Starting phenix.real_space_refine on Mon May 12 11:03:43 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8idd_35364/05_2025/8idd_35364.cif Found real_map, /net/cci-nas-00/data/ceres_data/8idd_35364/05_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_35364/05_2025/8idd_35364.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8idd_35364/05_2025/8idd_35364.map" model { file = "/net/cci-nas-00/data/ceres_data/8idd_35364/05_2025/8idd_35364.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8idd_35364/05_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-5687/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: 5.83, per 1000 atoms: 0.66 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: 2.48 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: 0.82 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: 2.26 Time building geometry restraints manager: 2.75 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: 3.330 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: 0.080 Process input model: 23.000 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:2.900 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 30.070 ------------------------------------------------------------------------------- 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 8890 Z= 0.204 Angle : 1.017 14.481 12102 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 Details of bonding type rmsd hydrogen bonds : bond 0.18239 ( 377) hydrogen bonds : angle 7.23826 ( 1104) SS BOND : bond 0.00201 ( 2) SS BOND : angle 2.06941 ( 4) covalent geometry : bond 0.00411 ( 8888) covalent geometry : angle 1.01666 (12098) *********************** 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 : 1.160 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: 0.1804 time to fit residues: 42.5883 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 : 0.950 ------------------------------------------------------------------------------- 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 A 197 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3539 r_free = 0.3539 target = 0.062561 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3266 r_free = 0.3266 target = 0.052845 restraints weight = 65792.242| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3295 r_free = 0.3295 target = 0.053844 restraints weight = 44055.598| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3312 r_free = 0.3312 target = 0.054436 restraints weight = 32402.356| |-----------------------------------------------------------------------------| r_work (final): 0.3300 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8039 moved from start: 0.1660 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 8890 Z= 0.150 Angle : 0.634 9.649 12102 Z= 0.325 Chirality : 0.041 0.132 1487 Planarity : 0.004 0.050 1554 Dihedral : 8.333 73.205 1347 Min Nonbonded Distance : 2.389 Molprobity Statistics. All-atom Clashscore : 9.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.04 % Favored : 95.96 % Rotamer: Outliers : 1.30 % Allowed : 11.26 % Favored : 87.44 % 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: -1.92 (0.23), residues: 1189 helix: -0.83 (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 0.008 0.001 ARG E 134 Details of bonding type rmsd hydrogen bonds : bond 0.03504 ( 377) hydrogen bonds : angle 4.78319 ( 1104) SS BOND : bond 0.00170 ( 2) SS BOND : angle 0.72380 ( 4) covalent geometry : bond 0.00327 ( 8888) covalent geometry : angle 0.63347 (12098) *********************** 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 141 residues out of total 990 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 130 time to evaluate : 1.097 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 47 MET cc_start: 0.8673 (mmm) cc_final: 0.8154 (mmm) REVERT: D 113 PHE cc_start: 0.8658 (m-80) cc_final: 0.8371 (m-80) REVERT: C 27 THR cc_start: 0.9207 (m) cc_final: 0.8986 (t) REVERT: C 137 LYS cc_start: 0.9140 (mmpt) cc_final: 0.8907 (mmmt) REVERT: C 222 VAL cc_start: 0.9076 (t) cc_final: 0.8866 (p) outliers start: 11 outliers final: 5 residues processed: 137 average time/residue: 0.1659 time to fit residues: 34.2345 Evaluate side-chains 119 residues out of total 990 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 114 time to evaluate : 0.986 ------------------------------------------------------------------------------- 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: 1.9990 chunk 11 optimal weight: 2.9990 chunk 94 optimal weight: 7.9990 chunk 53 optimal weight: 0.8980 chunk 67 optimal weight: 0.5980 chunk 41 optimal weight: 3.9990 chunk 48 optimal weight: 3.9990 chunk 5 optimal weight: 4.9990 chunk 59 optimal weight: 0.6980 chunk 62 optimal weight: 0.7980 chunk 96 optimal weight: 0.8980 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 252 ASN ** E 179 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 = 0.3535 r_free = 0.3535 target = 0.062669 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3257 r_free = 0.3257 target = 0.052864 restraints weight = 67040.249| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3287 r_free = 0.3287 target = 0.053883 restraints weight = 45028.269| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3311 r_free = 0.3311 target = 0.054634 restraints weight = 33038.740| |-----------------------------------------------------------------------------| r_work (final): 0.3297 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8041 moved from start: 0.1880 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 8890 Z= 0.117 Angle : 0.590 9.836 12102 Z= 0.297 Chirality : 0.040 0.140 1487 Planarity : 0.003 0.032 1554 Dihedral : 8.172 73.104 1347 Min Nonbonded Distance : 2.371 Molprobity Statistics. All-atom Clashscore : 8.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.87 % Favored : 96.13 % Rotamer: Outliers : 1.54 % Allowed : 14.57 % Favored : 83.89 % 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: -1.36 (0.24), residues: 1189 helix: -0.28 (0.21), residues: 609 sheet: -1.47 (0.64), residues: 71 loop : -1.50 (0.27), residues: 509 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP C 274 HIS 0.003 0.001 HIS A 197 PHE 0.010 0.001 PHE A 87 TYR 0.010 0.001 TYR C 215 ARG 0.005 0.000 ARG E 134 Details of bonding type rmsd hydrogen bonds : bond 0.03123 ( 377) hydrogen bonds : angle 4.48315 ( 1104) SS BOND : bond 0.00280 ( 2) SS BOND : angle 1.27297 ( 4) covalent geometry : bond 0.00259 ( 8888) covalent geometry : angle 0.58927 (12098) *********************** 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 133 residues out of total 990 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 120 time to evaluate : 1.078 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 47 MET cc_start: 0.8566 (mmm) cc_final: 0.8183 (mmm) REVERT: D 282 MET cc_start: 0.9007 (OUTLIER) cc_final: 0.8797 (tmm) REVERT: C 27 THR cc_start: 0.9207 (m) cc_final: 0.8994 (t) REVERT: C 137 LYS cc_start: 0.9216 (mmpt) cc_final: 0.8966 (mmmt) REVERT: A 47 MET cc_start: 0.9071 (mpp) cc_final: 0.8849 (mpp) REVERT: A 87 PHE cc_start: 0.8805 (m-10) cc_final: 0.8464 (m-10) outliers start: 13 outliers final: 10 residues processed: 128 average time/residue: 0.1670 time to fit residues: 31.9575 Evaluate side-chains 121 residues out of total 990 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 110 time to evaluate : 1.148 ------------------------------------------------------------------------------- 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: 0.9980 chunk 4 optimal weight: 3.9990 chunk 44 optimal weight: 0.6980 chunk 27 optimal weight: 0.7980 chunk 41 optimal weight: 3.9990 chunk 28 optimal weight: 0.8980 chunk 0 optimal weight: 10.0000 chunk 50 optimal weight: 0.8980 chunk 78 optimal weight: 0.9990 chunk 31 optimal weight: 2.9990 chunk 70 optimal weight: 3.9990 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 179 GLN E 191 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3515 r_free = 0.3515 target = 0.061666 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3235 r_free = 0.3235 target = 0.051797 restraints weight = 65917.516| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3264 r_free = 0.3264 target = 0.052791 restraints weight = 44069.427| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3286 r_free = 0.3286 target = 0.053499 restraints weight = 32332.870| |-----------------------------------------------------------------------------| r_work (final): 0.3284 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8061 moved from start: 0.2195 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 8890 Z= 0.119 Angle : 0.573 10.337 12102 Z= 0.289 Chirality : 0.040 0.165 1487 Planarity : 0.003 0.030 1554 Dihedral : 7.932 73.961 1347 Min Nonbonded Distance : 2.404 Molprobity Statistics. All-atom Clashscore : 9.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.12 % Favored : 95.88 % Rotamer: Outliers : 2.49 % Allowed : 16.47 % Favored : 81.04 % 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: -1.08 (0.25), residues: 1189 helix: 0.00 (0.22), residues: 617 sheet: -1.35 (0.65), residues: 71 loop : -1.45 (0.28), residues: 501 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 154 TYR 0.011 0.001 TYR C 215 ARG 0.003 0.000 ARG A 152 Details of bonding type rmsd hydrogen bonds : bond 0.02910 ( 377) hydrogen bonds : angle 4.25089 ( 1104) SS BOND : bond 0.00026 ( 2) SS BOND : angle 1.05255 ( 4) covalent geometry : bond 0.00266 ( 8888) covalent geometry : angle 0.57273 (12098) *********************** 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 136 residues out of total 990 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 115 time to evaluate : 1.012 Fit side-chains revert: symmetry clash REVERT: B 164 ASP cc_start: 0.7749 (m-30) cc_final: 0.7478 (m-30) REVERT: D 20 MET cc_start: 0.8271 (ttt) cc_final: 0.8000 (ttt) REVERT: D 144 LYS cc_start: 0.7793 (mmtt) cc_final: 0.7572 (mmtt) REVERT: D 191 MET cc_start: 0.8540 (tpp) cc_final: 0.8087 (tpp) REVERT: C 137 LYS cc_start: 0.9231 (mmpt) cc_final: 0.8907 (mmmt) outliers start: 21 outliers final: 13 residues processed: 129 average time/residue: 0.1529 time to fit residues: 29.7161 Evaluate side-chains 124 residues out of total 990 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 111 time to evaluate : 0.959 ------------------------------------------------------------------------------- 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 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 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: 0.5980 chunk 47 optimal weight: 0.9980 chunk 0 optimal weight: 10.0000 chunk 14 optimal weight: 0.6980 chunk 78 optimal weight: 1.9990 chunk 41 optimal weight: 3.9990 chunk 13 optimal weight: 0.9990 chunk 44 optimal weight: 0.6980 chunk 48 optimal weight: 1.9990 chunk 10 optimal weight: 0.5980 chunk 87 optimal weight: 0.8980 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 179 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 = 0.3512 r_free = 0.3512 target = 0.061317 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3238 r_free = 0.3238 target = 0.051676 restraints weight = 65121.206| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3268 r_free = 0.3268 target = 0.052693 restraints weight = 43327.396| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3290 r_free = 0.3290 target = 0.053414 restraints weight = 31580.541| |-----------------------------------------------------------------------------| r_work (final): 0.3284 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8055 moved from start: 0.2334 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 8890 Z= 0.112 Angle : 0.586 10.842 12102 Z= 0.292 Chirality : 0.040 0.149 1487 Planarity : 0.002 0.025 1554 Dihedral : 7.773 73.388 1347 Min Nonbonded Distance : 2.411 Molprobity Statistics. All-atom Clashscore : 9.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.87 % Favored : 96.13 % Rotamer: Outliers : 2.01 % Allowed : 18.48 % Favored : 79.50 % 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: -0.89 (0.25), residues: 1189 helix: 0.14 (0.22), residues: 605 sheet: -1.71 (0.78), residues: 51 loop : -1.28 (0.28), residues: 533 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.000 TRP C 274 HIS 0.002 0.001 HIS A 197 PHE 0.013 0.001 PHE A 46 TYR 0.011 0.001 TYR D 52 ARG 0.002 0.000 ARG A 152 Details of bonding type rmsd hydrogen bonds : bond 0.02866 ( 377) hydrogen bonds : angle 4.20281 ( 1104) SS BOND : bond 0.00013 ( 2) SS BOND : angle 0.77816 ( 4) covalent geometry : bond 0.00252 ( 8888) covalent geometry : angle 0.58553 (12098) *********************** 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 133 residues out of total 990 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 116 time to evaluate : 0.974 Fit side-chains revert: symmetry clash REVERT: B 164 ASP cc_start: 0.7783 (m-30) cc_final: 0.7543 (m-30) REVERT: D 144 LYS cc_start: 0.7788 (mmtt) cc_final: 0.7549 (mmtt) REVERT: C 24 MET cc_start: 0.8855 (tpp) cc_final: 0.8535 (tpp) REVERT: C 137 LYS cc_start: 0.9239 (mmpt) cc_final: 0.8912 (mmmt) REVERT: A 87 PHE cc_start: 0.8629 (m-10) cc_final: 0.8300 (m-10) outliers start: 17 outliers final: 13 residues processed: 128 average time/residue: 0.1587 time to fit residues: 30.7284 Evaluate side-chains 119 residues out of total 990 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 106 time to evaluate : 0.931 ------------------------------------------------------------------------------- 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: 0.4980 chunk 105 optimal weight: 1.9990 chunk 43 optimal weight: 4.9990 chunk 50 optimal weight: 0.9990 chunk 114 optimal weight: 4.9990 chunk 108 optimal weight: 6.9990 chunk 6 optimal weight: 4.9990 chunk 75 optimal weight: 7.9990 chunk 33 optimal weight: 0.9980 chunk 20 optimal weight: 3.9990 chunk 55 optimal weight: 0.9980 overall best weight: 1.0984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 179 GLN A 88 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3487 r_free = 0.3487 target = 0.060253 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3207 r_free = 0.3207 target = 0.050561 restraints weight = 66220.208| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3237 r_free = 0.3237 target = 0.051556 restraints weight = 43584.396| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3259 r_free = 0.3259 target = 0.052289 restraints weight = 31635.539| |-----------------------------------------------------------------------------| r_work (final): 0.3259 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8093 moved from start: 0.2676 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 8890 Z= 0.143 Angle : 0.618 11.996 12102 Z= 0.308 Chirality : 0.040 0.140 1487 Planarity : 0.003 0.025 1554 Dihedral : 7.725 72.185 1347 Min Nonbonded Distance : 2.412 Molprobity Statistics. All-atom Clashscore : 10.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.37 % Favored : 95.63 % Rotamer: Outliers : 2.13 % Allowed : 19.55 % Favored : 78.32 % 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: -0.72 (0.25), residues: 1189 helix: 0.32 (0.22), residues: 597 sheet: -1.55 (0.59), residues: 81 loop : -1.18 (0.29), residues: 511 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP D 214 HIS 0.003 0.001 HIS A 197 PHE 0.009 0.001 PHE D 5 TYR 0.012 0.001 TYR D 52 ARG 0.002 0.000 ARG C 99 Details of bonding type rmsd hydrogen bonds : bond 0.02892 ( 377) hydrogen bonds : angle 4.20861 ( 1104) SS BOND : bond 0.00046 ( 2) SS BOND : angle 0.67093 ( 4) covalent geometry : bond 0.00318 ( 8888) covalent geometry : angle 0.61795 (12098) *********************** 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 130 residues out of total 990 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 112 time to evaluate : 0.981 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 164 ASP cc_start: 0.7811 (m-30) cc_final: 0.7522 (m-30) REVERT: D 144 LYS cc_start: 0.7885 (mmtt) cc_final: 0.7639 (mmtt) REVERT: D 208 LEU cc_start: 0.9463 (OUTLIER) cc_final: 0.9235 (mp) REVERT: D 282 MET cc_start: 0.9148 (tmm) cc_final: 0.8941 (tmm) REVERT: C 24 MET cc_start: 0.8902 (tpp) cc_final: 0.8574 (tpp) REVERT: C 137 LYS cc_start: 0.9192 (mmpt) cc_final: 0.8959 (mmmt) REVERT: A 87 PHE cc_start: 0.8567 (m-10) cc_final: 0.8330 (m-10) outliers start: 18 outliers final: 13 residues processed: 125 average time/residue: 0.1606 time to fit residues: 30.1700 Evaluate side-chains 120 residues out of total 990 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 106 time to evaluate : 0.962 ------------------------------------------------------------------------------- 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 208 LEU 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 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: 0.8980 chunk 92 optimal weight: 0.9980 chunk 54 optimal weight: 2.9990 chunk 63 optimal weight: 6.9990 chunk 12 optimal weight: 0.8980 chunk 22 optimal weight: 0.5980 chunk 98 optimal weight: 4.9990 chunk 4 optimal weight: 4.9990 chunk 48 optimal weight: 5.9990 chunk 79 optimal weight: 0.9990 chunk 20 optimal weight: 7.9990 overall best weight: 0.8782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 186 ASN ** D 180 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 179 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 = 0.3486 r_free = 0.3486 target = 0.060280 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3208 r_free = 0.3208 target = 0.050578 restraints weight = 66313.914| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 19)----------------| | r_work = 0.3238 r_free = 0.3238 target = 0.051587 restraints weight = 43490.166| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3260 r_free = 0.3260 target = 0.052332 restraints weight = 31458.394| |-----------------------------------------------------------------------------| r_work (final): 0.3254 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8094 moved from start: 0.2794 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 8890 Z= 0.125 Angle : 0.620 11.183 12102 Z= 0.306 Chirality : 0.040 0.133 1487 Planarity : 0.003 0.026 1554 Dihedral : 7.624 70.393 1347 Min Nonbonded Distance : 2.425 Molprobity Statistics. All-atom Clashscore : 10.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.54 % Favored : 95.46 % Rotamer: Outliers : 2.01 % Allowed : 20.38 % Favored : 77.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.69 (0.25), residues: 1189 helix: 0.32 (0.22), residues: 597 sheet: -1.61 (0.59), 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 0.007 0.001 PHE A 154 TYR 0.012 0.001 TYR D 52 ARG 0.002 0.000 ARG C 99 Details of bonding type rmsd hydrogen bonds : bond 0.02860 ( 377) hydrogen bonds : angle 4.19354 ( 1104) SS BOND : bond 0.00026 ( 2) SS BOND : angle 0.60052 ( 4) covalent geometry : bond 0.00285 ( 8888) covalent geometry : angle 0.61986 (12098) *********************** 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 134 residues out of total 990 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 117 time to evaluate : 1.052 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 164 ASP cc_start: 0.7861 (m-30) cc_final: 0.7567 (m-30) REVERT: D 20 MET cc_start: 0.7811 (ttt) cc_final: 0.7488 (tmm) REVERT: D 144 LYS cc_start: 0.7953 (mmtt) cc_final: 0.7745 (mmtt) REVERT: D 208 LEU cc_start: 0.9482 (OUTLIER) cc_final: 0.9248 (mp) REVERT: D 282 MET cc_start: 0.9139 (tmm) cc_final: 0.8910 (tmm) REVERT: C 20 MET cc_start: 0.8873 (tpp) cc_final: 0.8599 (tpp) REVERT: C 24 MET cc_start: 0.9018 (tpp) cc_final: 0.8657 (tpp) REVERT: C 137 LYS cc_start: 0.9231 (mmpt) cc_final: 0.8978 (mmmt) outliers start: 17 outliers final: 15 residues processed: 129 average time/residue: 0.1615 time to fit residues: 31.1998 Evaluate side-chains 125 residues out of total 990 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 109 time to evaluate : 0.990 ------------------------------------------------------------------------------- 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 208 LEU Chi-restraints excluded: chain D residue 226 LEU Chi-restraints excluded: chain D residue 278 LEU Chi-restraints excluded: chain D residue 289 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: 0.6980 chunk 14 optimal weight: 0.4980 chunk 49 optimal weight: 0.8980 chunk 34 optimal weight: 9.9990 chunk 20 optimal weight: 8.9990 chunk 1 optimal weight: 3.9990 chunk 90 optimal weight: 0.9990 chunk 21 optimal weight: 0.9990 chunk 32 optimal weight: 0.9990 chunk 6 optimal weight: 5.9990 chunk 105 optimal weight: 0.9980 overall best weight: 0.8182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 179 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 = 0.3486 r_free = 0.3486 target = 0.060123 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3206 r_free = 0.3206 target = 0.050476 restraints weight = 66769.784| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3235 r_free = 0.3235 target = 0.051465 restraints weight = 43696.520| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3259 r_free = 0.3259 target = 0.052232 restraints weight = 31570.620| |-----------------------------------------------------------------------------| r_work (final): 0.3264 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8078 moved from start: 0.2925 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 8890 Z= 0.124 Angle : 0.641 11.392 12102 Z= 0.318 Chirality : 0.040 0.157 1487 Planarity : 0.003 0.027 1554 Dihedral : 7.530 69.661 1347 Min Nonbonded Distance : 2.432 Molprobity Statistics. All-atom Clashscore : 10.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.29 % Favored : 95.71 % Rotamer: Outliers : 2.37 % Allowed : 20.02 % Favored : 77.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.68 (0.25), residues: 1189 helix: 0.31 (0.22), residues: 594 sheet: -1.56 (0.64), residues: 71 loop : -1.11 (0.29), residues: 524 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP C 274 HIS 0.003 0.001 HIS C 136 PHE 0.021 0.001 PHE A 87 TYR 0.011 0.001 TYR D 52 ARG 0.003 0.000 ARG A 184 Details of bonding type rmsd hydrogen bonds : bond 0.02870 ( 377) hydrogen bonds : angle 4.15266 ( 1104) SS BOND : bond 0.00003 ( 2) SS BOND : angle 0.55191 ( 4) covalent geometry : bond 0.00286 ( 8888) covalent geometry : angle 0.64069 (12098) *********************** 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 133 residues out of total 990 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 113 time to evaluate : 0.938 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 164 ASP cc_start: 0.7851 (m-30) cc_final: 0.7548 (m-30) REVERT: B 205 MET cc_start: 0.8864 (pmm) cc_final: 0.8643 (pmm) REVERT: C 24 MET cc_start: 0.9075 (tpp) cc_final: 0.8732 (tpp) REVERT: C 137 LYS cc_start: 0.9187 (mmpt) cc_final: 0.8942 (mmmt) outliers start: 20 outliers final: 15 residues processed: 128 average time/residue: 0.1534 time to fit residues: 29.8828 Evaluate side-chains 122 residues out of total 990 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 107 time to evaluate : 1.031 ------------------------------------------------------------------------------- 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 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 25 VAL 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: 0.2980 chunk 105 optimal weight: 0.8980 chunk 1 optimal weight: 7.9990 chunk 97 optimal weight: 4.9990 chunk 35 optimal weight: 0.0980 chunk 95 optimal weight: 7.9990 chunk 92 optimal weight: 3.9990 chunk 0 optimal weight: 10.0000 chunk 52 optimal weight: 3.9990 chunk 74 optimal weight: 0.9980 chunk 64 optimal weight: 1.9990 overall best weight: 0.8582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 197 HIS ** D 180 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 179 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 = 0.3480 r_free = 0.3480 target = 0.060287 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3202 r_free = 0.3202 target = 0.050534 restraints weight = 67314.830| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3233 r_free = 0.3233 target = 0.051548 restraints weight = 43880.782| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3251 r_free = 0.3251 target = 0.052207 restraints weight = 31573.364| |-----------------------------------------------------------------------------| r_work (final): 0.3250 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8099 moved from start: 0.3023 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 8890 Z= 0.130 Angle : 0.675 11.737 12102 Z= 0.334 Chirality : 0.041 0.159 1487 Planarity : 0.003 0.028 1554 Dihedral : 7.489 69.132 1347 Min Nonbonded Distance : 2.434 Molprobity Statistics. All-atom Clashscore : 11.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.63 % Favored : 95.37 % Rotamer: Outliers : 2.13 % Allowed : 20.73 % Favored : 77.13 % 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: 0.23 (0.22), residues: 613 sheet: -1.80 (0.78), residues: 51 loop : -1.23 (0.28), residues: 525 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP C 274 HIS 0.011 0.001 HIS B 197 PHE 0.026 0.001 PHE A 87 TYR 0.011 0.001 TYR D 52 ARG 0.002 0.000 ARG C 99 Details of bonding type rmsd hydrogen bonds : bond 0.02980 ( 377) hydrogen bonds : angle 4.25205 ( 1104) SS BOND : bond 0.00182 ( 2) SS BOND : angle 1.36776 ( 4) covalent geometry : bond 0.00299 ( 8888) covalent geometry : angle 0.67478 (12098) *********************** 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 128 residues out of total 990 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 110 time to evaluate : 1.072 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 164 ASP cc_start: 0.7895 (m-30) cc_final: 0.7670 (m-30) REVERT: C 24 MET cc_start: 0.9087 (tpp) cc_final: 0.8747 (tpp) REVERT: C 137 LYS cc_start: 0.9195 (mmpt) cc_final: 0.8954 (mmmt) outliers start: 18 outliers final: 16 residues processed: 122 average time/residue: 0.1593 time to fit residues: 29.9003 Evaluate side-chains 121 residues out of total 990 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 105 time to evaluate : 1.048 ------------------------------------------------------------------------------- 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 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 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: 3.9990 chunk 103 optimal weight: 1.9990 chunk 96 optimal weight: 6.9990 chunk 114 optimal weight: 7.9990 chunk 59 optimal weight: 6.9990 chunk 33 optimal weight: 3.9990 chunk 14 optimal weight: 0.0980 chunk 101 optimal weight: 4.9990 chunk 28 optimal weight: 0.9990 chunk 3 optimal weight: 2.9990 chunk 95 optimal weight: 9.9990 overall best weight: 2.0188 ------------------------------------------------------------------------------- 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** ** C 190 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 179 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 = 0.3394 r_free = 0.3394 target = 0.056672 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3108 r_free = 0.3108 target = 0.047013 restraints weight = 66258.309| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3139 r_free = 0.3139 target = 0.047999 restraints weight = 42160.062| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3161 r_free = 0.3161 target = 0.048705 restraints weight = 29966.485| |-----------------------------------------------------------------------------| r_work (final): 0.3155 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8195 moved from start: 0.3731 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.074 8890 Z= 0.234 Angle : 0.778 13.128 12102 Z= 0.392 Chirality : 0.044 0.173 1487 Planarity : 0.003 0.025 1554 Dihedral : 7.900 68.824 1345 Min Nonbonded Distance : 2.364 Molprobity Statistics. All-atom Clashscore : 16.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.72 % Favored : 94.28 % Rotamer: Outliers : 2.25 % Allowed : 21.09 % Favored : 76.66 % 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: -1.17 (0.25), residues: 1189 helix: -0.03 (0.21), residues: 639 sheet: -1.94 (0.60), residues: 75 loop : -1.51 (0.30), residues: 475 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP D 214 HIS 0.010 0.002 HIS B 197 PHE 0.021 0.002 PHE A 87 TYR 0.017 0.002 TYR D 215 ARG 0.005 0.001 ARG C 99 Details of bonding type rmsd hydrogen bonds : bond 0.03423 ( 377) hydrogen bonds : angle 4.57338 ( 1104) SS BOND : bond 0.00175 ( 2) SS BOND : angle 1.26397 ( 4) covalent geometry : bond 0.00515 ( 8888) covalent geometry : angle 0.77736 (12098) ********************** 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 121 residues out of total 990 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 102 time to evaluate : 1.046 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: D 191 MET cc_start: 0.8629 (tpp) cc_final: 0.8359 (tpp) REVERT: C 24 MET cc_start: 0.9129 (tpp) cc_final: 0.8757 (tpp) REVERT: C 137 LYS cc_start: 0.9320 (mmpt) cc_final: 0.9098 (mmmt) REVERT: A 161 LEU cc_start: 0.9214 (OUTLIER) cc_final: 0.8916 (tp) outliers start: 19 outliers final: 15 residues processed: 117 average time/residue: 0.1606 time to fit residues: 29.0870 Evaluate side-chains 115 residues out of total 990 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 99 time to evaluate : 1.055 ------------------------------------------------------------------------------- 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 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 216 THR 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 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: 0.9980 chunk 65 optimal weight: 0.0030 chunk 69 optimal weight: 0.6980 chunk 21 optimal weight: 6.9990 chunk 19 optimal weight: 5.9990 chunk 7 optimal weight: 6.9990 chunk 109 optimal weight: 0.9980 chunk 5 optimal weight: 2.9990 chunk 90 optimal weight: 0.7980 chunk 41 optimal weight: 2.9990 chunk 72 optimal weight: 0.9980 overall best weight: 0.6990 ------------------------------------------------------------------------------- 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** ** E 179 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 = 0.3448 r_free = 0.3448 target = 0.058732 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3161 r_free = 0.3161 target = 0.048838 restraints weight = 66068.809| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3194 r_free = 0.3194 target = 0.049883 restraints weight = 42429.229| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3218 r_free = 0.3218 target = 0.050638 restraints weight = 30143.394| |-----------------------------------------------------------------------------| r_work (final): 0.3215 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8125 moved from start: 0.3560 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 8890 Z= 0.130 Angle : 0.732 12.481 12102 Z= 0.356 Chirality : 0.043 0.257 1487 Planarity : 0.003 0.028 1554 Dihedral : 7.543 64.343 1345 Min Nonbonded Distance : 2.434 Molprobity Statistics. All-atom Clashscore : 12.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.54 % Favored : 95.46 % Rotamer: Outliers : 1.78 % Allowed : 22.63 % Favored : 75.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.06 (0.25), residues: 1189 helix: 0.06 (0.21), residues: 644 sheet: -1.99 (0.75), residues: 51 loop : -1.52 (0.29), residues: 494 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP C 274 HIS 0.011 0.001 HIS B 197 PHE 0.022 0.001 PHE A 87 TYR 0.015 0.001 TYR C 215 ARG 0.003 0.000 ARG E 134 Details of bonding type rmsd hydrogen bonds : bond 0.03091 ( 377) hydrogen bonds : angle 4.36738 ( 1104) SS BOND : bond 0.00047 ( 2) SS BOND : angle 1.12690 ( 4) covalent geometry : bond 0.00301 ( 8888) covalent geometry : angle 0.73185 (12098) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2673.31 seconds wall clock time: 47 minutes 42.56 seconds (2862.56 seconds total)