Starting phenix.real_space_refine on Sat Aug 23 01:20:42 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8idd_35364/08_2025/8idd_35364.cif Found real_map, /net/cci-nas-00/data/ceres_data/8idd_35364/08_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_35364/08_2025/8idd_35364.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8idd_35364/08_2025/8idd_35364.map" model { file = "/net/cci-nas-00/data/ceres_data/8idd_35364/08_2025/8idd_35364.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8idd_35364/08_2025/8idd_35364.cif" } resolution = 4.0 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 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): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/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, 'ARG:plan': 9, 'ASP:plan': 6, 'ASN:plan1': 2, 'GLU:plan': 7, 'PHE:plan': 1, 'HIS:plan': 1, 'TYR:plan': 1} 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: {'ARG:plan': 2, 'GLU:plan': 1, 'GLN:plan1': 2, 'ASN:plan1': 1, 'PHE:plan': 1, 'TYR:plan': 1} 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, 'ASN:plan1': 1, 'ARG:plan': 3, 'ASP:plan': 4, 'GLU:plan': 3, 'TYR:plan': 1} 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, 'ARG:plan': 8, 'ASP:plan': 6, 'ASN:plan1': 2, 'GLU:plan': 7, 'PHE:plan': 1, 'HIS:plan': 1, 'TYR:plan': 1} 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: 2.06, per 1000 atoms: 0.23 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: 0.59 Conformation dependent library (CDL) restraints added in 286.5 milliseconds Enol-peptide restraints added in 953.7 nanoseconds 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: 0.23 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: 1.08 Time building geometry restraints manager: 0.82 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 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: 3.720 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: 0.170 Check model and map are aligned: 0.020 Set scattering table: 0.030 Process input model: 7.830 Find NCS groups from input model: 0.120 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.140 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 13.060 ------------------------------------------------------------------------------- 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 : 5.72 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. 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 ARG 0.009 0.001 ARG E 134 TYR 0.018 0.002 TYR C 288 PHE 0.045 0.002 PHE A 46 TRP 0.009 0.001 TRP D 214 HIS 0.008 0.001 HIS A 197 Details of bonding type rmsd covalent geometry : bond 0.00411 ( 8888) covalent geometry : angle 1.01666 (12098) SS BOND : bond 0.00201 ( 2) SS BOND : angle 2.06941 ( 4) hydrogen bonds : bond 0.18239 ( 377) hydrogen bonds : angle 7.23826 ( 1104) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2378 Ramachandran restraints generated. 1189 Oldfield, 0 Emsley, 1189 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2378 Ramachandran restraints generated. 1189 Oldfield, 0 Emsley, 1189 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 166 residues out of total 990 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 164 time to evaluate : 0.320 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: 0.0579 time to fit residues: 13.9252 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 : 0.211 ------------------------------------------------------------------------------- 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 108 optimal weight: 2.9990 chunk 49 optimal weight: 0.7980 chunk 97 optimal weight: 7.9990 chunk 113 optimal weight: 3.9990 chunk 53 optimal weight: 0.7980 chunk 5 optimal weight: 4.9990 chunk 33 optimal weight: 0.0970 chunk 65 optimal weight: 3.9990 chunk 62 optimal weight: 0.9990 chunk 51 optimal weight: 0.0040 chunk 100 optimal weight: 5.9990 overall best weight: 0.5392 ------------------------------------------------------------------------------- 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 C 136 HIS E 179 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3583 r_free = 0.3583 target = 0.064318 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3314 r_free = 0.3314 target = 0.054521 restraints weight = 66071.276| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3344 r_free = 0.3344 target = 0.055550 restraints weight = 44728.498| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3362 r_free = 0.3362 target = 0.056218 restraints weight = 33067.679| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3380 r_free = 0.3380 target = 0.056806 restraints weight = 26501.437| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.3393 r_free = 0.3393 target = 0.057260 restraints weight = 21714.865| |-----------------------------------------------------------------------------| r_work (final): 0.3375 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7951 moved from start: 0.1419 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 8890 Z= 0.115 Angle : 0.619 9.988 12102 Z= 0.312 Chirality : 0.040 0.128 1487 Planarity : 0.004 0.041 1554 Dihedral : 8.323 75.129 1347 Min Nonbonded Distance : 2.401 Molprobity Statistics. All-atom Clashscore : 7.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.87 % Favored : 96.13 % Rotamer: Outliers : 1.30 % Allowed : 10.66 % Favored : 88.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -2.08 (0.23), residues: 1189 helix: -1.00 (0.20), residues: 595 sheet: -1.58 (0.65), residues: 71 loop : -1.69 (0.25), residues: 523 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG C 49 TYR 0.007 0.001 TYR C 215 PHE 0.015 0.001 PHE D 35 TRP 0.003 0.000 TRP C 274 HIS 0.007 0.001 HIS B 197 Details of bonding type rmsd covalent geometry : bond 0.00250 ( 8888) covalent geometry : angle 0.61885 (12098) SS BOND : bond 0.00096 ( 2) SS BOND : angle 0.82100 ( 4) hydrogen bonds : bond 0.03540 ( 377) hydrogen bonds : angle 4.80462 ( 1104) *********************** 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 146 residues out of total 990 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 135 time to evaluate : 0.236 Fit side-chains revert: symmetry clash REVERT: B 47 MET cc_start: 0.8636 (mmm) cc_final: 0.8059 (mmm) REVERT: D 113 PHE cc_start: 0.8560 (m-80) cc_final: 0.8244 (m-80) REVERT: C 137 LYS cc_start: 0.9123 (mmpt) cc_final: 0.8866 (mmmt) REVERT: C 222 VAL cc_start: 0.9012 (t) cc_final: 0.8809 (p) REVERT: A 47 MET cc_start: 0.9152 (mpp) cc_final: 0.8901 (mpp) outliers start: 11 outliers final: 4 residues processed: 142 average time/residue: 0.0596 time to fit residues: 13.0174 Evaluate side-chains 120 residues out of total 990 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 116 time to evaluate : 0.247 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 40 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 55 optimal weight: 0.6980 chunk 13 optimal weight: 1.9990 chunk 5 optimal weight: 3.9990 chunk 110 optimal weight: 3.9990 chunk 92 optimal weight: 2.9990 chunk 115 optimal weight: 0.0980 chunk 62 optimal weight: 0.0020 chunk 111 optimal weight: 0.6980 chunk 39 optimal weight: 3.9990 chunk 34 optimal weight: 9.9990 chunk 49 optimal weight: 0.8980 overall best weight: 0.4788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 190 ASN E 179 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3575 r_free = 0.3575 target = 0.064042 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3307 r_free = 0.3307 target = 0.054312 restraints weight = 65539.258| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3335 r_free = 0.3335 target = 0.055301 restraints weight = 44397.009| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3356 r_free = 0.3356 target = 0.056034 restraints weight = 33039.113| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3368 r_free = 0.3368 target = 0.056470 restraints weight = 26155.781| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.3385 r_free = 0.3385 target = 0.056982 restraints weight = 21816.886| |-----------------------------------------------------------------------------| r_work (final): 0.3380 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7934 moved from start: 0.1625 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 8890 Z= 0.101 Angle : 0.586 10.454 12102 Z= 0.290 Chirality : 0.039 0.145 1487 Planarity : 0.003 0.031 1554 Dihedral : 8.071 72.591 1347 Min Nonbonded Distance : 2.409 Molprobity Statistics. All-atom Clashscore : 7.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.53 % Favored : 96.47 % Rotamer: Outliers : 1.78 % Allowed : 14.45 % Favored : 83.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.37 (0.24), residues: 1189 helix: -0.34 (0.22), residues: 593 sheet: -1.43 (0.65), residues: 71 loop : -1.42 (0.27), residues: 525 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG E 134 TYR 0.008 0.001 TYR C 215 PHE 0.010 0.001 PHE D 35 TRP 0.004 0.000 TRP C 274 HIS 0.002 0.001 HIS B 197 Details of bonding type rmsd covalent geometry : bond 0.00223 ( 8888) covalent geometry : angle 0.58589 (12098) SS BOND : bond 0.00939 ( 2) SS BOND : angle 1.15964 ( 4) hydrogen bonds : bond 0.03147 ( 377) hydrogen bonds : angle 4.43122 ( 1104) *********************** 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 135 residues out of total 990 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 120 time to evaluate : 0.214 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 47 MET cc_start: 0.8432 (mmm) cc_final: 0.8078 (mmm) REVERT: D 113 PHE cc_start: 0.8380 (m-80) cc_final: 0.8179 (m-80) REVERT: D 182 ILE cc_start: 0.9054 (tp) cc_final: 0.8833 (tp) REVERT: C 137 LYS cc_start: 0.9138 (mmpt) cc_final: 0.8883 (mmmt) outliers start: 15 outliers final: 10 residues processed: 130 average time/residue: 0.0661 time to fit residues: 13.1729 Evaluate side-chains 126 residues out of total 990 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 116 time to evaluate : 0.374 ------------------------------------------------------------------------------- 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 190 ASN Chi-restraints excluded: chain D residue 226 LEU Chi-restraints excluded: chain D residue 289 LEU Chi-restraints excluded: chain C residue 30 ILE Chi-restraints excluded: chain C residue 285 LEU Chi-restraints excluded: chain 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=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 117 random chunks: chunk 109 optimal weight: 1.9990 chunk 31 optimal weight: 3.9990 chunk 32 optimal weight: 5.9990 chunk 93 optimal weight: 10.0000 chunk 107 optimal weight: 0.0670 chunk 17 optimal weight: 3.9990 chunk 42 optimal weight: 3.9990 chunk 38 optimal weight: 3.9990 chunk 28 optimal weight: 8.9990 chunk 56 optimal weight: 5.9990 chunk 0 optimal weight: 10.0000 overall best weight: 2.8126 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 186 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 190 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 100 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 179 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 191 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 = 0.3405 r_free = 0.3405 target = 0.057265 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3114 r_free = 0.3114 target = 0.047516 restraints weight = 69422.971| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3143 r_free = 0.3143 target = 0.048478 restraints weight = 44521.040| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3166 r_free = 0.3166 target = 0.049186 restraints weight = 31908.031| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3178 r_free = 0.3178 target = 0.049583 restraints weight = 24626.967| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3191 r_free = 0.3191 target = 0.050011 restraints weight = 20533.281| |-----------------------------------------------------------------------------| r_work (final): 0.3187 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8181 moved from start: 0.3007 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.088 8890 Z= 0.311 Angle : 0.768 10.810 12102 Z= 0.402 Chirality : 0.045 0.172 1487 Planarity : 0.004 0.031 1554 Dihedral : 8.684 75.229 1347 Min Nonbonded Distance : 2.375 Molprobity Statistics. All-atom Clashscore : 16.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.97 % Favored : 94.03 % Rotamer: Outliers : 2.96 % Allowed : 16.00 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.75 (0.24), residues: 1189 helix: -0.54 (0.20), residues: 641 sheet: -1.88 (0.61), residues: 75 loop : -1.79 (0.29), residues: 473 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG C 99 TYR 0.021 0.003 TYR D 215 PHE 0.022 0.002 PHE C 163 TRP 0.010 0.002 TRP D 214 HIS 0.007 0.001 HIS E 117 Details of bonding type rmsd covalent geometry : bond 0.00646 ( 8888) covalent geometry : angle 0.76779 (12098) SS BOND : bond 0.00730 ( 2) SS BOND : angle 1.09468 ( 4) hydrogen bonds : bond 0.03807 ( 377) hydrogen bonds : angle 4.89845 ( 1104) *********************** 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 134 residues out of total 990 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 109 time to evaluate : 0.281 Fit side-chains revert: symmetry clash REVERT: D 20 MET cc_start: 0.8603 (ttt) cc_final: 0.8156 (ttt) REVERT: D 191 MET cc_start: 0.8554 (tpp) cc_final: 0.7683 (tpt) REVERT: C 20 MET cc_start: 0.8568 (tpp) cc_final: 0.8019 (tpt) REVERT: C 137 LYS cc_start: 0.9292 (mmpt) cc_final: 0.9067 (mmmt) outliers start: 25 outliers final: 15 residues processed: 128 average time/residue: 0.0580 time to fit residues: 11.4931 Evaluate side-chains 116 residues out of total 990 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 101 time to evaluate : 0.207 ------------------------------------------------------------------------------- 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 C residue 18 VAL Chi-restraints excluded: chain C residue 30 ILE Chi-restraints excluded: chain C residue 152 VAL Chi-restraints excluded: chain C residue 241 VAL Chi-restraints excluded: chain C residue 280 VAL Chi-restraints excluded: chain C residue 285 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 161 LEU Chi-restraints excluded: chain A residue 178 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 117 random chunks: chunk 36 optimal weight: 4.9990 chunk 30 optimal weight: 8.9990 chunk 37 optimal weight: 4.9990 chunk 0 optimal weight: 10.0000 chunk 109 optimal weight: 2.9990 chunk 55 optimal weight: 0.5980 chunk 49 optimal weight: 0.9980 chunk 85 optimal weight: 0.9980 chunk 34 optimal weight: 10.0000 chunk 76 optimal weight: 2.9990 chunk 52 optimal weight: 2.9990 overall best weight: 1.7184 ------------------------------------------------------------------------------- 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** D 190 ASN E 179 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3417 r_free = 0.3417 target = 0.057461 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3131 r_free = 0.3131 target = 0.047754 restraints weight = 68181.052| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3163 r_free = 0.3163 target = 0.048768 restraints weight = 43321.620| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3183 r_free = 0.3183 target = 0.049413 restraints weight = 30865.119| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3198 r_free = 0.3198 target = 0.049922 restraints weight = 24208.287| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3215 r_free = 0.3215 target = 0.050385 restraints weight = 19475.462| |-----------------------------------------------------------------------------| r_work (final): 0.3203 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8151 moved from start: 0.3192 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.074 8890 Z= 0.193 Angle : 0.658 9.756 12102 Z= 0.336 Chirality : 0.043 0.154 1487 Planarity : 0.003 0.026 1554 Dihedral : 8.202 68.458 1347 Min Nonbonded Distance : 2.412 Molprobity Statistics. All-atom Clashscore : 12.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.96 % Favored : 95.04 % Rotamer: Outliers : 2.84 % Allowed : 17.65 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.33 (0.25), residues: 1189 helix: -0.19 (0.21), residues: 632 sheet: -1.69 (0.61), residues: 71 loop : -1.60 (0.30), residues: 486 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 99 TYR 0.017 0.002 TYR D 52 PHE 0.017 0.001 PHE A 46 TRP 0.006 0.001 TRP C 274 HIS 0.003 0.001 HIS C 136 Details of bonding type rmsd covalent geometry : bond 0.00425 ( 8888) covalent geometry : angle 0.65770 (12098) SS BOND : bond 0.00162 ( 2) SS BOND : angle 0.69651 ( 4) hydrogen bonds : bond 0.03208 ( 377) hydrogen bonds : angle 4.55066 ( 1104) *********************** 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 137 residues out of total 990 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 113 time to evaluate : 0.354 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: D 20 MET cc_start: 0.8601 (ttt) cc_final: 0.7930 (ttt) REVERT: D 144 LYS cc_start: 0.7860 (mmtt) cc_final: 0.7575 (mmtt) REVERT: D 191 MET cc_start: 0.8685 (tpp) cc_final: 0.8473 (tpt) REVERT: C 20 MET cc_start: 0.8624 (tpp) cc_final: 0.8302 (tpt) REVERT: C 137 LYS cc_start: 0.9264 (mmpt) cc_final: 0.9029 (mmmt) REVERT: C 143 MET cc_start: 0.5678 (mmm) cc_final: 0.5092 (tpt) outliers start: 24 outliers final: 18 residues processed: 131 average time/residue: 0.0719 time to fit residues: 14.4510 Evaluate side-chains 124 residues out of total 990 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 106 time to evaluate : 0.210 ------------------------------------------------------------------------------- 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 190 ASN Chi-restraints excluded: chain D residue 226 LEU Chi-restraints excluded: chain D residue 265 TYR Chi-restraints excluded: chain C residue 165 VAL Chi-restraints excluded: chain C residue 285 LEU Chi-restraints excluded: chain C residue 290 THR Chi-restraints excluded: chain E residue 67 ASP Chi-restraints excluded: chain E residue 137 VAL Chi-restraints excluded: chain A residue 8 VAL Chi-restraints excluded: chain A residue 25 VAL Chi-restraints excluded: chain A residue 51 LEU Chi-restraints excluded: chain A residue 161 LEU Chi-restraints excluded: chain A residue 178 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 117 random chunks: chunk 93 optimal weight: 4.9990 chunk 39 optimal weight: 0.9980 chunk 15 optimal weight: 0.0980 chunk 51 optimal weight: 2.9990 chunk 32 optimal weight: 6.9990 chunk 23 optimal weight: 0.9990 chunk 28 optimal weight: 0.9980 chunk 57 optimal weight: 2.9990 chunk 112 optimal weight: 0.9980 chunk 19 optimal weight: 2.9990 chunk 86 optimal weight: 3.9990 overall best weight: 0.8182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 180 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 190 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 = 0.3444 r_free = 0.3444 target = 0.058542 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3156 r_free = 0.3156 target = 0.048612 restraints weight = 66843.971| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3187 r_free = 0.3187 target = 0.049636 restraints weight = 42620.973| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3209 r_free = 0.3209 target = 0.050366 restraints weight = 30403.994| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3221 r_free = 0.3221 target = 0.050749 restraints weight = 23604.366| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3238 r_free = 0.3238 target = 0.051259 restraints weight = 19595.184| |-----------------------------------------------------------------------------| r_work (final): 0.3237 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8111 moved from start: 0.3199 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 8890 Z= 0.129 Angle : 0.620 10.289 12102 Z= 0.312 Chirality : 0.041 0.150 1487 Planarity : 0.003 0.029 1554 Dihedral : 8.057 68.155 1347 Min Nonbonded Distance : 2.417 Molprobity Statistics. All-atom Clashscore : 10.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.71 % Favored : 95.29 % Rotamer: Outliers : 2.96 % Allowed : 18.84 % Favored : 78.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.15 (0.25), residues: 1189 helix: -0.00 (0.21), residues: 625 sheet: -2.02 (0.72), residues: 51 loop : -1.52 (0.29), residues: 513 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 99 TYR 0.015 0.001 TYR D 255 PHE 0.016 0.001 PHE A 46 TRP 0.003 0.001 TRP D 214 HIS 0.002 0.001 HIS A 197 Details of bonding type rmsd covalent geometry : bond 0.00296 ( 8888) covalent geometry : angle 0.62027 (12098) SS BOND : bond 0.00014 ( 2) SS BOND : angle 0.57738 ( 4) hydrogen bonds : bond 0.03075 ( 377) hydrogen bonds : angle 4.40599 ( 1104) *********************** 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 137 residues out of total 990 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 112 time to evaluate : 0.354 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: D 20 MET cc_start: 0.8491 (ttt) cc_final: 0.7859 (ttt) REVERT: D 144 LYS cc_start: 0.7861 (mmtt) cc_final: 0.7517 (mmtt) REVERT: C 137 LYS cc_start: 0.9211 (mmpt) cc_final: 0.8976 (mmmt) REVERT: C 143 MET cc_start: 0.5668 (mmm) cc_final: 0.5443 (tpp) REVERT: C 162 LEU cc_start: 0.8603 (tt) cc_final: 0.8347 (tp) outliers start: 25 outliers final: 19 residues processed: 128 average time/residue: 0.0658 time to fit residues: 12.9202 Evaluate side-chains 125 residues out of total 990 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 106 time to evaluate : 0.312 ------------------------------------------------------------------------------- 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 190 ASN Chi-restraints excluded: chain D residue 226 LEU Chi-restraints excluded: chain D residue 265 TYR Chi-restraints excluded: chain D residue 278 LEU Chi-restraints excluded: chain C residue 152 VAL Chi-restraints excluded: chain C residue 165 VAL Chi-restraints excluded: chain C residue 169 LEU Chi-restraints excluded: chain C residue 285 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 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 90 optimal weight: 0.9990 chunk 53 optimal weight: 0.8980 chunk 8 optimal weight: 3.9990 chunk 106 optimal weight: 5.9990 chunk 74 optimal weight: 0.6980 chunk 23 optimal weight: 0.9980 chunk 64 optimal weight: 2.9990 chunk 79 optimal weight: 2.9990 chunk 28 optimal weight: 1.9990 chunk 34 optimal weight: 7.9990 chunk 56 optimal weight: 0.5980 overall best weight: 0.8382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 180 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 190 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 179 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3443 r_free = 0.3443 target = 0.058497 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3158 r_free = 0.3158 target = 0.048680 restraints weight = 66484.800| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3190 r_free = 0.3190 target = 0.049717 restraints weight = 42346.760| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3207 r_free = 0.3207 target = 0.050321 restraints weight = 30191.102| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 22)----------------| | r_work = 0.3228 r_free = 0.3228 target = 0.050966 restraints weight = 23569.283| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3235 r_free = 0.3235 target = 0.051231 restraints weight = 18978.256| |-----------------------------------------------------------------------------| r_work (final): 0.3227 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8115 moved from start: 0.3215 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 8890 Z= 0.127 Angle : 0.639 10.989 12102 Z= 0.317 Chirality : 0.041 0.149 1487 Planarity : 0.003 0.032 1554 Dihedral : 7.931 68.438 1347 Min Nonbonded Distance : 2.420 Molprobity Statistics. All-atom Clashscore : 10.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.71 % Favored : 95.29 % Rotamer: Outliers : 2.73 % Allowed : 20.14 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.06 (0.25), residues: 1189 helix: 0.05 (0.21), residues: 624 sheet: -2.03 (0.72), residues: 51 loop : -1.43 (0.29), residues: 514 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 99 TYR 0.013 0.001 TYR D 52 PHE 0.015 0.001 PHE A 46 TRP 0.003 0.001 TRP C 214 HIS 0.003 0.001 HIS A 197 Details of bonding type rmsd covalent geometry : bond 0.00289 ( 8888) covalent geometry : angle 0.63824 (12098) SS BOND : bond 0.00270 ( 2) SS BOND : angle 1.25784 ( 4) hydrogen bonds : bond 0.02973 ( 377) hydrogen bonds : angle 4.31409 ( 1104) *********************** 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 133 residues out of total 990 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 110 time to evaluate : 0.358 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: D 144 LYS cc_start: 0.7798 (mmtt) cc_final: 0.7477 (mmtt) REVERT: C 20 MET cc_start: 0.8288 (mmm) cc_final: 0.7639 (tmm) REVERT: C 137 LYS cc_start: 0.9238 (mmpt) cc_final: 0.9002 (mmmt) REVERT: C 143 MET cc_start: 0.5794 (mmm) cc_final: 0.5336 (tpp) outliers start: 23 outliers final: 20 residues processed: 126 average time/residue: 0.0639 time to fit residues: 12.5895 Evaluate side-chains 126 residues out of total 990 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 106 time to evaluate : 0.343 ------------------------------------------------------------------------------- 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 265 TYR Chi-restraints excluded: chain D residue 278 LEU Chi-restraints excluded: chain C residue 18 VAL Chi-restraints excluded: chain C residue 152 VAL Chi-restraints excluded: chain C residue 165 VAL Chi-restraints excluded: chain C residue 169 LEU Chi-restraints excluded: chain C residue 285 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 117 random chunks: chunk 109 optimal weight: 0.4980 chunk 85 optimal weight: 3.9990 chunk 51 optimal weight: 0.0050 chunk 93 optimal weight: 5.9990 chunk 67 optimal weight: 0.9990 chunk 30 optimal weight: 0.0020 chunk 90 optimal weight: 5.9990 chunk 55 optimal weight: 1.9990 chunk 58 optimal weight: 3.9990 chunk 96 optimal weight: 3.9990 chunk 57 optimal weight: 0.8980 overall best weight: 0.4804 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 180 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 190 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 = 0.3468 r_free = 0.3468 target = 0.059379 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3190 r_free = 0.3190 target = 0.049699 restraints weight = 65283.555| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3222 r_free = 0.3222 target = 0.050748 restraints weight = 42396.540| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3246 r_free = 0.3246 target = 0.051499 restraints weight = 30077.972| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3260 r_free = 0.3260 target = 0.051995 restraints weight = 23030.942| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3272 r_free = 0.3272 target = 0.052404 restraints weight = 18691.567| |-----------------------------------------------------------------------------| r_work (final): 0.3268 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8069 moved from start: 0.3206 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= 0.111 Angle : 0.639 11.462 12102 Z= 0.314 Chirality : 0.041 0.187 1487 Planarity : 0.003 0.033 1554 Dihedral : 7.685 68.565 1347 Min Nonbonded Distance : 2.431 Molprobity Statistics. All-atom Clashscore : 9.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.71 % Favored : 95.29 % Rotamer: Outliers : 2.84 % Allowed : 20.85 % Favored : 76.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.93 (0.25), residues: 1189 helix: 0.12 (0.22), residues: 614 sheet: -1.90 (0.73), residues: 51 loop : -1.31 (0.28), residues: 524 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 43 TYR 0.011 0.001 TYR D 52 PHE 0.013 0.001 PHE A 87 TRP 0.003 0.000 TRP C 274 HIS 0.003 0.001 HIS A 197 Details of bonding type rmsd covalent geometry : bond 0.00251 ( 8888) covalent geometry : angle 0.63908 (12098) SS BOND : bond 0.00057 ( 2) SS BOND : angle 1.03448 ( 4) hydrogen bonds : bond 0.02950 ( 377) hydrogen bonds : angle 4.24158 ( 1104) *********************** 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 139 residues out of total 990 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 115 time to evaluate : 0.343 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: D 20 MET cc_start: 0.7740 (ttt) cc_final: 0.7505 (tmm) REVERT: D 144 LYS cc_start: 0.7755 (mmtt) cc_final: 0.7503 (mmtt) REVERT: C 137 LYS cc_start: 0.9232 (mmpt) cc_final: 0.8984 (mmmt) outliers start: 24 outliers final: 19 residues processed: 131 average time/residue: 0.0744 time to fit residues: 14.5732 Evaluate side-chains 125 residues out of total 990 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 106 time to evaluate : 0.341 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 190 ASN Chi-restraints excluded: chain D residue 226 LEU Chi-restraints excluded: chain D residue 265 TYR Chi-restraints excluded: chain D residue 278 LEU Chi-restraints excluded: chain C residue 18 VAL Chi-restraints excluded: chain C residue 152 VAL Chi-restraints excluded: chain C residue 165 VAL Chi-restraints excluded: chain C residue 169 LEU Chi-restraints excluded: chain C residue 190 ASN 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 113 optimal weight: 0.7980 chunk 107 optimal weight: 0.0170 chunk 43 optimal weight: 0.5980 chunk 33 optimal weight: 0.8980 chunk 76 optimal weight: 5.9990 chunk 102 optimal weight: 0.0770 chunk 0 optimal weight: 10.0000 chunk 90 optimal weight: 1.9990 chunk 71 optimal weight: 1.9990 chunk 54 optimal weight: 0.6980 chunk 14 optimal weight: 0.8980 overall best weight: 0.4376 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 180 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 190 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 = 0.3483 r_free = 0.3483 target = 0.059993 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3213 r_free = 0.3213 target = 0.050486 restraints weight = 65533.547| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3244 r_free = 0.3244 target = 0.051537 restraints weight = 42121.620| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3263 r_free = 0.3263 target = 0.052204 restraints weight = 30134.879| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3282 r_free = 0.3282 target = 0.052776 restraints weight = 23622.009| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3290 r_free = 0.3290 target = 0.053084 restraints weight = 19076.879| |-----------------------------------------------------------------------------| r_work (final): 0.3295 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8042 moved from start: 0.3178 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 8890 Z= 0.113 Angle : 0.690 12.073 12102 Z= 0.332 Chirality : 0.041 0.168 1487 Planarity : 0.003 0.034 1554 Dihedral : 7.489 69.380 1345 Min Nonbonded Distance : 2.434 Molprobity Statistics. All-atom Clashscore : 10.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.46 % Favored : 95.54 % Rotamer: Outliers : 2.25 % Allowed : 22.16 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.90 (0.25), residues: 1189 helix: 0.12 (0.22), residues: 616 sheet: -1.51 (0.60), residues: 71 loop : -1.27 (0.29), residues: 502 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 184 TYR 0.011 0.001 TYR C 215 PHE 0.016 0.001 PHE A 154 TRP 0.003 0.000 TRP C 274 HIS 0.003 0.001 HIS A 197 Details of bonding type rmsd covalent geometry : bond 0.00256 ( 8888) covalent geometry : angle 0.69034 (12098) SS BOND : bond 0.00061 ( 2) SS BOND : angle 0.91974 ( 4) hydrogen bonds : bond 0.02927 ( 377) hydrogen bonds : angle 4.15862 ( 1104) *********************** 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 134 residues out of total 990 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 115 time to evaluate : 0.209 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: D 20 MET cc_start: 0.7802 (ttt) cc_final: 0.7601 (tmm) REVERT: D 46 ASP cc_start: 0.8423 (p0) cc_final: 0.8178 (p0) REVERT: D 53 LEU cc_start: 0.8845 (OUTLIER) cc_final: 0.8487 (mt) REVERT: D 144 LYS cc_start: 0.7777 (mmtt) cc_final: 0.7541 (mmtt) REVERT: C 137 LYS cc_start: 0.9194 (mmpt) cc_final: 0.8944 (mmmt) outliers start: 19 outliers final: 16 residues processed: 128 average time/residue: 0.0731 time to fit residues: 14.4210 Evaluate side-chains 125 residues out of total 990 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 108 time to evaluate : 0.277 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 190 ASN Chi-restraints excluded: chain D residue 226 LEU Chi-restraints excluded: chain D residue 265 TYR Chi-restraints excluded: chain D residue 268 ILE Chi-restraints excluded: chain D residue 278 LEU Chi-restraints excluded: chain C residue 165 VAL Chi-restraints excluded: chain C residue 169 LEU Chi-restraints excluded: chain E residue 67 ASP Chi-restraints excluded: chain A residue 8 VAL Chi-restraints excluded: chain A residue 25 VAL Chi-restraints excluded: chain A residue 161 LEU Chi-restraints excluded: chain A residue 178 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 117 random chunks: chunk 106 optimal weight: 5.9990 chunk 9 optimal weight: 2.9990 chunk 48 optimal weight: 0.3980 chunk 30 optimal weight: 6.9990 chunk 94 optimal weight: 10.0000 chunk 56 optimal weight: 1.9990 chunk 70 optimal weight: 0.9980 chunk 103 optimal weight: 0.5980 chunk 19 optimal weight: 10.0000 chunk 20 optimal weight: 0.3980 chunk 11 optimal weight: 3.9990 overall best weight: 0.8782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 = 0.3468 r_free = 0.3468 target = 0.059328 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3188 r_free = 0.3188 target = 0.049615 restraints weight = 66484.074| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3218 r_free = 0.3218 target = 0.050643 restraints weight = 42755.994| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3242 r_free = 0.3242 target = 0.051388 restraints weight = 30595.647| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3255 r_free = 0.3255 target = 0.051849 restraints weight = 23564.039| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3270 r_free = 0.3270 target = 0.052303 restraints weight = 19261.732| |-----------------------------------------------------------------------------| r_work (final): 0.3263 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8079 moved from start: 0.3304 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= 0.131 Angle : 0.691 11.941 12102 Z= 0.338 Chirality : 0.043 0.228 1487 Planarity : 0.003 0.033 1554 Dihedral : 7.471 69.763 1345 Min Nonbonded Distance : 2.428 Molprobity Statistics. All-atom Clashscore : 11.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.54 % Favored : 95.46 % Rotamer: Outliers : 2.25 % Allowed : 21.92 % Favored : 75.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.95 (0.25), residues: 1189 helix: 0.07 (0.22), residues: 622 sheet: -1.50 (0.60), residues: 71 loop : -1.30 (0.29), residues: 496 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 147 TYR 0.010 0.001 TYR D 52 PHE 0.021 0.001 PHE A 87 TRP 0.004 0.001 TRP D 214 HIS 0.003 0.001 HIS A 197 Details of bonding type rmsd covalent geometry : bond 0.00301 ( 8888) covalent geometry : angle 0.69121 (12098) SS BOND : bond 0.00024 ( 2) SS BOND : angle 0.88195 ( 4) hydrogen bonds : bond 0.02979 ( 377) hydrogen bonds : angle 4.19465 ( 1104) ********************** 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 128 residues out of total 990 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 109 time to evaluate : 0.351 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 20 MET cc_start: 0.7892 (ttt) cc_final: 0.7630 (tmm) REVERT: D 46 ASP cc_start: 0.8496 (p0) cc_final: 0.8214 (p0) REVERT: D 53 LEU cc_start: 0.8869 (OUTLIER) cc_final: 0.8516 (mt) REVERT: C 137 LYS cc_start: 0.9273 (mmpt) cc_final: 0.9018 (mmmt) outliers start: 19 outliers final: 17 residues processed: 120 average time/residue: 0.0612 time to fit residues: 11.4987 Evaluate side-chains 125 residues out of total 990 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 107 time to evaluate : 0.348 ------------------------------------------------------------------------------- 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 265 TYR Chi-restraints excluded: chain D residue 268 ILE Chi-restraints excluded: chain D residue 278 LEU Chi-restraints excluded: chain C residue 18 VAL Chi-restraints excluded: chain C residue 165 VAL Chi-restraints excluded: chain C residue 169 LEU Chi-restraints excluded: chain E residue 67 ASP Chi-restraints excluded: chain A residue 8 VAL Chi-restraints excluded: chain A residue 25 VAL Chi-restraints excluded: chain A residue 161 LEU Chi-restraints excluded: chain A residue 178 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 117 random chunks: chunk 81 optimal weight: 4.9990 chunk 47 optimal weight: 0.7980 chunk 21 optimal weight: 0.0060 chunk 22 optimal weight: 0.8980 chunk 74 optimal weight: 0.9980 chunk 16 optimal weight: 0.3980 chunk 37 optimal weight: 2.9990 chunk 7 optimal weight: 0.6980 chunk 114 optimal weight: 0.9980 chunk 115 optimal weight: 0.0270 chunk 14 optimal weight: 0.7980 overall best weight: 0.3854 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 180 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 = 0.3500 r_free = 0.3500 target = 0.060550 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3230 r_free = 0.3230 target = 0.050908 restraints weight = 65674.484| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3261 r_free = 0.3261 target = 0.051949 restraints weight = 42674.660| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3280 r_free = 0.3280 target = 0.052610 restraints weight = 30635.647| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3297 r_free = 0.3297 target = 0.053198 restraints weight = 24003.322| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3308 r_free = 0.3308 target = 0.053574 restraints weight = 19190.805| |-----------------------------------------------------------------------------| r_work (final): 0.3305 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8035 moved from start: 0.3287 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= 0.113 Angle : 0.687 12.315 12102 Z= 0.330 Chirality : 0.042 0.173 1487 Planarity : 0.003 0.033 1554 Dihedral : 7.320 68.900 1345 Min Nonbonded Distance : 2.435 Molprobity Statistics. All-atom Clashscore : 10.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.37 % Favored : 95.63 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.78 (0.25), residues: 1189 helix: 0.23 (0.22), residues: 613 sheet: -1.47 (0.60), residues: 71 loop : -1.22 (0.29), residues: 505 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 147 TYR 0.009 0.001 TYR C 215 PHE 0.022 0.001 PHE A 87 TRP 0.003 0.000 TRP C 274 HIS 0.003 0.001 HIS A 197 Details of bonding type rmsd covalent geometry : bond 0.00254 ( 8888) covalent geometry : angle 0.68685 (12098) SS BOND : bond 0.00083 ( 2) SS BOND : angle 0.83997 ( 4) hydrogen bonds : bond 0.02869 ( 377) hydrogen bonds : angle 4.08799 ( 1104) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1388.51 seconds wall clock time: 24 minutes 47.58 seconds (1487.58 seconds total)