0.8183 (OUTLIER) cc_final: 0.7966 (mt0) REVERT: G 105 ARG cc_start: 0.7258 (mtt180) cc_final: 0.7033 (tpp80) REVERT: G 148 ARG cc_start: 0.7677 (ptp-170) cc_final: 0.7464 (ptp90) REVERT: G 175 TYR cc_start: 0.7266 (OUTLIER) cc_final: 0.6577 (t80) REVERT: G 177 GLN cc_start: 0.7526 (pp30) cc_final: 0.7275 (pp30) REVERT: G 178 ARG cc_start: 0.7881 (tpp80) cc_final: 0.7444 (tpp80) REVERT: G 222 GLU cc_start: 0.7682 (mm-30) cc_final: 0.7222 (mm-30) REVERT: G 252 GLN cc_start: 0.7931 (tp-100) cc_final: 0.7558 (tp40) REVERT: G 275 GLU cc_start: 0.7096 (pp20) cc_final: 0.6731 (pp20) REVERT: H 21 ARG cc_start: 0.7711 (mmt90) cc_final: 0.7049 (mtt180) REVERT: H 35 LYS cc_start: 0.8638 (mmtm) cc_final: 0.8286 (mmtm) REVERT: H 65 GLN cc_start: 0.7724 (mp10) cc_final: 0.6955 (mp10) REVERT: H 68 GLU cc_start: 0.6803 (tp30) cc_final: 0.6291 (tp30) REVERT: H 70 PHE cc_start: 0.7067 (OUTLIER) cc_final: 0.6713 (m-10) REVERT: H 84 GLU cc_start: 0.7939 (pt0) cc_final: 0.7567 (pt0) REVERT: H 122 LYS cc_start: 0.8056 (pttt) cc_final: 0.7749 (pttt) REVERT: H 210 ILE cc_start: 0.8303 (tp) cc_final: 0.7917 (tp) REVERT: H 212 TYR cc_start: 0.7172 (t80) cc_final: 0.6926 (t80) REVERT: H 215 TYR cc_start: 0.7950 (t80) cc_final: 0.7438 (t80) REVERT: H 221 ARG cc_start: 0.7791 (ttm-80) cc_final: 0.7151 (ttm-80) REVERT: H 223 GLN cc_start: 0.8061 (tt0) cc_final: 0.7606 (tt0) REVERT: H 235 ARG cc_start: 0.7427 (tpp-160) cc_final: 0.6864 (mmm160) REVERT: H 237 PHE cc_start: 0.8016 (m-80) cc_final: 0.7694 (m-80) REVERT: H 249 ASP cc_start: 0.7266 (m-30) cc_final: 0.6880 (m-30) REVERT: H 252 GLN cc_start: 0.7478 (tm-30) cc_final: 0.6806 (tm-30) REVERT: H 253 GLN cc_start: 0.7960 (mm-40) cc_final: 0.7584 (mm-40) REVERT: H 275 GLU cc_start: 0.7393 (pt0) cc_final: 0.7086 (pt0) REVERT: Q 16 ARG cc_start: 0.7565 (ttp80) cc_final: 0.7322 (ttp80) REVERT: Q 19 GLN cc_start: 0.8081 (mt0) cc_final: 0.7800 (mt0) REVERT: Q 117 GLU cc_start: 0.7207 (pt0) cc_final: 0.6827 (pt0) REVERT: Q 170 ARG cc_start: 0.7615 (mtm-85) cc_final: 0.7393 (mtt90) REVERT: R 44 GLU cc_start: 0.7058 (tm-30) cc_final: 0.6848 (tm-30) REVERT: R 61 PRO cc_start: 0.8028 (Cg_exo) cc_final: 0.7705 (Cg_endo) REVERT: R 77 LEU cc_start: 0.5745 (mt) cc_final: 0.5524 (mt) REVERT: R 118 ARG cc_start: 0.7288 (ttp-170) cc_final: 0.6972 (ttp-170) REVERT: R 123 GLU cc_start: 0.6989 (mm-30) cc_final: 0.6742 (mm-30) REVERT: R 157 MET cc_start: 0.5654 (pmm) cc_final: 0.5380 (pmm) REVERT: S 27 LYS cc_start: 0.8543 (ptmt) cc_final: 0.7962 (ptmt) REVERT: S 56 ARG cc_start: 0.7824 (tmm160) cc_final: 0.6962 (tmm160) REVERT: T 11 ASN cc_start: 0.6255 (p0) cc_final: 0.5921 (p0) REVERT: T 13 GLU cc_start: 0.8044 (pm20) cc_final: 0.7672 (pm20) REVERT: T 17 GLU cc_start: 0.7730 (mt-10) cc_final: 0.7129 (mt-10) REVERT: T 19 GLN cc_start: 0.7976 (mm-40) cc_final: 0.7451 (tp40) REVERT: T 30 TYR cc_start: 0.7791 (m-80) cc_final: 0.6605 (m-80) REVERT: T 42 ASP cc_start: 0.7373 (t0) cc_final: 0.7050 (t0) REVERT: T 48 ARG cc_start: 0.7856 (mmm-85) cc_final: 0.7104 (mtt180) REVERT: T 59 ARG cc_start: 0.7357 (tpt-90) cc_final: 0.6807 (mmm160) REVERT: T 89 LEU cc_start: 0.6382 (tp) cc_final: 0.6017 (tp) REVERT: T 157 MET cc_start: 0.6301 (ttt) cc_final: 0.5969 (ttt) REVERT: T 165 PHE cc_start: 0.8581 (m-80) cc_final: 0.8073 (m-80) REVERT: T 170 ARG cc_start: 0.7509 (ptp-170) cc_final: 0.7057 (ptp-170) REVERT: U 16 GLU cc_start: 0.7224 (mm-30) cc_final: 0.6965 (mm-30) REVERT: U 32 LYS cc_start: 0.8373 (ttpp) cc_final: 0.8154 (ttpp) REVERT: U 35 LYS cc_start: 0.8603 (mmtm) cc_final: 0.8227 (mmtm) REVERT: U 68 GLU cc_start: 0.7323 (tp30) cc_final: 0.6788 (tp30) REVERT: U 70 PHE cc_start: 0.7142 (OUTLIER) cc_final: 0.6878 (m-10) REVERT: U 103 MET cc_start: 0.7057 (mtp) cc_final: 0.6557 (mtt) REVERT: U 143 ASP cc_start: 0.8182 (m-30) cc_final: 0.7891 (m-30) REVERT: U 144 PHE cc_start: 0.8026 (m-80) cc_final: 0.7763 (m-80) REVERT: U 148 ARG cc_start: 0.6830 (ptp90) cc_final: 0.6542 (ptp90) REVERT: U 170 LEU cc_start: 0.7294 (OUTLIER) cc_final: 0.6910 (mm) REVERT: U 178 ARG cc_start: 0.7049 (mmm160) cc_final: 0.6717 (mmm160) REVERT: U 210 ILE cc_start: 0.8507 (tp) cc_final: 0.8124 (tp) REVERT: U 212 TYR cc_start: 0.7033 (t80) cc_final: 0.6822 (t80) REVERT: U 222 GLU cc_start: 0.7776 (mm-30) cc_final: 0.7536 (mm-30) REVERT: U 223 GLN cc_start: 0.8008 (tt0) cc_final: 0.7512 (tt0) REVERT: U 235 ARG cc_start: 0.7663 (tpp-160) cc_final: 0.6898 (ttm-80) REVERT: U 238 PHE cc_start: 0.7929 (t80) cc_final: 0.7623 (t80) REVERT: U 253 GLN cc_start: 0.8024 (mm-40) cc_final: 0.7689 (mm-40) REVERT: U 257 ASP cc_start: 0.6868 (m-30) cc_final: 0.6330 (m-30) REVERT: U 275 GLU cc_start: 0.7178 (pp20) cc_final: 0.6784 (pp20) REVERT: V 13 LEU cc_start: 0.8445 (mt) cc_final: 0.8198 (mt) REVERT: V 14 LYS cc_start: 0.8186 (tttp) cc_final: 0.7848 (ttmm) REVERT: V 15 LYS cc_start: 0.8330 (tmtp) cc_final: 0.7932 (tmtp) REVERT: V 65 GLN cc_start: 0.7912 (OUTLIER) cc_final: 0.7448 (mt0) REVERT: V 68 GLU cc_start: 0.7646 (tp30) cc_final: 0.6795 (tp30) REVERT: V 69 PHE cc_start: 0.8320 (t80) cc_final: 0.7951 (t80) REVERT: V 105 ARG cc_start: 0.7524 (mtt180) cc_final: 0.6823 (ttm-80) REVERT: V 148 ARG cc_start: 0.7386 (ptp90) cc_final: 0.7065 (ptp90) REVERT: V 150 ARG cc_start: 0.6776 (mtm180) cc_final: 0.6353 (mmm160) REVERT: V 158 PHE cc_start: 0.8111 (t80) cc_final: 0.7543 (t80) REVERT: V 169 VAL cc_start: 0.7825 (OUTLIER) cc_final: 0.7503 (p) REVERT: V 181 LEU cc_start: 0.7752 (mt) cc_final: 0.7516 (mt) REVERT: V 188 ARG cc_start: 0.6967 (tpt-90) cc_final: 0.6681 (tpt-90) REVERT: V 192 ASP cc_start: 0.7310 (m-30) cc_final: 0.6594 (m-30) REVERT: V 216 ARG cc_start: 0.8046 (tpt90) cc_final: 0.7754 (tpt170) REVERT: V 222 GLU cc_start: 0.7830 (mm-30) cc_final: 0.7610 (mm-30) REVERT: V 265 ASP cc_start: 0.7476 (t0) cc_final: 0.7205 (t0) REVERT: W 15 LYS cc_start: 0.8310 (tmtp) cc_final: 0.7764 (tmtp) REVERT: W 32 LYS cc_start: 0.8010 (tppt) cc_final: 0.7586 (tppt) REVERT: W 62 ARG cc_start: 0.6946 (mtp85) cc_final: 0.6601 (mtp85) REVERT: W 64 GLU cc_start: 0.7529 (pm20) cc_final: 0.7170 (pm20) REVERT: W 85 MET cc_start: 0.8042 (mtm) cc_final: 0.7765 (mtp) REVERT: W 86 SER cc_start: 0.8777 (m) cc_final: 0.8348 (p) REVERT: W 100 LYS cc_start: 0.8239 (mtmm) cc_final: 0.7832 (mtmm) REVERT: W 105 ARG cc_start: 0.7863 (ttm-80) cc_final: 0.7560 (ttm-80) REVERT: W 129 ARG cc_start: 0.6751 (ttm110) cc_final: 0.6045 (mtt-85) REVERT: W 166 ASP cc_start: 0.7525 (p0) cc_final: 0.7215 (p0) REVERT: W 187 GLN cc_start: 0.8303 (mm-40) cc_final: 0.7871 (mm-40) REVERT: W 188 ARG cc_start: 0.8295 (tpp80) cc_final: 0.8082 (tpp80) REVERT: W 218 ASN cc_start: 0.8021 (t0) cc_final: 0.6827 (t0) REVERT: W 221 ARG cc_start: 0.7790 (mtt90) cc_final: 0.7147 (ttp-110) REVERT: W 222 GLU cc_start: 0.7779 (mm-30) cc_final: 0.7001 (mm-30) REVERT: X 15 LYS cc_start: 0.8459 (tmtp) cc_final: 0.7828 (tppt) REVERT: X 16 GLU cc_start: 0.7852 (mm-30) cc_final: 0.7356 (mm-30) REVERT: X 35 LYS cc_start: 0.8715 (OUTLIER) cc_final: 0.8366 (mtmm) REVERT: X 42 LEU cc_start: 0.8621 (OUTLIER) cc_final: 0.8266 (mt) REVERT: X 46 LEU cc_start: 0.8105 (mt) cc_final: 0.7837 (mp) REVERT: X 53 GLU cc_start: 0.7628 (tm-30) cc_final: 0.6536 (tm-30) REVERT: X 55 GLU cc_start: 0.7498 (mp0) cc_final: 0.7144 (mp0) REVERT: X 57 PHE cc_start: 0.7730 (t80) cc_final: 0.7513 (t80) REVERT: X 145 GLN cc_start: 0.8207 (mm-40) cc_final: 0.7677 (mm110) REVERT: X 158 PHE cc_start: 0.7874 (t80) cc_final: 0.7612 (t80) REVERT: X 168 ILE cc_start: 0.8311 (mm) cc_final: 0.8028 (mm) REVERT: X 171 THR cc_start: 0.7614 (m) cc_final: 0.7188 (t) REVERT: X 176 PHE cc_start: 0.8487 (m-10) cc_final: 0.8251 (m-80) REVERT: X 179 MET cc_start: 0.7061 (mmm) cc_final: 0.6362 (mmm) REVERT: X 182 ASP cc_start: 0.7281 (m-30) cc_final: 0.6934 (m-30) REVERT: X 225 GLN cc_start: 0.7549 (pt0) cc_final: 0.7205 (pt0) REVERT: X 247 GLN cc_start: 0.7228 (mm-40) cc_final: 0.6540 (mt0) REVERT: X 264 THR cc_start: 0.8206 (OUTLIER) cc_final: 0.7995 (p) outliers start: 109 outliers final: 69 residues processed: 1193 average time/residue: 0.2275 time to fit residues: 398.8990 Evaluate side-chains 1223 residues out of total 3024 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 85 poor density : 1138 time to evaluate : 1.088 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 81 LEU Chi-restraints excluded: chain B residue 35 VAL Chi-restraints excluded: chain B residue 64 VAL Chi-restraints excluded: chain B residue 146 ILE Chi-restraints excluded: chain C residue 12 SER Chi-restraints excluded: chain C residue 27 LYS Chi-restraints excluded: chain C residue 41 VAL Chi-restraints excluded: chain C residue 120 VAL Chi-restraints excluded: chain D residue 60 VAL Chi-restraints excluded: chain E residue 19 GLU Chi-restraints excluded: chain E residue 49 THR Chi-restraints excluded: chain E residue 100 LYS Chi-restraints excluded: chain E residue 145 GLN Chi-restraints excluded: chain E residue 175 TYR Chi-restraints excluded: chain E residue 179 MET Chi-restraints excluded: chain E residue 225 GLN Chi-restraints excluded: chain E residue 276 SER Chi-restraints excluded: chain F residue 18 ARG Chi-restraints excluded: chain F residue 35 LYS Chi-restraints excluded: chain F residue 62 ARG Chi-restraints excluded: chain F residue 93 GLU Chi-restraints excluded: chain F residue 217 MET Chi-restraints excluded: chain F residue 270 VAL Chi-restraints excluded: chain G residue 3 THR Chi-restraints excluded: chain G residue 5 THR Chi-restraints excluded: chain G residue 19 GLU Chi-restraints excluded: chain G residue 65 GLN Chi-restraints excluded: chain G residue 101 SER Chi-restraints excluded: chain G residue 117 THR Chi-restraints excluded: chain G residue 119 ASN Chi-restraints excluded: chain G residue 175 TYR Chi-restraints excluded: chain G residue 209 ASN Chi-restraints excluded: chain G residue 249 ASP Chi-restraints excluded: chain H residue 64 GLU Chi-restraints excluded: chain H residue 70 PHE Chi-restraints excluded: chain H residue 91 SER Chi-restraints excluded: chain H residue 119 ASN Chi-restraints excluded: chain H residue 193 LEU Chi-restraints excluded: chain H residue 197 SER Chi-restraints excluded: chain H residue 209 ASN Chi-restraints excluded: chain Q residue 21 VAL Chi-restraints excluded: chain Q residue 43 LEU Chi-restraints excluded: chain R residue 32 THR Chi-restraints excluded: chain R residue 81 LEU Chi-restraints excluded: chain R residue 120 VAL Chi-restraints excluded: chain S residue 117 GLU Chi-restraints excluded: chain T residue 4 THR Chi-restraints excluded: chain T residue 36 THR Chi-restraints excluded: chain T residue 41 VAL Chi-restraints excluded: chain T residue 120 VAL Chi-restraints excluded: chain T residue 144 ILE Chi-restraints excluded: chain U residue 18 ARG Chi-restraints excluded: chain U residue 64 GLU Chi-restraints excluded: chain U residue 70 PHE Chi-restraints excluded: chain U residue 119 ASN Chi-restraints excluded: chain U residue 120 TYR Chi-restraints excluded: chain U residue 170 LEU Chi-restraints excluded: chain U residue 252 GLN Chi-restraints excluded: chain V residue 65 GLN Chi-restraints excluded: chain V residue 77 ARG Chi-restraints excluded: chain V residue 120 TYR Chi-restraints excluded: chain V residue 169 VAL Chi-restraints excluded: chain V residue 252 GLN Chi-restraints excluded: chain W residue 6 LEU Chi-restraints excluded: chain W residue 8 GLU Chi-restraints excluded: chain W residue 18 ARG Chi-restraints excluded: chain W residue 38 ASP Chi-restraints excluded: chain W residue 77 ARG Chi-restraints excluded: chain W residue 81 LEU Chi-restraints excluded: chain W residue 159 HIS Chi-restraints excluded: chain W residue 177 GLN Chi-restraints excluded: chain W residue 225 GLN Chi-restraints excluded: chain W residue 246 VAL Chi-restraints excluded: chain W residue 273 LEU Chi-restraints excluded: chain X residue 35 LYS Chi-restraints excluded: chain X residue 42 LEU Chi-restraints excluded: chain X residue 79 GLN Chi-restraints excluded: chain X residue 82 VAL Chi-restraints excluded: chain X residue 86 SER Chi-restraints excluded: chain X residue 100 LYS Chi-restraints excluded: chain X residue 122 LYS Chi-restraints excluded: chain X residue 177 GLN Chi-restraints excluded: chain X residue 210 ILE Chi-restraints excluded: chain X residue 240 THR Chi-restraints excluded: chain X residue 264 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 360 random chunks: chunk 140 optimal weight: 2.9990 chunk 252 optimal weight: 0.9990 chunk 37 optimal weight: 0.0970 chunk 66 optimal weight: 50.0000 chunk 2 optimal weight: 2.9990 chunk 112 optimal weight: 6.9990 chunk 125 optimal weight: 1.9990 chunk 137 optimal weight: 0.3980 chunk 45 optimal weight: 8.9990 chunk 262 optimal weight: 4.9990 chunk 352 optimal weight: 4.9990 overall best weight: 1.2984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 119 HIS ** E 145 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 164 GLN E 219 GLN E 247 GLN ** F 123 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 159 HIS G 41 GLN ** G 104 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 159 HIS H 225 GLN R 119 HIS ** R 172 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** W 60 HIS ** W 123 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** X 253 GLN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3887 r_free = 0.3887 target = 0.128502 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3586 r_free = 0.3586 target = 0.109030 restraints weight = 62321.498| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3643 r_free = 0.3643 target = 0.112878 restraints weight = 32573.251| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3680 r_free = 0.3680 target = 0.115396 restraints weight = 19689.846| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 42)----------------| | r_work = 0.3705 r_free = 0.3705 target = 0.117089 restraints weight = 13179.900| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3720 r_free = 0.3720 target = 0.118131 restraints weight = 9623.657| |-----------------------------------------------------------------------------| r_work (final): 0.3716 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7197 moved from start: 0.7804 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.054 29416 Z= 0.170 Angle : 0.681 9.861 39856 Z= 0.347 Chirality : 0.047 0.201 4432 Planarity : 0.005 0.054 5200 Dihedral : 4.716 23.729 4024 Min Nonbonded Distance : 2.522 Molprobity Statistics. All-atom Clashscore : 13.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.59 % Favored : 96.41 % Rotamer: Outliers : 3.85 % Allowed : 21.82 % Favored : 74.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.55 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.16 (0.13), residues: 3624 helix: 0.07 (0.13), residues: 1608 sheet: -0.72 (0.19), residues: 608 loop : -1.69 (0.15), residues: 1408 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG X 178 TYR 0.038 0.002 TYR E 203 PHE 0.040 0.002 PHE Q 139 TRP 0.054 0.002 TRP C 141 HIS 0.007 0.001 HIS D 20 Details of bonding type rmsd covalent geometry : bond 0.00363 (29416) covalent geometry : angle 0.68085 (39856) hydrogen bonds : bond 0.03924 ( 1252) hydrogen bonds : angle 5.05733 ( 3636) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7248 Ramachandran restraints generated. 3624 Oldfield, 0 Emsley, 3624 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7248 Ramachandran restraints generated. 3624 Oldfield, 0 Emsley, 3624 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1296 residues out of total 3024 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 116 poor density : 1180 time to evaluate : 1.096 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: symmetry clash 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: symmetry clash 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: symmetry clash 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 5 TRP cc_start: 0.7365 (m100) cc_final: 0.6050 (m100) REVERT: A 19 GLN cc_start: 0.7743 (tm-30) cc_final: 0.7541 (tp40) REVERT: A 30 TYR cc_start: 0.7097 (m-80) cc_final: 0.6379 (m-80) REVERT: A 32 THR cc_start: 0.8085 (p) cc_final: 0.7850 (m) REVERT: A 59 ARG cc_start: 0.7372 (mmt180) cc_final: 0.7087 (tpp80) REVERT: A 123 GLU cc_start: 0.7089 (tp30) cc_final: 0.6802 (mm-30) REVERT: A 175 LEU cc_start: 0.7781 (tp) cc_final: 0.7546 (tp) REVERT: B 16 ARG cc_start: 0.7824 (ttp80) cc_final: 0.7344 (ttp80) REVERT: B 27 LYS cc_start: 0.7443 (ptmt) cc_final: 0.7067 (ptmt) REVERT: B 117 GLU cc_start: 0.7496 (pt0) cc_final: 0.7054 (pt0) REVERT: B 174 ARG cc_start: 0.7967 (mtp180) cc_final: 0.7502 (mtp180) REVERT: C 11 ASN cc_start: 0.7264 (t0) cc_final: 0.6536 (t0) REVERT: C 12 SER cc_start: 0.8678 (OUTLIER) cc_final: 0.8426 (p) REVERT: C 14 LYS cc_start: 0.8658 (mttm) cc_final: 0.8314 (mttm) REVERT: C 19 GLN cc_start: 0.7907 (mm-40) cc_final: 0.7562 (mm-40) REVERT: C 27 LYS cc_start: 0.8236 (OUTLIER) cc_final: 0.7921 (ptpp) REVERT: C 30 TYR cc_start: 0.7438 (m-80) cc_final: 0.6678 (m-80) REVERT: C 168 LEU cc_start: 0.8238 (tp) cc_final: 0.7898 (tp) REVERT: C 172 HIS cc_start: 0.7970 (m90) cc_final: 0.7695 (m-70) REVERT: C 174 ARG cc_start: 0.7876 (mtp180) cc_final: 0.7638 (mtp180) REVERT: D 7 TYR cc_start: 0.7564 (t80) cc_final: 0.7139 (t80) REVERT: D 9 THR cc_start: 0.8482 (t) cc_final: 0.8062 (m) REVERT: D 11 ASN cc_start: 0.7333 (t0) cc_final: 0.6685 (m110) REVERT: D 63 ILE cc_start: 0.7307 (OUTLIER) cc_final: 0.6620 (mt) REVERT: D 69 LEU cc_start: 0.7535 (tp) cc_final: 0.7242 (tp) REVERT: D 118 ARG cc_start: 0.7741 (mtm180) cc_final: 0.7279 (ptp-170) REVERT: E 15 LYS cc_start: 0.8588 (tmtp) cc_final: 0.7845 (tmtp) REVERT: E 16 GLU cc_start: 0.7866 (mm-30) cc_final: 0.7110 (mm-30) REVERT: E 53 GLU cc_start: 0.7664 (tm-30) cc_final: 0.7399 (tm-30) REVERT: E 80 ARG cc_start: 0.8009 (tpt170) cc_final: 0.7310 (tpt90) REVERT: E 103 MET cc_start: 0.6969 (mmm) cc_final: 0.6600 (mmt) REVERT: E 133 LYS cc_start: 0.6834 (mtmm) cc_final: 0.6302 (mtmm) REVERT: E 158 PHE cc_start: 0.7964 (t80) cc_final: 0.7728 (t80) REVERT: E 179 MET cc_start: 0.7082 (OUTLIER) cc_final: 0.6479 (mmt) REVERT: E 181 LEU cc_start: 0.7871 (mt) cc_final: 0.7512 (mp) REVERT: E 182 ASP cc_start: 0.7515 (m-30) cc_final: 0.7259 (m-30) REVERT: E 225 GLN cc_start: 0.7597 (OUTLIER) cc_final: 0.7297 (mt0) REVERT: E 275 GLU cc_start: 0.7587 (mt-10) cc_final: 0.7075 (mt-10) REVERT: F 12 LEU cc_start: 0.8159 (mm) cc_final: 0.7888 (mp) REVERT: F 15 LYS cc_start: 0.8318 (tmtp) cc_final: 0.8095 (tttp) REVERT: F 19 GLU cc_start: 0.7913 (pt0) cc_final: 0.7629 (pt0) REVERT: F 26 LEU cc_start: 0.7738 (mt) cc_final: 0.7235 (mp) REVERT: F 32 LYS cc_start: 0.8052 (tppt) cc_final: 0.7512 (tppt) REVERT: F 35 LYS cc_start: 0.8888 (OUTLIER) cc_final: 0.8688 (mmmm) REVERT: F 38 ASP cc_start: 0.8641 (p0) cc_final: 0.8398 (p0) REVERT: F 41 GLN cc_start: 0.8188 (tm-30) cc_final: 0.7954 (tm-30) REVERT: F 63 PHE cc_start: 0.8238 (t80) cc_final: 0.8007 (t80) REVERT: F 66 LEU cc_start: 0.8927 (mt) cc_final: 0.8534 (mp) REVERT: F 70 PHE cc_start: 0.8653 (m-80) cc_final: 0.8371 (m-80) REVERT: F 77 ARG cc_start: 0.7992 (mpt90) cc_final: 0.7364 (mpt90) REVERT: F 78 LEU cc_start: 0.8688 (tp) cc_final: 0.8419 (tt) REVERT: F 80 ARG cc_start: 0.7752 (tpt90) cc_final: 0.7128 (tpt90) REVERT: F 95 GLU cc_start: 0.7971 (mt-10) cc_final: 0.7620 (mt-10) REVERT: F 171 THR cc_start: 0.8017 (m) cc_final: 0.7237 (p) REVERT: F 188 ARG cc_start: 0.8564 (mmm-85) cc_final: 0.8159 (tpt90) REVERT: F 217 MET cc_start: 0.7211 (OUTLIER) cc_final: 0.6988 (mtt) REVERT: F 218 ASN cc_start: 0.7777 (t0) cc_final: 0.7418 (t0) REVERT: G 31 SER cc_start: 0.8525 (m) cc_final: 0.8210 (p) REVERT: G 65 GLN cc_start: 0.8179 (OUTLIER) cc_final: 0.7780 (mt0) REVERT: G 113 ARG cc_start: 0.7428 (mtt180) cc_final: 0.7142 (mtt180) REVERT: G 175 TYR cc_start: 0.7325 (OUTLIER) cc_final: 0.6602 (t80) REVERT: G 177 GLN cc_start: 0.7503 (pp30) cc_final: 0.7300 (pp30) REVERT: G 178 ARG cc_start: 0.7936 (tpp80) cc_final: 0.7467 (tpp80) REVERT: G 211 ARG cc_start: 0.7916 (mtp85) cc_final: 0.7675 (ttm-80) REVERT: G 222 GLU cc_start: 0.7633 (mm-30) cc_final: 0.7227 (mm-30) REVERT: G 235 ARG cc_start: 0.7230 (mmm160) cc_final: 0.6571 (mmm160) REVERT: G 252 GLN cc_start: 0.7890 (tp-100) cc_final: 0.7545 (tp40) REVERT: G 272 ARG cc_start: 0.7925 (mmp80) cc_final: 0.7374 (mmp80) REVERT: G 275 GLU cc_start: 0.6999 (pp20) cc_final: 0.6572 (pp20) REVERT: H 21 ARG cc_start: 0.7769 (mmt90) cc_final: 0.7278 (mtt180) REVERT: H 68 GLU cc_start: 0.6938 (tp30) cc_final: 0.6446 (tp30) REVERT: H 70 PHE cc_start: 0.7138 (OUTLIER) cc_final: 0.6777 (m-10) REVERT: H 84 GLU cc_start: 0.7908 (pt0) cc_final: 0.7546 (pt0) REVERT: H 118 THR cc_start: 0.7440 (t) cc_final: 0.7183 (m) REVERT: H 122 LYS cc_start: 0.8108 (pttt) cc_final: 0.7794 (pttt) REVERT: H 215 TYR cc_start: 0.7885 (t80) cc_final: 0.7347 (t80) REVERT: H 221 ARG cc_start: 0.7816 (ttm-80) cc_final: 0.7346 (ttm-80) REVERT: H 223 GLN cc_start: 0.8079 (tt0) cc_final: 0.7639 (tt0) REVERT: H 235 ARG cc_start: 0.7417 (tpp-160) cc_final: 0.6835 (mmm160) REVERT: H 237 PHE cc_start: 0.7981 (m-80) cc_final: 0.7631 (m-80) REVERT: H 275 GLU cc_start: 0.7341 (pt0) cc_final: 0.7050 (pt0) REVERT: Q 13 GLU cc_start: 0.7426 (tp30) cc_final: 0.6841 (tp30) REVERT: Q 101 GLN cc_start: 0.8249 (pm20) cc_final: 0.8035 (pm20) REVERT: Q 117 GLU cc_start: 0.7178 (pt0) cc_final: 0.6756 (pt0) REVERT: R 48 ARG cc_start: 0.7703 (ttm-80) cc_final: 0.7221 (ttm-80) REVERT: R 59 ARG cc_start: 0.7496 (tpp80) cc_final: 0.7242 (tpp80) REVERT: R 61 PRO cc_start: 0.7896 (Cg_exo) cc_final: 0.7595 (Cg_endo) REVERT: R 123 GLU cc_start: 0.6898 (mm-30) cc_final: 0.6211 (mm-30) REVERT: S 16 ARG cc_start: 0.8775 (mmm160) cc_final: 0.8382 (tpt90) REVERT: S 27 LYS cc_start: 0.8591 (ptmt) cc_final: 0.8050 (ptmt) REVERT: S 56 ARG cc_start: 0.7724 (tmm160) cc_final: 0.6967 (tmm160) REVERT: S 71 ILE cc_start: 0.7495 (mm) cc_final: 0.7244 (mm) REVERT: S 78 PRO cc_start: 0.7228 (Cg_exo) cc_final: 0.7020 (Cg_endo) REVERT: S 176 ARG cc_start: 0.8681 (mtm-85) cc_final: 0.8447 (mtm-85) REVERT: T 13 GLU cc_start: 0.7915 (pm20) cc_final: 0.7481 (pm20) REVERT: T 19 GLN cc_start: 0.7977 (mm-40) cc_final: 0.7492 (tp40) REVERT: T 30 TYR cc_start: 0.7842 (m-80) cc_final: 0.6701 (m-80) REVERT: T 42 ASP cc_start: 0.7415 (t0) cc_final: 0.7096 (t0) REVERT: T 48 ARG cc_start: 0.7838 (mmm-85) cc_final: 0.7278 (mtt90) REVERT: T 59 ARG cc_start: 0.7309 (tpt-90) cc_final: 0.6900 (tpt-90) REVERT: T 89 LEU cc_start: 0.6511 (tp) cc_final: 0.6148 (tp) REVERT: T 161 GLU cc_start: 0.8030 (pt0) cc_final: 0.7813 (pt0) REVERT: T 165 PHE cc_start: 0.8621 (m-80) cc_final: 0.8017 (m-80) REVERT: T 170 ARG cc_start: 0.7599 (ptp-170) cc_final: 0.7095 (ptp-170) REVERT: T 176 ARG cc_start: 0.8471 (ptp-110) cc_final: 0.7694 (ttm-80) REVERT: U 16 GLU cc_start: 0.7199 (mm-30) cc_final: 0.6958 (mm-30) REVERT: U 21 ARG cc_start: 0.7643 (mmt90) cc_final: 0.6886 (mtt180) REVERT: U 32 LYS cc_start: 0.8395 (ttpp) cc_final: 0.8082 (ttpp) REVERT: U 35 LYS cc_start: 0.8654 (mmtm) cc_final: 0.8307 (mmtm) REVERT: U 68 GLU cc_start: 0.7494 (tp30) cc_final: 0.6932 (tp30) REVERT: U 70 PHE cc_start: 0.7207 (OUTLIER) cc_final: 0.7003 (m-10) REVERT: U 143 ASP cc_start: 0.8137 (m-30) cc_final: 0.7832 (m-30) REVERT: U 144 PHE cc_start: 0.7973 (m-80) cc_final: 0.7733 (m-80) REVERT: U 148 ARG cc_start: 0.6875 (ptp90) cc_final: 0.6509 (ptp90) REVERT: U 170 LEU cc_start: 0.7194 (OUTLIER) cc_final: 0.6805 (mm) REVERT: U 194 LEU cc_start: 0.7988 (mt) cc_final: 0.7759 (mt) REVERT: U 210 ILE cc_start: 0.8542 (tp) cc_final: 0.8151 (tp) REVERT: U 212 TYR cc_start: 0.7069 (t80) cc_final: 0.6804 (t80) REVERT: U 222 GLU cc_start: 0.7803 (mm-30) cc_final: 0.7553 (mm-30) REVERT: U 223 GLN cc_start: 0.8022 (tt0) cc_final: 0.7516 (tt0) REVERT: U 235 ARG cc_start: 0.7643 (tpp-160) cc_final: 0.6990 (ttm-80) REVERT: U 238 PHE cc_start: 0.7917 (t80) cc_final: 0.7609 (t80) REVERT: U 253 GLN cc_start: 0.7957 (mm-40) cc_final: 0.7626 (mm-40) REVERT: U 257 ASP cc_start: 0.6822 (m-30) cc_final: 0.6564 (m-30) REVERT: V 13 LEU cc_start: 0.8496 (mt) cc_final: 0.8247 (mt) REVERT: V 15 LYS cc_start: 0.8291 (tmtp) cc_final: 0.7650 (tmtp) REVERT: V 16 GLU cc_start: 0.7924 (mm-30) cc_final: 0.7521 (mm-30) REVERT: V 68 GLU cc_start: 0.7759 (tp30) cc_final: 0.6971 (tp30) REVERT: V 69 PHE cc_start: 0.8558 (t80) cc_final: 0.8324 (t80) REVERT: V 105 ARG cc_start: 0.7525 (mtt180) cc_final: 0.6838 (ttm-80) REVERT: V 125 GLU cc_start: 0.7455 (mp0) cc_final: 0.7064 (mp0) REVERT: V 148 ARG cc_start: 0.7406 (ptp90) cc_final: 0.7009 (ptp90) REVERT: V 150 ARG cc_start: 0.6766 (mtm180) cc_final: 0.6353 (mmm160) REVERT: V 158 PHE cc_start: 0.8139 (t80) cc_final: 0.7573 (t80) REVERT: V 164 GLN cc_start: 0.6265 (mm110) cc_final: 0.5918 (mm110) REVERT: V 175 TYR cc_start: 0.7389 (m-80) cc_final: 0.6908 (t80) REVERT: V 188 ARG cc_start: 0.7058 (tpt-90) cc_final: 0.6808 (tpt-90) REVERT: V 192 ASP cc_start: 0.7339 (m-30) cc_final: 0.6684 (m-30) REVERT: V 216 ARG cc_start: 0.8070 (tpt90) cc_final: 0.7777 (tpt170) REVERT: V 222 GLU cc_start: 0.7822 (mm-30) cc_final: 0.7610 (mm-30) REVERT: V 263 PRO cc_start: 0.7815 (Cg_endo) cc_final: 0.7525 (Cg_exo) REVERT: V 265 ASP cc_start: 0.7281 (t0) cc_final: 0.6947 (t0) REVERT: W 15 LYS cc_start: 0.8335 (tmtp) cc_final: 0.7803 (tmtp) REVERT: W 32 LYS cc_start: 0.8037 (tppt) cc_final: 0.7627 (tppt) REVERT: W 56 LEU cc_start: 0.7800 (mm) cc_final: 0.7451 (mt) REVERT: W 59 MET cc_start: 0.7738 (ttp) cc_final: 0.7384 (tmm) REVERT: W 60 HIS cc_start: 0.8248 (m-70) cc_final: 0.7996 (m-70) REVERT: W 62 ARG cc_start: 0.6943 (mtp85) cc_final: 0.6599 (mtp85) REVERT: W 64 GLU cc_start: 0.7593 (pm20) cc_final: 0.7185 (pm20) REVERT: W 85 MET cc_start: 0.8070 (mtm) cc_final: 0.7786 (mtp) REVERT: W 86 SER cc_start: 0.8793 (m) cc_final: 0.8324 (p) REVERT: W 100 LYS cc_start: 0.8313 (mtmm) cc_final: 0.7897 (mtmm) REVERT: W 105 ARG cc_start: 0.7778 (ttm-80) cc_final: 0.7435 (ttm-80) REVERT: W 129 ARG cc_start: 0.6642 (ttm110) cc_final: 0.6043 (mmt180) REVERT: W 130 ASP cc_start: 0.7025 (m-30) cc_final: 0.6802 (m-30) REVERT: W 157 LYS cc_start: 0.8172 (mmtt) cc_final: 0.7919 (mmmt) REVERT: W 166 ASP cc_start: 0.7510 (p0) cc_final: 0.7167 (p0) REVERT: W 187 GLN cc_start: 0.8295 (mm-40) cc_final: 0.7959 (mm-40) REVERT: W 188 ARG cc_start: 0.8325 (tpp80) cc_final: 0.7824 (tpp80) REVERT: W 192 ASP cc_start: 0.7618 (m-30) cc_final: 0.6981 (m-30) REVERT: W 212 TYR cc_start: 0.7053 (t80) cc_final: 0.6606 (t80) REVERT: W 218 ASN cc_start: 0.8085 (t0) cc_final: 0.6830 (m110) REVERT: W 221 ARG cc_start: 0.7845 (mtt90) cc_final: 0.7202 (ttp-110) REVERT: W 222 GLU cc_start: 0.7819 (mm-30) cc_final: 0.7190 (mm-30) REVERT: X 15 LYS cc_start: 0.8469 (tmtp) cc_final: 0.7944 (tppt) REVERT: X 16 GLU cc_start: 0.7837 (mm-30) cc_final: 0.7249 (mm-30) REVERT: X 35 LYS cc_start: 0.8737 (OUTLIER) cc_final: 0.8394 (mtmm) REVERT: X 42 LEU cc_start: 0.8629 (OUTLIER) cc_final: 0.8235 (mt) REVERT: X 46 LEU cc_start: 0.8036 (mt) cc_final: 0.7697 (mp) REVERT: X 53 GLU cc_start: 0.7673 (tm-30) cc_final: 0.6604 (tm-30) REVERT: X 57 PHE cc_start: 0.7782 (t80) cc_final: 0.7479 (t80) REVERT: X 119 ASN cc_start: 0.8170 (p0) cc_final: 0.7943 (p0) REVERT: X 145 GLN cc_start: 0.8231 (mm-40) cc_final: 0.7706 (mm110) REVERT: X 158 PHE cc_start: 0.7852 (t80) cc_final: 0.7614 (t80) REVERT: X 168 ILE cc_start: 0.8315 (mm) cc_final: 0.8025 (mm) REVERT: X 171 THR cc_start: 0.7651 (m) cc_final: 0.7361 (t) REVERT: X 172 GLU cc_start: 0.7694 (tm-30) cc_final: 0.7397 (tm-30) REVERT: X 176 PHE cc_start: 0.8491 (m-10) cc_final: 0.8208 (m-80) REVERT: X 179 MET cc_start: 0.7036 (mmm) cc_final: 0.6358 (mmm) REVERT: X 225 GLN cc_start: 0.7558 (pt0) cc_final: 0.7242 (pt0) REVERT: X 247 GLN cc_start: 0.7432 (mm-40) cc_final: 0.6610 (mm-40) REVERT: X 264 THR cc_start: 0.8226 (t) cc_final: 0.7984 (p) outliers start: 116 outliers final: 70 residues processed: 1209 average time/residue: 0.2290 time to fit residues: 407.9570 Evaluate side-chains 1237 residues out of total 3024 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 84 poor density : 1153 time to evaluate : 0.911 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 81 LEU Chi-restraints excluded: chain B residue 146 ILE Chi-restraints excluded: chain C residue 12 SER Chi-restraints excluded: chain C residue 27 LYS Chi-restraints excluded: chain C residue 41 VAL Chi-restraints excluded: chain C residue 60 VAL Chi-restraints excluded: chain C residue 120 VAL Chi-restraints excluded: chain D residue 63 ILE Chi-restraints excluded: chain D residue 88 SER Chi-restraints excluded: chain E residue 49 THR Chi-restraints excluded: chain E residue 72 ILE Chi-restraints excluded: chain E residue 84 GLU Chi-restraints excluded: chain E residue 179 MET Chi-restraints excluded: chain E residue 225 GLN Chi-restraints excluded: chain E residue 276 SER Chi-restraints excluded: chain F residue 3 THR Chi-restraints excluded: chain F residue 18 ARG Chi-restraints excluded: chain F residue 35 LYS Chi-restraints excluded: chain F residue 62 ARG Chi-restraints excluded: chain F residue 154 GLU Chi-restraints excluded: chain F residue 170 LEU Chi-restraints excluded: chain F residue 177 GLN Chi-restraints excluded: chain F residue 217 MET Chi-restraints excluded: chain F residue 253 GLN Chi-restraints excluded: chain G residue 3 THR Chi-restraints excluded: chain G residue 5 THR Chi-restraints excluded: chain G residue 19 GLU Chi-restraints excluded: chain G residue 65 GLN Chi-restraints excluded: chain G residue 101 SER Chi-restraints excluded: chain G residue 117 THR Chi-restraints excluded: chain G residue 119 ASN Chi-restraints excluded: chain G residue 175 TYR Chi-restraints excluded: chain G residue 201 ILE Chi-restraints excluded: chain G residue 209 ASN Chi-restraints excluded: chain H residue 64 GLU Chi-restraints excluded: chain H residue 70 PHE Chi-restraints excluded: chain H residue 119 ASN Chi-restraints excluded: chain H residue 193 LEU Chi-restraints excluded: chain Q residue 9 THR Chi-restraints excluded: chain Q residue 43 LEU Chi-restraints excluded: chain R residue 32 THR Chi-restraints excluded: chain R residue 63 ILE Chi-restraints excluded: chain R residue 120 VAL Chi-restraints excluded: chain S residue 43 LEU Chi-restraints excluded: chain S residue 117 GLU Chi-restraints excluded: chain T residue 4 THR Chi-restraints excluded: chain T residue 10 THR Chi-restraints excluded: chain T residue 16 ARG Chi-restraints excluded: chain T residue 41 VAL Chi-restraints excluded: chain T residue 120 VAL Chi-restraints excluded: chain T residue 139 PHE Chi-restraints excluded: chain T residue 140 HIS Chi-restraints excluded: chain T residue 166 SER Chi-restraints excluded: chain U residue 18 ARG Chi-restraints excluded: chain U residue 64 GLU Chi-restraints excluded: chain U residue 70 PHE Chi-restraints excluded: chain U residue 120 TYR Chi-restraints excluded: chain U residue 170 LEU Chi-restraints excluded: chain U residue 252 GLN Chi-restraints excluded: chain V residue 4 LEU Chi-restraints excluded: chain V residue 77 ARG Chi-restraints excluded: chain V residue 84 GLU Chi-restraints excluded: chain V residue 118 THR Chi-restraints excluded: chain V residue 120 TYR Chi-restraints excluded: chain V residue 171 THR Chi-restraints excluded: chain W residue 6 LEU Chi-restraints excluded: chain W residue 8 GLU Chi-restraints excluded: chain W residue 38 ASP Chi-restraints excluded: chain W residue 77 ARG Chi-restraints excluded: chain W residue 81 LEU Chi-restraints excluded: chain W residue 122 LYS Chi-restraints excluded: chain W residue 134 GLN Chi-restraints excluded: chain W residue 159 HIS Chi-restraints excluded: chain W residue 206 SER Chi-restraints excluded: chain W residue 225 GLN Chi-restraints excluded: chain X residue 35 LYS Chi-restraints excluded: chain X residue 42 LEU Chi-restraints excluded: chain X residue 100 LYS Chi-restraints excluded: chain X residue 110 LEU Chi-restraints excluded: chain X residue 117 THR Chi-restraints excluded: chain X residue 122 LYS Chi-restraints excluded: chain X residue 177 GLN Chi-restraints excluded: chain X residue 210 ILE Chi-restraints excluded: chain X residue 223 GLN Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 360 random chunks: chunk 81 optimal weight: 7.9990 chunk 218 optimal weight: 2.9990 chunk 311 optimal weight: 2.9990 chunk 281 optimal weight: 4.9990 chunk 63 optimal weight: 5.9990 chunk 85 optimal weight: 3.9990 chunk 340 optimal weight: 0.8980 chunk 320 optimal weight: 2.9990 chunk 203 optimal weight: 0.7980 chunk 328 optimal weight: 1.9990 chunk 234 optimal weight: 4.9990 overall best weight: 1.9386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 119 HIS ** B 150 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 140 HIS ** E 145 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 247 GLN ** F 123 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 159 HIS G 65 GLN ** G 225 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 230 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 232 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 225 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 19 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 119 HIS ** R 172 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** T 101 GLN ** W 123 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3841 r_free = 0.3841 target = 0.125154 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3547 r_free = 0.3547 target = 0.106209 restraints weight = 62484.976| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3603 r_free = 0.3603 target = 0.109978 restraints weight = 32431.024| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3640 r_free = 0.3640 target = 0.112426 restraints weight = 19519.266| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 48)----------------| | r_work = 0.3665 r_free = 0.3665 target = 0.114073 restraints weight = 13081.020| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.3682 r_free = 0.3682 target = 0.115192 restraints weight = 9519.901| |-----------------------------------------------------------------------------| r_work (final): 0.3679 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7257 moved from start: 0.8494 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.067 29416 Z= 0.224 Angle : 0.729 9.987 39856 Z= 0.377 Chirality : 0.049 0.304 4432 Planarity : 0.005 0.070 5200 Dihedral : 5.026 25.109 4024 Min Nonbonded Distance : 2.483 Molprobity Statistics. All-atom Clashscore : 15.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.19 % Favored : 95.81 % Rotamer: Outliers : 4.48 % Allowed : 22.45 % Favored : 73.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.55 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.43 (0.13), residues: 3624 helix: -0.15 (0.12), residues: 1656 sheet: -0.92 (0.19), residues: 648 loop : -1.88 (0.15), residues: 1320 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG A 176 TYR 0.035 0.003 TYR X 203 PHE 0.023 0.002 PHE W 25 TRP 0.045 0.003 TRP C 141 HIS 0.008 0.001 HIS D 140 Details of bonding type rmsd covalent geometry : bond 0.00473 (29416) covalent geometry : angle 0.72934 (39856) hydrogen bonds : bond 0.04550 ( 1252) hydrogen bonds : angle 5.37459 ( 3636) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7248 Ramachandran restraints generated. 3624 Oldfield, 0 Emsley, 3624 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7248 Ramachandran restraints generated. 3624 Oldfield, 0 Emsley, 3624 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1394 residues out of total 3024 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 135 poor density : 1259 time to evaluate : 1.007 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: symmetry clash 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: symmetry clash 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: symmetry clash 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: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 19 GLN cc_start: 0.7872 (tm-30) cc_final: 0.7658 (tp40) REVERT: A 30 TYR cc_start: 0.7267 (m-80) cc_final: 0.6487 (m-80) REVERT: A 37 GLU cc_start: 0.7626 (mp0) cc_final: 0.7280 (mp0) REVERT: A 119 HIS cc_start: 0.6497 (m90) cc_final: 0.6191 (m-70) REVERT: A 123 GLU cc_start: 0.7202 (tp30) cc_final: 0.6493 (mm-30) REVERT: A 175 LEU cc_start: 0.7986 (tp) cc_final: 0.7772 (tp) REVERT: A 178 GLU cc_start: 0.7981 (mt-10) cc_final: 0.7768 (mt-10) REVERT: B 16 ARG cc_start: 0.7931 (ttp80) cc_final: 0.7500 (ttp80) REVERT: B 27 LYS cc_start: 0.7368 (ptmt) cc_final: 0.7007 (ptmt) REVERT: B 117 GLU cc_start: 0.7498 (pt0) cc_final: 0.7062 (pt0) REVERT: B 150 GLN cc_start: 0.8133 (tp40) cc_final: 0.7870 (tp-100) REVERT: C 12 SER cc_start: 0.8736 (OUTLIER) cc_final: 0.8470 (p) REVERT: C 19 GLN cc_start: 0.7900 (mm-40) cc_final: 0.7594 (mm-40) REVERT: C 27 LYS cc_start: 0.8326 (OUTLIER) cc_final: 0.8019 (ptpp) REVERT: C 30 TYR cc_start: 0.7358 (m-80) cc_final: 0.6757 (m-80) REVERT: C 48 ARG cc_start: 0.7969 (mmm-85) cc_final: 0.7564 (ttm170) REVERT: C 95 GLU cc_start: 0.8062 (mm-30) cc_final: 0.7755 (mp0) REVERT: C 119 HIS cc_start: 0.7207 (m170) cc_final: 0.6861 (m90) REVERT: C 121 LEU cc_start: 0.8283 (mt) cc_final: 0.8048 (mm) REVERT: C 148 LYS cc_start: 0.8251 (pttm) cc_final: 0.7908 (pttm) REVERT: C 164 SER cc_start: 0.8484 (p) cc_final: 0.8219 (t) REVERT: C 168 LEU cc_start: 0.8359 (tp) cc_final: 0.7954 (tp) REVERT: C 172 HIS cc_start: 0.8151 (m90) cc_final: 0.7786 (m-70) REVERT: C 174 ARG cc_start: 0.7907 (mtp180) cc_final: 0.7595 (mtp180) REVERT: C 176 ARG cc_start: 0.8729 (ptp-110) cc_final: 0.8202 (ttm-80) REVERT: D 11 ASN cc_start: 0.7706 (t0) cc_final: 0.7439 (t0) REVERT: D 38 ILE cc_start: 0.8458 (tt) cc_final: 0.7986 (tt) REVERT: D 50 LYS cc_start: 0.8242 (mmpt) cc_final: 0.7983 (mmpt) REVERT: D 63 ILE cc_start: 0.7437 (OUTLIER) cc_final: 0.6926 (mt) REVERT: D 69 LEU cc_start: 0.7568 (tp) cc_final: 0.7265 (tp) REVERT: D 83 LYS cc_start: 0.7898 (ttpt) cc_final: 0.7644 (ttpt) REVERT: D 118 ARG cc_start: 0.7909 (mtm180) cc_final: 0.7453 (ptp-170) REVERT: D 176 ARG cc_start: 0.8452 (mtp180) cc_final: 0.8130 (mtt-85) REVERT: E 15 LYS cc_start: 0.8597 (tmtp) cc_final: 0.7910 (tmtp) REVERT: E 16 GLU cc_start: 0.7895 (mm-30) cc_final: 0.7123 (mm-30) REVERT: E 46 LEU cc_start: 0.8516 (mt) cc_final: 0.8263 (mm) REVERT: E 80 ARG cc_start: 0.7979 (tpt170) cc_final: 0.7167 (tpt90) REVERT: E 89 PHE cc_start: 0.7928 (m-10) cc_final: 0.7699 (m-80) REVERT: E 133 LYS cc_start: 0.6925 (mtmm) cc_final: 0.6581 (mtmm) REVERT: E 158 PHE cc_start: 0.8002 (t80) cc_final: 0.7781 (t80) REVERT: E 177 GLN cc_start: 0.8445 (pp30) cc_final: 0.7997 (pp30) REVERT: E 179 MET cc_start: 0.7183 (OUTLIER) cc_final: 0.6567 (mmt) REVERT: E 217 MET cc_start: 0.7448 (mtt) cc_final: 0.6946 (mmm) REVERT: E 221 ARG cc_start: 0.7528 (mtt-85) cc_final: 0.6877 (mtt-85) REVERT: E 225 GLN cc_start: 0.7612 (OUTLIER) cc_final: 0.7293 (mt0) REVERT: E 272 ARG cc_start: 0.7886 (mmp80) cc_final: 0.6952 (mmp80) REVERT: E 275 GLU cc_start: 0.7655 (mt-10) cc_final: 0.7221 (mt-10) REVERT: F 12 LEU cc_start: 0.8335 (mm) cc_final: 0.8053 (mp) REVERT: F 19 GLU cc_start: 0.7913 (pt0) cc_final: 0.7585 (pt0) REVERT: F 26 LEU cc_start: 0.7735 (mt) cc_final: 0.7237 (mp) REVERT: F 32 LYS cc_start: 0.8103 (tppt) cc_final: 0.7560 (tppt) REVERT: F 38 ASP cc_start: 0.8648 (p0) cc_final: 0.8370 (p0) REVERT: F 41 GLN cc_start: 0.8161 (tm-30) cc_final: 0.7881 (tm-30) REVERT: F 63 PHE cc_start: 0.8292 (t80) cc_final: 0.8040 (t80) REVERT: F 66 LEU cc_start: 0.8887 (mt) cc_final: 0.8520 (mp) REVERT: F 70 PHE cc_start: 0.8688 (m-80) cc_final: 0.8424 (m-80) REVERT: F 77 ARG cc_start: 0.7993 (mpt90) cc_final: 0.7356 (mpt90) REVERT: F 80 ARG cc_start: 0.7790 (tpt90) cc_final: 0.7101 (tpt90) REVERT: F 95 GLU cc_start: 0.7963 (mt-10) cc_final: 0.7619 (mt-10) REVERT: F 157 LYS cc_start: 0.8282 (mmtp) cc_final: 0.7830 (mmmt) REVERT: F 172 GLU cc_start: 0.7613 (tt0) cc_final: 0.7329 (tt0) REVERT: F 188 ARG cc_start: 0.8619 (mmm-85) cc_final: 0.8222 (tpt90) REVERT: F 189 LEU cc_start: 0.8380 (OUTLIER) cc_final: 0.8125 (mp) REVERT: G 2 THR cc_start: 0.7728 (p) cc_final: 0.7361 (t) REVERT: G 65 GLN cc_start: 0.8185 (OUTLIER) cc_final: 0.7954 (mt0) REVERT: G 85 MET cc_start: 0.7958 (tpp) cc_final: 0.7439 (tpp) REVERT: G 103 MET cc_start: 0.6314 (mtp) cc_final: 0.5892 (mtp) REVERT: G 113 ARG cc_start: 0.7446 (mtt180) cc_final: 0.6408 (mtt180) REVERT: G 158 PHE cc_start: 0.7862 (t80) cc_final: 0.7546 (t80) REVERT: G 163 ASP cc_start: 0.6222 (p0) cc_final: 0.5129 (p0) REVERT: G 175 TYR cc_start: 0.7462 (OUTLIER) cc_final: 0.6659 (t80) REVERT: G 197 SER cc_start: 0.7697 (t) cc_final: 0.7472 (t) REVERT: G 211 ARG cc_start: 0.7946 (mtp85) cc_final: 0.7653 (ttm-80) REVERT: G 222 GLU cc_start: 0.7680 (mm-30) cc_final: 0.7193 (mm-30) REVERT: G 235 ARG cc_start: 0.7242 (mmm160) cc_final: 0.6594 (mmm160) REVERT: G 252 GLN cc_start: 0.7877 (tp-100) cc_final: 0.7556 (tp-100) REVERT: G 272 ARG cc_start: 0.7903 (mmp80) cc_final: 0.7497 (mmp80) REVERT: G 276 SER cc_start: 0.7615 (m) cc_final: 0.7376 (m) REVERT: H 21 ARG cc_start: 0.7757 (mmt90) cc_final: 0.7260 (mtt180) REVERT: H 68 GLU cc_start: 0.7154 (tp30) cc_final: 0.6565 (tp30) REVERT: H 84 GLU cc_start: 0.7892 (pt0) cc_final: 0.7586 (pt0) REVERT: H 122 LYS cc_start: 0.8082 (pttt) cc_final: 0.7811 (pttt) REVERT: H 164 GLN cc_start: 0.6609 (mt0) cc_final: 0.6276 (mm110) REVERT: H 187 GLN cc_start: 0.7885 (mm-40) cc_final: 0.7419 (mm-40) REVERT: H 188 ARG cc_start: 0.7636 (tpp80) cc_final: 0.7109 (tpp80) REVERT: H 215 TYR cc_start: 0.7893 (t80) cc_final: 0.7349 (t80) REVERT: H 221 ARG cc_start: 0.7839 (ttm-80) cc_final: 0.7201 (ttm-80) REVERT: H 225 GLN cc_start: 0.7618 (tt0) cc_final: 0.7216 (tt0) REVERT: H 235 ARG cc_start: 0.7378 (tpp-160) cc_final: 0.6783 (mmm160) REVERT: H 237 PHE cc_start: 0.7964 (m-80) cc_final: 0.7592 (m-80) REVERT: H 253 GLN cc_start: 0.7946 (mm-40) cc_final: 0.7637 (mp10) REVERT: H 275 GLU cc_start: 0.7330 (pt0) cc_final: 0.6974 (pt0) REVERT: Q 117 GLU cc_start: 0.7197 (pt0) cc_final: 0.6788 (pt0) REVERT: Q 170 ARG cc_start: 0.7570 (ptp90) cc_final: 0.7320 (ptp90) REVERT: R 13 GLU cc_start: 0.8181 (mm-30) cc_final: 0.7795 (mm-30) REVERT: R 28 LEU cc_start: 0.8479 (OUTLIER) cc_final: 0.8269 (tp) REVERT: R 44 GLU cc_start: 0.7267 (tm-30) cc_final: 0.6658 (tm-30) REVERT: R 48 ARG cc_start: 0.7758 (ttm-80) cc_final: 0.7206 (ttm-80) REVERT: R 61 PRO cc_start: 0.7813 (Cg_exo) cc_final: 0.7468 (Cg_endo) REVERT: R 118 ARG cc_start: 0.7317 (ttp-170) cc_final: 0.7074 (ttp-170) REVERT: R 123 GLU cc_start: 0.6880 (mm-30) cc_final: 0.5962 (mm-30) REVERT: R 171 LEU cc_start: 0.8052 (mt) cc_final: 0.7758 (mt) REVERT: R 174 ARG cc_start: 0.8320 (mtp85) cc_final: 0.7697 (mtp85) REVERT: S 5 TRP cc_start: 0.6768 (m100) cc_final: 0.6351 (m100) REVERT: S 11 ASN cc_start: 0.7290 (t0) cc_final: 0.7055 (t0) REVERT: S 16 ARG cc_start: 0.8834 (mmm160) cc_final: 0.8536 (tpt90) REVERT: S 71 ILE cc_start: 0.7407 (mm) cc_final: 0.7108 (mm) REVERT: S 78 PRO cc_start: 0.7406 (Cg_exo) cc_final: 0.7180 (Cg_endo) REVERT: S 118 ARG cc_start: 0.8024 (mtm180) cc_final: 0.7597 (ptp-170) REVERT: T 19 GLN cc_start: 0.8053 (mm-40) cc_final: 0.7564 (mm-40) REVERT: T 30 TYR cc_start: 0.7837 (m-80) cc_final: 0.6835 (m-80) REVERT: T 42 ASP cc_start: 0.7535 (t0) cc_final: 0.7125 (t0) REVERT: T 45 THR cc_start: 0.8400 (m) cc_final: 0.7962 (t) REVERT: T 59 ARG cc_start: 0.7407 (tpt-90) cc_final: 0.7049 (tpt-90) REVERT: T 89 LEU cc_start: 0.6448 (tp) cc_final: 0.6154 (tp) REVERT: T 165 PHE cc_start: 0.8674 (m-80) cc_final: 0.8236 (m-80) REVERT: T 170 ARG cc_start: 0.7575 (ptp-170) cc_final: 0.7104 (ptp-170) REVERT: T 176 ARG cc_start: 0.8582 (ptp-110) cc_final: 0.7977 (ttp-110) REVERT: T 178 GLU cc_start: 0.7373 (mt-10) cc_final: 0.7021 (mt-10) REVERT: U 21 ARG cc_start: 0.7742 (mmt90) cc_final: 0.7024 (mtt180) REVERT: U 32 LYS cc_start: 0.8404 (ttpp) cc_final: 0.8102 (ttpp) REVERT: U 35 LYS cc_start: 0.8651 (mmtm) cc_final: 0.8307 (mmtm) REVERT: U 68 GLU cc_start: 0.7633 (tp30) cc_final: 0.7018 (tp30) REVERT: U 103 MET cc_start: 0.7024 (mtt) cc_final: 0.6704 (mtt) REVERT: U 143 ASP cc_start: 0.8138 (m-30) cc_final: 0.7837 (m-30) REVERT: U 144 PHE cc_start: 0.8001 (m-80) cc_final: 0.7771 (m-80) REVERT: U 148 ARG cc_start: 0.6973 (ptp90) cc_final: 0.6602 (ptp90) REVERT: U 170 LEU cc_start: 0.7339 (OUTLIER) cc_final: 0.6926 (mm) REVERT: U 187 GLN cc_start: 0.8001 (mm-40) cc_final: 0.7644 (mm110) REVERT: U 210 ILE cc_start: 0.8514 (tp) cc_final: 0.8112 (tp) REVERT: U 222 GLU cc_start: 0.7806 (mm-30) cc_final: 0.7531 (mm-30) REVERT: U 223 GLN cc_start: 0.7993 (tt0) cc_final: 0.7525 (tt0) REVERT: U 235 ARG cc_start: 0.7601 (tpp-160) cc_final: 0.7370 (ttm-80) REVERT: U 253 GLN cc_start: 0.7951 (mm-40) cc_final: 0.7713 (mm-40) REVERT: U 257 ASP cc_start: 0.6773 (m-30) cc_final: 0.6543 (m-30) REVERT: V 15 LYS cc_start: 0.8275 (tmtp) cc_final: 0.7589 (tmtp) REVERT: V 16 GLU cc_start: 0.7900 (mm-30) cc_final: 0.7344 (mm-30) REVERT: V 17 PHE cc_start: 0.8651 (t80) cc_final: 0.8167 (t80) REVERT: V 65 GLN cc_start: 0.8121 (mt0) cc_final: 0.7497 (mt0) REVERT: V 68 GLU cc_start: 0.7919 (tp30) cc_final: 0.7630 (tm-30) REVERT: V 69 PHE cc_start: 0.8805 (t80) cc_final: 0.8096 (t80) REVERT: V 105 ARG cc_start: 0.7541 (mtt180) cc_final: 0.7000 (ttm-80) REVERT: V 113 ARG cc_start: 0.7568 (mtt180) cc_final: 0.7145 (mtt180) REVERT: V 122 LYS cc_start: 0.8385 (pttt) cc_final: 0.8151 (pttt) REVERT: V 125 GLU cc_start: 0.7513 (mp0) cc_final: 0.7175 (mp0) REVERT: V 148 ARG cc_start: 0.7360 (ptp90) cc_final: 0.6932 (ptp90) REVERT: V 150 ARG cc_start: 0.6774 (mtm180) cc_final: 0.6331 (mmm160) REVERT: V 158 PHE cc_start: 0.8216 (t80) cc_final: 0.7705 (t80) REVERT: V 163 ASP cc_start: 0.6002 (p0) cc_final: 0.5437 (t0) REVERT: V 164 GLN cc_start: 0.6817 (mm110) cc_final: 0.6174 (mm110) REVERT: V 188 ARG cc_start: 0.7203 (tpt-90) cc_final: 0.6878 (tpt-90) REVERT: V 192 ASP cc_start: 0.7425 (m-30) cc_final: 0.6697 (m-30) REVERT: V 222 GLU cc_start: 0.7850 (mm-30) cc_final: 0.7641 (mm-30) REVERT: V 263 PRO cc_start: 0.8061 (Cg_endo) cc_final: 0.7830 (Cg_exo) REVERT: W 15 LYS cc_start: 0.8358 (tmtp) cc_final: 0.7842 (tmtp) REVERT: W 32 LYS cc_start: 0.8119 (tppt) cc_final: 0.7743 (tppt) REVERT: W 55 GLU cc_start: 0.7627 (mt-10) cc_final: 0.7403 (mt-10) REVERT: W 59 MET cc_start: 0.7775 (ttp) cc_final: 0.7351 (tmm) REVERT: W 62 ARG cc_start: 0.6937 (mtp85) cc_final: 0.6597 (mtp85) REVERT: W 63 PHE cc_start: 0.8489 (t80) cc_final: 0.8257 (t80) REVERT: W 64 GLU cc_start: 0.7749 (pm20) cc_final: 0.7334 (pm20) REVERT: W 85 MET cc_start: 0.8092 (mtm) cc_final: 0.7854 (mtp) REVERT: W 86 SER cc_start: 0.8807 (m) cc_final: 0.8390 (t) REVERT: W 100 LYS cc_start: 0.8430 (mtmm) cc_final: 0.8111 (mtmm) REVERT: W 105 ARG cc_start: 0.7765 (ttm-80) cc_final: 0.7423 (ttm-80) REVERT: W 125 GLU cc_start: 0.7130 (OUTLIER) cc_final: 0.6789 (mt-10) REVERT: W 129 ARG cc_start: 0.6749 (ttm110) cc_final: 0.6284 (mtt-85) REVERT: W 157 LYS cc_start: 0.8228 (mmtt) cc_final: 0.7965 (mmtt) REVERT: W 166 ASP cc_start: 0.7521 (p0) cc_final: 0.7174 (p0) REVERT: W 187 GLN cc_start: 0.8388 (mm-40) cc_final: 0.8034 (mm-40) REVERT: W 188 ARG cc_start: 0.8385 (tpp80) cc_final: 0.7884 (tpp80) REVERT: W 192 ASP cc_start: 0.7669 (m-30) cc_final: 0.6984 (m-30) REVERT: W 212 TYR cc_start: 0.7319 (t80) cc_final: 0.6708 (t80) REVERT: W 218 ASN cc_start: 0.8137 (t0) cc_final: 0.7445 (m110) REVERT: W 221 ARG cc_start: 0.7903 (mtt90) cc_final: 0.7438 (mtt90) REVERT: X 15 LYS cc_start: 0.8460 (tmtp) cc_final: 0.8023 (tppt) REVERT: X 16 GLU cc_start: 0.7828 (mm-30) cc_final: 0.7203 (mm-30) REVERT: X 35 LYS cc_start: 0.8807 (OUTLIER) cc_final: 0.8424 (mtmm) REVERT: X 42 LEU cc_start: 0.8656 (OUTLIER) cc_final: 0.8335 (mp) REVERT: X 46 LEU cc_start: 0.8065 (mt) cc_final: 0.7686 (mp) REVERT: X 57 PHE cc_start: 0.7880 (t80) cc_final: 0.7623 (t80) REVERT: X 103 MET cc_start: 0.7308 (mmm) cc_final: 0.7100 (mmm) REVERT: X 156 ILE cc_start: 0.7668 (mt) cc_final: 0.7225 (mt) REVERT: X 158 PHE cc_start: 0.7843 (t80) cc_final: 0.7584 (t80) REVERT: X 168 ILE cc_start: 0.8390 (mm) cc_final: 0.8127 (mm) REVERT: X 171 THR cc_start: 0.7705 (m) cc_final: 0.7390 (t) REVERT: X 172 GLU cc_start: 0.7755 (tm-30) cc_final: 0.7402 (tm-30) REVERT: X 176 PHE cc_start: 0.8536 (m-10) cc_final: 0.8278 (m-80) REVERT: X 179 MET cc_start: 0.7176 (mmm) cc_final: 0.6500 (mmm) REVERT: X 182 ASP cc_start: 0.7276 (m-30) cc_final: 0.6947 (m-30) REVERT: X 225 GLN cc_start: 0.7555 (pt0) cc_final: 0.7233 (pt0) REVERT: X 241 HIS cc_start: 0.7403 (m90) cc_final: 0.7120 (m90) REVERT: X 249 ASP cc_start: 0.7914 (m-30) cc_final: 0.7702 (m-30) REVERT: X 264 THR cc_start: 0.8216 (OUTLIER) cc_final: 0.7941 (p) outliers start: 135 outliers final: 86 residues processed: 1291 average time/residue: 0.2213 time to fit residues: 422.4989 Evaluate side-chains 1327 residues out of total 3024 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 100 poor density : 1227 time to evaluate : 1.108 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 140 HIS Chi-restraints excluded: chain B residue 34 LYS Chi-restraints excluded: chain B residue 35 VAL Chi-restraints excluded: chain B residue 94 CYS Chi-restraints excluded: chain B residue 103 THR Chi-restraints excluded: chain C residue 4 THR Chi-restraints excluded: chain C residue 12 SER Chi-restraints excluded: chain C residue 27 LYS Chi-restraints excluded: chain C residue 41 VAL Chi-restraints excluded: chain C residue 60 VAL Chi-restraints excluded: chain C residue 85 PHE Chi-restraints excluded: chain C residue 120 VAL Chi-restraints excluded: chain D residue 63 ILE Chi-restraints excluded: chain D residue 88 SER Chi-restraints excluded: chain D residue 166 SER Chi-restraints excluded: chain E residue 49 THR Chi-restraints excluded: chain E residue 72 ILE Chi-restraints excluded: chain E residue 179 MET Chi-restraints excluded: chain E residue 201 ILE Chi-restraints excluded: chain E residue 223 GLN Chi-restraints excluded: chain E residue 225 GLN Chi-restraints excluded: chain E residue 240 THR Chi-restraints excluded: chain E residue 276 SER Chi-restraints excluded: chain F residue 3 THR Chi-restraints excluded: chain F residue 6 LEU Chi-restraints excluded: chain F residue 62 ARG Chi-restraints excluded: chain F residue 170 LEU Chi-restraints excluded: chain F residue 177 GLN Chi-restraints excluded: chain F residue 189 LEU Chi-restraints excluded: chain F residue 253 GLN Chi-restraints excluded: chain G residue 3 THR Chi-restraints excluded: chain G residue 5 THR Chi-restraints excluded: chain G residue 19 GLU Chi-restraints excluded: chain G residue 55 GLU Chi-restraints excluded: chain G residue 65 GLN Chi-restraints excluded: chain G residue 70 PHE Chi-restraints excluded: chain G residue 117 THR Chi-restraints excluded: chain G residue 119 ASN Chi-restraints excluded: chain G residue 175 TYR Chi-restraints excluded: chain G residue 201 ILE Chi-restraints excluded: chain G residue 209 ASN Chi-restraints excluded: chain H residue 30 PHE Chi-restraints excluded: chain H residue 64 GLU Chi-restraints excluded: chain H residue 91 SER Chi-restraints excluded: chain H residue 114 THR Chi-restraints excluded: chain H residue 119 ASN Chi-restraints excluded: chain H residue 193 LEU Chi-restraints excluded: chain Q residue 9 THR Chi-restraints excluded: chain R residue 28 LEU Chi-restraints excluded: chain R residue 32 THR Chi-restraints excluded: chain R residue 63 ILE Chi-restraints excluded: chain R residue 120 VAL Chi-restraints excluded: chain S residue 117 GLU Chi-restraints excluded: chain T residue 4 THR Chi-restraints excluded: chain T residue 41 VAL Chi-restraints excluded: chain T residue 120 VAL Chi-restraints excluded: chain U residue 18 ARG Chi-restraints excluded: chain U residue 64 GLU Chi-restraints excluded: chain U residue 117 THR Chi-restraints excluded: chain U residue 119 ASN Chi-restraints excluded: chain U residue 120 TYR Chi-restraints excluded: chain U residue 150 ARG Chi-restraints excluded: chain U residue 170 LEU Chi-restraints excluded: chain U residue 252 GLN Chi-restraints excluded: chain V residue 4 LEU Chi-restraints excluded: chain V residue 77 ARG Chi-restraints excluded: chain V residue 84 GLU Chi-restraints excluded: chain V residue 118 THR Chi-restraints excluded: chain V residue 119 ASN Chi-restraints excluded: chain V residue 120 TYR Chi-restraints excluded: chain V residue 171 THR Chi-restraints excluded: chain V residue 177 GLN Chi-restraints excluded: chain W residue 6 LEU Chi-restraints excluded: chain W residue 8 GLU Chi-restraints excluded: chain W residue 38 ASP Chi-restraints excluded: chain W residue 73 SER Chi-restraints excluded: chain W residue 77 ARG Chi-restraints excluded: chain W residue 81 LEU Chi-restraints excluded: chain W residue 122 LYS Chi-restraints excluded: chain W residue 125 GLU Chi-restraints excluded: chain W residue 134 GLN Chi-restraints excluded: chain W residue 154 GLU Chi-restraints excluded: chain W residue 159 HIS Chi-restraints excluded: chain W residue 170 LEU Chi-restraints excluded: chain W residue 177 GLN Chi-restraints excluded: chain W residue 206 SER Chi-restraints excluded: chain W residue 225 GLN Chi-restraints excluded: chain W residue 273 LEU Chi-restraints excluded: chain X residue 35 LYS Chi-restraints excluded: chain X residue 42 LEU Chi-restraints excluded: chain X residue 43 ILE Chi-restraints excluded: chain X residue 79 GLN Chi-restraints excluded: chain X residue 100 LYS Chi-restraints excluded: chain X residue 110 LEU Chi-restraints excluded: chain X residue 117 THR Chi-restraints excluded: chain X residue 177 GLN Chi-restraints excluded: chain X residue 209 ASN Chi-restraints excluded: chain X residue 210 ILE Chi-restraints excluded: chain X residue 223 GLN Chi-restraints excluded: chain X residue 264 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 360 random chunks: chunk 93 optimal weight: 0.9980 chunk 302 optimal weight: 2.9990 chunk 122 optimal weight: 2.9990 chunk 282 optimal weight: 0.5980 chunk 161 optimal weight: 5.9990 chunk 139 optimal weight: 10.0000 chunk 274 optimal weight: 0.2980 chunk 293 optimal weight: 0.8980 chunk 195 optimal weight: 9.9990 chunk 154 optimal weight: 2.9990 chunk 92 optimal weight: 2.9990 overall best weight: 1.1582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 150 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 11 ASN ** E 145 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 247 GLN ** F 123 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 159 HIS ** G 41 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 65 GLN ** G 123 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 225 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 230 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 232 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 225 GLN ** Q 140 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 19 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 119 HIS ** R 172 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** T 101 GLN X 123 HIS Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3858 r_free = 0.3858 target = 0.126187 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3562 r_free = 0.3562 target = 0.107103 restraints weight = 62147.503| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3619 r_free = 0.3619 target = 0.110901 restraints weight = 32340.140| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3656 r_free = 0.3656 target = 0.113359 restraints weight = 19505.823| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3680 r_free = 0.3680 target = 0.114985 restraints weight = 13075.740| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 37)----------------| | r_work = 0.3697 r_free = 0.3697 target = 0.116130 restraints weight = 9564.225| |-----------------------------------------------------------------------------| r_work (final): 0.3694 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7233 moved from start: 0.8720 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.055 29416 Z= 0.159 Angle : 0.698 10.150 39856 Z= 0.355 Chirality : 0.047 0.277 4432 Planarity : 0.005 0.056 5200 Dihedral : 4.759 27.039 4024 Min Nonbonded Distance : 2.504 Molprobity Statistics. All-atom Clashscore : 13.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.45 % Favored : 96.55 % Rotamer: Outliers : 3.98 % Allowed : 24.47 % Favored : 71.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.55 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.12 (0.13), residues: 3624 helix: 0.08 (0.13), residues: 1656 sheet: -0.61 (0.20), residues: 608 loop : -1.75 (0.15), residues: 1360 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG A 16 TYR 0.032 0.002 TYR X 203 PHE 0.021 0.002 PHE G 57 TRP 0.061 0.002 TRP Q 141 HIS 0.008 0.001 HIS H 60 Details of bonding type rmsd covalent geometry : bond 0.00348 (29416) covalent geometry : angle 0.69803 (39856) hydrogen bonds : bond 0.03845 ( 1252) hydrogen bonds : angle 5.15331 ( 3636) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7248 Ramachandran restraints generated. 3624 Oldfield, 0 Emsley, 3624 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7248 Ramachandran restraints generated. 3624 Oldfield, 0 Emsley, 3624 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1343 residues out of total 3024 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 120 poor density : 1223 time to evaluate : 1.066 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: symmetry clash 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: symmetry clash 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 19 GLN cc_start: 0.7753 (tm-30) cc_final: 0.7515 (tp40) REVERT: A 30 TYR cc_start: 0.7266 (m-80) cc_final: 0.6450 (m-80) REVERT: A 37 GLU cc_start: 0.7560 (mp0) cc_final: 0.7119 (mp0) REVERT: A 119 HIS cc_start: 0.6486 (m90) cc_final: 0.6129 (m-70) REVERT: A 123 GLU cc_start: 0.7235 (tp30) cc_final: 0.6614 (mm-30) REVERT: A 175 LEU cc_start: 0.7969 (tp) cc_final: 0.7744 (tp) REVERT: A 178 GLU cc_start: 0.7998 (mt-10) cc_final: 0.7749 (mt-10) REVERT: B 16 ARG cc_start: 0.7967 (ttp80) cc_final: 0.7533 (ttp80) REVERT: B 27 LYS cc_start: 0.7334 (ptmt) cc_final: 0.6926 (ptmt) REVERT: B 66 HIS cc_start: 0.7381 (t70) cc_final: 0.7163 (t-90) REVERT: B 117 GLU cc_start: 0.7508 (pt0) cc_final: 0.7038 (pt0) REVERT: B 174 ARG cc_start: 0.8089 (mtp180) cc_final: 0.7636 (mtp180) REVERT: C 12 SER cc_start: 0.8732 (OUTLIER) cc_final: 0.8488 (p) REVERT: C 14 LYS cc_start: 0.8694 (mttm) cc_final: 0.8211 (mttm) REVERT: C 19 GLN cc_start: 0.7997 (mm-40) cc_final: 0.7665 (mm-40) REVERT: C 27 LYS cc_start: 0.8274 (OUTLIER) cc_final: 0.7985 (ptpp) REVERT: C 30 TYR cc_start: 0.7397 (m-80) cc_final: 0.6672 (m-80) REVERT: C 95 GLU cc_start: 0.8083 (mm-30) cc_final: 0.7759 (mp0) REVERT: C 119 HIS cc_start: 0.7218 (m170) cc_final: 0.6964 (m90) REVERT: C 164 SER cc_start: 0.8420 (p) cc_final: 0.8052 (t) REVERT: C 168 LEU cc_start: 0.8411 (tp) cc_final: 0.8007 (tp) REVERT: C 172 HIS cc_start: 0.8168 (m90) cc_final: 0.7805 (m-70) REVERT: C 174 ARG cc_start: 0.7916 (mtp180) cc_final: 0.7211 (mtp180) REVERT: C 176 ARG cc_start: 0.8708 (ptp-110) cc_final: 0.8204 (ttm-80) REVERT: D 11 ASN cc_start: 0.7526 (t0) cc_final: 0.7126 (t0) REVERT: D 38 ILE cc_start: 0.8443 (tt) cc_final: 0.7993 (tt) REVERT: D 45 THR cc_start: 0.8636 (p) cc_final: 0.8432 (t) REVERT: D 50 LYS cc_start: 0.8248 (mmpt) cc_final: 0.7993 (mmpt) REVERT: D 69 LEU cc_start: 0.7441 (tp) cc_final: 0.7150 (tp) REVERT: D 83 LYS cc_start: 0.7866 (ttpt) cc_final: 0.7559 (ttpt) REVERT: D 118 ARG cc_start: 0.7796 (mtm180) cc_final: 0.7398 (ptp-170) REVERT: D 176 ARG cc_start: 0.8411 (mtp180) cc_final: 0.7907 (mtt-85) REVERT: E 15 LYS cc_start: 0.8619 (tmtp) cc_final: 0.7956 (tmtp) REVERT: E 16 GLU cc_start: 0.7931 (mm-30) cc_final: 0.7116 (mm-30) REVERT: E 46 LEU cc_start: 0.8464 (mt) cc_final: 0.8238 (mm) REVERT: E 53 GLU cc_start: 0.7600 (tm-30) cc_final: 0.7314 (tm-30) REVERT: E 89 PHE cc_start: 0.7990 (m-10) cc_final: 0.7711 (m-80) REVERT: E 133 LYS cc_start: 0.6899 (mtmm) cc_final: 0.6393 (mtmm) REVERT: E 145 GLN cc_start: 0.8242 (tp40) cc_final: 0.8022 (mm-40) REVERT: E 158 PHE cc_start: 0.7994 (t80) cc_final: 0.7762 (t80) REVERT: E 177 GLN cc_start: 0.8366 (pp30) cc_final: 0.7971 (pp30) REVERT: E 179 MET cc_start: 0.7102 (OUTLIER) cc_final: 0.6458 (mmt) REVERT: E 225 GLN cc_start: 0.7596 (OUTLIER) cc_final: 0.7394 (mt0) REVERT: E 264 THR cc_start: 0.8358 (t) cc_final: 0.7987 (p) REVERT: E 272 ARG cc_start: 0.7849 (mmp80) cc_final: 0.6968 (mmp80) REVERT: E 275 GLU cc_start: 0.7642 (mt-10) cc_final: 0.7226 (mt-10) REVERT: F 12 LEU cc_start: 0.8352 (mm) cc_final: 0.8063 (mp) REVERT: F 19 GLU cc_start: 0.7879 (pt0) cc_final: 0.7565 (pt0) REVERT: F 26 LEU cc_start: 0.7834 (mt) cc_final: 0.7274 (mp) REVERT: F 32 LYS cc_start: 0.8074 (tppt) cc_final: 0.7532 (tppt) REVERT: F 38 ASP cc_start: 0.8659 (p0) cc_final: 0.8343 (p0) REVERT: F 55 GLU cc_start: 0.7378 (pm20) cc_final: 0.7076 (pm20) REVERT: F 63 PHE cc_start: 0.8242 (t80) cc_final: 0.7988 (t80) REVERT: F 66 LEU cc_start: 0.8911 (mt) cc_final: 0.8515 (mp) REVERT: F 70 PHE cc_start: 0.8650 (m-80) cc_final: 0.8355 (m-80) REVERT: F 77 ARG cc_start: 0.7964 (mpt90) cc_final: 0.7318 (mpt90) REVERT: F 78 LEU cc_start: 0.8707 (tp) cc_final: 0.8462 (tt) REVERT: F 95 GLU cc_start: 0.7957 (mt-10) cc_final: 0.7647 (mt-10) REVERT: F 133 LYS cc_start: 0.7493 (mttt) cc_final: 0.7135 (mtpp) REVERT: F 172 GLU cc_start: 0.7551 (tt0) cc_final: 0.7252 (tt0) REVERT: F 179 MET cc_start: 0.6971 (mmm) cc_final: 0.6765 (mmm) REVERT: F 188 ARG cc_start: 0.8583 (mmm-85) cc_final: 0.8230 (tpt90) REVERT: F 217 MET cc_start: 0.7213 (OUTLIER) cc_final: 0.6913 (mtt) REVERT: F 218 ASN cc_start: 0.7896 (t0) cc_final: 0.7444 (t0) REVERT: G 2 THR cc_start: 0.7856 (p) cc_final: 0.7531 (t) REVERT: G 85 MET cc_start: 0.7794 (tpp) cc_final: 0.7398 (tpp) REVERT: G 103 MET cc_start: 0.6360 (mtp) cc_final: 0.6031 (mtp) REVERT: G 113 ARG cc_start: 0.6962 (mtt180) cc_final: 0.6682 (mtt180) REVERT: G 175 TYR cc_start: 0.7470 (OUTLIER) cc_final: 0.6722 (t80) REVERT: G 178 ARG cc_start: 0.7990 (tpp80) cc_final: 0.7686 (tpp80) REVERT: G 197 SER cc_start: 0.7760 (t) cc_final: 0.7501 (t) REVERT: G 211 ARG cc_start: 0.7867 (mtp85) cc_final: 0.7577 (ttm-80) REVERT: G 222 GLU cc_start: 0.7648 (mm-30) cc_final: 0.7188 (mm-30) REVERT: G 235 ARG cc_start: 0.7256 (mmm160) cc_final: 0.6489 (mmm160) REVERT: G 252 GLN cc_start: 0.7822 (tp-100) cc_final: 0.7520 (tp-100) REVERT: G 276 SER cc_start: 0.7606 (m) cc_final: 0.7355 (m) REVERT: H 21 ARG cc_start: 0.7747 (mmt90) cc_final: 0.7319 (mtt180) REVERT: H 65 GLN cc_start: 0.7726 (mp10) cc_final: 0.6982 (mp10) REVERT: H 68 GLU cc_start: 0.7132 (tp30) cc_final: 0.6500 (tp30) REVERT: H 84 GLU cc_start: 0.7889 (pt0) cc_final: 0.7565 (pt0) REVERT: H 122 LYS cc_start: 0.8060 (pttt) cc_final: 0.7812 (pttt) REVERT: H 164 GLN cc_start: 0.6619 (mt0) cc_final: 0.6324 (mm110) REVERT: H 188 ARG cc_start: 0.7606 (tpp80) cc_final: 0.7088 (tpp80) REVERT: H 215 TYR cc_start: 0.7804 (t80) cc_final: 0.7226 (t80) REVERT: H 221 ARG cc_start: 0.7826 (ttm-80) cc_final: 0.7367 (mtm-85) REVERT: H 223 GLN cc_start: 0.8025 (tt0) cc_final: 0.7741 (tp40) REVERT: H 225 GLN cc_start: 0.7618 (OUTLIER) cc_final: 0.7236 (tt0) REVERT: H 235 ARG cc_start: 0.7390 (tpp-160) cc_final: 0.6726 (tpp80) REVERT: H 237 PHE cc_start: 0.7956 (m-80) cc_final: 0.7609 (m-80) REVERT: H 253 GLN cc_start: 0.7950 (mm-40) cc_final: 0.7682 (mp10) REVERT: H 275 GLU cc_start: 0.7313 (pt0) cc_final: 0.7106 (pt0) REVERT: Q 56 ARG cc_start: 0.7599 (mtt-85) cc_final: 0.7020 (mtt-85) REVERT: Q 117 GLU cc_start: 0.7139 (pt0) cc_final: 0.6710 (pt0) REVERT: Q 161 GLU cc_start: 0.7513 (tp30) cc_final: 0.6986 (tp30) REVERT: Q 170 ARG cc_start: 0.7494 (ptp90) cc_final: 0.7277 (ptp90) REVERT: R 13 GLU cc_start: 0.8175 (mm-30) cc_final: 0.7497 (mm-30) REVERT: R 44 GLU cc_start: 0.7230 (tm-30) cc_final: 0.6564 (tm-30) REVERT: R 48 ARG cc_start: 0.7808 (ttm-80) cc_final: 0.7360 (ttm-80) REVERT: R 61 PRO cc_start: 0.7856 (Cg_exo) cc_final: 0.7543 (Cg_endo) REVERT: R 118 ARG cc_start: 0.7309 (ttp-170) cc_final: 0.7063 (ttp-170) REVERT: R 123 GLU cc_start: 0.6866 (mm-30) cc_final: 0.5993 (mm-30) REVERT: R 162 LYS cc_start: 0.8179 (ttpm) cc_final: 0.7602 (tttm) REVERT: R 171 LEU cc_start: 0.8030 (mt) cc_final: 0.7747 (mt) REVERT: R 174 ARG cc_start: 0.8235 (mtp85) cc_final: 0.7545 (mtp85) REVERT: S 9 THR cc_start: 0.8504 (t) cc_final: 0.8281 (m) REVERT: S 11 ASN cc_start: 0.7283 (t0) cc_final: 0.7083 (t0) REVERT: S 16 ARG cc_start: 0.8828 (mmm160) cc_final: 0.8560 (tpt90) REVERT: S 63 ILE cc_start: 0.7211 (tt) cc_final: 0.6566 (mt) REVERT: S 71 ILE cc_start: 0.7374 (mm) cc_final: 0.7079 (mm) REVERT: S 118 ARG cc_start: 0.7992 (mtm180) cc_final: 0.7549 (ptp-170) REVERT: T 19 GLN cc_start: 0.8039 (mm-40) cc_final: 0.7459 (mm-40) REVERT: T 30 TYR cc_start: 0.7830 (m-80) cc_final: 0.6724 (m-80) REVERT: T 42 ASP cc_start: 0.7525 (t0) cc_final: 0.7017 (t0) REVERT: T 45 THR cc_start: 0.8389 (m) cc_final: 0.7881 (p) REVERT: T 59 ARG cc_start: 0.7399 (tpt-90) cc_final: 0.7022 (tpt-90) REVERT: T 165 PHE cc_start: 0.8572 (m-80) cc_final: 0.8180 (m-80) REVERT: T 170 ARG cc_start: 0.7546 (ptp-170) cc_final: 0.6981 (ptp-170) REVERT: T 176 ARG cc_start: 0.8588 (ptp-110) cc_final: 0.7961 (ttp-110) REVERT: U 21 ARG cc_start: 0.7725 (mmt90) cc_final: 0.7024 (mtt180) REVERT: U 32 LYS cc_start: 0.8376 (ttpp) cc_final: 0.8112 (ttpp) REVERT: U 35 LYS cc_start: 0.8668 (mmtm) cc_final: 0.8330 (mmtm) REVERT: U 59 MET cc_start: 0.7726 (tpt) cc_final: 0.7421 (tpp) REVERT: U 68 GLU cc_start: 0.7564 (tp30) cc_final: 0.6958 (tp30) REVERT: U 103 MET cc_start: 0.7008 (mtt) cc_final: 0.6596 (mtt) REVERT: U 143 ASP cc_start: 0.8112 (m-30) cc_final: 0.7800 (m-30) REVERT: U 144 PHE cc_start: 0.7988 (m-80) cc_final: 0.7760 (m-80) REVERT: U 148 ARG cc_start: 0.6962 (ptp90) cc_final: 0.6602 (ptp90) REVERT: U 170 LEU cc_start: 0.7321 (OUTLIER) cc_final: 0.6803 (mm) REVERT: U 187 GLN cc_start: 0.7952 (mm-40) cc_final: 0.7655 (mm110) REVERT: U 210 ILE cc_start: 0.8495 (tp) cc_final: 0.8112 (tp) REVERT: U 212 TYR cc_start: 0.7095 (t80) cc_final: 0.6851 (t80) REVERT: U 222 GLU cc_start: 0.7817 (mm-30) cc_final: 0.7539 (mm-30) REVERT: U 223 GLN cc_start: 0.7972 (tt0) cc_final: 0.7482 (tt0) REVERT: U 235 ARG cc_start: 0.7630 (tpp-160) cc_final: 0.7410 (ttm-80) REVERT: U 253 GLN cc_start: 0.7940 (mm-40) cc_final: 0.7719 (mm-40) REVERT: U 257 ASP cc_start: 0.6811 (m-30) cc_final: 0.6573 (m-30) REVERT: V 15 LYS cc_start: 0.8232 (tmtp) cc_final: 0.7532 (tmtp) REVERT: V 16 GLU cc_start: 0.7883 (mm-30) cc_final: 0.7342 (mm-30) REVERT: V 17 PHE cc_start: 0.8577 (t80) cc_final: 0.8138 (t80) REVERT: V 62 ARG cc_start: 0.7263 (mmt90) cc_final: 0.6930 (ttm110) REVERT: V 68 GLU cc_start: 0.7851 (tp30) cc_final: 0.7549 (tm-30) REVERT: V 69 PHE cc_start: 0.8746 (t80) cc_final: 0.8059 (t80) REVERT: V 77 ARG cc_start: 0.7951 (OUTLIER) cc_final: 0.7644 (tpt90) REVERT: V 105 ARG cc_start: 0.7595 (mtt180) cc_final: 0.7019 (ttm-80) REVERT: V 113 ARG cc_start: 0.7507 (mtt180) cc_final: 0.7158 (mtt180) REVERT: V 125 GLU cc_start: 0.7461 (mp0) cc_final: 0.7074 (mp0) REVERT: V 148 ARG cc_start: 0.7370 (ptp90) cc_final: 0.6876 (ptp90) REVERT: V 150 ARG cc_start: 0.6838 (mtm180) cc_final: 0.6368 (mmm160) REVERT: V 158 PHE cc_start: 0.8179 (t80) cc_final: 0.7708 (t80) REVERT: V 192 ASP cc_start: 0.7404 (m-30) cc_final: 0.6676 (m-30) REVERT: W 15 LYS cc_start: 0.8358 (tmtp) cc_final: 0.7842 (tmtp) REVERT: W 32 LYS cc_start: 0.8078 (tppt) cc_final: 0.7700 (tppt) REVERT: W 55 GLU cc_start: 0.7661 (mt-10) cc_final: 0.7428 (mt-10) REVERT: W 59 MET cc_start: 0.7849 (ttp) cc_final: 0.7270 (tmm) REVERT: W 62 ARG cc_start: 0.6943 (mtp85) cc_final: 0.6593 (mtp85) REVERT: W 63 PHE cc_start: 0.8474 (t80) cc_final: 0.8232 (t80) REVERT: W 64 GLU cc_start: 0.7660 (pm20) cc_final: 0.7285 (pm20) REVERT: W 80 ARG cc_start: 0.7925 (tpt170) cc_final: 0.7716 (tpt-90) REVERT: W 85 MET cc_start: 0.8096 (mtm) cc_final: 0.7842 (mtp) REVERT: W 86 SER cc_start: 0.8741 (m) cc_final: 0.8277 (p) REVERT: W 88 SER cc_start: 0.8429 (m) cc_final: 0.8117 (p) REVERT: W 100 LYS cc_start: 0.8443 (mtmm) cc_final: 0.8175 (mtmm) REVERT: W 105 ARG cc_start: 0.7699 (ttm-80) cc_final: 0.7326 (ttm-80) REVERT: W 125 GLU cc_start: 0.7084 (OUTLIER) cc_final: 0.6851 (mt-10) REVERT: W 129 ARG cc_start: 0.6797 (ttm110) cc_final: 0.6110 (mmm160) REVERT: W 130 ASP cc_start: 0.6595 (m-30) cc_final: 0.6378 (m-30) REVERT: W 157 LYS cc_start: 0.8241 (mmtt) cc_final: 0.8021 (mmtt) REVERT: W 166 ASP cc_start: 0.7502 (p0) cc_final: 0.7173 (p0) REVERT: W 179 MET cc_start: 0.6792 (mmm) cc_final: 0.6003 (mmm) REVERT: W 187 GLN cc_start: 0.8355 (mm-40) cc_final: 0.8025 (mm-40) REVERT: W 188 ARG cc_start: 0.8340 (tpp80) cc_final: 0.7802 (tpp80) REVERT: W 192 ASP cc_start: 0.7613 (m-30) cc_final: 0.6923 (m-30) REVERT: W 212 TYR cc_start: 0.7218 (t80) cc_final: 0.6655 (t80) REVERT: W 218 ASN cc_start: 0.8177 (t0) cc_final: 0.7918 (t0) REVERT: W 221 ARG cc_start: 0.7918 (mtt90) cc_final: 0.7415 (mtt90) REVERT: W 245 LEU cc_start: 0.8463 (mt) cc_final: 0.7994 (mp) REVERT: X 15 LYS cc_start: 0.8470 (tmtp) cc_final: 0.8019 (tppt) REVERT: X 16 GLU cc_start: 0.7852 (mm-30) cc_final: 0.7215 (mm-30) REVERT: X 35 LYS cc_start: 0.8805 (OUTLIER) cc_final: 0.8455 (mtmm) REVERT: X 42 LEU cc_start: 0.8601 (OUTLIER) cc_final: 0.8276 (mp) REVERT: X 46 LEU cc_start: 0.8030 (mt) cc_final: 0.7709 (mp) REVERT: X 65 GLN cc_start: 0.7462 (mt0) cc_final: 0.7087 (mp10) REVERT: X 155 VAL cc_start: 0.8134 (t) cc_final: 0.7847 (p) REVERT: X 158 PHE cc_start: 0.7808 (t80) cc_final: 0.7495 (t80) REVERT: X 168 ILE cc_start: 0.8371 (mm) cc_final: 0.8094 (mm) REVERT: X 170 LEU cc_start: 0.7829 (OUTLIER) cc_final: 0.7561 (tp) REVERT: X 171 THR cc_start: 0.7586 (m) cc_final: 0.7151 (t) REVERT: X 172 GLU cc_start: 0.7668 (tm-30) cc_final: 0.7353 (tm-30) REVERT: X 182 ASP cc_start: 0.7290 (m-30) cc_final: 0.6973 (m-30) REVERT: X 218 ASN cc_start: 0.7654 (t0) cc_final: 0.7429 (t0) REVERT: X 225 GLN cc_start: 0.7622 (pt0) cc_final: 0.7356 (pt0) REVERT: X 247 GLN cc_start: 0.7640 (mm-40) cc_final: 0.6761 (mm-40) REVERT: X 252 GLN cc_start: 0.7703 (pp30) cc_final: 0.7389 (pp30) REVERT: X 253 GLN cc_start: 0.8368 (mm110) cc_final: 0.8104 (tp40) REVERT: X 264 THR cc_start: 0.8272 (OUTLIER) cc_final: 0.8016 (p) outliers start: 120 outliers final: 83 residues processed: 1251 average time/residue: 0.2357 time to fit residues: 433.3463 Evaluate side-chains 1302 residues out of total 3024 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 97 poor density : 1205 time to evaluate : 1.102 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 32 THR Chi-restraints excluded: chain A residue 40 ASP Chi-restraints excluded: chain A residue 140 HIS Chi-restraints excluded: chain A residue 157 MET Chi-restraints excluded: chain B residue 35 VAL Chi-restraints excluded: chain B residue 94 CYS Chi-restraints excluded: chain B residue 103 THR Chi-restraints excluded: chain C residue 12 SER Chi-restraints excluded: chain C residue 27 LYS Chi-restraints excluded: chain C residue 60 VAL Chi-restraints excluded: chain C residue 120 VAL Chi-restraints excluded: chain D residue 88 SER Chi-restraints excluded: chain D residue 96 VAL Chi-restraints excluded: chain E residue 49 THR Chi-restraints excluded: chain E residue 72 ILE Chi-restraints excluded: chain E residue 84 GLU Chi-restraints excluded: chain E residue 97 LEU Chi-restraints excluded: chain E residue 179 MET Chi-restraints excluded: chain E residue 225 GLN Chi-restraints excluded: chain E residue 240 THR Chi-restraints excluded: chain E residue 259 ILE Chi-restraints excluded: chain E residue 276 SER Chi-restraints excluded: chain F residue 3 THR Chi-restraints excluded: chain F residue 18 ARG Chi-restraints excluded: chain F residue 93 GLU Chi-restraints excluded: chain F residue 170 LEU Chi-restraints excluded: chain F residue 217 MET Chi-restraints excluded: chain G residue 3 THR Chi-restraints excluded: chain G residue 5 THR Chi-restraints excluded: chain G residue 19 GLU Chi-restraints excluded: chain G residue 88 SER Chi-restraints excluded: chain G residue 114 THR Chi-restraints excluded: chain G residue 117 THR Chi-restraints excluded: chain G residue 119 ASN Chi-restraints excluded: chain G residue 175 TYR Chi-restraints excluded: chain G residue 204 SER Chi-restraints excluded: chain G residue 208 THR Chi-restraints excluded: chain G residue 209 ASN Chi-restraints excluded: chain H residue 14 LYS Chi-restraints excluded: chain H residue 64 GLU Chi-restraints excluded: chain H residue 119 ASN Chi-restraints excluded: chain H residue 193 LEU Chi-restraints excluded: chain H residue 225 GLN Chi-restraints excluded: chain Q residue 9 THR Chi-restraints excluded: chain Q residue 43 LEU Chi-restraints excluded: chain R residue 32 THR Chi-restraints excluded: chain R residue 120 VAL Chi-restraints excluded: chain S residue 60 VAL Chi-restraints excluded: chain S residue 117 GLU Chi-restraints excluded: chain T residue 10 THR Chi-restraints excluded: chain T residue 28 LEU Chi-restraints excluded: chain T residue 41 VAL Chi-restraints excluded: chain T residue 120 VAL Chi-restraints excluded: chain T residue 164 SER Chi-restraints excluded: chain U residue 18 ARG Chi-restraints excluded: chain U residue 64 GLU Chi-restraints excluded: chain U residue 119 ASN Chi-restraints excluded: chain U residue 120 TYR Chi-restraints excluded: chain U residue 170 LEU Chi-restraints excluded: chain U residue 177 GLN Chi-restraints excluded: chain U residue 252 GLN Chi-restraints excluded: chain V residue 4 LEU Chi-restraints excluded: chain V residue 5 THR Chi-restraints excluded: chain V residue 77 ARG Chi-restraints excluded: chain V residue 84 GLU Chi-restraints excluded: chain V residue 118 THR Chi-restraints excluded: chain V residue 119 ASN Chi-restraints excluded: chain V residue 120 TYR Chi-restraints excluded: chain V residue 169 VAL Chi-restraints excluded: chain V residue 170 LEU Chi-restraints excluded: chain V residue 171 THR Chi-restraints excluded: chain W residue 6 LEU Chi-restraints excluded: chain W residue 8 GLU Chi-restraints excluded: chain W residue 38 ASP Chi-restraints excluded: chain W residue 73 SER Chi-restraints excluded: chain W residue 77 ARG Chi-restraints excluded: chain W residue 122 LYS Chi-restraints excluded: chain W residue 125 GLU Chi-restraints excluded: chain W residue 134 GLN Chi-restraints excluded: chain W residue 154 GLU Chi-restraints excluded: chain W residue 159 HIS Chi-restraints excluded: chain W residue 170 LEU Chi-restraints excluded: chain W residue 177 GLN Chi-restraints excluded: chain W residue 225 GLN Chi-restraints excluded: chain X residue 35 LYS Chi-restraints excluded: chain X residue 42 LEU Chi-restraints excluded: chain X residue 43 ILE Chi-restraints excluded: chain X residue 50 LEU Chi-restraints excluded: chain X residue 79 GLN Chi-restraints excluded: chain X residue 100 LYS Chi-restraints excluded: chain X residue 110 LEU Chi-restraints excluded: chain X residue 117 THR Chi-restraints excluded: chain X residue 170 LEU Chi-restraints excluded: chain X residue 177 GLN Chi-restraints excluded: chain X residue 210 ILE Chi-restraints excluded: chain X residue 223 GLN Chi-restraints excluded: chain X residue 264 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 360 random chunks: chunk 260 optimal weight: 0.9980 chunk 318 optimal weight: 0.7980 chunk 212 optimal weight: 0.5980 chunk 150 optimal weight: 2.9990 chunk 217 optimal weight: 0.8980 chunk 120 optimal weight: 1.9990 chunk 171 optimal weight: 2.9990 chunk 149 optimal weight: 2.9990 chunk 73 optimal weight: 0.7980 chunk 98 optimal weight: 0.3980 chunk 340 optimal weight: 0.8980 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 65 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 145 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 164 GLN ** F 123 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 41 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 123 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 225 GLN G 230 HIS G 232 GLN H 225 GLN H 260 GLN Q 19 GLN ** R 19 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 119 HIS ** R 172 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** S 119 HIS S 140 HIS T 101 GLN T 172 HIS U 225 GLN X 41 GLN X 123 HIS Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3864 r_free = 0.3864 target = 0.127053 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3563 r_free = 0.3563 target = 0.107444 restraints weight = 62205.350| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3621 r_free = 0.3621 target = 0.111369 restraints weight = 31882.777| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3658 r_free = 0.3658 target = 0.113934 restraints weight = 19093.693| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3682 r_free = 0.3682 target = 0.115600 restraints weight = 12674.440| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 39)----------------| | r_work = 0.3701 r_free = 0.3701 target = 0.116821 restraints weight = 9187.158| |-----------------------------------------------------------------------------| r_work (final): 0.3698 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7232 moved from start: 0.8910 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.056 29416 Z= 0.133 Angle : 0.698 9.614 39856 Z= 0.352 Chirality : 0.047 0.261 4432 Planarity : 0.005 0.084 5200 Dihedral : 4.547 21.051 4024 Min Nonbonded Distance : 2.488 Molprobity Statistics. All-atom Clashscore : 12.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.34 % Favored : 96.66 % Rotamer: Outliers : 3.78 % Allowed : 26.39 % Favored : 69.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.55 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.97 (0.13), residues: 3624 helix: 0.27 (0.13), residues: 1656 sheet: -0.64 (0.19), residues: 680 loop : -1.74 (0.16), residues: 1288 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.016 0.001 ARG S 176 TYR 0.027 0.002 TYR H 212 PHE 0.038 0.002 PHE H 17 TRP 0.065 0.002 TRP Q 141 HIS 0.008 0.001 HIS S 140 Details of bonding type rmsd covalent geometry : bond 0.00305 (29416) covalent geometry : angle 0.69834 (39856) hydrogen bonds : bond 0.03488 ( 1252) hydrogen bonds : angle 4.97713 ( 3636) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7248 Ramachandran restraints generated. 3624 Oldfield, 0 Emsley, 3624 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7248 Ramachandran restraints generated. 3624 Oldfield, 0 Emsley, 3624 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1319 residues out of total 3024 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 114 poor density : 1205 time to evaluate : 1.204 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: symmetry clash 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: symmetry clash 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: symmetry clash 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: symmetry clash REVERT: A 19 GLN cc_start: 0.7821 (tm-30) cc_final: 0.7599 (tp-100) REVERT: A 30 TYR cc_start: 0.7262 (m-80) cc_final: 0.6701 (m-80) REVERT: A 37 GLU cc_start: 0.7496 (mp0) cc_final: 0.6734 (mp0) REVERT: A 50 LYS cc_start: 0.8324 (mmmt) cc_final: 0.7937 (mmmt) REVERT: A 119 HIS cc_start: 0.6506 (m90) cc_final: 0.6083 (m-70) REVERT: A 123 GLU cc_start: 0.7281 (tp30) cc_final: 0.6804 (mm-30) REVERT: A 174 ARG cc_start: 0.8404 (mtm-85) cc_final: 0.7404 (mtp85) REVERT: A 175 LEU cc_start: 0.8004 (tp) cc_final: 0.7785 (tp) REVERT: A 178 GLU cc_start: 0.8089 (mt-10) cc_final: 0.7826 (mt-10) REVERT: B 16 ARG cc_start: 0.8093 (ttp80) cc_final: 0.7617 (ttp80) REVERT: B 27 LYS cc_start: 0.7334 (ptmt) cc_final: 0.7021 (ptmt) REVERT: B 111 CYS cc_start: 0.7366 (t) cc_final: 0.6633 (t) REVERT: B 117 GLU cc_start: 0.7553 (pt0) cc_final: 0.7053 (pt0) REVERT: C 12 SER cc_start: 0.8835 (p) cc_final: 0.8572 (p) REVERT: C 14 LYS cc_start: 0.8763 (mttm) cc_final: 0.8262 (mttm) REVERT: C 19 GLN cc_start: 0.8066 (mm-40) cc_final: 0.7717 (mm-40) REVERT: C 27 LYS cc_start: 0.8274 (OUTLIER) cc_final: 0.7960 (ptpp) REVERT: C 30 TYR cc_start: 0.7393 (m-80) cc_final: 0.6698 (m-80) REVERT: C 164 SER cc_start: 0.8384 (p) cc_final: 0.8066 (t) REVERT: C 168 LEU cc_start: 0.8457 (tp) cc_final: 0.8062 (tp) REVERT: C 172 HIS cc_start: 0.8241 (m90) cc_final: 0.7891 (m-70) REVERT: C 176 ARG cc_start: 0.8744 (ptp-110) cc_final: 0.8263 (ttm-80) REVERT: D 11 ASN cc_start: 0.7191 (t0) cc_final: 0.6964 (t0) REVERT: D 38 ILE cc_start: 0.8444 (tt) cc_final: 0.7858 (tt) REVERT: D 50 LYS cc_start: 0.8285 (mmpt) cc_final: 0.7972 (mmpt) REVERT: D 56 ARG cc_start: 0.7996 (mtt-85) cc_final: 0.7345 (mmt180) REVERT: D 69 LEU cc_start: 0.7427 (tp) cc_final: 0.7129 (tp) REVERT: D 118 ARG cc_start: 0.7754 (mtm180) cc_final: 0.7422 (ptp-170) REVERT: D 176 ARG cc_start: 0.8414 (mtp180) cc_final: 0.7947 (mtt-85) REVERT: E 15 LYS cc_start: 0.8607 (tmtp) cc_final: 0.7985 (tmtp) REVERT: E 16 GLU cc_start: 0.7956 (mm-30) cc_final: 0.7072 (mm-30) REVERT: E 46 LEU cc_start: 0.8529 (mt) cc_final: 0.8298 (mm) REVERT: E 53 GLU cc_start: 0.7490 (tm-30) cc_final: 0.7273 (tm-30) REVERT: E 89 PHE cc_start: 0.8001 (m-10) cc_final: 0.7712 (m-80) REVERT: E 133 LYS cc_start: 0.6814 (mtmm) cc_final: 0.6279 (mtmm) REVERT: E 145 GLN cc_start: 0.8147 (tp40) cc_final: 0.7871 (mm-40) REVERT: E 158 PHE cc_start: 0.7942 (t80) cc_final: 0.7685 (t80) REVERT: E 177 GLN cc_start: 0.8333 (OUTLIER) cc_final: 0.7944 (pp30) REVERT: E 217 MET cc_start: 0.7500 (mtt) cc_final: 0.7149 (mmm) REVERT: E 264 THR cc_start: 0.8358 (t) cc_final: 0.7973 (p) REVERT: E 272 ARG cc_start: 0.7911 (mmp80) cc_final: 0.7173 (mmp80) REVERT: E 275 GLU cc_start: 0.7690 (mt-10) cc_final: 0.7249 (mt-10) REVERT: F 12 LEU cc_start: 0.8341 (mm) cc_final: 0.8046 (mp) REVERT: F 19 GLU cc_start: 0.7966 (pt0) cc_final: 0.7642 (pt0) REVERT: F 26 LEU cc_start: 0.7683 (mt) cc_final: 0.7110 (mp) REVERT: F 32 LYS cc_start: 0.8041 (tppt) cc_final: 0.7488 (tppt) REVERT: F 38 ASP cc_start: 0.8690 (p0) cc_final: 0.8345 (p0) REVERT: F 52 PHE cc_start: 0.6686 (m-80) cc_final: 0.6480 (m-80) REVERT: F 55 GLU cc_start: 0.7405 (pm20) cc_final: 0.7203 (pm20) REVERT: F 63 PHE cc_start: 0.8254 (t80) cc_final: 0.8015 (t80) REVERT: F 66 LEU cc_start: 0.8911 (mt) cc_final: 0.8484 (mp) REVERT: F 70 PHE cc_start: 0.8737 (m-80) cc_final: 0.8436 (m-80) REVERT: F 77 ARG cc_start: 0.7976 (mpt90) cc_final: 0.7432 (mpt90) REVERT: F 80 ARG cc_start: 0.7655 (tpt90) cc_final: 0.7108 (tpt90) REVERT: F 91 SER cc_start: 0.8360 (t) cc_final: 0.7590 (p) REVERT: F 95 GLU cc_start: 0.8060 (mt-10) cc_final: 0.7763 (mt-10) REVERT: F 133 LYS cc_start: 0.7438 (mttt) cc_final: 0.7179 (mtpp) REVERT: F 171 THR cc_start: 0.7957 (m) cc_final: 0.7227 (p) REVERT: F 172 GLU cc_start: 0.7652 (tt0) cc_final: 0.7199 (tt0) REVERT: F 188 ARG cc_start: 0.8606 (mmm-85) cc_final: 0.8261 (tpt90) REVERT: F 217 MET cc_start: 0.7234 (OUTLIER) cc_final: 0.6950 (mtt) REVERT: F 218 ASN cc_start: 0.7856 (t0) cc_final: 0.7389 (t0) REVERT: G 2 THR cc_start: 0.7888 (p) cc_final: 0.7620 (t) REVERT: G 13 LEU cc_start: 0.8559 (mt) cc_final: 0.8197 (mt) REVERT: G 31 SER cc_start: 0.8485 (m) cc_final: 0.8250 (p) REVERT: G 66 LEU cc_start: 0.8504 (OUTLIER) cc_final: 0.8192 (mm) REVERT: G 77 ARG cc_start: 0.8096 (mpt90) cc_final: 0.7718 (mpt90) REVERT: G 88 SER cc_start: 0.8647 (OUTLIER) cc_final: 0.8379 (p) REVERT: G 103 MET cc_start: 0.6494 (mtp) cc_final: 0.6129 (mtp) REVERT: G 113 ARG cc_start: 0.6979 (mtt180) cc_final: 0.6704 (mtt180) REVERT: G 163 ASP cc_start: 0.7401 (m-30) cc_final: 0.7061 (m-30) REVERT: G 175 TYR cc_start: 0.7468 (OUTLIER) cc_final: 0.6710 (t80) REVERT: G 222 GLU cc_start: 0.7694 (mm-30) cc_final: 0.7255 (mm-30) REVERT: G 235 ARG cc_start: 0.7228 (mmm160) cc_final: 0.6749 (mmm160) REVERT: G 252 GLN cc_start: 0.7844 (tp-100) cc_final: 0.7443 (tp40) REVERT: H 15 LYS cc_start: 0.8512 (tmtp) cc_final: 0.7931 (tmtp) REVERT: H 21 ARG cc_start: 0.7771 (mmt90) cc_final: 0.7206 (mtt180) REVERT: H 59 MET cc_start: 0.7212 (ptt) cc_final: 0.6208 (tmm) REVERT: H 65 GLN cc_start: 0.7774 (mp10) cc_final: 0.7151 (mp10) REVERT: H 68 GLU cc_start: 0.7119 (tp30) cc_final: 0.6414 (tp30) REVERT: H 79 GLN cc_start: 0.8445 (mt0) cc_final: 0.8231 (mp10) REVERT: H 122 LYS cc_start: 0.8060 (pttt) cc_final: 0.7717 (pttt) REVERT: H 140 SER cc_start: 0.7747 (p) cc_final: 0.7461 (p) REVERT: H 215 TYR cc_start: 0.7801 (t80) cc_final: 0.7143 (t80) REVERT: H 221 ARG cc_start: 0.7897 (ttm-80) cc_final: 0.7390 (mtm-85) REVERT: H 222 GLU cc_start: 0.7830 (mm-30) cc_final: 0.7479 (mm-30) REVERT: H 223 GLN cc_start: 0.8041 (tt0) cc_final: 0.7736 (tp40) REVERT: H 225 GLN cc_start: 0.7748 (tt0) cc_final: 0.7433 (tt0) REVERT: H 235 ARG cc_start: 0.7359 (tpp-160) cc_final: 0.6691 (tpp80) REVERT: H 237 PHE cc_start: 0.7933 (m-80) cc_final: 0.7605 (m-80) REVERT: H 253 GLN cc_start: 0.7973 (mm-40) cc_final: 0.7697 (mp10) REVERT: H 275 GLU cc_start: 0.7366 (pt0) cc_final: 0.6905 (pt0) REVERT: Q 101 GLN cc_start: 0.8330 (pm20) cc_final: 0.7622 (tp40) REVERT: Q 117 GLU cc_start: 0.7166 (pt0) cc_final: 0.6726 (pt0) REVERT: Q 141 TRP cc_start: 0.6034 (m-90) cc_final: 0.5575 (m100) REVERT: Q 161 GLU cc_start: 0.7734 (tp30) cc_final: 0.7201 (tp30) REVERT: Q 170 ARG cc_start: 0.7548 (ptp90) cc_final: 0.7265 (ptp90) REVERT: Q 174 ARG cc_start: 0.8252 (mtp180) cc_final: 0.7652 (mtp180) REVERT: R 44 GLU cc_start: 0.7270 (tm-30) cc_final: 0.6621 (tm-30) REVERT: R 48 ARG cc_start: 0.7883 (ttm-80) cc_final: 0.7358 (ttm-80) REVERT: R 61 PRO cc_start: 0.7823 (Cg_exo) cc_final: 0.7536 (Cg_endo) REVERT: R 118 ARG cc_start: 0.7381 (ttp-170) cc_final: 0.7061 (ttp-170) REVERT: R 123 GLU cc_start: 0.6832 (mm-30) cc_final: 0.6057 (mm-30) REVERT: R 171 LEU cc_start: 0.8121 (mt) cc_final: 0.7829 (mt) REVERT: R 174 ARG cc_start: 0.8178 (mtp85) cc_final: 0.7594 (mtp85) REVERT: S 9 THR cc_start: 0.8347 (t) cc_final: 0.8098 (m) REVERT: S 16 ARG cc_start: 0.8900 (mmm160) cc_final: 0.8588 (tpt90) REVERT: S 63 ILE cc_start: 0.7058 (tt) cc_final: 0.6429 (mt) REVERT: S 71 ILE cc_start: 0.7425 (mm) cc_final: 0.7135 (mm) REVERT: S 118 ARG cc_start: 0.7971 (mtm180) cc_final: 0.7602 (ptp-170) REVERT: S 176 ARG cc_start: 0.8840 (mtm110) cc_final: 0.8421 (mtm110) REVERT: T 19 GLN cc_start: 0.8112 (mm-40) cc_final: 0.7623 (mm-40) REVERT: T 30 TYR cc_start: 0.7826 (m-80) cc_final: 0.6976 (m-80) REVERT: T 42 ASP cc_start: 0.7527 (t0) cc_final: 0.7152 (t0) REVERT: T 45 THR cc_start: 0.8387 (m) cc_final: 0.8104 (m) REVERT: T 59 ARG cc_start: 0.7487 (tpt-90) cc_final: 0.7022 (tpt-90) REVERT: T 170 ARG cc_start: 0.7667 (ptp-170) cc_final: 0.7052 (ptp-170) REVERT: T 176 ARG cc_start: 0.8624 (ptp-110) cc_final: 0.7918 (ttm-80) REVERT: U 21 ARG cc_start: 0.7787 (mmt90) cc_final: 0.7017 (mtt180) REVERT: U 23 ILE cc_start: 0.8104 (mt) cc_final: 0.7815 (mm) REVERT: U 32 LYS cc_start: 0.8373 (ttpp) cc_final: 0.8134 (ttpp) REVERT: U 59 MET cc_start: 0.7901 (tpt) cc_final: 0.7112 (tpp) REVERT: U 68 GLU cc_start: 0.7587 (tp30) cc_final: 0.6855 (tp30) REVERT: U 70 PHE cc_start: 0.7459 (OUTLIER) cc_final: 0.7235 (m-80) REVERT: U 103 MET cc_start: 0.7106 (mtt) cc_final: 0.6663 (mtt) REVERT: U 143 ASP cc_start: 0.8115 (m-30) cc_final: 0.7815 (m-30) REVERT: U 144 PHE cc_start: 0.7982 (m-80) cc_final: 0.7711 (m-80) REVERT: U 148 ARG cc_start: 0.6973 (ptp90) cc_final: 0.6562 (ptp90) REVERT: U 164 GLN cc_start: 0.6689 (mt0) cc_final: 0.6328 (mm110) REVERT: U 170 LEU cc_start: 0.7271 (OUTLIER) cc_final: 0.6776 (mm) REVERT: U 187 GLN cc_start: 0.8017 (mm-40) cc_final: 0.7737 (mm-40) REVERT: U 210 ILE cc_start: 0.8453 (tp) cc_final: 0.8041 (tp) REVERT: U 222 GLU cc_start: 0.7963 (mm-30) cc_final: 0.7611 (mm-30) REVERT: U 223 GLN cc_start: 0.7997 (tt0) cc_final: 0.7775 (tt0) REVERT: U 235 ARG cc_start: 0.7638 (tpp-160) cc_final: 0.7419 (ttm-80) REVERT: V 15 LYS cc_start: 0.8208 (tmtp) cc_final: 0.7513 (tmtp) REVERT: V 16 GLU cc_start: 0.7889 (mm-30) cc_final: 0.7355 (mm-30) REVERT: V 17 PHE cc_start: 0.8587 (t80) cc_final: 0.8122 (t80) REVERT: V 62 ARG cc_start: 0.7362 (mmt90) cc_final: 0.6993 (ttm110) REVERT: V 68 GLU cc_start: 0.7952 (tp30) cc_final: 0.7581 (tm-30) REVERT: V 69 PHE cc_start: 0.8813 (t80) cc_final: 0.8090 (t80) REVERT: V 77 ARG cc_start: 0.8067 (OUTLIER) cc_final: 0.7698 (tpt90) REVERT: V 105 ARG cc_start: 0.7623 (mtt180) cc_final: 0.7030 (ttm-80) REVERT: V 113 ARG cc_start: 0.7581 (mtt180) cc_final: 0.7215 (mtt180) REVERT: V 125 GLU cc_start: 0.7519 (mp0) cc_final: 0.7054 (mp0) REVERT: V 148 ARG cc_start: 0.7395 (ptp90) cc_final: 0.6868 (ptp90) REVERT: V 150 ARG cc_start: 0.6904 (mtm180) cc_final: 0.6439 (mmm160) REVERT: V 158 PHE cc_start: 0.8122 (t80) cc_final: 0.7645 (t80) REVERT: V 192 ASP cc_start: 0.7426 (m-30) cc_final: 0.6655 (m-30) REVERT: V 222 GLU cc_start: 0.7756 (mm-30) cc_final: 0.7156 (mm-30) REVERT: W 15 LYS cc_start: 0.8402 (tmtp) cc_final: 0.7868 (tmtp) REVERT: W 26 LEU cc_start: 0.7908 (mt) cc_final: 0.7596 (mp) REVERT: W 32 LYS cc_start: 0.8071 (tppt) cc_final: 0.7657 (tppt) REVERT: W 55 GLU cc_start: 0.7713 (mt-10) cc_final: 0.7446 (mt-10) REVERT: W 59 MET cc_start: 0.7917 (ttp) cc_final: 0.7457 (tmm) REVERT: W 62 ARG cc_start: 0.7021 (mtp85) cc_final: 0.6639 (mtp85) REVERT: W 63 PHE cc_start: 0.8472 (t80) cc_final: 0.8261 (t80) REVERT: W 64 GLU cc_start: 0.7718 (pm20) cc_final: 0.7320 (pm20) REVERT: W 80 ARG cc_start: 0.7899 (tpt170) cc_final: 0.7654 (tpt-90) REVERT: W 85 MET cc_start: 0.8236 (mtm) cc_final: 0.7927 (mtp) REVERT: W 86 SER cc_start: 0.8790 (m) cc_final: 0.8282 (p) REVERT: W 88 SER cc_start: 0.8418 (m) cc_final: 0.8048 (p) REVERT: W 91 SER cc_start: 0.8441 (t) cc_final: 0.8041 (p) REVERT: W 100 LYS cc_start: 0.8531 (mtmm) cc_final: 0.8225 (mtmm) REVERT: W 105 ARG cc_start: 0.7741 (ttm-80) cc_final: 0.7343 (ttm-80) REVERT: W 125 GLU cc_start: 0.7115 (OUTLIER) cc_final: 0.6891 (mt-10) REVERT: W 129 ARG cc_start: 0.6936 (ttm110) cc_final: 0.6477 (mtt-85) REVERT: W 157 LYS cc_start: 0.8287 (mmtt) cc_final: 0.8038 (mmtt) REVERT: W 159 HIS cc_start: 0.8533 (OUTLIER) cc_final: 0.7700 (t-90) REVERT: W 166 ASP cc_start: 0.7509 (p0) cc_final: 0.7229 (p0) REVERT: W 179 MET cc_start: 0.6975 (mmm) cc_final: 0.6044 (mmm) REVERT: W 187 GLN cc_start: 0.8375 (mm-40) cc_final: 0.8025 (mm-40) REVERT: W 188 ARG cc_start: 0.8348 (tpp80) cc_final: 0.7631 (tpp80) REVERT: W 192 ASP cc_start: 0.7588 (m-30) cc_final: 0.6815 (m-30) REVERT: W 212 TYR cc_start: 0.7262 (t80) cc_final: 0.6735 (t80) REVERT: W 221 ARG cc_start: 0.7954 (mtt90) cc_final: 0.7509 (ttp-110) REVERT: W 245 LEU cc_start: 0.8445 (mt) cc_final: 0.7934 (mt) REVERT: W 260 GLN cc_start: 0.7570 (tp40) cc_final: 0.7338 (tp-100) REVERT: X 15 LYS cc_start: 0.8504 (tmtp) cc_final: 0.7981 (tppt) REVERT: X 16 GLU cc_start: 0.7922 (mm-30) cc_final: 0.7193 (mm-30) REVERT: X 42 LEU cc_start: 0.8557 (mm) cc_final: 0.8232 (mp) REVERT: X 46 LEU cc_start: 0.8067 (mt) cc_final: 0.7747 (mp) REVERT: X 55 GLU cc_start: 0.7562 (mp0) cc_final: 0.7359 (mp0) REVERT: X 65 GLN cc_start: 0.7325 (mt0) cc_final: 0.6920 (mp10) REVERT: X 89 PHE cc_start: 0.7694 (m-10) cc_final: 0.7384 (m-10) REVERT: X 155 VAL cc_start: 0.8074 (t) cc_final: 0.7791 (p) REVERT: X 158 PHE cc_start: 0.7748 (t80) cc_final: 0.7508 (t80) REVERT: X 168 ILE cc_start: 0.8338 (mm) cc_final: 0.8067 (mm) REVERT: X 172 GLU cc_start: 0.7589 (tm-30) cc_final: 0.7384 (tm-30) REVERT: X 178 ARG cc_start: 0.8292 (mmm-85) cc_final: 0.8092 (mmm-85) REVERT: X 179 MET cc_start: 0.7112 (mmm) cc_final: 0.6297 (mmm) REVERT: X 182 ASP cc_start: 0.7303 (m-30) cc_final: 0.7006 (m-30) REVERT: X 218 ASN cc_start: 0.7598 (t0) cc_final: 0.7331 (t0) REVERT: X 225 GLN cc_start: 0.7680 (pt0) cc_final: 0.7416 (pt0) REVERT: X 249 ASP cc_start: 0.7844 (OUTLIER) cc_final: 0.7398 (t0) REVERT: X 252 GLN cc_start: 0.7653 (pp30) cc_final: 0.7299 (pp30) REVERT: X 253 GLN cc_start: 0.8394 (mm110) cc_final: 0.8107 (tp40) REVERT: X 264 THR cc_start: 0.8351 (t) cc_final: 0.8068 (p) outliers start: 114 outliers final: 79 residues processed: 1229 average time/residue: 0.2255 time to fit residues: 407.9626 Evaluate side-chains 1286 residues out of total 3024 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 91 poor density : 1195 time to evaluate : 1.124 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 32 THR Chi-restraints excluded: chain B residue 35 VAL Chi-restraints excluded: chain B residue 103 THR Chi-restraints excluded: chain C residue 27 LYS Chi-restraints excluded: chain C residue 120 VAL Chi-restraints excluded: chain C residue 153 THR Chi-restraints excluded: chain D residue 60 VAL Chi-restraints excluded: chain D residue 63 ILE Chi-restraints excluded: chain D residue 88 SER Chi-restraints excluded: chain D residue 96 VAL Chi-restraints excluded: chain D residue 166 SER Chi-restraints excluded: chain E residue 49 THR Chi-restraints excluded: chain E residue 84 GLU Chi-restraints excluded: chain E residue 97 LEU Chi-restraints excluded: chain E residue 177 GLN Chi-restraints excluded: chain E residue 223 GLN Chi-restraints excluded: chain E residue 240 THR Chi-restraints excluded: chain F residue 18 ARG Chi-restraints excluded: chain F residue 93 GLU Chi-restraints excluded: chain F residue 154 GLU Chi-restraints excluded: chain F residue 159 HIS Chi-restraints excluded: chain F residue 170 LEU Chi-restraints excluded: chain F residue 217 MET Chi-restraints excluded: chain F residue 222 GLU Chi-restraints excluded: chain G residue 3 THR Chi-restraints excluded: chain G residue 5 THR Chi-restraints excluded: chain G residue 19 GLU Chi-restraints excluded: chain G residue 66 LEU Chi-restraints excluded: chain G residue 88 SER Chi-restraints excluded: chain G residue 115 ILE Chi-restraints excluded: chain G residue 117 THR Chi-restraints excluded: chain G residue 119 ASN Chi-restraints excluded: chain G residue 175 TYR Chi-restraints excluded: chain G residue 208 THR Chi-restraints excluded: chain G residue 209 ASN Chi-restraints excluded: chain H residue 14 LYS Chi-restraints excluded: chain H residue 119 ASN Chi-restraints excluded: chain H residue 193 LEU Chi-restraints excluded: chain H residue 210 ILE Chi-restraints excluded: chain Q residue 19 GLN Chi-restraints excluded: chain Q residue 43 LEU Chi-restraints excluded: chain Q residue 139 PHE Chi-restraints excluded: chain R residue 32 THR Chi-restraints excluded: chain R residue 120 VAL Chi-restraints excluded: chain R residue 128 GLU Chi-restraints excluded: chain S residue 38 ILE Chi-restraints excluded: chain S residue 60 VAL Chi-restraints excluded: chain T residue 28 LEU Chi-restraints excluded: chain T residue 36 THR Chi-restraints excluded: chain T residue 41 VAL Chi-restraints excluded: chain T residue 120 VAL Chi-restraints excluded: chain U residue 18 ARG Chi-restraints excluded: chain U residue 64 GLU Chi-restraints excluded: chain U residue 70 PHE Chi-restraints excluded: chain U residue 117 THR Chi-restraints excluded: chain U residue 119 ASN Chi-restraints excluded: chain U residue 120 TYR Chi-restraints excluded: chain U residue 150 ARG Chi-restraints excluded: chain U residue 170 LEU Chi-restraints excluded: chain U residue 177 GLN Chi-restraints excluded: chain U residue 252 GLN Chi-restraints excluded: chain V residue 4 LEU Chi-restraints excluded: chain V residue 77 ARG Chi-restraints excluded: chain V residue 84 GLU Chi-restraints excluded: chain V residue 118 THR Chi-restraints excluded: chain V residue 119 ASN Chi-restraints excluded: chain V residue 120 TYR Chi-restraints excluded: chain V residue 170 LEU Chi-restraints excluded: chain V residue 171 THR Chi-restraints excluded: chain W residue 6 LEU Chi-restraints excluded: chain W residue 8 GLU Chi-restraints excluded: chain W residue 38 ASP Chi-restraints excluded: chain W residue 77 ARG Chi-restraints excluded: chain W residue 122 LYS Chi-restraints excluded: chain W residue 125 GLU Chi-restraints excluded: chain W residue 134 GLN Chi-restraints excluded: chain W residue 154 GLU Chi-restraints excluded: chain W residue 159 HIS Chi-restraints excluded: chain W residue 177 GLN Chi-restraints excluded: chain W residue 225 GLN Chi-restraints excluded: chain W residue 252 GLN Chi-restraints excluded: chain W residue 273 LEU Chi-restraints excluded: chain X residue 50 LEU Chi-restraints excluded: chain X residue 79 GLN Chi-restraints excluded: chain X residue 103 MET Chi-restraints excluded: chain X residue 117 THR Chi-restraints excluded: chain X residue 170 LEU Chi-restraints excluded: chain X residue 177 GLN Chi-restraints excluded: chain X residue 210 ILE Chi-restraints excluded: chain X residue 240 THR Chi-restraints excluded: chain X residue 249 ASP Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 360 random chunks: chunk 0 optimal weight: 4.9990 chunk 338 optimal weight: 0.9980 chunk 52 optimal weight: 0.9980 chunk 169 optimal weight: 0.3980 chunk 172 optimal weight: 4.9990 chunk 281 optimal weight: 3.9990 chunk 127 optimal weight: 2.9990 chunk 142 optimal weight: 3.9990 chunk 293 optimal weight: 2.9990 chunk 11 optimal weight: 2.9990 chunk 246 optimal weight: 0.0050 overall best weight: 1.0796 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 65 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 145 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 123 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 41 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 123 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Q 19 GLN ** R 19 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 119 HIS ** R 172 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** V 164 GLN ** W 123 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** X 123 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3846 r_free = 0.3846 target = 0.125770 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3543 r_free = 0.3543 target = 0.106272 restraints weight = 62385.193| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3601 r_free = 0.3601 target = 0.110148 restraints weight = 31982.958| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3638 r_free = 0.3638 target = 0.112684 restraints weight = 19173.452| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 49)----------------| | r_work = 0.3663 r_free = 0.3663 target = 0.114388 restraints weight = 12745.055| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 42)----------------| | r_work = 0.3681 r_free = 0.3681 target = 0.115549 restraints weight = 9222.782| |-----------------------------------------------------------------------------| r_work (final): 0.3672 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7255 moved from start: 0.9123 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 29416 Z= 0.155 Angle : 0.714 9.433 39856 Z= 0.362 Chirality : 0.048 0.251 4432 Planarity : 0.005 0.077 5200 Dihedral : 4.598 21.032 4024 Min Nonbonded Distance : 2.480 Molprobity Statistics. All-atom Clashscore : 14.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.75 % Favored : 96.25 % Rotamer: Outliers : 3.58 % Allowed : 26.99 % Favored : 69.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.55 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.95 (0.14), residues: 3624 helix: 0.27 (0.13), residues: 1656 sheet: -0.65 (0.19), residues: 680 loop : -1.70 (0.16), residues: 1288 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG S 176 TYR 0.030 0.002 TYR H 212 PHE 0.035 0.002 PHE X 57 TRP 0.060 0.002 TRP Q 141 HIS 0.012 0.001 HIS D 140 Details of bonding type rmsd covalent geometry : bond 0.00346 (29416) covalent geometry : angle 0.71407 (39856) hydrogen bonds : bond 0.03707 ( 1252) hydrogen bonds : angle 5.04555 ( 3636) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7248 Ramachandran restraints generated. 3624 Oldfield, 0 Emsley, 3624 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7248 Ramachandran restraints generated. 3624 Oldfield, 0 Emsley, 3624 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1319 residues out of total 3024 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 108 poor density : 1211 time to evaluate : 1.056 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: symmetry clash 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: symmetry clash 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: symmetry clash 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 19 GLN cc_start: 0.7854 (tm-30) cc_final: 0.7612 (tp40) REVERT: A 30 TYR cc_start: 0.7319 (m-80) cc_final: 0.6371 (m-80) REVERT: A 37 GLU cc_start: 0.7452 (mp0) cc_final: 0.6976 (mp0) REVERT: A 119 HIS cc_start: 0.6549 (m90) cc_final: 0.6195 (m-70) REVERT: A 123 GLU cc_start: 0.7310 (tp30) cc_final: 0.6864 (mm-30) REVERT: A 175 LEU cc_start: 0.8019 (tp) cc_final: 0.7810 (tp) REVERT: A 178 GLU cc_start: 0.8118 (mt-10) cc_final: 0.7854 (mt-10) REVERT: B 16 ARG cc_start: 0.8073 (ttp80) cc_final: 0.7581 (ttp80) REVERT: B 27 LYS cc_start: 0.7324 (ptmt) cc_final: 0.7007 (ptmt) REVERT: B 111 CYS cc_start: 0.7404 (t) cc_final: 0.6662 (t) REVERT: B 117 GLU cc_start: 0.7571 (pt0) cc_final: 0.7053 (pt0) REVERT: C 12 SER cc_start: 0.8809 (p) cc_final: 0.8553 (p) REVERT: C 14 LYS cc_start: 0.8778 (mttm) cc_final: 0.8003 (mttm) REVERT: C 19 GLN cc_start: 0.8074 (mm-40) cc_final: 0.7731 (mm-40) REVERT: C 27 LYS cc_start: 0.8321 (OUTLIER) cc_final: 0.7998 (ptpp) REVERT: C 30 TYR cc_start: 0.7405 (m-80) cc_final: 0.6739 (m-80) REVERT: C 65 GLU cc_start: 0.6797 (tm-30) cc_final: 0.5917 (tm-30) REVERT: C 95 GLU cc_start: 0.8163 (mm-30) cc_final: 0.7808 (mp0) REVERT: C 164 SER cc_start: 0.8369 (p) cc_final: 0.8016 (t) REVERT: C 168 LEU cc_start: 0.8479 (tp) cc_final: 0.8047 (tp) REVERT: C 172 HIS cc_start: 0.8303 (m90) cc_final: 0.7959 (m-70) REVERT: C 174 ARG cc_start: 0.8028 (mtp180) cc_final: 0.7322 (mtp180) REVERT: C 176 ARG cc_start: 0.8767 (ptp-110) cc_final: 0.8231 (ttm-80) REVERT: D 11 ASN cc_start: 0.7322 (t0) cc_final: 0.7117 (t0) REVERT: D 38 ILE cc_start: 0.8437 (tt) cc_final: 0.7902 (tt) REVERT: D 50 LYS cc_start: 0.8309 (mmpt) cc_final: 0.7965 (mmpt) REVERT: D 69 LEU cc_start: 0.7319 (tp) cc_final: 0.7036 (tp) REVERT: D 118 ARG cc_start: 0.7844 (mtm180) cc_final: 0.7513 (ptp-170) REVERT: D 162 LYS cc_start: 0.7583 (mmmt) cc_final: 0.7316 (mmmt) REVERT: D 176 ARG cc_start: 0.8390 (mtp180) cc_final: 0.7924 (mtt-85) REVERT: E 15 LYS cc_start: 0.8614 (tmtp) cc_final: 0.7996 (tmtp) REVERT: E 16 GLU cc_start: 0.7962 (mm-30) cc_final: 0.7084 (mm-30) REVERT: E 46 LEU cc_start: 0.8503 (mt) cc_final: 0.8292 (mm) REVERT: E 53 GLU cc_start: 0.7523 (tm-30) cc_final: 0.7275 (tm-30) REVERT: E 89 PHE cc_start: 0.8005 (m-10) cc_final: 0.7727 (m-80) REVERT: E 133 LYS cc_start: 0.6846 (mtmm) cc_final: 0.6492 (mtmm) REVERT: E 145 GLN cc_start: 0.8084 (tp40) cc_final: 0.7781 (mm-40) REVERT: E 158 PHE cc_start: 0.7939 (t80) cc_final: 0.7617 (t80) REVERT: E 177 GLN cc_start: 0.8375 (OUTLIER) cc_final: 0.7896 (pp30) REVERT: E 179 MET cc_start: 0.7184 (OUTLIER) cc_final: 0.6515 (mmt) REVERT: E 217 MET cc_start: 0.7523 (mtt) cc_final: 0.7143 (mmm) REVERT: E 225 GLN cc_start: 0.7835 (mt0) cc_final: 0.7436 (mt0) REVERT: E 235 ARG cc_start: 0.6925 (tpp80) cc_final: 0.6467 (tpp80) REVERT: E 253 GLN cc_start: 0.8120 (mm-40) cc_final: 0.7853 (mm-40) REVERT: E 264 THR cc_start: 0.8353 (t) cc_final: 0.7963 (p) REVERT: E 272 ARG cc_start: 0.7914 (mmp80) cc_final: 0.7246 (mmp80) REVERT: E 275 GLU cc_start: 0.7695 (mt-10) cc_final: 0.7269 (mt-10) REVERT: F 12 LEU cc_start: 0.8347 (mm) cc_final: 0.8077 (mp) REVERT: F 26 LEU cc_start: 0.7696 (mt) cc_final: 0.7139 (mp) REVERT: F 32 LYS cc_start: 0.8059 (tppt) cc_final: 0.7505 (tppt) REVERT: F 38 ASP cc_start: 0.8671 (p0) cc_final: 0.8343 (p0) REVERT: F 52 PHE cc_start: 0.6737 (m-80) cc_final: 0.6439 (m-80) REVERT: F 66 LEU cc_start: 0.8915 (mt) cc_final: 0.8525 (mp) REVERT: F 70 PHE cc_start: 0.8756 (m-80) cc_final: 0.8411 (m-80) REVERT: F 77 ARG cc_start: 0.8006 (mpt90) cc_final: 0.7362 (mpt90) REVERT: F 78 LEU cc_start: 0.8705 (tp) cc_final: 0.8495 (tt) REVERT: F 91 SER cc_start: 0.8381 (t) cc_final: 0.7638 (p) REVERT: F 95 GLU cc_start: 0.8034 (mt-10) cc_final: 0.7804 (mt-10) REVERT: F 133 LYS cc_start: 0.7503 (mttt) cc_final: 0.7165 (mtpp) REVERT: F 171 THR cc_start: 0.7959 (m) cc_final: 0.7214 (p) REVERT: F 172 GLU cc_start: 0.7658 (tt0) cc_final: 0.7177 (tt0) REVERT: F 188 ARG cc_start: 0.8605 (mmm-85) cc_final: 0.8290 (tpt90) REVERT: F 217 MET cc_start: 0.7249 (OUTLIER) cc_final: 0.6962 (mtt) REVERT: F 218 ASN cc_start: 0.7881 (t0) cc_final: 0.7401 (t0) REVERT: G 2 THR cc_start: 0.7973 (p) cc_final: 0.7672 (t) REVERT: G 31 SER cc_start: 0.8493 (OUTLIER) cc_final: 0.8241 (p) REVERT: G 66 LEU cc_start: 0.8535 (OUTLIER) cc_final: 0.8183 (mm) REVERT: G 77 ARG cc_start: 0.8114 (mpt90) cc_final: 0.7737 (mpt90) REVERT: G 88 SER cc_start: 0.8626 (OUTLIER) cc_final: 0.8373 (p) REVERT: G 103 MET cc_start: 0.6477 (mtp) cc_final: 0.6115 (mtp) REVERT: G 113 ARG cc_start: 0.7046 (mtt180) cc_final: 0.6783 (mtt180) REVERT: G 163 ASP cc_start: 0.7384 (m-30) cc_final: 0.7162 (m-30) REVERT: G 175 TYR cc_start: 0.7492 (OUTLIER) cc_final: 0.6709 (t80) REVERT: G 178 ARG cc_start: 0.8068 (tpp80) cc_final: 0.7713 (tpp80) REVERT: G 222 GLU cc_start: 0.7709 (mm-30) cc_final: 0.7262 (mm-30) REVERT: G 235 ARG cc_start: 0.7227 (mmm160) cc_final: 0.6839 (mmm160) REVERT: H 15 LYS cc_start: 0.8492 (tmtp) cc_final: 0.7919 (tmtp) REVERT: H 21 ARG cc_start: 0.7792 (mmt90) cc_final: 0.7200 (mtt180) REVERT: H 65 GLN cc_start: 0.7815 (mp10) cc_final: 0.7174 (mp10) REVERT: H 68 GLU cc_start: 0.7165 (tp30) cc_final: 0.6482 (tp30) REVERT: H 79 GLN cc_start: 0.8449 (mt0) cc_final: 0.8233 (mp10) REVERT: H 122 LYS cc_start: 0.8022 (pttt) cc_final: 0.7749 (pttt) REVERT: H 140 SER cc_start: 0.7705 (p) cc_final: 0.7409 (p) REVERT: H 188 ARG cc_start: 0.7650 (tpp80) cc_final: 0.7161 (tpp80) REVERT: H 215 TYR cc_start: 0.7806 (t80) cc_final: 0.7138 (t80) REVERT: H 221 ARG cc_start: 0.7890 (ttm-80) cc_final: 0.7414 (ttm-80) REVERT: H 223 GLN cc_start: 0.7982 (tt0) cc_final: 0.7689 (tp40) REVERT: H 235 ARG cc_start: 0.7329 (tpp-160) cc_final: 0.6652 (tpp80) REVERT: H 237 PHE cc_start: 0.7938 (m-80) cc_final: 0.7613 (m-80) REVERT: H 245 LEU cc_start: 0.7639 (mt) cc_final: 0.7399 (mt) REVERT: H 253 GLN cc_start: 0.7938 (mm-40) cc_final: 0.7588 (mp10) REVERT: H 275 GLU cc_start: 0.7372 (pt0) cc_final: 0.6979 (pt0) REVERT: Q 34 LYS cc_start: 0.8375 (tttm) cc_final: 0.8172 (tttm) REVERT: Q 56 ARG cc_start: 0.7603 (mtt-85) cc_final: 0.7159 (mtt-85) REVERT: Q 59 ARG cc_start: 0.8171 (mmt180) cc_final: 0.7758 (mmt90) REVERT: Q 101 GLN cc_start: 0.8386 (pm20) cc_final: 0.7623 (tp40) REVERT: Q 117 GLU cc_start: 0.7167 (pt0) cc_final: 0.6739 (pt0) REVERT: Q 141 TRP cc_start: 0.6077 (m-90) cc_final: 0.5676 (m100) REVERT: Q 161 GLU cc_start: 0.7861 (tp30) cc_final: 0.7253 (tp30) REVERT: Q 170 ARG cc_start: 0.7593 (ptp90) cc_final: 0.7276 (ptp90) REVERT: Q 174 ARG cc_start: 0.8356 (mtp180) cc_final: 0.7785 (mtp180) REVERT: R 13 GLU cc_start: 0.8057 (mm-30) cc_final: 0.7734 (mm-30) REVERT: R 44 GLU cc_start: 0.7301 (tm-30) cc_final: 0.7061 (tm-30) REVERT: R 61 PRO cc_start: 0.7731 (Cg_exo) cc_final: 0.7417 (Cg_endo) REVERT: R 118 ARG cc_start: 0.7421 (ttp-170) cc_final: 0.7034 (ttp-170) REVERT: R 119 HIS cc_start: 0.6637 (m170) cc_final: 0.6366 (m-70) REVERT: R 162 LYS cc_start: 0.8167 (ttpm) cc_final: 0.7444 (tttm) REVERT: R 174 ARG cc_start: 0.8163 (mtp85) cc_final: 0.7718 (mtp85) REVERT: S 16 ARG cc_start: 0.8918 (OUTLIER) cc_final: 0.8643 (tpt90) REVERT: S 59 ARG cc_start: 0.7260 (mmt180) cc_final: 0.6693 (mmt180) REVERT: S 71 ILE cc_start: 0.7433 (mm) cc_final: 0.7133 (mm) REVERT: S 176 ARG cc_start: 0.8829 (mtm110) cc_final: 0.8436 (mtm110) REVERT: T 19 GLN cc_start: 0.8126 (mm-40) cc_final: 0.7632 (mm-40) REVERT: T 30 TYR cc_start: 0.7826 (m-80) cc_final: 0.6990 (m-80) REVERT: T 42 ASP cc_start: 0.7607 (t0) cc_final: 0.7205 (t0) REVERT: T 59 ARG cc_start: 0.7492 (tpt-90) cc_final: 0.7002 (tpt-90) REVERT: T 170 ARG cc_start: 0.7624 (ptp-170) cc_final: 0.7015 (ptp-170) REVERT: T 176 ARG cc_start: 0.8635 (ptp-110) cc_final: 0.7992 (ttp-110) REVERT: U 21 ARG cc_start: 0.7809 (mmt90) cc_final: 0.7051 (mtt180) REVERT: U 32 LYS cc_start: 0.8379 (ttpp) cc_final: 0.8135 (ttpp) REVERT: U 35 LYS cc_start: 0.8694 (mmtm) cc_final: 0.8436 (mttm) REVERT: U 59 MET cc_start: 0.7927 (tpt) cc_final: 0.7248 (tpp) REVERT: U 68 GLU cc_start: 0.7647 (tp30) cc_final: 0.6889 (tp30) REVERT: U 103 MET cc_start: 0.7052 (mtt) cc_final: 0.6656 (mtt) REVERT: U 143 ASP cc_start: 0.8144 (m-30) cc_final: 0.7799 (m-30) REVERT: U 144 PHE cc_start: 0.7989 (m-80) cc_final: 0.7737 (m-80) REVERT: U 148 ARG cc_start: 0.7000 (ptp90) cc_final: 0.6562 (ptp90) REVERT: U 170 LEU cc_start: 0.7336 (OUTLIER) cc_final: 0.6836 (mm) REVERT: U 187 GLN cc_start: 0.8048 (mm-40) cc_final: 0.7766 (mm-40) REVERT: U 210 ILE cc_start: 0.8459 (tp) cc_final: 0.8058 (tp) REVERT: U 222 GLU cc_start: 0.7935 (mm-30) cc_final: 0.7613 (mm-30) REVERT: U 223 GLN cc_start: 0.7987 (tt0) cc_final: 0.7431 (tt0) REVERT: U 235 ARG cc_start: 0.7764 (tpp-160) cc_final: 0.7278 (ttm-80) REVERT: V 15 LYS cc_start: 0.8209 (tmtp) cc_final: 0.7559 (tmtp) REVERT: V 16 GLU cc_start: 0.7884 (mm-30) cc_final: 0.7331 (mm-30) REVERT: V 55 GLU cc_start: 0.7775 (pm20) cc_final: 0.7517 (pm20) REVERT: V 68 GLU cc_start: 0.7984 (tp30) cc_final: 0.7593 (tm-30) REVERT: V 69 PHE cc_start: 0.8855 (t80) cc_final: 0.8186 (t80) REVERT: V 77 ARG cc_start: 0.8048 (OUTLIER) cc_final: 0.7770 (tpt170) REVERT: V 101 SER cc_start: 0.8206 (t) cc_final: 0.7882 (m) REVERT: V 105 ARG cc_start: 0.7607 (mtt180) cc_final: 0.6905 (ttm-80) REVERT: V 113 ARG cc_start: 0.7555 (mtt180) cc_final: 0.7232 (mtt180) REVERT: V 125 GLU cc_start: 0.7523 (mp0) cc_final: 0.7079 (mp0) REVERT: V 148 ARG cc_start: 0.7379 (ptp90) cc_final: 0.6875 (ptp90) REVERT: V 150 ARG cc_start: 0.6907 (mtm180) cc_final: 0.6455 (mmm160) REVERT: V 158 PHE cc_start: 0.8121 (t80) cc_final: 0.7664 (t80) REVERT: V 192 ASP cc_start: 0.7435 (m-30) cc_final: 0.6668 (m-30) REVERT: V 222 GLU cc_start: 0.7758 (mm-30) cc_final: 0.7156 (mm-30) REVERT: V 269 SER cc_start: 0.7475 (t) cc_final: 0.7009 (t) REVERT: W 15 LYS cc_start: 0.8391 (tmtp) cc_final: 0.7855 (tmtp) REVERT: W 26 LEU cc_start: 0.7955 (mt) cc_final: 0.7568 (mp) REVERT: W 32 LYS cc_start: 0.8087 (tppt) cc_final: 0.7683 (tppt) REVERT: W 55 GLU cc_start: 0.7738 (mt-10) cc_final: 0.7490 (mt-10) REVERT: W 59 MET cc_start: 0.7905 (ttp) cc_final: 0.7540 (tmm) REVERT: W 62 ARG cc_start: 0.7098 (mtp85) cc_final: 0.6735 (mtp85) REVERT: W 63 PHE cc_start: 0.8481 (t80) cc_final: 0.8246 (t80) REVERT: W 64 GLU cc_start: 0.7737 (pm20) cc_final: 0.7303 (pm20) REVERT: W 80 ARG cc_start: 0.7908 (tpt170) cc_final: 0.7680 (tpt-90) REVERT: W 85 MET cc_start: 0.8218 (mtm) cc_final: 0.7921 (mtp) REVERT: W 86 SER cc_start: 0.8785 (m) cc_final: 0.8297 (p) REVERT: W 88 SER cc_start: 0.8442 (m) cc_final: 0.8059 (p) REVERT: W 91 SER cc_start: 0.8479 (t) cc_final: 0.8070 (p) REVERT: W 100 LYS cc_start: 0.8563 (mtmm) cc_final: 0.8255 (mtmm) REVERT: W 105 ARG cc_start: 0.7744 (ttm-80) cc_final: 0.7298 (ttm-80) REVERT: W 125 GLU cc_start: 0.7160 (OUTLIER) cc_final: 0.6878 (mt-10) REVERT: W 157 LYS cc_start: 0.8312 (mmtt) cc_final: 0.7873 (mmmt) REVERT: W 159 HIS cc_start: 0.8526 (OUTLIER) cc_final: 0.7770 (t-90) REVERT: W 166 ASP cc_start: 0.7496 (p0) cc_final: 0.7211 (p0) REVERT: W 179 MET cc_start: 0.6981 (mmm) cc_final: 0.6174 (mmm) REVERT: W 187 GLN cc_start: 0.8415 (mm-40) cc_final: 0.8075 (mm-40) REVERT: W 188 ARG cc_start: 0.8374 (tpp80) cc_final: 0.7661 (tpp80) REVERT: W 192 ASP cc_start: 0.7659 (m-30) cc_final: 0.6858 (m-30) REVERT: W 212 TYR cc_start: 0.7316 (t80) cc_final: 0.6656 (t80) REVERT: W 221 ARG cc_start: 0.7975 (mtt90) cc_final: 0.7392 (mtt90) REVERT: W 225 GLN cc_start: 0.7982 (OUTLIER) cc_final: 0.7771 (mt0) REVERT: W 245 LEU cc_start: 0.8494 (mt) cc_final: 0.7989 (mt) REVERT: W 260 GLN cc_start: 0.7505 (tp40) cc_final: 0.6808 (tp40) REVERT: X 15 LYS cc_start: 0.8453 (tmtp) cc_final: 0.7989 (tppt) REVERT: X 16 GLU cc_start: 0.7929 (mm-30) cc_final: 0.7227 (mm-30) REVERT: X 42 LEU cc_start: 0.8578 (mm) cc_final: 0.8233 (mp) REVERT: X 46 LEU cc_start: 0.8089 (mt) cc_final: 0.7751 (mp) REVERT: X 55 GLU cc_start: 0.7570 (mp0) cc_final: 0.7324 (mp0) REVERT: X 65 GLN cc_start: 0.7414 (mt0) cc_final: 0.7013 (mp10) REVERT: X 155 VAL cc_start: 0.8077 (t) cc_final: 0.7778 (p) REVERT: X 158 PHE cc_start: 0.7771 (t80) cc_final: 0.7504 (t80) REVERT: X 168 ILE cc_start: 0.8321 (mm) cc_final: 0.8051 (mm) REVERT: X 172 GLU cc_start: 0.7697 (tm-30) cc_final: 0.7408 (tm-30) REVERT: X 176 PHE cc_start: 0.8461 (m-10) cc_final: 0.8137 (m-80) REVERT: X 182 ASP cc_start: 0.7294 (m-30) cc_final: 0.6994 (m-30) REVERT: X 218 ASN cc_start: 0.7595 (t0) cc_final: 0.7354 (t0) REVERT: X 225 GLN cc_start: 0.7662 (pt0) cc_final: 0.7387 (pt0) REVERT: X 249 ASP cc_start: 0.7910 (OUTLIER) cc_final: 0.7581 (t0) REVERT: X 253 GLN cc_start: 0.8467 (mm110) cc_final: 0.8223 (tp40) REVERT: X 264 THR cc_start: 0.8323 (t) cc_final: 0.8043 (p) outliers start: 108 outliers final: 83 residues processed: 1236 average time/residue: 0.2328 time to fit residues: 422.1187 Evaluate side-chains 1296 residues out of total 3024 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 98 poor density : 1198 time to evaluate : 1.095 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 32 THR Chi-restraints excluded: chain A residue 157 MET Chi-restraints excluded: chain B residue 21 VAL Chi-restraints excluded: chain B residue 35 VAL Chi-restraints excluded: chain B residue 103 THR Chi-restraints excluded: chain C residue 27 LYS Chi-restraints excluded: chain C residue 120 VAL Chi-restraints excluded: chain C residue 153 THR Chi-restraints excluded: chain D residue 60 VAL Chi-restraints excluded: chain D residue 63 ILE Chi-restraints excluded: chain D residue 88 SER Chi-restraints excluded: chain D residue 96 VAL Chi-restraints excluded: chain E residue 49 THR Chi-restraints excluded: chain E residue 84 GLU Chi-restraints excluded: chain E residue 97 LEU Chi-restraints excluded: chain E residue 175 TYR Chi-restraints excluded: chain E residue 177 GLN Chi-restraints excluded: chain E residue 179 MET Chi-restraints excluded: chain E residue 240 THR Chi-restraints excluded: chain E residue 259 ILE Chi-restraints excluded: chain F residue 3 THR Chi-restraints excluded: chain F residue 93 GLU Chi-restraints excluded: chain F residue 154 GLU Chi-restraints excluded: chain F residue 159 HIS Chi-restraints excluded: chain F residue 170 LEU Chi-restraints excluded: chain F residue 217 MET Chi-restraints excluded: chain G residue 3 THR Chi-restraints excluded: chain G residue 5 THR Chi-restraints excluded: chain G residue 31 SER Chi-restraints excluded: chain G residue 66 LEU Chi-restraints excluded: chain G residue 70 PHE Chi-restraints excluded: chain G residue 88 SER Chi-restraints excluded: chain G residue 114 THR Chi-restraints excluded: chain G residue 115 ILE Chi-restraints excluded: chain G residue 117 THR Chi-restraints excluded: chain G residue 119 ASN Chi-restraints excluded: chain G residue 170 LEU Chi-restraints excluded: chain G residue 175 TYR Chi-restraints excluded: chain G residue 204 SER Chi-restraints excluded: chain G residue 208 THR Chi-restraints excluded: chain G residue 209 ASN Chi-restraints excluded: chain H residue 14 LYS Chi-restraints excluded: chain H residue 64 GLU Chi-restraints excluded: chain H residue 119 ASN Chi-restraints excluded: chain H residue 193 LEU Chi-restraints excluded: chain H residue 210 ILE Chi-restraints excluded: chain Q residue 19 GLN Chi-restraints excluded: chain Q residue 43 LEU Chi-restraints excluded: chain R residue 32 THR Chi-restraints excluded: chain R residue 128 GLU Chi-restraints excluded: chain S residue 16 ARG Chi-restraints excluded: chain S residue 38 ILE Chi-restraints excluded: chain S residue 60 VAL Chi-restraints excluded: chain T residue 28 LEU Chi-restraints excluded: chain T residue 36 THR Chi-restraints excluded: chain T residue 41 VAL Chi-restraints excluded: chain T residue 120 VAL Chi-restraints excluded: chain U residue 18 ARG Chi-restraints excluded: chain U residue 64 GLU Chi-restraints excluded: chain U residue 119 ASN Chi-restraints excluded: chain U residue 120 TYR Chi-restraints excluded: chain U residue 134 GLN Chi-restraints excluded: chain U residue 150 ARG Chi-restraints excluded: chain U residue 170 LEU Chi-restraints excluded: chain U residue 177 GLN Chi-restraints excluded: chain U residue 252 GLN Chi-restraints excluded: chain V residue 4 LEU Chi-restraints excluded: chain V residue 5 THR Chi-restraints excluded: chain V residue 77 ARG Chi-restraints excluded: chain V residue 84 GLU Chi-restraints excluded: chain V residue 118 THR Chi-restraints excluded: chain V residue 119 ASN Chi-restraints excluded: chain V residue 120 TYR Chi-restraints excluded: chain V residue 170 LEU Chi-restraints excluded: chain V residue 171 THR Chi-restraints excluded: chain W residue 6 LEU Chi-restraints excluded: chain W residue 8 GLU Chi-restraints excluded: chain W residue 38 ASP Chi-restraints excluded: chain W residue 77 ARG Chi-restraints excluded: chain W residue 122 LYS Chi-restraints excluded: chain W residue 125 GLU Chi-restraints excluded: chain W residue 134 GLN Chi-restraints excluded: chain W residue 154 GLU Chi-restraints excluded: chain W residue 159 HIS Chi-restraints excluded: chain W residue 170 LEU Chi-restraints excluded: chain W residue 177 GLN Chi-restraints excluded: chain W residue 225 GLN Chi-restraints excluded: chain W residue 252 GLN Chi-restraints excluded: chain W residue 273 LEU Chi-restraints excluded: chain X residue 50 LEU Chi-restraints excluded: chain X residue 79 GLN Chi-restraints excluded: chain X residue 103 MET Chi-restraints excluded: chain X residue 117 THR Chi-restraints excluded: chain X residue 170 LEU Chi-restraints excluded: chain X residue 177 GLN Chi-restraints excluded: chain X residue 210 ILE Chi-restraints excluded: chain X residue 240 THR Chi-restraints excluded: chain X residue 249 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 360 random chunks: chunk 89 optimal weight: 0.9990 chunk 118 optimal weight: 0.5980 chunk 228 optimal weight: 9.9990 chunk 239 optimal weight: 3.9990 chunk 321 optimal weight: 2.9990 chunk 129 optimal weight: 0.9990 chunk 268 optimal weight: 0.6980 chunk 163 optimal weight: 0.9990 chunk 70 optimal weight: 0.0470 chunk 330 optimal weight: 1.9990 chunk 72 optimal weight: 0.8980 overall best weight: 0.6480 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 150 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 65 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 145 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 164 GLN ** E 252 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 123 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 41 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 123 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 159 HIS ** R 19 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 20 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 172 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 123 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** X 123 HIS X 252 GLN X 253 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3862 r_free = 0.3862 target = 0.126913 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3563 r_free = 0.3563 target = 0.107484 restraints weight = 61947.837| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3621 r_free = 0.3621 target = 0.111369 restraints weight = 31690.521| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3658 r_free = 0.3658 target = 0.113917 restraints weight = 18958.608| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.3683 r_free = 0.3683 target = 0.115640 restraints weight = 12541.332| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.3700 r_free = 0.3700 target = 0.116796 restraints weight = 9038.779| |-----------------------------------------------------------------------------| r_work (final): 0.3694 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7229 moved from start: 0.9244 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 29416 Z= 0.132 Angle : 0.714 10.774 39856 Z= 0.359 Chirality : 0.047 0.241 4432 Planarity : 0.005 0.069 5200 Dihedral : 4.521 26.345 4024 Min Nonbonded Distance : 2.471 Molprobity Statistics. All-atom Clashscore : 13.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.37 % Favored : 96.63 % Rotamer: Outliers : 3.28 % Allowed : 27.82 % Favored : 68.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.55 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.78 (0.14), residues: 3624 helix: 0.39 (0.13), residues: 1648 sheet: -0.43 (0.20), residues: 600 loop : -1.61 (0.15), residues: 1376 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG A 176 TYR 0.032 0.002 TYR U 212 PHE 0.035 0.001 PHE X 57 TRP 0.064 0.002 TRP T 86 HIS 0.012 0.001 HIS D 140 Details of bonding type rmsd covalent geometry : bond 0.00304 (29416) covalent geometry : angle 0.71365 (39856) hydrogen bonds : bond 0.03343 ( 1252) hydrogen bonds : angle 4.94356 ( 3636) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7248 Ramachandran restraints generated. 3624 Oldfield, 0 Emsley, 3624 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7248 Ramachandran restraints generated. 3624 Oldfield, 0 Emsley, 3624 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1307 residues out of total 3024 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 99 poor density : 1208 time to evaluate : 1.075 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: symmetry clash 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: symmetry clash 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: symmetry clash 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: symmetry clash REVERT: A 19 GLN cc_start: 0.7830 (tm-30) cc_final: 0.7590 (tp40) REVERT: A 30 TYR cc_start: 0.7293 (m-80) cc_final: 0.6313 (m-80) REVERT: A 37 GLU cc_start: 0.7298 (mp0) cc_final: 0.6881 (mp0) REVERT: A 119 HIS cc_start: 0.6527 (m90) cc_final: 0.6163 (m-70) REVERT: A 123 GLU cc_start: 0.7268 (tp30) cc_final: 0.6755 (mm-30) REVERT: A 171 LEU cc_start: 0.8551 (mt) cc_final: 0.8208 (mt) REVERT: A 174 ARG cc_start: 0.8414 (mtm-85) cc_final: 0.7545 (mtp85) REVERT: A 175 LEU cc_start: 0.7969 (tp) cc_final: 0.7758 (tp) REVERT: A 178 GLU cc_start: 0.8118 (mt-10) cc_final: 0.7849 (mt-10) REVERT: B 16 ARG cc_start: 0.8096 (ttp80) cc_final: 0.7590 (ttp80) REVERT: B 27 LYS cc_start: 0.7323 (ptmt) cc_final: 0.7009 (ptmt) REVERT: B 59 ARG cc_start: 0.7986 (mmt180) cc_final: 0.7566 (mmt180) REVERT: B 111 CYS cc_start: 0.7461 (t) cc_final: 0.6685 (t) REVERT: B 117 GLU cc_start: 0.7548 (pt0) cc_final: 0.7030 (pt0) REVERT: C 12 SER cc_start: 0.8785 (p) cc_final: 0.8512 (p) REVERT: C 14 LYS cc_start: 0.8776 (mttm) cc_final: 0.8027 (mttm) REVERT: C 19 GLN cc_start: 0.8073 (mm-40) cc_final: 0.7694 (mm-40) REVERT: C 27 LYS cc_start: 0.8291 (OUTLIER) cc_final: 0.7979 (ptpp) REVERT: C 30 TYR cc_start: 0.7420 (m-80) cc_final: 0.6751 (m-80) REVERT: C 65 GLU cc_start: 0.6757 (tm-30) cc_final: 0.6033 (tm-30) REVERT: C 89 LEU cc_start: 0.7084 (mm) cc_final: 0.6838 (tt) REVERT: C 164 SER cc_start: 0.8268 (p) cc_final: 0.7927 (t) REVERT: C 168 LEU cc_start: 0.8455 (tp) cc_final: 0.8202 (tp) REVERT: C 174 ARG cc_start: 0.7994 (mtp180) cc_final: 0.7350 (mtp180) REVERT: C 176 ARG cc_start: 0.8757 (ptp-110) cc_final: 0.8205 (ttm-80) REVERT: D 50 LYS cc_start: 0.8311 (mmpt) cc_final: 0.8073 (ptmt) REVERT: D 56 ARG cc_start: 0.8012 (mmt180) cc_final: 0.7554 (mmt180) REVERT: D 69 LEU cc_start: 0.7273 (tp) cc_final: 0.7038 (tp) REVERT: D 176 ARG cc_start: 0.8386 (mtp180) cc_final: 0.7953 (mtt-85) REVERT: E 15 LYS cc_start: 0.8602 (tmtp) cc_final: 0.8002 (tmtp) REVERT: E 16 GLU cc_start: 0.7970 (mm-30) cc_final: 0.7076 (mm-30) REVERT: E 46 LEU cc_start: 0.8501 (mt) cc_final: 0.8298 (mm) REVERT: E 53 GLU cc_start: 0.7455 (tm-30) cc_final: 0.7224 (tm-30) REVERT: E 62 ARG cc_start: 0.6729 (mmp80) cc_final: 0.6528 (mmp80) REVERT: E 89 PHE cc_start: 0.7984 (m-10) cc_final: 0.7620 (m-80) REVERT: E 133 LYS cc_start: 0.6832 (mtmm) cc_final: 0.6318 (mtmm) REVERT: E 145 GLN cc_start: 0.8097 (tp40) cc_final: 0.7583 (mm-40) REVERT: E 158 PHE cc_start: 0.7907 (t80) cc_final: 0.7653 (t80) REVERT: E 178 ARG cc_start: 0.8182 (mmm-85) cc_final: 0.7964 (mmm-85) REVERT: E 179 MET cc_start: 0.7179 (OUTLIER) cc_final: 0.6522 (mmt) REVERT: E 217 MET cc_start: 0.7503 (mtt) cc_final: 0.6972 (mmm) REVERT: E 225 GLN cc_start: 0.7821 (mt0) cc_final: 0.7466 (mt0) REVERT: E 235 ARG cc_start: 0.6864 (tpp80) cc_final: 0.6351 (tpp80) REVERT: E 253 GLN cc_start: 0.8154 (mm-40) cc_final: 0.7813 (mm-40) REVERT: E 264 THR cc_start: 0.8345 (t) cc_final: 0.7954 (p) REVERT: E 272 ARG cc_start: 0.7891 (mmp80) cc_final: 0.7223 (mmp80) REVERT: E 275 GLU cc_start: 0.7682 (mt-10) cc_final: 0.7246 (mt-10) REVERT: F 12 LEU cc_start: 0.8391 (mm) cc_final: 0.8103 (mp) REVERT: F 26 LEU cc_start: 0.7670 (mt) cc_final: 0.7193 (mp) REVERT: F 32 LYS cc_start: 0.8003 (tppt) cc_final: 0.7489 (tppt) REVERT: F 38 ASP cc_start: 0.8670 (p0) cc_final: 0.8328 (p0) REVERT: F 52 PHE cc_start: 0.6512 (m-80) cc_final: 0.6262 (m-80) REVERT: F 66 LEU cc_start: 0.8924 (mt) cc_final: 0.8517 (mp) REVERT: F 68 GLU cc_start: 0.7185 (tp30) cc_final: 0.6689 (tp30) REVERT: F 70 PHE cc_start: 0.8727 (m-80) cc_final: 0.8363 (m-80) REVERT: F 77 ARG cc_start: 0.7960 (mpt90) cc_final: 0.7423 (mpt90) REVERT: F 80 ARG cc_start: 0.7670 (tpt90) cc_final: 0.7331 (tpt90) REVERT: F 91 SER cc_start: 0.8316 (t) cc_final: 0.7658 (p) REVERT: F 95 GLU cc_start: 0.8044 (mt-10) cc_final: 0.7837 (mt-10) REVERT: F 133 LYS cc_start: 0.7441 (mttt) cc_final: 0.7154 (mtpp) REVERT: F 171 THR cc_start: 0.7923 (m) cc_final: 0.6951 (p) REVERT: F 172 GLU cc_start: 0.7647 (tt0) cc_final: 0.7280 (tt0) REVERT: F 179 MET cc_start: 0.7156 (mmm) cc_final: 0.6791 (mmm) REVERT: F 188 ARG cc_start: 0.8567 (mmm-85) cc_final: 0.8252 (tpt90) REVERT: F 205 PHE cc_start: 0.7457 (m-80) cc_final: 0.7178 (t80) REVERT: F 217 MET cc_start: 0.7225 (OUTLIER) cc_final: 0.6936 (mtt) REVERT: F 218 ASN cc_start: 0.7849 (t0) cc_final: 0.7392 (t0) REVERT: G 2 THR cc_start: 0.7956 (p) cc_final: 0.7730 (t) REVERT: G 13 LEU cc_start: 0.8562 (mt) cc_final: 0.8201 (mt) REVERT: G 66 LEU cc_start: 0.8489 (OUTLIER) cc_final: 0.8152 (mm) REVERT: G 77 ARG cc_start: 0.8101 (mpt90) cc_final: 0.7715 (mpt90) REVERT: G 88 SER cc_start: 0.8580 (OUTLIER) cc_final: 0.8353 (p) REVERT: G 103 MET cc_start: 0.6494 (mtp) cc_final: 0.6136 (mtp) REVERT: G 113 ARG cc_start: 0.6993 (mtt180) cc_final: 0.6713 (mtt180) REVERT: G 122 LYS cc_start: 0.8066 (pttt) cc_final: 0.7505 (pttt) REVERT: G 175 TYR cc_start: 0.7503 (OUTLIER) cc_final: 0.6751 (t80) REVERT: G 222 GLU cc_start: 0.7692 (mm-30) cc_final: 0.7258 (mm-30) REVERT: G 235 ARG cc_start: 0.7299 (mmm160) cc_final: 0.6919 (mmm160) REVERT: G 275 GLU cc_start: 0.7006 (pp20) cc_final: 0.6593 (pp20) REVERT: H 15 LYS cc_start: 0.8472 (tmtp) cc_final: 0.7906 (tmtp) REVERT: H 21 ARG cc_start: 0.7754 (mmt90) cc_final: 0.6886 (mtt180) REVERT: H 65 GLN cc_start: 0.7803 (mp10) cc_final: 0.6765 (mp10) REVERT: H 68 GLU cc_start: 0.7153 (tp30) cc_final: 0.6435 (tp30) REVERT: H 122 LYS cc_start: 0.7999 (pttt) cc_final: 0.7705 (pttt) REVERT: H 188 ARG cc_start: 0.7604 (tpp80) cc_final: 0.7144 (tpp80) REVERT: H 221 ARG cc_start: 0.7904 (ttm-80) cc_final: 0.7296 (ttm-80) REVERT: H 223 GLN cc_start: 0.8030 (tt0) cc_final: 0.7754 (tp40) REVERT: H 235 ARG cc_start: 0.7359 (tpp-160) cc_final: 0.6644 (tpp80) REVERT: H 237 PHE cc_start: 0.7896 (m-80) cc_final: 0.7621 (m-80) REVERT: H 245 LEU cc_start: 0.7580 (mt) cc_final: 0.7320 (mt) REVERT: H 253 GLN cc_start: 0.7923 (mm-40) cc_final: 0.7579 (mp10) REVERT: H 275 GLU cc_start: 0.7359 (pt0) cc_final: 0.6900 (pt0) REVERT: Q 56 ARG cc_start: 0.7560 (mtt-85) cc_final: 0.7169 (mtt-85) REVERT: Q 101 GLN cc_start: 0.8377 (pm20) cc_final: 0.7615 (tp40) REVERT: Q 117 GLU cc_start: 0.7136 (pt0) cc_final: 0.6674 (pt0) REVERT: Q 141 TRP cc_start: 0.5921 (m-90) cc_final: 0.5611 (m100) REVERT: Q 161 GLU cc_start: 0.7990 (tp30) cc_final: 0.7360 (tp30) REVERT: Q 170 ARG cc_start: 0.7573 (ptp90) cc_final: 0.7219 (ptp90) REVERT: Q 174 ARG cc_start: 0.8352 (mtp180) cc_final: 0.7756 (mtp180) REVERT: R 61 PRO cc_start: 0.7673 (Cg_exo) cc_final: 0.7406 (Cg_endo) REVERT: R 118 ARG cc_start: 0.7417 (ttp-170) cc_final: 0.7112 (ttp-170) REVERT: R 162 LYS cc_start: 0.8286 (ttpm) cc_final: 0.7556 (tttm) REVERT: R 174 ARG cc_start: 0.8193 (mtp85) cc_final: 0.7980 (mtp85) REVERT: S 5 TRP cc_start: 0.6846 (m100) cc_final: 0.6216 (m100) REVERT: S 52 ILE cc_start: 0.7830 (mm) cc_final: 0.7622 (mm) REVERT: S 59 ARG cc_start: 0.7217 (mmt180) cc_final: 0.6650 (mmt180) REVERT: S 71 ILE cc_start: 0.7370 (mm) cc_final: 0.7087 (mm) REVERT: S 107 ARG cc_start: 0.6394 (mtm-85) cc_final: 0.6187 (mtm-85) REVERT: S 118 ARG cc_start: 0.8214 (ptp-170) cc_final: 0.7967 (ptp-170) REVERT: S 176 ARG cc_start: 0.8833 (mtm110) cc_final: 0.8419 (mtm110) REVERT: T 19 GLN cc_start: 0.8068 (mm-40) cc_final: 0.7567 (mm-40) REVERT: T 30 TYR cc_start: 0.7822 (m-80) cc_final: 0.6977 (m-80) REVERT: T 42 ASP cc_start: 0.7633 (t0) cc_final: 0.6974 (t0) REVERT: T 45 THR cc_start: 0.8409 (m) cc_final: 0.7968 (p) REVERT: T 59 ARG cc_start: 0.7536 (tpt-90) cc_final: 0.7073 (tpt-90) REVERT: T 170 ARG cc_start: 0.7588 (ptp-170) cc_final: 0.6971 (ptp-170) REVERT: T 176 ARG cc_start: 0.8622 (ptp-110) cc_final: 0.8046 (ttp-110) REVERT: U 21 ARG cc_start: 0.7827 (mmt90) cc_final: 0.7103 (mtt180) REVERT: U 23 ILE cc_start: 0.8106 (mt) cc_final: 0.7850 (mm) REVERT: U 32 LYS cc_start: 0.8366 (ttpp) cc_final: 0.8111 (ttpp) REVERT: U 35 LYS cc_start: 0.8665 (mmtm) cc_final: 0.8379 (mttm) REVERT: U 59 MET cc_start: 0.7901 (tpt) cc_final: 0.7268 (tpp) REVERT: U 60 HIS cc_start: 0.6838 (m90) cc_final: 0.6221 (m90) REVERT: U 68 GLU cc_start: 0.7567 (tp30) cc_final: 0.6798 (tp30) REVERT: U 103 MET cc_start: 0.7079 (mtt) cc_final: 0.6662 (mtt) REVERT: U 143 ASP cc_start: 0.8054 (m-30) cc_final: 0.7733 (m-30) REVERT: U 144 PHE cc_start: 0.7982 (m-80) cc_final: 0.7737 (m-80) REVERT: U 148 ARG cc_start: 0.6996 (ptp90) cc_final: 0.6572 (ptp90) REVERT: U 164 GLN cc_start: 0.6738 (mt0) cc_final: 0.6399 (mm110) REVERT: U 170 LEU cc_start: 0.7393 (OUTLIER) cc_final: 0.6875 (mm) REVERT: U 187 GLN cc_start: 0.8051 (mm-40) cc_final: 0.7769 (mm-40) REVERT: U 210 ILE cc_start: 0.8451 (tp) cc_final: 0.8049 (tp) REVERT: U 222 GLU cc_start: 0.7928 (mm-30) cc_final: 0.7570 (mm-30) REVERT: U 223 GLN cc_start: 0.7962 (tt0) cc_final: 0.7401 (tt0) REVERT: U 235 ARG cc_start: 0.7775 (tpp-160) cc_final: 0.7283 (ttm-80) REVERT: U 253 GLN cc_start: 0.7898 (mm-40) cc_final: 0.7670 (mm-40) REVERT: V 15 LYS cc_start: 0.8189 (tmtp) cc_final: 0.7533 (tmtp) REVERT: V 16 GLU cc_start: 0.7895 (mm-30) cc_final: 0.7402 (mm-30) REVERT: V 62 ARG cc_start: 0.7325 (mmt90) cc_final: 0.7038 (ttm110) REVERT: V 68 GLU cc_start: 0.7972 (tp30) cc_final: 0.7269 (tp30) REVERT: V 70 PHE cc_start: 0.8470 (t80) cc_final: 0.8161 (t80) REVERT: V 77 ARG cc_start: 0.8035 (OUTLIER) cc_final: 0.7615 (tpt170) REVERT: V 101 SER cc_start: 0.8233 (t) cc_final: 0.7861 (m) REVERT: V 105 ARG cc_start: 0.7565 (mtt180) cc_final: 0.6872 (ttm-80) REVERT: V 113 ARG cc_start: 0.7543 (mtt180) cc_final: 0.7180 (mtt180) REVERT: V 125 GLU cc_start: 0.7472 (mp0) cc_final: 0.7005 (mp0) REVERT: V 148 ARG cc_start: 0.7380 (ptp90) cc_final: 0.6850 (ptp90) REVERT: V 150 ARG cc_start: 0.6897 (mtm180) cc_final: 0.6454 (mmm160) REVERT: V 158 PHE cc_start: 0.8070 (t80) cc_final: 0.7644 (t80) REVERT: V 192 ASP cc_start: 0.7402 (m-30) cc_final: 0.6625 (m-30) REVERT: V 222 GLU cc_start: 0.7784 (mm-30) cc_final: 0.7151 (mm-30) REVERT: V 231 SER cc_start: 0.8542 (t) cc_final: 0.8222 (p) REVERT: V 252 GLN cc_start: 0.8091 (tm-30) cc_final: 0.7871 (tm-30) REVERT: V 269 SER cc_start: 0.7521 (t) cc_final: 0.6988 (t) REVERT: W 15 LYS cc_start: 0.8384 (tmtp) cc_final: 0.7866 (tmtp) REVERT: W 26 LEU cc_start: 0.7930 (mt) cc_final: 0.7576 (mp) REVERT: W 32 LYS cc_start: 0.8064 (tppt) cc_final: 0.7648 (tppt) REVERT: W 46 LEU cc_start: 0.8415 (mt) cc_final: 0.8079 (mt) REVERT: W 55 GLU cc_start: 0.7745 (mt-10) cc_final: 0.7485 (mt-10) REVERT: W 59 MET cc_start: 0.7919 (ttp) cc_final: 0.7555 (tmm) REVERT: W 62 ARG cc_start: 0.7144 (mtp85) cc_final: 0.6747 (mtp85) REVERT: W 63 PHE cc_start: 0.8411 (t80) cc_final: 0.8141 (t80) REVERT: W 64 GLU cc_start: 0.7654 (pm20) cc_final: 0.7287 (pm20) REVERT: W 85 MET cc_start: 0.8208 (mtm) cc_final: 0.7961 (mtp) REVERT: W 86 SER cc_start: 0.8765 (m) cc_final: 0.8253 (p) REVERT: W 88 SER cc_start: 0.8412 (m) cc_final: 0.8043 (p) REVERT: W 91 SER cc_start: 0.8453 (t) cc_final: 0.8054 (p) REVERT: W 100 LYS cc_start: 0.8551 (mtmm) cc_final: 0.8250 (mtmm) REVERT: W 105 ARG cc_start: 0.7732 (ttm-80) cc_final: 0.7293 (ttm-80) REVERT: W 107 LEU cc_start: 0.8166 (tp) cc_final: 0.7936 (tt) REVERT: W 125 GLU cc_start: 0.7159 (OUTLIER) cc_final: 0.6815 (mp0) REVERT: W 129 ARG cc_start: 0.7021 (ttm110) cc_final: 0.6587 (mtt-85) REVERT: W 157 LYS cc_start: 0.8324 (mmtt) cc_final: 0.8020 (mmmt) REVERT: W 159 HIS cc_start: 0.8503 (OUTLIER) cc_final: 0.7765 (t-90) REVERT: W 166 ASP cc_start: 0.7462 (p0) cc_final: 0.7188 (p0) REVERT: W 179 MET cc_start: 0.6991 (mmm) cc_final: 0.6180 (mmm) REVERT: W 187 GLN cc_start: 0.8377 (mm-40) cc_final: 0.8026 (mm-40) REVERT: W 188 ARG cc_start: 0.8311 (tpp80) cc_final: 0.7593 (tpp80) REVERT: W 192 ASP cc_start: 0.7607 (m-30) cc_final: 0.6831 (m-30) REVERT: W 212 TYR cc_start: 0.7232 (t80) cc_final: 0.6654 (t80) REVERT: W 221 ARG cc_start: 0.7905 (mtt90) cc_final: 0.7300 (mtt90) REVERT: W 245 LEU cc_start: 0.8496 (mt) cc_final: 0.7785 (mt) REVERT: W 260 GLN cc_start: 0.7486 (tp40) cc_final: 0.6733 (tp40) REVERT: X 15 LYS cc_start: 0.8506 (tmtp) cc_final: 0.8002 (tppt) REVERT: X 16 GLU cc_start: 0.7945 (mm-30) cc_final: 0.7229 (mm-30) REVERT: X 42 LEU cc_start: 0.8546 (mm) cc_final: 0.8200 (mp) REVERT: X 46 LEU cc_start: 0.8057 (mt) cc_final: 0.7715 (mp) REVERT: X 55 GLU cc_start: 0.7579 (mp0) cc_final: 0.7366 (mp0) REVERT: X 65 GLN cc_start: 0.7362 (mt0) cc_final: 0.6988 (mp10) REVERT: X 155 VAL cc_start: 0.8044 (t) cc_final: 0.7752 (p) REVERT: X 168 ILE cc_start: 0.8307 (mm) cc_final: 0.8045 (mm) REVERT: X 170 LEU cc_start: 0.7740 (OUTLIER) cc_final: 0.7478 (tp) REVERT: X 176 PHE cc_start: 0.8421 (m-10) cc_final: 0.8070 (m-80) REVERT: X 179 MET cc_start: 0.7143 (mmm) cc_final: 0.6343 (mmm) REVERT: X 182 ASP cc_start: 0.7291 (m-30) cc_final: 0.6985 (m-30) REVERT: X 218 ASN cc_start: 0.7551 (t0) cc_final: 0.7299 (t0) REVERT: X 225 GLN cc_start: 0.7706 (pt0) cc_final: 0.7449 (pt0) REVERT: X 247 GLN cc_start: 0.7646 (mm-40) cc_final: 0.6672 (mm110) REVERT: X 249 ASP cc_start: 0.7883 (OUTLIER) cc_final: 0.7525 (t0) REVERT: X 252 GLN cc_start: 0.7605 (OUTLIER) cc_final: 0.7402 (pp30) REVERT: X 264 THR cc_start: 0.8360 (t) cc_final: 0.8077 (p) outliers start: 99 outliers final: 78 residues processed: 1231 average time/residue: 0.2239 time to fit residues: 406.5054 Evaluate side-chains 1285 residues out of total 3024 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 91 poor density : 1194 time to evaluate : 1.082 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 32 THR Chi-restraints excluded: chain B residue 21 VAL Chi-restraints excluded: chain B residue 35 VAL Chi-restraints excluded: chain B residue 103 THR Chi-restraints excluded: chain C residue 27 LYS Chi-restraints excluded: chain C residue 120 VAL Chi-restraints excluded: chain C residue 153 THR Chi-restraints excluded: chain C residue 159 LEU Chi-restraints excluded: chain D residue 63 ILE Chi-restraints excluded: chain D residue 96 VAL Chi-restraints excluded: chain E residue 49 THR Chi-restraints excluded: chain E residue 84 GLU Chi-restraints excluded: chain E residue 97 LEU Chi-restraints excluded: chain E residue 179 MET Chi-restraints excluded: chain E residue 240 THR Chi-restraints excluded: chain E residue 259 ILE Chi-restraints excluded: chain F residue 93 GLU Chi-restraints excluded: chain F residue 125 GLU Chi-restraints excluded: chain F residue 154 GLU Chi-restraints excluded: chain F residue 159 HIS Chi-restraints excluded: chain F residue 170 LEU Chi-restraints excluded: chain F residue 217 MET Chi-restraints excluded: chain G residue 3 THR Chi-restraints excluded: chain G residue 5 THR Chi-restraints excluded: chain G residue 66 LEU Chi-restraints excluded: chain G residue 70 PHE Chi-restraints excluded: chain G residue 88 SER Chi-restraints excluded: chain G residue 114 THR Chi-restraints excluded: chain G residue 115 ILE Chi-restraints excluded: chain G residue 117 THR Chi-restraints excluded: chain G residue 119 ASN Chi-restraints excluded: chain G residue 170 LEU Chi-restraints excluded: chain G residue 175 TYR Chi-restraints excluded: chain G residue 208 THR Chi-restraints excluded: chain G residue 209 ASN Chi-restraints excluded: chain H residue 14 LYS Chi-restraints excluded: chain H residue 64 GLU Chi-restraints excluded: chain H residue 119 ASN Chi-restraints excluded: chain H residue 193 LEU Chi-restraints excluded: chain H residue 210 ILE Chi-restraints excluded: chain Q residue 43 LEU Chi-restraints excluded: chain R residue 32 THR Chi-restraints excluded: chain R residue 128 GLU Chi-restraints excluded: chain S residue 60 VAL Chi-restraints excluded: chain T residue 28 LEU Chi-restraints excluded: chain T residue 36 THR Chi-restraints excluded: chain T residue 41 VAL Chi-restraints excluded: chain T residue 120 VAL Chi-restraints excluded: chain T residue 164 SER Chi-restraints excluded: chain U residue 18 ARG Chi-restraints excluded: chain U residue 64 GLU Chi-restraints excluded: chain U residue 117 THR Chi-restraints excluded: chain U residue 119 ASN Chi-restraints excluded: chain U residue 120 TYR Chi-restraints excluded: chain U residue 134 GLN Chi-restraints excluded: chain U residue 150 ARG Chi-restraints excluded: chain U residue 170 LEU Chi-restraints excluded: chain U residue 177 GLN Chi-restraints excluded: chain U residue 252 GLN Chi-restraints excluded: chain V residue 4 LEU Chi-restraints excluded: chain V residue 5 THR Chi-restraints excluded: chain V residue 77 ARG Chi-restraints excluded: chain V residue 84 GLU Chi-restraints excluded: chain V residue 118 THR Chi-restraints excluded: chain V residue 119 ASN Chi-restraints excluded: chain V residue 120 TYR Chi-restraints excluded: chain V residue 170 LEU Chi-restraints excluded: chain V residue 171 THR Chi-restraints excluded: chain W residue 6 LEU Chi-restraints excluded: chain W residue 38 ASP Chi-restraints excluded: chain W residue 77 ARG Chi-restraints excluded: chain W residue 122 LYS Chi-restraints excluded: chain W residue 125 GLU Chi-restraints excluded: chain W residue 134 GLN Chi-restraints excluded: chain W residue 154 GLU Chi-restraints excluded: chain W residue 159 HIS Chi-restraints excluded: chain W residue 170 LEU Chi-restraints excluded: chain W residue 177 GLN Chi-restraints excluded: chain W residue 225 GLN Chi-restraints excluded: chain W residue 252 GLN Chi-restraints excluded: chain W residue 273 LEU Chi-restraints excluded: chain X residue 50 LEU Chi-restraints excluded: chain X residue 79 GLN Chi-restraints excluded: chain X residue 103 MET Chi-restraints excluded: chain X residue 117 THR Chi-restraints excluded: chain X residue 170 LEU Chi-restraints excluded: chain X residue 177 GLN Chi-restraints excluded: chain X residue 210 ILE Chi-restraints excluded: chain X residue 240 THR Chi-restraints excluded: chain X residue 249 ASP Chi-restraints excluded: chain X residue 252 GLN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 360 random chunks: chunk 356 optimal weight: 3.9990 chunk 267 optimal weight: 0.5980 chunk 109 optimal weight: 0.9980 chunk 142 optimal weight: 0.1980 chunk 294 optimal weight: 0.2980 chunk 234 optimal weight: 4.9990 chunk 194 optimal weight: 1.9990 chunk 293 optimal weight: 4.9990 chunk 129 optimal weight: 0.0970 chunk 218 optimal weight: 8.9990 chunk 350 optimal weight: 0.6980 overall best weight: 0.3778 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 150 GLN ** E 65 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 145 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 164 GLN ** E 252 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 123 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 41 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 123 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 252 GLN ** H 225 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 19 GLN ** R 19 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 20 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** R 119 HIS ** R 172 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 140 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** W 241 HIS X 123 HIS ** X 252 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3888 r_free = 0.3888 target = 0.128519 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3597 r_free = 0.3597 target = 0.109344 restraints weight = 62328.274| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3653 r_free = 0.3653 target = 0.113160 restraints weight = 32331.466| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3689 r_free = 0.3689 target = 0.115655 restraints weight = 19415.087| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.3714 r_free = 0.3714 target = 0.117317 restraints weight = 12916.717| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 39)----------------| | r_work = 0.3731 r_free = 0.3731 target = 0.118470 restraints weight = 9378.578| |-----------------------------------------------------------------------------| r_work (final): 0.3727 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7177 moved from start: 0.9346 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 29416 Z= 0.125 Angle : 0.715 10.354 39856 Z= 0.357 Chirality : 0.046 0.247 4432 Planarity : 0.005 0.075 5200 Dihedral : 4.411 24.041 4024 Min Nonbonded Distance : 2.476 Molprobity Statistics. All-atom Clashscore : 13.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.15 % Favored : 96.85 % Rotamer: Outliers : 3.32 % Allowed : 28.81 % Favored : 67.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.55 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.65 (0.14), residues: 3624 helix: 0.51 (0.13), residues: 1616 sheet: -0.36 (0.20), residues: 600 loop : -1.51 (0.16), residues: 1408 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG S 176 TYR 0.031 0.002 TYR H 212 PHE 0.035 0.001 PHE X 57 TRP 0.076 0.002 TRP T 86 HIS 0.011 0.001 HIS D 140 Details of bonding type rmsd covalent geometry : bond 0.00287 (29416) covalent geometry : angle 0.71474 (39856) hydrogen bonds : bond 0.03174 ( 1252) hydrogen bonds : angle 4.87406 ( 3636) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7438.82 seconds wall clock time: 128 minutes 2.39 seconds (7682.39 seconds total)