Starting phenix.real_space_refine on Wed Mar 4 12:26:31 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7aho_11789/03_2026/7aho_11789.cif Found real_map, /net/cci-nas-00/data/ceres_data/7aho_11789/03_2026/7aho_11789.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.18 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/7aho_11789/03_2026/7aho_11789.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7aho_11789/03_2026/7aho_11789.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7aho_11789/03_2026/7aho_11789.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7aho_11789/03_2026/7aho_11789.map" } resolution = 4.18 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= 0.003 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 6 5.49 5 S 69 5.16 5 C 8482 2.51 5 N 2355 2.21 5 O 2609 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 28 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 13521 Number of models: 1 Model: "" Number of chains: 9 Chain: "A" Number of atoms: 2338 Number of conformers: 1 Conformer: "" Number of residues, atoms: 305, 2338 Classifications: {'peptide': 305} Link IDs: {'PTRANS': 10, 'TRANS': 294} Chain breaks: 2 Chain: "B" Number of atoms: 2284 Number of conformers: 1 Conformer: "" Number of residues, atoms: 299, 2284 Classifications: {'peptide': 299} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 10, 'TRANS': 288} Chain breaks: 2 Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "C" Number of atoms: 2340 Number of conformers: 1 Conformer: "" Number of residues, atoms: 306, 2340 Classifications: {'peptide': 306} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 10, 'TRANS': 295} Chain breaks: 2 Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "D" Number of atoms: 2185 Number of conformers: 1 Conformer: "" Number of residues, atoms: 283, 2185 Classifications: {'peptide': 283} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PTRANS': 8, 'TRANS': 274} Chain breaks: 2 Unresolved non-hydrogen bonds: 20 Unresolved non-hydrogen angles: 25 Unresolved non-hydrogen dihedrals: 17 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ARG:plan': 1, 'PHE:plan': 1, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 14 Chain: "E" Number of atoms: 2115 Number of conformers: 1 Conformer: "" Number of residues, atoms: 273, 2115 Classifications: {'peptide': 273} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 8, 'TRANS': 264} Chain breaks: 2 Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 8 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'HIS:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "F" Number of atoms: 2178 Number of conformers: 1 Conformer: "" Number of residues, atoms: 282, 2178 Classifications: {'peptide': 282} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'PTRANS': 8, 'TRANS': 273} Chain breaks: 2 Unresolved non-hydrogen bonds: 26 Unresolved non-hydrogen angles: 33 Unresolved non-hydrogen dihedrals: 23 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'HIS:plan': 1, 'ARG:plan': 1, 'PHE:plan': 1, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 19 Chain: "A" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'ADP': 1} Classifications: {'undetermined': 1} Chain: "B" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'ADP': 1} Classifications: {'undetermined': 1} Chain: "C" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'ADP': 1} Classifications: {'undetermined': 1} Time building chain proxies: 2.89, per 1000 atoms: 0.21 Number of scatterers: 13521 At special positions: 0 Unit cell: (73.29, 126.687, 131.922, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 69 16.00 P 6 15.00 O 2609 8.00 N 2355 7.00 C 8482 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 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=2, symmetry=0 Number of additional bonds: simple=2, symmetry=0 Coordination: Other bonds: Time building additional restraints: 1.05 Conformation dependent library (CDL) restraints added in 519.5 milliseconds 3424 Ramachandran restraints generated. 1712 Oldfield, 0 Emsley, 1712 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3246 Finding SS restraints... Secondary structure from input PDB file: 93 helices and 18 sheets defined 49.0% alpha, 8.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.61 Creating SS restraints... Processing helix chain 'A' and resid 56 through 72 removed outlier: 3.537A pdb=" N GLU A 61 " --> pdb=" O GLU A 57 " (cutoff:3.500A) removed outlier: 3.944A pdb=" N ALA A 62 " --> pdb=" O ASN A 58 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N LEU A 69 " --> pdb=" O VAL A 65 " (cutoff:3.500A) Processing helix chain 'A' and resid 95 through 101 removed outlier: 3.695A pdb=" N LEU A 101 " --> pdb=" O ILE A 97 " (cutoff:3.500A) Processing helix chain 'A' and resid 113 through 115 No H-bonds generated for 'chain 'A' and resid 113 through 115' Processing helix chain 'A' and resid 121 through 131 removed outlier: 3.550A pdb=" N VAL A 125 " --> pdb=" O LYS A 121 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N LEU A 126 " --> pdb=" O LYS A 122 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N MET A 127 " --> pdb=" O THR A 123 " (cutoff:3.500A) Processing helix chain 'A' and resid 151 through 155 removed outlier: 3.688A pdb=" N LEU A 154 " --> pdb=" O LEU A 151 " (cutoff:3.500A) Processing helix chain 'A' and resid 184 through 200 removed outlier: 4.136A pdb=" N ILE A 190 " --> pdb=" O LEU A 186 " (cutoff:3.500A) removed outlier: 3.905A pdb=" N ASN A 191 " --> pdb=" O ARG A 187 " (cutoff:3.500A) removed outlier: 3.833A pdb=" N LYS A 192 " --> pdb=" O GLY A 188 " (cutoff:3.500A) removed outlier: 3.942A pdb=" N VAL A 193 " --> pdb=" O GLU A 189 " (cutoff:3.500A) removed outlier: 3.891A pdb=" N ASP A 199 " --> pdb=" O ASN A 195 " (cutoff:3.500A) Processing helix chain 'A' and resid 214 through 218 Processing helix chain 'A' and resid 219 through 230 removed outlier: 3.724A pdb=" N TYR A 225 " --> pdb=" O GLU A 221 " (cutoff:3.500A) Processing helix chain 'A' and resid 257 through 261 removed outlier: 3.728A pdb=" N GLY A 260 " --> pdb=" O SER A 257 " (cutoff:3.500A) Processing helix chain 'A' and resid 265 through 267 No H-bonds generated for 'chain 'A' and resid 265 through 267' Processing helix chain 'A' and resid 280 through 293 removed outlier: 3.886A pdb=" N GLN A 284 " --> pdb=" O GLN A 280 " (cutoff:3.500A) removed outlier: 3.852A pdb=" N ILE A 285 " --> pdb=" O GLU A 281 " (cutoff:3.500A) removed outlier: 4.271A pdb=" N ILE A 286 " --> pdb=" O MET A 282 " (cutoff:3.500A) removed outlier: 3.757A pdb=" N GLU A 293 " --> pdb=" O ARG A 289 " (cutoff:3.500A) Processing helix chain 'A' and resid 298 through 312 removed outlier: 3.721A pdb=" N HIS A 304 " --> pdb=" O GLU A 300 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N GLU A 307 " --> pdb=" O ASN A 303 " (cutoff:3.500A) Processing helix chain 'A' and resid 315 through 320 removed outlier: 3.560A pdb=" N GLN A 319 " --> pdb=" O ARG A 315 " (cutoff:3.500A) Processing helix chain 'A' and resid 320 through 332 removed outlier: 4.181A pdb=" N ILE A 330 " --> pdb=" O LEU A 326 " (cutoff:3.500A) Processing helix chain 'A' and resid 337 through 346 removed outlier: 3.737A pdb=" N VAL A 341 " --> pdb=" O GLU A 337 " (cutoff:3.500A) removed outlier: 4.107A pdb=" N GLU A 343 " --> pdb=" O GLU A 339 " (cutoff:3.500A) Processing helix chain 'A' and resid 350 through 360 removed outlier: 4.031A pdb=" N LYS A 356 " --> pdb=" O LYS A 352 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N LEU A 358 " --> pdb=" O SER A 354 " (cutoff:3.500A) Processing helix chain 'B' and resid 26 through 33 removed outlier: 5.018A pdb=" N SER B 31 " --> pdb=" O ARG B 28 " (cutoff:3.500A) removed outlier: 3.954A pdb=" N SER B 33 " --> pdb=" O ALA B 30 " (cutoff:3.500A) Processing helix chain 'B' and resid 56 through 72 removed outlier: 3.520A pdb=" N ALA B 62 " --> pdb=" O ASN B 58 " (cutoff:3.500A) Processing helix chain 'B' and resid 91 through 101 Processing helix chain 'B' and resid 121 through 131 removed outlier: 3.718A pdb=" N VAL B 125 " --> pdb=" O LYS B 121 " (cutoff:3.500A) removed outlier: 4.034A pdb=" N ASN B 129 " --> pdb=" O VAL B 125 " (cutoff:3.500A) Processing helix chain 'B' and resid 151 through 155 Processing helix chain 'B' and resid 189 through 201 removed outlier: 3.646A pdb=" N VAL B 193 " --> pdb=" O GLU B 189 " (cutoff:3.500A) removed outlier: 4.116A pdb=" N VAL B 194 " --> pdb=" O ILE B 190 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N ASN B 195 " --> pdb=" O ASN B 191 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N ILE B 198 " --> pdb=" O VAL B 194 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N ASP B 199 " --> pdb=" O ASN B 195 " (cutoff:3.500A) Processing helix chain 'B' and resid 215 through 218 Processing helix chain 'B' and resid 219 through 230 removed outlier: 3.731A pdb=" N THR B 224 " --> pdb=" O ILE B 220 " (cutoff:3.500A) removed outlier: 4.471A pdb=" N TYR B 225 " --> pdb=" O GLU B 221 " (cutoff:3.500A) Processing helix chain 'B' and resid 257 through 261 removed outlier: 3.631A pdb=" N GLY B 260 " --> pdb=" O SER B 257 " (cutoff:3.500A) Processing helix chain 'B' and resid 262 through 267 Processing helix chain 'B' and resid 278 through 294 removed outlier: 3.574A pdb=" N GLN B 284 " --> pdb=" O GLN B 280 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N ILE B 285 " --> pdb=" O GLU B 281 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N LYS B 287 " --> pdb=" O LYS B 283 " (cutoff:3.500A) Processing helix chain 'B' and resid 298 through 310 removed outlier: 3.616A pdb=" N HIS B 304 " --> pdb=" O GLU B 300 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N THR B 310 " --> pdb=" O GLY B 306 " (cutoff:3.500A) Processing helix chain 'B' and resid 313 through 320 removed outlier: 3.974A pdb=" N SER B 317 " --> pdb=" O THR B 313 " (cutoff:3.500A) Processing helix chain 'B' and resid 320 through 332 removed outlier: 3.599A pdb=" N LEU B 326 " --> pdb=" O THR B 322 " (cutoff:3.500A) removed outlier: 3.853A pdb=" N ALA B 328 " --> pdb=" O ALA B 324 " (cutoff:3.500A) Processing helix chain 'B' and resid 337 through 347 removed outlier: 3.596A pdb=" N VAL B 341 " --> pdb=" O GLU B 337 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N GLU B 343 " --> pdb=" O GLU B 339 " (cutoff:3.500A) removed outlier: 4.500A pdb=" N GLU B 346 " --> pdb=" O GLU B 342 " (cutoff:3.500A) Processing helix chain 'B' and resid 353 through 358 removed outlier: 3.932A pdb=" N LEU B 358 " --> pdb=" O SER B 354 " (cutoff:3.500A) Processing helix chain 'C' and resid 26 through 31 removed outlier: 4.218A pdb=" N SER C 31 " --> pdb=" O GLN C 27 " (cutoff:3.500A) Processing helix chain 'C' and resid 56 through 72 removed outlier: 4.086A pdb=" N GLU C 61 " --> pdb=" O GLU C 57 " (cutoff:3.500A) removed outlier: 3.986A pdb=" N ALA C 62 " --> pdb=" O ASN C 58 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N LYS C 71 " --> pdb=" O VAL C 67 " (cutoff:3.500A) Processing helix chain 'C' and resid 89 through 101 removed outlier: 3.605A pdb=" N ALA C 94 " --> pdb=" O LYS C 90 " (cutoff:3.500A) removed outlier: 4.402A pdb=" N ALA C 98 " --> pdb=" O ALA C 94 " (cutoff:3.500A) Processing helix chain 'C' and resid 113 through 115 No H-bonds generated for 'chain 'C' and resid 113 through 115' Processing helix chain 'C' and resid 121 through 134 removed outlier: 3.576A pdb=" N VAL C 125 " --> pdb=" O LYS C 121 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N ALA C 133 " --> pdb=" O ASN C 129 " (cutoff:3.500A) removed outlier: 3.915A pdb=" N ILE C 134 " --> pdb=" O PHE C 130 " (cutoff:3.500A) Processing helix chain 'C' and resid 184 through 198 removed outlier: 3.868A pdb=" N LYS C 192 " --> pdb=" O GLY C 188 " (cutoff:3.500A) removed outlier: 3.884A pdb=" N VAL C 193 " --> pdb=" O GLU C 189 " (cutoff:3.500A) Processing helix chain 'C' and resid 215 through 218 Processing helix chain 'C' and resid 219 through 228 removed outlier: 3.632A pdb=" N THR C 224 " --> pdb=" O ILE C 220 " (cutoff:3.500A) removed outlier: 4.654A pdb=" N TYR C 225 " --> pdb=" O GLU C 221 " (cutoff:3.500A) Processing helix chain 'C' and resid 264 through 267 Processing helix chain 'C' and resid 280 through 292 removed outlier: 3.706A pdb=" N GLN C 284 " --> pdb=" O GLN C 280 " (cutoff:3.500A) removed outlier: 3.901A pdb=" N ILE C 285 " --> pdb=" O GLU C 281 " (cutoff:3.500A) removed outlier: 4.113A pdb=" N ILE C 286 " --> pdb=" O MET C 282 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N THR C 292 " --> pdb=" O ILE C 288 " (cutoff:3.500A) Processing helix chain 'C' and resid 301 through 306 Processing helix chain 'C' and resid 313 through 319 removed outlier: 4.258A pdb=" N SER C 317 " --> pdb=" O THR C 313 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N VAL C 318 " --> pdb=" O LEU C 314 " (cutoff:3.500A) removed outlier: 3.969A pdb=" N GLN C 319 " --> pdb=" O ARG C 315 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 313 through 319' Processing helix chain 'C' and resid 320 through 332 Processing helix chain 'C' and resid 337 through 346 removed outlier: 3.958A pdb=" N GLU C 342 " --> pdb=" O LYS C 338 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N ILE C 344 " --> pdb=" O HIS C 340 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N GLU C 346 " --> pdb=" O GLU C 342 " (cutoff:3.500A) Processing helix chain 'C' and resid 350 through 355 Processing helix chain 'C' and resid 356 through 361 Processing helix chain 'D' and resid 64 through 78 removed outlier: 3.836A pdb=" N ALA D 71 " --> pdb=" O ALA D 67 " (cutoff:3.500A) removed outlier: 3.765A pdb=" N GLU D 76 " --> pdb=" O GLY D 72 " (cutoff:3.500A) Processing helix chain 'D' and resid 100 through 108 removed outlier: 3.874A pdb=" N GLY D 104 " --> pdb=" O ALA D 100 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N ALA D 108 " --> pdb=" O GLY D 104 " (cutoff:3.500A) Processing helix chain 'D' and resid 121 through 124 removed outlier: 3.598A pdb=" N PHE D 124 " --> pdb=" O SER D 121 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 121 through 124' Processing helix chain 'D' and resid 129 through 139 removed outlier: 4.073A pdb=" N THR D 135 " --> pdb=" O THR D 131 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N ARG D 139 " --> pdb=" O THR D 135 " (cutoff:3.500A) Processing helix chain 'D' and resid 161 through 166 removed outlier: 4.017A pdb=" N ILE D 165 " --> pdb=" O GLU D 161 " (cutoff:3.500A) Processing helix chain 'D' and resid 189 through 202 removed outlier: 3.504A pdb=" N ALA D 193 " --> pdb=" O GLU D 189 " (cutoff:3.500A) removed outlier: 4.913A pdb=" N GLU D 200 " --> pdb=" O ALA D 196 " (cutoff:3.500A) removed outlier: 4.094A pdb=" N GLU D 201 " --> pdb=" O GLU D 197 " (cutoff:3.500A) removed outlier: 3.752A pdb=" N GLY D 202 " --> pdb=" O TRP D 198 " (cutoff:3.500A) Processing helix chain 'D' and resid 215 through 219 Processing helix chain 'D' and resid 220 through 231 removed outlier: 3.501A pdb=" N PHE D 224 " --> pdb=" O ASP D 220 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N LEU D 231 " --> pdb=" O LEU D 227 " (cutoff:3.500A) Processing helix chain 'D' and resid 258 through 261 removed outlier: 3.527A pdb=" N ILE D 261 " --> pdb=" O PRO D 258 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 258 through 261' Processing helix chain 'D' and resid 265 through 267 No H-bonds generated for 'chain 'D' and resid 265 through 267' Processing helix chain 'D' and resid 278 through 293 removed outlier: 3.695A pdb=" N THR D 282 " --> pdb=" O SER D 278 " (cutoff:3.500A) removed outlier: 3.785A pdb=" N LYS D 283 " --> pdb=" O GLU D 279 " (cutoff:3.500A) removed outlier: 3.980A pdb=" N GLN D 284 " --> pdb=" O LYS D 280 " (cutoff:3.500A) removed outlier: 3.860A pdb=" N ILE D 285 " --> pdb=" O ASP D 281 " (cutoff:3.500A) Processing helix chain 'D' and resid 299 through 312 removed outlier: 3.646A pdb=" N THR D 303 " --> pdb=" O GLU D 299 " (cutoff:3.500A) removed outlier: 3.886A pdb=" N VAL D 304 " --> pdb=" O ASP D 300 " (cutoff:3.500A) Processing helix chain 'D' and resid 318 through 325 removed outlier: 3.856A pdb=" N THR D 322 " --> pdb=" O ILE D 318 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N ALA D 323 " --> pdb=" O GLN D 319 " (cutoff:3.500A) Processing helix chain 'D' and resid 352 through 360 removed outlier: 3.821A pdb=" N GLN D 356 " --> pdb=" O SER D 352 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N MET D 358 " --> pdb=" O SER D 354 " (cutoff:3.500A) removed outlier: 3.909A pdb=" N GLU D 360 " --> pdb=" O GLN D 356 " (cutoff:3.500A) Processing helix chain 'E' and resid 66 through 80 removed outlier: 3.762A pdb=" N ALA E 71 " --> pdb=" O ALA E 67 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N GLY E 72 " --> pdb=" O ARG E 68 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N MET E 77 " --> pdb=" O VAL E 73 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N ARG E 79 " --> pdb=" O LEU E 75 " (cutoff:3.500A) Processing helix chain 'E' and resid 93 through 96 removed outlier: 3.979A pdb=" N THR E 96 " --> pdb=" O GLN E 93 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 93 through 96' Processing helix chain 'E' and resid 97 through 103 removed outlier: 3.892A pdb=" N ILE E 101 " --> pdb=" O GLY E 97 " (cutoff:3.500A) Processing helix chain 'E' and resid 104 through 106 No H-bonds generated for 'chain 'E' and resid 104 through 106' Processing helix chain 'E' and resid 131 through 140 removed outlier: 3.508A pdb=" N GLN E 136 " --> pdb=" O GLU E 132 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N ALA E 137 " --> pdb=" O ALA E 133 " (cutoff:3.500A) Processing helix chain 'E' and resid 189 through 196 Processing helix chain 'E' and resid 197 through 201 removed outlier: 3.993A pdb=" N GLU E 200 " --> pdb=" O GLU E 197 " (cutoff:3.500A) Processing helix chain 'E' and resid 216 through 219 Processing helix chain 'E' and resid 220 through 225 Processing helix chain 'E' and resid 225 through 231 removed outlier: 3.510A pdb=" N ARG E 229 " --> pdb=" O SER E 225 " (cutoff:3.500A) removed outlier: 3.750A pdb=" N LEU E 231 " --> pdb=" O LEU E 227 " (cutoff:3.500A) Processing helix chain 'E' and resid 262 through 266 Processing helix chain 'E' and resid 278 through 292 removed outlier: 3.681A pdb=" N GLN E 284 " --> pdb=" O LYS E 280 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N ILE E 285 " --> pdb=" O ASP E 281 " (cutoff:3.500A) removed outlier: 3.798A pdb=" N GLU E 291 " --> pdb=" O ARG E 287 " (cutoff:3.500A) Processing helix chain 'E' and resid 301 through 309 removed outlier: 3.803A pdb=" N ARG E 307 " --> pdb=" O THR E 303 " (cutoff:3.500A) Processing helix chain 'E' and resid 315 through 329 removed outlier: 3.976A pdb=" N ILE E 321 " --> pdb=" O ALA E 317 " (cutoff:3.500A) removed outlier: 3.785A pdb=" N THR E 322 " --> pdb=" O ILE E 318 " (cutoff:3.500A) removed outlier: 3.753A pdb=" N ALA E 323 " --> pdb=" O GLN E 319 " (cutoff:3.500A) removed outlier: 3.739A pdb=" N SER E 325 " --> pdb=" O ILE E 321 " (cutoff:3.500A) removed outlier: 3.770A pdb=" N LEU E 326 " --> pdb=" O THR E 322 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N CYS E 328 " --> pdb=" O ALA E 324 " (cutoff:3.500A) Processing helix chain 'E' and resid 337 through 347 removed outlier: 3.946A pdb=" N ILE E 341 " --> pdb=" O GLN E 337 " (cutoff:3.500A) removed outlier: 4.064A pdb=" N LYS E 342 " --> pdb=" O VAL E 338 " (cutoff:3.500A) removed outlier: 3.833A pdb=" N SER E 346 " --> pdb=" O LYS E 342 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N LEU E 347 " --> pdb=" O ARG E 343 " (cutoff:3.500A) Processing helix chain 'E' and resid 356 through 361 removed outlier: 4.198A pdb=" N TYR E 361 " --> pdb=" O TYR E 357 " (cutoff:3.500A) Processing helix chain 'F' and resid 64 through 80 removed outlier: 3.733A pdb=" N ARG F 69 " --> pdb=" O LEU F 65 " (cutoff:3.500A) removed outlier: 4.818A pdb=" N ALA F 70 " --> pdb=" O ALA F 66 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N ILE F 78 " --> pdb=" O VAL F 74 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N ARG F 79 " --> pdb=" O LEU F 75 " (cutoff:3.500A) removed outlier: 3.848A pdb=" N GLU F 80 " --> pdb=" O GLU F 76 " (cutoff:3.500A) Processing helix chain 'F' and resid 103 through 108 Processing helix chain 'F' and resid 121 through 124 Processing helix chain 'F' and resid 134 through 140 Processing helix chain 'F' and resid 159 through 166 removed outlier: 3.646A pdb=" N ASP F 163 " --> pdb=" O LEU F 159 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N VAL F 164 " --> pdb=" O HIS F 160 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N ILE F 165 " --> pdb=" O GLU F 161 " (cutoff:3.500A) Processing helix chain 'F' and resid 188 through 202 removed outlier: 3.568A pdb=" N ASN F 192 " --> pdb=" O ARG F 188 " (cutoff:3.500A) removed outlier: 5.680A pdb=" N ALA F 193 " --> pdb=" O GLU F 189 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N ALA F 196 " --> pdb=" O ASN F 192 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N ARG F 199 " --> pdb=" O VAL F 195 " (cutoff:3.500A) removed outlier: 4.416A pdb=" N GLU F 200 " --> pdb=" O ALA F 196 " (cutoff:3.500A) removed outlier: 4.230A pdb=" N GLU F 201 " --> pdb=" O GLU F 197 " (cutoff:3.500A) Processing helix chain 'F' and resid 215 through 219 Processing helix chain 'F' and resid 220 through 228 removed outlier: 5.373A pdb=" N PHE F 226 " --> pdb=" O GLU F 222 " (cutoff:3.500A) removed outlier: 4.076A pdb=" N LEU F 227 " --> pdb=" O SER F 223 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N ASN F 228 " --> pdb=" O PHE F 224 " (cutoff:3.500A) Processing helix chain 'F' and resid 265 through 267 No H-bonds generated for 'chain 'F' and resid 265 through 267' Processing helix chain 'F' and resid 278 through 290 removed outlier: 4.065A pdb=" N LYS F 283 " --> pdb=" O GLU F 279 " (cutoff:3.500A) removed outlier: 4.350A pdb=" N GLN F 284 " --> pdb=" O LYS F 280 " (cutoff:3.500A) removed outlier: 4.033A pdb=" N ILE F 285 " --> pdb=" O ASP F 281 " (cutoff:3.500A) Processing helix chain 'F' and resid 298 through 310 Processing helix chain 'F' and resid 313 through 320 removed outlier: 3.520A pdb=" N ALA F 317 " --> pdb=" O SER F 313 " (cutoff:3.500A) Processing helix chain 'F' and resid 321 through 329 removed outlier: 3.529A pdb=" N LEU F 326 " --> pdb=" O THR F 322 " (cutoff:3.500A) removed outlier: 3.854A pdb=" N VAL F 327 " --> pdb=" O ALA F 323 " (cutoff:3.500A) Processing helix chain 'F' and resid 337 through 348 removed outlier: 3.815A pdb=" N VAL F 344 " --> pdb=" O ASP F 340 " (cutoff:3.500A) Processing helix chain 'F' and resid 355 through 360 removed outlier: 3.572A pdb=" N LYS F 359 " --> pdb=" O THR F 355 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 49 through 50 removed outlier: 3.629A pdb=" N ALA A 50 " --> pdb=" O LEU A 53 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N LEU A 53 " --> pdb=" O ALA A 50 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA1 Processing sheet with id=AA2, first strand: chain 'A' and resid 107 through 111 removed outlier: 6.383A pdb=" N LEU A 210 " --> pdb=" O ILE A 239 " (cutoff:3.500A) removed outlier: 6.641A pdb=" N VAL A 80 " --> pdb=" O PHE A 240 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N LEU A 81 " --> pdb=" O MET A 270 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 148 through 149 Processing sheet with id=AA4, first strand: chain 'A' and resid 348 through 349 removed outlier: 4.585A pdb=" N ILE F 271 " --> pdb=" O TYR A 349 " (cutoff:3.500A) removed outlier: 7.015A pdb=" N ALA F 87 " --> pdb=" O LEU F 270 " (cutoff:3.500A) removed outlier: 7.769A pdb=" N VAL F 272 " --> pdb=" O ALA F 87 " (cutoff:3.500A) removed outlier: 6.293A pdb=" N LEU F 89 " --> pdb=" O VAL F 272 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N ALA F 242 " --> pdb=" O ILE F 213 " (cutoff:3.500A) removed outlier: 5.799A pdb=" N THR F 116 " --> pdb=" O PHE F 212 " (cutoff:3.500A) removed outlier: 6.590A pdb=" N ASP F 214 " --> pdb=" O THR F 116 " (cutoff:3.500A) removed outlier: 6.865A pdb=" N ILE F 118 " --> pdb=" O ASP F 214 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 110 through 111 removed outlier: 6.736A pdb=" N MET B 110 " --> pdb=" O ASP B 213 " (cutoff:3.500A) removed outlier: 6.323A pdb=" N LEU B 210 " --> pdb=" O ILE B 239 " (cutoff:3.500A) removed outlier: 7.822A pdb=" N ALA B 241 " --> pdb=" O LEU B 210 " (cutoff:3.500A) removed outlier: 7.049A pdb=" N VAL B 212 " --> pdb=" O ALA B 241 " (cutoff:3.500A) removed outlier: 6.433A pdb=" N VAL B 80 " --> pdb=" O PHE B 240 " (cutoff:3.500A) removed outlier: 7.122A pdb=" N ALA B 79 " --> pdb=" O MET B 270 " (cutoff:3.500A) removed outlier: 7.444A pdb=" N ILE B 272 " --> pdb=" O ALA B 79 " (cutoff:3.500A) removed outlier: 6.092A pdb=" N LEU B 81 " --> pdb=" O ILE B 272 " (cutoff:3.500A) removed outlier: 4.247A pdb=" N ILE B 271 " --> pdb=" O LEU E 349 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 149 through 150 Processing sheet with id=AA7, first strand: chain 'B' and resid 348 through 349 removed outlier: 3.605A pdb=" N TYR B 349 " --> pdb=" O ILE D 271 " (cutoff:3.500A) removed outlier: 4.587A pdb=" N ILE D 271 " --> pdb=" O TYR B 349 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'C' and resid 49 through 50 Processing sheet with id=AA9, first strand: chain 'C' and resid 110 through 111 removed outlier: 6.733A pdb=" N MET C 110 " --> pdb=" O ASP C 213 " (cutoff:3.500A) removed outlier: 5.992A pdb=" N VAL C 80 " --> pdb=" O PHE C 240 " (cutoff:3.500A) removed outlier: 7.768A pdb=" N SER C 242 " --> pdb=" O VAL C 80 " (cutoff:3.500A) removed outlier: 5.916A pdb=" N LEU C 82 " --> pdb=" O SER C 242 " (cutoff:3.500A) removed outlier: 7.043A pdb=" N ALA C 79 " --> pdb=" O MET C 270 " (cutoff:3.500A) removed outlier: 7.885A pdb=" N ILE C 272 " --> pdb=" O ALA C 79 " (cutoff:3.500A) removed outlier: 6.555A pdb=" N LEU C 81 " --> pdb=" O ILE C 272 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'C' and resid 135 through 137 Processing sheet with id=AB2, first strand: chain 'C' and resid 246 through 248 removed outlier: 3.650A pdb=" N SER C 257 " --> pdb=" O CYS C 247 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'C' and resid 348 through 349 removed outlier: 3.585A pdb=" N ILE E 271 " --> pdb=" O TYR C 349 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N ASP E 214 " --> pdb=" O ILE E 118 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'D' and resid 115 through 119 removed outlier: 5.783A pdb=" N THR D 116 " --> pdb=" O PHE D 212 " (cutoff:3.500A) removed outlier: 6.697A pdb=" N ASP D 214 " --> pdb=" O THR D 116 " (cutoff:3.500A) removed outlier: 6.460A pdb=" N ILE D 118 " --> pdb=" O ASP D 214 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB4 Processing sheet with id=AB5, first strand: chain 'D' and resid 248 through 249 Processing sheet with id=AB6, first strand: chain 'E' and resid 143 through 144 Processing sheet with id=AB7, first strand: chain 'E' and resid 247 through 249 Processing sheet with id=AB8, first strand: chain 'F' and resid 157 through 158 removed outlier: 3.557A pdb=" N GLY F 143 " --> pdb=" O ILE F 207 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'F' and resid 247 through 249 418 hydrogen bonds defined for protein. 1173 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 2.00 Time building geometry restraints manager: 1.46 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 4540 1.34 - 1.46: 2102 1.46 - 1.57: 6911 1.57 - 1.69: 9 1.69 - 1.81: 120 Bond restraints: 13682 Sorted by residual: bond pdb=" C4 ADP C 501 " pdb=" C5 ADP C 501 " ideal model delta sigma weight residual 1.490 1.460 0.030 2.00e-02 2.50e+03 2.27e+00 bond pdb=" C THR C 322 " pdb=" N PRO C 323 " ideal model delta sigma weight residual 1.334 1.369 -0.035 2.34e-02 1.83e+03 2.24e+00 bond pdb=" C GLY D 95 " pdb=" N THR D 96 " ideal model delta sigma weight residual 1.332 1.311 0.021 1.40e-02 5.10e+03 2.24e+00 bond pdb=" C4 ADP A 501 " pdb=" C5 ADP A 501 " ideal model delta sigma weight residual 1.490 1.463 0.027 2.00e-02 2.50e+03 1.83e+00 bond pdb=" C4 ADP B 501 " pdb=" C5 ADP B 501 " ideal model delta sigma weight residual 1.490 1.463 0.027 2.00e-02 2.50e+03 1.79e+00 ... (remaining 13677 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.29: 17921 2.29 - 4.57: 468 4.57 - 6.86: 65 6.86 - 9.14: 9 9.14 - 11.43: 4 Bond angle restraints: 18467 Sorted by residual: angle pdb=" C GLY F 333 " pdb=" N THR F 334 " pdb=" CA THR F 334 " ideal model delta sigma weight residual 121.54 132.97 -11.43 1.91e+00 2.74e-01 3.58e+01 angle pdb=" N GLN E 93 " pdb=" CA GLN E 93 " pdb=" C GLN E 93 " ideal model delta sigma weight residual 110.13 104.28 5.85 1.15e+00 7.56e-01 2.59e+01 angle pdb=" C ARG D 331 " pdb=" N LYS D 332 " pdb=" CA LYS D 332 " ideal model delta sigma weight residual 121.54 131.08 -9.54 1.91e+00 2.74e-01 2.50e+01 angle pdb=" C GLU F 293 " pdb=" N ASP F 294 " pdb=" CA ASP F 294 " ideal model delta sigma weight residual 121.54 130.73 -9.19 1.91e+00 2.74e-01 2.32e+01 angle pdb=" C GLY D 333 " pdb=" N THR D 334 " pdb=" CA THR D 334 " ideal model delta sigma weight residual 121.54 130.35 -8.81 1.91e+00 2.74e-01 2.13e+01 ... (remaining 18462 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 27.88: 8042 27.88 - 55.77: 350 55.77 - 83.65: 34 83.65 - 111.54: 5 111.54 - 139.42: 3 Dihedral angle restraints: 8434 sinusoidal: 3419 harmonic: 5015 Sorted by residual: dihedral pdb=" O1B ADP B 501 " pdb=" O3A ADP B 501 " pdb=" PB ADP B 501 " pdb=" PA ADP B 501 " ideal model delta sinusoidal sigma weight residual 300.00 160.58 139.42 1 2.00e+01 2.50e-03 4.22e+01 dihedral pdb=" O1B ADP C 501 " pdb=" O3A ADP C 501 " pdb=" PB ADP C 501 " pdb=" PA ADP C 501 " ideal model delta sinusoidal sigma weight residual -60.00 66.40 -126.40 1 2.00e+01 2.50e-03 3.82e+01 dihedral pdb=" C5' ADP C 501 " pdb=" O5' ADP C 501 " pdb=" PA ADP C 501 " pdb=" O2A ADP C 501 " ideal model delta sinusoidal sigma weight residual -60.00 57.96 -117.95 1 2.00e+01 2.50e-03 3.53e+01 ... (remaining 8431 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.060: 1648 0.060 - 0.120: 451 0.120 - 0.180: 82 0.180 - 0.240: 17 0.240 - 0.300: 2 Chirality restraints: 2200 Sorted by residual: chirality pdb=" CB ILE F 247 " pdb=" CA ILE F 247 " pdb=" CG1 ILE F 247 " pdb=" CG2 ILE F 247 " both_signs ideal model delta sigma weight residual False 2.64 2.35 0.30 2.00e-01 2.50e+01 2.25e+00 chirality pdb=" CB THR C 313 " pdb=" CA THR C 313 " pdb=" OG1 THR C 313 " pdb=" CG2 THR C 313 " both_signs ideal model delta sigma weight residual False 2.55 2.27 0.28 2.00e-01 2.50e+01 1.99e+00 chirality pdb=" CB VAL C 215 " pdb=" CA VAL C 215 " pdb=" CG1 VAL C 215 " pdb=" CG2 VAL C 215 " both_signs ideal model delta sigma weight residual False -2.63 -2.39 -0.24 2.00e-01 2.50e+01 1.43e+00 ... (remaining 2197 not shown) Planarity restraints: 2352 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C THR A 322 " 0.046 5.00e-02 4.00e+02 6.80e-02 7.40e+00 pdb=" N PRO A 323 " -0.118 5.00e-02 4.00e+02 pdb=" CA PRO A 323 " 0.033 5.00e-02 4.00e+02 pdb=" CD PRO A 323 " 0.039 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C SER B 257 " -0.041 5.00e-02 4.00e+02 6.21e-02 6.17e+00 pdb=" N PRO B 258 " 0.107 5.00e-02 4.00e+02 pdb=" CA PRO B 258 " -0.032 5.00e-02 4.00e+02 pdb=" CD PRO B 258 " -0.034 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C THR B 278 " -0.040 5.00e-02 4.00e+02 6.09e-02 5.93e+00 pdb=" N PRO B 279 " 0.105 5.00e-02 4.00e+02 pdb=" CA PRO B 279 " -0.031 5.00e-02 4.00e+02 pdb=" CD PRO B 279 " -0.034 5.00e-02 4.00e+02 ... (remaining 2349 not shown) Histogram of nonbonded interaction distances: 2.25 - 2.78: 3347 2.78 - 3.31: 12226 3.31 - 3.84: 21467 3.84 - 4.37: 25975 4.37 - 4.90: 42085 Nonbonded interactions: 105100 Sorted by model distance: nonbonded pdb=" OG SER C 117 " pdb=" O ILE C 120 " model vdw 2.254 3.040 nonbonded pdb=" OG SER E 257 " pdb=" O ILE E 261 " model vdw 2.256 3.040 nonbonded pdb=" OG1 THR B 88 " pdb=" O MET B 275 " model vdw 2.270 3.040 nonbonded pdb=" O THR D 131 " pdb=" OG1 THR D 135 " model vdw 2.274 3.040 nonbonded pdb=" OH TYR C 116 " pdb=" O MET C 217 " model vdw 2.277 3.040 ... (remaining 105095 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 26 through 138 or resid 147 through 155 or resid 188 throu \ gh 501)) selection = (chain 'B' and (resid 26 through 362 or resid 501)) selection = (chain 'C' and (resid 26 through 138 or resid 147 through 155 or resid 188 throu \ gh 362 or resid 501)) } ncs_group { reference = (chain 'D' and (resid 61 through 164 or resid 188 through 363)) selection = (chain 'E' and (resid 61 through 146 or resid 157 through 363)) selection = (chain 'F' and (resid 61 through 146 or resid 157 through 164 or resid 188 throu \ gh 363)) } 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=0.01 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.740 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.150 Check model and map are aligned: 0.030 Set scattering table: 0.030 Process input model: 12.410 Find NCS groups from input model: 0.260 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.180 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 15.840 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7720 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 : 0.006 0.060 13684 Z= 0.275 Angle : 0.921 11.431 18467 Z= 0.506 Chirality : 0.058 0.300 2200 Planarity : 0.006 0.068 2352 Dihedral : 15.599 139.419 5188 Min Nonbonded Distance : 2.254 Molprobity Statistics. All-atom Clashscore : 6.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.61 % Favored : 95.39 % Rotamer: Outliers : 0.21 % Allowed : 9.62 % Favored : 90.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: -5.45 (0.15), residues: 1712 helix: -4.50 (0.08), residues: 821 sheet: -2.84 (0.32), residues: 219 loop : -2.33 (0.21), residues: 672 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG B 273 TYR 0.021 0.002 TYR E 345 PHE 0.028 0.002 PHE C 223 TRP 0.011 0.002 TRP F 198 HIS 0.009 0.002 HIS A 152 Details of bonding type rmsd covalent geometry : bond 0.00604 (13682) covalent geometry : angle 0.92056 (18467) hydrogen bonds : bond 0.29918 ( 418) hydrogen bonds : angle 10.23650 ( 1173) Misc. bond : bond 0.00021 ( 2) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3424 Ramachandran restraints generated. 1712 Oldfield, 0 Emsley, 1712 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3424 Ramachandran restraints generated. 1712 Oldfield, 0 Emsley, 1712 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 388 residues out of total 1471 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 385 time to evaluate : 0.454 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 27 GLN cc_start: 0.6893 (tm-30) cc_final: 0.6576 (tm-30) REVERT: A 81 LEU cc_start: 0.8881 (tt) cc_final: 0.8667 (tt) REVERT: A 114 GLU cc_start: 0.8024 (tm-30) cc_final: 0.7629 (tp30) REVERT: A 227 HIS cc_start: 0.8271 (t-90) cc_final: 0.8001 (t-170) REVERT: A 282 MET cc_start: 0.8031 (mmt) cc_final: 0.7498 (mmt) REVERT: A 295 ILE cc_start: 0.9081 (mm) cc_final: 0.8826 (mm) REVERT: A 303 ASN cc_start: 0.7654 (m-40) cc_final: 0.7405 (m110) REVERT: B 121 LYS cc_start: 0.7856 (ptmt) cc_final: 0.7023 (mttm) REVERT: B 196 LYS cc_start: 0.8697 (tttt) cc_final: 0.8463 (tttp) REVERT: B 197 TYR cc_start: 0.6403 (m-10) cc_final: 0.5657 (m-80) REVERT: B 338 LYS cc_start: 0.8276 (tttt) cc_final: 0.8043 (tttt) REVERT: C 58 ASN cc_start: 0.8600 (t0) cc_final: 0.8244 (t0) REVERT: C 69 LEU cc_start: 0.9273 (mp) cc_final: 0.9055 (mp) REVERT: C 91 THR cc_start: 0.8686 (m) cc_final: 0.8269 (p) REVERT: C 131 ARG cc_start: 0.7987 (mtp180) cc_final: 0.7394 (mtp-110) REVERT: C 134 ILE cc_start: 0.8679 (mt) cc_final: 0.8453 (mm) REVERT: C 225 TYR cc_start: 0.8553 (t80) cc_final: 0.8205 (t80) REVERT: C 319 GLN cc_start: 0.8328 (mm-40) cc_final: 0.7366 (tm-30) REVERT: C 350 ASP cc_start: 0.8139 (p0) cc_final: 0.7781 (p0) REVERT: D 140 ARG cc_start: 0.8351 (ttm170) cc_final: 0.8147 (ptp-170) REVERT: D 308 ILE cc_start: 0.8956 (mm) cc_final: 0.8160 (mm) REVERT: E 128 MET cc_start: 0.3750 (ptp) cc_final: 0.3034 (pmm) REVERT: E 139 ARG cc_start: 0.5826 (mtm-85) cc_final: 0.5586 (mmt90) REVERT: E 140 ARG cc_start: 0.8197 (mtt180) cc_final: 0.7949 (mtp180) REVERT: E 161 GLU cc_start: 0.6135 (mt-10) cc_final: 0.5926 (mp0) REVERT: E 199 ARG cc_start: 0.6306 (mtm180) cc_final: 0.5177 (tmm160) REVERT: E 203 LYS cc_start: 0.4244 (mmtt) cc_final: 0.2500 (tptm) REVERT: E 221 ILE cc_start: 0.9162 (tp) cc_final: 0.8800 (tp) REVERT: E 225 SER cc_start: 0.8842 (t) cc_final: 0.8547 (t) REVERT: E 316 TYR cc_start: 0.8591 (t80) cc_final: 0.8347 (t80) REVERT: E 319 GLN cc_start: 0.7671 (mt0) cc_final: 0.6910 (mm-40) REVERT: E 330 LYS cc_start: 0.8669 (mmmt) cc_final: 0.8452 (mtpt) REVERT: F 68 ARG cc_start: 0.7004 (mtp180) cc_final: 0.6708 (mtp-110) REVERT: F 75 LEU cc_start: 0.8811 (mt) cc_final: 0.8260 (mt) REVERT: F 82 LYS cc_start: 0.8111 (mmtt) cc_final: 0.7854 (mttm) REVERT: F 220 ASP cc_start: 0.8093 (p0) cc_final: 0.7751 (m-30) REVERT: F 228 ASN cc_start: 0.7621 (t0) cc_final: 0.7336 (t0) REVERT: F 319 GLN cc_start: 0.8756 (mt0) cc_final: 0.7806 (tt0) outliers start: 3 outliers final: 1 residues processed: 388 average time/residue: 0.1318 time to fit residues: 70.3946 Evaluate side-chains 277 residues out of total 1471 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 276 time to evaluate : 0.505 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 172 random chunks: chunk 98 optimal weight: 0.4980 chunk 107 optimal weight: 2.9990 chunk 10 optimal weight: 0.9980 chunk 66 optimal weight: 1.9990 chunk 130 optimal weight: 0.7980 chunk 124 optimal weight: 1.9990 chunk 103 optimal weight: 0.0270 chunk 77 optimal weight: 1.9990 chunk 122 optimal weight: 6.9990 chunk 91 optimal weight: 0.9990 chunk 149 optimal weight: 3.9990 overall best weight: 0.6640 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 325 ASN A 340 HIS B 191 ASN C 34 HIS C 99 GLN C 227 HIS C 304 HIS D 64 GLN D 107 GLN D 160 HIS D 217 HIS D 319 GLN D 337 GLN D 362 GLN E 64 GLN E 160 HIS F 259 HIS F 319 GLN F 337 GLN Total number of N/Q/H flips: 19 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3366 r_free = 0.3366 target = 0.111233 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3165 r_free = 0.3165 target = 0.097926 restraints weight = 27900.768| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3204 r_free = 0.3204 target = 0.100402 restraints weight = 16662.664| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3233 r_free = 0.3233 target = 0.102202 restraints weight = 11216.762| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3252 r_free = 0.3252 target = 0.103414 restraints weight = 8168.367| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3265 r_free = 0.3265 target = 0.104257 restraints weight = 6398.999| |-----------------------------------------------------------------------------| r_work (final): 0.3263 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3262 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3262 r_free = 0.3262 target_work(ls_wunit_k1) = 0.104 | | occupancies: max = 1.00 min = 0.01 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3261 r_free = 0.3261 target_work(ls_wunit_k1) = 0.104 | | occupancies: max = 1.00 min = 0.47 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3261 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7634 moved from start: 0.2280 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 13684 Z= 0.128 Angle : 0.630 8.767 18467 Z= 0.325 Chirality : 0.044 0.169 2200 Planarity : 0.005 0.049 2352 Dihedral : 8.195 103.843 1908 Min Nonbonded Distance : 2.469 Molprobity Statistics. All-atom Clashscore : 8.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.32 % Favored : 95.68 % Rotamer: Outliers : 0.14 % Allowed : 5.56 % Favored : 94.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -4.38 (0.17), residues: 1712 helix: -3.47 (0.12), residues: 853 sheet: -2.43 (0.32), residues: 229 loop : -1.83 (0.23), residues: 630 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 273 TYR 0.015 0.002 TYR E 345 PHE 0.014 0.001 PHE D 115 TRP 0.021 0.002 TRP E 198 HIS 0.004 0.001 HIS C 304 Details of bonding type rmsd covalent geometry : bond 0.00277 (13682) covalent geometry : angle 0.63033 (18467) hydrogen bonds : bond 0.04527 ( 418) hydrogen bonds : angle 5.81542 ( 1173) Misc. bond : bond 0.00011 ( 2) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3424 Ramachandran restraints generated. 1712 Oldfield, 0 Emsley, 1712 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3424 Ramachandran restraints generated. 1712 Oldfield, 0 Emsley, 1712 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 361 residues out of total 1471 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 359 time to evaluate : 0.431 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 63 CYS cc_start: 0.8890 (m) cc_final: 0.8539 (m) REVERT: A 114 GLU cc_start: 0.7772 (tm-30) cc_final: 0.7389 (tp30) REVERT: A 227 HIS cc_start: 0.8116 (t-90) cc_final: 0.7655 (t-170) REVERT: A 282 MET cc_start: 0.7977 (mmt) cc_final: 0.7404 (mmt) REVERT: A 303 ASN cc_start: 0.8082 (m-40) cc_final: 0.7745 (m-40) REVERT: B 121 LYS cc_start: 0.7770 (ptmt) cc_final: 0.6967 (mttp) REVERT: B 127 MET cc_start: 0.8715 (mmm) cc_final: 0.8327 (mmp) REVERT: B 197 TYR cc_start: 0.6493 (m-10) cc_final: 0.5627 (m-80) REVERT: B 271 ILE cc_start: 0.8749 (mp) cc_final: 0.8457 (mt) REVERT: C 58 ASN cc_start: 0.8751 (t0) cc_final: 0.8335 (t0) REVERT: C 134 ILE cc_start: 0.8513 (mt) cc_final: 0.8186 (mm) REVERT: C 197 TYR cc_start: 0.7381 (m-80) cc_final: 0.7180 (m-80) REVERT: C 225 TYR cc_start: 0.8820 (t80) cc_final: 0.8377 (t80) REVERT: C 240 PHE cc_start: 0.8734 (m-80) cc_final: 0.8508 (m-80) REVERT: C 319 GLN cc_start: 0.8255 (mm-40) cc_final: 0.7425 (tm-30) REVERT: C 323 PRO cc_start: 0.9291 (Cg_exo) cc_final: 0.9028 (Cg_endo) REVERT: D 140 ARG cc_start: 0.8332 (ttm170) cc_final: 0.7759 (ttm110) REVERT: D 217 HIS cc_start: 0.7490 (OUTLIER) cc_final: 0.7214 (p90) REVERT: D 308 ILE cc_start: 0.8886 (mm) cc_final: 0.8112 (mm) REVERT: E 76 GLU cc_start: 0.6958 (mm-30) cc_final: 0.6729 (mm-30) REVERT: E 128 MET cc_start: 0.3688 (ptp) cc_final: 0.3149 (pmm) REVERT: E 132 GLU cc_start: 0.7441 (tp30) cc_final: 0.7216 (tp30) REVERT: E 140 ARG cc_start: 0.8184 (mtt180) cc_final: 0.7739 (mtp85) REVERT: E 199 ARG cc_start: 0.6244 (mtm180) cc_final: 0.5211 (tmm160) REVERT: E 203 LYS cc_start: 0.3819 (mmtt) cc_final: 0.2233 (tptm) REVERT: E 221 ILE cc_start: 0.8929 (tp) cc_final: 0.8697 (tp) REVERT: E 319 GLN cc_start: 0.7678 (mt0) cc_final: 0.6838 (mm-40) REVERT: E 327 VAL cc_start: 0.8741 (m) cc_final: 0.8418 (p) REVERT: E 330 LYS cc_start: 0.8589 (mmmt) cc_final: 0.8305 (mtpt) REVERT: E 350 ASP cc_start: 0.8825 (p0) cc_final: 0.8239 (p0) REVERT: F 68 ARG cc_start: 0.7001 (mtp180) cc_final: 0.6720 (mtp-110) REVERT: F 77 MET cc_start: 0.9158 (ttp) cc_final: 0.7484 (tmm) REVERT: F 82 LYS cc_start: 0.8045 (mmtt) cc_final: 0.7444 (mttm) REVERT: F 105 MET cc_start: 0.8053 (mmp) cc_final: 0.7344 (mmt) outliers start: 2 outliers final: 0 residues processed: 361 average time/residue: 0.1119 time to fit residues: 59.0010 Evaluate side-chains 272 residues out of total 1471 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 271 time to evaluate : 0.490 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 172 random chunks: chunk 30 optimal weight: 7.9990 chunk 45 optimal weight: 0.0070 chunk 66 optimal weight: 3.9990 chunk 40 optimal weight: 0.6980 chunk 163 optimal weight: 3.9990 chunk 94 optimal weight: 0.0770 chunk 112 optimal weight: 2.9990 chunk 78 optimal weight: 3.9990 chunk 61 optimal weight: 0.0000 chunk 11 optimal weight: 0.0020 chunk 114 optimal weight: 3.9990 overall best weight: 0.1568 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 32 HIS C 304 HIS D 166 ASN D 319 GLN ** E 244 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3414 r_free = 0.3414 target = 0.114593 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3224 r_free = 0.3224 target = 0.101640 restraints weight = 27498.512| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3263 r_free = 0.3263 target = 0.104154 restraints weight = 16109.314| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3291 r_free = 0.3291 target = 0.106046 restraints weight = 10642.167| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3309 r_free = 0.3309 target = 0.107249 restraints weight = 7636.024| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3324 r_free = 0.3324 target = 0.108198 restraints weight = 5921.695| |-----------------------------------------------------------------------------| r_work (final): 0.3323 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3324 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3324 r_free = 0.3324 target_work(ls_wunit_k1) = 0.108 | | occupancies: max = 1.00 min = 0.47 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3324 r_free = 0.3324 target_work(ls_wunit_k1) = 0.108 | | occupancies: max = 1.00 min = 0.70 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3324 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7554 moved from start: 0.3094 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 13684 Z= 0.103 Angle : 0.592 8.022 18467 Z= 0.298 Chirality : 0.044 0.194 2200 Planarity : 0.004 0.039 2352 Dihedral : 7.091 93.736 1908 Min Nonbonded Distance : 2.464 Molprobity Statistics. All-atom Clashscore : 7.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.68 % Favored : 96.32 % Rotamer: Outliers : 0.00 % Allowed : 3.71 % Favored : 96.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.38 (0.18), residues: 1712 helix: -2.60 (0.14), residues: 841 sheet: -2.26 (0.33), residues: 229 loop : -1.34 (0.23), residues: 642 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG B 268 TYR 0.020 0.001 TYR A 197 PHE 0.023 0.001 PHE B 223 TRP 0.007 0.001 TRP D 198 HIS 0.005 0.001 HIS E 160 Details of bonding type rmsd covalent geometry : bond 0.00220 (13682) covalent geometry : angle 0.59198 (18467) hydrogen bonds : bond 0.03375 ( 418) hydrogen bonds : angle 5.00782 ( 1173) Misc. bond : bond 0.00020 ( 2) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3424 Ramachandran restraints generated. 1712 Oldfield, 0 Emsley, 1712 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3424 Ramachandran restraints generated. 1712 Oldfield, 0 Emsley, 1712 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 386 residues out of total 1471 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 386 time to evaluate : 0.504 Fit side-chains revert: symmetry clash REVERT: A 63 CYS cc_start: 0.8766 (m) cc_final: 0.8504 (m) REVERT: A 200 GLN cc_start: 0.7633 (tt0) cc_final: 0.6887 (tp40) REVERT: A 282 MET cc_start: 0.8016 (mmt) cc_final: 0.7510 (mmt) REVERT: A 303 ASN cc_start: 0.8065 (m-40) cc_final: 0.7682 (m-40) REVERT: A 310 THR cc_start: 0.8639 (t) cc_final: 0.8228 (t) REVERT: B 121 LYS cc_start: 0.7899 (ptmt) cc_final: 0.7191 (mttm) REVERT: B 127 MET cc_start: 0.8715 (mmm) cc_final: 0.8098 (mmm) REVERT: B 197 TYR cc_start: 0.6348 (m-10) cc_final: 0.5604 (m-80) REVERT: B 231 GLU cc_start: 0.7327 (mt-10) cc_final: 0.6908 (tt0) REVERT: B 275 MET cc_start: 0.8298 (mmm) cc_final: 0.8057 (mmm) REVERT: B 304 HIS cc_start: 0.6889 (t-170) cc_final: 0.6630 (t-90) REVERT: C 75 MET cc_start: 0.6211 (tpt) cc_final: 0.5993 (tpt) REVERT: C 108 CYS cc_start: 0.7647 (p) cc_final: 0.7233 (t) REVERT: C 225 TYR cc_start: 0.8823 (t80) cc_final: 0.8373 (t80) REVERT: C 314 LEU cc_start: 0.8625 (tt) cc_final: 0.8337 (tt) REVERT: C 323 PRO cc_start: 0.9195 (Cg_exo) cc_final: 0.8946 (Cg_endo) REVERT: D 140 ARG cc_start: 0.8297 (ttm170) cc_final: 0.7932 (ttm170) REVERT: D 308 ILE cc_start: 0.8665 (mm) cc_final: 0.8012 (mm) REVERT: E 128 MET cc_start: 0.3596 (ptp) cc_final: 0.3062 (pmm) REVERT: E 131 THR cc_start: 0.7967 (p) cc_final: 0.7662 (t) REVERT: E 132 GLU cc_start: 0.7767 (tp30) cc_final: 0.7368 (tp30) REVERT: E 140 ARG cc_start: 0.7963 (mtt180) cc_final: 0.7571 (mtp85) REVERT: E 199 ARG cc_start: 0.6092 (mtm180) cc_final: 0.5166 (tmm160) REVERT: E 203 LYS cc_start: 0.3570 (mmtt) cc_final: 0.2054 (tptt) REVERT: E 232 GLU cc_start: 0.7666 (mm-30) cc_final: 0.7461 (mp0) REVERT: E 327 VAL cc_start: 0.8597 (m) cc_final: 0.8361 (p) REVERT: E 330 LYS cc_start: 0.8596 (mmmt) cc_final: 0.8185 (mtmt) REVERT: E 350 ASP cc_start: 0.8669 (p0) cc_final: 0.8066 (p0) REVERT: F 68 ARG cc_start: 0.7051 (mtp180) cc_final: 0.6753 (mmm160) REVERT: F 77 MET cc_start: 0.8977 (ttp) cc_final: 0.7616 (tmm) REVERT: F 313 SER cc_start: 0.7872 (t) cc_final: 0.7671 (p) outliers start: 0 outliers final: 0 residues processed: 386 average time/residue: 0.1184 time to fit residues: 65.9117 Evaluate side-chains 277 residues out of total 1471 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 277 time to evaluate : 0.413 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 172 random chunks: chunk 91 optimal weight: 4.9990 chunk 27 optimal weight: 0.7980 chunk 15 optimal weight: 1.9990 chunk 100 optimal weight: 3.9990 chunk 40 optimal weight: 3.9990 chunk 167 optimal weight: 0.0570 chunk 69 optimal weight: 0.9980 chunk 14 optimal weight: 1.9990 chunk 46 optimal weight: 2.9990 chunk 151 optimal weight: 0.4980 chunk 102 optimal weight: 0.8980 overall best weight: 0.6498 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 216 HIS C 259 HIS C 304 HIS D 217 HIS D 319 GLN E 228 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3396 r_free = 0.3396 target = 0.113220 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3208 r_free = 0.3208 target = 0.100862 restraints weight = 27936.081| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3244 r_free = 0.3244 target = 0.103129 restraints weight = 17101.687| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3270 r_free = 0.3270 target = 0.104746 restraints weight = 11638.933| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 21)----------------| | r_work = 0.3286 r_free = 0.3286 target = 0.105809 restraints weight = 8586.897| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 38)----------------| | r_work = 0.3301 r_free = 0.3301 target = 0.106720 restraints weight = 6818.880| |-----------------------------------------------------------------------------| r_work (final): 0.3302 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3301 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3301 r_free = 0.3301 target_work(ls_wunit_k1) = 0.107 | | occupancies: max = 1.00 min = 0.70 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3301 r_free = 0.3301 target_work(ls_wunit_k1) = 0.107 | | occupancies: max = 1.00 min = 1.00 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3301 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7583 moved from start: 0.3423 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 13684 Z= 0.115 Angle : 0.604 7.697 18467 Z= 0.298 Chirality : 0.046 0.482 2200 Planarity : 0.003 0.035 2352 Dihedral : 6.749 88.939 1908 Min Nonbonded Distance : 2.392 Molprobity Statistics. All-atom Clashscore : 7.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.45 % Favored : 96.55 % Rotamer: Outliers : 0.14 % Allowed : 3.85 % Favored : 96.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.83 (0.19), residues: 1712 helix: -2.13 (0.16), residues: 843 sheet: -2.02 (0.34), residues: 224 loop : -1.09 (0.24), residues: 645 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 315 TYR 0.017 0.001 TYR A 197 PHE 0.014 0.001 PHE B 223 TRP 0.006 0.001 TRP D 198 HIS 0.005 0.001 HIS A 227 Details of bonding type rmsd covalent geometry : bond 0.00259 (13682) covalent geometry : angle 0.60377 (18467) hydrogen bonds : bond 0.03089 ( 418) hydrogen bonds : angle 4.87753 ( 1173) Misc. bond : bond 0.00278 ( 2) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3424 Ramachandran restraints generated. 1712 Oldfield, 0 Emsley, 1712 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3424 Ramachandran restraints generated. 1712 Oldfield, 0 Emsley, 1712 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 350 residues out of total 1471 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 348 time to evaluate : 0.508 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 63 CYS cc_start: 0.8766 (m) cc_final: 0.8506 (m) REVERT: A 127 MET cc_start: 0.6837 (ttt) cc_final: 0.6618 (ttm) REVERT: A 282 MET cc_start: 0.7902 (mmt) cc_final: 0.7583 (mmt) REVERT: A 295 ILE cc_start: 0.9423 (mp) cc_final: 0.9105 (mm) REVERT: A 310 THR cc_start: 0.8706 (t) cc_final: 0.8368 (t) REVERT: B 121 LYS cc_start: 0.7927 (ptmt) cc_final: 0.7251 (mttm) REVERT: B 127 MET cc_start: 0.8662 (mmm) cc_final: 0.8392 (mmp) REVERT: B 231 GLU cc_start: 0.7277 (mt-10) cc_final: 0.6810 (tt0) REVERT: B 275 MET cc_start: 0.8191 (mmm) cc_final: 0.7970 (mmm) REVERT: B 304 HIS cc_start: 0.6986 (t-170) cc_final: 0.6577 (t-90) REVERT: C 75 MET cc_start: 0.6270 (tpt) cc_final: 0.5985 (tpt) REVERT: C 131 ARG cc_start: 0.8564 (mtp180) cc_final: 0.8342 (mtt-85) REVERT: C 225 TYR cc_start: 0.8853 (t80) cc_final: 0.8392 (t80) REVERT: C 254 ASP cc_start: 0.8035 (t0) cc_final: 0.7679 (t0) REVERT: C 323 PRO cc_start: 0.9247 (Cg_exo) cc_final: 0.9004 (Cg_endo) REVERT: D 140 ARG cc_start: 0.8374 (ttm170) cc_final: 0.8065 (ttm170) REVERT: D 217 HIS cc_start: 0.7471 (OUTLIER) cc_final: 0.7175 (p90) REVERT: D 288 ILE cc_start: 0.8952 (pt) cc_final: 0.8706 (tp) REVERT: D 308 ILE cc_start: 0.8790 (mm) cc_final: 0.8217 (mm) REVERT: D 358 MET cc_start: 0.7444 (mpp) cc_final: 0.7138 (mpp) REVERT: E 105 MET cc_start: 0.8783 (mpp) cc_final: 0.8539 (mpp) REVERT: E 128 MET cc_start: 0.3571 (ptp) cc_final: 0.2966 (pmm) REVERT: E 131 THR cc_start: 0.7972 (p) cc_final: 0.7664 (t) REVERT: E 132 GLU cc_start: 0.7789 (tp30) cc_final: 0.6927 (tp30) REVERT: E 135 THR cc_start: 0.7998 (m) cc_final: 0.7731 (m) REVERT: E 136 GLN cc_start: 0.8480 (pm20) cc_final: 0.7738 (pm20) REVERT: E 140 ARG cc_start: 0.8107 (mtt180) cc_final: 0.7620 (mtp85) REVERT: E 199 ARG cc_start: 0.6077 (mtm180) cc_final: 0.5176 (tmm160) REVERT: E 203 LYS cc_start: 0.3406 (mmtt) cc_final: 0.2239 (tptm) REVERT: E 221 ILE cc_start: 0.8966 (tp) cc_final: 0.8716 (tp) REVERT: E 327 VAL cc_start: 0.8658 (m) cc_final: 0.8458 (p) REVERT: E 345 TYR cc_start: 0.7687 (t80) cc_final: 0.7462 (t80) REVERT: E 358 MET cc_start: 0.8180 (mmm) cc_final: 0.7858 (mmm) REVERT: F 68 ARG cc_start: 0.7100 (mtp180) cc_final: 0.6879 (mmm160) REVERT: F 77 MET cc_start: 0.9050 (ttp) cc_final: 0.7698 (tmm) REVERT: F 231 LEU cc_start: 0.8728 (tt) cc_final: 0.8474 (tp) REVERT: F 297 MET cc_start: 0.7550 (ttm) cc_final: 0.7341 (ttp) outliers start: 2 outliers final: 0 residues processed: 350 average time/residue: 0.1071 time to fit residues: 55.7019 Evaluate side-chains 267 residues out of total 1471 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 266 time to evaluate : 0.527 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 172 random chunks: chunk 72 optimal weight: 0.0570 chunk 103 optimal weight: 3.9990 chunk 15 optimal weight: 1.9990 chunk 16 optimal weight: 0.9980 chunk 92 optimal weight: 6.9990 chunk 2 optimal weight: 0.0020 chunk 46 optimal weight: 3.9990 chunk 98 optimal weight: 2.9990 chunk 64 optimal weight: 4.9990 chunk 45 optimal weight: 0.8980 chunk 122 optimal weight: 0.0570 overall best weight: 0.4024 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 129 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 129 ASN C 246 ASN C 304 HIS D 319 GLN E 228 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3408 r_free = 0.3408 target = 0.114345 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3222 r_free = 0.3222 target = 0.101868 restraints weight = 27821.982| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3257 r_free = 0.3257 target = 0.104118 restraints weight = 16911.697| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3282 r_free = 0.3282 target = 0.105762 restraints weight = 11508.346| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 39)----------------| | r_work = 0.3301 r_free = 0.3301 target = 0.106954 restraints weight = 8479.379| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3313 r_free = 0.3313 target = 0.107722 restraints weight = 6672.737| |-----------------------------------------------------------------------------| r_work (final): 0.3317 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7563 moved from start: 0.3732 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 13684 Z= 0.101 Angle : 0.586 7.595 18467 Z= 0.288 Chirality : 0.045 0.446 2200 Planarity : 0.003 0.035 2352 Dihedral : 6.516 90.824 1908 Min Nonbonded Distance : 2.439 Molprobity Statistics. All-atom Clashscore : 8.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.50 % Favored : 96.50 % Rotamer: Outliers : 0.00 % Allowed : 3.50 % Favored : 96.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.40 (0.19), residues: 1712 helix: -1.78 (0.16), residues: 832 sheet: -1.87 (0.35), residues: 223 loop : -0.88 (0.24), residues: 657 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG D 331 TYR 0.018 0.001 TYR D 357 PHE 0.011 0.001 PHE F 348 TRP 0.007 0.001 TRP D 198 HIS 0.007 0.001 HIS C 32 Details of bonding type rmsd covalent geometry : bond 0.00225 (13682) covalent geometry : angle 0.58624 (18467) hydrogen bonds : bond 0.02867 ( 418) hydrogen bonds : angle 4.65254 ( 1173) Misc. bond : bond 0.00287 ( 2) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3424 Ramachandran restraints generated. 1712 Oldfield, 0 Emsley, 1712 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3424 Ramachandran restraints generated. 1712 Oldfield, 0 Emsley, 1712 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 341 residues out of total 1471 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 341 time to evaluate : 0.410 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 63 CYS cc_start: 0.8723 (m) cc_final: 0.8438 (m) REVERT: A 127 MET cc_start: 0.7161 (ttt) cc_final: 0.6871 (ttm) REVERT: A 247 CYS cc_start: 0.8358 (p) cc_final: 0.7365 (t) REVERT: A 275 MET cc_start: 0.7554 (mtm) cc_final: 0.7228 (mtm) REVERT: A 282 MET cc_start: 0.7847 (mmt) cc_final: 0.7175 (mmt) REVERT: A 295 ILE cc_start: 0.9422 (mp) cc_final: 0.9085 (mm) REVERT: A 310 THR cc_start: 0.8657 (t) cc_final: 0.8395 (t) REVERT: B 70 ILE cc_start: 0.8074 (mt) cc_final: 0.7786 (mt) REVERT: B 121 LYS cc_start: 0.7981 (ptmt) cc_final: 0.7302 (mttm) REVERT: B 127 MET cc_start: 0.8576 (mmm) cc_final: 0.8211 (mmm) REVERT: B 231 GLU cc_start: 0.7220 (mt-10) cc_final: 0.6811 (tt0) REVERT: B 237 ILE cc_start: 0.8664 (tp) cc_final: 0.8441 (tt) REVERT: B 275 MET cc_start: 0.8242 (mmm) cc_final: 0.8031 (mmm) REVERT: B 304 HIS cc_start: 0.6783 (t-170) cc_final: 0.6571 (t-90) REVERT: C 148 ASP cc_start: 0.6400 (m-30) cc_final: 0.5557 (p0) REVERT: C 225 TYR cc_start: 0.8864 (t80) cc_final: 0.8374 (t80) REVERT: C 323 PRO cc_start: 0.9211 (Cg_exo) cc_final: 0.8958 (Cg_endo) REVERT: D 105 MET cc_start: 0.8440 (tpp) cc_final: 0.8181 (tpp) REVERT: D 140 ARG cc_start: 0.8223 (ttm170) cc_final: 0.7790 (ttp-170) REVERT: D 288 ILE cc_start: 0.8880 (pt) cc_final: 0.8571 (tp) REVERT: D 308 ILE cc_start: 0.8742 (mm) cc_final: 0.8249 (mm) REVERT: E 98 LYS cc_start: 0.8653 (mtmt) cc_final: 0.8375 (mtmm) REVERT: E 128 MET cc_start: 0.3600 (ptp) cc_final: 0.3005 (pmm) REVERT: E 131 THR cc_start: 0.7975 (p) cc_final: 0.7686 (t) REVERT: E 140 ARG cc_start: 0.8062 (mtt180) cc_final: 0.7724 (mtp85) REVERT: E 199 ARG cc_start: 0.6083 (mtm180) cc_final: 0.5178 (tmm160) REVERT: E 203 LYS cc_start: 0.3412 (mmtt) cc_final: 0.2289 (tptm) REVERT: E 221 ILE cc_start: 0.8960 (tp) cc_final: 0.8704 (tp) REVERT: E 284 GLN cc_start: 0.7837 (tp40) cc_final: 0.7581 (tp40) REVERT: E 345 TYR cc_start: 0.7646 (t80) cc_final: 0.7384 (t80) REVERT: E 358 MET cc_start: 0.8082 (mmm) cc_final: 0.7824 (mmm) REVERT: F 77 MET cc_start: 0.8945 (ttp) cc_final: 0.7833 (tmm) REVERT: F 128 MET cc_start: 0.6992 (mtt) cc_final: 0.6743 (mtt) REVERT: F 231 LEU cc_start: 0.8713 (tt) cc_final: 0.8427 (tp) outliers start: 0 outliers final: 0 residues processed: 341 average time/residue: 0.1040 time to fit residues: 52.9612 Evaluate side-chains 265 residues out of total 1471 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 265 time to evaluate : 0.461 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 172 random chunks: chunk 168 optimal weight: 0.0370 chunk 112 optimal weight: 5.9990 chunk 49 optimal weight: 0.4980 chunk 101 optimal weight: 5.9990 chunk 128 optimal weight: 2.9990 chunk 80 optimal weight: 2.9990 chunk 53 optimal weight: 0.1980 chunk 41 optimal weight: 0.1980 chunk 153 optimal weight: 0.9990 chunk 46 optimal weight: 1.9990 chunk 63 optimal weight: 0.9990 overall best weight: 0.3860 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 304 HIS D 136 GLN D 217 HIS D 319 GLN E 228 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3424 r_free = 0.3424 target = 0.115210 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3239 r_free = 0.3239 target = 0.102845 restraints weight = 27828.692| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 47)----------------| | r_work = 0.3275 r_free = 0.3275 target = 0.105165 restraints weight = 16888.712| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3301 r_free = 0.3301 target = 0.106800 restraints weight = 11405.589| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3317 r_free = 0.3317 target = 0.107849 restraints weight = 8370.623| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 37)----------------| | r_work = 0.3330 r_free = 0.3330 target = 0.108721 restraints weight = 6626.087| |-----------------------------------------------------------------------------| r_work (final): 0.3333 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7550 moved from start: 0.3991 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 13684 Z= 0.100 Angle : 0.581 7.808 18467 Z= 0.287 Chirality : 0.045 0.420 2200 Planarity : 0.003 0.035 2352 Dihedral : 6.219 84.056 1908 Min Nonbonded Distance : 2.370 Molprobity Statistics. All-atom Clashscore : 8.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.10 % Favored : 96.90 % Rotamer: Outliers : 0.07 % Allowed : 1.58 % Favored : 98.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.10 (0.20), residues: 1712 helix: -1.48 (0.17), residues: 830 sheet: -1.77 (0.35), residues: 219 loop : -0.80 (0.24), residues: 663 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG D 307 TYR 0.014 0.001 TYR A 197 PHE 0.011 0.001 PHE F 348 TRP 0.006 0.001 TRP D 198 HIS 0.009 0.001 HIS D 160 Details of bonding type rmsd covalent geometry : bond 0.00225 (13682) covalent geometry : angle 0.58097 (18467) hydrogen bonds : bond 0.02667 ( 418) hydrogen bonds : angle 4.56470 ( 1173) Misc. bond : bond 0.00300 ( 2) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3424 Ramachandran restraints generated. 1712 Oldfield, 0 Emsley, 1712 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3424 Ramachandran restraints generated. 1712 Oldfield, 0 Emsley, 1712 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 346 residues out of total 1471 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 345 time to evaluate : 0.516 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 63 CYS cc_start: 0.8733 (m) cc_final: 0.8470 (m) REVERT: A 127 MET cc_start: 0.7076 (ttt) cc_final: 0.6786 (ttm) REVERT: A 187 ARG cc_start: 0.7347 (ttt180) cc_final: 0.7136 (tmt170) REVERT: A 282 MET cc_start: 0.7789 (mmt) cc_final: 0.7309 (mmt) REVERT: B 121 LYS cc_start: 0.7974 (ptmt) cc_final: 0.7328 (mttm) REVERT: B 127 MET cc_start: 0.8561 (mmm) cc_final: 0.8188 (mmm) REVERT: B 231 GLU cc_start: 0.7233 (mt-10) cc_final: 0.6868 (tt0) REVERT: C 148 ASP cc_start: 0.6199 (m-30) cc_final: 0.5377 (p0) REVERT: C 225 TYR cc_start: 0.8834 (t80) cc_final: 0.8350 (t80) REVERT: C 254 ASP cc_start: 0.7766 (t0) cc_final: 0.7543 (t0) REVERT: C 323 PRO cc_start: 0.9189 (Cg_exo) cc_final: 0.8926 (Cg_endo) REVERT: D 308 ILE cc_start: 0.8731 (mm) cc_final: 0.8266 (mm) REVERT: E 128 MET cc_start: 0.3714 (ptp) cc_final: 0.3173 (pmm) REVERT: E 131 THR cc_start: 0.8074 (p) cc_final: 0.7704 (t) REVERT: E 140 ARG cc_start: 0.8015 (mtt180) cc_final: 0.7713 (mtp85) REVERT: E 199 ARG cc_start: 0.6077 (mtm180) cc_final: 0.5292 (ttp80) REVERT: E 203 LYS cc_start: 0.3286 (mmtt) cc_final: 0.2279 (tptm) REVERT: E 319 GLN cc_start: 0.7565 (mt0) cc_final: 0.6955 (mm-40) REVERT: E 345 TYR cc_start: 0.7715 (t80) cc_final: 0.7373 (t80) REVERT: F 68 ARG cc_start: 0.7086 (mtp180) cc_final: 0.6852 (mmm160) REVERT: F 77 MET cc_start: 0.8955 (ttp) cc_final: 0.8454 (tmm) REVERT: F 105 MET cc_start: 0.7337 (mmp) cc_final: 0.6364 (tpp) REVERT: F 128 MET cc_start: 0.6851 (mtt) cc_final: 0.5219 (mmp) REVERT: F 194 LYS cc_start: 0.8245 (tptm) cc_final: 0.7503 (tppt) REVERT: F 231 LEU cc_start: 0.8785 (tt) cc_final: 0.8488 (tp) outliers start: 1 outliers final: 0 residues processed: 346 average time/residue: 0.1104 time to fit residues: 55.6805 Evaluate side-chains 250 residues out of total 1471 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 250 time to evaluate : 0.409 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 172 random chunks: chunk 119 optimal weight: 4.9990 chunk 139 optimal weight: 0.0980 chunk 56 optimal weight: 0.9980 chunk 112 optimal weight: 0.9980 chunk 104 optimal weight: 0.7980 chunk 102 optimal weight: 3.9990 chunk 40 optimal weight: 0.6980 chunk 153 optimal weight: 4.9990 chunk 107 optimal weight: 4.9990 chunk 86 optimal weight: 3.9990 chunk 23 optimal weight: 5.9990 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 129 ASN B 56 GLN C 304 HIS D 217 HIS D 319 GLN E 356 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3408 r_free = 0.3408 target = 0.114198 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3217 r_free = 0.3217 target = 0.101639 restraints weight = 27839.461| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3253 r_free = 0.3253 target = 0.103874 restraints weight = 17087.648| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3279 r_free = 0.3279 target = 0.105552 restraints weight = 11695.473| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3296 r_free = 0.3296 target = 0.106630 restraints weight = 8637.939| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3308 r_free = 0.3308 target = 0.107405 restraints weight = 6843.620| |-----------------------------------------------------------------------------| r_work (final): 0.3309 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7577 moved from start: 0.4080 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 13684 Z= 0.115 Angle : 0.587 7.915 18467 Z= 0.290 Chirality : 0.045 0.453 2200 Planarity : 0.003 0.037 2352 Dihedral : 6.097 81.363 1908 Min Nonbonded Distance : 2.433 Molprobity Statistics. All-atom Clashscore : 8.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.50 % Favored : 96.50 % Rotamer: Outliers : 0.14 % Allowed : 1.65 % Favored : 98.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.94 (0.20), residues: 1712 helix: -1.31 (0.17), residues: 846 sheet: -1.75 (0.35), residues: 215 loop : -0.76 (0.24), residues: 651 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 131 TYR 0.017 0.001 TYR B 277 PHE 0.015 0.001 PHE F 348 TRP 0.006 0.001 TRP D 198 HIS 0.007 0.001 HIS D 160 Details of bonding type rmsd covalent geometry : bond 0.00265 (13682) covalent geometry : angle 0.58656 (18467) hydrogen bonds : bond 0.02766 ( 418) hydrogen bonds : angle 4.50006 ( 1173) Misc. bond : bond 0.00251 ( 2) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3424 Ramachandran restraints generated. 1712 Oldfield, 0 Emsley, 1712 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3424 Ramachandran restraints generated. 1712 Oldfield, 0 Emsley, 1712 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 326 residues out of total 1471 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 324 time to evaluate : 0.482 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 63 CYS cc_start: 0.8757 (m) cc_final: 0.8508 (m) REVERT: A 127 MET cc_start: 0.7176 (ttt) cc_final: 0.6936 (ttm) REVERT: A 282 MET cc_start: 0.7771 (mmt) cc_final: 0.7301 (mmt) REVERT: B 121 LYS cc_start: 0.8006 (ptmt) cc_final: 0.7345 (mttm) REVERT: B 127 MET cc_start: 0.8549 (mmm) cc_final: 0.8195 (mmm) REVERT: B 231 GLU cc_start: 0.7128 (mt-10) cc_final: 0.6843 (tt0) REVERT: B 341 VAL cc_start: 0.9152 (t) cc_final: 0.8850 (t) REVERT: C 58 ASN cc_start: 0.8618 (t0) cc_final: 0.8292 (t0) REVERT: C 131 ARG cc_start: 0.8275 (mtt-85) cc_final: 0.7187 (mtp-110) REVERT: C 148 ASP cc_start: 0.6336 (m-30) cc_final: 0.5443 (p0) REVERT: C 225 TYR cc_start: 0.8833 (t80) cc_final: 0.8334 (t80) REVERT: C 254 ASP cc_start: 0.7902 (t0) cc_final: 0.7644 (t0) REVERT: C 307 GLU cc_start: 0.6592 (mt-10) cc_final: 0.6272 (mp0) REVERT: C 323 PRO cc_start: 0.9218 (Cg_exo) cc_final: 0.8953 (Cg_endo) REVERT: C 350 ASP cc_start: 0.7986 (p0) cc_final: 0.7654 (p0) REVERT: D 140 ARG cc_start: 0.8272 (ttm170) cc_final: 0.5537 (tpt90) REVERT: D 308 ILE cc_start: 0.8734 (mm) cc_final: 0.8260 (mm) REVERT: E 128 MET cc_start: 0.3881 (ptp) cc_final: 0.3339 (pmm) REVERT: E 130 LYS cc_start: 0.6761 (tttp) cc_final: 0.6232 (tttp) REVERT: E 131 THR cc_start: 0.8238 (p) cc_final: 0.7861 (t) REVERT: E 203 LYS cc_start: 0.3335 (mmtt) cc_final: 0.2367 (tptm) REVERT: E 345 TYR cc_start: 0.7765 (t80) cc_final: 0.7460 (t80) REVERT: F 68 ARG cc_start: 0.7126 (mtp180) cc_final: 0.6847 (mmm160) REVERT: F 77 MET cc_start: 0.8996 (ttp) cc_final: 0.8589 (tmm) REVERT: F 105 MET cc_start: 0.7430 (mmp) cc_final: 0.6516 (tpp) REVERT: F 128 MET cc_start: 0.6973 (mtt) cc_final: 0.5184 (mmp) REVERT: F 231 LEU cc_start: 0.8798 (tt) cc_final: 0.8507 (tp) outliers start: 2 outliers final: 0 residues processed: 326 average time/residue: 0.1112 time to fit residues: 53.6000 Evaluate side-chains 250 residues out of total 1471 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 250 time to evaluate : 0.419 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 172 random chunks: chunk 80 optimal weight: 1.9990 chunk 85 optimal weight: 2.9990 chunk 156 optimal weight: 0.8980 chunk 112 optimal weight: 0.9990 chunk 145 optimal weight: 2.9990 chunk 48 optimal weight: 0.9980 chunk 137 optimal weight: 0.7980 chunk 47 optimal weight: 0.2980 chunk 4 optimal weight: 0.9980 chunk 75 optimal weight: 2.9990 chunk 157 optimal weight: 0.9990 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 304 HIS B 304 HIS C 259 HIS C 304 HIS ** E 217 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3389 r_free = 0.3389 target = 0.113070 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3207 r_free = 0.3207 target = 0.101068 restraints weight = 27761.695| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3242 r_free = 0.3242 target = 0.103339 restraints weight = 16790.748| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3265 r_free = 0.3265 target = 0.104819 restraints weight = 11288.671| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3284 r_free = 0.3284 target = 0.105991 restraints weight = 8379.414| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.3297 r_free = 0.3297 target = 0.106839 restraints weight = 6538.578| |-----------------------------------------------------------------------------| r_work (final): 0.3299 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7583 moved from start: 0.4150 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 13684 Z= 0.121 Angle : 0.599 8.647 18467 Z= 0.296 Chirality : 0.045 0.481 2200 Planarity : 0.003 0.037 2352 Dihedral : 6.005 81.996 1908 Min Nonbonded Distance : 2.387 Molprobity Statistics. All-atom Clashscore : 8.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.50 % Favored : 96.50 % Rotamer: Outliers : 0.00 % Allowed : 1.10 % Favored : 98.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.84 (0.20), residues: 1712 helix: -1.21 (0.17), residues: 848 sheet: -1.69 (0.35), residues: 215 loop : -0.74 (0.24), residues: 649 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 273 TYR 0.018 0.001 TYR A 277 PHE 0.014 0.001 PHE F 348 TRP 0.007 0.001 TRP E 198 HIS 0.006 0.001 HIS D 160 Details of bonding type rmsd covalent geometry : bond 0.00278 (13682) covalent geometry : angle 0.59868 (18467) hydrogen bonds : bond 0.02746 ( 418) hydrogen bonds : angle 4.50089 ( 1173) Misc. bond : bond 0.00300 ( 2) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3424 Ramachandran restraints generated. 1712 Oldfield, 0 Emsley, 1712 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3424 Ramachandran restraints generated. 1712 Oldfield, 0 Emsley, 1712 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 324 residues out of total 1471 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 324 time to evaluate : 0.514 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 63 CYS cc_start: 0.8765 (m) cc_final: 0.8564 (m) REVERT: A 282 MET cc_start: 0.7736 (mmt) cc_final: 0.7356 (mmt) REVERT: A 319 GLN cc_start: 0.8156 (pp30) cc_final: 0.7842 (pp30) REVERT: B 121 LYS cc_start: 0.7992 (ptmt) cc_final: 0.7354 (mttm) REVERT: B 127 MET cc_start: 0.8488 (mmm) cc_final: 0.8222 (mmm) REVERT: B 231 GLU cc_start: 0.7044 (mt-10) cc_final: 0.6826 (tt0) REVERT: B 304 HIS cc_start: 0.6672 (t-90) cc_final: 0.6296 (t-90) REVERT: C 58 ASN cc_start: 0.8605 (t0) cc_final: 0.8256 (t0) REVERT: C 148 ASP cc_start: 0.6304 (m-30) cc_final: 0.5468 (p0) REVERT: C 225 TYR cc_start: 0.8800 (t80) cc_final: 0.8314 (t80) REVERT: C 254 ASP cc_start: 0.7905 (t0) cc_final: 0.7641 (t0) REVERT: C 323 PRO cc_start: 0.9206 (Cg_exo) cc_final: 0.8960 (Cg_endo) REVERT: C 350 ASP cc_start: 0.8007 (p0) cc_final: 0.7645 (p0) REVERT: D 140 ARG cc_start: 0.8256 (ttm170) cc_final: 0.7508 (ttm170) REVERT: D 308 ILE cc_start: 0.8737 (mm) cc_final: 0.8378 (mm) REVERT: E 128 MET cc_start: 0.3877 (ptp) cc_final: 0.3535 (ptp) REVERT: E 130 LYS cc_start: 0.6697 (tttp) cc_final: 0.6065 (mptt) REVERT: E 203 LYS cc_start: 0.3242 (mmtt) cc_final: 0.2089 (tptm) REVERT: E 345 TYR cc_start: 0.7841 (t80) cc_final: 0.7541 (t80) REVERT: F 77 MET cc_start: 0.8955 (ttp) cc_final: 0.8571 (tmm) REVERT: F 128 MET cc_start: 0.6885 (mtt) cc_final: 0.5127 (mmp) outliers start: 0 outliers final: 0 residues processed: 324 average time/residue: 0.1075 time to fit residues: 51.3400 Evaluate side-chains 244 residues out of total 1471 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 244 time to evaluate : 0.490 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 172 random chunks: chunk 128 optimal weight: 0.3980 chunk 22 optimal weight: 2.9990 chunk 93 optimal weight: 0.0070 chunk 38 optimal weight: 4.9990 chunk 145 optimal weight: 3.9990 chunk 108 optimal weight: 0.9990 chunk 37 optimal weight: 0.9980 chunk 26 optimal weight: 0.5980 chunk 101 optimal weight: 0.4980 chunk 164 optimal weight: 1.9990 chunk 42 optimal weight: 6.9990 overall best weight: 0.4998 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 304 HIS C 259 HIS C 304 HIS D 217 HIS D 319 GLN E 284 GLN F 228 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3406 r_free = 0.3406 target = 0.114361 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3215 r_free = 0.3215 target = 0.101683 restraints weight = 27802.139| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3252 r_free = 0.3252 target = 0.104054 restraints weight = 16515.736| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3280 r_free = 0.3280 target = 0.105815 restraints weight = 11039.788| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3296 r_free = 0.3296 target = 0.106937 restraints weight = 8010.166| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.3311 r_free = 0.3311 target = 0.107889 restraints weight = 6274.668| |-----------------------------------------------------------------------------| r_work (final): 0.3310 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7562 moved from start: 0.4327 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 13684 Z= 0.106 Angle : 0.590 9.217 18467 Z= 0.292 Chirality : 0.045 0.501 2200 Planarity : 0.003 0.037 2352 Dihedral : 5.913 80.126 1908 Min Nonbonded Distance : 2.360 Molprobity Statistics. All-atom Clashscore : 8.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.62 % Favored : 96.38 % Rotamer: Outliers : 0.07 % Allowed : 0.55 % Favored : 99.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.68 (0.20), residues: 1712 helix: -1.09 (0.17), residues: 839 sheet: -1.72 (0.36), residues: 207 loop : -0.63 (0.24), residues: 666 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 273 TYR 0.012 0.001 TYR F 302 PHE 0.015 0.001 PHE F 348 TRP 0.007 0.001 TRP E 198 HIS 0.006 0.001 HIS D 160 Details of bonding type rmsd covalent geometry : bond 0.00240 (13682) covalent geometry : angle 0.59019 (18467) hydrogen bonds : bond 0.02659 ( 418) hydrogen bonds : angle 4.39104 ( 1173) Misc. bond : bond 0.00317 ( 2) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3424 Ramachandran restraints generated. 1712 Oldfield, 0 Emsley, 1712 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3424 Ramachandran restraints generated. 1712 Oldfield, 0 Emsley, 1712 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 316 residues out of total 1471 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 315 time to evaluate : 0.532 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 63 CYS cc_start: 0.8745 (m) cc_final: 0.8525 (m) REVERT: A 275 MET cc_start: 0.7419 (mtm) cc_final: 0.7067 (mtm) REVERT: A 282 MET cc_start: 0.7662 (mmt) cc_final: 0.7439 (mmt) REVERT: B 121 LYS cc_start: 0.7916 (ptmt) cc_final: 0.7282 (mttm) REVERT: B 127 MET cc_start: 0.8431 (mmm) cc_final: 0.8205 (mmm) REVERT: B 304 HIS cc_start: 0.6819 (t-90) cc_final: 0.6422 (t-90) REVERT: C 58 ASN cc_start: 0.8573 (t0) cc_final: 0.8221 (t0) REVERT: C 148 ASP cc_start: 0.6256 (m-30) cc_final: 0.5398 (p0) REVERT: C 225 TYR cc_start: 0.8804 (t80) cc_final: 0.8337 (t80) REVERT: C 254 ASP cc_start: 0.7886 (t0) cc_final: 0.7634 (t0) REVERT: C 323 PRO cc_start: 0.9190 (Cg_exo) cc_final: 0.8947 (Cg_endo) REVERT: C 350 ASP cc_start: 0.7948 (p0) cc_final: 0.7605 (p0) REVERT: D 132 GLU cc_start: 0.7018 (mm-30) cc_final: 0.6770 (mm-30) REVERT: D 140 ARG cc_start: 0.8232 (ttm170) cc_final: 0.7520 (ttm170) REVERT: D 308 ILE cc_start: 0.8737 (mm) cc_final: 0.8336 (mm) REVERT: E 128 MET cc_start: 0.3809 (ptp) cc_final: 0.3499 (ptp) REVERT: E 130 LYS cc_start: 0.6765 (tttp) cc_final: 0.6206 (tttp) REVERT: E 199 ARG cc_start: 0.6143 (mtm180) cc_final: 0.5405 (ttp80) REVERT: E 203 LYS cc_start: 0.3340 (mmtt) cc_final: 0.2212 (tptm) REVERT: E 345 TYR cc_start: 0.7755 (t80) cc_final: 0.7473 (t80) REVERT: F 105 MET cc_start: 0.7269 (mmp) cc_final: 0.6095 (tpp) REVERT: F 128 MET cc_start: 0.6890 (mtt) cc_final: 0.5221 (mmp) REVERT: F 244 ASN cc_start: 0.7682 (p0) cc_final: 0.7043 (t0) REVERT: F 310 LEU cc_start: 0.9043 (mt) cc_final: 0.7930 (pp) outliers start: 1 outliers final: 0 residues processed: 316 average time/residue: 0.1028 time to fit residues: 48.6623 Evaluate side-chains 246 residues out of total 1471 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 246 time to evaluate : 0.433 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 172 random chunks: chunk 106 optimal weight: 0.7980 chunk 29 optimal weight: 0.9990 chunk 41 optimal weight: 2.9990 chunk 61 optimal weight: 6.9990 chunk 117 optimal weight: 7.9990 chunk 83 optimal weight: 4.9990 chunk 35 optimal weight: 2.9990 chunk 21 optimal weight: 0.9980 chunk 168 optimal weight: 0.5980 chunk 139 optimal weight: 3.9990 chunk 81 optimal weight: 0.0870 overall best weight: 0.6960 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 304 HIS C 304 HIS D 217 HIS D 319 GLN ** E 217 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 160 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3398 r_free = 0.3398 target = 0.113813 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3216 r_free = 0.3216 target = 0.101718 restraints weight = 27697.715| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3251 r_free = 0.3251 target = 0.103965 restraints weight = 16887.158| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3277 r_free = 0.3277 target = 0.105629 restraints weight = 11447.374| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3294 r_free = 0.3294 target = 0.106742 restraints weight = 8356.451| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 39)----------------| | r_work = 0.3307 r_free = 0.3307 target = 0.107584 restraints weight = 6576.536| |-----------------------------------------------------------------------------| r_work (final): 0.3306 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7574 moved from start: 0.4375 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 13684 Z= 0.118 Angle : 0.609 9.701 18467 Z= 0.303 Chirality : 0.045 0.522 2200 Planarity : 0.003 0.038 2352 Dihedral : 5.920 79.518 1908 Min Nonbonded Distance : 2.380 Molprobity Statistics. All-atom Clashscore : 8.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.56 % Favored : 96.44 % Rotamer: Outliers : 0.07 % Allowed : 0.27 % Favored : 99.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: -1.57 (0.20), residues: 1712 helix: -0.99 (0.18), residues: 841 sheet: -1.65 (0.36), residues: 206 loop : -0.61 (0.24), residues: 665 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG B 273 TYR 0.011 0.001 TYR A 197 PHE 0.014 0.001 PHE F 348 TRP 0.007 0.001 TRP E 198 HIS 0.006 0.001 HIS D 160 Details of bonding type rmsd covalent geometry : bond 0.00271 (13682) covalent geometry : angle 0.60854 (18467) hydrogen bonds : bond 0.02734 ( 418) hydrogen bonds : angle 4.56987 ( 1173) Misc. bond : bond 0.00374 ( 2) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3424 Ramachandran restraints generated. 1712 Oldfield, 0 Emsley, 1712 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3424 Ramachandran restraints generated. 1712 Oldfield, 0 Emsley, 1712 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 308 residues out of total 1471 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 307 time to evaluate : 0.461 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 63 CYS cc_start: 0.8780 (m) cc_final: 0.8548 (m) REVERT: A 275 MET cc_start: 0.7425 (mtm) cc_final: 0.7041 (mtm) REVERT: A 282 MET cc_start: 0.7750 (mmt) cc_final: 0.7509 (mmt) REVERT: B 121 LYS cc_start: 0.7899 (ptmt) cc_final: 0.7271 (mttm) REVERT: B 127 MET cc_start: 0.8415 (mmm) cc_final: 0.8214 (mmm) REVERT: B 304 HIS cc_start: 0.6885 (t-90) cc_final: 0.6464 (t-90) REVERT: C 58 ASN cc_start: 0.8533 (t0) cc_final: 0.8184 (t0) REVERT: C 148 ASP cc_start: 0.6210 (m-30) cc_final: 0.5442 (p0) REVERT: C 225 TYR cc_start: 0.8800 (t80) cc_final: 0.8322 (t80) REVERT: C 254 ASP cc_start: 0.7924 (t0) cc_final: 0.7684 (t0) REVERT: C 323 PRO cc_start: 0.9199 (Cg_exo) cc_final: 0.8945 (Cg_endo) REVERT: C 350 ASP cc_start: 0.7956 (p0) cc_final: 0.7549 (p0) REVERT: D 77 MET cc_start: 0.8865 (ttm) cc_final: 0.8658 (ttm) REVERT: D 308 ILE cc_start: 0.8622 (mm) cc_final: 0.8403 (mm) REVERT: E 128 MET cc_start: 0.3789 (ptp) cc_final: 0.3542 (ptp) REVERT: E 130 LYS cc_start: 0.6804 (tttp) cc_final: 0.6164 (mptt) REVERT: E 203 LYS cc_start: 0.3390 (mmtt) cc_final: 0.2224 (tptm) REVERT: E 342 LYS cc_start: 0.8931 (mtmm) cc_final: 0.8714 (mtmm) REVERT: E 345 TYR cc_start: 0.7732 (t80) cc_final: 0.7395 (t80) REVERT: E 358 MET cc_start: 0.7967 (tpt) cc_final: 0.7458 (tpt) REVERT: F 128 MET cc_start: 0.6877 (mtt) cc_final: 0.5222 (mmp) REVERT: F 244 ASN cc_start: 0.7686 (p0) cc_final: 0.7080 (t0) REVERT: F 310 LEU cc_start: 0.9035 (mt) cc_final: 0.7925 (pp) outliers start: 1 outliers final: 0 residues processed: 308 average time/residue: 0.1025 time to fit residues: 47.8630 Evaluate side-chains 252 residues out of total 1471 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 252 time to evaluate : 0.368 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 172 random chunks: chunk 152 optimal weight: 0.9990 chunk 84 optimal weight: 0.8980 chunk 57 optimal weight: 0.8980 chunk 169 optimal weight: 0.7980 chunk 18 optimal weight: 0.6980 chunk 21 optimal weight: 2.9990 chunk 144 optimal weight: 3.9990 chunk 42 optimal weight: 0.0170 chunk 154 optimal weight: 2.9990 chunk 168 optimal weight: 2.9990 chunk 135 optimal weight: 0.8980 overall best weight: 0.6618 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 304 HIS C 304 HIS D 217 HIS D 319 GLN ** E 217 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3398 r_free = 0.3398 target = 0.113910 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3216 r_free = 0.3216 target = 0.101808 restraints weight = 27937.362| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3251 r_free = 0.3251 target = 0.104107 restraints weight = 16901.930| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3276 r_free = 0.3276 target = 0.105724 restraints weight = 11352.165| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3294 r_free = 0.3294 target = 0.106851 restraints weight = 8289.701| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 41)----------------| | r_work = 0.3309 r_free = 0.3309 target = 0.107799 restraints weight = 6473.781| |-----------------------------------------------------------------------------| r_work (final): 0.3310 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7569 moved from start: 0.4447 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 13684 Z= 0.115 Angle : 0.600 9.268 18467 Z= 0.298 Chirality : 0.045 0.483 2200 Planarity : 0.003 0.038 2352 Dihedral : 5.799 78.564 1908 Min Nonbonded Distance : 2.337 Molprobity Statistics. All-atom Clashscore : 8.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.74 % Favored : 96.26 % Rotamer: Outliers : 0.07 % Allowed : 0.55 % Favored : 99.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.47 (0.20), residues: 1712 helix: -0.92 (0.18), residues: 840 sheet: -1.63 (0.36), residues: 206 loop : -0.52 (0.24), residues: 666 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 273 TYR 0.014 0.001 TYR F 302 PHE 0.013 0.001 PHE F 348 TRP 0.008 0.001 TRP F 198 HIS 0.006 0.001 HIS D 160 Details of bonding type rmsd covalent geometry : bond 0.00265 (13682) covalent geometry : angle 0.60006 (18467) hydrogen bonds : bond 0.02698 ( 418) hydrogen bonds : angle 4.48834 ( 1173) Misc. bond : bond 0.00339 ( 2) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1987.95 seconds wall clock time: 35 minutes 11.70 seconds (2111.70 seconds total)