Starting phenix.real_space_refine on Thu Jul 31 15:44:43 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7aho_11789/07_2025/7aho_11789.cif Found real_map, /net/cci-nas-00/data/ceres_data/7aho_11789/07_2025/7aho_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/7aho_11789/07_2025/7aho_11789.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7aho_11789/07_2025/7aho_11789.map" model { file = "/net/cci-nas-00/data/ceres_data/7aho_11789/07_2025/7aho_11789.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7aho_11789/07_2025/7aho_11789.cif" } resolution = 4.18 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.003 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): 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/modules/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: {'PHE:plan': 1, 'ARG: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: {'PHE:plan': 1, 'ARG:plan': 1, 'ASN:plan1': 1, 'HIS:plan': 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: 10.94, per 1000 atoms: 0.81 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: 3.78 Conformation dependent library (CDL) restraints added in 2.6 seconds 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: 1.77 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: 4.21 Time building geometry restraints manager: 4.47 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 362 or resid 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: 1.610 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.470 Check model and map are aligned: 0.090 Set scattering table: 0.130 Process input model: 37.500 Find NCS groups from input model: 1.090 Set up NCS constraints: 0.090 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:3.290 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 44.290 ------------------------------------------------------------------------------- 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -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 TRP 0.011 0.002 TRP F 198 HIS 0.009 0.002 HIS A 152 PHE 0.028 0.002 PHE C 223 TYR 0.021 0.002 TYR E 345 ARG 0.012 0.001 ARG B 273 Details of bonding type rmsd hydrogen bonds : bond 0.29918 ( 418) hydrogen bonds : angle 10.23650 ( 1173) covalent geometry : bond 0.00604 (13682) covalent geometry : angle 0.92056 (18467) 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 : 1.652 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: 0.7630 (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: 0.3034 time to fit residues: 161.2216 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 : 1.575 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 172 random chunks: chunk 145 optimal weight: 0.9990 chunk 130 optimal weight: 0.7980 chunk 72 optimal weight: 0.8980 chunk 44 optimal weight: 0.9980 chunk 87 optimal weight: 2.9990 chunk 69 optimal weight: 2.9990 chunk 134 optimal weight: 1.9990 chunk 52 optimal weight: 0.6980 chunk 81 optimal weight: 0.8980 chunk 100 optimal weight: 3.9990 chunk 156 optimal weight: 0.9990 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 ** E 217 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 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 = 0.3353 r_free = 0.3353 target = 0.110379 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3151 r_free = 0.3151 target = 0.097079 restraints weight = 28054.335| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3190 r_free = 0.3190 target = 0.099531 restraints weight = 16764.076| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3219 r_free = 0.3219 target = 0.101320 restraints weight = 11257.156| |-----------------------------------------------------------------------------| r_work (final): 0.3216 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3215 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3215 r_free = 0.3215 target_work(ls_wunit_k1) = 0.101 | | occupancies: max = 1.00 min = 0.01 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3214 r_free = 0.3214 target_work(ls_wunit_k1) = 0.101 | | occupancies: max = 1.00 min = 0.56 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3214 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7682 moved from start: 0.2142 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.057 13684 Z= 0.146 Angle : 0.653 8.965 18467 Z= 0.338 Chirality : 0.045 0.169 2200 Planarity : 0.005 0.052 2352 Dihedral : 8.447 109.423 1908 Min Nonbonded Distance : 2.467 Molprobity Statistics. All-atom Clashscore : 8.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.44 % Favored : 95.56 % Rotamer: Outliers : 0.21 % Allowed : 5.63 % Favored : 94.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.42 (0.16), residues: 1712 helix: -3.48 (0.12), residues: 855 sheet: -2.49 (0.31), residues: 229 loop : -1.88 (0.22), residues: 628 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.003 TRP E 198 HIS 0.004 0.001 HIS C 304 PHE 0.014 0.001 PHE D 115 TYR 0.016 0.002 TYR E 345 ARG 0.004 0.000 ARG D 69 Details of bonding type rmsd hydrogen bonds : bond 0.05087 ( 418) hydrogen bonds : angle 6.01375 ( 1173) covalent geometry : bond 0.00322 (13682) covalent geometry : angle 0.65286 (18467) Misc. bond : bond 0.00018 ( 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 352 residues out of total 1471 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 349 time to evaluate : 1.586 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 114 GLU cc_start: 0.7830 (tm-30) cc_final: 0.7459 (tp30) REVERT: A 227 HIS cc_start: 0.8152 (t-90) cc_final: 0.7865 (t-170) REVERT: A 282 MET cc_start: 0.7992 (mmt) cc_final: 0.7431 (mmt) REVERT: A 303 ASN cc_start: 0.8127 (m-40) cc_final: 0.7782 (m-40) REVERT: B 121 LYS cc_start: 0.7790 (ptmt) cc_final: 0.6997 (mttm) REVERT: B 127 MET cc_start: 0.8795 (mmm) cc_final: 0.8444 (mmp) REVERT: B 197 TYR cc_start: 0.6563 (m-10) cc_final: 0.5667 (m-80) REVERT: B 271 ILE cc_start: 0.8782 (mp) cc_final: 0.8514 (mt) REVERT: B 295 ILE cc_start: 0.8214 (pt) cc_final: 0.7980 (mm) REVERT: C 58 ASN cc_start: 0.8768 (t0) cc_final: 0.8335 (t0) REVERT: C 134 ILE cc_start: 0.8533 (mt) cc_final: 0.8222 (mm) REVERT: C 197 TYR cc_start: 0.7407 (m-80) cc_final: 0.7167 (m-80) REVERT: C 225 TYR cc_start: 0.8797 (t80) cc_final: 0.8363 (t80) REVERT: C 319 GLN cc_start: 0.8292 (mm-40) cc_final: 0.7434 (tm-30) REVERT: C 323 PRO cc_start: 0.9322 (Cg_exo) cc_final: 0.9078 (Cg_endo) REVERT: D 140 ARG cc_start: 0.8337 (ttm170) cc_final: 0.7766 (ttm110) REVERT: D 217 HIS cc_start: 0.7517 (OUTLIER) cc_final: 0.7227 (p90) REVERT: D 308 ILE cc_start: 0.8894 (mm) cc_final: 0.8335 (mm) REVERT: E 76 GLU cc_start: 0.7014 (mm-30) cc_final: 0.6790 (mm-30) REVERT: E 128 MET cc_start: 0.3659 (ptp) cc_final: 0.3055 (pmm) REVERT: E 140 ARG cc_start: 0.8220 (mtt180) cc_final: 0.7790 (mtp85) REVERT: E 199 ARG cc_start: 0.6238 (mtm180) cc_final: 0.5191 (tmm160) REVERT: E 203 LYS cc_start: 0.3847 (mmtt) cc_final: 0.2258 (tptm) REVERT: E 221 ILE cc_start: 0.8964 (tp) cc_final: 0.8729 (tp) REVERT: E 228 ASN cc_start: 0.8272 (t0) cc_final: 0.7869 (t0) REVERT: E 319 GLN cc_start: 0.7746 (mt0) cc_final: 0.6945 (mm-40) REVERT: E 327 VAL cc_start: 0.8797 (m) cc_final: 0.8459 (p) REVERT: E 330 LYS cc_start: 0.8646 (mmmt) cc_final: 0.8333 (mtpt) REVERT: E 350 ASP cc_start: 0.8890 (p0) cc_final: 0.8314 (p0) REVERT: F 68 ARG cc_start: 0.6998 (mtp180) cc_final: 0.6696 (mtp-110) REVERT: F 77 MET cc_start: 0.9211 (ttp) cc_final: 0.8786 (ttm) REVERT: F 82 LYS cc_start: 0.8045 (mmtt) cc_final: 0.7670 (mttm) REVERT: F 105 MET cc_start: 0.8058 (mmp) cc_final: 0.7465 (mmt) REVERT: F 158 SER cc_start: 0.7806 (m) cc_final: 0.7602 (t) REVERT: F 218 MET cc_start: 0.9107 (mmm) cc_final: 0.8804 (mmt) REVERT: F 220 ASP cc_start: 0.8189 (p0) cc_final: 0.7574 (m-30) REVERT: F 263 ILE cc_start: 0.8026 (tp) cc_final: 0.7820 (tp) outliers start: 3 outliers final: 0 residues processed: 352 average time/residue: 0.2545 time to fit residues: 129.6127 Evaluate side-chains 268 residues out of total 1471 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 267 time to evaluate : 1.553 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 172 random chunks: chunk 54 optimal weight: 2.9990 chunk 164 optimal weight: 6.9990 chunk 111 optimal weight: 3.9990 chunk 26 optimal weight: 0.9980 chunk 112 optimal weight: 4.9990 chunk 72 optimal weight: 3.9990 chunk 32 optimal weight: 5.9990 chunk 76 optimal weight: 2.9990 chunk 148 optimal weight: 0.9990 chunk 165 optimal weight: 1.9990 chunk 82 optimal weight: 1.9990 overall best weight: 1.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 32 HIS A 304 HIS C 246 ASN C 259 HIS C 304 HIS D 166 ASN D 319 GLN ** E 217 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3321 r_free = 0.3321 target = 0.108154 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3116 r_free = 0.3116 target = 0.094827 restraints weight = 28515.030| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3155 r_free = 0.3155 target = 0.097270 restraints weight = 17096.849| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3183 r_free = 0.3183 target = 0.099016 restraints weight = 11460.049| |-----------------------------------------------------------------------------| r_work (final): 0.3182 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3182 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3182 r_free = 0.3182 target_work(ls_wunit_k1) = 0.099 | | occupancies: max = 1.00 min = 0.56 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3182 r_free = 0.3182 target_work(ls_wunit_k1) = 0.099 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3182 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7729 moved from start: 0.2641 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.054 13684 Z= 0.207 Angle : 0.685 8.310 18467 Z= 0.348 Chirality : 0.047 0.211 2200 Planarity : 0.004 0.067 2352 Dihedral : 8.045 106.157 1908 Min Nonbonded Distance : 2.443 Molprobity Statistics. All-atom Clashscore : 8.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.49 % Favored : 94.51 % Rotamer: Outliers : 0.00 % Allowed : 5.56 % Favored : 94.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.65 (0.18), residues: 1712 helix: -2.70 (0.14), residues: 859 sheet: -2.37 (0.34), residues: 212 loop : -1.66 (0.23), residues: 641 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP E 198 HIS 0.005 0.001 HIS E 160 PHE 0.021 0.002 PHE B 223 TYR 0.020 0.002 TYR A 197 ARG 0.010 0.000 ARG C 60 Details of bonding type rmsd hydrogen bonds : bond 0.04075 ( 418) hydrogen bonds : angle 5.57750 ( 1173) covalent geometry : bond 0.00468 (13682) covalent geometry : angle 0.68487 (18467) Misc. bond : bond 0.00022 ( 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 319 residues out of total 1471 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 319 time to evaluate : 1.605 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 63 CYS cc_start: 0.8896 (m) cc_final: 0.8382 (m) REVERT: A 114 GLU cc_start: 0.7944 (tm-30) cc_final: 0.7386 (tp30) REVERT: A 227 HIS cc_start: 0.8205 (t-90) cc_final: 0.7920 (t-170) REVERT: A 282 MET cc_start: 0.8072 (mmt) cc_final: 0.7358 (mmt) REVERT: A 303 ASN cc_start: 0.8078 (m-40) cc_final: 0.7719 (m-40) REVERT: B 121 LYS cc_start: 0.7903 (ptmt) cc_final: 0.7111 (mttm) REVERT: B 127 MET cc_start: 0.8796 (mmm) cc_final: 0.8374 (mmp) REVERT: B 197 TYR cc_start: 0.6622 (m-10) cc_final: 0.5738 (m-80) REVERT: B 217 MET cc_start: 0.7695 (tpp) cc_final: 0.7389 (tpp) REVERT: B 231 GLU cc_start: 0.7210 (mt-10) cc_final: 0.6758 (tt0) REVERT: B 237 ILE cc_start: 0.8743 (tp) cc_final: 0.8479 (tt) REVERT: B 271 ILE cc_start: 0.8784 (mp) cc_final: 0.8536 (mt) REVERT: B 338 LYS cc_start: 0.8090 (tttt) cc_final: 0.7852 (mttt) REVERT: C 58 ASN cc_start: 0.8689 (t0) cc_final: 0.8252 (t0) REVERT: C 108 CYS cc_start: 0.7687 (p) cc_final: 0.7191 (t) REVERT: C 225 TYR cc_start: 0.8827 (t80) cc_final: 0.8450 (t80) REVERT: C 240 PHE cc_start: 0.8798 (m-80) cc_final: 0.8582 (m-80) REVERT: C 307 GLU cc_start: 0.7517 (mt-10) cc_final: 0.7070 (mt-10) REVERT: C 319 GLN cc_start: 0.8412 (mm-40) cc_final: 0.7408 (tm-30) REVERT: C 323 PRO cc_start: 0.9312 (Cg_exo) cc_final: 0.9073 (Cg_endo) REVERT: C 350 ASP cc_start: 0.8279 (p0) cc_final: 0.7909 (p0) REVERT: D 140 ARG cc_start: 0.8409 (ttm170) cc_final: 0.7913 (ttm110) REVERT: D 308 ILE cc_start: 0.8904 (mm) cc_final: 0.8341 (mm) REVERT: E 128 MET cc_start: 0.3643 (ptp) cc_final: 0.2876 (pmm) REVERT: E 131 THR cc_start: 0.8022 (p) cc_final: 0.7790 (t) REVERT: E 132 GLU cc_start: 0.7788 (tp30) cc_final: 0.7498 (tp30) REVERT: E 140 ARG cc_start: 0.8258 (mtt180) cc_final: 0.8052 (mtp180) REVERT: E 199 ARG cc_start: 0.6289 (mtm180) cc_final: 0.5193 (tmm160) REVERT: E 203 LYS cc_start: 0.3887 (mmtt) cc_final: 0.2450 (tppt) REVERT: E 327 VAL cc_start: 0.8787 (m) cc_final: 0.8495 (p) REVERT: E 330 LYS cc_start: 0.8590 (mmmt) cc_final: 0.8295 (mtpt) REVERT: F 68 ARG cc_start: 0.7032 (mtp180) cc_final: 0.6700 (mmm160) REVERT: F 105 MET cc_start: 0.7986 (mmp) cc_final: 0.6333 (mtt) REVERT: F 158 SER cc_start: 0.7816 (m) cc_final: 0.7563 (t) outliers start: 0 outliers final: 0 residues processed: 319 average time/residue: 0.2662 time to fit residues: 122.1023 Evaluate side-chains 257 residues out of total 1471 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 257 time to evaluate : 1.623 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 172 random chunks: chunk 139 optimal weight: 0.9990 chunk 152 optimal weight: 0.2980 chunk 119 optimal weight: 4.9990 chunk 170 optimal weight: 5.9990 chunk 34 optimal weight: 0.5980 chunk 41 optimal weight: 7.9990 chunk 10 optimal weight: 0.9990 chunk 9 optimal weight: 0.1980 chunk 11 optimal weight: 1.9990 chunk 138 optimal weight: 1.9990 chunk 67 optimal weight: 6.9990 overall best weight: 0.6184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 340 HIS B 32 HIS C 304 HIS D 217 HIS D 319 GLN D 356 GLN E 284 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3373 r_free = 0.3373 target = 0.111728 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3175 r_free = 0.3175 target = 0.098569 restraints weight = 27887.970| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3214 r_free = 0.3214 target = 0.101029 restraints weight = 16626.012| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3241 r_free = 0.3241 target = 0.102769 restraints weight = 11155.306| |-----------------------------------------------------------------------------| r_work (final): 0.3242 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3241 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3241 r_free = 0.3241 target_work(ls_wunit_k1) = 0.103 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3241 r_free = 0.3241 target_work(ls_wunit_k1) = 0.103 | | occupancies: max = 1.00 min = 0.97 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3241 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7655 moved from start: 0.3052 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= 0.117 Angle : 0.607 7.843 18467 Z= 0.305 Chirality : 0.045 0.163 2200 Planarity : 0.004 0.049 2352 Dihedral : 7.338 95.396 1908 Min Nonbonded Distance : 2.477 Molprobity Statistics. All-atom Clashscore : 8.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.97 % Favored : 96.03 % Rotamer: Outliers : 0.07 % Allowed : 3.23 % Favored : 96.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.04 (0.19), residues: 1712 helix: -2.18 (0.15), residues: 847 sheet: -2.16 (0.35), residues: 212 loop : -1.39 (0.23), residues: 653 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP E 198 HIS 0.009 0.001 HIS A 152 PHE 0.012 0.001 PHE E 348 TYR 0.019 0.002 TYR A 197 ARG 0.004 0.000 ARG C 60 Details of bonding type rmsd hydrogen bonds : bond 0.03348 ( 418) hydrogen bonds : angle 5.06291 ( 1173) covalent geometry : bond 0.00262 (13682) covalent geometry : angle 0.60723 (18467) Misc. bond : bond 0.00023 ( 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 340 residues out of total 1471 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 339 time to evaluate : 1.426 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 63 CYS cc_start: 0.8856 (m) cc_final: 0.8455 (m) REVERT: A 114 GLU cc_start: 0.7796 (tm-30) cc_final: 0.7230 (tp30) REVERT: A 247 CYS cc_start: 0.8388 (p) cc_final: 0.7586 (t) REVERT: A 282 MET cc_start: 0.7932 (mmt) cc_final: 0.7320 (mmt) REVERT: A 295 ILE cc_start: 0.9428 (mp) cc_final: 0.9129 (mm) REVERT: B 121 LYS cc_start: 0.7919 (ptmt) cc_final: 0.7183 (mttm) REVERT: B 127 MET cc_start: 0.8703 (mmm) cc_final: 0.8374 (mmp) REVERT: B 197 TYR cc_start: 0.6556 (m-10) cc_final: 0.5726 (m-80) REVERT: B 231 GLU cc_start: 0.7152 (mt-10) cc_final: 0.6756 (tt0) REVERT: B 338 LYS cc_start: 0.7921 (tttt) cc_final: 0.7501 (mttt) REVERT: C 58 ASN cc_start: 0.8691 (t0) cc_final: 0.8290 (t0) REVERT: C 108 CYS cc_start: 0.7773 (p) cc_final: 0.7383 (t) REVERT: C 225 TYR cc_start: 0.8841 (t80) cc_final: 0.8404 (t80) REVERT: C 319 GLN cc_start: 0.8308 (mm-40) cc_final: 0.7363 (tm-30) REVERT: C 323 PRO cc_start: 0.9245 (Cg_exo) cc_final: 0.8975 (Cg_endo) REVERT: D 140 ARG cc_start: 0.8383 (ttm170) cc_final: 0.8025 (ttm170) REVERT: D 308 ILE cc_start: 0.8769 (mm) cc_final: 0.8344 (mm) REVERT: D 358 MET cc_start: 0.7708 (mpp) cc_final: 0.7310 (mpp) REVERT: E 62 VAL cc_start: 0.7908 (m) cc_final: 0.7701 (m) REVERT: E 105 MET cc_start: 0.8764 (mpp) cc_final: 0.8530 (mpp) REVERT: E 128 MET cc_start: 0.3733 (ptp) cc_final: 0.2942 (pmm) REVERT: E 140 ARG cc_start: 0.8080 (mtt180) cc_final: 0.7823 (mtp180) REVERT: E 203 LYS cc_start: 0.3729 (mmtt) cc_final: 0.2345 (tptm) REVERT: E 327 VAL cc_start: 0.8710 (m) cc_final: 0.8454 (p) REVERT: F 68 ARG cc_start: 0.7019 (mtp180) cc_final: 0.6692 (mmm160) REVERT: F 158 SER cc_start: 0.7720 (m) cc_final: 0.7485 (t) REVERT: F 313 SER cc_start: 0.7943 (t) cc_final: 0.7650 (p) REVERT: F 315 ARG cc_start: 0.7417 (ptm160) cc_final: 0.6843 (ptm160) outliers start: 1 outliers final: 0 residues processed: 340 average time/residue: 0.2491 time to fit residues: 122.6706 Evaluate side-chains 260 residues out of total 1471 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 260 time to evaluate : 1.424 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 172 random chunks: chunk 74 optimal weight: 0.8980 chunk 95 optimal weight: 2.9990 chunk 49 optimal weight: 0.4980 chunk 13 optimal weight: 0.8980 chunk 151 optimal weight: 1.9990 chunk 43 optimal weight: 0.0370 chunk 11 optimal weight: 2.9990 chunk 166 optimal weight: 7.9990 chunk 28 optimal weight: 3.9990 chunk 15 optimal weight: 1.9990 chunk 2 optimal weight: 10.0000 overall best weight: 0.8660 ------------------------------------------------------------------------------- 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 Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3362 r_free = 0.3362 target = 0.110970 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3161 r_free = 0.3161 target = 0.097882 restraints weight = 28147.078| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3201 r_free = 0.3201 target = 0.100372 restraints weight = 16799.882| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3228 r_free = 0.3228 target = 0.102133 restraints weight = 11253.895| |-----------------------------------------------------------------------------| r_work (final): 0.3229 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3229 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3229 r_free = 0.3229 target_work(ls_wunit_k1) = 0.102 | | occupancies: max = 1.00 min = 0.97 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3229 r_free = 0.3229 target_work(ls_wunit_k1) = 0.102 | | occupancies: max = 1.00 min = 0.99 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3229 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7668 moved from start: 0.3298 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 13684 Z= 0.128 Angle : 0.603 7.766 18467 Z= 0.302 Chirality : 0.045 0.164 2200 Planarity : 0.004 0.043 2352 Dihedral : 6.985 89.672 1908 Min Nonbonded Distance : 2.454 Molprobity Statistics. All-atom Clashscore : 8.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.50 % Favored : 95.50 % Rotamer: Outliers : 0.00 % Allowed : 3.43 % Favored : 96.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.63 (0.19), residues: 1712 helix: -1.80 (0.16), residues: 850 sheet: -2.04 (0.35), residues: 213 loop : -1.23 (0.24), residues: 649 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.002 TRP E 198 HIS 0.005 0.001 HIS A 152 PHE 0.010 0.001 PHE D 115 TYR 0.018 0.002 TYR A 197 ARG 0.005 0.000 ARG A 315 Details of bonding type rmsd hydrogen bonds : bond 0.03108 ( 418) hydrogen bonds : angle 4.88975 ( 1173) covalent geometry : bond 0.00292 (13682) covalent geometry : angle 0.60329 (18467) Misc. bond : bond 0.00029 ( 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 326 residues out of total 1471 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 326 time to evaluate : 1.436 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 63 CYS cc_start: 0.8694 (m) cc_final: 0.8390 (m) REVERT: A 114 GLU cc_start: 0.7843 (tm-30) cc_final: 0.7226 (tp30) REVERT: A 116 TYR cc_start: 0.6897 (m-10) cc_final: 0.6395 (m-10) REVERT: A 127 MET cc_start: 0.6808 (ttt) cc_final: 0.6604 (ttt) REVERT: A 247 CYS cc_start: 0.8362 (p) cc_final: 0.7587 (t) REVERT: A 282 MET cc_start: 0.7948 (mmt) cc_final: 0.7490 (mmt) REVERT: A 303 ASN cc_start: 0.8290 (m110) cc_final: 0.7988 (m-40) REVERT: B 121 LYS cc_start: 0.7923 (ptmt) cc_final: 0.7220 (mttm) REVERT: B 127 MET cc_start: 0.8660 (mmm) cc_final: 0.8433 (mmp) REVERT: B 217 MET cc_start: 0.7552 (tpp) cc_final: 0.7334 (tpp) REVERT: B 231 GLU cc_start: 0.7022 (mt-10) cc_final: 0.6702 (tt0) REVERT: B 304 HIS cc_start: 0.7000 (t-170) cc_final: 0.6716 (t-90) REVERT: B 338 LYS cc_start: 0.8077 (tttt) cc_final: 0.7641 (mttt) REVERT: C 58 ASN cc_start: 0.8724 (t0) cc_final: 0.8310 (t0) REVERT: C 108 CYS cc_start: 0.7871 (p) cc_final: 0.7492 (t) REVERT: C 225 TYR cc_start: 0.8858 (t80) cc_final: 0.8443 (t80) REVERT: C 319 GLN cc_start: 0.8288 (mm-40) cc_final: 0.7337 (tm-30) REVERT: C 323 PRO cc_start: 0.9250 (Cg_exo) cc_final: 0.8984 (Cg_endo) REVERT: C 350 ASP cc_start: 0.8115 (p0) cc_final: 0.7827 (p0) REVERT: D 105 MET cc_start: 0.8433 (tpp) cc_final: 0.8197 (tpp) REVERT: D 140 ARG cc_start: 0.8470 (ttm170) cc_final: 0.8264 (ttm170) REVERT: D 308 ILE cc_start: 0.8738 (mm) cc_final: 0.8350 (mm) REVERT: D 358 MET cc_start: 0.7524 (mpp) cc_final: 0.7163 (mpp) REVERT: E 98 LYS cc_start: 0.8639 (mtmt) cc_final: 0.8426 (mtmm) REVERT: E 128 MET cc_start: 0.3676 (ptp) cc_final: 0.2936 (pmm) REVERT: E 140 ARG cc_start: 0.8190 (mtt180) cc_final: 0.7919 (mtp180) REVERT: E 203 LYS cc_start: 0.3650 (mmtt) cc_final: 0.2132 (tptm) REVERT: E 228 ASN cc_start: 0.8182 (t0) cc_final: 0.7912 (t0) REVERT: E 327 VAL cc_start: 0.8675 (m) cc_final: 0.8441 (p) REVERT: F 68 ARG cc_start: 0.7043 (mtp180) cc_final: 0.6809 (mmm160) REVERT: F 105 MET cc_start: 0.8132 (mmp) cc_final: 0.7000 (tpp) REVERT: F 158 SER cc_start: 0.7758 (m) cc_final: 0.7301 (t) REVERT: F 313 SER cc_start: 0.7849 (t) cc_final: 0.7550 (p) outliers start: 0 outliers final: 0 residues processed: 326 average time/residue: 0.2462 time to fit residues: 116.6976 Evaluate side-chains 256 residues out of total 1471 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 256 time to evaluate : 1.472 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 172 random chunks: chunk 112 optimal weight: 5.9990 chunk 41 optimal weight: 0.8980 chunk 11 optimal weight: 2.9990 chunk 39 optimal weight: 0.5980 chunk 69 optimal weight: 4.9990 chunk 77 optimal weight: 2.9990 chunk 145 optimal weight: 0.8980 chunk 168 optimal weight: 0.7980 chunk 101 optimal weight: 0.8980 chunk 28 optimal weight: 0.8980 chunk 66 optimal weight: 2.9990 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 56 GLN C 304 HIS D 217 HIS D 319 GLN E 362 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3367 r_free = 0.3367 target = 0.111479 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3169 r_free = 0.3169 target = 0.098418 restraints weight = 28271.475| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3208 r_free = 0.3208 target = 0.100891 restraints weight = 16937.391| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3234 r_free = 0.3234 target = 0.102552 restraints weight = 11364.151| |-----------------------------------------------------------------------------| r_work (final): 0.3235 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3235 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3235 r_free = 0.3235 target_work(ls_wunit_k1) = 0.103 | | occupancies: max = 1.00 min = 0.99 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3235 r_free = 0.3235 target_work(ls_wunit_k1) = 0.103 | | occupancies: max = 1.00 min = 0.97 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3235 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7657 moved from start: 0.3562 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 13684 Z= 0.127 Angle : 0.616 8.520 18467 Z= 0.306 Chirality : 0.045 0.234 2200 Planarity : 0.004 0.042 2352 Dihedral : 6.779 90.215 1908 Min Nonbonded Distance : 2.461 Molprobity Statistics. All-atom Clashscore : 8.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.09 % Favored : 95.91 % Rotamer: Outliers : 0.07 % Allowed : 2.47 % Favored : 97.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.39 (0.19), residues: 1712 helix: -1.58 (0.17), residues: 856 sheet: -1.96 (0.35), residues: 214 loop : -1.12 (0.24), residues: 642 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP E 198 HIS 0.005 0.001 HIS A 152 PHE 0.011 0.001 PHE D 226 TYR 0.018 0.002 TYR A 116 ARG 0.011 0.000 ARG B 244 Details of bonding type rmsd hydrogen bonds : bond 0.02989 ( 418) hydrogen bonds : angle 4.82063 ( 1173) covalent geometry : bond 0.00291 (13682) covalent geometry : angle 0.61636 (18467) Misc. bond : bond 0.00027 ( 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 323 residues out of total 1471 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 322 time to evaluate : 1.601 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 63 CYS cc_start: 0.8816 (m) cc_final: 0.8527 (m) REVERT: A 114 GLU cc_start: 0.7773 (tm-30) cc_final: 0.7208 (tp30) REVERT: A 127 MET cc_start: 0.7041 (ttt) cc_final: 0.6790 (ttm) REVERT: A 228 ARG cc_start: 0.8087 (ttp-170) cc_final: 0.7870 (mtp-110) REVERT: A 247 CYS cc_start: 0.8389 (p) cc_final: 0.7574 (t) REVERT: A 282 MET cc_start: 0.7912 (mmt) cc_final: 0.7491 (mmt) REVERT: A 303 ASN cc_start: 0.8284 (m110) cc_final: 0.7988 (m-40) REVERT: B 70 ILE cc_start: 0.8013 (mt) cc_final: 0.7724 (mt) REVERT: B 121 LYS cc_start: 0.7933 (ptmt) cc_final: 0.7258 (mttm) REVERT: B 231 GLU cc_start: 0.6906 (mt-10) cc_final: 0.6664 (tt0) REVERT: B 237 ILE cc_start: 0.8705 (tp) cc_final: 0.8498 (tt) REVERT: B 304 HIS cc_start: 0.6976 (t-170) cc_final: 0.6616 (t-90) REVERT: B 338 LYS cc_start: 0.7902 (tttt) cc_final: 0.7420 (mttt) REVERT: C 58 ASN cc_start: 0.8689 (t0) cc_final: 0.8208 (t0) REVERT: C 108 CYS cc_start: 0.7843 (p) cc_final: 0.7450 (t) REVERT: C 225 TYR cc_start: 0.8861 (t80) cc_final: 0.8406 (t80) REVERT: C 254 ASP cc_start: 0.8236 (t0) cc_final: 0.7876 (t0) REVERT: C 319 GLN cc_start: 0.8260 (mm-40) cc_final: 0.7341 (tm-30) REVERT: C 323 PRO cc_start: 0.9242 (Cg_exo) cc_final: 0.8981 (Cg_endo) REVERT: C 350 ASP cc_start: 0.8081 (p0) cc_final: 0.7758 (p0) REVERT: D 140 ARG cc_start: 0.8368 (ttm170) cc_final: 0.8160 (ttm170) REVERT: D 308 ILE cc_start: 0.8718 (mm) cc_final: 0.8341 (mm) REVERT: D 358 MET cc_start: 0.7624 (mpp) cc_final: 0.7226 (mpp) REVERT: E 128 MET cc_start: 0.3737 (ptp) cc_final: 0.3062 (pmm) REVERT: E 130 LYS cc_start: 0.7021 (tttp) cc_final: 0.6390 (tttp) REVERT: E 140 ARG cc_start: 0.8135 (mtt180) cc_final: 0.7878 (mtp180) REVERT: E 203 LYS cc_start: 0.3380 (mmtt) cc_final: 0.2225 (tptm) REVERT: E 228 ASN cc_start: 0.8184 (t0) cc_final: 0.7933 (t0) REVERT: E 327 VAL cc_start: 0.8709 (m) cc_final: 0.8464 (p) REVERT: F 68 ARG cc_start: 0.7056 (mtp180) cc_final: 0.6826 (mmm160) REVERT: F 105 MET cc_start: 0.8132 (mmp) cc_final: 0.7015 (tpp) REVERT: F 128 MET cc_start: 0.7025 (mtt) cc_final: 0.6787 (mtt) REVERT: F 158 SER cc_start: 0.7633 (m) cc_final: 0.7359 (t) REVERT: F 313 SER cc_start: 0.7900 (t) cc_final: 0.7598 (p) outliers start: 1 outliers final: 0 residues processed: 323 average time/residue: 0.2513 time to fit residues: 117.4587 Evaluate side-chains 253 residues out of total 1471 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 253 time to evaluate : 1.416 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 172 random chunks: chunk 10 optimal weight: 2.9990 chunk 15 optimal weight: 0.9990 chunk 142 optimal weight: 3.9990 chunk 27 optimal weight: 0.7980 chunk 125 optimal weight: 6.9990 chunk 17 optimal weight: 0.9980 chunk 42 optimal weight: 0.5980 chunk 149 optimal weight: 0.9990 chunk 150 optimal weight: 1.9990 chunk 19 optimal weight: 3.9990 chunk 75 optimal weight: 1.9990 overall best weight: 0.8784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 304 HIS D 136 GLN D 217 HIS D 319 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3370 r_free = 0.3370 target = 0.111604 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3181 r_free = 0.3181 target = 0.099183 restraints weight = 28323.566| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3216 r_free = 0.3216 target = 0.101422 restraints weight = 17481.507| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3243 r_free = 0.3243 target = 0.103094 restraints weight = 11988.794| |-----------------------------------------------------------------------------| r_work (final): 0.3243 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3243 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3243 r_free = 0.3243 target_work(ls_wunit_k1) = 0.103 | | occupancies: max = 1.00 min = 0.97 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3244 r_free = 0.3244 target_work(ls_wunit_k1) = 0.103 | | occupancies: max = 1.00 min = 1.00 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3244 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7656 moved from start: 0.3691 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 13684 Z= 0.127 Angle : 0.603 7.478 18467 Z= 0.301 Chirality : 0.045 0.200 2200 Planarity : 0.004 0.040 2352 Dihedral : 6.609 90.341 1908 Min Nonbonded Distance : 2.460 Molprobity Statistics. All-atom Clashscore : 8.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.91 % Favored : 96.09 % Rotamer: Outliers : 0.07 % Allowed : 1.85 % Favored : 98.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.15 (0.20), residues: 1712 helix: -1.36 (0.17), residues: 845 sheet: -1.85 (0.36), residues: 213 loop : -1.06 (0.24), residues: 654 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP E 198 HIS 0.004 0.001 HIS A 152 PHE 0.011 0.001 PHE D 226 TYR 0.016 0.001 TYR A 197 ARG 0.006 0.000 ARG A 250 Details of bonding type rmsd hydrogen bonds : bond 0.02935 ( 418) hydrogen bonds : angle 4.74530 ( 1173) covalent geometry : bond 0.00292 (13682) covalent geometry : angle 0.60326 (18467) Misc. bond : bond 0.00022 ( 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 324 residues out of total 1471 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 323 time to evaluate : 1.901 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 63 CYS cc_start: 0.8800 (m) cc_final: 0.8495 (m) REVERT: A 114 GLU cc_start: 0.7773 (tm-30) cc_final: 0.7517 (tm-30) REVERT: A 127 MET cc_start: 0.7068 (ttt) cc_final: 0.6856 (ttm) REVERT: A 247 CYS cc_start: 0.8456 (p) cc_final: 0.7568 (t) REVERT: A 303 ASN cc_start: 0.8270 (m110) cc_final: 0.7825 (m110) REVERT: B 121 LYS cc_start: 0.7859 (ptmt) cc_final: 0.7182 (mttm) REVERT: B 127 MET cc_start: 0.8983 (mmp) cc_final: 0.8519 (mmp) REVERT: B 338 LYS cc_start: 0.7919 (tttt) cc_final: 0.7435 (mttt) REVERT: C 58 ASN cc_start: 0.8649 (t0) cc_final: 0.8197 (t0) REVERT: C 108 CYS cc_start: 0.7826 (p) cc_final: 0.7440 (t) REVERT: C 225 TYR cc_start: 0.8849 (t80) cc_final: 0.8392 (t80) REVERT: C 254 ASP cc_start: 0.8133 (t0) cc_final: 0.7867 (t0) REVERT: C 319 GLN cc_start: 0.8277 (mm-40) cc_final: 0.7346 (tm-30) REVERT: C 323 PRO cc_start: 0.9226 (Cg_exo) cc_final: 0.8964 (Cg_endo) REVERT: D 140 ARG cc_start: 0.8320 (ttm170) cc_final: 0.8101 (ttm170) REVERT: D 308 ILE cc_start: 0.8699 (mm) cc_final: 0.8200 (mm) REVERT: E 128 MET cc_start: 0.3775 (ptp) cc_final: 0.3164 (pmm) REVERT: E 130 LYS cc_start: 0.6889 (tttp) cc_final: 0.6363 (tttp) REVERT: E 140 ARG cc_start: 0.8115 (mtt180) cc_final: 0.7886 (mtp180) REVERT: E 203 LYS cc_start: 0.3480 (mmtt) cc_final: 0.2339 (tptm) REVERT: E 327 VAL cc_start: 0.8673 (m) cc_final: 0.8440 (p) REVERT: E 345 TYR cc_start: 0.8105 (t80) cc_final: 0.7728 (t80) REVERT: F 68 ARG cc_start: 0.7069 (mtp180) cc_final: 0.6843 (mmm160) REVERT: F 105 MET cc_start: 0.8138 (mmp) cc_final: 0.7024 (tpp) REVERT: F 128 MET cc_start: 0.7140 (mtt) cc_final: 0.6923 (mtt) REVERT: F 158 SER cc_start: 0.7680 (m) cc_final: 0.7425 (t) REVERT: F 313 SER cc_start: 0.7902 (t) cc_final: 0.7613 (p) outliers start: 1 outliers final: 0 residues processed: 324 average time/residue: 0.2461 time to fit residues: 116.9120 Evaluate side-chains 255 residues out of total 1471 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 255 time to evaluate : 1.751 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 172 random chunks: chunk 143 optimal weight: 4.9990 chunk 56 optimal weight: 1.9990 chunk 14 optimal weight: 0.9980 chunk 77 optimal weight: 3.9990 chunk 101 optimal weight: 0.0970 chunk 126 optimal weight: 0.8980 chunk 8 optimal weight: 1.9990 chunk 87 optimal weight: 0.8980 chunk 140 optimal weight: 0.7980 chunk 102 optimal weight: 2.9990 chunk 132 optimal weight: 0.9990 overall best weight: 0.7378 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 56 GLN C 304 HIS C 340 HIS D 136 GLN D 319 GLN F 228 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3375 r_free = 0.3375 target = 0.112092 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3186 r_free = 0.3186 target = 0.099676 restraints weight = 28266.973| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3221 r_free = 0.3221 target = 0.101902 restraints weight = 17360.163| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3249 r_free = 0.3249 target = 0.103604 restraints weight = 11807.731| |-----------------------------------------------------------------------------| r_work (final): 0.3250 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7642 moved from start: 0.3875 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= 0.119 Angle : 0.606 7.477 18467 Z= 0.303 Chirality : 0.045 0.190 2200 Planarity : 0.004 0.039 2352 Dihedral : 6.401 90.607 1908 Min Nonbonded Distance : 2.386 Molprobity Statistics. All-atom Clashscore : 7.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.86 % Favored : 96.14 % Rotamer: Outliers : 0.00 % Allowed : 0.96 % Favored : 99.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.05 (0.20), residues: 1712 helix: -1.29 (0.17), residues: 853 sheet: -1.73 (0.36), residues: 212 loop : -1.02 (0.24), residues: 647 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP E 198 HIS 0.006 0.001 HIS A 152 PHE 0.014 0.001 PHE A 223 TYR 0.019 0.001 TYR A 116 ARG 0.006 0.000 ARG A 250 Details of bonding type rmsd hydrogen bonds : bond 0.02860 ( 418) hydrogen bonds : angle 4.70480 ( 1173) covalent geometry : bond 0.00270 (13682) covalent geometry : angle 0.60612 (18467) Misc. bond : bond 0.00020 ( 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 321 residues out of total 1471 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 321 time to evaluate : 1.495 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 63 CYS cc_start: 0.8801 (m) cc_final: 0.8522 (m) REVERT: A 74 LYS cc_start: 0.8205 (ttpt) cc_final: 0.7700 (mptt) REVERT: A 127 MET cc_start: 0.7114 (ttt) cc_final: 0.6878 (ttm) REVERT: A 303 ASN cc_start: 0.8269 (m110) cc_final: 0.7856 (m110) REVERT: A 319 GLN cc_start: 0.7975 (pp30) cc_final: 0.7553 (pp30) REVERT: B 121 LYS cc_start: 0.7834 (ptmt) cc_final: 0.7187 (mttm) REVERT: B 127 MET cc_start: 0.8945 (mmp) cc_final: 0.8451 (mmp) REVERT: B 304 HIS cc_start: 0.6893 (t-90) cc_final: 0.6509 (t-90) REVERT: B 338 LYS cc_start: 0.7937 (tttt) cc_final: 0.7441 (mttt) REVERT: C 58 ASN cc_start: 0.8746 (t0) cc_final: 0.8311 (t0) REVERT: C 108 CYS cc_start: 0.7815 (p) cc_final: 0.7400 (t) REVERT: C 225 TYR cc_start: 0.8848 (t80) cc_final: 0.8376 (t80) REVERT: C 254 ASP cc_start: 0.8000 (t0) cc_final: 0.7699 (t0) REVERT: C 270 MET cc_start: 0.8435 (ptp) cc_final: 0.8100 (ptp) REVERT: C 275 MET cc_start: 0.7918 (ttt) cc_final: 0.7519 (ttt) REVERT: C 307 GLU cc_start: 0.7373 (mt-10) cc_final: 0.7095 (mt-10) REVERT: C 319 GLN cc_start: 0.8277 (mm-40) cc_final: 0.7333 (tm-30) REVERT: C 323 PRO cc_start: 0.9238 (Cg_exo) cc_final: 0.8956 (Cg_endo) REVERT: D 140 ARG cc_start: 0.8294 (ttm170) cc_final: 0.8081 (ttm170) REVERT: D 308 ILE cc_start: 0.8661 (mm) cc_final: 0.8292 (mm) REVERT: E 128 MET cc_start: 0.3708 (ptp) cc_final: 0.3169 (pmm) REVERT: E 130 LYS cc_start: 0.6919 (tttp) cc_final: 0.6448 (tttp) REVERT: E 203 LYS cc_start: 0.3386 (mmtt) cc_final: 0.2249 (tptm) REVERT: E 327 VAL cc_start: 0.8658 (m) cc_final: 0.8452 (p) REVERT: E 345 TYR cc_start: 0.8098 (t80) cc_final: 0.7732 (t80) REVERT: F 68 ARG cc_start: 0.7066 (mtp180) cc_final: 0.6858 (mmm160) REVERT: F 105 MET cc_start: 0.8044 (mmp) cc_final: 0.7156 (tpp) REVERT: F 128 MET cc_start: 0.7144 (mtt) cc_final: 0.6944 (mtt) REVERT: F 158 SER cc_start: 0.7786 (m) cc_final: 0.7510 (t) REVERT: F 313 SER cc_start: 0.7877 (t) cc_final: 0.7602 (p) outliers start: 0 outliers final: 0 residues processed: 321 average time/residue: 0.2446 time to fit residues: 115.0357 Evaluate side-chains 257 residues out of total 1471 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 257 time to evaluate : 1.501 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 172 random chunks: chunk 71 optimal weight: 3.9990 chunk 15 optimal weight: 0.7980 chunk 114 optimal weight: 0.9980 chunk 69 optimal weight: 0.9980 chunk 41 optimal weight: 0.9980 chunk 3 optimal weight: 1.9990 chunk 86 optimal weight: 2.9990 chunk 55 optimal weight: 0.6980 chunk 112 optimal weight: 0.3980 chunk 20 optimal weight: 0.9980 chunk 135 optimal weight: 4.9990 overall best weight: 0.7780 ------------------------------------------------------------------------------- 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 56 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 304 HIS D 136 GLN D 217 HIS D 319 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3380 r_free = 0.3380 target = 0.112416 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3192 r_free = 0.3192 target = 0.100037 restraints weight = 27733.348| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.3229 r_free = 0.3229 target = 0.102318 restraints weight = 17154.434| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3253 r_free = 0.3253 target = 0.103901 restraints weight = 11735.332| |-----------------------------------------------------------------------------| r_work (final): 0.3254 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7638 moved from start: 0.4021 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 13684 Z= 0.121 Angle : 0.614 7.410 18467 Z= 0.306 Chirality : 0.045 0.187 2200 Planarity : 0.004 0.038 2352 Dihedral : 6.238 90.279 1908 Min Nonbonded Distance : 2.386 Molprobity Statistics. All-atom Clashscore : 8.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.15 % Favored : 95.85 % Rotamer: Outliers : 0.07 % Allowed : 0.89 % Favored : 99.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.97 (0.20), residues: 1712 helix: -1.24 (0.17), residues: 860 sheet: -1.64 (0.36), residues: 213 loop : -0.95 (0.24), residues: 639 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP E 198 HIS 0.004 0.001 HIS A 227 PHE 0.015 0.001 PHE A 223 TYR 0.013 0.001 TYR A 116 ARG 0.010 0.000 ARG B 268 Details of bonding type rmsd hydrogen bonds : bond 0.02805 ( 418) hydrogen bonds : angle 4.65654 ( 1173) covalent geometry : bond 0.00276 (13682) covalent geometry : angle 0.61426 (18467) Misc. bond : bond 0.00027 ( 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 312 residues out of total 1471 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 311 time to evaluate : 1.439 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 63 CYS cc_start: 0.8855 (m) cc_final: 0.8542 (m) REVERT: A 127 MET cc_start: 0.7144 (ttt) cc_final: 0.6872 (ttm) REVERT: A 242 SER cc_start: 0.9097 (t) cc_final: 0.8479 (m) REVERT: A 303 ASN cc_start: 0.8306 (m110) cc_final: 0.7816 (m110) REVERT: A 319 GLN cc_start: 0.7894 (pp30) cc_final: 0.7501 (pp30) REVERT: B 121 LYS cc_start: 0.7895 (ptmt) cc_final: 0.7223 (mttm) REVERT: B 127 MET cc_start: 0.8930 (mmp) cc_final: 0.8447 (mmp) REVERT: B 300 GLU cc_start: 0.8180 (mp0) cc_final: 0.7954 (mp0) REVERT: B 304 HIS cc_start: 0.6937 (t-90) cc_final: 0.6505 (t-90) REVERT: B 338 LYS cc_start: 0.7943 (tttt) cc_final: 0.7454 (mttt) REVERT: C 58 ASN cc_start: 0.8668 (t0) cc_final: 0.8221 (t0) REVERT: C 108 CYS cc_start: 0.7823 (p) cc_final: 0.7394 (t) REVERT: C 217 MET cc_start: 0.8645 (mmm) cc_final: 0.8240 (mtp) REVERT: C 225 TYR cc_start: 0.8812 (t80) cc_final: 0.8333 (t80) REVERT: C 254 ASP cc_start: 0.7968 (t0) cc_final: 0.7722 (t0) REVERT: C 319 GLN cc_start: 0.8269 (mm-40) cc_final: 0.8052 (mp10) REVERT: C 323 PRO cc_start: 0.9224 (Cg_exo) cc_final: 0.8986 (Cg_endo) REVERT: D 140 ARG cc_start: 0.8280 (ttm170) cc_final: 0.8066 (ttm170) REVERT: D 308 ILE cc_start: 0.8732 (mm) cc_final: 0.8361 (mm) REVERT: E 128 MET cc_start: 0.3798 (ptp) cc_final: 0.3206 (pmm) REVERT: E 203 LYS cc_start: 0.3354 (mmtt) cc_final: 0.2169 (tptm) REVERT: E 235 MET cc_start: 0.7458 (mtm) cc_final: 0.7241 (mtt) REVERT: E 327 VAL cc_start: 0.8601 (m) cc_final: 0.8368 (p) REVERT: E 345 TYR cc_start: 0.8068 (t80) cc_final: 0.7621 (t80) REVERT: F 105 MET cc_start: 0.8002 (mmp) cc_final: 0.7216 (tpp) REVERT: F 128 MET cc_start: 0.7075 (mtt) cc_final: 0.5371 (mmp) REVERT: F 158 SER cc_start: 0.7733 (m) cc_final: 0.7361 (t) REVERT: F 313 SER cc_start: 0.7946 (t) cc_final: 0.7669 (p) outliers start: 1 outliers final: 0 residues processed: 312 average time/residue: 0.2369 time to fit residues: 109.1377 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 : 2.167 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 172 random chunks: chunk 65 optimal weight: 0.0370 chunk 53 optimal weight: 0.1980 chunk 137 optimal weight: 7.9990 chunk 70 optimal weight: 5.9990 chunk 136 optimal weight: 0.9980 chunk 66 optimal weight: 0.7980 chunk 99 optimal weight: 5.9990 chunk 11 optimal weight: 2.9990 chunk 67 optimal weight: 0.0770 chunk 12 optimal weight: 3.9990 chunk 104 optimal weight: 3.9990 overall best weight: 0.4216 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 129 ASN A 284 GLN A 340 HIS ** C 56 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 304 HIS C 340 HIS D 136 GLN D 217 HIS D 319 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3393 r_free = 0.3393 target = 0.113524 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3209 r_free = 0.3209 target = 0.101278 restraints weight = 27967.447| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3244 r_free = 0.3244 target = 0.103554 restraints weight = 17042.983| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3270 r_free = 0.3270 target = 0.105234 restraints weight = 11498.871| |-----------------------------------------------------------------------------| r_work (final): 0.3270 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7614 moved from start: 0.4220 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.041 13684 Z= 0.110 Angle : 0.617 7.378 18467 Z= 0.307 Chirality : 0.045 0.198 2200 Planarity : 0.004 0.059 2352 Dihedral : 6.077 87.663 1908 Min Nonbonded Distance : 2.390 Molprobity Statistics. All-atom Clashscore : 8.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.80 % Favored : 96.20 % Rotamer: Outliers : 0.07 % Allowed : 0.48 % Favored : 99.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.84 (0.20), residues: 1712 helix: -1.16 (0.17), residues: 853 sheet: -1.53 (0.37), residues: 213 loop : -0.89 (0.24), residues: 646 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP E 198 HIS 0.004 0.001 HIS A 152 PHE 0.014 0.001 PHE A 223 TYR 0.018 0.001 TYR B 277 ARG 0.011 0.000 ARG B 268 Details of bonding type rmsd hydrogen bonds : bond 0.02692 ( 418) hydrogen bonds : angle 4.51634 ( 1173) covalent geometry : bond 0.00245 (13682) covalent geometry : angle 0.61708 (18467) Misc. bond : bond 0.00092 ( 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 324 residues out of total 1471 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 323 time to evaluate : 1.504 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 63 CYS cc_start: 0.8829 (m) cc_final: 0.8557 (m) REVERT: A 127 MET cc_start: 0.7212 (ttt) cc_final: 0.6952 (ttm) REVERT: A 228 ARG cc_start: 0.7767 (mtp-110) cc_final: 0.7505 (mtm110) REVERT: A 242 SER cc_start: 0.9073 (t) cc_final: 0.8483 (m) REVERT: A 303 ASN cc_start: 0.8224 (m110) cc_final: 0.7898 (m110) REVERT: A 308 ILE cc_start: 0.8038 (mm) cc_final: 0.7812 (mt) REVERT: A 319 GLN cc_start: 0.7915 (pp30) cc_final: 0.7540 (pp30) REVERT: B 121 LYS cc_start: 0.7891 (ptmt) cc_final: 0.7235 (mttm) REVERT: B 196 LYS cc_start: 0.8170 (tttt) cc_final: 0.7681 (tttm) REVERT: B 304 HIS cc_start: 0.6896 (t-90) cc_final: 0.6476 (t-90) REVERT: B 338 LYS cc_start: 0.7924 (tttt) cc_final: 0.7511 (mttt) REVERT: C 58 ASN cc_start: 0.8648 (t0) cc_final: 0.8195 (t0) REVERT: C 108 CYS cc_start: 0.7808 (p) cc_final: 0.7410 (t) REVERT: C 217 MET cc_start: 0.8619 (mmm) cc_final: 0.8393 (mmm) REVERT: C 225 TYR cc_start: 0.8801 (t80) cc_final: 0.8303 (t80) REVERT: C 254 ASP cc_start: 0.7991 (t0) cc_final: 0.7725 (t0) REVERT: C 270 MET cc_start: 0.8363 (ptp) cc_final: 0.8078 (ptp) REVERT: C 323 PRO cc_start: 0.9197 (Cg_exo) cc_final: 0.8934 (Cg_endo) REVERT: C 350 ASP cc_start: 0.8014 (p0) cc_final: 0.7639 (p0) REVERT: D 140 ARG cc_start: 0.8267 (ttm170) cc_final: 0.7879 (ttm170) REVERT: D 297 MET cc_start: 0.7224 (tmm) cc_final: 0.7014 (tmm) REVERT: D 308 ILE cc_start: 0.8700 (mm) cc_final: 0.8278 (mm) REVERT: E 128 MET cc_start: 0.3555 (ptp) cc_final: 0.2992 (pmm) REVERT: E 130 LYS cc_start: 0.6860 (tttp) cc_final: 0.6436 (tttp) REVERT: E 203 LYS cc_start: 0.3193 (mmtt) cc_final: 0.2146 (tptm) REVERT: E 228 ASN cc_start: 0.8009 (t0) cc_final: 0.7701 (t0) REVERT: E 327 VAL cc_start: 0.8535 (m) cc_final: 0.8294 (p) REVERT: E 345 TYR cc_start: 0.8008 (t80) cc_final: 0.7552 (t80) REVERT: F 105 MET cc_start: 0.7987 (mmp) cc_final: 0.7431 (tpp) REVERT: F 128 MET cc_start: 0.7074 (mtt) cc_final: 0.5288 (mmp) REVERT: F 158 SER cc_start: 0.7687 (m) cc_final: 0.7390 (t) REVERT: F 313 SER cc_start: 0.7895 (t) cc_final: 0.7611 (p) outliers start: 1 outliers final: 0 residues processed: 324 average time/residue: 0.2642 time to fit residues: 128.9484 Evaluate side-chains 257 residues out of total 1471 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 257 time to evaluate : 1.507 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 172 random chunks: chunk 53 optimal weight: 0.7980 chunk 8 optimal weight: 0.8980 chunk 31 optimal weight: 0.7980 chunk 166 optimal weight: 6.9990 chunk 30 optimal weight: 5.9990 chunk 154 optimal weight: 1.9990 chunk 48 optimal weight: 5.9990 chunk 159 optimal weight: 3.9990 chunk 128 optimal weight: 0.1980 chunk 145 optimal weight: 1.9990 chunk 112 optimal weight: 0.3980 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 304 HIS ** A 340 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 216 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 56 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 304 HIS D 217 HIS D 319 GLN E 356 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3415 r_free = 0.3415 target = 0.114386 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3215 r_free = 0.3215 target = 0.101364 restraints weight = 28190.074| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3256 r_free = 0.3256 target = 0.103966 restraints weight = 16720.769| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3283 r_free = 0.3283 target = 0.105667 restraints weight = 11039.222| |-----------------------------------------------------------------------------| r_work (final): 0.3282 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7618 moved from start: 0.4333 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 13684 Z= 0.116 Angle : 0.622 7.335 18467 Z= 0.309 Chirality : 0.045 0.178 2200 Planarity : 0.004 0.056 2352 Dihedral : 5.972 87.927 1908 Min Nonbonded Distance : 2.385 Molprobity Statistics. All-atom Clashscore : 8.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.09 % Favored : 95.91 % Rotamer: Outliers : 0.14 % Allowed : 0.34 % Favored : 99.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.76 (0.20), residues: 1712 helix: -1.13 (0.17), residues: 854 sheet: -1.49 (0.37), residues: 212 loop : -0.78 (0.25), residues: 646 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP E 198 HIS 0.004 0.001 HIS A 152 PHE 0.013 0.001 PHE A 223 TYR 0.021 0.001 TYR B 277 ARG 0.009 0.000 ARG E 329 Details of bonding type rmsd hydrogen bonds : bond 0.02716 ( 418) hydrogen bonds : angle 4.65042 ( 1173) covalent geometry : bond 0.00265 (13682) covalent geometry : angle 0.62241 (18467) Misc. bond : bond 0.00079 ( 2) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4125.31 seconds wall clock time: 72 minutes 36.84 seconds (4356.84 seconds total)