Starting phenix.real_space_refine on Sat Feb 17 10:14:36 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7d06_30525/02_2024/7d06_30525_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7d06_30525/02_2024/7d06_30525.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7d06_30525/02_2024/7d06_30525.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7d06_30525/02_2024/7d06_30525.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7d06_30525/02_2024/7d06_30525_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7d06_30525/02_2024/7d06_30525_updated.pdb" } resolution = 3.1 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= 0.008 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 12 5.49 5 S 88 5.16 5 C 11778 2.51 5 N 2978 2.21 5 O 3472 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 13": "OE1" <-> "OE2" Residue "A GLU 81": "OE1" <-> "OE2" Residue "A GLU 95": "OE1" <-> "OE2" Residue "A GLU 116": "OE1" <-> "OE2" Residue "A GLU 130": "OE1" <-> "OE2" Residue "B GLU 15": "OE1" <-> "OE2" Residue "B GLU 25": "OE1" <-> "OE2" Residue "B GLU 109": "OE1" <-> "OE2" Residue "B GLU 135": "OE1" <-> "OE2" Residue "B GLU 236": "OE1" <-> "OE2" Residue "B GLU 270": "OE1" <-> "OE2" Residue "B ARG 272": "NH1" <-> "NH2" Residue "C GLU 18": "OE1" <-> "OE2" Residue "C GLU 21": "OE1" <-> "OE2" Residue "C GLU 47": "OE1" <-> "OE2" Residue "C PHE 72": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 90": "OE1" <-> "OE2" Residue "D GLU 13": "OE1" <-> "OE2" Residue "D GLU 81": "OE1" <-> "OE2" Residue "D GLU 95": "OE1" <-> "OE2" Residue "D GLU 116": "OE1" <-> "OE2" Residue "D GLU 130": "OE1" <-> "OE2" Residue "E GLU 15": "OE1" <-> "OE2" Residue "E GLU 25": "OE1" <-> "OE2" Residue "E GLU 109": "OE1" <-> "OE2" Residue "E GLU 135": "OE1" <-> "OE2" Residue "E GLU 236": "OE1" <-> "OE2" Residue "E GLU 270": "OE1" <-> "OE2" Residue "E ARG 272": "NH1" <-> "NH2" Residue "F GLU 18": "OE1" <-> "OE2" Residue "F GLU 21": "OE1" <-> "OE2" Residue "F GLU 47": "OE1" <-> "OE2" Residue "F PHE 72": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F GLU 90": "OE1" <-> "OE2" Residue "G ARG 4": "NH1" <-> "NH2" Residue "G PHE 84": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G GLU 100": "OE1" <-> "OE2" Residue "G GLU 186": "OE1" <-> "OE2" Residue "H ARG 4": "NH1" <-> "NH2" Residue "H GLU 7": "OE1" <-> "OE2" Residue "H PHE 46": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H PHE 84": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H GLU 100": "OE1" <-> "OE2" Residue "H GLU 156": "OE1" <-> "OE2" Residue "I ARG 78": "NH1" <-> "NH2" Residue "I PHE 84": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I TYR 145": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J ARG 4": "NH1" <-> "NH2" Residue "J GLU 142": "OE1" <-> "OE2" Residue "J GLU 156": "OE1" <-> "OE2" Residue "J GLU 186": "OE1" <-> "OE2" Residue "K ARG 4": "NH1" <-> "NH2" Residue "K GLU 96": "OE1" <-> "OE2" Residue "L GLU 96": "OE1" <-> "OE2" Residue "L GLU 100": "OE1" <-> "OE2" Residue "L GLU 142": "OE1" <-> "OE2" Residue "L GLU 186": "OE1" <-> "OE2" Time to flip residues: 0.11s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 18328 Number of models: 1 Model: "" Number of chains: 15 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: "A" Number of atoms: 294 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 294 Unusual residues: {'PGV': 6} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 12 Planarities with less than four sites: {'PGV:plan-3': 1} Unresolved non-hydrogen planarities: 4 Chain: "D" Number of atoms: 243 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 243 Unusual residues: {'PGV': 5} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 12 Planarities with less than four sites: {'PGV:plan-3': 1} Unresolved non-hydrogen planarities: 4 Chain: "I" Number of atoms: 51 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 51 Unusual residues: {'PGV': 1} Classifications: {'undetermined': 1} Time building chain proxies: 9.89, per 1000 atoms: 0.54 Number of scatterers: 18328 At special positions: 0 Unit cell: (134.788, 121.744, 153.267, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 88 16.00 P 12 15.00 O 3472 8.00 N 2978 7.00 C 11778 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: 6.93 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: 82 helices and 15 sheets defined 42.4% alpha, 10.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 3.95 Creating SS restraints... Processing helix chain 'A' and resid 3 through 29 Processing helix chain 'A' and resid 37 through 48 removed outlier: 3.627A pdb=" N HIS A 46 " --> pdb=" O VAL A 42 " (cutoff:3.500A) Processing helix chain 'A' and resid 51 through 77 removed outlier: 4.329A pdb=" N LEU A 54 " --> pdb=" O MET A 51 " (cutoff:3.500A) removed outlier: 3.740A pdb=" N ILE A 55 " --> pdb=" O SER A 52 " (cutoff:3.500A) removed outlier: 3.924A pdb=" N ILE A 56 " --> pdb=" O LEU A 53 " (cutoff:3.500A) removed outlier: 3.818A pdb=" N THR A 57 " --> pdb=" O LEU A 54 " (cutoff:3.500A) removed outlier: 3.797A pdb=" N VAL A 58 " --> pdb=" O ILE A 55 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N SER A 59 " --> pdb=" O ILE A 56 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N GLY A 60 " --> pdb=" O THR A 57 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N PHE A 62 " --> pdb=" O SER A 59 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N ILE A 63 " --> pdb=" O GLY A 60 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N GLY A 64 " --> pdb=" O LEU A 61 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N LEU A 65 " --> pdb=" O PHE A 62 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N LEU A 67 " --> pdb=" O GLY A 64 " (cutoff:3.500A) removed outlier: 3.739A pdb=" N GLY A 68 " --> pdb=" O LEU A 65 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N GLN A 70 " --> pdb=" O LEU A 67 " (cutoff:3.500A) removed outlier: 4.184A pdb=" N GLY A 71 " --> pdb=" O GLY A 68 " (cutoff:3.500A) removed outlier: 3.883A pdb=" N TYR A 72 " --> pdb=" O LEU A 69 " (cutoff:3.500A) removed outlier: 3.784A pdb=" N ILE A 74 " --> pdb=" O GLY A 71 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N LEU A 75 " --> pdb=" O TYR A 72 " (cutoff:3.500A) removed outlier: 4.211A pdb=" N VAL A 76 " --> pdb=" O SER A 73 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N ASN A 77 " --> pdb=" O ILE A 74 " (cutoff:3.500A) Processing helix chain 'A' and resid 81 through 94 removed outlier: 4.481A pdb=" N GLY A 85 " --> pdb=" O SER A 82 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N THR A 86 " --> pdb=" O MET A 83 " (cutoff:3.500A) removed outlier: 3.877A pdb=" N VAL A 88 " --> pdb=" O GLY A 85 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N SER A 89 " --> pdb=" O THR A 86 " (cutoff:3.500A) removed outlier: 3.886A pdb=" N LEU A 90 " --> pdb=" O MET A 87 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N LEU A 92 " --> pdb=" O SER A 89 " (cutoff:3.500A) removed outlier: 3.975A pdb=" N LEU A 93 " --> pdb=" O LEU A 90 " (cutoff:3.500A) removed outlier: 4.097A pdb=" N ARG A 94 " --> pdb=" O THR A 91 " (cutoff:3.500A) Processing helix chain 'A' and resid 96 through 108 removed outlier: 3.634A pdb=" N ALA A 101 " --> pdb=" O ALA A 97 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N ALA A 102 " --> pdb=" O PRO A 98 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N GLY A 107 " --> pdb=" O LEU A 103 " (cutoff:3.500A) Processing helix chain 'A' and resid 113 through 122 removed outlier: 3.657A pdb=" N GLY A 118 " --> pdb=" O THR A 114 " (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 141 through 171 removed outlier: 3.527A pdb=" N TRP A 146 " --> pdb=" O SER A 142 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N GLY A 148 " --> pdb=" O ARG A 144 " (cutoff:3.500A) Proline residue: A 153 - end of helix removed outlier: 3.806A pdb=" N VAL A 157 " --> pdb=" O PRO A 153 " (cutoff:3.500A) removed outlier: 3.883A pdb=" N ILE A 158 " --> pdb=" O MET A 154 " (cutoff:3.500A) Processing helix chain 'A' and resid 179 through 189 removed outlier: 3.530A pdb=" N ASN A 189 " --> pdb=" O GLY A 185 " (cutoff:3.500A) Processing helix chain 'A' and resid 192 through 195 No H-bonds generated for 'chain 'A' and resid 192 through 195' Processing helix chain 'A' and resid 197 through 219 removed outlier: 3.534A pdb=" N LYS A 202 " --> pdb=" O ASN A 198 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N ALA A 214 " --> pdb=" O CYS A 210 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N GLY A 218 " --> pdb=" O ALA A 214 " (cutoff:3.500A) Processing helix chain 'A' and resid 225 through 254 removed outlier: 3.886A pdb=" N ALA A 229 " --> pdb=" O PRO A 225 " (cutoff:3.500A) removed outlier: 3.880A pdb=" N THR A 230 " --> pdb=" O GLU A 226 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N ALA A 231 " --> pdb=" O GLY A 227 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N THR A 233 " --> pdb=" O ALA A 229 " (cutoff:3.500A) removed outlier: 3.746A pdb=" N VAL A 236 " --> pdb=" O MET A 232 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N VAL A 237 " --> pdb=" O THR A 233 " (cutoff:3.500A) removed outlier: 3.852A pdb=" N PHE A 248 " --> pdb=" O LEU A 244 " (cutoff:3.500A) removed outlier: 3.867A pdb=" N VAL A 249 " --> pdb=" O GLY A 245 " (cutoff:3.500A) Processing helix chain 'B' and resid 52 through 60 removed outlier: 3.841A pdb=" N LEU B 55 " --> pdb=" O LYS B 52 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N LEU B 56 " --> pdb=" O THR B 53 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N ARG B 57 " --> pdb=" O THR B 54 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N ILE B 59 " --> pdb=" O LEU B 56 " (cutoff:3.500A) removed outlier: 4.417A pdb=" N GLY B 60 " --> pdb=" O ARG B 57 " (cutoff:3.500A) Processing helix chain 'B' and resid 82 through 91 removed outlier: 3.747A pdb=" N ALA B 87 " --> pdb=" O GLN B 83 " (cutoff:3.500A) removed outlier: 3.820A pdb=" N ALA B 90 " --> pdb=" O PHE B 86 " (cutoff:3.500A) removed outlier: 4.336A pdb=" N ARG B 91 " --> pdb=" O ALA B 87 " (cutoff:3.500A) Processing helix chain 'B' and resid 106 through 111 removed outlier: 3.535A pdb=" N VAL B 111 " --> pdb=" O VAL B 107 " (cutoff:3.500A) Processing helix chain 'B' and resid 113 through 117 Processing helix chain 'B' and resid 123 through 137 removed outlier: 3.733A pdb=" N GLU B 128 " --> pdb=" O ASN B 124 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N ALA B 131 " --> pdb=" O ALA B 127 " (cutoff:3.500A) Processing helix chain 'B' and resid 155 through 164 removed outlier: 3.623A pdb=" N LEU B 160 " --> pdb=" O ARG B 156 " (cutoff:3.500A) Processing helix chain 'B' and resid 184 through 198 removed outlier: 3.656A pdb=" N ARG B 193 " --> pdb=" O THR B 189 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N ARG B 196 " --> pdb=" O ILE B 192 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N GLU B 197 " --> pdb=" O ARG B 193 " (cutoff:3.500A) Processing helix chain 'B' and resid 210 through 213 No H-bonds generated for 'chain 'B' and resid 210 through 213' Processing helix chain 'B' and resid 236 through 239 No H-bonds generated for 'chain 'B' and resid 236 through 239' Processing helix chain 'B' and resid 245 through 250 Processing helix chain 'C' and resid 22 through 33 removed outlier: 3.687A pdb=" N GLY C 27 " --> pdb=" O GLN C 23 " (cutoff:3.500A) removed outlier: 3.850A pdb=" N ILE C 30 " --> pdb=" O ALA C 26 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N ILE C 31 " --> pdb=" O GLY C 27 " (cutoff:3.500A) removed outlier: 3.950A pdb=" N LYS C 33 " --> pdb=" O ALA C 29 " (cutoff:3.500A) Processing helix chain 'C' and resid 53 through 62 removed outlier: 3.673A pdb=" N GLN C 59 " --> pdb=" O ALA C 55 " (cutoff:3.500A) Processing helix chain 'C' and resid 79 through 85 removed outlier: 3.529A pdb=" N GLN C 84 " --> pdb=" O LEU C 80 " (cutoff:3.500A) Processing helix chain 'D' and resid 3 through 29 Processing helix chain 'D' and resid 37 through 48 removed outlier: 3.626A pdb=" N HIS D 46 " --> pdb=" O VAL D 42 " (cutoff:3.500A) Processing helix chain 'D' and resid 51 through 77 removed outlier: 4.330A pdb=" N LEU D 54 " --> pdb=" O MET D 51 " (cutoff:3.500A) removed outlier: 3.739A pdb=" N ILE D 55 " --> pdb=" O SER D 52 " (cutoff:3.500A) removed outlier: 3.924A pdb=" N ILE D 56 " --> pdb=" O LEU D 53 " (cutoff:3.500A) removed outlier: 3.818A pdb=" N THR D 57 " --> pdb=" O LEU D 54 " (cutoff:3.500A) removed outlier: 3.796A pdb=" N VAL D 58 " --> pdb=" O ILE D 55 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N SER D 59 " --> pdb=" O ILE D 56 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N GLY D 60 " --> pdb=" O THR D 57 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N PHE D 62 " --> pdb=" O SER D 59 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N ILE D 63 " --> pdb=" O GLY D 60 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N GLY D 64 " --> pdb=" O LEU D 61 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N LEU D 65 " --> pdb=" O PHE D 62 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N LEU D 67 " --> pdb=" O GLY D 64 " (cutoff:3.500A) removed outlier: 3.739A pdb=" N GLY D 68 " --> pdb=" O LEU D 65 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N GLN D 70 " --> pdb=" O LEU D 67 " (cutoff:3.500A) removed outlier: 4.183A pdb=" N GLY D 71 " --> pdb=" O GLY D 68 " (cutoff:3.500A) removed outlier: 3.883A pdb=" N TYR D 72 " --> pdb=" O LEU D 69 " (cutoff:3.500A) removed outlier: 3.784A pdb=" N ILE D 74 " --> pdb=" O GLY D 71 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N LEU D 75 " --> pdb=" O TYR D 72 " (cutoff:3.500A) removed outlier: 4.210A pdb=" N VAL D 76 " --> pdb=" O SER D 73 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N ASN D 77 " --> pdb=" O ILE D 74 " (cutoff:3.500A) Processing helix chain 'D' and resid 81 through 94 removed outlier: 3.500A pdb=" N LEU D 84 " --> pdb=" O GLU D 81 " (cutoff:3.500A) removed outlier: 4.480A pdb=" N GLY D 85 " --> pdb=" O SER D 82 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N THR D 86 " --> pdb=" O MET D 83 " (cutoff:3.500A) removed outlier: 3.876A pdb=" N VAL D 88 " --> pdb=" O GLY D 85 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N SER D 89 " --> pdb=" O THR D 86 " (cutoff:3.500A) removed outlier: 3.886A pdb=" N LEU D 90 " --> pdb=" O MET D 87 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N LEU D 92 " --> pdb=" O SER D 89 " (cutoff:3.500A) removed outlier: 3.975A pdb=" N LEU D 93 " --> pdb=" O LEU D 90 " (cutoff:3.500A) removed outlier: 4.097A pdb=" N ARG D 94 " --> pdb=" O THR D 91 " (cutoff:3.500A) Processing helix chain 'D' and resid 96 through 108 removed outlier: 3.634A pdb=" N ALA D 101 " --> pdb=" O ALA D 97 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N ALA D 102 " --> pdb=" O PRO D 98 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N GLY D 107 " --> pdb=" O LEU D 103 " (cutoff:3.500A) Processing helix chain 'D' and resid 113 through 122 removed outlier: 3.658A pdb=" N GLY D 118 " --> pdb=" O THR D 114 " (cutoff:3.500A) Processing helix chain 'D' and resid 125 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 141 through 171 removed outlier: 3.527A pdb=" N TRP D 146 " --> pdb=" O SER D 142 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N GLY D 148 " --> pdb=" O ARG D 144 " (cutoff:3.500A) Proline residue: D 153 - end of helix removed outlier: 3.806A pdb=" N VAL D 157 " --> pdb=" O PRO D 153 " (cutoff:3.500A) removed outlier: 3.883A pdb=" N ILE D 158 " --> pdb=" O MET D 154 " (cutoff:3.500A) Processing helix chain 'D' and resid 179 through 189 removed outlier: 3.531A pdb=" N ASN D 189 " --> pdb=" O GLY D 185 " (cutoff:3.500A) Processing helix chain 'D' and resid 192 through 195 No H-bonds generated for 'chain 'D' and resid 192 through 195' Processing helix chain 'D' and resid 197 through 219 removed outlier: 3.534A pdb=" N LYS D 202 " --> pdb=" O ASN D 198 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N ALA D 214 " --> pdb=" O CYS D 210 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N GLY D 218 " --> pdb=" O ALA D 214 " (cutoff:3.500A) Processing helix chain 'D' and resid 225 through 254 removed outlier: 3.886A pdb=" N ALA D 229 " --> pdb=" O PRO D 225 " (cutoff:3.500A) removed outlier: 3.881A pdb=" N THR D 230 " --> pdb=" O GLU D 226 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N ALA D 231 " --> pdb=" O GLY D 227 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N THR D 233 " --> pdb=" O ALA D 229 " (cutoff:3.500A) removed outlier: 3.746A pdb=" N VAL D 236 " --> pdb=" O MET D 232 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N VAL D 237 " --> pdb=" O THR D 233 " (cutoff:3.500A) removed outlier: 3.852A pdb=" N PHE D 248 " --> pdb=" O LEU D 244 " (cutoff:3.500A) removed outlier: 3.867A pdb=" N VAL D 249 " --> pdb=" O GLY D 245 " (cutoff:3.500A) Processing helix chain 'E' and resid 52 through 60 removed outlier: 3.840A pdb=" N LEU E 55 " --> pdb=" O LYS E 52 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N LEU E 56 " --> pdb=" O THR E 53 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N ARG E 57 " --> pdb=" O THR E 54 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N ILE E 59 " --> pdb=" O LEU E 56 " (cutoff:3.500A) removed outlier: 4.417A pdb=" N GLY E 60 " --> pdb=" O ARG E 57 " (cutoff:3.500A) Processing helix chain 'E' and resid 82 through 91 removed outlier: 3.747A pdb=" N ALA E 87 " --> pdb=" O GLN E 83 " (cutoff:3.500A) removed outlier: 3.821A pdb=" N ALA E 90 " --> pdb=" O PHE E 86 " (cutoff:3.500A) removed outlier: 4.336A pdb=" N ARG E 91 " --> pdb=" O ALA E 87 " (cutoff:3.500A) Processing helix chain 'E' and resid 106 through 111 removed outlier: 3.626A pdb=" N VAL E 111 " --> pdb=" O VAL E 107 " (cutoff:3.500A) Processing helix chain 'E' and resid 113 through 117 Processing helix chain 'E' and resid 123 through 137 removed outlier: 3.733A pdb=" N GLU E 128 " --> pdb=" O ASN E 124 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N ALA E 131 " --> pdb=" O ALA E 127 " (cutoff:3.500A) Processing helix chain 'E' and resid 155 through 164 removed outlier: 3.624A pdb=" N LEU E 160 " --> pdb=" O ARG E 156 " (cutoff:3.500A) Processing helix chain 'E' and resid 184 through 198 removed outlier: 3.656A pdb=" N ARG E 193 " --> pdb=" O THR E 189 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N ARG E 196 " --> pdb=" O ILE E 192 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N GLU E 197 " --> pdb=" O ARG E 193 " (cutoff:3.500A) Processing helix chain 'E' and resid 210 through 213 No H-bonds generated for 'chain 'E' and resid 210 through 213' Processing helix chain 'E' and resid 236 through 239 No H-bonds generated for 'chain 'E' and resid 236 through 239' Processing helix chain 'E' and resid 245 through 250 Processing helix chain 'F' and resid 22 through 33 removed outlier: 3.687A pdb=" N GLY F 27 " --> pdb=" O GLN F 23 " (cutoff:3.500A) removed outlier: 3.850A pdb=" N ILE F 30 " --> pdb=" O ALA F 26 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N ILE F 31 " --> pdb=" O GLY F 27 " (cutoff:3.500A) removed outlier: 3.950A pdb=" N LYS F 33 " --> pdb=" O ALA F 29 " (cutoff:3.500A) Processing helix chain 'F' and resid 53 through 62 removed outlier: 3.673A pdb=" N GLN F 59 " --> pdb=" O ALA F 55 " (cutoff:3.500A) Processing helix chain 'F' and resid 79 through 85 removed outlier: 3.530A pdb=" N GLN F 84 " --> pdb=" O LEU F 80 " (cutoff:3.500A) Processing helix chain 'G' and resid 4 through 26 removed outlier: 3.788A pdb=" N VAL G 10 " --> pdb=" O SER G 6 " (cutoff:3.500A) Processing helix chain 'G' and resid 96 through 109 removed outlier: 4.613A pdb=" N LYS G 103 " --> pdb=" O GLU G 100 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N ASN G 104 " --> pdb=" O VAL G 101 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N ALA G 105 " --> pdb=" O GLN G 102 " (cutoff:3.500A) removed outlier: 4.445A pdb=" N LEU G 106 " --> pdb=" O LYS G 103 " (cutoff:3.500A) removed outlier: 3.799A pdb=" N LEU G 109 " --> pdb=" O LEU G 106 " (cutoff:3.500A) Processing helix chain 'G' and resid 112 through 115 No H-bonds generated for 'chain 'G' and resid 112 through 115' Processing helix chain 'G' and resid 126 through 131 removed outlier: 3.903A pdb=" N ILE G 131 " --> pdb=" O GLU G 127 " (cutoff:3.500A) Processing helix chain 'G' and resid 185 through 190 Processing helix chain 'H' and resid 4 through 29 removed outlier: 3.893A pdb=" N ILE H 15 " --> pdb=" O GLY H 11 " (cutoff:3.500A) Processing helix chain 'H' and resid 88 through 91 No H-bonds generated for 'chain 'H' and resid 88 through 91' Processing helix chain 'H' and resid 95 through 109 removed outlier: 3.608A pdb=" N LYS H 103 " --> pdb=" O LYS H 99 " (cutoff:3.500A) removed outlier: 3.840A pdb=" N ASN H 104 " --> pdb=" O GLU H 100 " (cutoff:3.500A) removed outlier: 3.876A pdb=" N ALA H 105 " --> pdb=" O VAL H 101 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N LEU H 106 " --> pdb=" O GLN H 102 " (cutoff:3.500A) 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 134 removed outlier: 3.899A pdb=" N ILE H 131 " --> pdb=" O GLU H 127 " (cutoff:3.500A) removed outlier: 4.239A pdb=" N SER H 132 " --> pdb=" O GLN H 128 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N ASN H 133 " --> pdb=" O GLN H 129 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N MET H 134 " --> pdb=" O LEU H 130 " (cutoff:3.500A) Processing helix chain 'H' and resid 185 through 192 removed outlier: 3.807A pdb=" N ILE H 189 " --> pdb=" O LEU H 185 " (cutoff:3.500A) Processing helix chain 'I' and resid 4 through 25 removed outlier: 3.569A pdb=" N ALA I 9 " --> pdb=" O THR I 5 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N ILE I 15 " --> pdb=" O GLY I 11 " (cutoff:3.500A) Processing helix chain 'I' and resid 88 through 91 No H-bonds generated for 'chain 'I' and resid 88 through 91' Processing helix chain 'I' and resid 96 through 109 Processing helix chain 'I' and resid 112 through 117 removed outlier: 4.176A pdb=" N THR I 116 " --> pdb=" O SER I 112 " (cutoff:3.500A) removed outlier: 3.814A pdb=" N GLN I 117 " --> pdb=" O SER I 113 " (cutoff:3.500A) No H-bonds generated for 'chain 'I' and resid 112 through 117' Processing helix chain 'I' and resid 124 through 134 removed outlier: 3.789A pdb=" N ILE I 131 " --> pdb=" O GLU I 127 " (cutoff:3.500A) removed outlier: 3.761A pdb=" N SER I 132 " --> pdb=" O GLN I 128 " (cutoff:3.500A) Processing helix chain 'I' and resid 185 through 192 Processing helix chain 'J' and resid 6 through 26 Processing helix chain 'J' and resid 95 through 109 removed outlier: 3.612A pdb=" N LYS J 99 " --> pdb=" O ALA J 95 " (cutoff:3.500A) removed outlier: 4.282A pdb=" N ASN J 104 " --> pdb=" O GLU J 100 " (cutoff:3.500A) Processing helix chain 'J' and resid 125 through 131 removed outlier: 4.124A pdb=" N LEU J 130 " --> pdb=" O MET J 126 " (cutoff:3.500A) Processing helix chain 'J' and resid 185 through 192 removed outlier: 3.592A pdb=" N SER J 190 " --> pdb=" O GLU J 186 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N PHE J 192 " --> pdb=" O LEU J 188 " (cutoff:3.500A) Processing helix chain 'K' and resid 4 through 29 removed outlier: 3.605A pdb=" N VAL K 10 " --> pdb=" O SER K 6 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N ILE K 15 " --> pdb=" O GLY K 11 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N PHE K 22 " --> pdb=" O GLY K 18 " (cutoff:3.500A) Processing helix chain 'K' and resid 95 through 109 removed outlier: 3.754A pdb=" N ASN K 104 " --> pdb=" O GLU K 100 " (cutoff:3.500A) removed outlier: 3.777A pdb=" N ASP K 107 " --> pdb=" O LYS K 103 " (cutoff:3.500A) Processing helix chain 'K' and resid 112 through 117 removed outlier: 4.453A pdb=" N THR K 116 " --> pdb=" O SER K 112 " (cutoff:3.500A) removed outlier: 4.033A pdb=" N GLN K 117 " --> pdb=" O SER K 113 " (cutoff:3.500A) No H-bonds generated for 'chain 'K' and resid 112 through 117' Processing helix chain 'K' and resid 125 through 131 removed outlier: 3.877A pdb=" N LEU K 130 " --> pdb=" O MET K 126 " (cutoff:3.500A) removed outlier: 3.960A pdb=" N ILE K 131 " --> pdb=" O GLU K 127 " (cutoff:3.500A) Processing helix chain 'K' and resid 185 through 192 removed outlier: 3.833A pdb=" N ILE K 189 " --> pdb=" O LEU K 185 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N LYS K 191 " --> pdb=" O ASP K 187 " (cutoff:3.500A) Processing helix chain 'L' and resid 4 through 27 removed outlier: 3.515A pdb=" N ILE L 15 " --> pdb=" O GLY L 11 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N PHE L 22 " --> pdb=" O GLY L 18 " (cutoff:3.500A) Processing helix chain 'L' and resid 95 through 108 removed outlier: 3.604A pdb=" N GLU L 100 " --> pdb=" O GLU L 96 " (cutoff:3.500A) removed outlier: 4.061A pdb=" N LYS L 103 " --> pdb=" O LYS L 99 " (cutoff:3.500A) Processing helix chain 'L' and resid 125 through 133 removed outlier: 4.056A pdb=" N GLN L 129 " --> pdb=" O THR L 125 " (cutoff:3.500A) removed outlier: 3.998A pdb=" N LEU L 130 " --> pdb=" O MET L 126 " (cutoff:3.500A) removed outlier: 4.148A pdb=" N ILE L 131 " --> pdb=" O GLU L 127 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N SER L 132 " --> pdb=" O GLN L 128 " (cutoff:3.500A) Processing helix chain 'L' and resid 185 through 191 Processing sheet with id= A, first strand: chain 'B' and resid 69 through 72 removed outlier: 3.781A pdb=" N GLU B 69 " --> pdb=" O LYS B 17 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N LYS B 17 " --> pdb=" O GLU B 69 " (cutoff:3.500A) removed outlier: 6.696A pdb=" N ILE B 36 " --> pdb=" O LEU B 13 " (cutoff:3.500A) removed outlier: 4.546A pdb=" N GLU B 15 " --> pdb=" O LEU B 34 " (cutoff:3.500A) removed outlier: 6.517A pdb=" N LEU B 34 " --> pdb=" O GLU B 15 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'B' and resid 228 through 232 removed outlier: 6.431A pdb=" N VAL B 222 " --> pdb=" O GLN B 229 " (cutoff:3.500A) removed outlier: 4.223A pdb=" N GLU B 231 " --> pdb=" O ILE B 220 " (cutoff:3.500A) removed outlier: 6.590A pdb=" N ILE B 220 " --> pdb=" O GLU B 231 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N SER B 207 " --> pdb=" O ILE B 44 " (cutoff:3.500A) removed outlier: 6.788A pdb=" N ILE B 171 " --> pdb=" O ILE B 204 " (cutoff:3.500A) removed outlier: 8.217A pdb=" N VAL B 206 " --> pdb=" O ILE B 171 " (cutoff:3.500A) removed outlier: 7.041A pdb=" N TYR B 173 " --> pdb=" O VAL B 206 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N ASP B 174 " --> pdb=" O LEU B 95 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'E' and resid 69 through 72 removed outlier: 3.781A pdb=" N GLU E 69 " --> pdb=" O LYS E 17 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N LYS E 17 " --> pdb=" O GLU E 69 " (cutoff:3.500A) removed outlier: 6.696A pdb=" N ILE E 36 " --> pdb=" O LEU E 13 " (cutoff:3.500A) removed outlier: 4.546A pdb=" N GLU E 15 " --> pdb=" O LEU E 34 " (cutoff:3.500A) removed outlier: 6.517A pdb=" N LEU E 34 " --> pdb=" O GLU E 15 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'E' and resid 228 through 232 removed outlier: 6.430A pdb=" N VAL E 222 " --> pdb=" O GLN E 229 " (cutoff:3.500A) removed outlier: 4.223A pdb=" N GLU E 231 " --> pdb=" O ILE E 220 " (cutoff:3.500A) removed outlier: 6.589A pdb=" N ILE E 220 " --> pdb=" O GLU E 231 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N SER E 207 " --> pdb=" O ILE E 44 " (cutoff:3.500A) removed outlier: 6.787A pdb=" N ILE E 171 " --> pdb=" O ILE E 204 " (cutoff:3.500A) removed outlier: 8.217A pdb=" N VAL E 206 " --> pdb=" O ILE E 171 " (cutoff:3.500A) removed outlier: 7.041A pdb=" N TYR E 173 " --> pdb=" O VAL E 206 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N ASP E 174 " --> pdb=" O LEU E 95 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'G' and resid 41 through 46 removed outlier: 3.572A pdb=" N SER G 70 " --> pdb=" O THR G 83 " (cutoff:3.500A) removed outlier: 6.165A pdb=" N ASP G 85 " --> pdb=" O VAL G 68 " (cutoff:3.500A) removed outlier: 5.597A pdb=" N VAL G 68 " --> pdb=" O ASP G 85 " (cutoff:3.500A) removed outlier: 6.359A pdb=" N VAL G 58 " --> pdb=" O ILE G 65 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'G' and resid 145 through 149 Processing sheet with id= G, first strand: chain 'H' and resid 41 through 46 removed outlier: 6.287A pdb=" N ASP H 85 " --> pdb=" O VAL H 68 " (cutoff:3.500A) removed outlier: 5.591A pdb=" N VAL H 68 " --> pdb=" O ASP H 85 " (cutoff:3.500A) removed outlier: 6.561A pdb=" N VAL H 58 " --> pdb=" O ILE H 65 " (cutoff:3.500A) removed outlier: 6.798A pdb=" N LEU H 159 " --> pdb=" O THR H 59 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'I' and resid 41 through 46 removed outlier: 3.916A pdb=" N LEU I 79 " --> pdb=" O ASP I 74 " (cutoff:3.500A) removed outlier: 6.223A pdb=" N ASP I 85 " --> pdb=" O VAL I 68 " (cutoff:3.500A) removed outlier: 5.626A pdb=" N VAL I 68 " --> pdb=" O ASP I 85 " (cutoff:3.500A) removed outlier: 6.708A pdb=" N VAL I 58 " --> pdb=" O ILE I 65 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'I' and resid 145 through 149 Processing sheet with id= J, first strand: chain 'J' and resid 42 through 46 removed outlier: 6.665A pdb=" N ASP J 85 " --> pdb=" O VAL J 68 " (cutoff:3.500A) removed outlier: 5.825A pdb=" N VAL J 68 " --> pdb=" O ASP J 85 " (cutoff:3.500A) removed outlier: 6.461A pdb=" N VAL J 58 " --> pdb=" O ILE J 65 " (cutoff:3.500A) Processing sheet with id= K, first strand: chain 'J' and resid 145 through 150 Processing sheet with id= L, first strand: chain 'K' and resid 41 through 46 removed outlier: 3.626A pdb=" N THR K 72 " --> pdb=" O THR K 81 " (cutoff:3.500A) removed outlier: 6.084A pdb=" N ASP K 85 " --> pdb=" O VAL K 68 " (cutoff:3.500A) removed outlier: 5.522A pdb=" N VAL K 68 " --> pdb=" O ASP K 85 " (cutoff:3.500A) removed outlier: 6.447A pdb=" N VAL K 58 " --> pdb=" O ILE K 65 " (cutoff:3.500A) Processing sheet with id= M, first strand: chain 'K' and resid 145 through 149 Processing sheet with id= N, first strand: chain 'L' and resid 41 through 46 removed outlier: 6.238A pdb=" N ASP L 85 " --> pdb=" O VAL L 68 " (cutoff:3.500A) removed outlier: 5.668A pdb=" N VAL L 68 " --> pdb=" O ASP L 85 " (cutoff:3.500A) removed outlier: 6.526A pdb=" N VAL L 58 " --> pdb=" O ILE L 65 " (cutoff:3.500A) Processing sheet with id= O, first strand: chain 'L' and resid 145 through 149 623 hydrogen bonds defined for protein. 1746 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: 4.91 Time building geometry restraints manager: 7.40 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.17 - 1.30: 3035 1.30 - 1.43: 4276 1.43 - 1.56: 10999 1.56 - 1.68: 76 1.68 - 1.81: 168 Bond restraints: 18554 Sorted by residual: bond pdb=" C11 PGV A 304 " pdb=" C12 PGV A 304 " ideal model delta sigma weight residual 1.332 1.553 -0.221 2.00e-02 2.50e+03 1.22e+02 bond pdb=" C11 PGV A 303 " pdb=" C12 PGV A 303 " ideal model delta sigma weight residual 1.332 1.552 -0.220 2.00e-02 2.50e+03 1.21e+02 bond pdb=" C11 PGV D 304 " pdb=" C12 PGV D 304 " ideal model delta sigma weight residual 1.332 1.552 -0.220 2.00e-02 2.50e+03 1.21e+02 bond pdb=" C11 PGV D 303 " pdb=" C12 PGV D 303 " ideal model delta sigma weight residual 1.332 1.552 -0.220 2.00e-02 2.50e+03 1.21e+02 bond pdb=" C11 PGV D 302 " pdb=" C12 PGV D 302 " ideal model delta sigma weight residual 1.332 1.552 -0.220 2.00e-02 2.50e+03 1.21e+02 ... (remaining 18549 not shown) Histogram of bond angle deviations from ideal: 80.19 - 90.96: 12 90.96 - 101.73: 79 101.73 - 112.50: 9914 112.50 - 123.27: 14271 123.27 - 134.03: 718 Bond angle restraints: 24994 Sorted by residual: angle pdb=" C19 PGV D 305 " pdb=" C20 PGV D 305 " pdb=" C21 PGV D 305 " ideal model delta sigma weight residual 113.71 80.19 33.52 3.00e+00 1.11e-01 1.25e+02 angle pdb=" C19 PGV A 301 " pdb=" C20 PGV A 301 " pdb=" C21 PGV A 301 " ideal model delta sigma weight residual 113.71 81.12 32.59 3.00e+00 1.11e-01 1.18e+02 angle pdb=" C19 PGV D 301 " pdb=" C20 PGV D 301 " pdb=" C21 PGV D 301 " ideal model delta sigma weight residual 113.71 81.14 32.57 3.00e+00 1.11e-01 1.18e+02 angle pdb=" C19 PGV A 305 " pdb=" C20 PGV A 305 " pdb=" C21 PGV A 305 " ideal model delta sigma weight residual 113.71 81.47 32.24 3.00e+00 1.11e-01 1.16e+02 angle pdb=" C19 PGV A 306 " pdb=" C20 PGV A 306 " pdb=" C21 PGV A 306 " ideal model delta sigma weight residual 113.71 82.13 31.58 3.00e+00 1.11e-01 1.11e+02 ... (remaining 24989 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 30.10: 10561 30.10 - 60.19: 678 60.19 - 90.29: 64 90.29 - 120.39: 9 120.39 - 150.48: 12 Dihedral angle restraints: 11324 sinusoidal: 4582 harmonic: 6742 Sorted by residual: dihedral pdb=" CA GLU L 156 " pdb=" C GLU L 156 " pdb=" N LYS L 157 " pdb=" CA LYS L 157 " ideal model delta harmonic sigma weight residual 180.00 151.19 28.81 0 5.00e+00 4.00e-02 3.32e+01 dihedral pdb=" CA GLU I 156 " pdb=" C GLU I 156 " pdb=" N LYS I 157 " pdb=" CA LYS I 157 " ideal model delta harmonic sigma weight residual 180.00 152.00 28.00 0 5.00e+00 4.00e-02 3.14e+01 dihedral pdb=" CA THR B 119 " pdb=" C THR B 119 " pdb=" N LYS B 120 " pdb=" CA LYS B 120 " ideal model delta harmonic sigma weight residual 180.00 153.67 26.33 0 5.00e+00 4.00e-02 2.77e+01 ... (remaining 11321 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.087: 2563 0.087 - 0.174: 368 0.174 - 0.261: 46 0.261 - 0.348: 3 0.348 - 0.435: 2 Chirality restraints: 2982 Sorted by residual: chirality pdb=" CB THR B 119 " pdb=" CA THR B 119 " pdb=" OG1 THR B 119 " pdb=" CG2 THR B 119 " both_signs ideal model delta sigma weight residual False 2.55 2.12 0.43 2.00e-01 2.50e+01 4.73e+00 chirality pdb=" CB THR E 119 " pdb=" CA THR E 119 " pdb=" OG1 THR E 119 " pdb=" CG2 THR E 119 " both_signs ideal model delta sigma weight residual False 2.55 2.12 0.43 2.00e-01 2.50e+01 4.69e+00 chirality pdb=" CA ASN H 35 " pdb=" N ASN H 35 " pdb=" C ASN H 35 " pdb=" CB ASN H 35 " both_signs ideal model delta sigma weight residual False 2.51 2.24 0.27 2.00e-01 2.50e+01 1.82e+00 ... (remaining 2979 not shown) Planarity restraints: 3134 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C10 PGV D 303 " 0.166 2.00e-02 2.50e+03 3.24e-01 1.05e+03 pdb=" C11 PGV D 303 " -0.428 2.00e-02 2.50e+03 pdb=" C12 PGV D 303 " 0.428 2.00e-02 2.50e+03 pdb=" C13 PGV D 303 " -0.166 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C10 PGV A 303 " -0.166 2.00e-02 2.50e+03 3.24e-01 1.05e+03 pdb=" C11 PGV A 303 " 0.428 2.00e-02 2.50e+03 pdb=" C12 PGV A 303 " -0.427 2.00e-02 2.50e+03 pdb=" C13 PGV A 303 " 0.166 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C10 PGV A 304 " 0.160 2.00e-02 2.50e+03 2.78e-01 7.73e+02 pdb=" C11 PGV A 304 " -0.360 2.00e-02 2.50e+03 pdb=" C12 PGV A 304 " 0.359 2.00e-02 2.50e+03 pdb=" C13 PGV A 304 " -0.159 2.00e-02 2.50e+03 ... (remaining 3131 not shown) Histogram of nonbonded interaction distances: 2.02 - 2.60: 216 2.60 - 3.17: 14337 3.17 - 3.75: 26127 3.75 - 4.32: 37785 4.32 - 4.90: 62734 Nonbonded interactions: 141199 Sorted by model distance: nonbonded pdb=" O MET E 105 " pdb=" OG SER E 106 " model vdw 2.021 2.440 nonbonded pdb=" O MET B 105 " pdb=" OG SER B 106 " model vdw 2.082 2.440 nonbonded pdb=" O06 PGV D 305 " pdb=" O12 PGV D 305 " model vdw 2.112 2.440 nonbonded pdb=" OD1 ASN G 94 " pdb=" N ALA G 95 " model vdw 2.129 2.520 nonbonded pdb=" O LEU L 73 " pdb=" O ASP L 74 " model vdw 2.143 3.040 ... (remaining 141194 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' and (resid 1 through 256 or resid 301 through 305)) 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' and resid 3 through 193) 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 individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.390 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: 2.920 Check model and map are aligned: 0.280 Set scattering table: 0.180 Process input model: 48.570 Find NCS groups from input model: 1.230 Set up NCS constraints: 0.140 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.870 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 56.600 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8281 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 : 0.012 0.221 18554 Z= 0.847 Angle : 1.544 33.516 24994 Z= 0.713 Chirality : 0.063 0.435 2982 Planarity : 0.016 0.324 3134 Dihedral : 19.877 150.482 6996 Min Nonbonded Distance : 2.021 Molprobity Statistics. All-atom Clashscore : 10.56 Ramachandran Plot: Outliers : 1.02 % Allowed : 10.38 % Favored : 88.60 % Rotamer: Outliers : 4.91 % Allowed : 9.82 % Favored : 85.27 % 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: -5.86 (0.12), residues: 2350 helix: -4.75 (0.05), residues: 992 sheet: -2.06 (0.29), residues: 278 loop : -3.44 (0.15), residues: 1080 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP A 212 HIS 0.005 0.002 HIS B 263 PHE 0.030 0.003 PHE C 17 TYR 0.039 0.003 TYR J 40 ARG 0.004 0.001 ARG B 190 *********************** 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 537 residues out of total 1994 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 92 poor density : 445 time to evaluate : 2.265 Fit side-chains REVERT: A 120 MET cc_start: 0.9144 (mtt) cc_final: 0.8916 (mtt) REVERT: A 188 ASN cc_start: 0.8657 (t0) cc_final: 0.8289 (t0) REVERT: B 17 LYS cc_start: 0.8533 (mtpt) cc_final: 0.8324 (mtmm) REVERT: B 120 LYS cc_start: 0.8653 (mppt) cc_final: 0.8397 (mmtt) REVERT: B 185 LYS cc_start: 0.9016 (ttmt) cc_final: 0.8732 (mtpt) REVERT: B 190 ARG cc_start: 0.7932 (mpp80) cc_final: 0.7698 (mtm180) REVERT: B 262 SER cc_start: 0.5448 (OUTLIER) cc_final: 0.4927 (m) REVERT: C 33 LYS cc_start: 0.7190 (OUTLIER) cc_final: 0.6905 (pttp) REVERT: C 34 GLN cc_start: 0.7401 (tp-100) cc_final: 0.7158 (tp40) REVERT: C 67 LYS cc_start: 0.7543 (OUTLIER) cc_final: 0.7293 (tppt) REVERT: C 93 HIS cc_start: 0.6548 (m90) cc_final: 0.6303 (m-70) REVERT: E 17 LYS cc_start: 0.8570 (mtpt) cc_final: 0.8263 (mtpt) REVERT: E 25 GLU cc_start: 0.6839 (OUTLIER) cc_final: 0.6615 (mt-10) REVERT: E 33 SER cc_start: 0.8859 (OUTLIER) cc_final: 0.8647 (p) REVERT: F 30 ILE cc_start: 0.7108 (mt) cc_final: 0.6828 (mp) REVERT: F 45 GLN cc_start: 0.7128 (OUTLIER) cc_final: 0.6601 (mp10) REVERT: F 73 LYS cc_start: 0.8339 (OUTLIER) cc_final: 0.8015 (ttmm) REVERT: G 141 ASP cc_start: 0.7866 (p0) cc_final: 0.7566 (p0) REVERT: G 160 LYS cc_start: 0.8785 (ttpt) cc_final: 0.8397 (tttp) REVERT: H 45 GLN cc_start: 0.8058 (mt0) cc_final: 0.7853 (mt0) REVERT: H 50 ASN cc_start: 0.8600 (t0) cc_final: 0.8280 (t0) REVERT: H 97 GLN cc_start: 0.8047 (mp10) cc_final: 0.7612 (mp10) REVERT: H 187 ASP cc_start: 0.7242 (t0) cc_final: 0.7035 (t0) REVERT: I 43 LYS cc_start: 0.8778 (ptpp) cc_final: 0.8525 (ptmm) REVERT: I 191 LYS cc_start: 0.8544 (OUTLIER) cc_final: 0.8085 (tttt) REVERT: J 43 LYS cc_start: 0.8370 (ptpp) cc_final: 0.8067 (pttp) REVERT: J 133 ASN cc_start: 0.6886 (m-40) cc_final: 0.6615 (m-40) REVERT: J 134 MET cc_start: 0.6031 (pmm) cc_final: 0.5609 (pmm) REVERT: J 147 MET cc_start: 0.8458 (ptm) cc_final: 0.8256 (ptp) REVERT: K 135 ASN cc_start: 0.5731 (OUTLIER) cc_final: 0.5438 (p0) outliers start: 92 outliers final: 27 residues processed: 513 average time/residue: 0.3334 time to fit residues: 246.4050 Evaluate side-chains 363 residues out of total 1994 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 327 time to evaluate : 2.144 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 262 SER Chi-restraints excluded: chain C residue 1 VAL Chi-restraints excluded: chain C residue 2 VAL Chi-restraints excluded: chain C residue 33 LYS Chi-restraints excluded: chain C residue 66 GLN Chi-restraints excluded: chain C residue 67 LYS Chi-restraints excluded: chain C residue 70 LEU Chi-restraints excluded: chain D residue 215 VAL Chi-restraints excluded: chain E residue 25 GLU Chi-restraints excluded: chain E residue 33 SER Chi-restraints excluded: chain E residue 103 THR Chi-restraints excluded: chain E residue 105 MET Chi-restraints excluded: chain E residue 235 GLU Chi-restraints excluded: chain E residue 246 LYS Chi-restraints excluded: chain E residue 249 LEU Chi-restraints excluded: chain F residue 1 VAL Chi-restraints excluded: chain F residue 2 VAL Chi-restraints excluded: chain F residue 40 ILE Chi-restraints excluded: chain F residue 45 GLN Chi-restraints excluded: chain F residue 67 LYS Chi-restraints excluded: chain F residue 70 LEU Chi-restraints excluded: chain F residue 73 LYS Chi-restraints excluded: chain G residue 93 PHE Chi-restraints excluded: chain H residue 35 ASN Chi-restraints excluded: chain H residue 36 LEU Chi-restraints excluded: chain I residue 63 VAL Chi-restraints excluded: chain I residue 78 ARG Chi-restraints excluded: chain I residue 191 LYS Chi-restraints excluded: chain K residue 32 VAL Chi-restraints excluded: chain K residue 36 LEU Chi-restraints excluded: chain K residue 135 ASN Chi-restraints excluded: chain L residue 77 THR Chi-restraints excluded: chain L residue 188 LEU Chi-restraints excluded: chain L residue 190 SER Chi-restraints excluded: chain L residue 192 PHE Chi-restraints excluded: chain L residue 193 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 234 random chunks: chunk 197 optimal weight: 3.9990 chunk 177 optimal weight: 0.3980 chunk 98 optimal weight: 6.9990 chunk 60 optimal weight: 3.9990 chunk 119 optimal weight: 6.9990 chunk 94 optimal weight: 0.8980 chunk 183 optimal weight: 4.9990 chunk 70 optimal weight: 1.9990 chunk 111 optimal weight: 5.9990 chunk 136 optimal weight: 7.9990 chunk 212 optimal weight: 0.0980 overall best weight: 1.4784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 46 HIS A 139 GLN A 191 GLN B 144 GLN C 66 GLN C 93 HIS D 46 HIS D 139 GLN D 191 GLN F 89 GLN G 45 GLN G 97 GLN H 35 ASN H 45 GLN H 50 ASN ** H 102 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 45 GLN I 104 ASN L 102 GLN L 128 GLN Total number of N/Q/H flips: 19 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8226 moved from start: 0.1973 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 18554 Z= 0.204 Angle : 0.688 10.502 24994 Z= 0.357 Chirality : 0.044 0.249 2982 Planarity : 0.005 0.057 3134 Dihedral : 17.428 142.034 3095 Min Nonbonded Distance : 2.044 Molprobity Statistics. All-atom Clashscore : 7.92 Ramachandran Plot: Outliers : 0.34 % Allowed : 8.81 % Favored : 90.85 % Rotamer: Outliers : 3.47 % Allowed : 14.89 % Favored : 81.64 % 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: -4.08 (0.14), residues: 2350 helix: -2.68 (0.11), residues: 1034 sheet: -1.51 (0.31), residues: 278 loop : -2.99 (0.16), residues: 1038 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP D 212 HIS 0.004 0.001 HIS C 71 PHE 0.017 0.001 PHE A 182 TYR 0.014 0.001 TYR B 173 ARG 0.005 0.000 ARG I 55 *********************** 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 424 residues out of total 1994 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 65 poor density : 359 time to evaluate : 2.063 Fit side-chains revert: symmetry clash REVERT: A 138 LYS cc_start: 0.8665 (mtpp) cc_final: 0.8421 (mmmm) REVERT: A 188 ASN cc_start: 0.8560 (t0) cc_final: 0.8275 (t0) REVERT: B 135 GLU cc_start: 0.8128 (tm-30) cc_final: 0.7911 (tm-30) REVERT: B 262 SER cc_start: 0.5043 (OUTLIER) cc_final: 0.4480 (m) REVERT: E 17 LYS cc_start: 0.8703 (mtpt) cc_final: 0.8453 (mtpt) REVERT: F 23 GLN cc_start: 0.8330 (mt0) cc_final: 0.8044 (mm-40) REVERT: F 61 LEU cc_start: 0.8124 (OUTLIER) cc_final: 0.7877 (tp) REVERT: F 70 LEU cc_start: 0.7020 (OUTLIER) cc_final: 0.6603 (mt) REVERT: G 85 ASP cc_start: 0.8405 (OUTLIER) cc_final: 0.8005 (p0) REVERT: H 26 MET cc_start: 0.8208 (mmp) cc_final: 0.7864 (mmp) REVERT: H 50 ASN cc_start: 0.8519 (t0) cc_final: 0.8302 (t0) REVERT: H 60 MET cc_start: 0.8234 (tpp) cc_final: 0.7882 (tpp) REVERT: H 97 GLN cc_start: 0.7943 (mp10) cc_final: 0.7540 (mp10) REVERT: H 141 ASP cc_start: 0.8220 (OUTLIER) cc_final: 0.7773 (p0) REVERT: I 78 ARG cc_start: 0.7436 (OUTLIER) cc_final: 0.7197 (mmt90) REVERT: I 185 LEU cc_start: 0.7994 (OUTLIER) cc_final: 0.7719 (pp) REVERT: I 186 GLU cc_start: 0.8229 (mm-30) cc_final: 0.7966 (mm-30) REVERT: I 191 LYS cc_start: 0.8647 (ttmt) cc_final: 0.8155 (tttt) REVERT: J 43 LYS cc_start: 0.8120 (ptpp) cc_final: 0.7903 (pttp) REVERT: J 134 MET cc_start: 0.6032 (pmm) cc_final: 0.5637 (pmm) REVERT: J 147 MET cc_start: 0.8328 (ptm) cc_final: 0.7842 (ptp) REVERT: K 26 MET cc_start: 0.8074 (mmp) cc_final: 0.7840 (mmp) REVERT: K 85 ASP cc_start: 0.8059 (p0) cc_final: 0.7854 (p0) REVERT: K 192 PHE cc_start: 0.7246 (t80) cc_final: 0.6952 (t80) REVERT: L 24 LEU cc_start: 0.8285 (OUTLIER) cc_final: 0.8080 (tt) outliers start: 65 outliers final: 36 residues processed: 403 average time/residue: 0.3245 time to fit residues: 191.6477 Evaluate side-chains 361 residues out of total 1994 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 317 time to evaluate : 2.082 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 19 LEU Chi-restraints excluded: chain B residue 124 ASN Chi-restraints excluded: chain B residue 262 SER Chi-restraints excluded: chain C residue 1 VAL Chi-restraints excluded: chain C residue 10 VAL Chi-restraints excluded: chain C residue 40 ILE Chi-restraints excluded: chain C residue 51 THR Chi-restraints excluded: chain C residue 61 LEU Chi-restraints excluded: chain E residue 103 THR Chi-restraints excluded: chain E residue 249 LEU Chi-restraints excluded: chain E residue 250 THR Chi-restraints excluded: chain E residue 271 VAL Chi-restraints excluded: chain F residue 1 VAL Chi-restraints excluded: chain F residue 2 VAL Chi-restraints excluded: chain F residue 40 ILE Chi-restraints excluded: chain F residue 45 GLN Chi-restraints excluded: chain F residue 51 THR Chi-restraints excluded: chain F residue 61 LEU Chi-restraints excluded: chain F residue 70 LEU Chi-restraints excluded: chain G residue 85 ASP Chi-restraints excluded: chain G residue 90 LEU Chi-restraints excluded: chain G residue 91 THR Chi-restraints excluded: chain G residue 93 PHE Chi-restraints excluded: chain G residue 150 THR Chi-restraints excluded: chain H residue 35 ASN Chi-restraints excluded: chain H residue 135 ASN Chi-restraints excluded: chain H residue 141 ASP Chi-restraints excluded: chain H residue 143 ASP Chi-restraints excluded: chain I residue 12 ILE Chi-restraints excluded: chain I residue 63 VAL Chi-restraints excluded: chain I residue 78 ARG Chi-restraints excluded: chain I residue 136 SER Chi-restraints excluded: chain I residue 143 ASP Chi-restraints excluded: chain I residue 185 LEU Chi-restraints excluded: chain J residue 143 ASP Chi-restraints excluded: chain K residue 36 LEU Chi-restraints excluded: chain K residue 63 VAL Chi-restraints excluded: chain K residue 141 ASP Chi-restraints excluded: chain K residue 168 ASN Chi-restraints excluded: chain K residue 184 ASP Chi-restraints excluded: chain L residue 24 LEU Chi-restraints excluded: chain L residue 167 LEU Chi-restraints excluded: chain L residue 192 PHE Chi-restraints excluded: chain L residue 193 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 234 random chunks: chunk 118 optimal weight: 0.9980 chunk 65 optimal weight: 7.9990 chunk 176 optimal weight: 20.0000 chunk 144 optimal weight: 8.9990 chunk 58 optimal weight: 4.9990 chunk 212 optimal weight: 20.0000 chunk 229 optimal weight: 8.9990 chunk 189 optimal weight: 40.0000 chunk 211 optimal weight: 5.9990 chunk 72 optimal weight: 5.9990 chunk 170 optimal weight: 8.9990 overall best weight: 5.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 208 HIS F 89 GLN ** H 102 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 102 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8309 moved from start: 0.2289 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.058 18554 Z= 0.464 Angle : 0.752 11.259 24994 Z= 0.385 Chirality : 0.048 0.277 2982 Planarity : 0.005 0.056 3134 Dihedral : 16.686 162.697 3045 Min Nonbonded Distance : 1.979 Molprobity Statistics. All-atom Clashscore : 8.73 Ramachandran Plot: Outliers : 0.21 % Allowed : 10.47 % Favored : 89.32 % Rotamer: Outliers : 5.34 % Allowed : 15.42 % Favored : 79.24 % 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: -3.13 (0.15), residues: 2350 helix: -1.46 (0.14), residues: 1044 sheet: -1.30 (0.32), residues: 278 loop : -2.93 (0.16), residues: 1028 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP A 212 HIS 0.005 0.001 HIS E 118 PHE 0.033 0.002 PHE C 17 TYR 0.023 0.002 TYR G 40 ARG 0.004 0.001 ARG E 272 *********************** 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 425 residues out of total 1994 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 100 poor density : 325 time to evaluate : 2.017 Fit side-chains revert: symmetry clash REVERT: B 17 LYS cc_start: 0.8823 (mttm) cc_final: 0.8590 (mttp) REVERT: B 120 LYS cc_start: 0.8668 (mppt) cc_final: 0.8343 (mmtt) REVERT: B 262 SER cc_start: 0.4967 (OUTLIER) cc_final: 0.4587 (m) REVERT: E 17 LYS cc_start: 0.8878 (mtpt) cc_final: 0.8632 (mtpt) REVERT: F 81 LYS cc_start: 0.8637 (mttt) cc_final: 0.8435 (mttt) REVERT: G 7 GLU cc_start: 0.7554 (mt-10) cc_final: 0.7349 (mt-10) REVERT: H 60 MET cc_start: 0.8320 (tpp) cc_final: 0.7882 (ttt) REVERT: H 93 PHE cc_start: 0.6822 (OUTLIER) cc_final: 0.5867 (p90) REVERT: H 141 ASP cc_start: 0.8380 (OUTLIER) cc_final: 0.7794 (p0) REVERT: I 185 LEU cc_start: 0.8057 (OUTLIER) cc_final: 0.7800 (pp) REVERT: I 186 GLU cc_start: 0.8217 (mm-30) cc_final: 0.7959 (mm-30) REVERT: I 191 LYS cc_start: 0.8662 (ttmt) cc_final: 0.8072 (tttt) REVERT: J 73 LEU cc_start: 0.8556 (OUTLIER) cc_final: 0.8283 (tt) REVERT: J 98 LEU cc_start: 0.8110 (OUTLIER) cc_final: 0.7755 (mt) REVERT: J 134 MET cc_start: 0.5988 (pmm) cc_final: 0.5596 (pmm) REVERT: K 85 ASP cc_start: 0.8290 (p0) cc_final: 0.7888 (p0) REVERT: K 93 PHE cc_start: 0.7235 (OUTLIER) cc_final: 0.6582 (p90) REVERT: K 192 PHE cc_start: 0.7038 (t80) cc_final: 0.6796 (t80) REVERT: L 42 MET cc_start: 0.8085 (mmm) cc_final: 0.7774 (mtt) outliers start: 100 outliers final: 69 residues processed: 390 average time/residue: 0.3257 time to fit residues: 193.5769 Evaluate side-chains 374 residues out of total 1994 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 76 poor density : 298 time to evaluate : 2.050 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 ILE Chi-restraints excluded: chain A residue 124 GLU Chi-restraints excluded: chain A residue 177 VAL Chi-restraints excluded: chain B residue 19 LEU Chi-restraints excluded: chain B residue 32 ILE Chi-restraints excluded: chain B residue 103 THR Chi-restraints excluded: chain B residue 124 ASN Chi-restraints excluded: chain B residue 154 MET Chi-restraints excluded: chain B residue 181 ASP Chi-restraints excluded: chain B residue 262 SER Chi-restraints excluded: chain C residue 10 VAL Chi-restraints excluded: chain C residue 12 SER Chi-restraints excluded: chain C residue 40 ILE Chi-restraints excluded: chain C residue 41 VAL Chi-restraints excluded: chain C residue 51 THR Chi-restraints excluded: chain C residue 61 LEU Chi-restraints excluded: chain D residue 81 GLU Chi-restraints excluded: chain D residue 177 VAL Chi-restraints excluded: chain D residue 215 VAL Chi-restraints excluded: chain D residue 233 THR Chi-restraints excluded: chain E residue 27 VAL Chi-restraints excluded: chain E residue 75 LYS Chi-restraints excluded: chain E residue 103 THR Chi-restraints excluded: chain E residue 169 ASP Chi-restraints excluded: chain E residue 188 LEU Chi-restraints excluded: chain E residue 189 THR Chi-restraints excluded: chain E residue 249 LEU Chi-restraints excluded: chain E residue 250 THR Chi-restraints excluded: chain F residue 1 VAL Chi-restraints excluded: chain F residue 2 VAL Chi-restraints excluded: chain F residue 51 THR Chi-restraints excluded: chain F residue 64 THR Chi-restraints excluded: chain F residue 70 LEU Chi-restraints excluded: chain G residue 63 VAL Chi-restraints excluded: chain G residue 85 ASP Chi-restraints excluded: chain G residue 87 ASP Chi-restraints excluded: chain G residue 90 LEU Chi-restraints excluded: chain G residue 91 THR Chi-restraints excluded: chain G residue 143 ASP Chi-restraints excluded: chain G residue 150 THR Chi-restraints excluded: chain G residue 153 LEU Chi-restraints excluded: chain G residue 167 LEU Chi-restraints excluded: chain H residue 35 ASN Chi-restraints excluded: chain H residue 93 PHE Chi-restraints excluded: chain H residue 128 GLN Chi-restraints excluded: chain H residue 135 ASN Chi-restraints excluded: chain H residue 141 ASP Chi-restraints excluded: chain H residue 143 ASP Chi-restraints excluded: chain H residue 167 LEU Chi-restraints excluded: chain H residue 174 ASP Chi-restraints excluded: chain H residue 188 LEU Chi-restraints excluded: chain I residue 63 VAL Chi-restraints excluded: chain I residue 78 ARG Chi-restraints excluded: chain I residue 87 ASP Chi-restraints excluded: chain I residue 136 SER Chi-restraints excluded: chain I residue 175 THR Chi-restraints excluded: chain I residue 185 LEU Chi-restraints excluded: chain J residue 21 LEU Chi-restraints excluded: chain J residue 73 LEU Chi-restraints excluded: chain J residue 96 GLU Chi-restraints excluded: chain J residue 98 LEU Chi-restraints excluded: chain J residue 143 ASP Chi-restraints excluded: chain K residue 32 VAL Chi-restraints excluded: chain K residue 36 LEU Chi-restraints excluded: chain K residue 63 VAL Chi-restraints excluded: chain K residue 93 PHE Chi-restraints excluded: chain K residue 135 ASN Chi-restraints excluded: chain K residue 141 ASP Chi-restraints excluded: chain K residue 168 ASN Chi-restraints excluded: chain K residue 183 MET Chi-restraints excluded: chain K residue 184 ASP Chi-restraints excluded: chain L residue 19 ILE Chi-restraints excluded: chain L residue 63 VAL Chi-restraints excluded: chain L residue 97 GLN Chi-restraints excluded: chain L residue 167 LEU Chi-restraints excluded: chain L residue 193 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 234 random chunks: chunk 210 optimal weight: 3.9990 chunk 160 optimal weight: 0.5980 chunk 110 optimal weight: 8.9990 chunk 23 optimal weight: 0.8980 chunk 101 optimal weight: 0.8980 chunk 142 optimal weight: 7.9990 chunk 213 optimal weight: 3.9990 chunk 226 optimal weight: 30.0000 chunk 111 optimal weight: 0.0020 chunk 202 optimal weight: 4.9990 chunk 60 optimal weight: 10.0000 overall best weight: 1.2790 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 264 GLN E 264 GLN H 50 ASN ** H 102 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 104 ASN ** L 102 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8231 moved from start: 0.2634 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 18554 Z= 0.163 Angle : 0.595 11.638 24994 Z= 0.309 Chirality : 0.042 0.288 2982 Planarity : 0.004 0.053 3134 Dihedral : 15.804 177.546 3035 Min Nonbonded Distance : 2.084 Molprobity Statistics. All-atom Clashscore : 7.87 Ramachandran Plot: Outliers : 0.21 % Allowed : 8.72 % Favored : 91.06 % Rotamer: Outliers : 4.32 % Allowed : 17.08 % Favored : 78.60 % 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: -2.27 (0.16), residues: 2350 helix: -0.53 (0.16), residues: 1042 sheet: -1.06 (0.33), residues: 278 loop : -2.68 (0.17), residues: 1030 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 212 HIS 0.008 0.001 HIS B 118 PHE 0.012 0.001 PHE C 17 TYR 0.013 0.001 TYR G 145 ARG 0.005 0.000 ARG E 82 *********************** 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 417 residues out of total 1994 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 81 poor density : 336 time to evaluate : 2.152 Fit side-chains REVERT: A 138 LYS cc_start: 0.8693 (mtpp) cc_final: 0.8403 (mmmm) REVERT: B 17 LYS cc_start: 0.8792 (mttm) cc_final: 0.8554 (mttp) REVERT: B 120 LYS cc_start: 0.8543 (mppt) cc_final: 0.8241 (mmtt) REVERT: B 135 GLU cc_start: 0.8169 (tm-30) cc_final: 0.7968 (tm-30) REVERT: D 226 GLU cc_start: 0.7885 (pp20) cc_final: 0.7369 (pp20) REVERT: E 17 LYS cc_start: 0.8830 (mtpt) cc_final: 0.8607 (mtpt) REVERT: F 70 LEU cc_start: 0.6737 (OUTLIER) cc_final: 0.6362 (mt) REVERT: F 81 LYS cc_start: 0.8559 (mttt) cc_final: 0.8332 (mttt) REVERT: H 60 MET cc_start: 0.8270 (tpp) cc_final: 0.7815 (ttt) REVERT: H 141 ASP cc_start: 0.8218 (OUTLIER) cc_final: 0.7723 (p0) REVERT: I 78 ARG cc_start: 0.7680 (OUTLIER) cc_final: 0.7448 (mmt90) REVERT: I 191 LYS cc_start: 0.8594 (ttmt) cc_final: 0.8012 (tttt) REVERT: J 43 LYS cc_start: 0.8137 (ptpp) cc_final: 0.7927 (pttp) REVERT: J 73 LEU cc_start: 0.8311 (OUTLIER) cc_final: 0.7925 (tt) REVERT: J 134 MET cc_start: 0.6015 (pmm) cc_final: 0.5660 (pmm) REVERT: J 141 ASP cc_start: 0.7968 (OUTLIER) cc_final: 0.7520 (p0) REVERT: K 85 ASP cc_start: 0.8186 (p0) cc_final: 0.7739 (p0) REVERT: L 24 LEU cc_start: 0.8355 (OUTLIER) cc_final: 0.8067 (tt) REVERT: L 42 MET cc_start: 0.7906 (mmm) cc_final: 0.7673 (mtt) REVERT: L 135 ASN cc_start: 0.7914 (OUTLIER) cc_final: 0.7683 (p0) outliers start: 81 outliers final: 46 residues processed: 392 average time/residue: 0.3039 time to fit residues: 177.3856 Evaluate side-chains 373 residues out of total 1994 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 53 poor density : 320 time to evaluate : 2.064 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 87 MET Chi-restraints excluded: chain A residue 129 MET Chi-restraints excluded: chain B residue 19 LEU Chi-restraints excluded: chain B residue 32 ILE Chi-restraints excluded: chain B residue 118 HIS Chi-restraints excluded: chain B residue 124 ASN Chi-restraints excluded: chain B residue 164 ILE Chi-restraints excluded: chain C residue 10 VAL Chi-restraints excluded: chain C residue 51 THR Chi-restraints excluded: chain C residue 61 LEU Chi-restraints excluded: chain D residue 87 MET Chi-restraints excluded: chain E residue 103 THR Chi-restraints excluded: chain E residue 118 HIS Chi-restraints excluded: chain E residue 145 LEU Chi-restraints excluded: chain E residue 169 ASP Chi-restraints excluded: chain E residue 188 LEU Chi-restraints excluded: chain E residue 249 LEU Chi-restraints excluded: chain E residue 271 VAL Chi-restraints excluded: chain F residue 2 VAL Chi-restraints excluded: chain F residue 51 THR Chi-restraints excluded: chain F residue 64 THR Chi-restraints excluded: chain F residue 70 LEU Chi-restraints excluded: chain G residue 36 LEU Chi-restraints excluded: chain G residue 63 VAL Chi-restraints excluded: chain G residue 85 ASP Chi-restraints excluded: chain G residue 87 ASP Chi-restraints excluded: chain G residue 90 LEU Chi-restraints excluded: chain G residue 150 THR Chi-restraints excluded: chain H residue 35 ASN Chi-restraints excluded: chain H residue 50 ASN Chi-restraints excluded: chain H residue 135 ASN Chi-restraints excluded: chain H residue 141 ASP Chi-restraints excluded: chain H residue 143 ASP Chi-restraints excluded: chain H residue 167 LEU Chi-restraints excluded: chain I residue 63 VAL Chi-restraints excluded: chain I residue 78 ARG Chi-restraints excluded: chain I residue 87 ASP Chi-restraints excluded: chain I residue 136 SER Chi-restraints excluded: chain I residue 143 ASP Chi-restraints excluded: chain I residue 175 THR Chi-restraints excluded: chain J residue 73 LEU Chi-restraints excluded: chain J residue 141 ASP Chi-restraints excluded: chain J residue 143 ASP Chi-restraints excluded: chain K residue 28 VAL Chi-restraints excluded: chain K residue 36 LEU Chi-restraints excluded: chain K residue 63 VAL Chi-restraints excluded: chain K residue 141 ASP Chi-restraints excluded: chain K residue 168 ASN Chi-restraints excluded: chain K residue 183 MET Chi-restraints excluded: chain K residue 184 ASP Chi-restraints excluded: chain L residue 24 LEU Chi-restraints excluded: chain L residue 135 ASN Chi-restraints excluded: chain L residue 167 LEU 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: 4.9990 chunk 3 optimal weight: 0.9980 chunk 168 optimal weight: 5.9990 chunk 93 optimal weight: 0.9980 chunk 193 optimal weight: 20.0000 chunk 156 optimal weight: 0.3980 chunk 0 optimal weight: 10.0000 chunk 115 optimal weight: 1.9990 chunk 203 optimal weight: 10.0000 chunk 57 optimal weight: 0.4980 overall best weight: 0.9782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 89 GLN H 50 ASN ** H 102 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 102 GLN ** L 102 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8217 moved from start: 0.2810 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.039 18554 Z= 0.151 Angle : 0.578 11.542 24994 Z= 0.299 Chirality : 0.041 0.213 2982 Planarity : 0.003 0.050 3134 Dihedral : 15.178 168.426 3031 Min Nonbonded Distance : 2.032 Molprobity Statistics. All-atom Clashscore : 8.03 Ramachandran Plot: Outliers : 0.13 % Allowed : 8.89 % Favored : 90.98 % Rotamer: Outliers : 4.11 % Allowed : 17.88 % Favored : 78.01 % 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: -1.76 (0.17), residues: 2350 helix: 0.02 (0.16), residues: 1040 sheet: -0.92 (0.33), residues: 278 loop : -2.53 (0.17), residues: 1032 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP D 212 HIS 0.007 0.001 HIS B 118 PHE 0.011 0.001 PHE G 13 TYR 0.016 0.001 TYR G 145 ARG 0.005 0.000 ARG E 140 *********************** 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 416 residues out of total 1994 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 77 poor density : 339 time to evaluate : 2.084 Fit side-chains revert: symmetry clash REVERT: A 138 LYS cc_start: 0.8668 (mtpp) cc_final: 0.8395 (mmmm) REVERT: B 17 LYS cc_start: 0.8796 (mttm) cc_final: 0.8560 (mttp) REVERT: B 135 GLU cc_start: 0.8126 (tm-30) cc_final: 0.7907 (tm-30) REVERT: B 246 LYS cc_start: 0.8153 (tptm) cc_final: 0.7854 (ptpt) REVERT: D 186 MET cc_start: 0.8791 (ttp) cc_final: 0.8561 (ttp) REVERT: D 226 GLU cc_start: 0.7853 (pp20) cc_final: 0.7639 (pm20) REVERT: E 17 LYS cc_start: 0.8849 (mtpt) cc_final: 0.8636 (mtpt) REVERT: E 105 MET cc_start: 0.8422 (mtt) cc_final: 0.8020 (mtt) REVERT: F 30 ILE cc_start: 0.6890 (OUTLIER) cc_final: 0.6651 (mp) REVERT: F 81 LYS cc_start: 0.8610 (mttt) cc_final: 0.8385 (mttt) REVERT: H 60 MET cc_start: 0.8257 (tpp) cc_final: 0.7785 (ttt) REVERT: H 93 PHE cc_start: 0.6780 (OUTLIER) cc_final: 0.6011 (p90) REVERT: H 141 ASP cc_start: 0.8249 (OUTLIER) cc_final: 0.7757 (p0) REVERT: J 43 LYS cc_start: 0.8133 (ptpp) cc_final: 0.7929 (pttp) REVERT: J 73 LEU cc_start: 0.8174 (OUTLIER) cc_final: 0.7906 (tt) REVERT: J 134 MET cc_start: 0.5958 (pmm) cc_final: 0.5649 (pmm) REVERT: J 141 ASP cc_start: 0.7944 (OUTLIER) cc_final: 0.7467 (p0) REVERT: K 85 ASP cc_start: 0.8153 (p0) cc_final: 0.7705 (p0) REVERT: K 93 PHE cc_start: 0.7024 (OUTLIER) cc_final: 0.6571 (p90) REVERT: K 187 ASP cc_start: 0.6603 (t70) cc_final: 0.6400 (t0) REVERT: L 21 LEU cc_start: 0.8479 (OUTLIER) cc_final: 0.8261 (mm) REVERT: L 24 LEU cc_start: 0.8336 (OUTLIER) cc_final: 0.8058 (tt) outliers start: 77 outliers final: 52 residues processed: 390 average time/residue: 0.3092 time to fit residues: 179.6549 Evaluate side-chains 379 residues out of total 1994 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 60 poor density : 319 time to evaluate : 1.855 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 129 MET Chi-restraints excluded: chain B residue 19 LEU Chi-restraints excluded: chain B residue 32 ILE Chi-restraints excluded: chain B residue 118 HIS Chi-restraints excluded: chain B residue 124 ASN Chi-restraints excluded: chain B residue 137 VAL Chi-restraints excluded: chain B residue 145 LEU Chi-restraints excluded: chain B residue 164 ILE Chi-restraints excluded: chain C residue 10 VAL Chi-restraints excluded: chain C residue 12 SER Chi-restraints excluded: chain C residue 40 ILE Chi-restraints excluded: chain C residue 51 THR Chi-restraints excluded: chain D residue 81 GLU Chi-restraints excluded: chain D residue 87 MET Chi-restraints excluded: chain E residue 103 THR Chi-restraints excluded: chain E residue 118 HIS Chi-restraints excluded: chain E residue 145 LEU Chi-restraints excluded: chain E residue 169 ASP Chi-restraints excluded: chain E residue 188 LEU Chi-restraints excluded: chain E residue 271 VAL Chi-restraints excluded: chain F residue 2 VAL Chi-restraints excluded: chain F residue 30 ILE Chi-restraints excluded: chain F residue 51 THR Chi-restraints excluded: chain F residue 64 THR Chi-restraints excluded: chain F residue 80 LEU Chi-restraints excluded: chain G residue 21 LEU Chi-restraints excluded: chain G residue 36 LEU Chi-restraints excluded: chain G residue 63 VAL Chi-restraints excluded: chain G residue 85 ASP Chi-restraints excluded: chain G residue 87 ASP Chi-restraints excluded: chain G residue 90 LEU Chi-restraints excluded: chain G residue 91 THR Chi-restraints excluded: chain G residue 143 ASP Chi-restraints excluded: chain G residue 150 THR Chi-restraints excluded: chain G residue 167 LEU Chi-restraints excluded: chain H residue 35 ASN Chi-restraints excluded: chain H residue 93 PHE Chi-restraints excluded: chain H residue 135 ASN Chi-restraints excluded: chain H residue 141 ASP Chi-restraints excluded: chain H residue 143 ASP Chi-restraints excluded: chain H residue 167 LEU Chi-restraints excluded: chain H residue 174 ASP Chi-restraints excluded: chain I residue 63 VAL Chi-restraints excluded: chain I residue 87 ASP Chi-restraints excluded: chain I residue 143 ASP Chi-restraints excluded: chain J residue 73 LEU Chi-restraints excluded: chain J residue 96 GLU Chi-restraints excluded: chain J residue 141 ASP Chi-restraints excluded: chain J residue 143 ASP Chi-restraints excluded: chain K residue 36 LEU Chi-restraints excluded: chain K residue 63 VAL Chi-restraints excluded: chain K residue 93 PHE Chi-restraints excluded: chain K residue 135 ASN Chi-restraints excluded: chain K residue 141 ASP Chi-restraints excluded: chain K residue 143 ASP Chi-restraints excluded: chain K residue 168 ASN Chi-restraints excluded: chain K residue 184 ASP Chi-restraints excluded: chain L residue 21 LEU Chi-restraints excluded: chain L residue 24 LEU Chi-restraints excluded: chain L residue 167 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 234 random chunks: chunk 76 optimal weight: 5.9990 chunk 203 optimal weight: 8.9990 chunk 44 optimal weight: 8.9990 chunk 132 optimal weight: 30.0000 chunk 55 optimal weight: 0.7980 chunk 226 optimal weight: 0.0970 chunk 187 optimal weight: 7.9990 chunk 104 optimal weight: 3.9990 chunk 18 optimal weight: 0.9980 chunk 74 optimal weight: 1.9990 chunk 118 optimal weight: 3.9990 overall best weight: 1.5782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 155 ASN G 45 GLN H 50 ASN I 102 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8222 moved from start: 0.2939 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 18554 Z= 0.182 Angle : 0.584 11.806 24994 Z= 0.302 Chirality : 0.042 0.288 2982 Planarity : 0.003 0.050 3134 Dihedral : 14.677 157.766 3023 Min Nonbonded Distance : 2.118 Molprobity Statistics. All-atom Clashscore : 7.46 Ramachandran Plot: Outliers : 0.17 % Allowed : 9.11 % Favored : 90.72 % Rotamer: Outliers : 4.43 % Allowed : 18.04 % Favored : 77.53 % 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: -1.48 (0.17), residues: 2350 helix: 0.34 (0.17), residues: 1040 sheet: -0.85 (0.33), residues: 278 loop : -2.47 (0.18), residues: 1032 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP D 183 HIS 0.008 0.001 HIS B 118 PHE 0.015 0.001 PHE G 13 TYR 0.016 0.001 TYR G 145 ARG 0.009 0.000 ARG I 78 *********************** 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 417 residues out of total 1994 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 83 poor density : 334 time to evaluate : 1.569 Fit side-chains revert: symmetry clash REVERT: A 138 LYS cc_start: 0.8668 (mtpp) cc_final: 0.8390 (mmmm) REVERT: B 17 LYS cc_start: 0.8769 (mttm) cc_final: 0.8547 (mttp) REVERT: B 120 LYS cc_start: 0.8583 (mppt) cc_final: 0.8302 (mmtt) REVERT: B 135 GLU cc_start: 0.8118 (tm-30) cc_final: 0.7878 (tm-30) REVERT: B 246 LYS cc_start: 0.8208 (tptm) cc_final: 0.7872 (ptpt) REVERT: D 226 GLU cc_start: 0.7835 (pp20) cc_final: 0.7631 (pm20) REVERT: E 105 MET cc_start: 0.8425 (mtt) cc_final: 0.8050 (mtt) REVERT: F 30 ILE cc_start: 0.6761 (OUTLIER) cc_final: 0.6457 (mp) REVERT: F 81 LYS cc_start: 0.8612 (mttt) cc_final: 0.8374 (mttt) REVERT: H 60 MET cc_start: 0.8264 (tpp) cc_final: 0.7815 (ttt) REVERT: H 93 PHE cc_start: 0.6761 (OUTLIER) cc_final: 0.6086 (p90) REVERT: H 141 ASP cc_start: 0.8252 (OUTLIER) cc_final: 0.7692 (p0) REVERT: I 16 ILE cc_start: 0.8533 (mm) cc_final: 0.8331 (mm) REVERT: J 73 LEU cc_start: 0.8183 (OUTLIER) cc_final: 0.7917 (tt) REVERT: J 134 MET cc_start: 0.5981 (pmm) cc_final: 0.5708 (pmm) REVERT: J 141 ASP cc_start: 0.7917 (OUTLIER) cc_final: 0.7353 (p0) REVERT: K 85 ASP cc_start: 0.8223 (p0) cc_final: 0.7852 (p0) REVERT: K 93 PHE cc_start: 0.6980 (OUTLIER) cc_final: 0.6604 (p90) REVERT: K 187 ASP cc_start: 0.6701 (t70) cc_final: 0.6498 (t0) REVERT: L 21 LEU cc_start: 0.8517 (OUTLIER) cc_final: 0.8309 (mm) REVERT: L 24 LEU cc_start: 0.8348 (OUTLIER) cc_final: 0.8061 (tt) outliers start: 83 outliers final: 61 residues processed: 388 average time/residue: 0.3118 time to fit residues: 180.1229 Evaluate side-chains 393 residues out of total 1994 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 69 poor density : 324 time to evaluate : 2.044 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 87 MET Chi-restraints excluded: chain A residue 129 MET Chi-restraints excluded: chain A residue 177 VAL Chi-restraints excluded: chain B residue 19 LEU Chi-restraints excluded: chain B residue 32 ILE Chi-restraints excluded: chain B residue 118 HIS Chi-restraints excluded: chain B residue 124 ASN Chi-restraints excluded: chain B residue 145 LEU Chi-restraints excluded: chain B residue 164 ILE Chi-restraints excluded: chain C residue 10 VAL Chi-restraints excluded: chain C residue 12 SER Chi-restraints excluded: chain C residue 40 ILE Chi-restraints excluded: chain C residue 51 THR Chi-restraints excluded: chain D residue 81 GLU Chi-restraints excluded: chain D residue 87 MET Chi-restraints excluded: chain E residue 75 LYS Chi-restraints excluded: chain E residue 80 MET Chi-restraints excluded: chain E residue 118 HIS Chi-restraints excluded: chain E residue 137 VAL Chi-restraints excluded: chain E residue 142 THR Chi-restraints excluded: chain E residue 145 LEU Chi-restraints excluded: chain E residue 169 ASP Chi-restraints excluded: chain E residue 188 LEU Chi-restraints excluded: chain E residue 271 VAL Chi-restraints excluded: chain F residue 2 VAL Chi-restraints excluded: chain F residue 30 ILE Chi-restraints excluded: chain F residue 51 THR Chi-restraints excluded: chain F residue 64 THR Chi-restraints excluded: chain F residue 80 LEU Chi-restraints excluded: chain G residue 21 LEU Chi-restraints excluded: chain G residue 36 LEU Chi-restraints excluded: chain G residue 63 VAL Chi-restraints excluded: chain G residue 85 ASP Chi-restraints excluded: chain G residue 87 ASP Chi-restraints excluded: chain G residue 90 LEU Chi-restraints excluded: chain G residue 143 ASP Chi-restraints excluded: chain G residue 150 THR Chi-restraints excluded: chain H residue 35 ASN Chi-restraints excluded: chain H residue 93 PHE Chi-restraints excluded: chain H residue 135 ASN Chi-restraints excluded: chain H residue 141 ASP Chi-restraints excluded: chain H residue 143 ASP Chi-restraints excluded: chain H residue 167 LEU Chi-restraints excluded: chain H residue 174 ASP Chi-restraints excluded: chain H residue 188 LEU Chi-restraints excluded: chain I residue 63 VAL Chi-restraints excluded: chain I residue 87 ASP Chi-restraints excluded: chain I residue 143 ASP Chi-restraints excluded: chain I residue 175 THR Chi-restraints excluded: chain J residue 21 LEU Chi-restraints excluded: chain J residue 73 LEU Chi-restraints excluded: chain J residue 96 GLU Chi-restraints excluded: chain J residue 141 ASP Chi-restraints excluded: chain J residue 143 ASP Chi-restraints excluded: chain K residue 28 VAL Chi-restraints excluded: chain K residue 36 LEU Chi-restraints excluded: chain K residue 63 VAL Chi-restraints excluded: chain K residue 93 PHE Chi-restraints excluded: chain K residue 135 ASN Chi-restraints excluded: chain K residue 141 ASP Chi-restraints excluded: chain K residue 143 ASP Chi-restraints excluded: chain K residue 168 ASN Chi-restraints excluded: chain K residue 183 MET Chi-restraints excluded: chain K residue 184 ASP Chi-restraints excluded: chain L residue 21 LEU Chi-restraints excluded: chain L residue 24 LEU Chi-restraints excluded: chain L residue 32 VAL Chi-restraints excluded: chain L residue 63 VAL Chi-restraints excluded: chain L residue 167 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 234 random chunks: chunk 218 optimal weight: 4.9990 chunk 25 optimal weight: 9.9990 chunk 128 optimal weight: 9.9990 chunk 165 optimal weight: 8.9990 chunk 190 optimal weight: 0.0370 chunk 126 optimal weight: 6.9990 chunk 225 optimal weight: 0.3980 chunk 141 optimal weight: 9.9990 chunk 137 optimal weight: 5.9990 chunk 104 optimal weight: 0.9980 chunk 139 optimal weight: 10.0000 overall best weight: 2.4862 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 264 GLN E 155 ASN F 89 GLN G 45 GLN H 50 ASN I 102 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8246 moved from start: 0.2971 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 18554 Z= 0.243 Angle : 0.607 12.073 24994 Z= 0.312 Chirality : 0.043 0.248 2982 Planarity : 0.004 0.050 3134 Dihedral : 14.401 147.594 3022 Min Nonbonded Distance : 2.035 Molprobity Statistics. All-atom Clashscore : 7.65 Ramachandran Plot: Outliers : 0.17 % Allowed : 9.53 % Favored : 90.30 % Rotamer: Outliers : 4.96 % Allowed : 18.30 % Favored : 76.73 % 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: -1.40 (0.17), residues: 2350 helix: 0.44 (0.17), residues: 1040 sheet: -0.80 (0.33), residues: 278 loop : -2.47 (0.18), residues: 1032 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP D 183 HIS 0.007 0.001 HIS E 118 PHE 0.018 0.001 PHE F 17 TYR 0.017 0.001 TYR G 145 ARG 0.008 0.000 ARG I 78 *********************** 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 416 residues out of total 1994 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 93 poor density : 323 time to evaluate : 2.193 Fit side-chains revert: symmetry clash REVERT: A 138 LYS cc_start: 0.8697 (mtpp) cc_final: 0.8404 (mmmm) REVERT: B 17 LYS cc_start: 0.8773 (mttm) cc_final: 0.8545 (mttp) REVERT: B 63 LEU cc_start: 0.8618 (OUTLIER) cc_final: 0.8382 (mt) REVERT: B 246 LYS cc_start: 0.8213 (tptm) cc_final: 0.7880 (ptpt) REVERT: D 226 GLU cc_start: 0.7827 (pp20) cc_final: 0.7624 (pm20) REVERT: F 30 ILE cc_start: 0.6858 (OUTLIER) cc_final: 0.6512 (mp) REVERT: F 70 LEU cc_start: 0.6733 (OUTLIER) cc_final: 0.6476 (mt) REVERT: F 81 LYS cc_start: 0.8631 (mttt) cc_final: 0.8393 (mttt) REVERT: H 60 MET cc_start: 0.8290 (tpp) cc_final: 0.7853 (ttt) REVERT: H 93 PHE cc_start: 0.6831 (OUTLIER) cc_final: 0.6148 (p90) REVERT: H 141 ASP cc_start: 0.8157 (OUTLIER) cc_final: 0.7682 (p0) REVERT: I 27 LYS cc_start: 0.8662 (OUTLIER) cc_final: 0.7937 (tmmt) REVERT: J 42 MET cc_start: 0.8622 (mtp) cc_final: 0.8085 (mtp) REVERT: J 73 LEU cc_start: 0.8176 (OUTLIER) cc_final: 0.7910 (tt) REVERT: J 134 MET cc_start: 0.5997 (pmm) cc_final: 0.5687 (pmm) REVERT: J 141 ASP cc_start: 0.7946 (OUTLIER) cc_final: 0.7357 (p0) REVERT: K 85 ASP cc_start: 0.8230 (p0) cc_final: 0.7942 (p0) REVERT: K 93 PHE cc_start: 0.7001 (OUTLIER) cc_final: 0.6507 (p90) REVERT: K 187 ASP cc_start: 0.6737 (t70) cc_final: 0.6526 (t0) REVERT: L 21 LEU cc_start: 0.8548 (OUTLIER) cc_final: 0.8341 (mm) REVERT: L 24 LEU cc_start: 0.8380 (OUTLIER) cc_final: 0.8084 (tt) REVERT: L 135 ASN cc_start: 0.7889 (OUTLIER) cc_final: 0.7684 (p0) outliers start: 93 outliers final: 67 residues processed: 383 average time/residue: 0.3290 time to fit residues: 191.0037 Evaluate side-chains 397 residues out of total 1994 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 79 poor density : 318 time to evaluate : 2.184 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 87 MET Chi-restraints excluded: chain A residue 124 GLU Chi-restraints excluded: chain A residue 129 MET Chi-restraints excluded: chain A residue 177 VAL Chi-restraints excluded: chain B residue 19 LEU Chi-restraints excluded: chain B residue 32 ILE Chi-restraints excluded: chain B residue 63 LEU Chi-restraints excluded: chain B residue 118 HIS Chi-restraints excluded: chain B residue 124 ASN Chi-restraints excluded: chain B residue 145 LEU Chi-restraints excluded: chain B residue 164 ILE Chi-restraints excluded: chain C residue 10 VAL Chi-restraints excluded: chain C residue 12 SER Chi-restraints excluded: chain C residue 40 ILE Chi-restraints excluded: chain C residue 51 THR Chi-restraints excluded: chain C residue 64 THR Chi-restraints excluded: chain D residue 81 GLU Chi-restraints excluded: chain D residue 87 MET Chi-restraints excluded: chain D residue 177 VAL Chi-restraints excluded: chain E residue 75 LYS Chi-restraints excluded: chain E residue 80 MET Chi-restraints excluded: chain E residue 118 HIS Chi-restraints excluded: chain E residue 137 VAL Chi-restraints excluded: chain E residue 142 THR Chi-restraints excluded: chain E residue 145 LEU Chi-restraints excluded: chain E residue 169 ASP Chi-restraints excluded: chain E residue 188 LEU Chi-restraints excluded: chain E residue 249 LEU Chi-restraints excluded: chain E residue 250 THR Chi-restraints excluded: chain E residue 271 VAL Chi-restraints excluded: chain F residue 2 VAL Chi-restraints excluded: chain F residue 30 ILE Chi-restraints excluded: chain F residue 51 THR Chi-restraints excluded: chain F residue 64 THR Chi-restraints excluded: chain F residue 70 LEU Chi-restraints excluded: chain G residue 21 LEU Chi-restraints excluded: chain G residue 36 LEU Chi-restraints excluded: chain G residue 63 VAL Chi-restraints excluded: chain G residue 85 ASP Chi-restraints excluded: chain G residue 87 ASP Chi-restraints excluded: chain G residue 90 LEU Chi-restraints excluded: chain G residue 143 ASP Chi-restraints excluded: chain G residue 150 THR Chi-restraints excluded: chain H residue 35 ASN Chi-restraints excluded: chain H residue 93 PHE Chi-restraints excluded: chain H residue 135 ASN Chi-restraints excluded: chain H residue 141 ASP Chi-restraints excluded: chain H residue 143 ASP Chi-restraints excluded: chain H residue 167 LEU Chi-restraints excluded: chain H residue 174 ASP Chi-restraints excluded: chain H residue 188 LEU Chi-restraints excluded: chain I residue 27 LYS Chi-restraints excluded: chain I residue 63 VAL Chi-restraints excluded: chain I residue 87 ASP Chi-restraints excluded: chain I residue 143 ASP Chi-restraints excluded: chain I residue 175 THR Chi-restraints excluded: chain J residue 21 LEU Chi-restraints excluded: chain J residue 73 LEU Chi-restraints excluded: chain J residue 96 GLU Chi-restraints excluded: chain J residue 141 ASP Chi-restraints excluded: chain J residue 143 ASP Chi-restraints excluded: chain J residue 180 GLN Chi-restraints excluded: chain K residue 28 VAL Chi-restraints excluded: chain K residue 36 LEU Chi-restraints excluded: chain K residue 63 VAL Chi-restraints excluded: chain K residue 90 LEU Chi-restraints excluded: chain K residue 93 PHE Chi-restraints excluded: chain K residue 135 ASN Chi-restraints excluded: chain K residue 141 ASP Chi-restraints excluded: chain K residue 143 ASP Chi-restraints excluded: chain K residue 168 ASN Chi-restraints excluded: chain K residue 183 MET Chi-restraints excluded: chain K residue 184 ASP Chi-restraints excluded: chain L residue 21 LEU Chi-restraints excluded: chain L residue 24 LEU Chi-restraints excluded: chain L residue 32 VAL Chi-restraints excluded: chain L residue 63 VAL Chi-restraints excluded: chain L residue 135 ASN Chi-restraints excluded: chain L residue 167 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 234 random chunks: chunk 90 optimal weight: 7.9990 chunk 134 optimal weight: 1.9990 chunk 67 optimal weight: 7.9990 chunk 44 optimal weight: 6.9990 chunk 43 optimal weight: 0.9990 chunk 143 optimal weight: 2.9990 chunk 153 optimal weight: 1.9990 chunk 111 optimal weight: 3.9990 chunk 21 optimal weight: 0.7980 chunk 177 optimal weight: 7.9990 chunk 205 optimal weight: 6.9990 overall best weight: 1.7588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 155 ASN G 45 GLN H 50 ASN I 45 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8229 moved from start: 0.3077 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 18554 Z= 0.195 Angle : 0.584 11.953 24994 Z= 0.303 Chirality : 0.043 0.280 2982 Planarity : 0.003 0.052 3134 Dihedral : 14.010 140.636 3022 Min Nonbonded Distance : 2.108 Molprobity Statistics. All-atom Clashscore : 7.63 Ramachandran Plot: Outliers : 0.17 % Allowed : 9.23 % Favored : 90.60 % Rotamer: Outliers : 4.80 % Allowed : 18.68 % Favored : 76.52 % 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: -1.25 (0.17), residues: 2350 helix: 0.60 (0.17), residues: 1040 sheet: -0.75 (0.33), residues: 278 loop : -2.43 (0.18), residues: 1032 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP D 183 HIS 0.007 0.001 HIS B 118 PHE 0.014 0.001 PHE G 13 TYR 0.016 0.001 TYR G 145 ARG 0.007 0.000 ARG I 78 *********************** 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 419 residues out of total 1994 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 90 poor density : 329 time to evaluate : 2.010 Fit side-chains revert: symmetry clash REVERT: A 138 LYS cc_start: 0.8666 (mtpp) cc_final: 0.8380 (mmmm) REVERT: B 17 LYS cc_start: 0.8753 (mttm) cc_final: 0.8538 (mttp) REVERT: B 63 LEU cc_start: 0.8562 (OUTLIER) cc_final: 0.8332 (mt) REVERT: B 120 LYS cc_start: 0.8598 (mppt) cc_final: 0.8312 (mmtt) REVERT: B 246 LYS cc_start: 0.8200 (tptm) cc_final: 0.7881 (ptpt) REVERT: C 66 GLN cc_start: 0.6992 (tm-30) cc_final: 0.6746 (tm-30) REVERT: F 30 ILE cc_start: 0.6857 (OUTLIER) cc_final: 0.6543 (mp) REVERT: F 79 MET cc_start: 0.8633 (mmm) cc_final: 0.8064 (mmm) REVERT: H 60 MET cc_start: 0.8262 (tpp) cc_final: 0.7830 (ttt) REVERT: H 93 PHE cc_start: 0.6780 (OUTLIER) cc_final: 0.6104 (p90) REVERT: H 141 ASP cc_start: 0.8107 (OUTLIER) cc_final: 0.7611 (p0) REVERT: I 27 LYS cc_start: 0.8658 (OUTLIER) cc_final: 0.7935 (tmmt) REVERT: J 73 LEU cc_start: 0.8159 (OUTLIER) cc_final: 0.7900 (tt) REVERT: J 134 MET cc_start: 0.5959 (pmm) cc_final: 0.5678 (pmm) REVERT: J 141 ASP cc_start: 0.7922 (OUTLIER) cc_final: 0.7420 (p0) REVERT: K 85 ASP cc_start: 0.8223 (p0) cc_final: 0.7930 (p0) REVERT: K 187 ASP cc_start: 0.6639 (t70) cc_final: 0.6425 (t0) REVERT: L 21 LEU cc_start: 0.8571 (OUTLIER) cc_final: 0.8363 (mm) REVERT: L 24 LEU cc_start: 0.8427 (OUTLIER) cc_final: 0.8221 (tt) REVERT: L 135 ASN cc_start: 0.7874 (OUTLIER) cc_final: 0.7673 (p0) outliers start: 90 outliers final: 68 residues processed: 385 average time/residue: 0.2936 time to fit residues: 170.6003 Evaluate side-chains 401 residues out of total 1994 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 78 poor density : 323 time to evaluate : 2.188 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 87 MET Chi-restraints excluded: chain A residue 124 GLU Chi-restraints excluded: chain A residue 129 MET Chi-restraints excluded: chain A residue 177 VAL Chi-restraints excluded: chain B residue 19 LEU Chi-restraints excluded: chain B residue 32 ILE Chi-restraints excluded: chain B residue 63 LEU Chi-restraints excluded: chain B residue 118 HIS Chi-restraints excluded: chain B residue 124 ASN Chi-restraints excluded: chain B residue 142 THR Chi-restraints excluded: chain B residue 145 LEU Chi-restraints excluded: chain B residue 164 ILE Chi-restraints excluded: chain C residue 10 VAL Chi-restraints excluded: chain C residue 12 SER Chi-restraints excluded: chain C residue 40 ILE Chi-restraints excluded: chain C residue 51 THR Chi-restraints excluded: chain C residue 64 THR Chi-restraints excluded: chain D residue 81 GLU Chi-restraints excluded: chain D residue 87 MET Chi-restraints excluded: chain E residue 16 VAL Chi-restraints excluded: chain E residue 75 LYS Chi-restraints excluded: chain E residue 80 MET Chi-restraints excluded: chain E residue 103 THR Chi-restraints excluded: chain E residue 118 HIS Chi-restraints excluded: chain E residue 137 VAL Chi-restraints excluded: chain E residue 142 THR Chi-restraints excluded: chain E residue 145 LEU Chi-restraints excluded: chain E residue 169 ASP Chi-restraints excluded: chain E residue 188 LEU Chi-restraints excluded: chain E residue 249 LEU Chi-restraints excluded: chain E residue 271 VAL Chi-restraints excluded: chain F residue 2 VAL Chi-restraints excluded: chain F residue 30 ILE Chi-restraints excluded: chain F residue 51 THR Chi-restraints excluded: chain F residue 64 THR Chi-restraints excluded: chain G residue 21 LEU Chi-restraints excluded: chain G residue 36 LEU Chi-restraints excluded: chain G residue 63 VAL Chi-restraints excluded: chain G residue 85 ASP Chi-restraints excluded: chain G residue 87 ASP Chi-restraints excluded: chain G residue 90 LEU Chi-restraints excluded: chain G residue 143 ASP Chi-restraints excluded: chain G residue 150 THR Chi-restraints excluded: chain H residue 35 ASN Chi-restraints excluded: chain H residue 93 PHE Chi-restraints excluded: chain H residue 135 ASN Chi-restraints excluded: chain H residue 141 ASP Chi-restraints excluded: chain H residue 143 ASP Chi-restraints excluded: chain H residue 167 LEU Chi-restraints excluded: chain H residue 174 ASP Chi-restraints excluded: chain H residue 188 LEU Chi-restraints excluded: chain I residue 27 LYS Chi-restraints excluded: chain I residue 63 VAL Chi-restraints excluded: chain I residue 87 ASP Chi-restraints excluded: chain I residue 143 ASP Chi-restraints excluded: chain I residue 175 THR Chi-restraints excluded: chain J residue 21 LEU Chi-restraints excluded: chain J residue 73 LEU Chi-restraints excluded: chain J residue 96 GLU Chi-restraints excluded: chain J residue 141 ASP Chi-restraints excluded: chain J residue 143 ASP Chi-restraints excluded: chain K residue 28 VAL Chi-restraints excluded: chain K residue 34 THR Chi-restraints excluded: chain K residue 36 LEU Chi-restraints excluded: chain K residue 63 VAL Chi-restraints excluded: chain K residue 90 LEU Chi-restraints excluded: chain K residue 135 ASN Chi-restraints excluded: chain K residue 141 ASP Chi-restraints excluded: chain K residue 168 ASN Chi-restraints excluded: chain K residue 183 MET Chi-restraints excluded: chain K residue 184 ASP Chi-restraints excluded: chain L residue 21 LEU Chi-restraints excluded: chain L residue 24 LEU Chi-restraints excluded: chain L residue 32 VAL Chi-restraints excluded: chain L residue 63 VAL Chi-restraints excluded: chain L residue 135 ASN Chi-restraints excluded: chain L residue 167 LEU Chi-restraints excluded: chain L residue 184 ASP Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 234 random chunks: chunk 216 optimal weight: 3.9990 chunk 197 optimal weight: 0.7980 chunk 210 optimal weight: 4.9990 chunk 126 optimal weight: 7.9990 chunk 91 optimal weight: 3.9990 chunk 165 optimal weight: 7.9990 chunk 64 optimal weight: 4.9990 chunk 189 optimal weight: 7.9990 chunk 198 optimal weight: 6.9990 chunk 209 optimal weight: 0.9990 chunk 138 optimal weight: 0.9980 overall best weight: 2.1586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 155 ASN G 45 GLN H 50 ASN I 45 GLN J 102 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8238 moved from start: 0.3112 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 18554 Z= 0.222 Angle : 0.597 12.059 24994 Z= 0.309 Chirality : 0.043 0.251 2982 Planarity : 0.004 0.049 3134 Dihedral : 13.741 133.478 3022 Min Nonbonded Distance : 2.078 Molprobity Statistics. All-atom Clashscore : 7.68 Ramachandran Plot: Outliers : 0.17 % Allowed : 9.49 % Favored : 90.34 % Rotamer: Outliers : 4.70 % Allowed : 18.62 % Favored : 76.68 % 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: -1.19 (0.17), residues: 2350 helix: 0.67 (0.17), residues: 1040 sheet: -0.73 (0.33), residues: 278 loop : -2.42 (0.18), residues: 1032 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP D 183 HIS 0.009 0.001 HIS E 263 PHE 0.018 0.001 PHE L 13 TYR 0.017 0.001 TYR G 145 ARG 0.008 0.000 ARG I 78 *********************** 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 411 residues out of total 1994 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 88 poor density : 323 time to evaluate : 2.123 Fit side-chains revert: symmetry clash REVERT: A 138 LYS cc_start: 0.8675 (mtpp) cc_final: 0.8380 (mmmm) REVERT: B 17 LYS cc_start: 0.8746 (mttm) cc_final: 0.8531 (mttp) REVERT: B 63 LEU cc_start: 0.8579 (OUTLIER) cc_final: 0.8354 (mt) REVERT: B 135 GLU cc_start: 0.8254 (tm-30) cc_final: 0.7981 (tm-30) REVERT: B 246 LYS cc_start: 0.8216 (tptm) cc_final: 0.7899 (ptpt) REVERT: C 66 GLN cc_start: 0.6945 (tm-30) cc_final: 0.6725 (tm-30) REVERT: F 30 ILE cc_start: 0.6870 (OUTLIER) cc_final: 0.6543 (mp) REVERT: H 60 MET cc_start: 0.8285 (tpp) cc_final: 0.7854 (ttt) REVERT: H 93 PHE cc_start: 0.6790 (OUTLIER) cc_final: 0.6098 (p90) REVERT: H 141 ASP cc_start: 0.8128 (OUTLIER) cc_final: 0.7604 (p0) REVERT: I 27 LYS cc_start: 0.8664 (OUTLIER) cc_final: 0.7942 (tmmt) REVERT: J 42 MET cc_start: 0.8656 (mtp) cc_final: 0.8080 (mtp) REVERT: J 73 LEU cc_start: 0.8175 (OUTLIER) cc_final: 0.7947 (tt) REVERT: J 134 MET cc_start: 0.5985 (pmm) cc_final: 0.5694 (pmm) REVERT: J 141 ASP cc_start: 0.7951 (OUTLIER) cc_final: 0.7434 (p0) REVERT: K 85 ASP cc_start: 0.8209 (p0) cc_final: 0.7925 (p0) REVERT: K 187 ASP cc_start: 0.6731 (t70) cc_final: 0.6519 (t0) REVERT: L 21 LEU cc_start: 0.8574 (OUTLIER) cc_final: 0.8366 (mm) REVERT: L 24 LEU cc_start: 0.8383 (OUTLIER) cc_final: 0.8082 (tt) REVERT: L 135 ASN cc_start: 0.7877 (OUTLIER) cc_final: 0.7675 (p0) outliers start: 88 outliers final: 70 residues processed: 378 average time/residue: 0.2916 time to fit residues: 164.6628 Evaluate side-chains 398 residues out of total 1994 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 80 poor density : 318 time to evaluate : 1.824 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 87 MET Chi-restraints excluded: chain A residue 124 GLU Chi-restraints excluded: chain A residue 129 MET Chi-restraints excluded: chain A residue 177 VAL Chi-restraints excluded: chain B residue 19 LEU Chi-restraints excluded: chain B residue 32 ILE Chi-restraints excluded: chain B residue 63 LEU Chi-restraints excluded: chain B residue 80 MET Chi-restraints excluded: chain B residue 118 HIS Chi-restraints excluded: chain B residue 124 ASN Chi-restraints excluded: chain B residue 142 THR Chi-restraints excluded: chain B residue 145 LEU Chi-restraints excluded: chain B residue 164 ILE Chi-restraints excluded: chain C residue 10 VAL Chi-restraints excluded: chain C residue 12 SER Chi-restraints excluded: chain C residue 40 ILE Chi-restraints excluded: chain C residue 51 THR Chi-restraints excluded: chain C residue 64 THR Chi-restraints excluded: chain D residue 81 GLU Chi-restraints excluded: chain D residue 87 MET Chi-restraints excluded: chain E residue 75 LYS Chi-restraints excluded: chain E residue 80 MET Chi-restraints excluded: chain E residue 103 THR Chi-restraints excluded: chain E residue 118 HIS Chi-restraints excluded: chain E residue 137 VAL Chi-restraints excluded: chain E residue 142 THR Chi-restraints excluded: chain E residue 145 LEU Chi-restraints excluded: chain E residue 169 ASP Chi-restraints excluded: chain E residue 188 LEU Chi-restraints excluded: chain E residue 249 LEU Chi-restraints excluded: chain E residue 250 THR Chi-restraints excluded: chain E residue 271 VAL Chi-restraints excluded: chain F residue 2 VAL Chi-restraints excluded: chain F residue 30 ILE Chi-restraints excluded: chain F residue 51 THR Chi-restraints excluded: chain F residue 64 THR Chi-restraints excluded: chain G residue 21 LEU Chi-restraints excluded: chain G residue 36 LEU Chi-restraints excluded: chain G residue 63 VAL Chi-restraints excluded: chain G residue 85 ASP Chi-restraints excluded: chain G residue 87 ASP Chi-restraints excluded: chain G residue 90 LEU Chi-restraints excluded: chain G residue 143 ASP Chi-restraints excluded: chain G residue 150 THR Chi-restraints excluded: chain G residue 153 LEU Chi-restraints excluded: chain H residue 35 ASN Chi-restraints excluded: chain H residue 93 PHE Chi-restraints excluded: chain H residue 135 ASN Chi-restraints excluded: chain H residue 141 ASP Chi-restraints excluded: chain H residue 143 ASP Chi-restraints excluded: chain H residue 167 LEU Chi-restraints excluded: chain H residue 174 ASP Chi-restraints excluded: chain H residue 188 LEU Chi-restraints excluded: chain I residue 27 LYS Chi-restraints excluded: chain I residue 63 VAL Chi-restraints excluded: chain I residue 87 ASP Chi-restraints excluded: chain I residue 136 SER Chi-restraints excluded: chain I residue 143 ASP Chi-restraints excluded: chain I residue 175 THR Chi-restraints excluded: chain J residue 21 LEU Chi-restraints excluded: chain J residue 73 LEU Chi-restraints excluded: chain J residue 96 GLU Chi-restraints excluded: chain J residue 141 ASP Chi-restraints excluded: chain J residue 143 ASP Chi-restraints excluded: chain J residue 180 GLN Chi-restraints excluded: chain K residue 28 VAL Chi-restraints excluded: chain K residue 36 LEU Chi-restraints excluded: chain K residue 63 VAL Chi-restraints excluded: chain K residue 90 LEU Chi-restraints excluded: chain K residue 135 ASN Chi-restraints excluded: chain K residue 141 ASP Chi-restraints excluded: chain K residue 168 ASN Chi-restraints excluded: chain K residue 183 MET Chi-restraints excluded: chain K residue 184 ASP Chi-restraints excluded: chain L residue 21 LEU Chi-restraints excluded: chain L residue 24 LEU Chi-restraints excluded: chain L residue 32 VAL Chi-restraints excluded: chain L residue 63 VAL Chi-restraints excluded: chain L residue 135 ASN Chi-restraints excluded: chain L residue 167 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 234 random chunks: chunk 222 optimal weight: 10.0000 chunk 135 optimal weight: 2.9990 chunk 105 optimal weight: 0.9980 chunk 154 optimal weight: 0.7980 chunk 233 optimal weight: 0.5980 chunk 214 optimal weight: 0.0870 chunk 185 optimal weight: 2.9990 chunk 19 optimal weight: 0.8980 chunk 143 optimal weight: 4.9990 chunk 113 optimal weight: 4.9990 chunk 147 optimal weight: 3.9990 overall best weight: 0.6758 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 155 ASN G 45 GLN H 50 ASN ** H 102 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 97 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8188 moved from start: 0.3328 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.040 18554 Z= 0.142 Angle : 0.563 11.690 24994 Z= 0.293 Chirality : 0.041 0.252 2982 Planarity : 0.003 0.050 3134 Dihedral : 13.232 128.199 3022 Min Nonbonded Distance : 2.028 Molprobity Statistics. All-atom Clashscore : 7.41 Ramachandran Plot: Outliers : 0.13 % Allowed : 8.51 % Favored : 91.36 % Rotamer: Outliers : 3.84 % Allowed : 19.21 % Favored : 76.95 % 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: -0.87 (0.18), residues: 2350 helix: 1.03 (0.17), residues: 1026 sheet: -0.58 (0.33), residues: 274 loop : -2.30 (0.18), residues: 1050 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 6 HIS 0.007 0.001 HIS E 263 PHE 0.012 0.001 PHE I 192 TYR 0.016 0.001 TYR G 145 ARG 0.008 0.000 ARG I 78 ********************** 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 407 residues out of total 1994 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 72 poor density : 335 time to evaluate : 2.122 Fit side-chains revert: symmetry clash REVERT: A 138 LYS cc_start: 0.8584 (mtpp) cc_final: 0.8285 (mmmm) REVERT: B 63 LEU cc_start: 0.8331 (OUTLIER) cc_final: 0.8053 (mt) REVERT: B 135 GLU cc_start: 0.8197 (tm-30) cc_final: 0.7910 (tm-30) REVERT: B 246 LYS cc_start: 0.8191 (tptm) cc_final: 0.7908 (ptpt) REVERT: F 30 ILE cc_start: 0.6952 (OUTLIER) cc_final: 0.6681 (mp) REVERT: H 47 ASP cc_start: 0.8174 (p0) cc_final: 0.7944 (p0) REVERT: H 60 MET cc_start: 0.8237 (tpp) cc_final: 0.7805 (ttt) REVERT: H 93 PHE cc_start: 0.6690 (OUTLIER) cc_final: 0.6082 (p90) REVERT: H 141 ASP cc_start: 0.8013 (OUTLIER) cc_final: 0.7602 (p0) REVERT: I 27 LYS cc_start: 0.8646 (OUTLIER) cc_final: 0.7933 (tmmt) REVERT: J 73 LEU cc_start: 0.7999 (OUTLIER) cc_final: 0.7758 (tt) REVERT: J 134 MET cc_start: 0.5925 (pmm) cc_final: 0.5669 (pmm) REVERT: J 141 ASP cc_start: 0.7963 (OUTLIER) cc_final: 0.7448 (p0) REVERT: K 85 ASP cc_start: 0.8103 (p0) cc_final: 0.7819 (p0) REVERT: K 187 ASP cc_start: 0.6639 (t70) cc_final: 0.6411 (t0) REVERT: L 21 LEU cc_start: 0.8534 (OUTLIER) cc_final: 0.8312 (mm) REVERT: L 24 LEU cc_start: 0.8405 (OUTLIER) cc_final: 0.8125 (tt) REVERT: L 26 MET cc_start: 0.7902 (mmm) cc_final: 0.7525 (mmt) REVERT: L 135 ASN cc_start: 0.7841 (OUTLIER) cc_final: 0.7622 (p0) outliers start: 72 outliers final: 55 residues processed: 381 average time/residue: 0.3026 time to fit residues: 172.7205 Evaluate side-chains 393 residues out of total 1994 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 65 poor density : 328 time to evaluate : 2.023 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 87 MET Chi-restraints excluded: chain A residue 124 GLU Chi-restraints excluded: chain A residue 129 MET Chi-restraints excluded: chain B residue 19 LEU Chi-restraints excluded: chain B residue 63 LEU Chi-restraints excluded: chain B residue 80 MET Chi-restraints excluded: chain B residue 118 HIS Chi-restraints excluded: chain B residue 119 THR Chi-restraints excluded: chain B residue 124 ASN Chi-restraints excluded: chain B residue 142 THR Chi-restraints excluded: chain B residue 145 LEU Chi-restraints excluded: chain B residue 164 ILE Chi-restraints excluded: chain C residue 10 VAL Chi-restraints excluded: chain C residue 12 SER Chi-restraints excluded: chain C residue 51 THR Chi-restraints excluded: chain C residue 64 THR Chi-restraints excluded: chain D residue 87 MET Chi-restraints excluded: chain E residue 75 LYS Chi-restraints excluded: chain E residue 103 THR Chi-restraints excluded: chain E residue 118 HIS Chi-restraints excluded: chain E residue 137 VAL Chi-restraints excluded: chain E residue 142 THR Chi-restraints excluded: chain E residue 145 LEU Chi-restraints excluded: chain E residue 169 ASP Chi-restraints excluded: chain E residue 188 LEU Chi-restraints excluded: chain E residue 249 LEU Chi-restraints excluded: chain E residue 271 VAL Chi-restraints excluded: chain F residue 2 VAL Chi-restraints excluded: chain F residue 30 ILE Chi-restraints excluded: chain F residue 51 THR Chi-restraints excluded: chain F residue 64 THR Chi-restraints excluded: chain G residue 21 LEU Chi-restraints excluded: chain G residue 36 LEU Chi-restraints excluded: chain G residue 63 VAL Chi-restraints excluded: chain G residue 85 ASP Chi-restraints excluded: chain G residue 90 LEU Chi-restraints excluded: chain G residue 143 ASP Chi-restraints excluded: chain G residue 150 THR Chi-restraints excluded: chain H residue 35 ASN Chi-restraints excluded: chain H residue 93 PHE Chi-restraints excluded: chain H residue 135 ASN Chi-restraints excluded: chain H residue 141 ASP Chi-restraints excluded: chain H residue 143 ASP Chi-restraints excluded: chain H residue 167 LEU Chi-restraints excluded: chain I residue 27 LYS Chi-restraints excluded: chain I residue 63 VAL Chi-restraints excluded: chain I residue 87 ASP Chi-restraints excluded: chain I residue 136 SER Chi-restraints excluded: chain I residue 143 ASP Chi-restraints excluded: chain I residue 175 THR Chi-restraints excluded: chain J residue 73 LEU Chi-restraints excluded: chain J residue 141 ASP Chi-restraints excluded: chain K residue 36 LEU Chi-restraints excluded: chain K residue 63 VAL Chi-restraints excluded: chain K residue 90 LEU Chi-restraints excluded: chain K residue 135 ASN Chi-restraints excluded: chain K residue 141 ASP Chi-restraints excluded: chain K residue 168 ASN Chi-restraints excluded: chain K residue 183 MET Chi-restraints excluded: chain K residue 184 ASP Chi-restraints excluded: chain L residue 21 LEU Chi-restraints excluded: chain L residue 24 LEU Chi-restraints excluded: chain L residue 63 VAL Chi-restraints excluded: chain L residue 135 ASN Chi-restraints excluded: chain L residue 167 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 234 random chunks: chunk 197 optimal weight: 0.2980 chunk 56 optimal weight: 0.7980 chunk 171 optimal weight: 9.9990 chunk 27 optimal weight: 7.9990 chunk 51 optimal weight: 0.0870 chunk 185 optimal weight: 4.9990 chunk 77 optimal weight: 6.9990 chunk 190 optimal weight: 10.0000 chunk 23 optimal weight: 0.8980 chunk 34 optimal weight: 7.9990 chunk 163 optimal weight: 10.0000 overall best weight: 1.4160 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 67 GLN E 155 ASN F 89 GLN G 45 GLN H 50 ASN I 102 GLN I 104 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3756 r_free = 0.3756 target = 0.147785 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3223 r_free = 0.3223 target = 0.105402 restraints weight = 24583.019| |-----------------------------------------------------------------------------| r_work (start): 0.3177 rms_B_bonded: 1.82 r_work: 0.2947 rms_B_bonded: 2.84 restraints_weight: 0.5000 r_work: 0.2801 rms_B_bonded: 4.52 restraints_weight: 0.2500 r_work (final): 0.2801 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8589 moved from start: 0.3363 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 18554 Z= 0.176 Angle : 0.582 12.026 24994 Z= 0.301 Chirality : 0.042 0.246 2982 Planarity : 0.003 0.049 3134 Dihedral : 13.017 123.656 3022 Min Nonbonded Distance : 2.050 Molprobity Statistics. All-atom Clashscore : 7.87 Ramachandran Plot: Outliers : 0.13 % Allowed : 8.98 % Favored : 90.89 % Rotamer: Outliers : 3.68 % Allowed : 19.32 % Favored : 77.00 % 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: -0.79 (0.18), residues: 2350 helix: 1.12 (0.17), residues: 1026 sheet: -0.62 (0.33), residues: 278 loop : -2.27 (0.18), residues: 1046 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP D 183 HIS 0.007 0.001 HIS E 263 PHE 0.018 0.001 PHE L 13 TYR 0.018 0.001 TYR G 145 ARG 0.007 0.000 ARG I 78 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4432.05 seconds wall clock time: 81 minutes 51.23 seconds (4911.23 seconds total)