Starting phenix.real_space_refine on Thu Mar 13 13:47:04 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8idd_35364/03_2025/8idd_35364.cif Found real_map, /net/cci-nas-00/data/ceres_data/8idd_35364/03_2025/8idd_35364.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8idd_35364/03_2025/8idd_35364.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8idd_35364/03_2025/8idd_35364.map" model { file = "/net/cci-nas-00/data/ceres_data/8idd_35364/03_2025/8idd_35364.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8idd_35364/03_2025/8idd_35364.cif" } resolution = 4.0 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.015 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 6 5.49 5 S 45 5.16 5 C 5531 2.51 5 N 1556 2.21 5 O 1630 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 3 residue(s): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/chem_data/mon_lib" Total number of atoms: 8768 Number of models: 1 Model: "" Number of chains: 7 Chain: "B" Number of atoms: 1570 Number of conformers: 1 Conformer: "" Number of residues, atoms: 225, 1570 Classifications: {'peptide': 225} Incomplete info: {'truncation_to_alanine': 49} Link IDs: {'PTRANS': 9, 'TRANS': 215} Unresolved non-hydrogen bonds: 195 Unresolved non-hydrogen angles: 242 Unresolved non-hydrogen dihedrals: 155 Unresolved non-hydrogen chiralities: 13 Planarities with less than four sites: {'GLN:plan1': 3, 'HIS:plan': 1, 'TYR:plan': 1, 'ASN:plan1': 2, 'ASP:plan': 6, 'PHE:plan': 1, 'GLU:plan': 7, 'ARG:plan': 9} Unresolved non-hydrogen planarities: 127 Chain: "D" Number of atoms: 2227 Number of conformers: 1 Conformer: "" Number of residues, atoms: 295, 2227 Classifications: {'peptide': 295} Incomplete info: {'truncation_to_alanine': 13} Link IDs: {'PTRANS': 6, 'TRANS': 288} Unresolved non-hydrogen bonds: 59 Unresolved non-hydrogen angles: 72 Unresolved non-hydrogen dihedrals: 51 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLN:plan1': 2, 'TYR:plan': 1, 'ASN:plan1': 1, 'PHE:plan': 1, 'GLU:plan': 1, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 38 Chain: "C" Number of atoms: 2257 Number of conformers: 1 Conformer: "" Number of residues, atoms: 295, 2257 Classifications: {'peptide': 295} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'PTRANS': 6, 'TRANS': 288} Unresolved non-hydrogen bonds: 28 Unresolved non-hydrogen angles: 34 Unresolved non-hydrogen dihedrals: 25 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 1, 'TYR:plan': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 16 Chain: "E" Number of atoms: 1076 Number of conformers: 1 Conformer: "" Number of residues, atoms: 159, 1076 Classifications: {'peptide': 159} Incomplete info: {'truncation_to_alanine': 30} Link IDs: {'PTRANS': 1, 'TRANS': 157} Unresolved non-hydrogen bonds: 114 Unresolved non-hydrogen angles: 141 Unresolved non-hydrogen dihedrals: 90 Unresolved non-hydrogen chiralities: 8 Planarities with less than four sites: {'GLN:plan1': 5, 'TYR:plan': 1, 'ASN:plan1': 1, 'ASP:plan': 4, 'GLU:plan': 3, 'ARG:plan': 3} Unresolved non-hydrogen planarities: 69 Chain: "A" Number of atoms: 1576 Number of conformers: 1 Conformer: "" Number of residues, atoms: 225, 1576 Classifications: {'peptide': 225} Incomplete info: {'truncation_to_alanine': 48} Link IDs: {'PTRANS': 9, 'TRANS': 215} Unresolved non-hydrogen bonds: 189 Unresolved non-hydrogen angles: 235 Unresolved non-hydrogen dihedrals: 150 Unresolved non-hydrogen chiralities: 13 Planarities with less than four sites: {'GLN:plan1': 3, 'HIS:plan': 1, 'TYR:plan': 1, 'ASN:plan1': 2, 'ASP:plan': 6, 'PHE:plan': 1, 'GLU:plan': 7, 'ARG:plan': 8} Unresolved non-hydrogen planarities: 122 Chain: "B" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 31 Unusual residues: {'ATP': 1} Classifications: {'undetermined': 1} Chain: "A" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 31 Unusual residues: {'ATP': 1} Classifications: {'undetermined': 1} Time building chain proxies: 6.39, per 1000 atoms: 0.73 Number of scatterers: 8768 At special positions: 0 Unit cell: (101.76, 99.64, 201.4, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 45 16.00 P 6 15.00 O 1630 8.00 N 1556 7.00 C 5531 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=2, symmetry=0 Simple disulfide: pdb=" SG CYS D 73 " - pdb=" SG CYS D 78 " distance=2.03 Simple disulfide: pdb=" SG CYS C 73 " - pdb=" SG CYS C 78 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 2.28 Conformation dependent library (CDL) restraints added in 1.1 seconds 2378 Ramachandran restraints generated. 1189 Oldfield, 0 Emsley, 1189 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2254 Finding SS restraints... Secondary structure from input PDB file: 53 helices and 8 sheets defined 57.0% alpha, 4.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.89 Creating SS restraints... Processing helix chain 'B' and resid 42 through 51 Processing helix chain 'B' and resid 75 through 82 removed outlier: 4.358A pdb=" N VAL B 82 " --> pdb=" O LYS B 78 " (cutoff:3.500A) Processing helix chain 'B' and resid 97 through 108 removed outlier: 3.578A pdb=" N VAL B 102 " --> pdb=" O VAL B 98 " (cutoff:3.500A) removed outlier: 3.816A pdb=" N ALA B 105 " --> pdb=" O ASN B 101 " (cutoff:3.500A) removed outlier: 4.303A pdb=" N LEU B 106 " --> pdb=" O VAL B 102 " (cutoff:3.500A) Processing helix chain 'B' and resid 112 through 118 removed outlier: 3.553A pdb=" N ILE B 116 " --> pdb=" O ARG B 112 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N ASN B 117 " --> pdb=" O THR B 113 " (cutoff:3.500A) Processing helix chain 'B' and resid 119 through 128 removed outlier: 3.717A pdb=" N GLU B 125 " --> pdb=" O PRO B 121 " (cutoff:3.500A) removed outlier: 4.482A pdb=" N THR B 126 " --> pdb=" O GLU B 122 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N VAL B 127 " --> pdb=" O VAL B 123 " (cutoff:3.500A) removed outlier: 3.900A pdb=" N GLY B 128 " --> pdb=" O LEU B 124 " (cutoff:3.500A) Processing helix chain 'B' and resid 144 through 151 Processing helix chain 'B' and resid 175 through 189 removed outlier: 4.052A pdb=" N ASP B 180 " --> pdb=" O ARG B 176 " (cutoff:3.500A) removed outlier: 4.489A pdb=" N LEU B 181 " --> pdb=" O ASP B 177 " (cutoff:3.500A) removed outlier: 3.873A pdb=" N LEU B 182 " --> pdb=" O ILE B 178 " (cutoff:3.500A) removed outlier: 3.971A pdb=" N GLU B 183 " --> pdb=" O MET B 179 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N THR B 188 " --> pdb=" O ARG B 184 " (cutoff:3.500A) removed outlier: 3.783A pdb=" N GLY B 189 " --> pdb=" O ILE B 185 " (cutoff:3.500A) Processing helix chain 'B' and resid 201 through 206 removed outlier: 4.411A pdb=" N MET B 205 " --> pdb=" O ILE B 201 " (cutoff:3.500A) removed outlier: 4.150A pdb=" N ARG B 206 " --> pdb=" O VAL B 202 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 201 through 206' Processing helix chain 'D' and resid 3 through 17 removed outlier: 3.957A pdb=" N LEU D 7 " --> pdb=" O PHE D 3 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N ASN D 8 " --> pdb=" O GLY D 4 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N LEU D 11 " --> pdb=" O LEU D 7 " (cutoff:3.500A) Processing helix chain 'D' and resid 20 through 54 removed outlier: 4.187A pdb=" N LEU D 26 " --> pdb=" O ILE D 22 " (cutoff:3.500A) removed outlier: 3.965A pdb=" N ALA D 29 " --> pdb=" O ILE D 25 " (cutoff:3.500A) removed outlier: 4.258A pdb=" N PHE D 35 " --> pdb=" O SER D 31 " (cutoff:3.500A) removed outlier: 4.180A pdb=" N ASP D 54 " --> pdb=" O ALA D 50 " (cutoff:3.500A) Processing helix chain 'D' and resid 63 through 68 Processing helix chain 'D' and resid 75 through 81 removed outlier: 3.713A pdb=" N LYS D 79 " --> pdb=" O THR D 75 " (cutoff:3.500A) Processing helix chain 'D' and resid 101 through 109 removed outlier: 3.678A pdb=" N ALA D 106 " --> pdb=" O ALA D 102 " (cutoff:3.500A) removed outlier: 4.619A pdb=" N ILE D 107 " --> pdb=" O TYR D 103 " (cutoff:3.500A) Processing helix chain 'D' and resid 118 through 122 removed outlier: 3.534A pdb=" N SER D 121 " --> pdb=" O GLY D 118 " (cutoff:3.500A) removed outlier: 4.313A pdb=" N PHE D 122 " --> pdb=" O LYS D 119 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 118 through 122' Processing helix chain 'D' and resid 139 through 143 removed outlier: 3.871A pdb=" N MET D 143 " --> pdb=" O ASP D 140 " (cutoff:3.500A) Processing helix chain 'D' and resid 163 through 190 removed outlier: 3.501A pdb=" N LEU D 169 " --> pdb=" O VAL D 165 " (cutoff:3.500A) removed outlier: 3.799A pdb=" N ASN D 171 " --> pdb=" O ASP D 167 " (cutoff:3.500A) removed outlier: 3.919A pdb=" N ALA D 172 " --> pdb=" O GLY D 168 " (cutoff:3.500A) removed outlier: 4.404A pdb=" N LEU D 186 " --> pdb=" O ILE D 182 " (cutoff:3.500A) removed outlier: 4.234A pdb=" N LEU D 187 " --> pdb=" O GLY D 183 " (cutoff:3.500A) Processing helix chain 'D' and resid 190 through 199 removed outlier: 3.782A pdb=" N VAL D 194 " --> pdb=" O ASN D 190 " (cutoff:3.500A) removed outlier: 4.036A pdb=" N TYR D 197 " --> pdb=" O GLN D 193 " (cutoff:3.500A) Processing helix chain 'D' and resid 199 through 209 removed outlier: 3.510A pdb=" N ILE D 203 " --> pdb=" O ARG D 199 " (cutoff:3.500A) Processing helix chain 'D' and resid 217 through 247 removed outlier: 4.388A pdb=" N GLU D 223 " --> pdb=" O PRO D 219 " (cutoff:3.500A) removed outlier: 4.425A pdb=" N ALA D 224 " --> pdb=" O PHE D 220 " (cutoff:3.500A) removed outlier: 3.966A pdb=" N ALA D 227 " --> pdb=" O GLU D 223 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N ALA D 237 " --> pdb=" O GLY D 233 " (cutoff:3.500A) Processing helix chain 'D' and resid 253 through 258 removed outlier: 3.518A pdb=" N ALA D 257 " --> pdb=" O GLN D 253 " (cutoff:3.500A) Processing helix chain 'D' and resid 264 through 293 removed outlier: 3.970A pdb=" N ILE D 268 " --> pdb=" O ASP D 264 " (cutoff:3.500A) removed outlier: 3.949A pdb=" N LEU D 269 " --> pdb=" O TYR D 265 " (cutoff:3.500A) removed outlier: 3.739A pdb=" N ILE D 271 " --> pdb=" O ASP D 267 " (cutoff:3.500A) Proline residue: D 273 - end of helix removed outlier: 3.513A pdb=" N LEU D 278 " --> pdb=" O TRP D 274 " (cutoff:3.500A) removed outlier: 3.932A pdb=" N ALA D 281 " --> pdb=" O LEU D 277 " (cutoff:3.500A) removed outlier: 4.031A pdb=" N THR D 286 " --> pdb=" O MET D 282 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N TYR D 288 " --> pdb=" O GLY D 284 " (cutoff:3.500A) removed outlier: 3.833A pdb=" N LEU D 289 " --> pdb=" O LEU D 285 " (cutoff:3.500A) removed outlier: 4.114A pdb=" N THR D 290 " --> pdb=" O THR D 286 " (cutoff:3.500A) removed outlier: 4.394A pdb=" N LEU D 291 " --> pdb=" O ALA D 287 " (cutoff:3.500A) Processing helix chain 'C' and resid 2 through 5 removed outlier: 3.886A pdb=" N PHE C 5 " --> pdb=" O ARG C 2 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 2 through 5' Processing helix chain 'C' and resid 6 through 17 removed outlier: 4.102A pdb=" N VAL C 10 " --> pdb=" O LEU C 6 " (cutoff:3.500A) removed outlier: 3.771A pdb=" N LEU C 11 " --> pdb=" O LEU C 7 " (cutoff:3.500A) removed outlier: 4.659A pdb=" N THR C 12 " --> pdb=" O ASN C 8 " (cutoff:3.500A) Processing helix chain 'C' and resid 19 through 48 removed outlier: 3.571A pdb=" N ALA C 23 " --> pdb=" O THR C 19 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N SER C 31 " --> pdb=" O THR C 27 " (cutoff:3.500A) Processing helix chain 'C' and resid 63 through 68 Processing helix chain 'C' and resid 75 through 83 Processing helix chain 'C' and resid 84 through 88 removed outlier: 3.904A pdb=" N ARG C 88 " --> pdb=" O ILE C 85 " (cutoff:3.500A) Processing helix chain 'C' and resid 98 through 102 removed outlier: 3.774A pdb=" N ALA C 102 " --> pdb=" O ARG C 99 " (cutoff:3.500A) Processing helix chain 'C' and resid 105 through 110 removed outlier: 3.561A pdb=" N LYS C 109 " --> pdb=" O ASP C 105 " (cutoff:3.500A) Processing helix chain 'C' and resid 135 through 140 removed outlier: 4.217A pdb=" N ASP C 140 " --> pdb=" O HIS C 136 " (cutoff:3.500A) Processing helix chain 'C' and resid 141 through 143 No H-bonds generated for 'chain 'C' and resid 141 through 143' Processing helix chain 'C' and resid 159 through 199 removed outlier: 3.730A pdb=" N LEU C 169 " --> pdb=" O VAL C 165 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N SER C 170 " --> pdb=" O LEU C 166 " (cutoff:3.500A) removed outlier: 4.329A pdb=" N LEU C 186 " --> pdb=" O ILE C 182 " (cutoff:3.500A) removed outlier: 4.002A pdb=" N LEU C 187 " --> pdb=" O GLY C 183 " (cutoff:3.500A) removed outlier: 3.961A pdb=" N VAL C 192 " --> pdb=" O ILE C 188 " (cutoff:3.500A) removed outlier: 3.965A pdb=" N GLN C 193 " --> pdb=" O ALA C 189 " (cutoff:3.500A) Processing helix chain 'C' and resid 199 through 210 removed outlier: 3.728A pdb=" N ILE C 203 " --> pdb=" O ARG C 199 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N ARG C 207 " --> pdb=" O ILE C 203 " (cutoff:3.500A) removed outlier: 4.593A pdb=" N LEU C 208 " --> pdb=" O GLY C 204 " (cutoff:3.500A) Processing helix chain 'C' and resid 212 through 246 removed outlier: 3.986A pdb=" N GLN C 217 " --> pdb=" O ARG C 213 " (cutoff:3.500A) Proline residue: C 219 - end of helix removed outlier: 5.280A pdb=" N GLU C 223 " --> pdb=" O PRO C 219 " (cutoff:3.500A) removed outlier: 4.266A pdb=" N ALA C 224 " --> pdb=" O PHE C 220 " (cutoff:3.500A) removed outlier: 4.019A pdb=" N MET C 240 " --> pdb=" O VAL C 236 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N VAL C 241 " --> pdb=" O ALA C 237 " (cutoff:3.500A) Processing helix chain 'C' and resid 252 through 258 removed outlier: 4.301A pdb=" N GLN C 256 " --> pdb=" O ASN C 252 " (cutoff:3.500A) Processing helix chain 'C' and resid 264 through 270 removed outlier: 3.799A pdb=" N ILE C 268 " --> pdb=" O TYR C 265 " (cutoff:3.500A) Processing helix chain 'C' and resid 271 through 289 removed outlier: 4.237A pdb=" N THR C 286 " --> pdb=" O MET C 282 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N LEU C 289 " --> pdb=" O LEU C 285 " (cutoff:3.500A) Processing helix chain 'E' and resid 52 through 56 removed outlier: 3.599A pdb=" N GLN E 56 " --> pdb=" O ARG E 52 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 52 through 56' Processing helix chain 'E' and resid 57 through 64 removed outlier: 3.960A pdb=" N LEU E 61 " --> pdb=" O THR E 57 " (cutoff:3.500A) removed outlier: 3.996A pdb=" N HIS E 62 " --> pdb=" O THR E 58 " (cutoff:3.500A) Processing helix chain 'E' and resid 65 through 110 removed outlier: 3.921A pdb=" N ASP E 84 " --> pdb=" O GLN E 80 " (cutoff:3.500A) removed outlier: 4.306A pdb=" N ARG E 86 " --> pdb=" O LEU E 82 " (cutoff:3.500A) removed outlier: 4.787A pdb=" N THR E 87 " --> pdb=" O ALA E 83 " (cutoff:3.500A) removed outlier: 3.766A pdb=" N LEU E 96 " --> pdb=" O ALA E 92 " (cutoff:3.500A) removed outlier: 4.443A pdb=" N THR E 101 " --> pdb=" O ALA E 97 " (cutoff:3.500A) removed outlier: 4.315A pdb=" N ALA E 102 " --> pdb=" O THR E 98 " (cutoff:3.500A) removed outlier: 3.984A pdb=" N LYS E 105 " --> pdb=" O THR E 101 " (cutoff:3.500A) removed outlier: 4.226A pdb=" N THR E 110 " --> pdb=" O VAL E 106 " (cutoff:3.500A) Processing helix chain 'E' and resid 118 through 122 removed outlier: 3.653A pdb=" N ALA E 121 " --> pdb=" O GLY E 118 " (cutoff:3.500A) Processing helix chain 'E' and resid 128 through 133 removed outlier: 3.972A pdb=" N ASP E 133 " --> pdb=" O GLN E 129 " (cutoff:3.500A) Processing helix chain 'E' and resid 133 through 186 removed outlier: 3.830A pdb=" N VAL E 137 " --> pdb=" O ASP E 133 " (cutoff:3.500A) removed outlier: 4.021A pdb=" N VAL E 140 " --> pdb=" O SER E 136 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N HIS E 143 " --> pdb=" O ARG E 139 " (cutoff:3.500A) removed outlier: 3.733A pdb=" N GLN E 144 " --> pdb=" O VAL E 140 " (cutoff:3.500A) removed outlier: 3.887A pdb=" N MET E 145 " --> pdb=" O MET E 141 " (cutoff:3.500A) removed outlier: 3.875A pdb=" N SER E 146 " --> pdb=" O ALA E 142 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N ALA E 182 " --> pdb=" O GLU E 178 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N VAL E 183 " --> pdb=" O GLN E 179 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N ARG E 184 " --> pdb=" O ALA E 180 " (cutoff:3.500A) removed outlier: 3.903A pdb=" N ASN E 186 " --> pdb=" O ALA E 182 " (cutoff:3.500A) Processing helix chain 'E' and resid 186 through 191 Processing helix chain 'E' and resid 192 through 203 removed outlier: 3.517A pdb=" N VAL E 196 " --> pdb=" O SER E 192 " (cutoff:3.500A) removed outlier: 3.843A pdb=" N LYS E 202 " --> pdb=" O ILE E 198 " (cutoff:3.500A) removed outlier: 4.013A pdb=" N SER E 203 " --> pdb=" O ALA E 199 " (cutoff:3.500A) Processing helix chain 'A' and resid 43 through 51 Processing helix chain 'A' and resid 97 through 103 removed outlier: 3.665A pdb=" N VAL A 102 " --> pdb=" O VAL A 98 " (cutoff:3.500A) Processing helix chain 'A' and resid 104 through 110 removed outlier: 3.694A pdb=" N ILE A 109 " --> pdb=" O ALA A 105 " (cutoff:3.500A) removed outlier: 3.764A pdb=" N GLY A 110 " --> pdb=" O LEU A 106 " (cutoff:3.500A) Processing helix chain 'A' and resid 119 through 125 Processing helix chain 'A' and resid 141 through 143 No H-bonds generated for 'chain 'A' and resid 141 through 143' Processing helix chain 'A' and resid 144 through 154 removed outlier: 3.985A pdb=" N ALA A 151 " --> pdb=" O ARG A 147 " (cutoff:3.500A) Processing helix chain 'A' and resid 175 through 180 removed outlier: 3.649A pdb=" N ASP A 180 " --> pdb=" O ARG A 176 " (cutoff:3.500A) Processing helix chain 'A' and resid 180 through 189 removed outlier: 3.652A pdb=" N ARG A 184 " --> pdb=" O ASP A 180 " (cutoff:3.500A) removed outlier: 3.801A pdb=" N ILE A 185 " --> pdb=" O LEU A 181 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'B' and resid 6 through 9 removed outlier: 3.518A pdb=" N ASP B 6 " --> pdb=" O ASP B 60 " (cutoff:3.500A) removed outlier: 3.776A pdb=" N ASP B 60 " --> pdb=" O ASP B 6 " (cutoff:3.500A) removed outlier: 4.327A pdb=" N VAL B 8 " --> pdb=" O SER B 58 " (cutoff:3.500A) removed outlier: 6.020A pdb=" N SER B 58 " --> pdb=" O VAL B 8 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA1 Processing sheet with id=AA2, first strand: chain 'B' and resid 33 through 34 removed outlier: 6.586A pdb=" N VAL B 33 " --> pdb=" O MET B 194 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N ALA B 195 " --> pdb=" O ALA B 163 " (cutoff:3.500A) removed outlier: 5.601A pdb=" N GLY B 84 " --> pdb=" O LEU B 162 " (cutoff:3.500A) removed outlier: 7.150A pdb=" N ASP B 164 " --> pdb=" O GLY B 84 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'D' and resid 57 through 58 removed outlier: 4.463A pdb=" N ALA D 93 " --> pdb=" O LYS D 129 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'C' and resid 59 through 62 removed outlier: 7.751A pdb=" N GLN C 59 " --> pdb=" O VAL C 152 " (cutoff:3.500A) removed outlier: 5.632A pdb=" N VAL C 152 " --> pdb=" O GLN C 59 " (cutoff:3.500A) removed outlier: 6.951A pdb=" N PHE C 61 " --> pdb=" O LEU C 150 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'C' and resid 91 through 94 removed outlier: 7.112A pdb=" N LYS C 129 " --> pdb=" O LYS C 92 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 6 through 9 removed outlier: 3.738A pdb=" N ASP A 6 " --> pdb=" O ASP A 60 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N ASP A 60 " --> pdb=" O ASP A 6 " (cutoff:3.500A) removed outlier: 4.175A pdb=" N VAL A 8 " --> pdb=" O SER A 58 " (cutoff:3.500A) removed outlier: 5.768A pdb=" N SER A 58 " --> pdb=" O VAL A 8 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA6 Processing sheet with id=AA7, first strand: chain 'A' and resid 32 through 33 removed outlier: 6.222A pdb=" N VAL A 33 " --> pdb=" O MET A 194 " (cutoff:3.500A) removed outlier: 6.294A pdb=" N GLY A 84 " --> pdb=" O LEU A 162 " (cutoff:3.500A) removed outlier: 7.537A pdb=" N ASP A 164 " --> pdb=" O GLY A 84 " (cutoff:3.500A) removed outlier: 6.243A pdb=" N VAL A 86 " --> pdb=" O ASP A 164 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 212 through 213 377 hydrogen bonds defined for protein. 1104 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: 2.24 Time building geometry restraints manager: 2.70 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 2438 1.33 - 1.46: 1620 1.46 - 1.58: 4737 1.58 - 1.70: 9 1.70 - 1.82: 84 Bond restraints: 8888 Sorted by residual: bond pdb=" SD MET C 24 " pdb=" CE MET C 24 " ideal model delta sigma weight residual 1.791 1.744 0.047 2.50e-02 1.60e+03 3.52e+00 bond pdb=" CG1 ILE D 25 " pdb=" CD1 ILE D 25 " ideal model delta sigma weight residual 1.513 1.448 0.065 3.90e-02 6.57e+02 2.74e+00 bond pdb=" CA ILE A 178 " pdb=" C ILE A 178 " ideal model delta sigma weight residual 1.520 1.538 -0.018 1.20e-02 6.94e+03 2.29e+00 bond pdb=" C VAL B 76 " pdb=" N PRO B 77 " ideal model delta sigma weight residual 1.335 1.354 -0.019 1.28e-02 6.10e+03 2.26e+00 bond pdb=" C THR D 272 " pdb=" N PRO D 273 " ideal model delta sigma weight residual 1.336 1.354 -0.018 1.23e-02 6.61e+03 2.18e+00 ... (remaining 8883 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.90: 11816 2.90 - 5.79: 226 5.79 - 8.69: 42 8.69 - 11.58: 13 11.58 - 14.48: 1 Bond angle restraints: 12098 Sorted by residual: angle pdb=" N ALA C 142 " pdb=" CA ALA C 142 " pdb=" C ALA C 142 " ideal model delta sigma weight residual 114.56 108.25 6.31 1.27e+00 6.20e-01 2.47e+01 angle pdb=" N ILE C 205 " pdb=" CA ILE C 205 " pdb=" C ILE C 205 " ideal model delta sigma weight residual 113.53 108.70 4.83 9.80e-01 1.04e+00 2.43e+01 angle pdb=" CB MET C 20 " pdb=" CG MET C 20 " pdb=" SD MET C 20 " ideal model delta sigma weight residual 112.70 127.18 -14.48 3.00e+00 1.11e-01 2.33e+01 angle pdb=" N VAL A 123 " pdb=" CA VAL A 123 " pdb=" C VAL A 123 " ideal model delta sigma weight residual 113.42 108.15 5.27 1.17e+00 7.31e-01 2.03e+01 angle pdb=" C ASP B 89 " pdb=" N PHE B 90 " pdb=" CA PHE B 90 " ideal model delta sigma weight residual 121.54 129.72 -8.18 1.91e+00 2.74e-01 1.84e+01 ... (remaining 12093 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.89: 4999 16.89 - 33.78: 317 33.78 - 50.67: 62 50.67 - 67.57: 14 67.57 - 84.46: 11 Dihedral angle restraints: 5403 sinusoidal: 1938 harmonic: 3465 Sorted by residual: dihedral pdb=" CA ASP A 89 " pdb=" C ASP A 89 " pdb=" N PHE A 90 " pdb=" CA PHE A 90 " ideal model delta harmonic sigma weight residual 180.00 157.33 22.67 0 5.00e+00 4.00e-02 2.06e+01 dihedral pdb=" CA ASN C 190 " pdb=" C ASN C 190 " pdb=" N MET C 191 " pdb=" CA MET C 191 " ideal model delta harmonic sigma weight residual 180.00 159.30 20.70 0 5.00e+00 4.00e-02 1.71e+01 dihedral pdb=" CA ASN D 190 " pdb=" C ASN D 190 " pdb=" N MET D 191 " pdb=" CA MET D 191 " ideal model delta harmonic sigma weight residual 180.00 159.96 20.04 0 5.00e+00 4.00e-02 1.61e+01 ... (remaining 5400 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.070: 1219 0.070 - 0.141: 233 0.141 - 0.211: 31 0.211 - 0.281: 3 0.281 - 0.352: 1 Chirality restraints: 1487 Sorted by residual: chirality pdb=" CB ILE A 178 " pdb=" CA ILE A 178 " pdb=" CG1 ILE A 178 " pdb=" CG2 ILE A 178 " both_signs ideal model delta sigma weight residual False 2.64 2.29 0.35 2.00e-01 2.50e+01 3.09e+00 chirality pdb=" CB VAL A 108 " pdb=" CA VAL A 108 " pdb=" CG1 VAL A 108 " pdb=" CG2 VAL A 108 " both_signs ideal model delta sigma weight residual False -2.63 -2.41 -0.22 2.00e-01 2.50e+01 1.22e+00 chirality pdb=" CA THR C 272 " pdb=" N THR C 272 " pdb=" C THR C 272 " pdb=" CB THR C 272 " both_signs ideal model delta sigma weight residual False 2.53 2.31 0.21 2.00e-01 2.50e+01 1.15e+00 ... (remaining 1484 not shown) Planarity restraints: 1554 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ILE A 178 " 0.020 2.00e-02 2.50e+03 4.14e-02 1.72e+01 pdb=" C ILE A 178 " -0.072 2.00e-02 2.50e+03 pdb=" O ILE A 178 " 0.027 2.00e-02 2.50e+03 pdb=" N MET A 179 " 0.024 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE A 46 " -0.015 2.00e-02 2.50e+03 1.95e-02 6.64e+00 pdb=" CG PHE A 46 " 0.045 2.00e-02 2.50e+03 pdb=" CD1 PHE A 46 " -0.014 2.00e-02 2.50e+03 pdb=" CD2 PHE A 46 " -0.014 2.00e-02 2.50e+03 pdb=" CE1 PHE A 46 " -0.001 2.00e-02 2.50e+03 pdb=" CE2 PHE A 46 " -0.000 2.00e-02 2.50e+03 pdb=" CZ PHE A 46 " -0.000 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA VAL A 63 " -0.012 2.00e-02 2.50e+03 2.33e-02 5.43e+00 pdb=" C VAL A 63 " 0.040 2.00e-02 2.50e+03 pdb=" O VAL A 63 " -0.015 2.00e-02 2.50e+03 pdb=" N SER A 64 " -0.014 2.00e-02 2.50e+03 ... (remaining 1551 not shown) Histogram of nonbonded interaction distances: 2.30 - 2.82: 2657 2.82 - 3.34: 8563 3.34 - 3.86: 14220 3.86 - 4.38: 15927 4.38 - 4.90: 26279 Nonbonded interactions: 67646 Sorted by model distance: nonbonded pdb=" OH TYR D 52 " pdb=" O ASN D 258 " model vdw 2.302 3.040 nonbonded pdb=" O GLU B 31 " pdb=" OG1 THR B 191 " model vdw 2.315 3.040 nonbonded pdb=" O LEU A 159 " pdb=" OG1 THR A 190 " model vdw 2.316 3.040 nonbonded pdb=" O ILE D 268 " pdb=" OG1 THR D 272 " model vdw 2.317 3.040 nonbonded pdb=" ND2 ASN E 85 " pdb=" OG SER E 169 " model vdw 2.323 3.120 ... (remaining 67641 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 1 through 175 or (resid 176 and (name N or name CA or name \ C or name O or name CB )) or resid 177 through 225 or resid 301)) selection = chain 'B' } ncs_group { reference = (chain 'C' and (resid 1 through 11 or (resid 12 and (name N or name CA or name C \ or name O or name CB )) or resid 13 through 15 or (resid 16 and (name N or name \ CA or name C or name O or name CB )) or resid 17 through 108 or (resid 109 and \ (name N or name CA or name C or name O or name CB )) or resid 110 through 133 or \ (resid 134 through 135 and (name N or name CA or name C or name O or name CB )) \ or resid 136 or (resid 137 and (name N or name CA or name C or name O or name C \ B )) or resid 138 through 152 or (resid 153 through 155 and (name N or name CA o \ r name C or name O or name CB )) or resid 156 through 219 or (resid 220 and (nam \ e N or name CA or name C or name O or name CB )) or resid 221 through 291 or (re \ sid 292 and (name N or name CA or name C or name O or name CB )) or resid 293 or \ (resid 294 and (name N or name CA or name C or name O or name CB )) or resid 29 \ 5)) selection = (chain 'D' and (resid 1 through 115 or (resid 116 through 117 and (name N or nam \ e CA or name C or name O or name CB )) or resid 118 through 143 or (resid 144 an \ d (name N or name CA or name C or name O or name CB )) or resid 145 through 196 \ or (resid 197 and (name N or name CA or name C or name O or name CB )) or resid \ 198 through 199 or (resid 200 and (name N or name CA or name C or name O or name \ CB )) or resid 201 through 295)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 102.610 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: 0.350 Check model and map are aligned: 0.060 Set scattering table: 0.090 Process input model: 23.860 Find NCS groups from input model: 0.300 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:3.050 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 130.370 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7895 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.065 8888 Z= 0.270 Angle : 1.017 14.481 12098 Z= 0.523 Chirality : 0.056 0.352 1487 Planarity : 0.005 0.041 1554 Dihedral : 12.747 84.457 3143 Min Nonbonded Distance : 2.302 Molprobity Statistics. All-atom Clashscore : 5.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.71 % Favored : 95.29 % Rotamer: Outliers : 0.24 % Allowed : 0.95 % Favored : 98.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.26 (0.21), residues: 1189 helix: -2.33 (0.17), residues: 571 sheet: -1.76 (0.65), residues: 71 loop : -1.89 (0.23), residues: 547 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP D 214 HIS 0.008 0.001 HIS A 197 PHE 0.045 0.002 PHE A 46 TYR 0.018 0.002 TYR C 288 ARG 0.009 0.001 ARG E 134 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2378 Ramachandran restraints generated. 1189 Oldfield, 0 Emsley, 1189 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2378 Ramachandran restraints generated. 1189 Oldfield, 0 Emsley, 1189 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 166 residues out of total 990 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 164 time to evaluate : 0.891 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 79 LYS cc_start: 0.8570 (mmpt) cc_final: 0.8341 (mmmt) REVERT: D 113 PHE cc_start: 0.8350 (m-80) cc_final: 0.8083 (m-80) REVERT: D 278 LEU cc_start: 0.8465 (pp) cc_final: 0.7930 (mm) REVERT: C 20 MET cc_start: 0.8805 (tpp) cc_final: 0.7479 (tpt) REVERT: C 137 LYS cc_start: 0.9079 (mmpt) cc_final: 0.8783 (mmmt) REVERT: A 138 ASP cc_start: 0.8219 (t70) cc_final: 0.8008 (t70) outliers start: 2 outliers final: 1 residues processed: 164 average time/residue: 0.1789 time to fit residues: 42.3530 Evaluate side-chains 129 residues out of total 990 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 128 time to evaluate : 1.035 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 285 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 117 random chunks: chunk 98 optimal weight: 1.9990 chunk 88 optimal weight: 0.8980 chunk 49 optimal weight: 0.7980 chunk 30 optimal weight: 9.9990 chunk 59 optimal weight: 8.9990 chunk 47 optimal weight: 2.9990 chunk 91 optimal weight: 10.0000 chunk 35 optimal weight: 8.9990 chunk 55 optimal weight: 0.9990 chunk 68 optimal weight: 0.9980 chunk 106 optimal weight: 8.9990 overall best weight: 1.1384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 197 HIS ** D 252 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 136 HIS ** E 179 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 197 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3540 r_free = 0.3540 target = 0.062566 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3266 r_free = 0.3266 target = 0.052851 restraints weight = 65790.149| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3295 r_free = 0.3295 target = 0.053845 restraints weight = 44113.094| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3316 r_free = 0.3316 target = 0.054559 restraints weight = 32468.484| |-----------------------------------------------------------------------------| r_work (final): 0.3305 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8033 moved from start: 0.1652 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 8888 Z= 0.214 Angle : 0.634 9.679 12098 Z= 0.326 Chirality : 0.041 0.131 1487 Planarity : 0.004 0.050 1554 Dihedral : 8.334 73.265 1347 Min Nonbonded Distance : 2.389 Molprobity Statistics. All-atom Clashscore : 9.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.95 % Favored : 96.05 % Rotamer: Outliers : 1.18 % Allowed : 11.26 % Favored : 87.56 % 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: -1.93 (0.23), residues: 1189 helix: -0.84 (0.21), residues: 589 sheet: -1.63 (0.64), residues: 71 loop : -1.64 (0.26), residues: 529 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP C 274 HIS 0.007 0.001 HIS B 197 PHE 0.016 0.001 PHE C 163 TYR 0.008 0.001 TYR C 215 ARG 0.007 0.001 ARG E 134 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2378 Ramachandran restraints generated. 1189 Oldfield, 0 Emsley, 1189 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2378 Ramachandran restraints generated. 1189 Oldfield, 0 Emsley, 1189 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 140 residues out of total 990 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 130 time to evaluate : 0.933 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 47 MET cc_start: 0.8675 (mmm) cc_final: 0.8154 (mmm) REVERT: D 113 PHE cc_start: 0.8630 (m-80) cc_final: 0.8361 (m-80) REVERT: C 27 THR cc_start: 0.9185 (m) cc_final: 0.8962 (t) REVERT: C 137 LYS cc_start: 0.9131 (mmpt) cc_final: 0.8898 (mmmt) REVERT: C 222 VAL cc_start: 0.9081 (t) cc_final: 0.8872 (p) REVERT: A 164 ASP cc_start: 0.8252 (t0) cc_final: 0.8049 (p0) outliers start: 10 outliers final: 5 residues processed: 136 average time/residue: 0.1558 time to fit residues: 32.1927 Evaluate side-chains 120 residues out of total 990 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 115 time to evaluate : 1.324 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 40 LEU Chi-restraints excluded: chain D residue 53 LEU Chi-restraints excluded: chain D residue 226 LEU Chi-restraints excluded: chain C residue 285 LEU Chi-restraints excluded: chain A residue 161 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 117 random chunks: chunk 66 optimal weight: 0.6980 chunk 11 optimal weight: 0.0050 chunk 94 optimal weight: 5.9990 chunk 53 optimal weight: 0.9990 chunk 67 optimal weight: 0.5980 chunk 41 optimal weight: 3.9990 chunk 48 optimal weight: 4.9990 chunk 5 optimal weight: 4.9990 chunk 59 optimal weight: 0.5980 chunk 62 optimal weight: 2.9990 chunk 96 optimal weight: 4.9990 overall best weight: 0.5796 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 252 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3553 r_free = 0.3553 target = 0.063125 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3277 r_free = 0.3277 target = 0.053288 restraints weight = 66500.611| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3305 r_free = 0.3305 target = 0.054283 restraints weight = 44603.071| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3329 r_free = 0.3329 target = 0.055067 restraints weight = 32861.665| |-----------------------------------------------------------------------------| r_work (final): 0.3312 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8023 moved from start: 0.1804 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 8888 Z= 0.152 Angle : 0.584 10.006 12098 Z= 0.291 Chirality : 0.040 0.128 1487 Planarity : 0.003 0.032 1554 Dihedral : 8.150 73.039 1347 Min Nonbonded Distance : 2.410 Molprobity Statistics. All-atom Clashscore : 7.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.95 % Favored : 96.05 % Rotamer: Outliers : 1.54 % Allowed : 14.69 % Favored : 83.77 % 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: -1.38 (0.24), residues: 1189 helix: -0.29 (0.21), residues: 609 sheet: -1.48 (0.64), residues: 71 loop : -1.51 (0.27), residues: 509 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP C 274 HIS 0.002 0.001 HIS A 197 PHE 0.010 0.001 PHE D 35 TYR 0.010 0.001 TYR C 215 ARG 0.005 0.000 ARG E 134 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2378 Ramachandran restraints generated. 1189 Oldfield, 0 Emsley, 1189 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2378 Ramachandran restraints generated. 1189 Oldfield, 0 Emsley, 1189 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 137 residues out of total 990 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 124 time to evaluate : 0.984 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 47 MET cc_start: 0.8593 (mmm) cc_final: 0.8212 (mmm) REVERT: B 205 MET cc_start: 0.8806 (pmm) cc_final: 0.8593 (pmm) REVERT: D 113 PHE cc_start: 0.8529 (m-80) cc_final: 0.8278 (m-80) REVERT: D 282 MET cc_start: 0.8997 (OUTLIER) cc_final: 0.8795 (tmm) REVERT: C 27 THR cc_start: 0.9186 (m) cc_final: 0.8967 (t) REVERT: C 137 LYS cc_start: 0.9213 (mmpt) cc_final: 0.8946 (mmmt) REVERT: C 162 LEU cc_start: 0.8614 (tt) cc_final: 0.8412 (pp) outliers start: 13 outliers final: 10 residues processed: 132 average time/residue: 0.1799 time to fit residues: 35.4187 Evaluate side-chains 123 residues out of total 990 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 112 time to evaluate : 0.969 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 167 THR Chi-restraints excluded: chain D residue 40 LEU Chi-restraints excluded: chain D residue 53 LEU Chi-restraints excluded: chain D residue 226 LEU Chi-restraints excluded: chain D residue 282 MET Chi-restraints excluded: chain D residue 289 LEU Chi-restraints excluded: chain C residue 30 ILE Chi-restraints excluded: chain C residue 285 LEU Chi-restraints excluded: chain E residue 67 ASP Chi-restraints excluded: chain A residue 161 LEU Chi-restraints excluded: chain A residue 178 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 117 random chunks: chunk 82 optimal weight: 0.9990 chunk 4 optimal weight: 2.9990 chunk 44 optimal weight: 0.7980 chunk 27 optimal weight: 0.7980 chunk 41 optimal weight: 3.9990 chunk 28 optimal weight: 0.9980 chunk 0 optimal weight: 10.0000 chunk 50 optimal weight: 0.7980 chunk 78 optimal weight: 0.9980 chunk 31 optimal weight: 6.9990 chunk 70 optimal weight: 1.9990 overall best weight: 0.8780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 191 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3519 r_free = 0.3519 target = 0.062012 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3239 r_free = 0.3239 target = 0.052202 restraints weight = 66315.417| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3272 r_free = 0.3272 target = 0.053244 restraints weight = 44835.970| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3293 r_free = 0.3293 target = 0.053966 restraints weight = 32654.773| |-----------------------------------------------------------------------------| r_work (final): 0.3288 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8057 moved from start: 0.2165 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 8888 Z= 0.178 Angle : 0.581 10.373 12098 Z= 0.293 Chirality : 0.040 0.159 1487 Planarity : 0.003 0.029 1554 Dihedral : 7.938 74.002 1347 Min Nonbonded Distance : 2.363 Molprobity Statistics. All-atom Clashscore : 9.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.87 % Favored : 96.13 % Rotamer: Outliers : 2.01 % Allowed : 16.23 % Favored : 81.75 % 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: -1.10 (0.25), residues: 1189 helix: -0.02 (0.22), residues: 619 sheet: -1.34 (0.65), residues: 71 loop : -1.47 (0.28), residues: 499 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP C 274 HIS 0.002 0.001 HIS E 117 PHE 0.008 0.001 PHE A 87 TYR 0.010 0.001 TYR C 215 ARG 0.003 0.000 ARG E 134 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2378 Ramachandran restraints generated. 1189 Oldfield, 0 Emsley, 1189 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2378 Ramachandran restraints generated. 1189 Oldfield, 0 Emsley, 1189 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 129 residues out of total 990 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 112 time to evaluate : 0.927 Fit side-chains revert: symmetry clash REVERT: B 164 ASP cc_start: 0.7712 (m-30) cc_final: 0.7445 (m-30) REVERT: D 20 MET cc_start: 0.8315 (ttt) cc_final: 0.8014 (ttt) REVERT: D 144 LYS cc_start: 0.7795 (mmtt) cc_final: 0.7562 (mmtt) REVERT: C 137 LYS cc_start: 0.9219 (mmpt) cc_final: 0.8986 (mmmt) REVERT: A 87 PHE cc_start: 0.8774 (m-10) cc_final: 0.8475 (m-10) outliers start: 17 outliers final: 12 residues processed: 123 average time/residue: 0.1533 time to fit residues: 28.6891 Evaluate side-chains 123 residues out of total 990 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 111 time to evaluate : 0.893 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 167 THR Chi-restraints excluded: chain D residue 40 LEU Chi-restraints excluded: chain D residue 53 LEU Chi-restraints excluded: chain D residue 226 LEU Chi-restraints excluded: chain D residue 289 LEU Chi-restraints excluded: chain C residue 30 ILE Chi-restraints excluded: chain C residue 285 LEU Chi-restraints excluded: chain E residue 67 ASP Chi-restraints excluded: chain A residue 8 VAL Chi-restraints excluded: chain A residue 161 LEU Chi-restraints excluded: chain A residue 178 ILE Chi-restraints excluded: chain A residue 209 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 117 random chunks: chunk 73 optimal weight: 0.7980 chunk 47 optimal weight: 0.6980 chunk 0 optimal weight: 10.0000 chunk 14 optimal weight: 0.4980 chunk 78 optimal weight: 1.9990 chunk 41 optimal weight: 0.9980 chunk 13 optimal weight: 0.2980 chunk 44 optimal weight: 0.9990 chunk 48 optimal weight: 0.8980 chunk 10 optimal weight: 0.9990 chunk 87 optimal weight: 0.8980 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 88 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3523 r_free = 0.3523 target = 0.062037 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3245 r_free = 0.3245 target = 0.052290 restraints weight = 65866.288| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3277 r_free = 0.3277 target = 0.053313 restraints weight = 43865.528| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3294 r_free = 0.3294 target = 0.053930 restraints weight = 31972.623| |-----------------------------------------------------------------------------| r_work (final): 0.3289 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8047 moved from start: 0.2261 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 8888 Z= 0.163 Angle : 0.585 10.708 12098 Z= 0.290 Chirality : 0.040 0.135 1487 Planarity : 0.002 0.025 1554 Dihedral : 7.788 73.365 1347 Min Nonbonded Distance : 2.412 Molprobity Statistics. All-atom Clashscore : 8.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.04 % Favored : 95.96 % Rotamer: Outliers : 2.25 % Allowed : 18.01 % Favored : 79.74 % 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: -0.90 (0.25), residues: 1189 helix: 0.13 (0.22), residues: 609 sheet: -1.36 (0.64), residues: 71 loop : -1.31 (0.28), residues: 509 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.000 TRP C 274 HIS 0.002 0.000 HIS A 197 PHE 0.007 0.001 PHE A 87 TYR 0.010 0.001 TYR D 52 ARG 0.002 0.000 ARG E 134 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2378 Ramachandran restraints generated. 1189 Oldfield, 0 Emsley, 1189 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2378 Ramachandran restraints generated. 1189 Oldfield, 0 Emsley, 1189 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 136 residues out of total 990 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 117 time to evaluate : 1.006 Fit side-chains revert: symmetry clash REVERT: B 164 ASP cc_start: 0.7679 (m-30) cc_final: 0.7414 (m-30) REVERT: D 144 LYS cc_start: 0.7748 (mmtt) cc_final: 0.7490 (mmtt) REVERT: C 24 MET cc_start: 0.8817 (tpp) cc_final: 0.8463 (tpp) REVERT: C 137 LYS cc_start: 0.9229 (mmpt) cc_final: 0.8905 (mmmt) REVERT: A 87 PHE cc_start: 0.8462 (m-10) cc_final: 0.8144 (m-10) outliers start: 19 outliers final: 13 residues processed: 131 average time/residue: 0.1896 time to fit residues: 37.9797 Evaluate side-chains 123 residues out of total 990 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 110 time to evaluate : 1.023 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 167 THR Chi-restraints excluded: chain D residue 40 LEU Chi-restraints excluded: chain D residue 53 LEU Chi-restraints excluded: chain D residue 60 VAL Chi-restraints excluded: chain D residue 226 LEU Chi-restraints excluded: chain C residue 152 VAL Chi-restraints excluded: chain C residue 285 LEU Chi-restraints excluded: chain E residue 67 ASP Chi-restraints excluded: chain A residue 8 VAL Chi-restraints excluded: chain A residue 36 ILE Chi-restraints excluded: chain A residue 161 LEU Chi-restraints excluded: chain A residue 178 ILE Chi-restraints excluded: chain A residue 209 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 117 random chunks: chunk 78 optimal weight: 0.7980 chunk 105 optimal weight: 1.9990 chunk 43 optimal weight: 3.9990 chunk 50 optimal weight: 1.9990 chunk 114 optimal weight: 9.9990 chunk 108 optimal weight: 5.9990 chunk 6 optimal weight: 1.9990 chunk 75 optimal weight: 6.9990 chunk 33 optimal weight: 0.8980 chunk 20 optimal weight: 3.9990 chunk 55 optimal weight: 0.7980 overall best weight: 1.2984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3470 r_free = 0.3470 target = 0.059792 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3182 r_free = 0.3182 target = 0.050005 restraints weight = 66590.060| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3214 r_free = 0.3214 target = 0.051043 restraints weight = 43696.963| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3238 r_free = 0.3238 target = 0.051779 restraints weight = 31227.336| |-----------------------------------------------------------------------------| r_work (final): 0.3240 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8109 moved from start: 0.2772 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.055 8888 Z= 0.235 Angle : 0.645 11.318 12098 Z= 0.322 Chirality : 0.041 0.149 1487 Planarity : 0.003 0.025 1554 Dihedral : 7.837 72.261 1347 Min Nonbonded Distance : 2.409 Molprobity Statistics. All-atom Clashscore : 11.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.71 % Favored : 95.29 % Rotamer: Outliers : 2.61 % Allowed : 18.72 % Favored : 78.67 % 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 (0.25), residues: 1189 helix: 0.24 (0.22), residues: 597 sheet: -1.53 (0.58), residues: 81 loop : -1.19 (0.29), residues: 511 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP D 214 HIS 0.003 0.001 HIS E 117 PHE 0.010 0.001 PHE D 5 TYR 0.014 0.001 TYR D 52 ARG 0.005 0.000 ARG A 48 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2378 Ramachandran restraints generated. 1189 Oldfield, 0 Emsley, 1189 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2378 Ramachandran restraints generated. 1189 Oldfield, 0 Emsley, 1189 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 131 residues out of total 990 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 109 time to evaluate : 0.986 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 164 ASP cc_start: 0.7741 (m-30) cc_final: 0.7473 (m-30) REVERT: D 144 LYS cc_start: 0.7910 (mmtt) cc_final: 0.7702 (mmtt) REVERT: D 185 ILE cc_start: 0.8951 (OUTLIER) cc_final: 0.8743 (tp) REVERT: D 282 MET cc_start: 0.9040 (OUTLIER) cc_final: 0.8826 (tmm) REVERT: C 24 MET cc_start: 0.8884 (tpp) cc_final: 0.8571 (tpp) REVERT: C 137 LYS cc_start: 0.9230 (mmpt) cc_final: 0.8994 (mmmt) outliers start: 22 outliers final: 17 residues processed: 122 average time/residue: 0.1598 time to fit residues: 29.4277 Evaluate side-chains 124 residues out of total 990 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 105 time to evaluate : 0.994 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 88 GLN Chi-restraints excluded: chain B residue 167 THR Chi-restraints excluded: chain D residue 40 LEU Chi-restraints excluded: chain D residue 53 LEU Chi-restraints excluded: chain D residue 60 VAL Chi-restraints excluded: chain D residue 185 ILE Chi-restraints excluded: chain D residue 226 LEU Chi-restraints excluded: chain D residue 278 LEU Chi-restraints excluded: chain D residue 282 MET Chi-restraints excluded: chain D residue 289 LEU Chi-restraints excluded: chain C residue 22 ILE Chi-restraints excluded: chain C residue 30 ILE Chi-restraints excluded: chain C residue 152 VAL Chi-restraints excluded: chain C residue 285 LEU Chi-restraints excluded: chain E residue 67 ASP Chi-restraints excluded: chain A residue 8 VAL Chi-restraints excluded: chain A residue 51 LEU Chi-restraints excluded: chain A residue 161 LEU Chi-restraints excluded: chain A residue 178 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 117 random chunks: chunk 15 optimal weight: 1.9990 chunk 92 optimal weight: 10.0000 chunk 54 optimal weight: 0.8980 chunk 63 optimal weight: 7.9990 chunk 12 optimal weight: 0.0970 chunk 22 optimal weight: 2.9990 chunk 98 optimal weight: 0.9980 chunk 4 optimal weight: 3.9990 chunk 48 optimal weight: 1.9990 chunk 79 optimal weight: 0.0170 chunk 20 optimal weight: 6.9990 overall best weight: 0.8018 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 186 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3483 r_free = 0.3483 target = 0.060335 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3201 r_free = 0.3201 target = 0.050611 restraints weight = 66862.240| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3232 r_free = 0.3232 target = 0.051617 restraints weight = 43331.093| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3256 r_free = 0.3256 target = 0.052366 restraints weight = 31175.976| |-----------------------------------------------------------------------------| r_work (final): 0.3242 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8099 moved from start: 0.2814 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 8888 Z= 0.180 Angle : 0.629 11.009 12098 Z= 0.309 Chirality : 0.041 0.203 1487 Planarity : 0.003 0.026 1554 Dihedral : 7.661 69.709 1347 Min Nonbonded Distance : 2.428 Molprobity Statistics. All-atom Clashscore : 10.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.37 % Favored : 95.63 % Rotamer: Outliers : 1.66 % Allowed : 20.62 % Favored : 77.73 % 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: -0.69 (0.25), residues: 1189 helix: 0.31 (0.22), residues: 597 sheet: -1.60 (0.58), residues: 81 loop : -1.11 (0.29), residues: 511 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP C 274 HIS 0.002 0.001 HIS A 197 PHE 0.014 0.001 PHE A 46 TYR 0.012 0.001 TYR D 52 ARG 0.002 0.000 ARG C 99 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2378 Ramachandran restraints generated. 1189 Oldfield, 0 Emsley, 1189 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2378 Ramachandran restraints generated. 1189 Oldfield, 0 Emsley, 1189 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 127 residues out of total 990 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 113 time to evaluate : 0.926 Fit side-chains revert: symmetry clash REVERT: B 164 ASP cc_start: 0.7860 (m-30) cc_final: 0.7558 (m-30) REVERT: D 144 LYS cc_start: 0.7956 (mmtt) cc_final: 0.7748 (mmtt) REVERT: D 282 MET cc_start: 0.9056 (tmm) cc_final: 0.8835 (tmm) REVERT: C 20 MET cc_start: 0.8820 (tpp) cc_final: 0.8618 (tpp) REVERT: C 24 MET cc_start: 0.9049 (tpp) cc_final: 0.8727 (tpp) REVERT: C 137 LYS cc_start: 0.9221 (mmpt) cc_final: 0.8973 (mmmt) REVERT: C 162 LEU cc_start: 0.8666 (tt) cc_final: 0.8420 (tp) outliers start: 14 outliers final: 13 residues processed: 121 average time/residue: 0.1665 time to fit residues: 30.3133 Evaluate side-chains 118 residues out of total 990 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 105 time to evaluate : 0.960 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 167 THR Chi-restraints excluded: chain D residue 40 LEU Chi-restraints excluded: chain D residue 53 LEU Chi-restraints excluded: chain D residue 60 VAL Chi-restraints excluded: chain D residue 226 LEU Chi-restraints excluded: chain D residue 278 LEU Chi-restraints excluded: chain C residue 152 VAL Chi-restraints excluded: chain C residue 285 LEU Chi-restraints excluded: chain E residue 67 ASP Chi-restraints excluded: chain A residue 8 VAL Chi-restraints excluded: chain A residue 51 LEU Chi-restraints excluded: chain A residue 161 LEU Chi-restraints excluded: chain A residue 178 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 117 random chunks: chunk 45 optimal weight: 1.9990 chunk 14 optimal weight: 0.9990 chunk 49 optimal weight: 0.9990 chunk 34 optimal weight: 9.9990 chunk 20 optimal weight: 8.9990 chunk 1 optimal weight: 5.9990 chunk 90 optimal weight: 0.7980 chunk 21 optimal weight: 0.5980 chunk 32 optimal weight: 2.9990 chunk 6 optimal weight: 4.9990 chunk 105 optimal weight: 2.9990 overall best weight: 1.0786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 180 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3467 r_free = 0.3467 target = 0.059811 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3184 r_free = 0.3184 target = 0.050110 restraints weight = 67651.934| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3217 r_free = 0.3217 target = 0.051133 restraints weight = 43708.386| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3236 r_free = 0.3236 target = 0.051786 restraints weight = 31258.145| |-----------------------------------------------------------------------------| r_work (final): 0.3233 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8116 moved from start: 0.3008 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 8888 Z= 0.210 Angle : 0.649 11.575 12098 Z= 0.322 Chirality : 0.041 0.159 1487 Planarity : 0.003 0.027 1554 Dihedral : 7.623 69.339 1347 Min Nonbonded Distance : 2.431 Molprobity Statistics. All-atom Clashscore : 11.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.88 % Favored : 95.12 % Rotamer: Outliers : 2.49 % Allowed : 20.02 % Favored : 77.49 % 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: -0.74 (0.26), residues: 1189 helix: 0.28 (0.22), residues: 610 sheet: -1.57 (0.62), residues: 71 loop : -1.21 (0.29), residues: 508 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP D 214 HIS 0.002 0.001 HIS C 136 PHE 0.017 0.001 PHE A 87 TYR 0.012 0.001 TYR D 52 ARG 0.003 0.000 ARG A 48 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2378 Ramachandran restraints generated. 1189 Oldfield, 0 Emsley, 1189 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2378 Ramachandran restraints generated. 1189 Oldfield, 0 Emsley, 1189 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 129 residues out of total 990 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 108 time to evaluate : 0.902 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 164 ASP cc_start: 0.7878 (m-30) cc_final: 0.7603 (m-30) REVERT: B 205 MET cc_start: 0.8886 (pmm) cc_final: 0.8657 (pmm) REVERT: D 282 MET cc_start: 0.9056 (tmm) cc_final: 0.8783 (tmm) REVERT: C 24 MET cc_start: 0.9015 (tpp) cc_final: 0.8713 (tpp) REVERT: C 137 LYS cc_start: 0.9196 (mmpt) cc_final: 0.8963 (mmmt) REVERT: C 162 LEU cc_start: 0.8733 (tt) cc_final: 0.8508 (tp) outliers start: 21 outliers final: 16 residues processed: 123 average time/residue: 0.1538 time to fit residues: 29.2142 Evaluate side-chains 118 residues out of total 990 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 102 time to evaluate : 1.047 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 88 GLN Chi-restraints excluded: chain B residue 167 THR Chi-restraints excluded: chain D residue 40 LEU Chi-restraints excluded: chain D residue 53 LEU Chi-restraints excluded: chain D residue 60 VAL Chi-restraints excluded: chain D residue 226 LEU Chi-restraints excluded: chain D residue 278 LEU Chi-restraints excluded: chain C residue 152 VAL Chi-restraints excluded: chain C residue 221 LEU Chi-restraints excluded: chain E residue 67 ASP Chi-restraints excluded: chain E residue 137 VAL Chi-restraints excluded: chain A residue 8 VAL Chi-restraints excluded: chain A residue 25 VAL Chi-restraints excluded: chain A residue 51 LEU Chi-restraints excluded: chain A residue 161 LEU Chi-restraints excluded: chain A residue 178 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 117 random chunks: chunk 107 optimal weight: 0.1980 chunk 105 optimal weight: 0.9990 chunk 1 optimal weight: 8.9990 chunk 97 optimal weight: 1.9990 chunk 35 optimal weight: 0.6980 chunk 95 optimal weight: 7.9990 chunk 92 optimal weight: 9.9990 chunk 0 optimal weight: 10.0000 chunk 52 optimal weight: 0.7980 chunk 74 optimal weight: 0.6980 chunk 64 optimal weight: 0.8980 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 180 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3480 r_free = 0.3480 target = 0.060086 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3193 r_free = 0.3193 target = 0.050253 restraints weight = 67297.389| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3228 r_free = 0.3228 target = 0.051324 restraints weight = 44082.462| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3245 r_free = 0.3245 target = 0.051923 restraints weight = 31605.145| |-----------------------------------------------------------------------------| r_work (final): 0.3250 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8088 moved from start: 0.3008 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 8888 Z= 0.179 Angle : 0.664 11.851 12098 Z= 0.327 Chirality : 0.041 0.173 1487 Planarity : 0.003 0.027 1554 Dihedral : 7.428 68.178 1345 Min Nonbonded Distance : 2.438 Molprobity Statistics. All-atom Clashscore : 9.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.54 % Favored : 95.46 % Rotamer: Outliers : 1.90 % Allowed : 21.33 % Favored : 76.78 % 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: -0.83 (0.25), residues: 1189 helix: 0.24 (0.22), residues: 619 sheet: -1.87 (0.77), residues: 51 loop : -1.34 (0.28), residues: 519 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP C 274 HIS 0.002 0.001 HIS A 197 PHE 0.023 0.001 PHE A 46 TYR 0.011 0.001 TYR C 215 ARG 0.002 0.000 ARG C 99 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2378 Ramachandran restraints generated. 1189 Oldfield, 0 Emsley, 1189 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2378 Ramachandran restraints generated. 1189 Oldfield, 0 Emsley, 1189 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 127 residues out of total 990 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 111 time to evaluate : 0.928 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: D 282 MET cc_start: 0.9032 (tmm) cc_final: 0.8818 (tmm) REVERT: C 24 MET cc_start: 0.9079 (tpp) cc_final: 0.8756 (tpp) REVERT: C 137 LYS cc_start: 0.9208 (mmpt) cc_final: 0.8966 (mmmt) REVERT: C 162 LEU cc_start: 0.8689 (tt) cc_final: 0.8471 (tp) outliers start: 16 outliers final: 15 residues processed: 123 average time/residue: 0.1548 time to fit residues: 29.0268 Evaluate side-chains 121 residues out of total 990 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 106 time to evaluate : 0.897 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 88 GLN Chi-restraints excluded: chain B residue 162 LEU Chi-restraints excluded: chain B residue 167 THR Chi-restraints excluded: chain D residue 40 LEU Chi-restraints excluded: chain D residue 53 LEU Chi-restraints excluded: chain D residue 60 VAL Chi-restraints excluded: chain D residue 226 LEU Chi-restraints excluded: chain D residue 278 LEU Chi-restraints excluded: chain C residue 152 VAL Chi-restraints excluded: chain C residue 221 LEU Chi-restraints excluded: chain E residue 67 ASP Chi-restraints excluded: chain A residue 8 VAL Chi-restraints excluded: chain A residue 25 VAL Chi-restraints excluded: chain A residue 161 LEU Chi-restraints excluded: chain A residue 178 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 117 random chunks: chunk 1 optimal weight: 4.9990 chunk 103 optimal weight: 0.9990 chunk 96 optimal weight: 8.9990 chunk 114 optimal weight: 4.9990 chunk 59 optimal weight: 5.9990 chunk 33 optimal weight: 0.9990 chunk 14 optimal weight: 0.0570 chunk 101 optimal weight: 3.9990 chunk 28 optimal weight: 0.8980 chunk 3 optimal weight: 2.9990 chunk 95 optimal weight: 10.0000 overall best weight: 1.1904 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 197 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 180 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3456 r_free = 0.3456 target = 0.058926 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3172 r_free = 0.3172 target = 0.049330 restraints weight = 67228.688| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3204 r_free = 0.3204 target = 0.050358 restraints weight = 43228.713| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3225 r_free = 0.3225 target = 0.051030 restraints weight = 30948.852| |-----------------------------------------------------------------------------| r_work (final): 0.3221 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8128 moved from start: 0.3315 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 8888 Z= 0.230 Angle : 0.709 13.604 12098 Z= 0.349 Chirality : 0.042 0.176 1487 Planarity : 0.003 0.035 1554 Dihedral : 7.524 68.674 1345 Min Nonbonded Distance : 2.427 Molprobity Statistics. All-atom Clashscore : 11.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.88 % Favored : 95.12 % Rotamer: Outliers : 1.90 % Allowed : 21.92 % Favored : 76.18 % 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: -0.71 (0.26), residues: 1189 helix: 0.31 (0.22), residues: 616 sheet: -1.56 (0.62), residues: 71 loop : -1.22 (0.30), residues: 502 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP D 214 HIS 0.011 0.001 HIS B 197 PHE 0.025 0.001 PHE A 46 TYR 0.012 0.002 TYR D 52 ARG 0.003 0.000 ARG C 49 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2378 Ramachandran restraints generated. 1189 Oldfield, 0 Emsley, 1189 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2378 Ramachandran restraints generated. 1189 Oldfield, 0 Emsley, 1189 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 122 residues out of total 990 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 106 time to evaluate : 0.904 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: D 282 MET cc_start: 0.9041 (tmm) cc_final: 0.8805 (tmm) REVERT: C 24 MET cc_start: 0.9069 (tpp) cc_final: 0.8767 (tpp) REVERT: C 137 LYS cc_start: 0.9264 (mmpt) cc_final: 0.9031 (mmmt) outliers start: 16 outliers final: 15 residues processed: 119 average time/residue: 0.1486 time to fit residues: 26.9907 Evaluate side-chains 117 residues out of total 990 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 102 time to evaluate : 0.781 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 88 GLN Chi-restraints excluded: chain B residue 162 LEU Chi-restraints excluded: chain B residue 167 THR Chi-restraints excluded: chain D residue 40 LEU Chi-restraints excluded: chain D residue 53 LEU Chi-restraints excluded: chain D residue 60 VAL Chi-restraints excluded: chain D residue 226 LEU Chi-restraints excluded: chain D residue 278 LEU Chi-restraints excluded: chain C residue 152 VAL Chi-restraints excluded: chain C residue 221 LEU Chi-restraints excluded: chain E residue 67 ASP Chi-restraints excluded: chain A residue 8 VAL Chi-restraints excluded: chain A residue 25 VAL Chi-restraints excluded: chain A residue 161 LEU Chi-restraints excluded: chain A residue 178 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 117 random chunks: chunk 77 optimal weight: 2.9990 chunk 65 optimal weight: 0.0870 chunk 69 optimal weight: 0.9980 chunk 21 optimal weight: 6.9990 chunk 19 optimal weight: 10.0000 chunk 7 optimal weight: 1.9990 chunk 109 optimal weight: 0.8980 chunk 5 optimal weight: 4.9990 chunk 90 optimal weight: 0.6980 chunk 41 optimal weight: 0.8980 chunk 72 optimal weight: 0.8980 overall best weight: 0.6958 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 197 HIS ** C 180 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3476 r_free = 0.3476 target = 0.060007 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3196 r_free = 0.3196 target = 0.050202 restraints weight = 66757.076| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3228 r_free = 0.3228 target = 0.051233 restraints weight = 43140.475| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3247 r_free = 0.3247 target = 0.051888 restraints weight = 30965.443| |-----------------------------------------------------------------------------| r_work (final): 0.3242 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8104 moved from start: 0.3272 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 8888 Z= 0.189 Angle : 0.712 12.654 12098 Z= 0.347 Chirality : 0.042 0.172 1487 Planarity : 0.003 0.028 1554 Dihedral : 7.411 67.202 1345 Min Nonbonded Distance : 2.435 Molprobity Statistics. All-atom Clashscore : 11.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.79 % Favored : 95.21 % Rotamer: Outliers : 2.13 % Allowed : 21.45 % Favored : 76.42 % 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: -0.78 (0.25), residues: 1189 helix: 0.28 (0.22), residues: 622 sheet: -1.93 (0.76), residues: 51 loop : -1.29 (0.28), residues: 516 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP C 274 HIS 0.010 0.001 HIS B 197 PHE 0.024 0.001 PHE A 46 TYR 0.012 0.001 TYR D 52 ARG 0.002 0.000 ARG A 147 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2829.97 seconds wall clock time: 50 minutes 53.87 seconds (3053.87 seconds total)