Starting phenix.real_space_refine on Sun Mar 17 13:10:03 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7d0a_30528/03_2024/7d0a_30528_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7d0a_30528/03_2024/7d0a_30528.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7d0a_30528/03_2024/7d0a_30528.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7d0a_30528/03_2024/7d0a_30528.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7d0a_30528/03_2024/7d0a_30528_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7d0a_30528/03_2024/7d0a_30528_updated.pdb" } resolution = 4.0 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.004 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians V 2 8.30 5 P 4 5.49 5 S 88 5.16 5 C 11342 2.51 5 N 2988 2.21 5 O 3380 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 116": "OE1" <-> "OE2" Residue "A GLU 130": "OE1" <-> "OE2" Residue "A GLU 226": "OE1" <-> "OE2" Residue "B ARG 26": "NH1" <-> "NH2" Residue "B GLU 84": "OE1" <-> "OE2" Residue "B GLU 109": "OE1" <-> "OE2" Residue "B GLU 123": "OE1" <-> "OE2" Residue "B GLU 128": "OE1" <-> "OE2" Residue "B GLU 135": "OE1" <-> "OE2" Residue "B GLU 143": "OE1" <-> "OE2" Residue "B GLU 258": "OE1" <-> "OE2" Residue "B GLU 270": "OE1" <-> "OE2" Residue "B ARG 272": "NH1" <-> "NH2" Residue "C GLU 8": "OE1" <-> "OE2" Residue "C GLU 47": "OE1" <-> "OE2" Residue "D ARG 9": "NH1" <-> "NH2" Residue "D GLU 116": "OE1" <-> "OE2" Residue "D GLU 130": "OE1" <-> "OE2" Residue "D GLU 226": "OE1" <-> "OE2" Residue "E ARG 26": "NH1" <-> "NH2" Residue "E GLU 84": "OE1" <-> "OE2" Residue "E GLU 109": "OE1" <-> "OE2" Residue "E GLU 123": "OE1" <-> "OE2" Residue "E GLU 128": "OE1" <-> "OE2" Residue "E GLU 135": "OE1" <-> "OE2" Residue "E GLU 143": "OE1" <-> "OE2" Residue "E TYR 221": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E GLU 258": "OE1" <-> "OE2" Residue "E GLU 270": "OE1" <-> "OE2" Residue "E ARG 272": "NH1" <-> "NH2" Residue "F GLU 8": "OE1" <-> "OE2" Residue "F GLU 47": "OE1" <-> "OE2" Residue "G ARG 4": "NH1" <-> "NH2" Residue "G PHE 46": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H ARG 4": "NH1" <-> "NH2" Residue "H GLU 7": "OE1" <-> "OE2" Residue "H ASP 47": "OD1" <-> "OD2" Residue "H GLU 96": "OE1" <-> "OE2" Residue "H GLU 100": "OE1" <-> "OE2" Residue "I ARG 4": "NH1" <-> "NH2" Residue "I ASP 38": "OD1" <-> "OD2" Residue "I TYR 40": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I ARG 78": "NH1" <-> "NH2" Residue "I GLU 186": "OE1" <-> "OE2" Residue "J ARG 4": "NH1" <-> "NH2" Residue "J ARG 78": "NH1" <-> "NH2" Residue "J GLU 100": "OE1" <-> "OE2" Residue "J GLU 142": "OE1" <-> "OE2" Residue "J TYR 145": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J GLU 186": "OE1" <-> "OE2" Residue "K ARG 4": "NH1" <-> "NH2" Residue "K GLU 186": "OE1" <-> "OE2" Residue "L ARG 4": "NH1" <-> "NH2" Residue "L GLU 7": "OE1" <-> "OE2" Residue "L PHE 84": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L GLU 156": "OE1" <-> "OE2" Time to flip residues: 0.06s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 17804 Number of models: 1 Model: "" Number of chains: 14 Chain: "A" Number of atoms: 1902 Number of conformers: 1 Conformer: "" Number of residues, atoms: 256, 1902 Classifications: {'peptide': 256} Link IDs: {'PTRANS': 7, 'TRANS': 248} Chain: "B" Number of atoms: 2032 Number of conformers: 1 Conformer: "" Number of residues, atoms: 263, 2032 Classifications: {'peptide': 263} Link IDs: {'PTRANS': 11, 'TRANS': 251} Chain: "C" Number of atoms: 763 Number of conformers: 1 Conformer: "" Number of residues, atoms: 95, 763 Classifications: {'peptide': 95} Link IDs: {'PTRANS': 3, 'TRANS': 91} Chain: "D" Number of atoms: 1902 Number of conformers: 1 Conformer: "" Number of residues, atoms: 256, 1902 Classifications: {'peptide': 256} Link IDs: {'PTRANS': 7, 'TRANS': 248} Chain: "E" Number of atoms: 2032 Number of conformers: 1 Conformer: "" Number of residues, atoms: 263, 2032 Classifications: {'peptide': 263} Link IDs: {'PTRANS': 11, 'TRANS': 251} Chain: "F" Number of atoms: 763 Number of conformers: 1 Conformer: "" Number of residues, atoms: 95, 763 Classifications: {'peptide': 95} Link IDs: {'PTRANS': 3, 'TRANS': 91} Chain: "G" Number of atoms: 1391 Number of conformers: 1 Conformer: "" Number of residues, atoms: 191, 1391 Classifications: {'peptide': 191} Incomplete info: {'truncation_to_alanine': 20} Link IDs: {'PTRANS': 4, 'TRANS': 186} Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 72 Unresolved non-hydrogen angles: 92 Unresolved non-hydrogen dihedrals: 59 Unresolved non-hydrogen chiralities: 5 Planarities with less than four sites: {'TYR:plan': 2, 'GLU:plan': 2, 'ARG:plan': 1, 'GLN:plan1': 3, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 45 Chain: "H" Number of atoms: 1391 Number of conformers: 1 Conformer: "" Number of residues, atoms: 191, 1391 Classifications: {'peptide': 191} Incomplete info: {'truncation_to_alanine': 20} Link IDs: {'PTRANS': 4, 'TRANS': 186} Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 72 Unresolved non-hydrogen angles: 92 Unresolved non-hydrogen dihedrals: 59 Unresolved non-hydrogen chiralities: 5 Planarities with less than four sites: {'TYR:plan': 2, 'GLU:plan': 2, 'ARG:plan': 1, 'GLN:plan1': 3, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 45 Chain: "I" Number of atoms: 1391 Number of conformers: 1 Conformer: "" Number of residues, atoms: 191, 1391 Classifications: {'peptide': 191} Incomplete info: {'truncation_to_alanine': 20} Link IDs: {'PTRANS': 4, 'TRANS': 186} Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 72 Unresolved non-hydrogen angles: 92 Unresolved non-hydrogen dihedrals: 59 Unresolved non-hydrogen chiralities: 5 Planarities with less than four sites: {'TYR:plan': 2, 'GLU:plan': 2, 'ARG:plan': 1, 'GLN:plan1': 3, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 45 Chain: "J" Number of atoms: 1391 Number of conformers: 1 Conformer: "" Number of residues, atoms: 191, 1391 Classifications: {'peptide': 191} Incomplete info: {'truncation_to_alanine': 20} Link IDs: {'PTRANS': 4, 'TRANS': 186} Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 72 Unresolved non-hydrogen angles: 92 Unresolved non-hydrogen dihedrals: 59 Unresolved non-hydrogen chiralities: 5 Planarities with less than four sites: {'TYR:plan': 2, 'GLU:plan': 2, 'ARG:plan': 1, 'GLN:plan1': 3, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 45 Chain: "K" Number of atoms: 1391 Number of conformers: 1 Conformer: "" Number of residues, atoms: 191, 1391 Classifications: {'peptide': 191} Incomplete info: {'truncation_to_alanine': 20} Link IDs: {'PTRANS': 4, 'TRANS': 186} Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 72 Unresolved non-hydrogen angles: 92 Unresolved non-hydrogen dihedrals: 59 Unresolved non-hydrogen chiralities: 5 Planarities with less than four sites: {'TYR:plan': 2, 'GLU:plan': 2, 'ARG:plan': 1, 'GLN:plan1': 3, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 45 Chain: "L" Number of atoms: 1391 Number of conformers: 1 Conformer: "" Number of residues, atoms: 191, 1391 Classifications: {'peptide': 191} Incomplete info: {'truncation_to_alanine': 20} Link IDs: {'PTRANS': 4, 'TRANS': 186} Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 72 Unresolved non-hydrogen angles: 92 Unresolved non-hydrogen dihedrals: 59 Unresolved non-hydrogen chiralities: 5 Planarities with less than four sites: {'TYR:plan': 2, 'GLU:plan': 2, 'ARG:plan': 1, 'GLN:plan1': 3, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 45 Chain: "B" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {'ADP': 1, 'VO4': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "E" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {'ADP': 1, 'VO4': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 9.63, per 1000 atoms: 0.54 Number of scatterers: 17804 At special positions: 0 Unit cell: (134.788, 126.092, 153.267, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) V 2 22.97 S 88 16.00 P 4 15.00 O 3380 8.00 N 2988 7.00 C 11342 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 6.79 Conformation dependent library (CDL) restraints added in 3.5 seconds 4700 Ramachandran restraints generated. 2350 Oldfield, 0 Emsley, 2350 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4328 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 78 helices and 16 sheets defined 41.2% alpha, 9.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 3.21 Creating SS restraints... Processing helix chain 'A' and resid 2 through 6 Processing helix chain 'A' and resid 10 through 29 removed outlier: 3.930A pdb=" N GLN A 27 " --> pdb=" O LEU A 23 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N ILE A 29 " --> pdb=" O LEU A 25 " (cutoff:3.500A) Processing helix chain 'A' and resid 37 through 47 Processing helix chain 'A' and resid 49 through 77 removed outlier: 4.657A pdb=" N LEU A 54 " --> pdb=" O VAL A 50 " (cutoff:3.500A) removed outlier: 5.226A pdb=" N ILE A 55 " --> pdb=" O MET A 51 " (cutoff:3.500A) removed outlier: 3.970A pdb=" N ILE A 56 " --> pdb=" O SER A 52 " (cutoff:3.500A) removed outlier: 3.863A pdb=" N THR A 57 " --> pdb=" O LEU A 53 " (cutoff:3.500A) removed outlier: 4.506A pdb=" N VAL A 58 " --> pdb=" O LEU A 54 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N ILE A 63 " --> pdb=" O SER A 59 " (cutoff:3.500A) removed outlier: 4.022A pdb=" N GLY A 64 " --> pdb=" O GLY A 60 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N LEU A 65 " --> pdb=" O LEU A 61 " (cutoff:3.500A) removed outlier: 3.944A pdb=" N LEU A 69 " --> pdb=" O LEU A 65 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N GLN A 70 " --> pdb=" O VAL A 66 " (cutoff:3.500A) removed outlier: 4.009A pdb=" N GLY A 71 " --> pdb=" O LEU A 67 " (cutoff:3.500A) removed outlier: 4.745A pdb=" N TYR A 72 " --> pdb=" O GLY A 68 " (cutoff:3.500A) removed outlier: 4.529A pdb=" N SER A 73 " --> pdb=" O LEU A 69 " (cutoff:3.500A) removed outlier: 3.848A pdb=" N ILE A 74 " --> pdb=" O GLN A 70 " (cutoff:3.500A) removed outlier: 4.771A pdb=" N ASN A 77 " --> pdb=" O SER A 73 " (cutoff:3.500A) Processing helix chain 'A' and resid 82 through 112 removed outlier: 4.089A pdb=" N GLY A 85 " --> pdb=" O SER A 82 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N MET A 87 " --> pdb=" O LEU A 84 " (cutoff:3.500A) removed outlier: 4.069A pdb=" N VAL A 88 " --> pdb=" O GLY A 85 " (cutoff:3.500A) removed outlier: 4.052A pdb=" N LEU A 90 " --> pdb=" O MET A 87 " (cutoff:3.500A) removed outlier: 3.880A pdb=" N THR A 91 " --> pdb=" O VAL A 88 " (cutoff:3.500A) removed outlier: 4.419A pdb=" N LEU A 93 " --> pdb=" O LEU A 90 " (cutoff:3.500A) removed outlier: 4.305A pdb=" N ARG A 94 " --> pdb=" O THR A 91 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N GLU A 95 " --> pdb=" O LEU A 92 " (cutoff:3.500A) removed outlier: 5.314A pdb=" N LEU A 96 " --> pdb=" O LEU A 93 " (cutoff:3.500A) removed outlier: 6.470A pdb=" N ALA A 97 " --> pdb=" O ARG A 94 " (cutoff:3.500A) Proline residue: A 98 - end of helix removed outlier: 4.018A pdb=" N ALA A 101 " --> pdb=" O PRO A 98 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N LEU A 103 " --> pdb=" O VAL A 100 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N LEU A 104 " --> pdb=" O ALA A 101 " (cutoff:3.500A) removed outlier: 4.219A pdb=" N ALA A 106 " --> pdb=" O LEU A 103 " (cutoff:3.500A) removed outlier: 4.807A pdb=" N ALA A 109 " --> pdb=" O ALA A 106 " (cutoff:3.500A) removed outlier: 4.524A pdb=" N GLY A 110 " --> pdb=" O GLY A 107 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N ALA A 112 " --> pdb=" O ALA A 109 " (cutoff:3.500A) Processing helix chain 'A' and resid 115 through 122 removed outlier: 3.784A pdb=" N MET A 120 " --> pdb=" O GLU A 116 " (cutoff:3.500A) removed outlier: 3.827A pdb=" N GLN A 122 " --> pdb=" O GLY A 118 " (cutoff:3.500A) Processing helix chain 'A' and resid 125 through 132 Processing helix chain 'A' and resid 136 through 139 No H-bonds generated for 'chain 'A' and resid 136 through 139' Processing helix chain 'A' and resid 142 through 174 removed outlier: 3.663A pdb=" N ALA A 147 " --> pdb=" O PRO A 143 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N VAL A 150 " --> pdb=" O TRP A 146 " (cutoff:3.500A) removed outlier: 3.963A pdb=" N LEU A 152 " --> pdb=" O GLY A 148 " (cutoff:3.500A) Proline residue: A 153 - end of helix removed outlier: 3.838A pdb=" N VAL A 157 " --> pdb=" O PRO A 153 " (cutoff:3.500A) removed outlier: 4.383A pdb=" N ILE A 158 " --> pdb=" O MET A 154 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N GLY A 167 " --> pdb=" O GLY A 163 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N LEU A 169 " --> pdb=" O VAL A 165 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N VAL A 170 " --> pdb=" O GLY A 166 " (cutoff:3.500A) removed outlier: 3.736A pdb=" N ASP A 173 " --> pdb=" O LEU A 169 " (cutoff:3.500A) Processing helix chain 'A' and resid 179 through 189 removed outlier: 3.581A pdb=" N MET A 186 " --> pdb=" O PHE A 182 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N ASN A 188 " --> pdb=" O SER A 184 " (cutoff:3.500A) removed outlier: 3.832A pdb=" N ASN A 189 " --> pdb=" O GLY A 185 " (cutoff:3.500A) Processing helix chain 'A' and resid 192 through 219 removed outlier: 4.929A pdb=" N VAL A 197 " --> pdb=" O GLY A 193 " (cutoff:3.500A) removed outlier: 4.341A pdb=" N ASN A 198 " --> pdb=" O HIS A 194 " (cutoff:3.500A) removed outlier: 3.780A pdb=" N LYS A 202 " --> pdb=" O ASN A 198 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N SER A 203 " --> pdb=" O GLY A 199 " (cutoff:3.500A) removed outlier: 3.974A pdb=" N VAL A 205 " --> pdb=" O ILE A 201 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N LEU A 209 " --> pdb=" O VAL A 205 " (cutoff:3.500A) removed outlier: 3.800A pdb=" N CYS A 210 " --> pdb=" O PHE A 206 " (cutoff:3.500A) removed outlier: 3.815A pdb=" N ILE A 213 " --> pdb=" O LEU A 209 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N ALA A 214 " --> pdb=" O CYS A 210 " (cutoff:3.500A) removed outlier: 4.204A pdb=" N GLY A 218 " --> pdb=" O ALA A 214 " (cutoff:3.500A) Processing helix chain 'A' and resid 227 through 245 Processing helix chain 'A' and resid 247 through 254 removed outlier: 3.797A pdb=" N ALA A 252 " --> pdb=" O PHE A 248 " (cutoff:3.500A) Processing helix chain 'B' and resid 54 through 60 Processing helix chain 'B' and resid 82 through 91 removed outlier: 4.498A pdb=" N ARG B 91 " --> pdb=" O ALA B 87 " (cutoff:3.500A) Processing helix chain 'B' and resid 107 through 118 removed outlier: 3.593A pdb=" N VAL B 111 " --> pdb=" O VAL B 107 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N ALA B 112 " --> pdb=" O TYR B 108 " (cutoff:3.500A) Proline residue: B 114 - end of helix removed outlier: 3.579A pdb=" N HIS B 118 " --> pdb=" O PRO B 114 " (cutoff:3.500A) Processing helix chain 'B' and resid 123 through 135 removed outlier: 4.018A pdb=" N LEU B 134 " --> pdb=" O VAL B 130 " (cutoff:3.500A) removed outlier: 4.011A pdb=" N GLU B 135 " --> pdb=" O ALA B 131 " (cutoff:3.500A) Processing helix chain 'B' and resid 152 through 163 removed outlier: 3.620A pdb=" N ARG B 156 " --> pdb=" O GLY B 152 " (cutoff:3.500A) removed outlier: 3.940A pdb=" N ARG B 157 " --> pdb=" O GLY B 153 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N VAL B 158 " --> pdb=" O MET B 154 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N ARG B 162 " --> pdb=" O VAL B 158 " (cutoff:3.500A) Processing helix chain 'B' and resid 182 through 199 removed outlier: 3.504A pdb=" N GLY B 186 " --> pdb=" O PRO B 182 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N ARG B 193 " --> pdb=" O THR B 189 " (cutoff:3.500A) removed outlier: 3.897A pdb=" N LEU B 195 " --> pdb=" O LEU B 191 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N ARG B 196 " --> pdb=" O ILE B 192 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N ALA B 198 " --> pdb=" O SER B 194 " (cutoff:3.500A) Processing helix chain 'B' and resid 210 through 214 Processing helix chain 'B' and resid 234 through 239 removed outlier: 3.535A pdb=" N GLN B 238 " --> pdb=" O PRO B 234 " (cutoff:3.500A) Processing helix chain 'C' and resid 22 through 33 removed outlier: 3.723A pdb=" N ALA C 26 " --> pdb=" O GLN C 22 " (cutoff:3.500A) removed outlier: 3.781A pdb=" N ILE C 30 " --> pdb=" O ALA C 26 " (cutoff:3.500A) removed outlier: 3.960A pdb=" N ILE C 31 " --> pdb=" O GLY C 27 " (cutoff:3.500A) removed outlier: 4.248A pdb=" N LYS C 33 " --> pdb=" O ALA C 29 " (cutoff:3.500A) Processing helix chain 'C' and resid 55 through 61 removed outlier: 4.253A pdb=" N LEU C 61 " --> pdb=" O LEU C 57 " (cutoff:3.500A) Processing helix chain 'C' and resid 80 through 82 No H-bonds generated for 'chain 'C' and resid 80 through 82' Processing helix chain 'D' and resid 2 through 29 removed outlier: 3.931A pdb=" N GLN D 27 " --> pdb=" O LEU D 23 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N ILE D 29 " --> pdb=" O LEU D 25 " (cutoff:3.500A) Processing helix chain 'D' and resid 37 through 47 Processing helix chain 'D' and resid 49 through 77 removed outlier: 4.658A pdb=" N LEU D 54 " --> pdb=" O VAL D 50 " (cutoff:3.500A) removed outlier: 5.227A pdb=" N ILE D 55 " --> pdb=" O MET D 51 " (cutoff:3.500A) removed outlier: 3.970A pdb=" N ILE D 56 " --> pdb=" O SER D 52 " (cutoff:3.500A) removed outlier: 3.862A pdb=" N THR D 57 " --> pdb=" O LEU D 53 " (cutoff:3.500A) removed outlier: 4.506A pdb=" N VAL D 58 " --> pdb=" O LEU D 54 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N ILE D 63 " --> pdb=" O SER D 59 " (cutoff:3.500A) removed outlier: 4.023A pdb=" N GLY D 64 " --> pdb=" O GLY D 60 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N LEU D 65 " --> pdb=" O LEU D 61 " (cutoff:3.500A) removed outlier: 3.944A pdb=" N LEU D 69 " --> pdb=" O LEU D 65 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N GLN D 70 " --> pdb=" O VAL D 66 " (cutoff:3.500A) removed outlier: 4.008A pdb=" N GLY D 71 " --> pdb=" O LEU D 67 " (cutoff:3.500A) removed outlier: 4.745A pdb=" N TYR D 72 " --> pdb=" O GLY D 68 " (cutoff:3.500A) removed outlier: 4.528A pdb=" N SER D 73 " --> pdb=" O LEU D 69 " (cutoff:3.500A) removed outlier: 3.849A pdb=" N ILE D 74 " --> pdb=" O GLN D 70 " (cutoff:3.500A) removed outlier: 4.771A pdb=" N ASN D 77 " --> pdb=" O SER D 73 " (cutoff:3.500A) Processing helix chain 'D' and resid 82 through 112 removed outlier: 4.089A pdb=" N GLY D 85 " --> pdb=" O SER D 82 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N MET D 87 " --> pdb=" O LEU D 84 " (cutoff:3.500A) removed outlier: 4.070A pdb=" N VAL D 88 " --> pdb=" O GLY D 85 " (cutoff:3.500A) removed outlier: 4.051A pdb=" N LEU D 90 " --> pdb=" O MET D 87 " (cutoff:3.500A) removed outlier: 3.879A pdb=" N THR D 91 " --> pdb=" O VAL D 88 " (cutoff:3.500A) removed outlier: 4.418A pdb=" N LEU D 93 " --> pdb=" O LEU D 90 " (cutoff:3.500A) removed outlier: 4.305A pdb=" N ARG D 94 " --> pdb=" O THR D 91 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N GLU D 95 " --> pdb=" O LEU D 92 " (cutoff:3.500A) removed outlier: 5.314A pdb=" N LEU D 96 " --> pdb=" O LEU D 93 " (cutoff:3.500A) removed outlier: 6.470A pdb=" N ALA D 97 " --> pdb=" O ARG D 94 " (cutoff:3.500A) Proline residue: D 98 - end of helix removed outlier: 4.019A pdb=" N ALA D 101 " --> pdb=" O PRO D 98 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N LEU D 103 " --> pdb=" O VAL D 100 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N LEU D 104 " --> pdb=" O ALA D 101 " (cutoff:3.500A) removed outlier: 4.220A pdb=" N ALA D 106 " --> pdb=" O LEU D 103 " (cutoff:3.500A) removed outlier: 4.808A pdb=" N ALA D 109 " --> pdb=" O ALA D 106 " (cutoff:3.500A) removed outlier: 4.524A pdb=" N GLY D 110 " --> pdb=" O GLY D 107 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N ALA D 112 " --> pdb=" O ALA D 109 " (cutoff:3.500A) Processing helix chain 'D' and resid 115 through 122 removed outlier: 3.784A pdb=" N MET D 120 " --> pdb=" O GLU D 116 " (cutoff:3.500A) removed outlier: 3.828A pdb=" N GLN D 122 " --> pdb=" O GLY D 118 " (cutoff:3.500A) Processing helix chain 'D' and resid 127 through 132 Processing helix chain 'D' and resid 136 through 139 No H-bonds generated for 'chain 'D' and resid 136 through 139' Processing helix chain 'D' and resid 142 through 174 removed outlier: 3.663A pdb=" N ALA D 147 " --> pdb=" O PRO D 143 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N VAL D 150 " --> pdb=" O TRP D 146 " (cutoff:3.500A) removed outlier: 3.964A pdb=" N LEU D 152 " --> pdb=" O GLY D 148 " (cutoff:3.500A) Proline residue: D 153 - end of helix removed outlier: 3.838A pdb=" N VAL D 157 " --> pdb=" O PRO D 153 " (cutoff:3.500A) removed outlier: 4.380A pdb=" N ILE D 158 " --> pdb=" O MET D 154 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N GLY D 167 " --> pdb=" O GLY D 163 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N LEU D 169 " --> pdb=" O VAL D 165 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N VAL D 170 " --> pdb=" O GLY D 166 " (cutoff:3.500A) removed outlier: 3.736A pdb=" N ASP D 173 " --> pdb=" O LEU D 169 " (cutoff:3.500A) Processing helix chain 'D' and resid 179 through 189 removed outlier: 3.581A pdb=" N MET D 186 " --> pdb=" O PHE D 182 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N ASN D 188 " --> pdb=" O SER D 184 " (cutoff:3.500A) removed outlier: 3.832A pdb=" N ASN D 189 " --> pdb=" O GLY D 185 " (cutoff:3.500A) Processing helix chain 'D' and resid 192 through 219 removed outlier: 4.929A pdb=" N VAL D 197 " --> pdb=" O GLY D 193 " (cutoff:3.500A) removed outlier: 4.341A pdb=" N ASN D 198 " --> pdb=" O HIS D 194 " (cutoff:3.500A) removed outlier: 3.780A pdb=" N LYS D 202 " --> pdb=" O ASN D 198 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N SER D 203 " --> pdb=" O GLY D 199 " (cutoff:3.500A) removed outlier: 3.974A pdb=" N VAL D 205 " --> pdb=" O ILE D 201 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N LEU D 209 " --> pdb=" O VAL D 205 " (cutoff:3.500A) removed outlier: 3.800A pdb=" N CYS D 210 " --> pdb=" O PHE D 206 " (cutoff:3.500A) removed outlier: 3.815A pdb=" N ILE D 213 " --> pdb=" O LEU D 209 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N ALA D 214 " --> pdb=" O CYS D 210 " (cutoff:3.500A) removed outlier: 4.204A pdb=" N GLY D 218 " --> pdb=" O ALA D 214 " (cutoff:3.500A) Processing helix chain 'D' and resid 227 through 245 Processing helix chain 'D' and resid 247 through 254 removed outlier: 3.798A pdb=" N ALA D 252 " --> pdb=" O PHE D 248 " (cutoff:3.500A) Processing helix chain 'E' and resid 54 through 60 Processing helix chain 'E' and resid 82 through 91 removed outlier: 4.497A pdb=" N ARG E 91 " --> pdb=" O ALA E 87 " (cutoff:3.500A) Processing helix chain 'E' and resid 107 through 118 removed outlier: 3.593A pdb=" N VAL E 111 " --> pdb=" O VAL E 107 " (cutoff:3.500A) removed outlier: 3.756A pdb=" N ALA E 112 " --> pdb=" O TYR E 108 " (cutoff:3.500A) Proline residue: E 114 - end of helix removed outlier: 3.579A pdb=" N HIS E 118 " --> pdb=" O PRO E 114 " (cutoff:3.500A) Processing helix chain 'E' and resid 123 through 135 removed outlier: 4.018A pdb=" N LEU E 134 " --> pdb=" O VAL E 130 " (cutoff:3.500A) removed outlier: 4.010A pdb=" N GLU E 135 " --> pdb=" O ALA E 131 " (cutoff:3.500A) Processing helix chain 'E' and resid 152 through 163 removed outlier: 3.620A pdb=" N ARG E 156 " --> pdb=" O GLY E 152 " (cutoff:3.500A) removed outlier: 3.939A pdb=" N ARG E 157 " --> pdb=" O GLY E 153 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N VAL E 158 " --> pdb=" O MET E 154 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N ARG E 162 " --> pdb=" O VAL E 158 " (cutoff:3.500A) Processing helix chain 'E' and resid 182 through 199 removed outlier: 3.504A pdb=" N GLY E 186 " --> pdb=" O PRO E 182 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N ARG E 193 " --> pdb=" O THR E 189 " (cutoff:3.500A) removed outlier: 3.897A pdb=" N LEU E 195 " --> pdb=" O LEU E 191 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N ARG E 196 " --> pdb=" O ILE E 192 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N ALA E 198 " --> pdb=" O SER E 194 " (cutoff:3.500A) Processing helix chain 'E' and resid 210 through 214 Processing helix chain 'E' and resid 234 through 239 removed outlier: 3.537A pdb=" N GLN E 238 " --> pdb=" O PRO E 234 " (cutoff:3.500A) Processing helix chain 'E' and resid 246 through 249 No H-bonds generated for 'chain 'E' and resid 246 through 249' Processing helix chain 'F' and resid 22 through 33 removed outlier: 3.723A pdb=" N ALA F 26 " --> pdb=" O GLN F 22 " (cutoff:3.500A) removed outlier: 3.781A pdb=" N ILE F 30 " --> pdb=" O ALA F 26 " (cutoff:3.500A) removed outlier: 3.962A pdb=" N ILE F 31 " --> pdb=" O GLY F 27 " (cutoff:3.500A) removed outlier: 4.247A pdb=" N LYS F 33 " --> pdb=" O ALA F 29 " (cutoff:3.500A) Processing helix chain 'F' and resid 55 through 61 removed outlier: 4.252A pdb=" N LEU F 61 " --> pdb=" O LEU F 57 " (cutoff:3.500A) Processing helix chain 'F' and resid 80 through 82 No H-bonds generated for 'chain 'F' and resid 80 through 82' Processing helix chain 'G' and resid 6 through 9 No H-bonds generated for 'chain 'G' and resid 6 through 9' Processing helix chain 'G' and resid 11 through 25 removed outlier: 3.813A pdb=" N ILE G 15 " --> pdb=" O GLY G 11 " (cutoff:3.500A) removed outlier: 3.949A pdb=" N PHE G 22 " --> pdb=" O GLY G 18 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N LEU G 24 " --> pdb=" O ALA G 20 " (cutoff:3.500A) Processing helix chain 'G' and resid 95 through 106 removed outlier: 3.774A pdb=" N LYS G 103 " --> pdb=" O LYS G 99 " (cutoff:3.500A) removed outlier: 4.151A pdb=" N ASN G 104 " --> pdb=" O GLU G 100 " (cutoff:3.500A) Processing helix chain 'G' and resid 125 through 134 removed outlier: 4.972A pdb=" N LEU G 130 " --> pdb=" O MET G 126 " (cutoff:3.500A) Processing helix chain 'G' and resid 185 through 192 removed outlier: 3.757A pdb=" N ILE G 189 " --> pdb=" O LEU G 185 " (cutoff:3.500A) removed outlier: 4.354A pdb=" N SER G 190 " --> pdb=" O GLU G 186 " (cutoff:3.500A) Processing helix chain 'H' and resid 4 through 29 removed outlier: 4.089A pdb=" N GLY H 11 " --> pdb=" O GLU H 7 " (cutoff:3.500A) removed outlier: 3.806A pdb=" N VAL H 14 " --> pdb=" O VAL H 10 " (cutoff:3.500A) removed outlier: 3.865A pdb=" N ILE H 15 " --> pdb=" O GLY H 11 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N LEU H 21 " --> pdb=" O PHE H 17 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N ALA H 25 " --> pdb=" O LEU H 21 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N LYS H 27 " --> pdb=" O PHE H 23 " (cutoff:3.500A) Processing helix chain 'H' and resid 95 through 103 removed outlier: 3.532A pdb=" N LYS H 103 " --> pdb=" O LYS H 99 " (cutoff:3.500A) Processing helix chain 'H' and resid 105 through 109 removed outlier: 3.518A pdb=" N LEU H 109 " --> pdb=" O ALA H 105 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 105 through 109' Processing helix chain 'H' and resid 112 through 115 No H-bonds generated for 'chain 'H' and resid 112 through 115' Processing helix chain 'H' and resid 124 through 130 removed outlier: 3.984A pdb=" N GLN H 129 " --> pdb=" O THR H 125 " (cutoff:3.500A) removed outlier: 3.817A pdb=" N LEU H 130 " --> pdb=" O MET H 126 " (cutoff:3.500A) Processing helix chain 'H' and resid 186 through 190 Processing helix chain 'I' and resid 4 through 29 removed outlier: 3.786A pdb=" N GLY I 18 " --> pdb=" O VAL I 14 " (cutoff:3.500A) removed outlier: 3.926A pdb=" N PHE I 23 " --> pdb=" O ILE I 19 " (cutoff:3.500A) removed outlier: 3.885A pdb=" N LEU I 24 " --> pdb=" O ALA I 20 " (cutoff:3.500A) removed outlier: 4.269A pdb=" N VAL I 28 " --> pdb=" O LEU I 24 " (cutoff:3.500A) removed outlier: 4.187A pdb=" N SER I 29 " --> pdb=" O ALA I 25 " (cutoff:3.500A) Processing helix chain 'I' and resid 95 through 109 removed outlier: 4.309A pdb=" N LYS I 99 " --> pdb=" O ALA I 95 " (cutoff:3.500A) removed outlier: 4.057A pdb=" N ASN I 104 " --> pdb=" O GLU I 100 " (cutoff:3.500A) Processing helix chain 'I' and resid 124 through 132 removed outlier: 3.600A pdb=" N GLN I 129 " --> pdb=" O THR I 125 " (cutoff:3.500A) removed outlier: 4.360A pdb=" N LEU I 130 " --> pdb=" O MET I 126 " (cutoff:3.500A) removed outlier: 4.308A pdb=" N ILE I 131 " --> pdb=" O GLU I 127 " (cutoff:3.500A) Processing helix chain 'I' and resid 185 through 190 Processing helix chain 'J' and resid 4 through 9 Processing helix chain 'J' and resid 11 through 27 removed outlier: 3.720A pdb=" N LEU J 24 " --> pdb=" O ALA J 20 " (cutoff:3.500A) Processing helix chain 'J' and resid 95 through 109 removed outlier: 3.611A pdb=" N LYS J 103 " --> pdb=" O LYS J 99 " (cutoff:3.500A) removed outlier: 3.907A pdb=" N ASN J 104 " --> pdb=" O GLU J 100 " (cutoff:3.500A) Processing helix chain 'J' and resid 112 through 114 No H-bonds generated for 'chain 'J' and resid 112 through 114' Processing helix chain 'J' and resid 128 through 132 Processing helix chain 'J' and resid 185 through 192 removed outlier: 4.095A pdb=" N ILE J 189 " --> pdb=" O LEU J 185 " (cutoff:3.500A) removed outlier: 5.108A pdb=" N SER J 190 " --> pdb=" O GLU J 186 " (cutoff:3.500A) Processing helix chain 'K' and resid 4 through 28 removed outlier: 4.029A pdb=" N LEU K 8 " --> pdb=" O ARG K 4 " (cutoff:3.500A) removed outlier: 3.888A pdb=" N ILE K 15 " --> pdb=" O GLY K 11 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N PHE K 17 " --> pdb=" O PHE K 13 " (cutoff:3.500A) removed outlier: 3.927A pdb=" N ILE K 19 " --> pdb=" O ILE K 15 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N MET K 26 " --> pdb=" O PHE K 22 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N LYS K 27 " --> pdb=" O PHE K 23 " (cutoff:3.500A) removed outlier: 4.360A pdb=" N VAL K 28 " --> pdb=" O LEU K 24 " (cutoff:3.500A) Processing helix chain 'K' and resid 95 through 108 removed outlier: 3.594A pdb=" N LYS K 99 " --> pdb=" O ALA K 95 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N LYS K 103 " --> pdb=" O LYS K 99 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N LEU K 106 " --> pdb=" O GLN K 102 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N ASP K 107 " --> pdb=" O LYS K 103 " (cutoff:3.500A) Processing helix chain 'K' and resid 124 through 131 removed outlier: 3.986A pdb=" N LEU K 130 " --> pdb=" O MET K 126 " (cutoff:3.500A) Processing helix chain 'K' and resid 185 through 192 removed outlier: 3.807A pdb=" N SER K 190 " --> pdb=" O GLU K 186 " (cutoff:3.500A) Processing helix chain 'L' and resid 4 through 27 Processing helix chain 'L' and resid 95 through 108 removed outlier: 3.507A pdb=" N ASN L 104 " --> pdb=" O GLU L 100 " (cutoff:3.500A) Processing helix chain 'L' and resid 112 through 117 Processing helix chain 'L' and resid 125 through 134 removed outlier: 3.739A pdb=" N LEU L 130 " --> pdb=" O MET L 126 " (cutoff:3.500A) removed outlier: 3.881A pdb=" N SER L 132 " --> pdb=" O GLN L 128 " (cutoff:3.500A) removed outlier: 4.226A pdb=" N ASN L 133 " --> pdb=" O GLN L 129 " (cutoff:3.500A) removed outlier: 3.864A pdb=" N MET L 134 " --> pdb=" O LEU L 130 " (cutoff:3.500A) Processing helix chain 'L' and resid 185 through 192 Processing sheet with id= A, first strand: chain 'B' and resid 70 through 72 removed outlier: 6.624A pdb=" N ILE B 36 " --> pdb=" O LEU B 13 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'B' and resid 41 through 43 removed outlier: 6.739A pdb=" N THR B 203 " --> pdb=" O THR B 42 " (cutoff:3.500A) removed outlier: 6.723A pdb=" N ILE B 171 " --> pdb=" O ILE B 204 " (cutoff:3.500A) removed outlier: 8.263A pdb=" N VAL B 206 " --> pdb=" O ILE B 171 " (cutoff:3.500A) removed outlier: 6.788A pdb=" N TYR B 173 " --> pdb=" O VAL B 206 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N GLY B 93 " --> pdb=" O LEU B 170 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'B' and resid 220 through 223 removed outlier: 3.646A pdb=" N GLY B 232 " --> pdb=" O ILE B 220 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N GLY B 230 " --> pdb=" O VAL B 222 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'E' and resid 70 through 72 removed outlier: 6.623A pdb=" N ILE E 36 " --> pdb=" O LEU E 13 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'E' and resid 228 through 232 removed outlier: 6.614A pdb=" N VAL E 222 " --> pdb=" O GLN E 229 " (cutoff:3.500A) removed outlier: 4.883A pdb=" N GLU E 231 " --> pdb=" O ILE E 220 " (cutoff:3.500A) removed outlier: 6.130A pdb=" N ILE E 220 " --> pdb=" O GLU E 231 " (cutoff:3.500A) removed outlier: 3.821A pdb=" N TYR E 219 " --> pdb=" O ILE E 41 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N ALA E 43 " --> pdb=" O TYR E 219 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N TYR E 221 " --> pdb=" O ALA E 43 " (cutoff:3.500A) removed outlier: 4.343A pdb=" N VAL E 223 " --> pdb=" O MET E 45 " (cutoff:3.500A) removed outlier: 6.604A pdb=" N THR E 203 " --> pdb=" O THR E 42 " (cutoff:3.500A) removed outlier: 7.741A pdb=" N ILE E 44 " --> pdb=" O THR E 203 " (cutoff:3.500A) removed outlier: 6.615A pdb=" N ILE E 205 " --> pdb=" O ILE E 44 " (cutoff:3.500A) removed outlier: 6.723A pdb=" N ILE E 171 " --> pdb=" O ILE E 204 " (cutoff:3.500A) removed outlier: 8.263A pdb=" N VAL E 206 " --> pdb=" O ILE E 171 " (cutoff:3.500A) removed outlier: 6.788A pdb=" N TYR E 173 " --> pdb=" O VAL E 206 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N GLY E 93 " --> pdb=" O LEU E 170 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'G' and resid 42 through 44 removed outlier: 3.860A pdb=" N LEU G 79 " --> pdb=" O ASP G 74 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N ASP G 74 " --> pdb=" O LEU G 79 " (cutoff:3.500A) removed outlier: 6.154A pdb=" N ASP G 85 " --> pdb=" O VAL G 68 " (cutoff:3.500A) removed outlier: 5.610A pdb=" N VAL G 68 " --> pdb=" O ASP G 85 " (cutoff:3.500A) removed outlier: 6.530A pdb=" N VAL G 58 " --> pdb=" O ILE G 65 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'G' and resid 145 through 150 removed outlier: 3.854A pdb=" N TYR G 145 " --> pdb=" O VAL G 162 " (cutoff:3.500A) removed outlier: 3.730A pdb=" N VAL G 162 " --> pdb=" O TYR G 145 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'H' and resid 40 through 43 removed outlier: 3.718A pdb=" N TYR H 40 " --> pdb=" O LEU H 86 " (cutoff:3.500A) removed outlier: 3.806A pdb=" N LEU H 79 " --> pdb=" O ASP H 74 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N ASP H 74 " --> pdb=" O LEU H 79 " (cutoff:3.500A) removed outlier: 6.637A pdb=" N ASP H 85 " --> pdb=" O VAL H 68 " (cutoff:3.500A) removed outlier: 5.493A pdb=" N VAL H 68 " --> pdb=" O ASP H 85 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N VAL H 63 " --> pdb=" O MET H 60 " (cutoff:3.500A) removed outlier: 6.400A pdb=" N VAL H 58 " --> pdb=" O ILE H 65 " (cutoff:3.500A) removed outlier: 8.192A pdb=" N LYS H 157 " --> pdb=" O LYS H 57 " (cutoff:3.500A) removed outlier: 9.339A pdb=" N THR H 59 " --> pdb=" O LYS H 157 " (cutoff:3.500A) removed outlier: 6.818A pdb=" N LEU H 159 " --> pdb=" O THR H 59 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'I' and resid 42 through 46 removed outlier: 3.569A pdb=" N ALA I 44 " --> pdb=" O VAL I 82 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N VAL I 82 " --> pdb=" O ALA I 44 " (cutoff:3.500A) removed outlier: 6.631A pdb=" N ASP I 85 " --> pdb=" O VAL I 68 " (cutoff:3.500A) removed outlier: 5.324A pdb=" N VAL I 68 " --> pdb=" O ASP I 85 " (cutoff:3.500A) removed outlier: 6.742A pdb=" N VAL I 58 " --> pdb=" O ILE I 65 " (cutoff:3.500A) Processing sheet with id= J, first strand: chain 'I' and resid 145 through 148 Processing sheet with id= K, first strand: chain 'J' and resid 41 through 46 removed outlier: 3.586A pdb=" N ALA J 80 " --> pdb=" O PHE J 46 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N LEU J 79 " --> pdb=" O ASP J 74 " (cutoff:3.500A) removed outlier: 6.488A pdb=" N ASP J 85 " --> pdb=" O VAL J 68 " (cutoff:3.500A) removed outlier: 5.564A pdb=" N VAL J 68 " --> pdb=" O ASP J 85 " (cutoff:3.500A) Processing sheet with id= L, first strand: chain 'J' and resid 145 through 150 Processing sheet with id= M, first strand: chain 'K' and resid 40 through 46 removed outlier: 4.057A pdb=" N LEU K 79 " --> pdb=" O ASP K 74 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N ASP K 74 " --> pdb=" O LEU K 79 " (cutoff:3.500A) Processing sheet with id= N, first strand: chain 'K' and resid 145 through 148 Processing sheet with id= O, first strand: chain 'L' and resid 42 through 46 removed outlier: 3.575A pdb=" N PHE L 84 " --> pdb=" O MET L 42 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N LEU L 79 " --> pdb=" O ASP L 74 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N SER L 70 " --> pdb=" O THR L 83 " (cutoff:3.500A) removed outlier: 6.148A pdb=" N ASP L 85 " --> pdb=" O VAL L 68 " (cutoff:3.500A) removed outlier: 5.646A pdb=" N VAL L 68 " --> pdb=" O ASP L 85 " (cutoff:3.500A) removed outlier: 6.338A pdb=" N VAL L 58 " --> pdb=" O ILE L 65 " (cutoff:3.500A) Processing sheet with id= P, first strand: chain 'L' and resid 145 through 148 540 hydrogen bonds defined for protein. 1539 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: 4.64 Time building geometry restraints manager: 7.29 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.99 - 1.16: 8 1.16 - 1.32: 3140 1.32 - 1.49: 6849 1.49 - 1.65: 7879 1.65 - 1.82: 168 Bond restraints: 18044 Sorted by residual: bond pdb=" O2 VO4 E 302 " pdb=" V VO4 E 302 " ideal model delta sigma weight residual 1.910 0.992 0.918 2.00e-02 2.50e+03 2.11e+03 bond pdb=" O2 VO4 B 302 " pdb=" V VO4 B 302 " ideal model delta sigma weight residual 1.910 0.992 0.918 2.00e-02 2.50e+03 2.11e+03 bond pdb=" O1 VO4 B 302 " pdb=" V VO4 B 302 " ideal model delta sigma weight residual 1.910 0.995 0.915 2.00e-02 2.50e+03 2.09e+03 bond pdb=" O3 VO4 B 302 " pdb=" V VO4 B 302 " ideal model delta sigma weight residual 1.910 0.995 0.915 2.00e-02 2.50e+03 2.09e+03 bond pdb=" O3 VO4 E 302 " pdb=" V VO4 E 302 " ideal model delta sigma weight residual 1.910 0.996 0.914 2.00e-02 2.50e+03 2.09e+03 ... (remaining 18039 not shown) Histogram of bond angle deviations from ideal: 89.52 - 107.42: 539 107.42 - 125.31: 23696 125.31 - 143.20: 209 143.20 - 161.10: 0 161.10 - 178.99: 4 Bond angle restraints: 24448 Sorted by residual: angle pdb=" O1 VO4 E 302 " pdb=" V VO4 E 302 " pdb=" O4 VO4 E 302 " ideal model delta sigma weight residual 109.47 178.99 -69.52 3.00e+00 1.11e-01 5.37e+02 angle pdb=" O1 VO4 B 302 " pdb=" V VO4 B 302 " pdb=" O4 VO4 B 302 " ideal model delta sigma weight residual 109.47 178.92 -69.45 3.00e+00 1.11e-01 5.36e+02 angle pdb=" O2 VO4 B 302 " pdb=" V VO4 B 302 " pdb=" O3 VO4 B 302 " ideal model delta sigma weight residual 109.47 177.93 -68.46 3.00e+00 1.11e-01 5.21e+02 angle pdb=" O2 VO4 E 302 " pdb=" V VO4 E 302 " pdb=" O3 VO4 E 302 " ideal model delta sigma weight residual 109.47 177.88 -68.41 3.00e+00 1.11e-01 5.20e+02 angle pdb=" O1 VO4 E 302 " pdb=" V VO4 E 302 " pdb=" O2 VO4 E 302 " ideal model delta sigma weight residual 109.47 89.52 19.95 3.00e+00 1.11e-01 4.42e+01 ... (remaining 24443 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.93: 9447 17.93 - 35.86: 967 35.86 - 53.79: 268 53.79 - 71.71: 121 71.71 - 89.64: 25 Dihedral angle restraints: 10828 sinusoidal: 4086 harmonic: 6742 Sorted by residual: dihedral pdb=" CA GLY K 88 " pdb=" C GLY K 88 " pdb=" N LYS K 89 " pdb=" CA LYS K 89 " ideal model delta harmonic sigma weight residual 180.00 150.07 29.93 0 5.00e+00 4.00e-02 3.58e+01 dihedral pdb=" CA GLY D 133 " pdb=" C GLY D 133 " pdb=" N VAL D 134 " pdb=" CA VAL D 134 " ideal model delta harmonic sigma weight residual 180.00 152.81 27.19 0 5.00e+00 4.00e-02 2.96e+01 dihedral pdb=" CA GLY A 133 " pdb=" C GLY A 133 " pdb=" N VAL A 134 " pdb=" CA VAL A 134 " ideal model delta harmonic sigma weight residual 180.00 152.82 27.18 0 5.00e+00 4.00e-02 2.96e+01 ... (remaining 10825 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 1.069: 2966 1.069 - 2.139: 0 2.139 - 3.208: 0 3.208 - 4.278: 0 4.278 - 5.347: 2 Chirality restraints: 2968 Sorted by residual: chirality pdb=" V VO4 E 302 " pdb=" O1 VO4 E 302 " pdb=" O2 VO4 E 302 " pdb=" O4 VO4 E 302 " both_signs ideal model delta sigma weight residual True 5.36 0.02 5.35 2.00e-01 2.50e+01 7.15e+02 chirality pdb=" V VO4 B 302 " pdb=" O1 VO4 B 302 " pdb=" O2 VO4 B 302 " pdb=" O4 VO4 B 302 " both_signs ideal model delta sigma weight residual True 5.36 0.02 5.35 2.00e-01 2.50e+01 7.14e+02 chirality pdb=" CB ILE F 15 " pdb=" CA ILE F 15 " pdb=" CG1 ILE F 15 " pdb=" CG2 ILE F 15 " both_signs ideal model delta sigma weight residual False 2.64 2.19 0.45 2.00e-01 2.50e+01 5.07e+00 ... (remaining 2965 not shown) Planarity restraints: 3102 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA THR B 142 " -0.018 2.00e-02 2.50e+03 3.67e-02 1.35e+01 pdb=" C THR B 142 " 0.063 2.00e-02 2.50e+03 pdb=" O THR B 142 " -0.024 2.00e-02 2.50e+03 pdb=" N GLU B 143 " -0.021 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA THR E 142 " 0.018 2.00e-02 2.50e+03 3.67e-02 1.35e+01 pdb=" C THR E 142 " -0.063 2.00e-02 2.50e+03 pdb=" O THR E 142 " 0.024 2.00e-02 2.50e+03 pdb=" N GLU E 143 " 0.021 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ALA A 97 " -0.057 5.00e-02 4.00e+02 8.52e-02 1.16e+01 pdb=" N PRO A 98 " 0.147 5.00e-02 4.00e+02 pdb=" CA PRO A 98 " -0.042 5.00e-02 4.00e+02 pdb=" CD PRO A 98 " -0.048 5.00e-02 4.00e+02 ... (remaining 3099 not shown) Histogram of nonbonded interaction distances: 2.10 - 2.66: 689 2.66 - 3.22: 17239 3.22 - 3.78: 28336 3.78 - 4.34: 36449 4.34 - 4.90: 57943 Nonbonded interactions: 140656 Sorted by model distance: nonbonded pdb=" O GLY I 155 " pdb=" CG GLU I 156 " model vdw 2.101 3.440 nonbonded pdb=" CA LEU C 61 " pdb=" OG1 THR C 64 " model vdw 2.197 3.470 nonbonded pdb=" CG1 VAL H 76 " pdb=" OE1 GLN I 97 " model vdw 2.202 3.460 nonbonded pdb=" OE2 GLU K 186 " pdb=" CE MET L 147 " model vdw 2.208 3.460 nonbonded pdb=" CA GLY D 8 " pdb=" CG1 VAL L 10 " model vdw 2.211 3.860 ... (remaining 140651 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'D' } ncs_group { reference = chain 'B' selection = chain 'E' } ncs_group { reference = chain 'C' selection = chain 'F' } ncs_group { reference = chain 'G' selection = chain 'H' selection = chain 'I' selection = chain 'J' selection = chain 'K' selection = chain 'L' } 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: 0.410 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: 0.010 Extract box with map and model: 2.760 Check model and map are aligned: 0.270 Set scattering table: 0.150 Process input model: 46.400 Find NCS groups from input model: 0.880 Set up NCS constraints: 0.110 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:3.100 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 54.090 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7798 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 : 0.021 0.918 18044 Z= 1.223 Angle : 1.527 69.522 24448 Z= 0.788 Chirality : 0.151 5.347 2968 Planarity : 0.007 0.085 3102 Dihedral : 17.850 89.643 6500 Min Nonbonded Distance : 2.101 Molprobity Statistics. All-atom Clashscore : 29.59 Ramachandran Plot: Outliers : 1.36 % Allowed : 11.40 % Favored : 87.23 % Rotamer: Outliers : 9.93 % Allowed : 12.49 % Favored : 77.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -5.59 (0.12), residues: 2350 helix: -4.25 (0.09), residues: 937 sheet: -2.71 (0.30), residues: 240 loop : -3.46 (0.15), residues: 1173 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP A 146 HIS 0.010 0.003 HIS F 93 PHE 0.046 0.003 PHE F 17 TYR 0.023 0.003 TYR J 145 ARG 0.007 0.001 ARG F 62 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4700 Ramachandran restraints generated. 2350 Oldfield, 0 Emsley, 2350 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4700 Ramachandran restraints generated. 2350 Oldfield, 0 Emsley, 2350 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 553 residues out of total 1994 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 186 poor density : 367 time to evaluate : 2.198 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: A 2 ASN cc_start: 0.8281 (m110) cc_final: 0.8053 (p0) REVERT: A 70 GLN cc_start: 0.7443 (mm-40) cc_final: 0.7108 (tm-30) REVERT: A 168 LYS cc_start: 0.8296 (tttm) cc_final: 0.7968 (ttmm) REVERT: A 179 GLU cc_start: 0.8514 (mp0) cc_final: 0.8248 (mp0) REVERT: B 81 SER cc_start: 0.6952 (OUTLIER) cc_final: 0.6639 (t) REVERT: B 219 TYR cc_start: 0.6115 (OUTLIER) cc_final: 0.5741 (m-80) REVERT: C 10 VAL cc_start: -0.0816 (OUTLIER) cc_final: -0.1408 (m) REVERT: C 71 HIS cc_start: 0.7933 (m90) cc_final: 0.7715 (m90) REVERT: C 84 GLN cc_start: 0.7173 (OUTLIER) cc_final: 0.6829 (mm-40) REVERT: D 30 PHE cc_start: 0.7730 (m-80) cc_final: 0.7487 (m-80) REVERT: D 74 ILE cc_start: 0.7596 (OUTLIER) cc_final: 0.7261 (tp) REVERT: E 146 MET cc_start: 0.9092 (tpp) cc_final: 0.8682 (mmm) REVERT: E 210 VAL cc_start: 0.8950 (OUTLIER) cc_final: 0.8748 (t) REVERT: E 249 LEU cc_start: 0.8941 (OUTLIER) cc_final: 0.8729 (mt) REVERT: F 10 VAL cc_start: 0.2270 (OUTLIER) cc_final: 0.1769 (t) REVERT: F 12 SER cc_start: 0.0511 (OUTLIER) cc_final: 0.0152 (t) REVERT: F 35 THR cc_start: 0.5355 (OUTLIER) cc_final: 0.5122 (m) REVERT: F 64 THR cc_start: 0.5496 (OUTLIER) cc_final: 0.4853 (p) REVERT: F 68 SER cc_start: 0.5430 (OUTLIER) cc_final: 0.4279 (m) REVERT: G 61 SER cc_start: 0.9003 (OUTLIER) cc_final: 0.8489 (p) REVERT: H 35 ASN cc_start: 0.8961 (p0) cc_final: 0.8669 (p0) REVERT: J 35 ASN cc_start: 0.7544 (OUTLIER) cc_final: 0.7146 (m-40) REVERT: J 96 GLU cc_start: 0.8759 (mp0) cc_final: 0.8438 (mp0) REVERT: L 10 VAL cc_start: 0.6717 (OUTLIER) cc_final: 0.6497 (t) REVERT: L 26 MET cc_start: 0.7918 (tpt) cc_final: 0.7705 (tpt) outliers start: 186 outliers final: 49 residues processed: 504 average time/residue: 0.3021 time to fit residues: 226.6484 Evaluate side-chains 286 residues out of total 1994 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 64 poor density : 222 time to evaluate : 2.024 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 95 GLU Chi-restraints excluded: chain A residue 128 SER Chi-restraints excluded: chain A residue 184 SER Chi-restraints excluded: chain A residue 211 THR Chi-restraints excluded: chain B residue 23 ARG Chi-restraints excluded: chain B residue 27 VAL Chi-restraints excluded: chain B residue 64 VAL Chi-restraints excluded: chain B residue 81 SER Chi-restraints excluded: chain B residue 103 THR Chi-restraints excluded: chain B residue 121 LEU Chi-restraints excluded: chain B residue 206 VAL Chi-restraints excluded: chain B residue 219 TYR Chi-restraints excluded: chain B residue 220 ILE Chi-restraints excluded: chain C residue 10 VAL Chi-restraints excluded: chain C residue 56 VAL Chi-restraints excluded: chain C residue 62 ARG Chi-restraints excluded: chain C residue 84 GLN Chi-restraints excluded: chain D residue 2 ASN Chi-restraints excluded: chain D residue 12 ILE Chi-restraints excluded: chain D residue 14 ARG Chi-restraints excluded: chain D residue 15 ILE Chi-restraints excluded: chain D residue 74 ILE Chi-restraints excluded: chain D residue 142 SER Chi-restraints excluded: chain D residue 165 VAL Chi-restraints excluded: chain D residue 226 GLU Chi-restraints excluded: chain E residue 18 ASN Chi-restraints excluded: chain E residue 41 ILE Chi-restraints excluded: chain E residue 42 THR Chi-restraints excluded: chain E residue 45 MET Chi-restraints excluded: chain E residue 103 THR Chi-restraints excluded: chain E residue 105 MET Chi-restraints excluded: chain E residue 134 LEU Chi-restraints excluded: chain E residue 142 THR Chi-restraints excluded: chain E residue 206 VAL Chi-restraints excluded: chain E residue 210 VAL Chi-restraints excluded: chain E residue 249 LEU Chi-restraints excluded: chain F residue 10 VAL Chi-restraints excluded: chain F residue 12 SER Chi-restraints excluded: chain F residue 35 THR Chi-restraints excluded: chain F residue 56 VAL Chi-restraints excluded: chain F residue 64 THR Chi-restraints excluded: chain F residue 68 SER Chi-restraints excluded: chain F residue 70 LEU Chi-restraints excluded: chain F residue 77 GLU Chi-restraints excluded: chain F residue 84 GLN Chi-restraints excluded: chain G residue 34 THR Chi-restraints excluded: chain G residue 36 LEU Chi-restraints excluded: chain G residue 61 SER Chi-restraints excluded: chain I residue 4 ARG Chi-restraints excluded: chain I residue 6 SER Chi-restraints excluded: chain I residue 154 LEU Chi-restraints excluded: chain I residue 157 LYS Chi-restraints excluded: chain J residue 35 ASN Chi-restraints excluded: chain J residue 36 LEU Chi-restraints excluded: chain J residue 37 SER Chi-restraints excluded: chain L residue 10 VAL Chi-restraints excluded: chain L residue 15 ILE Chi-restraints excluded: chain L residue 21 LEU Chi-restraints excluded: chain L residue 24 LEU Chi-restraints excluded: chain L residue 27 LYS Chi-restraints excluded: chain L residue 32 VAL Chi-restraints excluded: chain L residue 97 GLN Chi-restraints excluded: chain L residue 178 ASN Chi-restraints excluded: chain L residue 179 THR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 234 random chunks: chunk 197 optimal weight: 6.9990 chunk 177 optimal weight: 6.9990 chunk 98 optimal weight: 0.7980 chunk 60 optimal weight: 20.0000 chunk 119 optimal weight: 8.9990 chunk 94 optimal weight: 3.9990 chunk 183 optimal weight: 9.9990 chunk 70 optimal weight: 0.0770 chunk 111 optimal weight: 9.9990 chunk 136 optimal weight: 20.0000 chunk 212 optimal weight: 9.9990 overall best weight: 3.7744 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 44 GLN A 70 GLN B 35 ASN B 83 GLN C 6 ASN C 25 GLN ** C 34 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 48 HIS C 59 GLN ** C 71 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 44 GLN D 188 ASN D 189 ASN D 217 GLN E 35 ASN E 67 GLN E 247 GLN F 3 GLN F 48 HIS F 59 GLN ** F 66 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 50 ASN I 135 ASN J 133 ASN J 135 ASN ** K 94 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 35 ASN L 50 ASN Total number of N/Q/H flips: 24 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7845 moved from start: 0.2552 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 18044 Z= 0.267 Angle : 0.791 14.807 24448 Z= 0.407 Chirality : 0.046 0.205 2968 Planarity : 0.005 0.066 3102 Dihedral : 9.931 92.842 2638 Min Nonbonded Distance : 2.140 Molprobity Statistics. All-atom Clashscore : 16.75 Ramachandran Plot: Outliers : 0.13 % Allowed : 10.55 % Favored : 89.32 % Rotamer: Outliers : 6.30 % Allowed : 20.44 % Favored : 73.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.48 (0.14), residues: 2350 helix: -2.85 (0.12), residues: 981 sheet: -2.16 (0.30), residues: 254 loop : -3.27 (0.16), residues: 1115 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP D 146 HIS 0.008 0.002 HIS C 87 PHE 0.041 0.002 PHE L 13 TYR 0.020 0.002 TYR J 169 ARG 0.005 0.001 ARG H 67 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4700 Ramachandran restraints generated. 2350 Oldfield, 0 Emsley, 2350 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4700 Ramachandran restraints generated. 2350 Oldfield, 0 Emsley, 2350 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 374 residues out of total 1994 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 118 poor density : 256 time to evaluate : 1.954 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: A 70 GLN cc_start: 0.6719 (mm110) cc_final: 0.6334 (tp-100) REVERT: A 78 VAL cc_start: 0.9166 (m) cc_final: 0.8958 (p) REVERT: B 23 ARG cc_start: 0.4769 (OUTLIER) cc_final: 0.3721 (tpp80) REVERT: B 45 MET cc_start: 0.6998 (mtt) cc_final: 0.6752 (mtt) REVERT: B 146 MET cc_start: 0.8337 (tpp) cc_final: 0.7952 (mmm) REVERT: C 71 HIS cc_start: 0.8235 (m90) cc_final: 0.7952 (m90) REVERT: D 14 ARG cc_start: 0.7710 (OUTLIER) cc_final: 0.7249 (mmt180) REVERT: G 26 MET cc_start: 0.7538 (ppp) cc_final: 0.7330 (ppp) REVERT: G 46 PHE cc_start: 0.8795 (m-80) cc_final: 0.8470 (m-10) REVERT: G 134 MET cc_start: 0.8188 (ptm) cc_final: 0.7738 (ptp) REVERT: G 147 MET cc_start: 0.8502 (OUTLIER) cc_final: 0.8225 (ptp) REVERT: H 35 ASN cc_start: 0.8916 (p0) cc_final: 0.8610 (p0) REVERT: H 141 ASP cc_start: 0.8933 (OUTLIER) cc_final: 0.8727 (p0) REVERT: J 96 GLU cc_start: 0.8891 (mp0) cc_final: 0.8607 (mp0) REVERT: J 150 THR cc_start: 0.9186 (OUTLIER) cc_final: 0.8913 (m) REVERT: K 147 MET cc_start: 0.7313 (ptm) cc_final: 0.6819 (ptm) REVERT: L 24 LEU cc_start: 0.6200 (OUTLIER) cc_final: 0.5991 (tm) REVERT: L 100 GLU cc_start: 0.8316 (mt-10) cc_final: 0.7810 (tm-30) outliers start: 118 outliers final: 60 residues processed: 353 average time/residue: 0.2797 time to fit residues: 156.0208 Evaluate side-chains 284 residues out of total 1994 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 66 poor density : 218 time to evaluate : 2.120 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 26 LEU Chi-restraints excluded: chain A residue 89 SER Chi-restraints excluded: chain A residue 95 GLU Chi-restraints excluded: chain A residue 111 SER Chi-restraints excluded: chain A residue 128 SER Chi-restraints excluded: chain A residue 211 THR Chi-restraints excluded: chain A residue 237 VAL Chi-restraints excluded: chain A residue 246 PHE Chi-restraints excluded: chain B residue 23 ARG Chi-restraints excluded: chain B residue 50 THR Chi-restraints excluded: chain B residue 77 ILE Chi-restraints excluded: chain B residue 103 THR Chi-restraints excluded: chain B residue 129 LEU Chi-restraints excluded: chain B residue 136 SER Chi-restraints excluded: chain B residue 206 VAL Chi-restraints excluded: chain B residue 208 HIS Chi-restraints excluded: chain B residue 222 VAL Chi-restraints excluded: chain C residue 25 GLN Chi-restraints excluded: chain C residue 43 LEU Chi-restraints excluded: chain C residue 56 VAL Chi-restraints excluded: chain D residue 2 ASN Chi-restraints excluded: chain D residue 4 ILE Chi-restraints excluded: chain D residue 14 ARG Chi-restraints excluded: chain D residue 15 ILE Chi-restraints excluded: chain D residue 55 ILE Chi-restraints excluded: chain D residue 74 ILE Chi-restraints excluded: chain D residue 78 VAL Chi-restraints excluded: chain D residue 113 LEU Chi-restraints excluded: chain D residue 128 SER Chi-restraints excluded: chain D residue 162 ILE Chi-restraints excluded: chain D residue 164 ILE Chi-restraints excluded: chain D residue 249 VAL Chi-restraints excluded: chain E residue 75 LYS Chi-restraints excluded: chain E residue 103 THR Chi-restraints excluded: chain E residue 105 MET Chi-restraints excluded: chain E residue 201 LEU Chi-restraints excluded: chain E residue 206 VAL Chi-restraints excluded: chain F residue 19 ASN Chi-restraints excluded: chain F residue 30 ILE Chi-restraints excluded: chain F residue 54 LEU Chi-restraints excluded: chain F residue 64 THR Chi-restraints excluded: chain F residue 70 LEU Chi-restraints excluded: chain F residue 77 GLU Chi-restraints excluded: chain G residue 16 ILE Chi-restraints excluded: chain G residue 76 VAL Chi-restraints excluded: chain G residue 141 ASP Chi-restraints excluded: chain G residue 147 MET Chi-restraints excluded: chain H residue 141 ASP Chi-restraints excluded: chain H residue 188 LEU Chi-restraints excluded: chain I residue 4 ARG Chi-restraints excluded: chain I residue 63 VAL Chi-restraints excluded: chain I residue 76 VAL Chi-restraints excluded: chain I residue 182 THR Chi-restraints excluded: chain J residue 35 ASN Chi-restraints excluded: chain J residue 36 LEU Chi-restraints excluded: chain J residue 150 THR Chi-restraints excluded: chain K residue 35 ASN Chi-restraints excluded: chain K residue 135 ASN Chi-restraints excluded: chain K residue 150 THR Chi-restraints excluded: chain L residue 21 LEU Chi-restraints excluded: chain L residue 24 LEU Chi-restraints excluded: chain L residue 28 VAL Chi-restraints excluded: chain L residue 83 THR Chi-restraints excluded: chain L residue 150 THR Chi-restraints excluded: chain L residue 178 ASN Chi-restraints excluded: chain L residue 179 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 234 random chunks: chunk 118 optimal weight: 8.9990 chunk 65 optimal weight: 10.0000 chunk 176 optimal weight: 30.0000 chunk 144 optimal weight: 8.9990 chunk 58 optimal weight: 3.9990 chunk 212 optimal weight: 20.0000 chunk 229 optimal weight: 7.9990 chunk 189 optimal weight: 4.9990 chunk 211 optimal weight: 5.9990 chunk 72 optimal weight: 9.9990 chunk 170 optimal weight: 8.9990 overall best weight: 6.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 187 GLN ** B 238 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 3 GLN ** C 34 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 67 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 66 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 71 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 133 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 128 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 135 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 94 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7934 moved from start: 0.3278 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.047 18044 Z= 0.354 Angle : 0.800 10.260 24448 Z= 0.410 Chirality : 0.046 0.228 2968 Planarity : 0.005 0.066 3102 Dihedral : 8.469 105.030 2568 Min Nonbonded Distance : 2.024 Molprobity Statistics. All-atom Clashscore : 19.38 Ramachandran Plot: Outliers : 0.09 % Allowed : 11.70 % Favored : 88.21 % Rotamer: Outliers : 8.11 % Allowed : 22.09 % Favored : 69.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.89 (0.15), residues: 2350 helix: -2.06 (0.14), residues: 997 sheet: -1.79 (0.33), residues: 227 loop : -3.28 (0.16), residues: 1126 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP D 212 HIS 0.015 0.003 HIS A 46 PHE 0.034 0.002 PHE J 13 TYR 0.020 0.002 TYR J 169 ARG 0.005 0.001 ARG F 62 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4700 Ramachandran restraints generated. 2350 Oldfield, 0 Emsley, 2350 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4700 Ramachandran restraints generated. 2350 Oldfield, 0 Emsley, 2350 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 386 residues out of total 1994 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 152 poor density : 234 time to evaluate : 1.683 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: A 70 GLN cc_start: 0.7082 (mm110) cc_final: 0.6578 (tp-100) REVERT: A 78 VAL cc_start: 0.9256 (m) cc_final: 0.9000 (p) REVERT: B 92 MET cc_start: 0.7988 (ppp) cc_final: 0.7751 (mtt) REVERT: B 105 MET cc_start: 0.6946 (mtp) cc_final: 0.6653 (mtp) REVERT: B 146 MET cc_start: 0.8405 (tpp) cc_final: 0.8181 (mmp) REVERT: D 14 ARG cc_start: 0.7679 (OUTLIER) cc_final: 0.7259 (mmt180) REVERT: D 94 ARG cc_start: 0.6740 (OUTLIER) cc_final: 0.6474 (ptp-170) REVERT: D 120 MET cc_start: 0.7282 (OUTLIER) cc_final: 0.6970 (mtt) REVERT: E 146 MET cc_start: 0.8664 (tpp) cc_final: 0.8116 (mmm) REVERT: E 264 GLN cc_start: 0.8933 (OUTLIER) cc_final: 0.8476 (mp10) REVERT: G 134 MET cc_start: 0.8294 (ptm) cc_final: 0.7886 (ptp) REVERT: H 4 ARG cc_start: 0.5682 (ttt180) cc_final: 0.5368 (tpp-160) REVERT: H 35 ASN cc_start: 0.8996 (p0) cc_final: 0.8710 (p0) REVERT: H 141 ASP cc_start: 0.9035 (OUTLIER) cc_final: 0.8807 (p0) REVERT: J 96 GLU cc_start: 0.8786 (mp0) cc_final: 0.8484 (mp0) REVERT: J 150 THR cc_start: 0.9255 (OUTLIER) cc_final: 0.8999 (m) REVERT: K 147 MET cc_start: 0.7398 (ptm) cc_final: 0.6838 (ptm) REVERT: L 24 LEU cc_start: 0.6095 (OUTLIER) cc_final: 0.5888 (tm) REVERT: L 100 GLU cc_start: 0.8498 (mt-10) cc_final: 0.7845 (tm-30) REVERT: L 147 MET cc_start: 0.9141 (ppp) cc_final: 0.8491 (ppp) outliers start: 152 outliers final: 98 residues processed: 357 average time/residue: 0.2545 time to fit residues: 142.0914 Evaluate side-chains 318 residues out of total 1994 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 105 poor density : 213 time to evaluate : 2.039 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 26 LEU Chi-restraints excluded: chain A residue 94 ARG Chi-restraints excluded: chain A residue 120 MET Chi-restraints excluded: chain A residue 128 SER Chi-restraints excluded: chain A residue 130 GLU Chi-restraints excluded: chain A residue 188 ASN Chi-restraints excluded: chain A residue 211 THR Chi-restraints excluded: chain A residue 228 ILE Chi-restraints excluded: chain A residue 233 THR Chi-restraints excluded: chain A residue 237 VAL Chi-restraints excluded: chain A residue 242 CYS Chi-restraints excluded: chain A residue 246 PHE Chi-restraints excluded: chain A residue 249 VAL Chi-restraints excluded: chain B residue 50 THR Chi-restraints excluded: chain B residue 77 ILE Chi-restraints excluded: chain B residue 103 THR Chi-restraints excluded: chain B residue 129 LEU Chi-restraints excluded: chain B residue 136 SER Chi-restraints excluded: chain B residue 206 VAL Chi-restraints excluded: chain B residue 208 HIS Chi-restraints excluded: chain B residue 263 HIS Chi-restraints excluded: chain C residue 56 VAL Chi-restraints excluded: chain C residue 68 SER Chi-restraints excluded: chain C residue 72 PHE Chi-restraints excluded: chain D residue 2 ASN Chi-restraints excluded: chain D residue 11 VAL Chi-restraints excluded: chain D residue 14 ARG Chi-restraints excluded: chain D residue 15 ILE Chi-restraints excluded: chain D residue 30 PHE Chi-restraints excluded: chain D residue 55 ILE Chi-restraints excluded: chain D residue 74 ILE Chi-restraints excluded: chain D residue 78 VAL Chi-restraints excluded: chain D residue 94 ARG Chi-restraints excluded: chain D residue 120 MET Chi-restraints excluded: chain D residue 128 SER Chi-restraints excluded: chain D residue 140 ILE Chi-restraints excluded: chain D residue 164 ILE Chi-restraints excluded: chain D residue 170 VAL Chi-restraints excluded: chain D residue 228 ILE Chi-restraints excluded: chain D residue 242 CYS Chi-restraints excluded: chain D residue 246 PHE Chi-restraints excluded: chain D residue 249 VAL Chi-restraints excluded: chain E residue 18 ASN Chi-restraints excluded: chain E residue 45 MET Chi-restraints excluded: chain E residue 50 THR Chi-restraints excluded: chain E residue 75 LYS Chi-restraints excluded: chain E residue 77 ILE Chi-restraints excluded: chain E residue 81 SER Chi-restraints excluded: chain E residue 98 SER Chi-restraints excluded: chain E residue 103 THR Chi-restraints excluded: chain E residue 105 MET Chi-restraints excluded: chain E residue 201 LEU Chi-restraints excluded: chain E residue 206 VAL Chi-restraints excluded: chain E residue 264 GLN Chi-restraints excluded: chain F residue 17 PHE Chi-restraints excluded: chain F residue 19 ASN Chi-restraints excluded: chain F residue 30 ILE Chi-restraints excluded: chain F residue 35 THR Chi-restraints excluded: chain F residue 47 GLU Chi-restraints excluded: chain F residue 56 VAL Chi-restraints excluded: chain F residue 63 GLN Chi-restraints excluded: chain F residue 70 LEU Chi-restraints excluded: chain F residue 73 LYS Chi-restraints excluded: chain F residue 77 GLU Chi-restraints excluded: chain G residue 16 ILE Chi-restraints excluded: chain G residue 72 THR Chi-restraints excluded: chain G residue 76 VAL Chi-restraints excluded: chain G residue 135 ASN Chi-restraints excluded: chain G residue 141 ASP Chi-restraints excluded: chain G residue 150 THR Chi-restraints excluded: chain G residue 162 VAL Chi-restraints excluded: chain G residue 185 LEU Chi-restraints excluded: chain H residue 14 VAL Chi-restraints excluded: chain H residue 141 ASP Chi-restraints excluded: chain H residue 178 ASN Chi-restraints excluded: chain H residue 188 LEU Chi-restraints excluded: chain I residue 4 ARG Chi-restraints excluded: chain I residue 28 VAL Chi-restraints excluded: chain I residue 63 VAL Chi-restraints excluded: chain I residue 76 VAL Chi-restraints excluded: chain I residue 85 ASP Chi-restraints excluded: chain I residue 100 GLU Chi-restraints excluded: chain I residue 146 ILE Chi-restraints excluded: chain I residue 182 THR Chi-restraints excluded: chain I residue 185 LEU Chi-restraints excluded: chain J residue 35 ASN Chi-restraints excluded: chain J residue 36 LEU Chi-restraints excluded: chain J residue 150 THR Chi-restraints excluded: chain K residue 34 THR Chi-restraints excluded: chain K residue 35 ASN Chi-restraints excluded: chain K residue 135 ASN Chi-restraints excluded: chain K residue 150 THR Chi-restraints excluded: chain K residue 170 LEU Chi-restraints excluded: chain L residue 21 LEU Chi-restraints excluded: chain L residue 24 LEU Chi-restraints excluded: chain L residue 28 VAL Chi-restraints excluded: chain L residue 69 ASP Chi-restraints excluded: chain L residue 83 THR Chi-restraints excluded: chain L residue 142 GLU Chi-restraints excluded: chain L residue 145 TYR Chi-restraints excluded: chain L residue 150 THR Chi-restraints excluded: chain L residue 174 ASP Chi-restraints excluded: chain L residue 178 ASN Chi-restraints excluded: chain L residue 179 THR Chi-restraints excluded: chain L residue 182 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 234 random chunks: chunk 210 optimal weight: 7.9990 chunk 160 optimal weight: 10.0000 chunk 110 optimal weight: 10.0000 chunk 23 optimal weight: 4.9990 chunk 101 optimal weight: 6.9990 chunk 142 optimal weight: 0.0470 chunk 213 optimal weight: 2.9990 chunk 226 optimal weight: 0.0570 chunk 111 optimal weight: 8.9990 chunk 202 optimal weight: 9.9990 chunk 60 optimal weight: 20.0000 overall best weight: 3.0202 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 238 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 260 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 25 GLN ** C 34 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 67 GLN ** F 6 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 66 GLN ** H 128 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 135 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 94 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7876 moved from start: 0.3608 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 18044 Z= 0.212 Angle : 0.688 9.994 24448 Z= 0.349 Chirality : 0.043 0.182 2968 Planarity : 0.004 0.051 3102 Dihedral : 7.754 105.889 2560 Min Nonbonded Distance : 2.144 Molprobity Statistics. All-atom Clashscore : 15.47 Ramachandran Plot: Outliers : 0.09 % Allowed : 9.91 % Favored : 90.00 % Rotamer: Outliers : 6.19 % Allowed : 24.44 % Favored : 69.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.39 (0.16), residues: 2350 helix: -1.59 (0.15), residues: 986 sheet: -1.52 (0.33), residues: 241 loop : -3.06 (0.17), residues: 1123 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP D 146 HIS 0.014 0.002 HIS A 46 PHE 0.027 0.002 PHE C 17 TYR 0.017 0.001 TYR J 145 ARG 0.005 0.000 ARG K 4 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4700 Ramachandran restraints generated. 2350 Oldfield, 0 Emsley, 2350 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4700 Ramachandran restraints generated. 2350 Oldfield, 0 Emsley, 2350 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 373 residues out of total 1994 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 116 poor density : 257 time to evaluate : 1.871 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: A 70 GLN cc_start: 0.7155 (mm110) cc_final: 0.6600 (tp-100) REVERT: A 131 MET cc_start: 0.8352 (tpp) cc_final: 0.8001 (tpp) REVERT: A 154 MET cc_start: 0.8686 (mtt) cc_final: 0.8447 (mtt) REVERT: A 254 MET cc_start: 0.7677 (mmm) cc_final: 0.7164 (mmm) REVERT: B 143 GLU cc_start: 0.6029 (mt-10) cc_final: 0.5687 (mp0) REVERT: D 14 ARG cc_start: 0.7612 (OUTLIER) cc_final: 0.6897 (mmt180) REVERT: D 228 ILE cc_start: 0.7539 (OUTLIER) cc_final: 0.7248 (tt) REVERT: E 146 MET cc_start: 0.8618 (tpp) cc_final: 0.8158 (mmm) REVERT: G 12 ILE cc_start: 0.8509 (tt) cc_final: 0.8185 (tp) REVERT: G 36 LEU cc_start: 0.8292 (pp) cc_final: 0.8034 (pp) REVERT: G 46 PHE cc_start: 0.8811 (m-80) cc_final: 0.8421 (m-10) REVERT: G 96 GLU cc_start: 0.8719 (tp30) cc_final: 0.8395 (tp30) REVERT: H 4 ARG cc_start: 0.5988 (ttt180) cc_final: 0.5382 (tpp-160) REVERT: H 180 GLN cc_start: 0.8880 (tp40) cc_final: 0.8316 (tm-30) REVERT: K 147 MET cc_start: 0.7127 (ptm) cc_final: 0.6803 (ptm) REVERT: L 15 ILE cc_start: 0.8349 (tp) cc_final: 0.8139 (tt) REVERT: L 24 LEU cc_start: 0.6004 (OUTLIER) cc_final: 0.5760 (tm) REVERT: L 100 GLU cc_start: 0.8487 (mt-10) cc_final: 0.7903 (tm-30) outliers start: 116 outliers final: 80 residues processed: 349 average time/residue: 0.2604 time to fit residues: 141.0441 Evaluate side-chains 317 residues out of total 1994 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 83 poor density : 234 time to evaluate : 2.029 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 26 LEU Chi-restraints excluded: chain A residue 55 ILE Chi-restraints excluded: chain A residue 128 SER Chi-restraints excluded: chain A residue 130 GLU Chi-restraints excluded: chain A residue 149 ILE Chi-restraints excluded: chain A residue 155 LEU Chi-restraints excluded: chain A residue 211 THR Chi-restraints excluded: chain A residue 228 ILE Chi-restraints excluded: chain A residue 233 THR Chi-restraints excluded: chain A residue 242 CYS Chi-restraints excluded: chain A residue 246 PHE Chi-restraints excluded: chain A residue 249 VAL Chi-restraints excluded: chain B residue 77 ILE Chi-restraints excluded: chain B residue 103 THR Chi-restraints excluded: chain B residue 129 LEU Chi-restraints excluded: chain B residue 136 SER Chi-restraints excluded: chain B residue 206 VAL Chi-restraints excluded: chain B residue 208 HIS Chi-restraints excluded: chain B residue 267 LEU Chi-restraints excluded: chain C residue 25 GLN Chi-restraints excluded: chain C residue 50 ASN Chi-restraints excluded: chain C residue 56 VAL Chi-restraints excluded: chain D residue 2 ASN Chi-restraints excluded: chain D residue 11 VAL Chi-restraints excluded: chain D residue 14 ARG Chi-restraints excluded: chain D residue 15 ILE Chi-restraints excluded: chain D residue 55 ILE Chi-restraints excluded: chain D residue 74 ILE Chi-restraints excluded: chain D residue 78 VAL Chi-restraints excluded: chain D residue 94 ARG Chi-restraints excluded: chain D residue 128 SER Chi-restraints excluded: chain D residue 164 ILE Chi-restraints excluded: chain D residue 200 ILE Chi-restraints excluded: chain D residue 228 ILE Chi-restraints excluded: chain D residue 242 CYS Chi-restraints excluded: chain D residue 246 PHE Chi-restraints excluded: chain E residue 75 LYS Chi-restraints excluded: chain E residue 81 SER Chi-restraints excluded: chain E residue 95 LEU Chi-restraints excluded: chain E residue 98 SER Chi-restraints excluded: chain E residue 103 THR Chi-restraints excluded: chain E residue 105 MET Chi-restraints excluded: chain E residue 181 ASP Chi-restraints excluded: chain E residue 201 LEU Chi-restraints excluded: chain E residue 206 VAL Chi-restraints excluded: chain F residue 17 PHE Chi-restraints excluded: chain F residue 19 ASN Chi-restraints excluded: chain F residue 56 VAL Chi-restraints excluded: chain F residue 70 LEU Chi-restraints excluded: chain F residue 77 GLU Chi-restraints excluded: chain G residue 16 ILE Chi-restraints excluded: chain G residue 72 THR Chi-restraints excluded: chain G residue 76 VAL Chi-restraints excluded: chain G residue 94 ASN Chi-restraints excluded: chain G residue 135 ASN Chi-restraints excluded: chain G residue 141 ASP Chi-restraints excluded: chain G residue 150 THR Chi-restraints excluded: chain G residue 162 VAL Chi-restraints excluded: chain H residue 5 THR Chi-restraints excluded: chain H residue 10 VAL Chi-restraints excluded: chain H residue 21 LEU Chi-restraints excluded: chain H residue 188 LEU Chi-restraints excluded: chain I residue 4 ARG Chi-restraints excluded: chain I residue 28 VAL Chi-restraints excluded: chain I residue 63 VAL Chi-restraints excluded: chain I residue 85 ASP Chi-restraints excluded: chain I residue 146 ILE Chi-restraints excluded: chain I residue 185 LEU Chi-restraints excluded: chain J residue 35 ASN Chi-restraints excluded: chain J residue 36 LEU Chi-restraints excluded: chain K residue 35 ASN Chi-restraints excluded: chain K residue 135 ASN Chi-restraints excluded: chain K residue 145 TYR Chi-restraints excluded: chain K residue 150 THR Chi-restraints excluded: chain K residue 170 LEU Chi-restraints excluded: chain L residue 21 LEU Chi-restraints excluded: chain L residue 24 LEU Chi-restraints excluded: chain L residue 69 ASP Chi-restraints excluded: chain L residue 83 THR Chi-restraints excluded: chain L residue 150 THR Chi-restraints excluded: chain L residue 174 ASP Chi-restraints excluded: chain L residue 178 ASN Chi-restraints excluded: chain L residue 179 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 234 random chunks: chunk 188 optimal weight: 50.0000 chunk 128 optimal weight: 3.9990 chunk 3 optimal weight: 0.9990 chunk 168 optimal weight: 7.9990 chunk 93 optimal weight: 8.9990 chunk 193 optimal weight: 4.9990 chunk 156 optimal weight: 8.9990 chunk 0 optimal weight: 30.0000 chunk 115 optimal weight: 8.9990 chunk 203 optimal weight: 7.9990 chunk 57 optimal weight: 9.9990 overall best weight: 5.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 125 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 238 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 260 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 25 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 34 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 67 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 6 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 63 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 133 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 135 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 94 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7921 moved from start: 0.3871 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.046 18044 Z= 0.295 Angle : 0.733 8.326 24448 Z= 0.372 Chirality : 0.044 0.203 2968 Planarity : 0.004 0.053 3102 Dihedral : 7.710 110.976 2560 Min Nonbonded Distance : 2.084 Molprobity Statistics. All-atom Clashscore : 17.96 Ramachandran Plot: Outliers : 0.09 % Allowed : 11.28 % Favored : 88.64 % Rotamer: Outliers : 7.36 % Allowed : 25.03 % Favored : 67.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.28 (0.16), residues: 2350 helix: -1.44 (0.15), residues: 986 sheet: -1.39 (0.34), residues: 233 loop : -3.08 (0.17), residues: 1131 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP D 212 HIS 0.011 0.002 HIS A 46 PHE 0.029 0.002 PHE C 17 TYR 0.015 0.002 TYR J 145 ARG 0.003 0.000 ARG D 94 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4700 Ramachandran restraints generated. 2350 Oldfield, 0 Emsley, 2350 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4700 Ramachandran restraints generated. 2350 Oldfield, 0 Emsley, 2350 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 378 residues out of total 1994 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 138 poor density : 240 time to evaluate : 1.947 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: A 70 GLN cc_start: 0.7003 (mm110) cc_final: 0.6627 (tp-100) REVERT: A 154 MET cc_start: 0.8740 (mtt) cc_final: 0.8441 (mtt) REVERT: A 254 MET cc_start: 0.7809 (mmm) cc_final: 0.7298 (mmm) REVERT: D 14 ARG cc_start: 0.7544 (OUTLIER) cc_final: 0.7164 (mmt180) REVERT: E 146 MET cc_start: 0.8694 (tpp) cc_final: 0.8122 (mmm) REVERT: E 264 GLN cc_start: 0.8911 (OUTLIER) cc_final: 0.8431 (mp10) REVERT: G 46 PHE cc_start: 0.8844 (m-80) cc_final: 0.8396 (m-10) REVERT: G 96 GLU cc_start: 0.8711 (tp30) cc_final: 0.8439 (tp30) REVERT: H 4 ARG cc_start: 0.6030 (ttt180) cc_final: 0.5468 (tpp-160) REVERT: J 26 MET cc_start: 0.6729 (mmt) cc_final: 0.6527 (mmt) REVERT: J 93 PHE cc_start: 0.7037 (OUTLIER) cc_final: 0.6575 (m-80) REVERT: K 147 MET cc_start: 0.7235 (ptm) cc_final: 0.6926 (ptm) REVERT: L 15 ILE cc_start: 0.8336 (tp) cc_final: 0.8126 (tt) REVERT: L 24 LEU cc_start: 0.5950 (OUTLIER) cc_final: 0.5699 (tm) REVERT: L 100 GLU cc_start: 0.8530 (mt-10) cc_final: 0.7934 (tm-30) outliers start: 138 outliers final: 108 residues processed: 351 average time/residue: 0.2732 time to fit residues: 149.8919 Evaluate side-chains 332 residues out of total 1994 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 112 poor density : 220 time to evaluate : 1.874 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 26 LEU Chi-restraints excluded: chain A residue 45 MET Chi-restraints excluded: chain A residue 55 ILE Chi-restraints excluded: chain A residue 92 LEU Chi-restraints excluded: chain A residue 128 SER Chi-restraints excluded: chain A residue 130 GLU Chi-restraints excluded: chain A residue 149 ILE Chi-restraints excluded: chain A residue 155 LEU Chi-restraints excluded: chain A residue 188 ASN Chi-restraints excluded: chain A residue 200 ILE Chi-restraints excluded: chain A residue 215 VAL Chi-restraints excluded: chain A residue 228 ILE Chi-restraints excluded: chain A residue 233 THR Chi-restraints excluded: chain A residue 237 VAL Chi-restraints excluded: chain A residue 242 CYS Chi-restraints excluded: chain A residue 246 PHE Chi-restraints excluded: chain A residue 249 VAL Chi-restraints excluded: chain A residue 251 THR Chi-restraints excluded: chain B residue 50 THR Chi-restraints excluded: chain B residue 77 ILE Chi-restraints excluded: chain B residue 103 THR Chi-restraints excluded: chain B residue 107 VAL Chi-restraints excluded: chain B residue 129 LEU Chi-restraints excluded: chain B residue 136 SER Chi-restraints excluded: chain B residue 206 VAL Chi-restraints excluded: chain B residue 208 HIS Chi-restraints excluded: chain B residue 260 GLN Chi-restraints excluded: chain B residue 263 HIS Chi-restraints excluded: chain B residue 267 LEU Chi-restraints excluded: chain C residue 50 ASN Chi-restraints excluded: chain C residue 56 VAL Chi-restraints excluded: chain C residue 68 SER Chi-restraints excluded: chain C residue 77 GLU Chi-restraints excluded: chain D residue 2 ASN Chi-restraints excluded: chain D residue 14 ARG Chi-restraints excluded: chain D residue 15 ILE Chi-restraints excluded: chain D residue 55 ILE Chi-restraints excluded: chain D residue 56 ILE Chi-restraints excluded: chain D residue 74 ILE Chi-restraints excluded: chain D residue 78 VAL Chi-restraints excluded: chain D residue 128 SER Chi-restraints excluded: chain D residue 134 VAL Chi-restraints excluded: chain D residue 164 ILE Chi-restraints excluded: chain D residue 186 MET Chi-restraints excluded: chain D residue 200 ILE Chi-restraints excluded: chain D residue 228 ILE Chi-restraints excluded: chain D residue 242 CYS Chi-restraints excluded: chain D residue 246 PHE Chi-restraints excluded: chain E residue 75 LYS Chi-restraints excluded: chain E residue 81 SER Chi-restraints excluded: chain E residue 98 SER Chi-restraints excluded: chain E residue 103 THR Chi-restraints excluded: chain E residue 105 MET Chi-restraints excluded: chain E residue 145 LEU Chi-restraints excluded: chain E residue 154 MET Chi-restraints excluded: chain E residue 181 ASP Chi-restraints excluded: chain E residue 201 LEU Chi-restraints excluded: chain E residue 206 VAL Chi-restraints excluded: chain E residue 264 GLN Chi-restraints excluded: chain F residue 17 PHE Chi-restraints excluded: chain F residue 19 ASN Chi-restraints excluded: chain F residue 21 GLU Chi-restraints excluded: chain F residue 56 VAL Chi-restraints excluded: chain F residue 73 LYS Chi-restraints excluded: chain F residue 77 GLU Chi-restraints excluded: chain G residue 16 ILE Chi-restraints excluded: chain G residue 72 THR Chi-restraints excluded: chain G residue 76 VAL Chi-restraints excluded: chain G residue 135 ASN Chi-restraints excluded: chain G residue 141 ASP Chi-restraints excluded: chain G residue 150 THR Chi-restraints excluded: chain G residue 162 VAL Chi-restraints excluded: chain G residue 185 LEU Chi-restraints excluded: chain H residue 5 THR Chi-restraints excluded: chain H residue 10 VAL Chi-restraints excluded: chain H residue 19 ILE Chi-restraints excluded: chain H residue 21 LEU Chi-restraints excluded: chain H residue 76 VAL Chi-restraints excluded: chain H residue 143 ASP Chi-restraints excluded: chain H residue 188 LEU Chi-restraints excluded: chain I residue 28 VAL Chi-restraints excluded: chain I residue 32 VAL Chi-restraints excluded: chain I residue 50 ASN Chi-restraints excluded: chain I residue 63 VAL Chi-restraints excluded: chain I residue 76 VAL Chi-restraints excluded: chain I residue 85 ASP Chi-restraints excluded: chain I residue 146 ILE Chi-restraints excluded: chain I residue 182 THR Chi-restraints excluded: chain I residue 185 LEU Chi-restraints excluded: chain J residue 10 VAL Chi-restraints excluded: chain J residue 35 ASN Chi-restraints excluded: chain J residue 36 LEU Chi-restraints excluded: chain J residue 64 THR Chi-restraints excluded: chain J residue 93 PHE Chi-restraints excluded: chain J residue 150 THR Chi-restraints excluded: chain K residue 35 ASN Chi-restraints excluded: chain K residue 135 ASN Chi-restraints excluded: chain K residue 145 TYR Chi-restraints excluded: chain K residue 150 THR Chi-restraints excluded: chain K residue 170 LEU Chi-restraints excluded: chain L residue 8 LEU Chi-restraints excluded: chain L residue 21 LEU Chi-restraints excluded: chain L residue 24 LEU Chi-restraints excluded: chain L residue 28 VAL Chi-restraints excluded: chain L residue 69 ASP Chi-restraints excluded: chain L residue 83 THR Chi-restraints excluded: chain L residue 142 GLU Chi-restraints excluded: chain L residue 150 THR Chi-restraints excluded: chain L residue 174 ASP Chi-restraints excluded: chain L residue 178 ASN Chi-restraints excluded: chain L residue 179 THR Chi-restraints excluded: chain L residue 182 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 234 random chunks: chunk 76 optimal weight: 3.9990 chunk 203 optimal weight: 8.9990 chunk 44 optimal weight: 7.9990 chunk 132 optimal weight: 6.9990 chunk 55 optimal weight: 2.9990 chunk 226 optimal weight: 0.0040 chunk 187 optimal weight: 8.9990 chunk 104 optimal weight: 7.9990 chunk 18 optimal weight: 5.9990 chunk 74 optimal weight: 2.9990 chunk 118 optimal weight: 7.9990 overall best weight: 3.2000 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 125 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 238 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 260 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 25 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 34 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 67 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 6 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 63 GLN ** I 97 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 135 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 94 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7883 moved from start: 0.4099 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 18044 Z= 0.209 Angle : 0.692 14.156 24448 Z= 0.348 Chirality : 0.043 0.185 2968 Planarity : 0.004 0.047 3102 Dihedral : 7.319 111.623 2553 Min Nonbonded Distance : 2.154 Molprobity Statistics. All-atom Clashscore : 15.41 Ramachandran Plot: Outliers : 0.09 % Allowed : 9.66 % Favored : 90.26 % Rotamer: Outliers : 6.67 % Allowed : 26.09 % Favored : 67.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.93 (0.16), residues: 2350 helix: -1.08 (0.16), residues: 978 sheet: -1.42 (0.33), residues: 257 loop : -2.91 (0.17), residues: 1115 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.002 TRP A 6 HIS 0.011 0.001 HIS A 46 PHE 0.026 0.001 PHE C 17 TYR 0.015 0.001 TYR J 145 ARG 0.003 0.000 ARG G 67 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4700 Ramachandran restraints generated. 2350 Oldfield, 0 Emsley, 2350 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4700 Ramachandran restraints generated. 2350 Oldfield, 0 Emsley, 2350 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 371 residues out of total 1994 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 125 poor density : 246 time to evaluate : 2.107 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: A 70 GLN cc_start: 0.6857 (mm110) cc_final: 0.6524 (tp-100) REVERT: A 139 GLN cc_start: 0.8054 (tp40) cc_final: 0.7848 (tm-30) REVERT: A 154 MET cc_start: 0.8693 (mtt) cc_final: 0.8412 (mtt) REVERT: A 254 MET cc_start: 0.7714 (mmm) cc_final: 0.7242 (mmm) REVERT: D 14 ARG cc_start: 0.7630 (OUTLIER) cc_final: 0.7132 (mmt180) REVERT: D 198 ASN cc_start: 0.7802 (m-40) cc_final: 0.6268 (t0) REVERT: D 228 ILE cc_start: 0.7621 (OUTLIER) cc_final: 0.7295 (tt) REVERT: E 146 MET cc_start: 0.8692 (tpp) cc_final: 0.8147 (mmm) REVERT: E 264 GLN cc_start: 0.8863 (OUTLIER) cc_final: 0.8411 (mp10) REVERT: G 12 ILE cc_start: 0.8465 (tt) cc_final: 0.8136 (tp) REVERT: G 46 PHE cc_start: 0.8821 (m-80) cc_final: 0.8382 (m-10) REVERT: G 96 GLU cc_start: 0.8771 (tp30) cc_final: 0.8446 (tp30) REVERT: H 4 ARG cc_start: 0.5907 (ttt180) cc_final: 0.5426 (tpp-160) REVERT: H 180 GLN cc_start: 0.8916 (tp40) cc_final: 0.8352 (tm-30) REVERT: J 15 ILE cc_start: 0.8499 (OUTLIER) cc_final: 0.8224 (mt) REVERT: J 26 MET cc_start: 0.6684 (mmt) cc_final: 0.6477 (mmt) REVERT: J 93 PHE cc_start: 0.6942 (OUTLIER) cc_final: 0.6493 (m-80) REVERT: K 147 MET cc_start: 0.7164 (ptm) cc_final: 0.6851 (ptm) REVERT: L 15 ILE cc_start: 0.8329 (tp) cc_final: 0.8100 (tt) REVERT: L 24 LEU cc_start: 0.5713 (OUTLIER) cc_final: 0.5462 (tm) REVERT: L 100 GLU cc_start: 0.8480 (mt-10) cc_final: 0.7917 (tm-30) REVERT: L 147 MET cc_start: 0.9034 (ppp) cc_final: 0.8800 (ppp) outliers start: 125 outliers final: 98 residues processed: 348 average time/residue: 0.2711 time to fit residues: 146.0539 Evaluate side-chains 327 residues out of total 1994 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 104 poor density : 223 time to evaluate : 2.124 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 26 LEU Chi-restraints excluded: chain A residue 45 MET Chi-restraints excluded: chain A residue 55 ILE Chi-restraints excluded: chain A residue 92 LEU Chi-restraints excluded: chain A residue 130 GLU Chi-restraints excluded: chain A residue 149 ILE Chi-restraints excluded: chain A residue 155 LEU Chi-restraints excluded: chain A residue 188 ASN Chi-restraints excluded: chain A residue 200 ILE Chi-restraints excluded: chain A residue 228 ILE Chi-restraints excluded: chain A residue 233 THR Chi-restraints excluded: chain A residue 242 CYS Chi-restraints excluded: chain A residue 246 PHE Chi-restraints excluded: chain A residue 249 VAL Chi-restraints excluded: chain A residue 251 THR Chi-restraints excluded: chain B residue 50 THR Chi-restraints excluded: chain B residue 77 ILE Chi-restraints excluded: chain B residue 103 THR Chi-restraints excluded: chain B residue 107 VAL Chi-restraints excluded: chain B residue 129 LEU Chi-restraints excluded: chain B residue 136 SER Chi-restraints excluded: chain B residue 166 LEU Chi-restraints excluded: chain B residue 206 VAL Chi-restraints excluded: chain B residue 208 HIS Chi-restraints excluded: chain B residue 260 GLN Chi-restraints excluded: chain B residue 263 HIS Chi-restraints excluded: chain B residue 267 LEU Chi-restraints excluded: chain C residue 56 VAL Chi-restraints excluded: chain C residue 68 SER Chi-restraints excluded: chain C residue 77 GLU Chi-restraints excluded: chain D residue 2 ASN Chi-restraints excluded: chain D residue 14 ARG Chi-restraints excluded: chain D residue 15 ILE Chi-restraints excluded: chain D residue 55 ILE Chi-restraints excluded: chain D residue 56 ILE Chi-restraints excluded: chain D residue 74 ILE Chi-restraints excluded: chain D residue 78 VAL Chi-restraints excluded: chain D residue 128 SER Chi-restraints excluded: chain D residue 164 ILE Chi-restraints excluded: chain D residue 186 MET Chi-restraints excluded: chain D residue 200 ILE Chi-restraints excluded: chain D residue 228 ILE Chi-restraints excluded: chain D residue 242 CYS Chi-restraints excluded: chain D residue 246 PHE Chi-restraints excluded: chain E residue 75 LYS Chi-restraints excluded: chain E residue 77 ILE Chi-restraints excluded: chain E residue 81 SER Chi-restraints excluded: chain E residue 98 SER Chi-restraints excluded: chain E residue 103 THR Chi-restraints excluded: chain E residue 105 MET Chi-restraints excluded: chain E residue 145 LEU Chi-restraints excluded: chain E residue 181 ASP Chi-restraints excluded: chain E residue 201 LEU Chi-restraints excluded: chain E residue 206 VAL Chi-restraints excluded: chain E residue 264 GLN Chi-restraints excluded: chain F residue 17 PHE Chi-restraints excluded: chain F residue 19 ASN Chi-restraints excluded: chain F residue 56 VAL Chi-restraints excluded: chain F residue 73 LYS Chi-restraints excluded: chain F residue 77 GLU Chi-restraints excluded: chain G residue 16 ILE Chi-restraints excluded: chain G residue 72 THR Chi-restraints excluded: chain G residue 76 VAL Chi-restraints excluded: chain G residue 135 ASN Chi-restraints excluded: chain G residue 141 ASP Chi-restraints excluded: chain G residue 150 THR Chi-restraints excluded: chain G residue 162 VAL Chi-restraints excluded: chain G residue 185 LEU Chi-restraints excluded: chain H residue 5 THR Chi-restraints excluded: chain H residue 10 VAL Chi-restraints excluded: chain H residue 21 LEU Chi-restraints excluded: chain H residue 76 VAL Chi-restraints excluded: chain H residue 141 ASP Chi-restraints excluded: chain H residue 178 ASN Chi-restraints excluded: chain H residue 188 LEU Chi-restraints excluded: chain I residue 28 VAL Chi-restraints excluded: chain I residue 32 VAL Chi-restraints excluded: chain I residue 50 ASN Chi-restraints excluded: chain I residue 63 VAL Chi-restraints excluded: chain I residue 76 VAL Chi-restraints excluded: chain I residue 85 ASP Chi-restraints excluded: chain I residue 146 ILE Chi-restraints excluded: chain I residue 167 LEU Chi-restraints excluded: chain I residue 185 LEU Chi-restraints excluded: chain J residue 15 ILE Chi-restraints excluded: chain J residue 19 ILE Chi-restraints excluded: chain J residue 35 ASN Chi-restraints excluded: chain J residue 36 LEU Chi-restraints excluded: chain J residue 64 THR Chi-restraints excluded: chain J residue 93 PHE Chi-restraints excluded: chain J residue 150 THR Chi-restraints excluded: chain K residue 35 ASN Chi-restraints excluded: chain K residue 135 ASN Chi-restraints excluded: chain K residue 145 TYR Chi-restraints excluded: chain K residue 150 THR Chi-restraints excluded: chain K residue 170 LEU Chi-restraints excluded: chain L residue 21 LEU Chi-restraints excluded: chain L residue 24 LEU Chi-restraints excluded: chain L residue 69 ASP Chi-restraints excluded: chain L residue 83 THR Chi-restraints excluded: chain L residue 142 GLU Chi-restraints excluded: chain L residue 178 ASN Chi-restraints excluded: chain L residue 179 THR Chi-restraints excluded: chain L residue 182 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 234 random chunks: chunk 218 optimal weight: 20.0000 chunk 25 optimal weight: 7.9990 chunk 128 optimal weight: 7.9990 chunk 165 optimal weight: 7.9990 chunk 190 optimal weight: 10.0000 chunk 126 optimal weight: 6.9990 chunk 225 optimal weight: 4.9990 chunk 141 optimal weight: 9.9990 chunk 137 optimal weight: 10.0000 chunk 104 optimal weight: 8.9990 chunk 139 optimal weight: 6.9990 overall best weight: 6.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 125 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 238 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 260 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 25 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 34 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 77 ASN E 62 GLN ** E 67 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 6 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 34 GLN ** F 63 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 133 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 97 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 135 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 94 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7961 moved from start: 0.4356 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.045 18044 Z= 0.369 Angle : 0.798 11.931 24448 Z= 0.404 Chirality : 0.046 0.190 2968 Planarity : 0.005 0.056 3102 Dihedral : 7.614 119.913 2552 Min Nonbonded Distance : 2.054 Molprobity Statistics. All-atom Clashscore : 19.78 Ramachandran Plot: Outliers : 0.09 % Allowed : 12.00 % Favored : 87.91 % Rotamer: Outliers : 7.95 % Allowed : 26.95 % Favored : 65.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.14 (0.16), residues: 2350 helix: -1.16 (0.15), residues: 964 sheet: -1.35 (0.34), residues: 239 loop : -3.15 (0.17), residues: 1147 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.003 TRP A 6 HIS 0.008 0.002 HIS E 118 PHE 0.031 0.002 PHE C 17 TYR 0.017 0.002 TYR A 43 ARG 0.004 0.001 ARG L 67 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4700 Ramachandran restraints generated. 2350 Oldfield, 0 Emsley, 2350 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4700 Ramachandran restraints generated. 2350 Oldfield, 0 Emsley, 2350 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 374 residues out of total 1994 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 149 poor density : 225 time to evaluate : 2.081 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: A 70 GLN cc_start: 0.6910 (mm110) cc_final: 0.6610 (tp-100) REVERT: A 119 SER cc_start: 0.7615 (OUTLIER) cc_final: 0.7342 (m) REVERT: B 264 GLN cc_start: 0.7608 (OUTLIER) cc_final: 0.7246 (mm-40) REVERT: D 14 ARG cc_start: 0.7625 (OUTLIER) cc_final: 0.6850 (mmt180) REVERT: D 198 ASN cc_start: 0.7694 (m-40) cc_final: 0.7446 (t0) REVERT: D 217 GLN cc_start: 0.9323 (OUTLIER) cc_final: 0.8983 (tp40) REVERT: E 146 MET cc_start: 0.8823 (tpp) cc_final: 0.8219 (mmm) REVERT: E 223 VAL cc_start: 0.8315 (OUTLIER) cc_final: 0.8040 (p) REVERT: E 264 GLN cc_start: 0.8833 (OUTLIER) cc_final: 0.8375 (mp10) REVERT: H 4 ARG cc_start: 0.5930 (ttt180) cc_final: 0.5464 (tpp80) REVERT: H 180 GLN cc_start: 0.9000 (tp40) cc_final: 0.8431 (tt0) REVERT: I 169 TYR cc_start: 0.8174 (m-10) cc_final: 0.7948 (m-10) REVERT: J 15 ILE cc_start: 0.8527 (OUTLIER) cc_final: 0.8251 (mt) REVERT: J 26 MET cc_start: 0.6751 (mmt) cc_final: 0.6549 (mmt) REVERT: J 93 PHE cc_start: 0.6874 (OUTLIER) cc_final: 0.6448 (m-80) REVERT: K 7 GLU cc_start: 0.8784 (mm-30) cc_final: 0.8532 (tp30) REVERT: K 147 MET cc_start: 0.7336 (ptm) cc_final: 0.7094 (ptm) REVERT: L 100 GLU cc_start: 0.8454 (mt-10) cc_final: 0.7967 (tm-30) REVERT: L 147 MET cc_start: 0.9068 (ppp) cc_final: 0.8825 (ppp) outliers start: 149 outliers final: 118 residues processed: 342 average time/residue: 0.2600 time to fit residues: 139.2244 Evaluate side-chains 347 residues out of total 1994 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 126 poor density : 221 time to evaluate : 1.911 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 26 LEU Chi-restraints excluded: chain A residue 45 MET Chi-restraints excluded: chain A residue 55 ILE Chi-restraints excluded: chain A residue 56 ILE Chi-restraints excluded: chain A residue 74 ILE Chi-restraints excluded: chain A residue 92 LEU Chi-restraints excluded: chain A residue 119 SER Chi-restraints excluded: chain A residue 130 GLU Chi-restraints excluded: chain A residue 155 LEU Chi-restraints excluded: chain A residue 188 ASN Chi-restraints excluded: chain A residue 200 ILE Chi-restraints excluded: chain A residue 215 VAL Chi-restraints excluded: chain A residue 228 ILE Chi-restraints excluded: chain A residue 233 THR Chi-restraints excluded: chain A residue 242 CYS Chi-restraints excluded: chain A residue 246 PHE Chi-restraints excluded: chain A residue 249 VAL Chi-restraints excluded: chain A residue 251 THR Chi-restraints excluded: chain B residue 14 ILE Chi-restraints excluded: chain B residue 18 ASN Chi-restraints excluded: chain B residue 50 THR Chi-restraints excluded: chain B residue 77 ILE Chi-restraints excluded: chain B residue 103 THR Chi-restraints excluded: chain B residue 107 VAL Chi-restraints excluded: chain B residue 136 SER Chi-restraints excluded: chain B residue 166 LEU Chi-restraints excluded: chain B residue 206 VAL Chi-restraints excluded: chain B residue 208 HIS Chi-restraints excluded: chain B residue 222 VAL Chi-restraints excluded: chain B residue 260 GLN Chi-restraints excluded: chain B residue 263 HIS Chi-restraints excluded: chain B residue 264 GLN Chi-restraints excluded: chain B residue 267 LEU Chi-restraints excluded: chain C residue 43 LEU Chi-restraints excluded: chain C residue 56 VAL Chi-restraints excluded: chain C residue 57 LEU Chi-restraints excluded: chain C residue 68 SER Chi-restraints excluded: chain C residue 77 GLU Chi-restraints excluded: chain D residue 2 ASN Chi-restraints excluded: chain D residue 14 ARG Chi-restraints excluded: chain D residue 15 ILE Chi-restraints excluded: chain D residue 55 ILE Chi-restraints excluded: chain D residue 56 ILE Chi-restraints excluded: chain D residue 74 ILE Chi-restraints excluded: chain D residue 78 VAL Chi-restraints excluded: chain D residue 130 GLU Chi-restraints excluded: chain D residue 134 VAL Chi-restraints excluded: chain D residue 135 ASP Chi-restraints excluded: chain D residue 164 ILE Chi-restraints excluded: chain D residue 170 VAL Chi-restraints excluded: chain D residue 186 MET Chi-restraints excluded: chain D residue 196 VAL Chi-restraints excluded: chain D residue 200 ILE Chi-restraints excluded: chain D residue 204 ILE Chi-restraints excluded: chain D residue 217 GLN Chi-restraints excluded: chain D residue 228 ILE Chi-restraints excluded: chain D residue 242 CYS Chi-restraints excluded: chain D residue 246 PHE Chi-restraints excluded: chain E residue 75 LYS Chi-restraints excluded: chain E residue 98 SER Chi-restraints excluded: chain E residue 103 THR Chi-restraints excluded: chain E residue 105 MET Chi-restraints excluded: chain E residue 154 MET Chi-restraints excluded: chain E residue 181 ASP Chi-restraints excluded: chain E residue 201 LEU Chi-restraints excluded: chain E residue 206 VAL Chi-restraints excluded: chain E residue 223 VAL Chi-restraints excluded: chain E residue 264 GLN Chi-restraints excluded: chain F residue 11 VAL Chi-restraints excluded: chain F residue 17 PHE Chi-restraints excluded: chain F residue 19 ASN Chi-restraints excluded: chain F residue 21 GLU Chi-restraints excluded: chain F residue 30 ILE Chi-restraints excluded: chain F residue 56 VAL Chi-restraints excluded: chain F residue 73 LYS Chi-restraints excluded: chain G residue 16 ILE Chi-restraints excluded: chain G residue 72 THR Chi-restraints excluded: chain G residue 76 VAL Chi-restraints excluded: chain G residue 94 ASN Chi-restraints excluded: chain G residue 135 ASN Chi-restraints excluded: chain G residue 141 ASP Chi-restraints excluded: chain G residue 150 THR Chi-restraints excluded: chain G residue 162 VAL Chi-restraints excluded: chain G residue 185 LEU Chi-restraints excluded: chain H residue 5 THR Chi-restraints excluded: chain H residue 10 VAL Chi-restraints excluded: chain H residue 19 ILE Chi-restraints excluded: chain H residue 21 LEU Chi-restraints excluded: chain H residue 76 VAL Chi-restraints excluded: chain H residue 143 ASP Chi-restraints excluded: chain H residue 178 ASN Chi-restraints excluded: chain H residue 188 LEU Chi-restraints excluded: chain I residue 6 SER Chi-restraints excluded: chain I residue 28 VAL Chi-restraints excluded: chain I residue 32 VAL Chi-restraints excluded: chain I residue 63 VAL Chi-restraints excluded: chain I residue 76 VAL Chi-restraints excluded: chain I residue 85 ASP Chi-restraints excluded: chain I residue 146 ILE Chi-restraints excluded: chain I residue 167 LEU Chi-restraints excluded: chain I residue 182 THR Chi-restraints excluded: chain I residue 185 LEU Chi-restraints excluded: chain J residue 10 VAL Chi-restraints excluded: chain J residue 15 ILE Chi-restraints excluded: chain J residue 16 ILE Chi-restraints excluded: chain J residue 19 ILE Chi-restraints excluded: chain J residue 35 ASN Chi-restraints excluded: chain J residue 36 LEU Chi-restraints excluded: chain J residue 64 THR Chi-restraints excluded: chain J residue 93 PHE Chi-restraints excluded: chain J residue 150 THR Chi-restraints excluded: chain J residue 187 ASP Chi-restraints excluded: chain K residue 35 ASN Chi-restraints excluded: chain K residue 135 ASN Chi-restraints excluded: chain K residue 145 TYR Chi-restraints excluded: chain K residue 146 ILE Chi-restraints excluded: chain K residue 150 THR Chi-restraints excluded: chain K residue 170 LEU Chi-restraints excluded: chain L residue 21 LEU Chi-restraints excluded: chain L residue 28 VAL Chi-restraints excluded: chain L residue 69 ASP Chi-restraints excluded: chain L residue 83 THR Chi-restraints excluded: chain L residue 142 GLU Chi-restraints excluded: chain L residue 178 ASN Chi-restraints excluded: chain L residue 179 THR Chi-restraints excluded: chain L residue 182 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 234 random chunks: chunk 90 optimal weight: 20.0000 chunk 134 optimal weight: 9.9990 chunk 67 optimal weight: 7.9990 chunk 44 optimal weight: 5.9990 chunk 43 optimal weight: 2.9990 chunk 143 optimal weight: 2.9990 chunk 153 optimal weight: 7.9990 chunk 111 optimal weight: 0.9990 chunk 21 optimal weight: 5.9990 chunk 177 optimal weight: 5.9990 chunk 205 optimal weight: 2.9990 overall best weight: 3.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 125 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 238 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 260 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 34 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 67 GLN ** F 6 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 63 GLN ** G 133 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 97 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 135 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7896 moved from start: 0.4521 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 18044 Z= 0.215 Angle : 0.717 12.267 24448 Z= 0.360 Chirality : 0.043 0.178 2968 Planarity : 0.004 0.048 3102 Dihedral : 7.107 117.947 2547 Min Nonbonded Distance : 2.158 Molprobity Statistics. All-atom Clashscore : 15.78 Ramachandran Plot: Outliers : 0.09 % Allowed : 9.36 % Favored : 90.55 % Rotamer: Outliers : 6.46 % Allowed : 28.34 % Favored : 65.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.80 (0.17), residues: 2350 helix: -0.85 (0.16), residues: 972 sheet: -1.38 (0.33), residues: 261 loop : -2.96 (0.17), residues: 1117 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP A 6 HIS 0.006 0.001 HIS A 46 PHE 0.024 0.002 PHE C 17 TYR 0.016 0.001 TYR J 145 ARG 0.003 0.000 ARG B 82 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4700 Ramachandran restraints generated. 2350 Oldfield, 0 Emsley, 2350 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4700 Ramachandran restraints generated. 2350 Oldfield, 0 Emsley, 2350 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 364 residues out of total 1994 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 121 poor density : 243 time to evaluate : 2.012 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: A 70 GLN cc_start: 0.6822 (mm110) cc_final: 0.6500 (tp-100) REVERT: A 119 SER cc_start: 0.7481 (OUTLIER) cc_final: 0.7196 (m) REVERT: A 154 MET cc_start: 0.8753 (mtt) cc_final: 0.8477 (mtt) REVERT: A 254 MET cc_start: 0.7701 (mmm) cc_final: 0.7288 (mmm) REVERT: B 92 MET cc_start: 0.8326 (ppp) cc_final: 0.7780 (ptp) REVERT: D 14 ARG cc_start: 0.7534 (OUTLIER) cc_final: 0.6807 (mmt180) REVERT: E 223 VAL cc_start: 0.8405 (OUTLIER) cc_final: 0.8080 (p) REVERT: E 264 GLN cc_start: 0.8811 (OUTLIER) cc_final: 0.8354 (mp10) REVERT: G 12 ILE cc_start: 0.8512 (tt) cc_final: 0.8188 (tp) REVERT: G 46 PHE cc_start: 0.8810 (m-80) cc_final: 0.8272 (m-10) REVERT: H 4 ARG cc_start: 0.5969 (ttt180) cc_final: 0.5544 (tpp80) REVERT: H 134 MET cc_start: 0.5562 (ptt) cc_final: 0.5360 (ptt) REVERT: H 180 GLN cc_start: 0.8918 (tp40) cc_final: 0.8412 (tm-30) REVERT: I 169 TYR cc_start: 0.8130 (m-10) cc_final: 0.7899 (m-10) REVERT: J 15 ILE cc_start: 0.8449 (OUTLIER) cc_final: 0.8174 (mt) REVERT: J 26 MET cc_start: 0.6678 (mmt) cc_final: 0.6461 (mmt) REVERT: J 93 PHE cc_start: 0.6875 (OUTLIER) cc_final: 0.6322 (m-80) REVERT: K 147 MET cc_start: 0.7175 (ptm) cc_final: 0.6872 (ptm) REVERT: L 100 GLU cc_start: 0.8429 (mt-10) cc_final: 0.7897 (tm-30) REVERT: L 147 MET cc_start: 0.9081 (ppp) cc_final: 0.8854 (ppp) outliers start: 121 outliers final: 103 residues processed: 340 average time/residue: 0.2712 time to fit residues: 141.8944 Evaluate side-chains 333 residues out of total 1994 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 109 poor density : 224 time to evaluate : 1.938 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 45 MET Chi-restraints excluded: chain A residue 55 ILE Chi-restraints excluded: chain A residue 56 ILE Chi-restraints excluded: chain A residue 92 LEU Chi-restraints excluded: chain A residue 119 SER Chi-restraints excluded: chain A residue 130 GLU Chi-restraints excluded: chain A residue 155 LEU Chi-restraints excluded: chain A residue 188 ASN Chi-restraints excluded: chain A residue 200 ILE Chi-restraints excluded: chain A residue 228 ILE Chi-restraints excluded: chain A residue 233 THR Chi-restraints excluded: chain A residue 242 CYS Chi-restraints excluded: chain A residue 246 PHE Chi-restraints excluded: chain A residue 249 VAL Chi-restraints excluded: chain A residue 251 THR Chi-restraints excluded: chain B residue 14 ILE Chi-restraints excluded: chain B residue 77 ILE Chi-restraints excluded: chain B residue 107 VAL Chi-restraints excluded: chain B residue 129 LEU Chi-restraints excluded: chain B residue 136 SER Chi-restraints excluded: chain B residue 206 VAL Chi-restraints excluded: chain B residue 208 HIS Chi-restraints excluded: chain B residue 222 VAL Chi-restraints excluded: chain B residue 260 GLN Chi-restraints excluded: chain B residue 263 HIS Chi-restraints excluded: chain C residue 43 LEU Chi-restraints excluded: chain C residue 56 VAL Chi-restraints excluded: chain C residue 77 GLU Chi-restraints excluded: chain D residue 2 ASN Chi-restraints excluded: chain D residue 14 ARG Chi-restraints excluded: chain D residue 15 ILE Chi-restraints excluded: chain D residue 55 ILE Chi-restraints excluded: chain D residue 56 ILE Chi-restraints excluded: chain D residue 74 ILE Chi-restraints excluded: chain D residue 78 VAL Chi-restraints excluded: chain D residue 134 VAL Chi-restraints excluded: chain D residue 164 ILE Chi-restraints excluded: chain D residue 170 VAL Chi-restraints excluded: chain D residue 186 MET Chi-restraints excluded: chain D residue 196 VAL Chi-restraints excluded: chain D residue 200 ILE Chi-restraints excluded: chain D residue 228 ILE Chi-restraints excluded: chain D residue 242 CYS Chi-restraints excluded: chain D residue 246 PHE Chi-restraints excluded: chain E residue 18 ASN Chi-restraints excluded: chain E residue 75 LYS Chi-restraints excluded: chain E residue 98 SER Chi-restraints excluded: chain E residue 103 THR Chi-restraints excluded: chain E residue 105 MET Chi-restraints excluded: chain E residue 181 ASP Chi-restraints excluded: chain E residue 206 VAL Chi-restraints excluded: chain E residue 223 VAL Chi-restraints excluded: chain E residue 227 LYS Chi-restraints excluded: chain E residue 264 GLN Chi-restraints excluded: chain F residue 11 VAL Chi-restraints excluded: chain F residue 17 PHE Chi-restraints excluded: chain F residue 19 ASN Chi-restraints excluded: chain F residue 21 GLU Chi-restraints excluded: chain F residue 30 ILE Chi-restraints excluded: chain F residue 56 VAL Chi-restraints excluded: chain F residue 63 GLN Chi-restraints excluded: chain F residue 73 LYS Chi-restraints excluded: chain G residue 16 ILE Chi-restraints excluded: chain G residue 34 THR Chi-restraints excluded: chain G residue 72 THR Chi-restraints excluded: chain G residue 76 VAL Chi-restraints excluded: chain G residue 135 ASN Chi-restraints excluded: chain G residue 141 ASP Chi-restraints excluded: chain G residue 150 THR Chi-restraints excluded: chain G residue 162 VAL Chi-restraints excluded: chain G residue 185 LEU Chi-restraints excluded: chain H residue 5 THR Chi-restraints excluded: chain H residue 10 VAL Chi-restraints excluded: chain H residue 19 ILE Chi-restraints excluded: chain H residue 21 LEU Chi-restraints excluded: chain H residue 76 VAL Chi-restraints excluded: chain H residue 143 ASP Chi-restraints excluded: chain H residue 178 ASN Chi-restraints excluded: chain H residue 188 LEU Chi-restraints excluded: chain I residue 28 VAL Chi-restraints excluded: chain I residue 32 VAL Chi-restraints excluded: chain I residue 50 ASN Chi-restraints excluded: chain I residue 63 VAL Chi-restraints excluded: chain I residue 76 VAL Chi-restraints excluded: chain I residue 85 ASP Chi-restraints excluded: chain I residue 146 ILE Chi-restraints excluded: chain I residue 167 LEU Chi-restraints excluded: chain I residue 185 LEU Chi-restraints excluded: chain J residue 10 VAL Chi-restraints excluded: chain J residue 15 ILE Chi-restraints excluded: chain J residue 19 ILE Chi-restraints excluded: chain J residue 35 ASN Chi-restraints excluded: chain J residue 36 LEU Chi-restraints excluded: chain J residue 64 THR Chi-restraints excluded: chain J residue 93 PHE Chi-restraints excluded: chain J residue 150 THR Chi-restraints excluded: chain J residue 187 ASP Chi-restraints excluded: chain K residue 35 ASN Chi-restraints excluded: chain K residue 135 ASN Chi-restraints excluded: chain K residue 145 TYR Chi-restraints excluded: chain K residue 146 ILE Chi-restraints excluded: chain K residue 150 THR Chi-restraints excluded: chain K residue 170 LEU Chi-restraints excluded: chain L residue 21 LEU Chi-restraints excluded: chain L residue 69 ASP Chi-restraints excluded: chain L residue 83 THR Chi-restraints excluded: chain L residue 178 ASN Chi-restraints excluded: chain L residue 179 THR Chi-restraints excluded: chain L residue 182 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 234 random chunks: chunk 216 optimal weight: 6.9990 chunk 197 optimal weight: 3.9990 chunk 210 optimal weight: 8.9990 chunk 126 optimal weight: 4.9990 chunk 91 optimal weight: 8.9990 chunk 165 optimal weight: 7.9990 chunk 64 optimal weight: 2.9990 chunk 189 optimal weight: 20.0000 chunk 198 optimal weight: 0.9990 chunk 209 optimal weight: 6.9990 chunk 138 optimal weight: 6.9990 overall best weight: 3.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 125 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 238 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 260 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 19 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 34 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 67 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 6 ASN F 63 GLN G 180 GLN ** I 97 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 180 GLN ** J 135 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 94 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7912 moved from start: 0.4665 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 18044 Z= 0.247 Angle : 0.747 11.668 24448 Z= 0.374 Chirality : 0.044 0.217 2968 Planarity : 0.004 0.049 3102 Dihedral : 7.070 120.471 2546 Min Nonbonded Distance : 2.111 Molprobity Statistics. All-atom Clashscore : 17.29 Ramachandran Plot: Outliers : 0.09 % Allowed : 10.68 % Favored : 89.23 % Rotamer: Outliers : 6.19 % Allowed : 28.87 % Favored : 64.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.84 (0.16), residues: 2350 helix: -0.89 (0.16), residues: 1016 sheet: -1.34 (0.33), residues: 261 loop : -3.07 (0.17), residues: 1073 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP A 6 HIS 0.005 0.001 HIS A 46 PHE 0.025 0.002 PHE C 17 TYR 0.015 0.002 TYR J 145 ARG 0.019 0.000 ARG A 108 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4700 Ramachandran restraints generated. 2350 Oldfield, 0 Emsley, 2350 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4700 Ramachandran restraints generated. 2350 Oldfield, 0 Emsley, 2350 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 349 residues out of total 1994 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 116 poor density : 233 time to evaluate : 2.289 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: A 24 MET cc_start: 0.9150 (tmm) cc_final: 0.8833 (tmm) REVERT: A 43 TYR cc_start: 0.7644 (t80) cc_final: 0.7290 (t80) REVERT: A 70 GLN cc_start: 0.6803 (mm110) cc_final: 0.6560 (tp40) REVERT: A 119 SER cc_start: 0.7458 (OUTLIER) cc_final: 0.7129 (m) REVERT: A 154 MET cc_start: 0.8764 (mtt) cc_final: 0.8472 (mtt) REVERT: A 254 MET cc_start: 0.7736 (mmm) cc_final: 0.7373 (mmm) REVERT: B 133 LYS cc_start: 0.7544 (tptm) cc_final: 0.6744 (mmmm) REVERT: D 14 ARG cc_start: 0.7521 (OUTLIER) cc_final: 0.6803 (mmt180) REVERT: D 129 MET cc_start: 0.8392 (mmm) cc_final: 0.8185 (mmm) REVERT: E 223 VAL cc_start: 0.8402 (OUTLIER) cc_final: 0.8113 (p) REVERT: E 264 GLN cc_start: 0.8801 (OUTLIER) cc_final: 0.8336 (mp10) REVERT: G 12 ILE cc_start: 0.8545 (tt) cc_final: 0.8208 (tp) REVERT: G 46 PHE cc_start: 0.8831 (m-80) cc_final: 0.8296 (m-10) REVERT: H 4 ARG cc_start: 0.5961 (ttt180) cc_final: 0.5560 (tpp80) REVERT: H 180 GLN cc_start: 0.8914 (tp40) cc_final: 0.8300 (tm-30) REVERT: I 169 TYR cc_start: 0.8120 (m-10) cc_final: 0.7912 (m-10) REVERT: J 15 ILE cc_start: 0.8516 (OUTLIER) cc_final: 0.8243 (mt) REVERT: J 26 MET cc_start: 0.6683 (mmt) cc_final: 0.6465 (mmt) REVERT: J 93 PHE cc_start: 0.6879 (OUTLIER) cc_final: 0.6411 (m-80) REVERT: K 147 MET cc_start: 0.7261 (ptm) cc_final: 0.6973 (ptm) REVERT: L 100 GLU cc_start: 0.8445 (mt-10) cc_final: 0.7915 (tm-30) REVERT: L 147 MET cc_start: 0.9058 (ppp) cc_final: 0.8855 (ppp) outliers start: 116 outliers final: 102 residues processed: 325 average time/residue: 0.2622 time to fit residues: 133.3624 Evaluate side-chains 329 residues out of total 1994 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 108 poor density : 221 time to evaluate : 1.872 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 2 ASN Chi-restraints excluded: chain A residue 45 MET Chi-restraints excluded: chain A residue 55 ILE Chi-restraints excluded: chain A residue 56 ILE Chi-restraints excluded: chain A residue 89 SER Chi-restraints excluded: chain A residue 92 LEU Chi-restraints excluded: chain A residue 119 SER Chi-restraints excluded: chain A residue 130 GLU Chi-restraints excluded: chain A residue 155 LEU Chi-restraints excluded: chain A residue 188 ASN Chi-restraints excluded: chain A residue 200 ILE Chi-restraints excluded: chain A residue 228 ILE Chi-restraints excluded: chain A residue 233 THR Chi-restraints excluded: chain A residue 246 PHE Chi-restraints excluded: chain A residue 249 VAL Chi-restraints excluded: chain A residue 251 THR Chi-restraints excluded: chain B residue 14 ILE Chi-restraints excluded: chain B residue 77 ILE Chi-restraints excluded: chain B residue 107 VAL Chi-restraints excluded: chain B residue 129 LEU Chi-restraints excluded: chain B residue 136 SER Chi-restraints excluded: chain B residue 206 VAL Chi-restraints excluded: chain B residue 208 HIS Chi-restraints excluded: chain B residue 222 VAL Chi-restraints excluded: chain B residue 260 GLN Chi-restraints excluded: chain B residue 263 HIS Chi-restraints excluded: chain B residue 267 LEU Chi-restraints excluded: chain C residue 43 LEU Chi-restraints excluded: chain C residue 56 VAL Chi-restraints excluded: chain C residue 77 GLU Chi-restraints excluded: chain D residue 14 ARG Chi-restraints excluded: chain D residue 15 ILE Chi-restraints excluded: chain D residue 55 ILE Chi-restraints excluded: chain D residue 56 ILE Chi-restraints excluded: chain D residue 74 ILE Chi-restraints excluded: chain D residue 78 VAL Chi-restraints excluded: chain D residue 134 VAL Chi-restraints excluded: chain D residue 164 ILE Chi-restraints excluded: chain D residue 170 VAL Chi-restraints excluded: chain D residue 186 MET Chi-restraints excluded: chain D residue 196 VAL Chi-restraints excluded: chain D residue 200 ILE Chi-restraints excluded: chain D residue 228 ILE Chi-restraints excluded: chain D residue 242 CYS Chi-restraints excluded: chain D residue 246 PHE Chi-restraints excluded: chain E residue 18 ASN Chi-restraints excluded: chain E residue 75 LYS Chi-restraints excluded: chain E residue 81 SER Chi-restraints excluded: chain E residue 98 SER Chi-restraints excluded: chain E residue 105 MET Chi-restraints excluded: chain E residue 181 ASP Chi-restraints excluded: chain E residue 206 VAL Chi-restraints excluded: chain E residue 223 VAL Chi-restraints excluded: chain E residue 227 LYS Chi-restraints excluded: chain E residue 264 GLN Chi-restraints excluded: chain F residue 11 VAL Chi-restraints excluded: chain F residue 17 PHE Chi-restraints excluded: chain F residue 19 ASN Chi-restraints excluded: chain F residue 21 GLU Chi-restraints excluded: chain F residue 30 ILE Chi-restraints excluded: chain F residue 56 VAL Chi-restraints excluded: chain F residue 73 LYS Chi-restraints excluded: chain G residue 16 ILE Chi-restraints excluded: chain G residue 34 THR Chi-restraints excluded: chain G residue 72 THR Chi-restraints excluded: chain G residue 76 VAL Chi-restraints excluded: chain G residue 135 ASN Chi-restraints excluded: chain G residue 141 ASP Chi-restraints excluded: chain G residue 150 THR Chi-restraints excluded: chain G residue 162 VAL Chi-restraints excluded: chain G residue 185 LEU Chi-restraints excluded: chain H residue 5 THR Chi-restraints excluded: chain H residue 10 VAL Chi-restraints excluded: chain H residue 19 ILE Chi-restraints excluded: chain H residue 21 LEU Chi-restraints excluded: chain H residue 76 VAL Chi-restraints excluded: chain H residue 143 ASP Chi-restraints excluded: chain H residue 178 ASN Chi-restraints excluded: chain I residue 28 VAL Chi-restraints excluded: chain I residue 32 VAL Chi-restraints excluded: chain I residue 63 VAL Chi-restraints excluded: chain I residue 76 VAL Chi-restraints excluded: chain I residue 85 ASP Chi-restraints excluded: chain I residue 146 ILE Chi-restraints excluded: chain I residue 167 LEU Chi-restraints excluded: chain I residue 185 LEU Chi-restraints excluded: chain J residue 10 VAL Chi-restraints excluded: chain J residue 15 ILE Chi-restraints excluded: chain J residue 19 ILE Chi-restraints excluded: chain J residue 35 ASN Chi-restraints excluded: chain J residue 36 LEU Chi-restraints excluded: chain J residue 64 THR Chi-restraints excluded: chain J residue 93 PHE Chi-restraints excluded: chain J residue 150 THR Chi-restraints excluded: chain J residue 187 ASP Chi-restraints excluded: chain K residue 35 ASN Chi-restraints excluded: chain K residue 135 ASN Chi-restraints excluded: chain K residue 145 TYR Chi-restraints excluded: chain K residue 146 ILE Chi-restraints excluded: chain K residue 150 THR Chi-restraints excluded: chain K residue 170 LEU Chi-restraints excluded: chain L residue 8 LEU Chi-restraints excluded: chain L residue 21 LEU Chi-restraints excluded: chain L residue 83 THR Chi-restraints excluded: chain L residue 142 GLU Chi-restraints excluded: chain L residue 178 ASN Chi-restraints excluded: chain L residue 179 THR Chi-restraints excluded: chain L residue 182 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 234 random chunks: chunk 222 optimal weight: 5.9990 chunk 135 optimal weight: 7.9990 chunk 105 optimal weight: 8.9990 chunk 154 optimal weight: 2.9990 chunk 233 optimal weight: 0.9990 chunk 214 optimal weight: 8.9990 chunk 185 optimal weight: 2.9990 chunk 19 optimal weight: 8.9990 chunk 143 optimal weight: 10.0000 chunk 113 optimal weight: 9.9990 chunk 147 optimal weight: 0.0170 overall best weight: 2.6026 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 125 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 238 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 260 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 34 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 67 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 6 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 63 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 97 GLN ** J 135 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7880 moved from start: 0.4797 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 18044 Z= 0.197 Angle : 0.731 17.229 24448 Z= 0.364 Chirality : 0.043 0.196 2968 Planarity : 0.004 0.051 3102 Dihedral : 6.857 120.348 2543 Min Nonbonded Distance : 2.163 Molprobity Statistics. All-atom Clashscore : 15.61 Ramachandran Plot: Outliers : 0.09 % Allowed : 9.62 % Favored : 90.30 % Rotamer: Outliers : 5.44 % Allowed : 29.72 % Favored : 64.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.64 (0.17), residues: 2350 helix: -0.68 (0.16), residues: 997 sheet: -1.34 (0.32), residues: 269 loop : -2.95 (0.17), residues: 1084 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP A 6 HIS 0.005 0.001 HIS A 46 PHE 0.024 0.002 PHE C 17 TYR 0.016 0.001 TYR J 145 ARG 0.014 0.000 ARG A 108 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4700 Ramachandran restraints generated. 2350 Oldfield, 0 Emsley, 2350 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4700 Ramachandran restraints generated. 2350 Oldfield, 0 Emsley, 2350 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 331 residues out of total 1994 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 102 poor density : 229 time to evaluate : 1.993 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: A 43 TYR cc_start: 0.7642 (t80) cc_final: 0.7346 (t80) REVERT: A 70 GLN cc_start: 0.6867 (mm110) cc_final: 0.6602 (tp40) REVERT: B 92 MET cc_start: 0.8321 (ppp) cc_final: 0.7864 (ptp) REVERT: B 133 LYS cc_start: 0.7382 (tptm) cc_final: 0.6602 (mmmm) REVERT: D 14 ARG cc_start: 0.7493 (OUTLIER) cc_final: 0.6167 (mmt180) REVERT: D 217 GLN cc_start: 0.9312 (OUTLIER) cc_final: 0.8810 (tp40) REVERT: E 223 VAL cc_start: 0.8391 (OUTLIER) cc_final: 0.8102 (p) REVERT: E 264 GLN cc_start: 0.8801 (OUTLIER) cc_final: 0.8367 (mp10) REVERT: F 78 LYS cc_start: 0.9183 (mtmm) cc_final: 0.8893 (mtmm) REVERT: G 12 ILE cc_start: 0.8476 (tt) cc_final: 0.8138 (tp) REVERT: G 46 PHE cc_start: 0.8801 (m-80) cc_final: 0.8298 (m-10) REVERT: H 4 ARG cc_start: 0.6018 (ttt180) cc_final: 0.5581 (tpp80) REVERT: H 180 GLN cc_start: 0.8890 (tp40) cc_final: 0.8273 (tm-30) REVERT: I 169 TYR cc_start: 0.8101 (m-10) cc_final: 0.7885 (m-10) REVERT: J 15 ILE cc_start: 0.8438 (OUTLIER) cc_final: 0.8177 (mt) REVERT: J 93 PHE cc_start: 0.6859 (OUTLIER) cc_final: 0.6361 (m-80) REVERT: K 147 MET cc_start: 0.7282 (ptm) cc_final: 0.7009 (ptm) REVERT: L 26 MET cc_start: 0.8631 (tpt) cc_final: 0.8414 (tpt) REVERT: L 100 GLU cc_start: 0.8435 (mt-10) cc_final: 0.7906 (tm-30) REVERT: L 134 MET cc_start: 0.6645 (ptp) cc_final: 0.6349 (ptp) REVERT: L 147 MET cc_start: 0.9065 (ppp) cc_final: 0.8852 (ppp) outliers start: 102 outliers final: 91 residues processed: 311 average time/residue: 0.2596 time to fit residues: 125.6653 Evaluate side-chains 321 residues out of total 1994 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 97 poor density : 224 time to evaluate : 2.009 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 45 MET Chi-restraints excluded: chain A residue 55 ILE Chi-restraints excluded: chain A residue 56 ILE Chi-restraints excluded: chain A residue 92 LEU Chi-restraints excluded: chain A residue 130 GLU Chi-restraints excluded: chain A residue 155 LEU Chi-restraints excluded: chain A residue 200 ILE Chi-restraints excluded: chain A residue 215 VAL Chi-restraints excluded: chain A residue 228 ILE Chi-restraints excluded: chain A residue 233 THR Chi-restraints excluded: chain A residue 246 PHE Chi-restraints excluded: chain A residue 249 VAL Chi-restraints excluded: chain A residue 251 THR Chi-restraints excluded: chain B residue 14 ILE Chi-restraints excluded: chain B residue 77 ILE Chi-restraints excluded: chain B residue 107 VAL Chi-restraints excluded: chain B residue 136 SER Chi-restraints excluded: chain B residue 206 VAL Chi-restraints excluded: chain B residue 208 HIS Chi-restraints excluded: chain B residue 222 VAL Chi-restraints excluded: chain B residue 260 GLN Chi-restraints excluded: chain B residue 263 HIS Chi-restraints excluded: chain C residue 43 LEU Chi-restraints excluded: chain C residue 56 VAL Chi-restraints excluded: chain C residue 77 GLU Chi-restraints excluded: chain D residue 14 ARG Chi-restraints excluded: chain D residue 15 ILE Chi-restraints excluded: chain D residue 55 ILE Chi-restraints excluded: chain D residue 56 ILE Chi-restraints excluded: chain D residue 78 VAL Chi-restraints excluded: chain D residue 186 MET Chi-restraints excluded: chain D residue 200 ILE Chi-restraints excluded: chain D residue 217 GLN Chi-restraints excluded: chain D residue 228 ILE Chi-restraints excluded: chain D residue 242 CYS Chi-restraints excluded: chain D residue 246 PHE Chi-restraints excluded: chain E residue 18 ASN Chi-restraints excluded: chain E residue 75 LYS Chi-restraints excluded: chain E residue 81 SER Chi-restraints excluded: chain E residue 98 SER Chi-restraints excluded: chain E residue 105 MET Chi-restraints excluded: chain E residue 154 MET Chi-restraints excluded: chain E residue 181 ASP Chi-restraints excluded: chain E residue 206 VAL Chi-restraints excluded: chain E residue 223 VAL Chi-restraints excluded: chain E residue 227 LYS Chi-restraints excluded: chain E residue 264 GLN Chi-restraints excluded: chain F residue 11 VAL Chi-restraints excluded: chain F residue 17 PHE Chi-restraints excluded: chain F residue 19 ASN Chi-restraints excluded: chain F residue 21 GLU Chi-restraints excluded: chain F residue 56 VAL Chi-restraints excluded: chain F residue 73 LYS Chi-restraints excluded: chain G residue 16 ILE Chi-restraints excluded: chain G residue 34 THR Chi-restraints excluded: chain G residue 72 THR Chi-restraints excluded: chain G residue 76 VAL Chi-restraints excluded: chain G residue 141 ASP Chi-restraints excluded: chain G residue 150 THR Chi-restraints excluded: chain G residue 162 VAL Chi-restraints excluded: chain G residue 185 LEU Chi-restraints excluded: chain H residue 5 THR Chi-restraints excluded: chain H residue 10 VAL Chi-restraints excluded: chain H residue 19 ILE Chi-restraints excluded: chain H residue 21 LEU Chi-restraints excluded: chain H residue 76 VAL Chi-restraints excluded: chain H residue 178 ASN Chi-restraints excluded: chain I residue 28 VAL Chi-restraints excluded: chain I residue 32 VAL Chi-restraints excluded: chain I residue 50 ASN Chi-restraints excluded: chain I residue 76 VAL Chi-restraints excluded: chain I residue 85 ASP Chi-restraints excluded: chain I residue 146 ILE Chi-restraints excluded: chain I residue 167 LEU Chi-restraints excluded: chain I residue 185 LEU Chi-restraints excluded: chain J residue 10 VAL Chi-restraints excluded: chain J residue 15 ILE Chi-restraints excluded: chain J residue 19 ILE Chi-restraints excluded: chain J residue 35 ASN Chi-restraints excluded: chain J residue 36 LEU Chi-restraints excluded: chain J residue 64 THR Chi-restraints excluded: chain J residue 93 PHE Chi-restraints excluded: chain J residue 143 ASP Chi-restraints excluded: chain J residue 150 THR Chi-restraints excluded: chain J residue 187 ASP Chi-restraints excluded: chain K residue 35 ASN Chi-restraints excluded: chain K residue 135 ASN Chi-restraints excluded: chain K residue 145 TYR Chi-restraints excluded: chain K residue 146 ILE Chi-restraints excluded: chain K residue 150 THR Chi-restraints excluded: chain K residue 170 LEU Chi-restraints excluded: chain L residue 21 LEU Chi-restraints excluded: chain L residue 83 THR Chi-restraints excluded: chain L residue 142 GLU Chi-restraints excluded: chain L residue 178 ASN Chi-restraints excluded: chain L residue 179 THR Chi-restraints excluded: chain L residue 182 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 234 random chunks: chunk 197 optimal weight: 0.0970 chunk 56 optimal weight: 5.9990 chunk 171 optimal weight: 20.0000 chunk 27 optimal weight: 5.9990 chunk 51 optimal weight: 0.4980 chunk 185 optimal weight: 1.9990 chunk 77 optimal weight: 5.9990 chunk 190 optimal weight: 0.9990 chunk 23 optimal weight: 2.9990 chunk 34 optimal weight: 9.9990 chunk 163 optimal weight: 1.9990 overall best weight: 1.1184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 238 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 260 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 62 GLN ** F 6 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 63 GLN J 135 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3794 r_free = 0.3794 target = 0.097118 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3449 r_free = 0.3449 target = 0.079853 restraints weight = 71375.716| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3477 r_free = 0.3477 target = 0.080976 restraints weight = 47652.798| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3482 r_free = 0.3482 target = 0.081326 restraints weight = 32332.299| |-----------------------------------------------------------------------------| r_work (final): 0.3475 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7835 moved from start: 0.5018 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 18044 Z= 0.167 Angle : 0.728 17.016 24448 Z= 0.355 Chirality : 0.043 0.206 2968 Planarity : 0.004 0.052 3102 Dihedral : 6.554 119.274 2541 Min Nonbonded Distance : 2.203 Molprobity Statistics. All-atom Clashscore : 13.76 Ramachandran Plot: Outliers : 0.09 % Allowed : 9.02 % Favored : 90.89 % Rotamer: Outliers : 3.74 % Allowed : 31.27 % Favored : 64.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.40 (0.17), residues: 2350 helix: -0.44 (0.16), residues: 1004 sheet: -1.07 (0.34), residues: 253 loop : -2.90 (0.17), residues: 1093 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 6 HIS 0.005 0.001 HIS A 46 PHE 0.022 0.001 PHE C 17 TYR 0.024 0.001 TYR B 29 ARG 0.011 0.000 ARG A 108 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3475.15 seconds wall clock time: 63 minutes 52.10 seconds (3832.10 seconds total)