Starting phenix.real_space_refine on Tue Feb 3 23:19:23 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9odj_70364/02_2026/9odj_70364.cif Found real_map, /net/cci-nas-00/data/ceres_data/9odj_70364/02_2026/9odj_70364.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9odj_70364/02_2026/9odj_70364.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9odj_70364/02_2026/9odj_70364.map" model { file = "/net/cci-nas-00/data/ceres_data/9odj_70364/02_2026/9odj_70364.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9odj_70364/02_2026/9odj_70364.cif" } resolution = 3.0 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= 0.030 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians P 3 5.49 5 Mg 1 5.21 5 S 56 5.16 5 C 4841 2.51 5 N 1284 2.21 5 O 1373 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 8 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 7558 Number of models: 1 Model: "" Number of chains: 6 Chain: "B" Number of atoms: 2468 Number of conformers: 1 Conformer: "" Number of residues, atoms: 336, 2468 Classifications: {'peptide': 336} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 29} Link IDs: {'PTRANS': 5, 'TRANS': 330} Unresolved non-hydrogen bonds: 116 Unresolved non-hydrogen angles: 143 Unresolved non-hydrogen dihedrals: 89 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'ASP:plan': 8, 'GLN:plan1': 4, 'ARG:plan': 7, 'GLU:plan': 5, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 98 Chain: "C" Number of atoms: 355 Number of conformers: 1 Conformer: "" Number of residues, atoms: 53, 355 Classifications: {'peptide': 53} Incomplete info: {'truncation_to_alanine': 15} Link IDs: {'PTRANS': 4, 'TRANS': 48} Unresolved non-hydrogen bonds: 52 Unresolved non-hydrogen angles: 61 Unresolved non-hydrogen dihedrals: 43 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'GLN:plan1': 1, 'ARG:plan': 1, 'GLU:plan': 3, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 24 Chain: "D" Number of atoms: 2079 Number of conformers: 1 Conformer: "" Number of residues, atoms: 279, 2079 Classifications: {'peptide': 279} Incomplete info: {'truncation_to_alanine': 45} Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 268} Unresolved non-hydrogen bonds: 169 Unresolved non-hydrogen angles: 214 Unresolved non-hydrogen dihedrals: 147 Unresolved non-hydrogen chiralities: 17 Planarities with less than four sites: {'PHE:plan': 1, 'TYR:plan': 4, 'ARG:plan': 4, 'GLN:plan1': 1, 'ASP:plan': 1, 'HIS:plan': 1, 'TRP:plan': 1, 'GLU:plan': 1} Unresolved non-hydrogen planarities: 79 Chain: "A" Number of atoms: 2565 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 350, 2559 Classifications: {'peptide': 350} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 71} Link IDs: {'PTRANS': 4, 'TRANS': 345} Unresolved non-hydrogen bonds: 248 Unresolved non-hydrogen angles: 296 Unresolved non-hydrogen dihedrals: 200 Unresolved non-hydrogen chiralities: 7 Planarities with less than four sites: {'GLU:plan': 19, 'ASP:plan': 12, 'ARG:plan': 7, 'GLN:plan1': 2, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 158 Conformer: "B" Number of residues, atoms: 350, 2559 Classifications: {'peptide': 350} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 71} Link IDs: {'PTRANS': 4, 'TRANS': 345} Unresolved non-hydrogen bonds: 248 Unresolved non-hydrogen angles: 296 Unresolved non-hydrogen dihedrals: 200 Unresolved non-hydrogen chiralities: 7 Planarities with less than four sites: {'GLU:plan': 19, 'ASP:plan': 12, 'ARG:plan': 7, 'GLN:plan1': 2, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 158 bond proxies already assigned to first conformer: 2599 Chain: "D" Number of atoms: 58 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 58 Unusual residues: {'CLR': 1, 'EIG': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "A" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 33 Unusual residues: {' MG': 1, 'GTP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 2.45, per 1000 atoms: 0.32 Number of scatterers: 7558 At special positions: 0 Unit cell: (88.32, 99.84, 131.52, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 56 16.00 P 3 15.00 Mg 1 11.99 O 1373 8.00 N 1284 7.00 C 4841 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=1, symmetry=0 Simple disulfide: pdb=" SG CYS D 140 " - pdb=" SG CYS D 217 " 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: 0.66 Conformation dependent library (CDL) restraints added in 413.5 milliseconds 2022 Ramachandran restraints generated. 1011 Oldfield, 0 Emsley, 1011 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1932 Finding SS restraints... Secondary structure from input PDB file: 34 helices and 9 sheets defined 45.6% alpha, 17.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.30 Creating SS restraints... Processing helix chain 'B' and resid 5 through 22 Processing helix chain 'B' and resid 29 through 34 Processing helix chain 'C' and resid 10 through 21 Processing helix chain 'C' and resid 29 through 44 removed outlier: 3.593A pdb=" N LEU C 37 " --> pdb=" O ALA C 33 " (cutoff:3.500A) Processing helix chain 'C' and resid 55 through 59 removed outlier: 3.735A pdb=" N ASN C 59 " --> pdb=" O ALA C 56 " (cutoff:3.500A) Processing helix chain 'D' and resid 68 through 94 removed outlier: 3.913A pdb=" N TYR D 75 " --> pdb=" O ILE D 71 " (cutoff:3.500A) removed outlier: 4.552A pdb=" N SER D 76 " --> pdb=" O MET D 72 " (cutoff:3.500A) removed outlier: 3.804A pdb=" N VAL D 81 " --> pdb=" O ILE D 77 " (cutoff:3.500A) removed outlier: 4.260A pdb=" N GLY D 82 " --> pdb=" O VAL D 78 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N ILE D 93 " --> pdb=" O VAL D 89 " (cutoff:3.500A) removed outlier: 4.330A pdb=" N VAL D 94 " --> pdb=" O MET D 90 " (cutoff:3.500A) Processing helix chain 'D' and resid 101 through 118 Processing helix chain 'D' and resid 120 through 131 removed outlier: 3.604A pdb=" N GLN D 124 " --> pdb=" O THR D 120 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N TYR D 128 " --> pdb=" O GLN D 124 " (cutoff:3.500A) Processing helix chain 'D' and resid 148 through 157 removed outlier: 4.054A pdb=" N PHE D 152 " --> pdb=" O TYR D 148 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N THR D 153 " --> pdb=" O TYR D 149 " (cutoff:3.500A) removed outlier: 4.257A pdb=" N SER D 154 " --> pdb=" O ASN D 150 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N THR D 157 " --> pdb=" O THR D 153 " (cutoff:3.500A) Processing helix chain 'D' and resid 162 through 171 removed outlier: 3.605A pdb=" N TYR D 166 " --> pdb=" O SER D 162 " (cutoff:3.500A) Processing helix chain 'D' and resid 174 through 179 removed outlier: 3.698A pdb=" N PHE D 178 " --> pdb=" O LYS D 174 " (cutoff:3.500A) Processing helix chain 'D' and resid 180 through 195 Processing helix chain 'D' and resid 195 through 204 removed outlier: 3.731A pdb=" N GLY D 199 " --> pdb=" O SER D 195 " (cutoff:3.500A) Proline residue: D 201 - end of helix Processing helix chain 'D' and resid 224 through 241 removed outlier: 3.611A pdb=" N TRP D 228 " --> pdb=" O PRO D 224 " (cutoff:3.500A) removed outlier: 3.846A pdb=" N LEU D 232 " --> pdb=" O TRP D 228 " (cutoff:3.500A) removed outlier: 3.777A pdb=" N PHE D 239 " --> pdb=" O CYS D 235 " (cutoff:3.500A) Processing helix chain 'D' and resid 241 through 259 removed outlier: 4.009A pdb=" N TYR D 252 " --> pdb=" O ILE D 248 " (cutoff:3.500A) Processing helix chain 'D' and resid 268 through 303 removed outlier: 4.239A pdb=" N LEU D 275 " --> pdb=" O LYS D 271 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N ARG D 276 " --> pdb=" O ASP D 272 " (cutoff:3.500A) Proline residue: D 295 - end of helix Processing helix chain 'D' and resid 311 through 337 removed outlier: 4.029A pdb=" N ASN D 328 " --> pdb=" O LEU D 324 " (cutoff:3.500A) removed outlier: 5.081A pdb=" N SER D 329 " --> pdb=" O GLY D 325 " (cutoff:3.500A) removed outlier: 4.039A pdb=" N CYS D 330 " --> pdb=" O TYR D 326 " (cutoff:3.500A) Proline residue: D 333 - end of helix Processing helix chain 'A' and resid 9 through 31 Processing helix chain 'A' and resid 45 through 52 Processing helix chain 'A' and resid 69 through 91 removed outlier: 3.559A pdb=" N VAL A 73 " --> pdb=" O TYR A 69 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N ALA A 83 " --> pdb=" O GLN A 79 " (cutoff:3.500A) removed outlier: 4.253A pdb=" N GLY A 89 " --> pdb=" O ILE A 85 " (cutoff:3.500A) removed outlier: 4.256A pdb=" N ARG A 90 " --> pdb=" O ARG A 86 " (cutoff:3.500A) Processing helix chain 'A' and resid 97 through 111 removed outlier: 3.822A pdb=" N ALA A 101 " --> pdb=" O ASP A 97 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N VAL A 109 " --> pdb=" O ARG A 105 " (cutoff:3.500A) Processing helix chain 'A' and resid 112 through 114 No H-bonds generated for 'chain 'A' and resid 112 through 114' Processing helix chain 'A' and resid 120 through 133 removed outlier: 3.565A pdb=" N ASP A 133 " --> pdb=" O ARG A 129 " (cutoff:3.500A) Processing helix chain 'A' and resid 133 through 142 removed outlier: 3.694A pdb=" N GLN A 137 " --> pdb=" O ASP A 133 " (cutoff:3.500A) removed outlier: 3.971A pdb=" N ARG A 142 " --> pdb=" O ALA A 138 " (cutoff:3.500A) Processing helix chain 'A' and resid 143 through 146 Processing helix chain 'A' and resid 151 through 158 Processing helix chain 'A' and resid 158 through 163 Processing helix chain 'A' and resid 170 through 178 removed outlier: 3.777A pdb=" N ARG A 178 " --> pdb=" O VAL A 174 " (cutoff:3.500A) Processing helix chain 'A' and resid 207 through 216 removed outlier: 3.592A pdb=" N LYS A 210 " --> pdb=" O GLU A 207 " (cutoff:3.500A) removed outlier: 4.661A pdb=" N ILE A 212 " --> pdb=" O LYS A 209 " (cutoff:3.500A) removed outlier: 5.952A pdb=" N HIS A 213 " --> pdb=" O LYS A 210 " (cutoff:3.500A) Processing helix chain 'A' and resid 241 through 255 removed outlier: 3.611A pdb=" N GLU A 245 " --> pdb=" O ASN A 241 " (cutoff:3.500A) Processing helix chain 'A' and resid 270 through 278 Processing helix chain 'A' and resid 282 through 286 removed outlier: 4.073A pdb=" N ILE A 285 " --> pdb=" O PRO A 282 " (cutoff:3.500A) Processing helix chain 'A' and resid 295 through 309 removed outlier: 3.787A pdb=" N ALA A 301 " --> pdb=" O GLU A 297 " (cutoff:3.500A) Processing helix chain 'A' and resid 331 through 351 Processing sheet with id=AA1, first strand: chain 'B' and resid 47 through 51 removed outlier: 6.887A pdb=" N ILE B 338 " --> pdb=" O ARG B 48 " (cutoff:3.500A) removed outlier: 4.377A pdb=" N THR B 50 " --> pdb=" O LEU B 336 " (cutoff:3.500A) removed outlier: 6.300A pdb=" N LEU B 336 " --> pdb=" O THR B 50 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N CYS B 317 " --> pdb=" O GLY B 330 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 58 through 63 removed outlier: 3.749A pdb=" N ALA B 60 " --> pdb=" O ALA B 73 " (cutoff:3.500A) removed outlier: 3.763A pdb=" N LYS B 78 " --> pdb=" O SER B 74 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N HIS B 91 " --> pdb=" O ILE B 81 " (cutoff:3.500A) removed outlier: 6.942A pdb=" N ASP B 83 " --> pdb=" O LYS B 89 " (cutoff:3.500A) removed outlier: 6.200A pdb=" N LYS B 89 " --> pdb=" O ASP B 83 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 100 through 105 removed outlier: 6.846A pdb=" N GLY B 115 " --> pdb=" O MET B 101 " (cutoff:3.500A) removed outlier: 4.454A pdb=" N CYS B 103 " --> pdb=" O ALA B 113 " (cutoff:3.500A) removed outlier: 6.636A pdb=" N ALA B 113 " --> pdb=" O CYS B 103 " (cutoff:3.500A) removed outlier: 5.098A pdb=" N TYR B 105 " --> pdb=" O TYR B 111 " (cutoff:3.500A) removed outlier: 7.145A pdb=" N TYR B 111 " --> pdb=" O TYR B 105 " (cutoff:3.500A) removed outlier: 3.820A pdb=" N ARG B 137 " --> pdb=" O ILE B 123 " (cutoff:3.500A) removed outlier: 5.863A pdb=" N ASN B 125 " --> pdb=" O VAL B 135 " (cutoff:3.500A) removed outlier: 5.907A pdb=" N VAL B 135 " --> pdb=" O ASN B 125 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 146 through 151 removed outlier: 6.888A pdb=" N SER B 160 " --> pdb=" O SER B 147 " (cutoff:3.500A) removed outlier: 4.344A pdb=" N CYS B 149 " --> pdb=" O VAL B 158 " (cutoff:3.500A) removed outlier: 6.757A pdb=" N VAL B 158 " --> pdb=" O CYS B 149 " (cutoff:3.500A) removed outlier: 5.034A pdb=" N PHE B 151 " --> pdb=" O GLN B 156 " (cutoff:3.500A) removed outlier: 7.580A pdb=" N GLN B 156 " --> pdb=" O PHE B 151 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N ILE B 157 " --> pdb=" O TRP B 169 " (cutoff:3.500A) removed outlier: 4.175A pdb=" N THR B 165 " --> pdb=" O SER B 161 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N THR B 178 " --> pdb=" O LEU B 168 " (cutoff:3.500A) removed outlier: 5.763A pdb=" N ASP B 170 " --> pdb=" O GLN B 176 " (cutoff:3.500A) removed outlier: 5.939A pdb=" N GLN B 176 " --> pdb=" O ASP B 170 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 191 through 192 removed outlier: 6.727A pdb=" N ALA B 208 " --> pdb=" O THR B 221 " (cutoff:3.500A) removed outlier: 4.556A pdb=" N THR B 221 " --> pdb=" O ALA B 208 " (cutoff:3.500A) removed outlier: 6.737A pdb=" N LEU B 210 " --> pdb=" O ARG B 219 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 229 through 234 removed outlier: 7.007A pdb=" N GLY B 244 " --> pdb=" O ASN B 230 " (cutoff:3.500A) removed outlier: 4.408A pdb=" N ILE B 232 " --> pdb=" O ALA B 242 " (cutoff:3.500A) removed outlier: 6.705A pdb=" N ALA B 242 " --> pdb=" O ILE B 232 " (cutoff:3.500A) removed outlier: 5.096A pdb=" N PHE B 234 " --> pdb=" O ALA B 240 " (cutoff:3.500A) removed outlier: 7.279A pdb=" N ALA B 240 " --> pdb=" O PHE B 234 " (cutoff:3.500A) removed outlier: 6.529A pdb=" N CYS B 250 " --> pdb=" O THR B 263 " (cutoff:3.500A) removed outlier: 4.588A pdb=" N THR B 263 " --> pdb=" O CYS B 250 " (cutoff:3.500A) removed outlier: 6.801A pdb=" N LEU B 252 " --> pdb=" O LEU B 261 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N GLN B 259 " --> pdb=" O ASP B 254 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 273 through 278 removed outlier: 6.774A pdb=" N GLY B 288 " --> pdb=" O THR B 274 " (cutoff:3.500A) removed outlier: 4.771A pdb=" N VAL B 276 " --> pdb=" O LEU B 286 " (cutoff:3.500A) removed outlier: 6.870A pdb=" N LEU B 286 " --> pdb=" O VAL B 276 " (cutoff:3.500A) removed outlier: 4.726A pdb=" N PHE B 278 " --> pdb=" O LEU B 284 " (cutoff:3.500A) removed outlier: 6.845A pdb=" N LEU B 284 " --> pdb=" O PHE B 278 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N GLY B 306 " --> pdb=" O VAL B 296 " (cutoff:3.500A) removed outlier: 6.065A pdb=" N ASP B 298 " --> pdb=" O ARG B 304 " (cutoff:3.500A) removed outlier: 6.429A pdb=" N ARG B 304 " --> pdb=" O ASP B 298 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'D' and resid 206 through 211 Processing sheet with id=AA9, first strand: chain 'A' and resid 185 through 191 removed outlier: 6.276A pdb=" N VAL A 34 " --> pdb=" O LYS A 197 " (cutoff:3.500A) removed outlier: 7.763A pdb=" N PHE A 199 " --> pdb=" O VAL A 34 " (cutoff:3.500A) removed outlier: 6.981A pdb=" N LEU A 36 " --> pdb=" O PHE A 199 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N ALA A 220 " --> pdb=" O LYS A 35 " (cutoff:3.500A) removed outlier: 6.603A pdb=" N ILE A 221 " --> pdb=" O ILE A 265 " (cutoff:3.500A) removed outlier: 7.719A pdb=" N PHE A 267 " --> pdb=" O ILE A 221 " (cutoff:3.500A) removed outlier: 6.537A pdb=" N PHE A 223 " --> pdb=" O PHE A 267 " (cutoff:3.500A) removed outlier: 7.414A pdb=" N ASN A 269 " --> pdb=" O PHE A 223 " (cutoff:3.500A) removed outlier: 6.953A pdb=" N VAL A 225 " --> pdb=" O ASN A 269 " (cutoff:3.500A) removed outlier: 7.295A pdb=" N ILE A 264 " --> pdb=" O TYR A 320 " (cutoff:3.500A) removed outlier: 8.310A pdb=" N HIS A 322 " --> pdb=" O ILE A 264 " (cutoff:3.500A) removed outlier: 6.524A pdb=" N LEU A 266 " --> pdb=" O HIS A 322 " (cutoff:3.500A) 357 hydrogen bonds defined for protein. 1029 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: 1.25 Time building geometry restraints manager: 0.86 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.30: 1215 1.30 - 1.43: 2062 1.43 - 1.56: 4354 1.56 - 1.69: 5 1.69 - 1.82: 79 Bond restraints: 7715 Sorted by residual: bond pdb=" C08 EIG D 502 " pdb=" C10 EIG D 502 " ideal model delta sigma weight residual 1.541 1.314 0.227 2.00e-02 2.50e+03 1.29e+02 bond pdb=" N ILE D 198 " pdb=" CA ILE D 198 " ideal model delta sigma weight residual 1.456 1.493 -0.037 1.08e-02 8.57e+03 1.18e+01 bond pdb=" N LEU D 200 " pdb=" CA LEU D 200 " ideal model delta sigma weight residual 1.462 1.491 -0.029 8.50e-03 1.38e+04 1.18e+01 bond pdb=" N VAL B 133 " pdb=" CA VAL B 133 " ideal model delta sigma weight residual 1.457 1.492 -0.035 1.22e-02 6.72e+03 8.34e+00 bond pdb=" N THR B 128 " pdb=" CA THR B 128 " ideal model delta sigma weight residual 1.454 1.486 -0.033 1.18e-02 7.18e+03 7.60e+00 ... (remaining 7710 not shown) Histogram of bond angle deviations from ideal: 0.00 - 4.50: 10518 4.50 - 9.00: 25 9.00 - 13.49: 0 13.49 - 17.99: 1 17.99 - 22.49: 1 Bond angle restraints: 10545 Sorted by residual: angle pdb=" C12 EIG D 502 " pdb=" C08 EIG D 502 " pdb=" N01 EIG D 502 " ideal model delta sigma weight residual 113.08 90.59 22.49 3.00e+00 1.11e-01 5.62e+01 angle pdb=" C10 EIG D 502 " pdb=" C08 EIG D 502 " pdb=" N01 EIG D 502 " ideal model delta sigma weight residual 112.49 128.54 -16.05 3.00e+00 1.11e-01 2.86e+01 angle pdb=" N ILE D 198 " pdb=" CA ILE D 198 " pdb=" C ILE D 198 " ideal model delta sigma weight residual 113.42 108.66 4.76 1.17e+00 7.31e-01 1.66e+01 angle pdb=" CA VAL B 135 " pdb=" C VAL B 135 " pdb=" O VAL B 135 " ideal model delta sigma weight residual 121.59 118.05 3.54 1.03e+00 9.43e-01 1.18e+01 angle pdb=" N VAL D 143 " pdb=" CA VAL D 143 " pdb=" C VAL D 143 " ideal model delta sigma weight residual 111.62 108.92 2.70 7.90e-01 1.60e+00 1.17e+01 ... (remaining 10540 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 33.57: 4454 33.57 - 67.14: 148 67.14 - 100.71: 4 100.71 - 134.28: 2 134.28 - 167.85: 2 Dihedral angle restraints: 4610 sinusoidal: 1630 harmonic: 2980 Sorted by residual: dihedral pdb=" C5' GTP A 401 " pdb=" O5' GTP A 401 " pdb=" PA GTP A 401 " pdb=" O3A GTP A 401 " ideal model delta sinusoidal sigma weight residual 69.27 -122.88 -167.85 1 2.00e+01 2.50e-03 4.75e+01 dihedral pdb=" C8 GTP A 401 " pdb=" C1' GTP A 401 " pdb=" N9 GTP A 401 " pdb=" O4' GTP A 401 " ideal model delta sinusoidal sigma weight residual 104.59 -55.47 160.06 1 2.00e+01 2.50e-03 4.66e+01 dihedral pdb=" O2G GTP A 401 " pdb=" O3B GTP A 401 " pdb=" PG GTP A 401 " pdb=" PB GTP A 401 " ideal model delta sinusoidal sigma weight residual 177.30 46.76 130.54 1 2.00e+01 2.50e-03 3.96e+01 ... (remaining 4607 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.096: 1194 0.096 - 0.191: 63 0.191 - 0.287: 0 0.287 - 0.383: 1 0.383 - 0.478: 2 Chirality restraints: 1260 Sorted by residual: chirality pdb=" C10 EIG D 502 " pdb=" C08 EIG D 502 " pdb=" C13 EIG D 502 " pdb=" N02 EIG D 502 " both_signs ideal model delta sigma weight residual False 2.51 2.03 0.48 2.00e-01 2.50e+01 5.72e+00 chirality pdb=" C08 EIG D 502 " pdb=" C09 EIG D 502 " pdb=" C10 EIG D 502 " pdb=" C12 EIG D 502 " both_signs ideal model delta sigma weight residual False -2.77 -2.34 -0.43 2.00e-01 2.50e+01 4.62e+00 chirality pdb=" C14 EIG D 502 " pdb=" C13 EIG D 502 " pdb=" C15 EIG D 502 " pdb=" C17 EIG D 502 " both_signs ideal model delta sigma weight residual False -2.26 -2.62 0.36 2.00e-01 2.50e+01 3.29e+00 ... (remaining 1257 not shown) Planarity restraints: 1324 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG B 134 " -0.255 9.50e-02 1.11e+02 1.14e-01 8.06e+00 pdb=" NE ARG B 134 " 0.017 2.00e-02 2.50e+03 pdb=" CZ ARG B 134 " -0.001 2.00e-02 2.50e+03 pdb=" NH1 ARG B 134 " 0.004 2.00e-02 2.50e+03 pdb=" NH2 ARG B 134 " -0.008 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C MET D 243 " -0.042 5.00e-02 4.00e+02 6.39e-02 6.53e+00 pdb=" N PRO D 244 " 0.111 5.00e-02 4.00e+02 pdb=" CA PRO D 244 " -0.033 5.00e-02 4.00e+02 pdb=" CD PRO D 244 " -0.036 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ILE A 168 " -0.033 5.00e-02 4.00e+02 5.05e-02 4.09e+00 pdb=" N PRO A 169 " 0.087 5.00e-02 4.00e+02 pdb=" CA PRO A 169 " -0.026 5.00e-02 4.00e+02 pdb=" CD PRO A 169 " -0.028 5.00e-02 4.00e+02 ... (remaining 1321 not shown) Histogram of nonbonded interaction distances: 2.11 - 2.66: 105 2.66 - 3.22: 6808 3.22 - 3.78: 10688 3.78 - 4.34: 14733 4.34 - 4.90: 25644 Nonbonded interactions: 57978 Sorted by model distance: nonbonded pdb=" OG SER A 47 " pdb="MG MG A 402 " model vdw 2.105 2.170 nonbonded pdb=" ND2 ASN B 230 " pdb=" OD1 ASP B 246 " model vdw 2.198 3.120 nonbonded pdb=" OG SER B 281 " pdb=" OD2 ASP C 48 " model vdw 2.270 3.040 nonbonded pdb=" OG SER A 80 " pdb=" OD1 ASN A 149 " model vdw 2.287 3.040 nonbonded pdb=" N ASP B 186 " pdb=" OD1 ASP B 186 " model vdw 2.301 3.120 ... (remaining 57973 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 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. 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=0.50 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 3.990 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: 0.020 Extract box with map and model: 0.120 Check model and map are aligned: 0.020 Set scattering table: 0.010 Process input model: 8.930 Find NCS groups from input model: 0.190 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:6.500 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 19.800 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7882 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 : 0.005 0.227 7716 Z= 0.261 Angle : 0.765 22.490 10547 Z= 0.417 Chirality : 0.050 0.478 1260 Planarity : 0.005 0.114 1324 Dihedral : 16.348 167.854 2675 Min Nonbonded Distance : 2.105 Molprobity Statistics. All-atom Clashscore : 5.25 Ramachandran Plot: Outliers : 0.10 % Allowed : 2.87 % Favored : 97.03 % Rotamer: Outliers : 0.97 % Allowed : 20.89 % Favored : 78.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.35 % 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 are not related in a simple way. whole: -0.56 (0.26), residues: 1011 helix: 0.89 (0.26), residues: 441 sheet: 0.11 (0.39), residues: 165 loop : -2.04 (0.26), residues: 405 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 129 TYR 0.009 0.001 TYR D 149 PHE 0.015 0.001 PHE B 241 TRP 0.021 0.002 TRP B 82 HIS 0.005 0.001 HIS A 57 Details of bonding type rmsd covalent geometry : bond 0.00498 ( 7715) covalent geometry : angle 0.76431 (10545) SS BOND : bond 0.00337 ( 1) SS BOND : angle 1.50808 ( 2) hydrogen bonds : bond 0.14470 ( 357) hydrogen bonds : angle 5.06998 ( 1029) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2022 Ramachandran restraints generated. 1011 Oldfield, 0 Emsley, 1011 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2022 Ramachandran restraints generated. 1011 Oldfield, 0 Emsley, 1011 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 103 residues out of total 876 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 97 time to evaluate : 0.284 Fit side-chains REVERT: B 111 TYR cc_start: 0.9220 (m-80) cc_final: 0.8935 (m-80) REVERT: B 213 VAL cc_start: 0.9088 (m) cc_final: 0.8813 (t) REVERT: B 234 PHE cc_start: 0.9060 (OUTLIER) cc_final: 0.8045 (m-80) REVERT: A 318 GLU cc_start: 0.8415 (mm-30) cc_final: 0.8029 (mm-30) outliers start: 6 outliers final: 5 residues processed: 103 average time/residue: 0.4151 time to fit residues: 46.0348 Evaluate side-chains 93 residues out of total 876 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 87 time to evaluate : 0.292 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 70 LEU Chi-restraints excluded: chain B residue 186 ASP Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 290 ASP Chi-restraints excluded: chain B residue 294 CYS Chi-restraints excluded: chain B residue 318 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 49 optimal weight: 2.9990 chunk 97 optimal weight: 0.0070 chunk 53 optimal weight: 0.6980 chunk 5 optimal weight: 0.9980 chunk 33 optimal weight: 6.9990 chunk 65 optimal weight: 5.9990 chunk 62 optimal weight: 0.9990 chunk 51 optimal weight: 0.0370 chunk 38 optimal weight: 1.9990 chunk 61 optimal weight: 0.6980 chunk 45 optimal weight: 0.6980 overall best weight: 0.4276 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 36 ASN B 91 HIS A 79 GLN A 294 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3722 r_free = 0.3722 target = 0.146307 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3226 r_free = 0.3226 target = 0.104737 restraints weight = 11821.890| |-----------------------------------------------------------------------------| r_work (start): 0.3204 rms_B_bonded: 2.61 r_work: 0.3079 rms_B_bonded: 2.99 restraints_weight: 0.5000 r_work: 0.2940 rms_B_bonded: 4.89 restraints_weight: 0.2500 r_work (final): 0.2940 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2948 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2948 r_free = 0.2948 target_work(ls_wunit_k1) = 0.085 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2948 r_free = 0.2948 target_work(ls_wunit_k1) = 0.085 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2948 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8083 moved from start: 0.0913 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 7716 Z= 0.112 Angle : 0.538 7.925 10547 Z= 0.276 Chirality : 0.042 0.147 1260 Planarity : 0.004 0.049 1324 Dihedral : 9.912 158.657 1233 Min Nonbonded Distance : 2.126 Molprobity Statistics. All-atom Clashscore : 3.21 Ramachandran Plot: Outliers : 0.10 % Allowed : 2.57 % Favored : 97.33 % Rotamer: Outliers : 4.46 % Allowed : 18.11 % Favored : 77.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.35 % 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 are not related in a simple way. whole: -0.03 (0.26), residues: 1011 helix: 1.41 (0.26), residues: 442 sheet: 0.30 (0.39), residues: 173 loop : -1.89 (0.26), residues: 396 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 176 TYR 0.008 0.001 TYR A 154 PHE 0.014 0.001 PHE B 241 TRP 0.011 0.001 TRP D 293 HIS 0.005 0.001 HIS A 57 Details of bonding type rmsd covalent geometry : bond 0.00234 ( 7715) covalent geometry : angle 0.53781 (10545) SS BOND : bond 0.00115 ( 1) SS BOND : angle 0.94581 ( 2) hydrogen bonds : bond 0.05006 ( 357) hydrogen bonds : angle 4.08506 ( 1029) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2022 Ramachandran restraints generated. 1011 Oldfield, 0 Emsley, 1011 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2022 Ramachandran restraints generated. 1011 Oldfield, 0 Emsley, 1011 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 121 residues out of total 876 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 90 time to evaluate : 0.296 Fit side-chains REVERT: B 111 TYR cc_start: 0.9270 (m-80) cc_final: 0.9055 (m-80) REVERT: B 118 ASP cc_start: 0.8147 (OUTLIER) cc_final: 0.7539 (p0) REVERT: B 213 VAL cc_start: 0.9215 (m) cc_final: 0.8855 (t) REVERT: B 234 PHE cc_start: 0.9168 (OUTLIER) cc_final: 0.8207 (m-80) REVERT: B 258 ASP cc_start: 0.8383 (t0) cc_final: 0.7985 (t0) REVERT: B 325 MET cc_start: 0.8661 (OUTLIER) cc_final: 0.8385 (mmm) REVERT: D 112 LEU cc_start: 0.6576 (OUTLIER) cc_final: 0.6332 (tp) REVERT: D 263 ARG cc_start: 0.7948 (OUTLIER) cc_final: 0.6991 (mtm180) REVERT: D 264 MET cc_start: 0.7872 (mpp) cc_final: 0.7631 (pmm) REVERT: A 82 ILE cc_start: 0.6759 (OUTLIER) cc_final: 0.6362 (mp) REVERT: A 247 MET cc_start: 0.8160 (mtp) cc_final: 0.7890 (mtm) outliers start: 31 outliers final: 11 residues processed: 109 average time/residue: 0.3892 time to fit residues: 46.0668 Evaluate side-chains 102 residues out of total 876 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 85 time to evaluate : 0.288 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 70 LEU Chi-restraints excluded: chain B residue 118 ASP Chi-restraints excluded: chain B residue 173 THR Chi-restraints excluded: chain B residue 189 SER Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 263 THR Chi-restraints excluded: chain B residue 276 VAL Chi-restraints excluded: chain B residue 318 LEU Chi-restraints excluded: chain B residue 322 ASP Chi-restraints excluded: chain B residue 325 MET Chi-restraints excluded: chain C residue 25 ILE Chi-restraints excluded: chain D residue 112 LEU Chi-restraints excluded: chain D residue 194 LEU Chi-restraints excluded: chain D residue 263 ARG Chi-restraints excluded: chain D residue 291 VAL Chi-restraints excluded: chain A residue 82 ILE Chi-restraints excluded: chain A residue 168 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 13 optimal weight: 3.9990 chunk 10 optimal weight: 1.9990 chunk 43 optimal weight: 0.4980 chunk 53 optimal weight: 2.9990 chunk 68 optimal weight: 0.8980 chunk 39 optimal weight: 0.9990 chunk 83 optimal weight: 2.9990 chunk 27 optimal weight: 1.9990 chunk 63 optimal weight: 2.9990 chunk 59 optimal weight: 2.9990 chunk 22 optimal weight: 0.8980 overall best weight: 1.0584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 36 ASN B 110 ASN A 79 GLN A 294 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3686 r_free = 0.3686 target = 0.143099 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3151 r_free = 0.3151 target = 0.099231 restraints weight = 18641.720| |-----------------------------------------------------------------------------| r_work (start): 0.3126 rms_B_bonded: 3.23 r_work: 0.2986 rms_B_bonded: 3.47 restraints_weight: 0.5000 r_work (final): 0.2986 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2992 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2992 r_free = 0.2992 target_work(ls_wunit_k1) = 0.088 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2992 r_free = 0.2992 target_work(ls_wunit_k1) = 0.088 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2992 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8074 moved from start: 0.1084 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 7716 Z= 0.170 Angle : 0.589 10.829 10547 Z= 0.298 Chirality : 0.044 0.143 1260 Planarity : 0.004 0.049 1324 Dihedral : 9.754 162.357 1228 Min Nonbonded Distance : 2.087 Molprobity Statistics. All-atom Clashscore : 2.87 Ramachandran Plot: Outliers : 0.10 % Allowed : 3.27 % Favored : 96.63 % Rotamer: Outliers : 5.01 % Allowed : 18.25 % Favored : 76.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.35 % 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 are not related in a simple way. whole: -0.00 (0.26), residues: 1011 helix: 1.40 (0.26), residues: 447 sheet: 0.66 (0.40), residues: 163 loop : -2.00 (0.26), residues: 401 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 129 TYR 0.010 0.001 TYR A 154 PHE 0.017 0.002 PHE A 196 TRP 0.013 0.001 TRP B 82 HIS 0.005 0.001 HIS A 57 Details of bonding type rmsd covalent geometry : bond 0.00412 ( 7715) covalent geometry : angle 0.58884 (10545) SS BOND : bond 0.00068 ( 1) SS BOND : angle 1.11916 ( 2) hydrogen bonds : bond 0.05889 ( 357) hydrogen bonds : angle 4.11068 ( 1029) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2022 Ramachandran restraints generated. 1011 Oldfield, 0 Emsley, 1011 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2022 Ramachandran restraints generated. 1011 Oldfield, 0 Emsley, 1011 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 126 residues out of total 876 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 91 time to evaluate : 0.299 Fit side-chains REVERT: B 111 TYR cc_start: 0.9232 (m-80) cc_final: 0.8998 (m-80) REVERT: B 118 ASP cc_start: 0.8158 (OUTLIER) cc_final: 0.7561 (p0) REVERT: B 213 VAL cc_start: 0.9166 (m) cc_final: 0.8813 (t) REVERT: B 234 PHE cc_start: 0.9187 (OUTLIER) cc_final: 0.8323 (m-80) REVERT: B 258 ASP cc_start: 0.8294 (t0) cc_final: 0.8050 (t70) REVERT: D 112 LEU cc_start: 0.6487 (OUTLIER) cc_final: 0.6238 (tp) REVERT: D 196 SER cc_start: 0.7252 (p) cc_final: 0.6777 (m) REVERT: D 257 LEU cc_start: 0.7605 (OUTLIER) cc_final: 0.7293 (mp) REVERT: D 263 ARG cc_start: 0.7930 (OUTLIER) cc_final: 0.7020 (mtm180) REVERT: A 82 ILE cc_start: 0.6901 (OUTLIER) cc_final: 0.6518 (mp) REVERT: A 247 MET cc_start: 0.8100 (mtp) cc_final: 0.7810 (mtm) outliers start: 35 outliers final: 12 residues processed: 114 average time/residue: 0.3762 time to fit residues: 46.6884 Evaluate side-chains 107 residues out of total 876 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 89 time to evaluate : 0.298 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 70 LEU Chi-restraints excluded: chain B residue 118 ASP Chi-restraints excluded: chain B residue 173 THR Chi-restraints excluded: chain B residue 189 SER Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 263 THR Chi-restraints excluded: chain B residue 276 VAL Chi-restraints excluded: chain B residue 318 LEU Chi-restraints excluded: chain B residue 322 ASP Chi-restraints excluded: chain C residue 25 ILE Chi-restraints excluded: chain D residue 112 LEU Chi-restraints excluded: chain D residue 194 LEU Chi-restraints excluded: chain D residue 257 LEU Chi-restraints excluded: chain D residue 263 ARG Chi-restraints excluded: chain D residue 291 VAL Chi-restraints excluded: chain A residue 82 ILE Chi-restraints excluded: chain A residue 107 LEU Chi-restraints excluded: chain A residue 168 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 58 optimal weight: 0.6980 chunk 72 optimal weight: 0.6980 chunk 40 optimal weight: 1.9990 chunk 56 optimal weight: 0.7980 chunk 32 optimal weight: 0.6980 chunk 99 optimal weight: 0.9990 chunk 2 optimal weight: 0.8980 chunk 28 optimal weight: 1.9990 chunk 73 optimal weight: 1.9990 chunk 52 optimal weight: 0.9980 chunk 96 optimal weight: 0.4980 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 36 ASN ** D 150 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 79 GLN A 294 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3710 r_free = 0.3710 target = 0.145190 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3183 r_free = 0.3183 target = 0.101451 restraints weight = 22208.692| |-----------------------------------------------------------------------------| r_work (start): 0.3157 rms_B_bonded: 3.69 r_work: 0.3003 rms_B_bonded: 3.74 restraints_weight: 0.5000 r_work (final): 0.3003 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3006 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3006 r_free = 0.3006 target_work(ls_wunit_k1) = 0.089 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3006 r_free = 0.3006 target_work(ls_wunit_k1) = 0.089 | | occupancies: max = 1.00 min = 0.48 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3006 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8052 moved from start: 0.1304 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 7716 Z= 0.123 Angle : 0.526 6.295 10547 Z= 0.268 Chirality : 0.042 0.149 1260 Planarity : 0.003 0.047 1324 Dihedral : 9.226 163.822 1228 Min Nonbonded Distance : 2.109 Molprobity Statistics. All-atom Clashscore : 2.93 Ramachandran Plot: Outliers : 0.10 % Allowed : 2.67 % Favored : 97.23 % Rotamer: Outliers : 4.32 % Allowed : 19.36 % Favored : 76.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.35 % 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 are not related in a simple way. whole: 0.20 (0.27), residues: 1011 helix: 1.56 (0.26), residues: 448 sheet: 0.93 (0.41), residues: 157 loop : -1.93 (0.26), residues: 406 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 86 TYR 0.007 0.001 TYR D 148 PHE 0.014 0.001 PHE B 241 TRP 0.011 0.001 TRP B 82 HIS 0.004 0.001 HIS A 57 Details of bonding type rmsd covalent geometry : bond 0.00282 ( 7715) covalent geometry : angle 0.52593 (10545) SS BOND : bond 0.00020 ( 1) SS BOND : angle 1.16724 ( 2) hydrogen bonds : bond 0.04889 ( 357) hydrogen bonds : angle 3.91249 ( 1029) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2022 Ramachandran restraints generated. 1011 Oldfield, 0 Emsley, 1011 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2022 Ramachandran restraints generated. 1011 Oldfield, 0 Emsley, 1011 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 120 residues out of total 876 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 90 time to evaluate : 0.235 Fit side-chains REVERT: B 111 TYR cc_start: 0.9237 (m-80) cc_final: 0.9019 (m-80) REVERT: B 118 ASP cc_start: 0.8056 (OUTLIER) cc_final: 0.7496 (p0) REVERT: B 155 ASN cc_start: 0.8532 (t0) cc_final: 0.8307 (t0) REVERT: B 213 VAL cc_start: 0.9120 (m) cc_final: 0.8825 (t) REVERT: B 234 PHE cc_start: 0.9206 (OUTLIER) cc_final: 0.8353 (m-80) REVERT: B 258 ASP cc_start: 0.8260 (t0) cc_final: 0.8038 (t70) REVERT: D 112 LEU cc_start: 0.6450 (OUTLIER) cc_final: 0.6203 (tp) REVERT: D 257 LEU cc_start: 0.7494 (OUTLIER) cc_final: 0.7188 (mp) REVERT: D 263 ARG cc_start: 0.7949 (OUTLIER) cc_final: 0.6928 (mtm180) REVERT: A 82 ILE cc_start: 0.6774 (OUTLIER) cc_final: 0.6328 (mp) REVERT: A 247 MET cc_start: 0.8058 (mtp) cc_final: 0.7769 (mtm) outliers start: 30 outliers final: 14 residues processed: 112 average time/residue: 0.3346 time to fit residues: 40.7197 Evaluate side-chains 104 residues out of total 876 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 84 time to evaluate : 0.220 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 70 LEU Chi-restraints excluded: chain B residue 118 ASP Chi-restraints excluded: chain B residue 173 THR Chi-restraints excluded: chain B residue 189 SER Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 263 THR Chi-restraints excluded: chain B residue 276 VAL Chi-restraints excluded: chain B residue 318 LEU Chi-restraints excluded: chain B residue 322 ASP Chi-restraints excluded: chain C residue 25 ILE Chi-restraints excluded: chain D residue 112 LEU Chi-restraints excluded: chain D residue 194 LEU Chi-restraints excluded: chain D residue 257 LEU Chi-restraints excluded: chain D residue 263 ARG Chi-restraints excluded: chain D residue 291 VAL Chi-restraints excluded: chain D residue 302 ILE Chi-restraints excluded: chain A residue 82 ILE Chi-restraints excluded: chain A residue 107 LEU Chi-restraints excluded: chain A residue 108 PHE Chi-restraints excluded: chain A residue 168 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 93 optimal weight: 1.9990 chunk 90 optimal weight: 0.0980 chunk 98 optimal weight: 0.9980 chunk 70 optimal weight: 0.9980 chunk 48 optimal weight: 1.9990 chunk 16 optimal weight: 1.9990 chunk 84 optimal weight: 2.9990 chunk 27 optimal weight: 1.9990 chunk 71 optimal weight: 0.4980 chunk 59 optimal weight: 2.9990 chunk 68 optimal weight: 2.9990 overall best weight: 0.9182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 36 ASN A 294 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3697 r_free = 0.3697 target = 0.144025 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3164 r_free = 0.3164 target = 0.100361 restraints weight = 22190.343| |-----------------------------------------------------------------------------| r_work (start): 0.3137 rms_B_bonded: 3.82 r_work: 0.2982 rms_B_bonded: 3.76 restraints_weight: 0.5000 r_work (final): 0.2982 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2969 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2969 r_free = 0.2969 target_work(ls_wunit_k1) = 0.087 | | occupancies: max = 1.00 min = 0.48 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2969 r_free = 0.2969 target_work(ls_wunit_k1) = 0.087 | | occupancies: max = 1.00 min = 0.47 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2969 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8065 moved from start: 0.1336 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 7716 Z= 0.150 Angle : 0.557 8.898 10547 Z= 0.282 Chirality : 0.044 0.151 1260 Planarity : 0.003 0.050 1324 Dihedral : 9.216 166.039 1228 Min Nonbonded Distance : 2.093 Molprobity Statistics. All-atom Clashscore : 3.21 Ramachandran Plot: Outliers : 0.10 % Allowed : 3.56 % Favored : 96.34 % Rotamer: Outliers : 4.60 % Allowed : 19.36 % Favored : 76.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.35 % 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 are not related in a simple way. whole: 0.20 (0.27), residues: 1011 helix: 1.57 (0.26), residues: 448 sheet: 0.90 (0.41), residues: 157 loop : -1.93 (0.26), residues: 406 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 129 TYR 0.008 0.001 TYR A 154 PHE 0.016 0.001 PHE A 196 TRP 0.012 0.001 TRP B 82 HIS 0.005 0.001 HIS A 57 Details of bonding type rmsd covalent geometry : bond 0.00360 ( 7715) covalent geometry : angle 0.55684 (10545) SS BOND : bond 0.00315 ( 1) SS BOND : angle 1.22811 ( 2) hydrogen bonds : bond 0.05399 ( 357) hydrogen bonds : angle 3.96583 ( 1029) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2022 Ramachandran restraints generated. 1011 Oldfield, 0 Emsley, 1011 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2022 Ramachandran restraints generated. 1011 Oldfield, 0 Emsley, 1011 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 118 residues out of total 876 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 86 time to evaluate : 0.215 Fit side-chains REVERT: B 111 TYR cc_start: 0.9256 (m-80) cc_final: 0.9034 (m-80) REVERT: B 118 ASP cc_start: 0.8165 (OUTLIER) cc_final: 0.7584 (p0) REVERT: B 155 ASN cc_start: 0.8532 (t0) cc_final: 0.8298 (t0) REVERT: B 213 VAL cc_start: 0.9122 (m) cc_final: 0.8813 (t) REVERT: B 234 PHE cc_start: 0.9233 (OUTLIER) cc_final: 0.8436 (m-80) REVERT: B 258 ASP cc_start: 0.8278 (t0) cc_final: 0.8055 (t70) REVERT: D 112 LEU cc_start: 0.6494 (OUTLIER) cc_final: 0.6257 (tp) REVERT: D 257 LEU cc_start: 0.7551 (OUTLIER) cc_final: 0.7286 (mp) REVERT: D 263 ARG cc_start: 0.7914 (OUTLIER) cc_final: 0.6971 (mtm180) REVERT: D 264 MET cc_start: 0.7769 (mpp) cc_final: 0.7511 (pmm) REVERT: A 82 ILE cc_start: 0.6859 (OUTLIER) cc_final: 0.6423 (mp) REVERT: A 247 MET cc_start: 0.8072 (mtp) cc_final: 0.7780 (mtm) outliers start: 32 outliers final: 15 residues processed: 106 average time/residue: 0.3616 time to fit residues: 41.3976 Evaluate side-chains 104 residues out of total 876 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 83 time to evaluate : 0.315 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 33 ILE Chi-restraints excluded: chain B residue 70 LEU Chi-restraints excluded: chain B residue 118 ASP Chi-restraints excluded: chain B residue 173 THR Chi-restraints excluded: chain B residue 189 SER Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 263 THR Chi-restraints excluded: chain B residue 276 VAL Chi-restraints excluded: chain B residue 322 ASP Chi-restraints excluded: chain C residue 16 VAL Chi-restraints excluded: chain C residue 25 ILE Chi-restraints excluded: chain D residue 112 LEU Chi-restraints excluded: chain D residue 194 LEU Chi-restraints excluded: chain D residue 257 LEU Chi-restraints excluded: chain D residue 263 ARG Chi-restraints excluded: chain D residue 291 VAL Chi-restraints excluded: chain D residue 302 ILE Chi-restraints excluded: chain A residue 82 ILE Chi-restraints excluded: chain A residue 107 LEU Chi-restraints excluded: chain A residue 108 PHE Chi-restraints excluded: chain A residue 168 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 68 optimal weight: 1.9990 chunk 92 optimal weight: 0.8980 chunk 98 optimal weight: 0.6980 chunk 73 optimal weight: 1.9990 chunk 17 optimal weight: 2.9990 chunk 61 optimal weight: 2.9990 chunk 81 optimal weight: 1.9990 chunk 85 optimal weight: 2.9990 chunk 15 optimal weight: 0.7980 chunk 51 optimal weight: 0.9990 chunk 49 optimal weight: 0.9980 overall best weight: 0.8782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 36 ASN A 171 GLN A 294 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3698 r_free = 0.3698 target = 0.144115 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3190 r_free = 0.3190 target = 0.102099 restraints weight = 12266.725| |-----------------------------------------------------------------------------| r_work (start): 0.3169 rms_B_bonded: 2.64 r_work: 0.3042 rms_B_bonded: 3.00 restraints_weight: 0.5000 r_work: 0.2903 rms_B_bonded: 4.88 restraints_weight: 0.2500 r_work (final): 0.2903 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2912 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2912 r_free = 0.2912 target_work(ls_wunit_k1) = 0.083 | | occupancies: max = 1.00 min = 0.47 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2912 r_free = 0.2912 target_work(ls_wunit_k1) = 0.083 | | occupancies: max = 1.00 min = 0.46 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2912 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8125 moved from start: 0.1407 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 7716 Z= 0.144 Angle : 0.552 11.342 10547 Z= 0.278 Chirality : 0.043 0.151 1260 Planarity : 0.003 0.049 1324 Dihedral : 9.029 167.389 1226 Min Nonbonded Distance : 2.100 Molprobity Statistics. All-atom Clashscore : 3.21 Ramachandran Plot: Outliers : 0.10 % Allowed : 3.07 % Favored : 96.83 % Rotamer: Outliers : 5.15 % Allowed : 18.66 % Favored : 76.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.35 % 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 are not related in a simple way. whole: 0.26 (0.27), residues: 1011 helix: 1.63 (0.26), residues: 447 sheet: 0.93 (0.41), residues: 157 loop : -1.90 (0.26), residues: 407 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 129 TYR 0.008 0.001 TYR A 154 PHE 0.015 0.001 PHE A 196 TRP 0.012 0.001 TRP B 82 HIS 0.004 0.001 HIS A 57 Details of bonding type rmsd covalent geometry : bond 0.00344 ( 7715) covalent geometry : angle 0.55153 (10545) SS BOND : bond 0.00270 ( 1) SS BOND : angle 1.20688 ( 2) hydrogen bonds : bond 0.05240 ( 357) hydrogen bonds : angle 3.93575 ( 1029) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2022 Ramachandran restraints generated. 1011 Oldfield, 0 Emsley, 1011 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2022 Ramachandran restraints generated. 1011 Oldfield, 0 Emsley, 1011 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 121 residues out of total 876 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 85 time to evaluate : 0.326 Fit side-chains REVERT: B 111 TYR cc_start: 0.9309 (m-80) cc_final: 0.9093 (m-80) REVERT: B 118 ASP cc_start: 0.8250 (OUTLIER) cc_final: 0.7690 (p0) REVERT: B 155 ASN cc_start: 0.8602 (t0) cc_final: 0.8360 (t0) REVERT: B 213 VAL cc_start: 0.9176 (m) cc_final: 0.8850 (t) REVERT: B 234 PHE cc_start: 0.9254 (OUTLIER) cc_final: 0.8456 (m-80) REVERT: B 258 ASP cc_start: 0.8371 (t0) cc_final: 0.8147 (t70) REVERT: B 325 MET cc_start: 0.8808 (OUTLIER) cc_final: 0.8426 (mmm) REVERT: D 112 LEU cc_start: 0.6606 (OUTLIER) cc_final: 0.6352 (tp) REVERT: D 257 LEU cc_start: 0.7577 (OUTLIER) cc_final: 0.7296 (mp) REVERT: D 263 ARG cc_start: 0.7935 (OUTLIER) cc_final: 0.7127 (mtm180) REVERT: D 264 MET cc_start: 0.7836 (mpp) cc_final: 0.7576 (pmm) REVERT: A 43 GLU cc_start: 0.7630 (mm-30) cc_final: 0.7241 (mm-30) REVERT: A 82 ILE cc_start: 0.6888 (OUTLIER) cc_final: 0.6475 (mp) REVERT: A 247 MET cc_start: 0.8161 (mtp) cc_final: 0.7866 (mtm) outliers start: 36 outliers final: 16 residues processed: 110 average time/residue: 0.3463 time to fit residues: 41.1771 Evaluate side-chains 107 residues out of total 876 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 84 time to evaluate : 0.275 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 70 LEU Chi-restraints excluded: chain B residue 118 ASP Chi-restraints excluded: chain B residue 173 THR Chi-restraints excluded: chain B residue 189 SER Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 276 VAL Chi-restraints excluded: chain B residue 318 LEU Chi-restraints excluded: chain B residue 322 ASP Chi-restraints excluded: chain B residue 325 MET Chi-restraints excluded: chain C residue 16 VAL Chi-restraints excluded: chain C residue 25 ILE Chi-restraints excluded: chain D residue 112 LEU Chi-restraints excluded: chain D residue 147 ASP Chi-restraints excluded: chain D residue 194 LEU Chi-restraints excluded: chain D residue 257 LEU Chi-restraints excluded: chain D residue 263 ARG Chi-restraints excluded: chain D residue 291 VAL Chi-restraints excluded: chain D residue 302 ILE Chi-restraints excluded: chain A residue 82 ILE Chi-restraints excluded: chain A residue 107 LEU Chi-restraints excluded: chain A residue 108 PHE Chi-restraints excluded: chain A residue 168 ILE Chi-restraints excluded: chain A residue 243 MET Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 80 optimal weight: 0.9990 chunk 88 optimal weight: 1.9990 chunk 74 optimal weight: 4.9990 chunk 55 optimal weight: 0.5980 chunk 45 optimal weight: 3.9990 chunk 19 optimal weight: 0.9990 chunk 99 optimal weight: 0.8980 chunk 68 optimal weight: 0.8980 chunk 75 optimal weight: 3.9990 chunk 0 optimal weight: 20.0000 chunk 95 optimal weight: 0.9990 overall best weight: 0.8784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 36 ASN A 171 GLN A 294 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3698 r_free = 0.3698 target = 0.144103 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3193 r_free = 0.3193 target = 0.102321 restraints weight = 11823.945| |-----------------------------------------------------------------------------| r_work (start): 0.3169 rms_B_bonded: 2.59 r_work: 0.3043 rms_B_bonded: 2.96 restraints_weight: 0.5000 r_work: 0.2905 rms_B_bonded: 4.83 restraints_weight: 0.2500 r_work (final): 0.2905 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2913 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2913 r_free = 0.2913 target_work(ls_wunit_k1) = 0.083 | | occupancies: max = 1.00 min = 0.46 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2913 r_free = 0.2913 target_work(ls_wunit_k1) = 0.083 | | occupancies: max = 1.00 min = 0.46 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2913 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8122 moved from start: 0.1436 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 7716 Z= 0.145 Angle : 0.546 6.304 10547 Z= 0.277 Chirality : 0.043 0.147 1260 Planarity : 0.003 0.049 1324 Dihedral : 8.963 168.248 1226 Min Nonbonded Distance : 2.100 Molprobity Statistics. All-atom Clashscore : 3.28 Ramachandran Plot: Outliers : 0.10 % Allowed : 3.27 % Favored : 96.63 % Rotamer: Outliers : 4.32 % Allowed : 20.06 % Favored : 75.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.35 % 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 are not related in a simple way. whole: 0.26 (0.27), residues: 1011 helix: 1.63 (0.26), residues: 447 sheet: 0.91 (0.41), residues: 157 loop : -1.88 (0.26), residues: 407 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 129 TYR 0.008 0.001 TYR A 154 PHE 0.015 0.001 PHE A 196 TRP 0.012 0.001 TRP B 82 HIS 0.004 0.001 HIS A 57 Details of bonding type rmsd covalent geometry : bond 0.00345 ( 7715) covalent geometry : angle 0.54598 (10545) SS BOND : bond 0.00179 ( 1) SS BOND : angle 1.12587 ( 2) hydrogen bonds : bond 0.05261 ( 357) hydrogen bonds : angle 3.92937 ( 1029) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2022 Ramachandran restraints generated. 1011 Oldfield, 0 Emsley, 1011 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2022 Ramachandran restraints generated. 1011 Oldfield, 0 Emsley, 1011 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 117 residues out of total 876 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 87 time to evaluate : 0.211 Fit side-chains REVERT: B 111 TYR cc_start: 0.9309 (m-80) cc_final: 0.9094 (m-80) REVERT: B 118 ASP cc_start: 0.8248 (OUTLIER) cc_final: 0.7688 (p0) REVERT: B 155 ASN cc_start: 0.8601 (t0) cc_final: 0.8362 (t0) REVERT: B 213 VAL cc_start: 0.9165 (m) cc_final: 0.8866 (t) REVERT: B 234 PHE cc_start: 0.9253 (OUTLIER) cc_final: 0.8370 (m-80) REVERT: B 258 ASP cc_start: 0.8366 (t0) cc_final: 0.8139 (t70) REVERT: B 325 MET cc_start: 0.8799 (OUTLIER) cc_final: 0.8419 (mmm) REVERT: D 112 LEU cc_start: 0.6630 (OUTLIER) cc_final: 0.6371 (tp) REVERT: D 221 PHE cc_start: 0.6737 (m-80) cc_final: 0.6414 (m-80) REVERT: D 257 LEU cc_start: 0.7574 (OUTLIER) cc_final: 0.7291 (mp) REVERT: D 263 ARG cc_start: 0.7940 (OUTLIER) cc_final: 0.7635 (mtm180) REVERT: D 264 MET cc_start: 0.7815 (mpp) cc_final: 0.7580 (pmm) REVERT: A 43 GLU cc_start: 0.7647 (mm-30) cc_final: 0.7364 (mm-30) REVERT: A 82 ILE cc_start: 0.6919 (OUTLIER) cc_final: 0.6506 (mp) REVERT: A 247 MET cc_start: 0.8146 (mtp) cc_final: 0.7849 (mtm) outliers start: 30 outliers final: 16 residues processed: 108 average time/residue: 0.3730 time to fit residues: 43.6068 Evaluate side-chains 108 residues out of total 876 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 85 time to evaluate : 0.245 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 70 LEU Chi-restraints excluded: chain B residue 118 ASP Chi-restraints excluded: chain B residue 173 THR Chi-restraints excluded: chain B residue 189 SER Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 276 VAL Chi-restraints excluded: chain B residue 318 LEU Chi-restraints excluded: chain B residue 322 ASP Chi-restraints excluded: chain B residue 325 MET Chi-restraints excluded: chain C residue 16 VAL Chi-restraints excluded: chain C residue 25 ILE Chi-restraints excluded: chain D residue 112 LEU Chi-restraints excluded: chain D residue 147 ASP Chi-restraints excluded: chain D residue 194 LEU Chi-restraints excluded: chain D residue 257 LEU Chi-restraints excluded: chain D residue 263 ARG Chi-restraints excluded: chain D residue 291 VAL Chi-restraints excluded: chain D residue 302 ILE Chi-restraints excluded: chain A residue 82 ILE Chi-restraints excluded: chain A residue 107 LEU Chi-restraints excluded: chain A residue 108 PHE Chi-restraints excluded: chain A residue 168 ILE Chi-restraints excluded: chain A residue 243 MET Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 26 optimal weight: 0.1980 chunk 48 optimal weight: 0.8980 chunk 88 optimal weight: 0.0040 chunk 46 optimal weight: 2.9990 chunk 72 optimal weight: 0.9990 chunk 56 optimal weight: 0.6980 chunk 73 optimal weight: 0.0970 chunk 86 optimal weight: 0.9980 chunk 8 optimal weight: 0.9990 chunk 76 optimal weight: 0.9990 chunk 21 optimal weight: 0.8980 overall best weight: 0.3790 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 36 ASN ** D 150 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 171 GLN A 294 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3735 r_free = 0.3735 target = 0.147376 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3228 r_free = 0.3228 target = 0.104829 restraints weight = 13931.684| |-----------------------------------------------------------------------------| r_work (start): 0.3203 rms_B_bonded: 2.84 r_work: 0.3075 rms_B_bonded: 3.18 restraints_weight: 0.5000 r_work (final): 0.3075 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3081 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3081 r_free = 0.3081 target_work(ls_wunit_k1) = 0.094 | | occupancies: max = 1.00 min = 0.46 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3081 r_free = 0.3081 target_work(ls_wunit_k1) = 0.094 | | occupancies: max = 1.00 min = 0.47 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3081 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7984 moved from start: 0.1665 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 7716 Z= 0.094 Angle : 0.492 8.725 10547 Z= 0.249 Chirality : 0.041 0.150 1260 Planarity : 0.003 0.047 1324 Dihedral : 8.565 169.542 1226 Min Nonbonded Distance : 2.129 Molprobity Statistics. All-atom Clashscore : 3.00 Ramachandran Plot: Outliers : 0.10 % Allowed : 1.78 % Favored : 98.12 % Rotamer: Outliers : 3.48 % Allowed : 20.61 % Favored : 75.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.35 % 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 are not related in a simple way. whole: 0.49 (0.27), residues: 1011 helix: 1.82 (0.27), residues: 445 sheet: 0.96 (0.40), residues: 162 loop : -1.75 (0.26), residues: 404 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 86 TYR 0.006 0.001 TYR D 149 PHE 0.012 0.001 PHE B 241 TRP 0.011 0.001 TRP B 82 HIS 0.003 0.001 HIS A 57 Details of bonding type rmsd covalent geometry : bond 0.00200 ( 7715) covalent geometry : angle 0.49169 (10545) SS BOND : bond 0.00124 ( 1) SS BOND : angle 0.97088 ( 2) hydrogen bonds : bond 0.04083 ( 357) hydrogen bonds : angle 3.74371 ( 1029) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2022 Ramachandran restraints generated. 1011 Oldfield, 0 Emsley, 1011 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2022 Ramachandran restraints generated. 1011 Oldfield, 0 Emsley, 1011 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 116 residues out of total 876 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 92 time to evaluate : 0.176 Fit side-chains REVERT: B 111 TYR cc_start: 0.9204 (m-80) cc_final: 0.8977 (m-80) REVERT: B 118 ASP cc_start: 0.7876 (OUTLIER) cc_final: 0.7299 (p0) REVERT: B 155 ASN cc_start: 0.8460 (t0) cc_final: 0.8216 (t0) REVERT: B 173 THR cc_start: 0.8696 (OUTLIER) cc_final: 0.8418 (p) REVERT: B 213 VAL cc_start: 0.9089 (m) cc_final: 0.8864 (t) REVERT: B 234 PHE cc_start: 0.9170 (OUTLIER) cc_final: 0.8359 (m-80) REVERT: B 258 ASP cc_start: 0.8058 (t0) cc_final: 0.7853 (t70) REVERT: D 112 LEU cc_start: 0.6485 (OUTLIER) cc_final: 0.6247 (tp) REVERT: D 263 ARG cc_start: 0.7794 (OUTLIER) cc_final: 0.6949 (mtm180) REVERT: A 82 ILE cc_start: 0.6855 (OUTLIER) cc_final: 0.6473 (mp) REVERT: A 166 ASN cc_start: 0.8348 (p0) cc_final: 0.8042 (p0) REVERT: A 247 MET cc_start: 0.8012 (mtp) cc_final: 0.7705 (mtm) REVERT: A 324 THR cc_start: 0.8599 (t) cc_final: 0.8379 (t) outliers start: 24 outliers final: 11 residues processed: 108 average time/residue: 0.3851 time to fit residues: 44.6195 Evaluate side-chains 106 residues out of total 876 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 89 time to evaluate : 0.193 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 70 LEU Chi-restraints excluded: chain B residue 118 ASP Chi-restraints excluded: chain B residue 173 THR Chi-restraints excluded: chain B residue 189 SER Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 318 LEU Chi-restraints excluded: chain B residue 322 ASP Chi-restraints excluded: chain C residue 25 ILE Chi-restraints excluded: chain D residue 94 VAL Chi-restraints excluded: chain D residue 112 LEU Chi-restraints excluded: chain D residue 194 LEU Chi-restraints excluded: chain D residue 263 ARG Chi-restraints excluded: chain D residue 302 ILE Chi-restraints excluded: chain A residue 82 ILE Chi-restraints excluded: chain A residue 107 LEU Chi-restraints excluded: chain A residue 168 ILE Chi-restraints excluded: chain A residue 243 MET Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 83 optimal weight: 1.9990 chunk 71 optimal weight: 0.4980 chunk 37 optimal weight: 0.9990 chunk 32 optimal weight: 1.9990 chunk 53 optimal weight: 0.6980 chunk 18 optimal weight: 1.9990 chunk 49 optimal weight: 0.0470 chunk 72 optimal weight: 0.9990 chunk 31 optimal weight: 0.9980 chunk 88 optimal weight: 0.0770 chunk 33 optimal weight: 6.9990 overall best weight: 0.4636 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 36 ASN ** D 150 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 171 GLN A 294 ASN A 306 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3734 r_free = 0.3734 target = 0.147200 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3235 r_free = 0.3235 target = 0.105431 restraints weight = 11792.839| |-----------------------------------------------------------------------------| r_work (start): 0.3210 rms_B_bonded: 2.62 r_work: 0.3086 rms_B_bonded: 3.00 restraints_weight: 0.5000 r_work: 0.2948 rms_B_bonded: 4.89 restraints_weight: 0.2500 r_work (final): 0.2948 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2926 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2926 r_free = 0.2926 target_work(ls_wunit_k1) = 0.084 | | occupancies: max = 1.00 min = 0.47 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2926 r_free = 0.2926 target_work(ls_wunit_k1) = 0.084 | | occupancies: max = 1.00 min = 0.47 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2926 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8074 moved from start: 0.1776 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 7716 Z= 0.101 Angle : 0.503 11.363 10547 Z= 0.252 Chirality : 0.041 0.157 1260 Planarity : 0.003 0.047 1324 Dihedral : 8.460 173.867 1226 Min Nonbonded Distance : 2.118 Molprobity Statistics. All-atom Clashscore : 3.14 Ramachandran Plot: Outliers : 0.10 % Allowed : 2.38 % Favored : 97.52 % Rotamer: Outliers : 3.48 % Allowed : 20.61 % Favored : 75.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.35 % 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 are not related in a simple way. whole: 0.57 (0.27), residues: 1011 helix: 1.90 (0.26), residues: 445 sheet: 0.59 (0.40), residues: 172 loop : -1.58 (0.27), residues: 394 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 129 TYR 0.007 0.001 TYR D 149 PHE 0.013 0.001 PHE B 241 TRP 0.010 0.001 TRP B 82 HIS 0.004 0.001 HIS A 57 Details of bonding type rmsd covalent geometry : bond 0.00223 ( 7715) covalent geometry : angle 0.50263 (10545) SS BOND : bond 0.00155 ( 1) SS BOND : angle 0.96117 ( 2) hydrogen bonds : bond 0.04272 ( 357) hydrogen bonds : angle 3.73632 ( 1029) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2022 Ramachandran restraints generated. 1011 Oldfield, 0 Emsley, 1011 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2022 Ramachandran restraints generated. 1011 Oldfield, 0 Emsley, 1011 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 119 residues out of total 876 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 95 time to evaluate : 0.333 Fit side-chains REVERT: B 118 ASP cc_start: 0.8098 (OUTLIER) cc_final: 0.7538 (p0) REVERT: B 155 ASN cc_start: 0.8525 (t0) cc_final: 0.8263 (t0) REVERT: B 173 THR cc_start: 0.8716 (OUTLIER) cc_final: 0.8408 (p) REVERT: B 213 VAL cc_start: 0.9156 (m) cc_final: 0.8878 (t) REVERT: B 234 PHE cc_start: 0.9227 (OUTLIER) cc_final: 0.8473 (m-80) REVERT: B 258 ASP cc_start: 0.8233 (t0) cc_final: 0.8019 (t70) REVERT: D 112 LEU cc_start: 0.6582 (OUTLIER) cc_final: 0.6328 (tp) REVERT: D 196 SER cc_start: 0.7260 (p) cc_final: 0.6839 (m) REVERT: D 263 ARG cc_start: 0.7812 (OUTLIER) cc_final: 0.7043 (mtm180) REVERT: A 82 ILE cc_start: 0.6899 (OUTLIER) cc_final: 0.6448 (mp) REVERT: A 166 ASN cc_start: 0.8328 (p0) cc_final: 0.8081 (p0) REVERT: A 247 MET cc_start: 0.8105 (mtp) cc_final: 0.7827 (mtm) outliers start: 24 outliers final: 12 residues processed: 110 average time/residue: 0.3805 time to fit residues: 45.1165 Evaluate side-chains 111 residues out of total 876 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 93 time to evaluate : 0.311 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 70 LEU Chi-restraints excluded: chain B residue 118 ASP Chi-restraints excluded: chain B residue 173 THR Chi-restraints excluded: chain B residue 189 SER Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 318 LEU Chi-restraints excluded: chain B residue 322 ASP Chi-restraints excluded: chain C residue 25 ILE Chi-restraints excluded: chain D residue 112 LEU Chi-restraints excluded: chain D residue 194 LEU Chi-restraints excluded: chain D residue 263 ARG Chi-restraints excluded: chain D residue 291 VAL Chi-restraints excluded: chain D residue 302 ILE Chi-restraints excluded: chain A residue 82 ILE Chi-restraints excluded: chain A residue 107 LEU Chi-restraints excluded: chain A residue 108 PHE Chi-restraints excluded: chain A residue 168 ILE Chi-restraints excluded: chain A residue 243 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 50 optimal weight: 3.9990 chunk 93 optimal weight: 0.0070 chunk 27 optimal weight: 1.9990 chunk 24 optimal weight: 1.9990 chunk 81 optimal weight: 0.8980 chunk 37 optimal weight: 4.9990 chunk 97 optimal weight: 0.2980 chunk 8 optimal weight: 0.8980 chunk 78 optimal weight: 0.0060 chunk 56 optimal weight: 0.9980 chunk 52 optimal weight: 5.9990 overall best weight: 0.4214 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 36 ASN ** D 150 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 157 ASN A 171 GLN A 294 ASN A 306 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3743 r_free = 0.3743 target = 0.148025 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3235 r_free = 0.3235 target = 0.105380 restraints weight = 13924.058| |-----------------------------------------------------------------------------| r_work (start): 0.3208 rms_B_bonded: 2.85 r_work: 0.3080 rms_B_bonded: 3.19 restraints_weight: 0.5000 r_work (final): 0.3080 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3086 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3086 r_free = 0.3086 target_work(ls_wunit_k1) = 0.095 | | occupancies: max = 1.00 min = 0.47 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3086 r_free = 0.3086 target_work(ls_wunit_k1) = 0.095 | | occupancies: max = 1.00 min = 0.47 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3086 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7985 moved from start: 0.1852 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 7716 Z= 0.097 Angle : 0.497 11.270 10547 Z= 0.249 Chirality : 0.041 0.159 1260 Planarity : 0.003 0.047 1324 Dihedral : 8.332 176.456 1226 Min Nonbonded Distance : 2.119 Molprobity Statistics. All-atom Clashscore : 3.34 Ramachandran Plot: Outliers : 0.10 % Allowed : 2.18 % Favored : 97.72 % Rotamer: Outliers : 2.92 % Allowed : 21.03 % Favored : 76.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.35 % 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 are not related in a simple way. whole: 0.62 (0.27), residues: 1011 helix: 1.92 (0.26), residues: 447 sheet: 0.61 (0.40), residues: 173 loop : -1.54 (0.27), residues: 391 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 86 TYR 0.012 0.001 TYR B 111 PHE 0.012 0.001 PHE B 241 TRP 0.009 0.001 TRP B 82 HIS 0.003 0.001 HIS A 57 Details of bonding type rmsd covalent geometry : bond 0.00210 ( 7715) covalent geometry : angle 0.49684 (10545) SS BOND : bond 0.00307 ( 1) SS BOND : angle 0.88495 ( 2) hydrogen bonds : bond 0.04037 ( 357) hydrogen bonds : angle 3.69531 ( 1029) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2022 Ramachandran restraints generated. 1011 Oldfield, 0 Emsley, 1011 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2022 Ramachandran restraints generated. 1011 Oldfield, 0 Emsley, 1011 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 115 residues out of total 876 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 95 time to evaluate : 0.188 Fit side-chains REVERT: B 118 ASP cc_start: 0.7898 (OUTLIER) cc_final: 0.7345 (p0) REVERT: B 155 ASN cc_start: 0.8404 (t0) cc_final: 0.8152 (t0) REVERT: B 173 THR cc_start: 0.8705 (OUTLIER) cc_final: 0.8466 (p) REVERT: B 213 VAL cc_start: 0.9090 (m) cc_final: 0.8863 (t) REVERT: B 234 PHE cc_start: 0.9166 (OUTLIER) cc_final: 0.8446 (m-80) REVERT: D 112 LEU cc_start: 0.6484 (OUTLIER) cc_final: 0.6254 (tp) REVERT: D 263 ARG cc_start: 0.7730 (OUTLIER) cc_final: 0.7167 (mtm180) REVERT: A 82 ILE cc_start: 0.6851 (OUTLIER) cc_final: 0.6436 (mp) REVERT: A 166 ASN cc_start: 0.8215 (p0) cc_final: 0.7939 (p0) REVERT: A 247 MET cc_start: 0.7997 (mtp) cc_final: 0.7699 (mtm) REVERT: A 324 THR cc_start: 0.8565 (t) cc_final: 0.8345 (t) outliers start: 20 outliers final: 10 residues processed: 108 average time/residue: 0.4167 time to fit residues: 48.4709 Evaluate side-chains 110 residues out of total 876 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 94 time to evaluate : 0.303 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 70 LEU Chi-restraints excluded: chain B residue 100 VAL Chi-restraints excluded: chain B residue 118 ASP Chi-restraints excluded: chain B residue 173 THR Chi-restraints excluded: chain B residue 189 SER Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 318 LEU Chi-restraints excluded: chain B residue 322 ASP Chi-restraints excluded: chain C residue 25 ILE Chi-restraints excluded: chain D residue 112 LEU Chi-restraints excluded: chain D residue 194 LEU Chi-restraints excluded: chain D residue 263 ARG Chi-restraints excluded: chain D residue 302 ILE Chi-restraints excluded: chain A residue 82 ILE Chi-restraints excluded: chain A residue 168 ILE Chi-restraints excluded: chain A residue 243 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 26 optimal weight: 0.6980 chunk 3 optimal weight: 3.9990 chunk 41 optimal weight: 3.9990 chunk 37 optimal weight: 0.0370 chunk 90 optimal weight: 2.9990 chunk 69 optimal weight: 1.9990 chunk 21 optimal weight: 0.9990 chunk 1 optimal weight: 0.9980 chunk 7 optimal weight: 2.9990 chunk 12 optimal weight: 0.0020 chunk 55 optimal weight: 0.5980 overall best weight: 0.4666 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 36 ASN D 137 ASN ** D 150 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 149 ASN A 171 GLN A 294 ASN A 306 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3738 r_free = 0.3738 target = 0.147630 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3231 r_free = 0.3231 target = 0.105180 restraints weight = 13513.638| |-----------------------------------------------------------------------------| r_work (start): 0.3207 rms_B_bonded: 2.80 r_work: 0.3080 rms_B_bonded: 3.15 restraints_weight: 0.5000 r_work (final): 0.3080 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3084 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3084 r_free = 0.3084 target_work(ls_wunit_k1) = 0.095 | | occupancies: max = 1.00 min = 0.47 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3084 r_free = 0.3084 target_work(ls_wunit_k1) = 0.095 | | occupancies: max = 1.00 min = 0.47 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3084 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7985 moved from start: 0.1911 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 7716 Z= 0.100 Angle : 0.500 11.528 10547 Z= 0.251 Chirality : 0.041 0.161 1260 Planarity : 0.003 0.047 1324 Dihedral : 8.237 176.725 1226 Min Nonbonded Distance : 2.112 Molprobity Statistics. All-atom Clashscore : 3.14 Ramachandran Plot: Outliers : 0.10 % Allowed : 2.57 % Favored : 97.33 % Rotamer: Outliers : 3.06 % Allowed : 20.61 % Favored : 76.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.35 % 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 are not related in a simple way. whole: 0.67 (0.27), residues: 1011 helix: 2.00 (0.26), residues: 445 sheet: 0.59 (0.40), residues: 173 loop : -1.53 (0.27), residues: 393 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 86 TYR 0.007 0.001 TYR D 149 PHE 0.012 0.001 PHE B 241 TRP 0.010 0.001 TRP B 82 HIS 0.004 0.001 HIS A 57 Details of bonding type rmsd covalent geometry : bond 0.00221 ( 7715) covalent geometry : angle 0.50008 (10545) SS BOND : bond 0.00218 ( 1) SS BOND : angle 0.86297 ( 2) hydrogen bonds : bond 0.04117 ( 357) hydrogen bonds : angle 3.69777 ( 1029) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2616.44 seconds wall clock time: 45 minutes 13.75 seconds (2713.75 seconds total)