Starting phenix.real_space_refine on Thu Feb 5 01:06:12 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9pnd_71750/02_2026/9pnd_71750.cif Found real_map, /net/cci-nas-00/data/ceres_data/9pnd_71750/02_2026/9pnd_71750.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.19 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9pnd_71750/02_2026/9pnd_71750.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9pnd_71750/02_2026/9pnd_71750.map" model { file = "/net/cci-nas-00/data/ceres_data/9pnd_71750/02_2026/9pnd_71750.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9pnd_71750/02_2026/9pnd_71750.cif" } resolution = 3.19 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.005 sd= 0.104 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians P 10 5.49 5 Mg 4 5.21 5 S 98 5.16 5 C 8662 2.51 5 N 2340 2.21 5 O 2664 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 16 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 13778 Number of models: 1 Model: "" Number of chains: 12 Chain: "B" Number of atoms: 3363 Number of conformers: 1 Conformer: "" Number of residues, atoms: 428, 3363 Classifications: {'peptide': 428} Link IDs: {'PCIS': 1, 'PTRANS': 18, 'TRANS': 408} Chain: "D" Number of atoms: 3363 Number of conformers: 1 Conformer: "" Number of residues, atoms: 428, 3363 Classifications: {'peptide': 428} Link IDs: {'PCIS': 1, 'PTRANS': 18, 'TRANS': 408} Chain: "A" Number of atoms: 3427 Number of conformers: 1 Conformer: "" Number of residues, atoms: 439, 3427 Classifications: {'peptide': 439} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 1, 'PTRANS': 19, 'TRANS': 418} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 1 Chain: "C" Number of atoms: 3427 Number of conformers: 1 Conformer: "" Number of residues, atoms: 439, 3427 Classifications: {'peptide': 439} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 1, 'PTRANS': 19, 'TRANS': 418} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 1 Chain: "B" Number of atoms: 64 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 64 Unusual residues: {' MG': 1, 'EPB': 1, 'GDP': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "D" Number of atoms: 64 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 64 Unusual residues: {' MG': 1, 'EPB': 1, 'GDP': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "A" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 33 Unusual residues: {' MG': 1, 'GTP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "C" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 33 Unusual residues: {' MG': 1, 'GTP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "B" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "D" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "A" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "C" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Time building chain proxies: 3.40, per 1000 atoms: 0.25 Number of scatterers: 13778 At special positions: 0 Unit cell: (75.5563, 72.8088, 201.941, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 98 16.00 P 10 15.00 Mg 4 11.99 O 2664 8.00 N 2340 7.00 C 8662 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=0, symmetry=0 Time building additional restraints: 1.26 Conformation dependent library (CDL) restraints added in 530.4 milliseconds 3452 Ramachandran restraints generated. 1726 Oldfield, 0 Emsley, 1726 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3204 Finding SS restraints... Secondary structure from input PDB file: 76 helices and 10 sheets defined 52.2% alpha, 14.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.48 Creating SS restraints... Processing helix chain 'B' and resid 10 through 29 Processing helix chain 'B' and resid 46 through 49 removed outlier: 3.710A pdb=" N VAL B 49 " --> pdb=" O ARG B 46 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 46 through 49' Processing helix chain 'B' and resid 70 through 79 Processing helix chain 'B' and resid 86 through 88 No H-bonds generated for 'chain 'B' and resid 86 through 88' Processing helix chain 'B' and resid 109 through 127 removed outlier: 4.590A pdb=" N ASP B 114 " --> pdb=" O ALA B 110 " (cutoff:3.500A) removed outlier: 5.577A pdb=" N SER B 115 " --> pdb=" O GLU B 111 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N VAL B 119 " --> pdb=" O SER B 115 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N ASN B 126 " --> pdb=" O LYS B 122 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N CYS B 127 " --> pdb=" O GLU B 123 " (cutoff:3.500A) Processing helix chain 'B' and resid 142 through 159 removed outlier: 3.638A pdb=" N THR B 149 " --> pdb=" O SER B 145 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N GLU B 158 " --> pdb=" O LYS B 154 " (cutoff:3.500A) Processing helix chain 'B' and resid 180 through 196 removed outlier: 4.084A pdb=" N GLN B 191 " --> pdb=" O LEU B 187 " (cutoff:3.500A) removed outlier: 4.414A pdb=" N GLU B 194 " --> pdb=" O HIS B 190 " (cutoff:3.500A) Processing helix chain 'B' and resid 203 through 214 Processing helix chain 'B' and resid 221 through 237 removed outlier: 3.517A pdb=" N THR B 237 " --> pdb=" O MET B 233 " (cutoff:3.500A) Processing helix chain 'B' and resid 237 through 242 removed outlier: 3.911A pdb=" N ARG B 241 " --> pdb=" O THR B 237 " (cutoff:3.500A) Processing helix chain 'B' and resid 249 through 258 Processing helix chain 'B' and resid 285 through 294 removed outlier: 3.723A pdb=" N PHE B 294 " --> pdb=" O THR B 290 " (cutoff:3.500A) Processing helix chain 'B' and resid 304 through 308 Processing helix chain 'B' and resid 322 through 337 removed outlier: 3.633A pdb=" N VAL B 326 " --> pdb=" O SER B 322 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N GLU B 328 " --> pdb=" O LYS B 324 " (cutoff:3.500A) removed outlier: 4.255A pdb=" N MET B 330 " --> pdb=" O VAL B 326 " (cutoff:3.500A) removed outlier: 4.598A pdb=" N LEU B 331 " --> pdb=" O ASP B 327 " (cutoff:3.500A) Processing helix chain 'B' and resid 338 through 341 Processing helix chain 'B' and resid 374 through 391 removed outlier: 3.743A pdb=" N PHE B 378 " --> pdb=" O ILE B 374 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N ILE B 381 " --> pdb=" O LEU B 377 " (cutoff:3.500A) removed outlier: 4.158A pdb=" N ARG B 391 " --> pdb=" O ALA B 387 " (cutoff:3.500A) Processing helix chain 'B' and resid 395 through 401 removed outlier: 3.676A pdb=" N GLU B 401 " --> pdb=" O TRP B 397 " (cutoff:3.500A) Processing helix chain 'B' and resid 404 through 428 removed outlier: 3.972A pdb=" N PHE B 408 " --> pdb=" O ASP B 404 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N THR B 409 " --> pdb=" O GLU B 405 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N TYR B 425 " --> pdb=" O GLU B 421 " (cutoff:3.500A) Processing helix chain 'D' and resid 10 through 29 Processing helix chain 'D' and resid 40 through 46 removed outlier: 4.378A pdb=" N LEU D 44 " --> pdb=" O SER D 40 " (cutoff:3.500A) removed outlier: 4.095A pdb=" N ARG D 46 " --> pdb=" O LEU D 42 " (cutoff:3.500A) Processing helix chain 'D' and resid 47 through 49 No H-bonds generated for 'chain 'D' and resid 47 through 49' Processing helix chain 'D' and resid 69 through 79 removed outlier: 4.543A pdb=" N MET D 73 " --> pdb=" O GLU D 69 " (cutoff:3.500A) Processing helix chain 'D' and resid 86 through 88 No H-bonds generated for 'chain 'D' and resid 86 through 88' Processing helix chain 'D' and resid 100 through 106 removed outlier: 3.552A pdb=" N GLY D 104 " --> pdb=" O ASN D 100 " (cutoff:3.500A) Processing helix chain 'D' and resid 108 through 127 removed outlier: 3.832A pdb=" N LEU D 112 " --> pdb=" O GLU D 108 " (cutoff:3.500A) removed outlier: 4.312A pdb=" N ASP D 114 " --> pdb=" O ALA D 110 " (cutoff:3.500A) removed outlier: 4.844A pdb=" N SER D 115 " --> pdb=" O GLU D 111 " (cutoff:3.500A) removed outlier: 3.762A pdb=" N VAL D 119 " --> pdb=" O SER D 115 " (cutoff:3.500A) removed outlier: 3.864A pdb=" N CYS D 124 " --> pdb=" O VAL D 120 " (cutoff:3.500A) removed outlier: 4.119A pdb=" N GLU D 125 " --> pdb=" O ARG D 121 " (cutoff:3.500A) removed outlier: 3.986A pdb=" N ASN D 126 " --> pdb=" O LYS D 122 " (cutoff:3.500A) Processing helix chain 'D' and resid 142 through 159 removed outlier: 3.769A pdb=" N THR D 149 " --> pdb=" O SER D 145 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N LEU D 150 " --> pdb=" O GLY D 146 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N SER D 153 " --> pdb=" O THR D 149 " (cutoff:3.500A) Processing helix chain 'D' and resid 180 through 193 removed outlier: 3.924A pdb=" N HIS D 190 " --> pdb=" O THR D 186 " (cutoff:3.500A) removed outlier: 4.673A pdb=" N GLN D 191 " --> pdb=" O LEU D 187 " (cutoff:3.500A) Processing helix chain 'D' and resid 204 through 213 Processing helix chain 'D' and resid 221 through 237 removed outlier: 3.797A pdb=" N THR D 237 " --> pdb=" O MET D 233 " (cutoff:3.500A) Processing helix chain 'D' and resid 237 through 242 removed outlier: 3.759A pdb=" N ARG D 241 " --> pdb=" O THR D 237 " (cutoff:3.500A) Processing helix chain 'D' and resid 249 through 258 removed outlier: 3.644A pdb=" N ASN D 256 " --> pdb=" O LYS D 252 " (cutoff:3.500A) Processing helix chain 'D' and resid 276 through 281 removed outlier: 4.130A pdb=" N GLN D 280 " --> pdb=" O GLY D 277 " (cutoff:3.500A) Processing helix chain 'D' and resid 285 through 294 removed outlier: 3.640A pdb=" N GLN D 292 " --> pdb=" O GLU D 288 " (cutoff:3.500A) Processing helix chain 'D' and resid 295 through 299 Processing helix chain 'D' and resid 304 through 308 Processing helix chain 'D' and resid 322 through 337 removed outlier: 3.568A pdb=" N VAL D 326 " --> pdb=" O SER D 322 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N MET D 330 " --> pdb=" O VAL D 326 " (cutoff:3.500A) Processing helix chain 'D' and resid 338 through 341 Processing helix chain 'D' and resid 374 through 391 removed outlier: 3.702A pdb=" N PHE D 378 " --> pdb=" O ILE D 374 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N ILE D 381 " --> pdb=" O LEU D 377 " (cutoff:3.500A) removed outlier: 3.837A pdb=" N ARG D 391 " --> pdb=" O ALA D 387 " (cutoff:3.500A) Processing helix chain 'D' and resid 394 through 400 removed outlier: 3.888A pdb=" N TYR D 398 " --> pdb=" O PHE D 394 " (cutoff:3.500A) Processing helix chain 'D' and resid 404 through 427 removed outlier: 3.734A pdb=" N PHE D 408 " --> pdb=" O ASP D 404 " (cutoff:3.500A) Processing helix chain 'A' and resid 10 through 29 Processing helix chain 'A' and resid 71 through 81 removed outlier: 4.362A pdb=" N ILE A 75 " --> pdb=" O GLU A 71 " (cutoff:3.500A) removed outlier: 3.743A pdb=" N GLU A 77 " --> pdb=" O THR A 73 " (cutoff:3.500A) removed outlier: 3.833A pdb=" N VAL A 78 " --> pdb=" O VAL A 74 " (cutoff:3.500A) Processing helix chain 'A' and resid 82 through 85 removed outlier: 4.502A pdb=" N GLN A 85 " --> pdb=" O THR A 82 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 82 through 85' Processing helix chain 'A' and resid 88 through 90 No H-bonds generated for 'chain 'A' and resid 88 through 90' Processing helix chain 'A' and resid 102 through 108 Processing helix chain 'A' and resid 110 through 129 removed outlier: 3.968A pdb=" N ILE A 114 " --> pdb=" O ILE A 110 " (cutoff:3.500A) removed outlier: 5.005A pdb=" N ASP A 116 " --> pdb=" O LYS A 112 " (cutoff:3.500A) removed outlier: 5.701A pdb=" N LEU A 117 " --> pdb=" O GLU A 113 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N GLN A 128 " --> pdb=" O LYS A 124 " (cutoff:3.500A) Processing helix chain 'A' and resid 143 through 161 removed outlier: 4.400A pdb=" N THR A 150 " --> pdb=" O GLY A 146 " (cutoff:3.500A) Processing helix chain 'A' and resid 182 through 190 Processing helix chain 'A' and resid 190 through 197 removed outlier: 3.758A pdb=" N THR A 194 " --> pdb=" O THR A 190 " (cutoff:3.500A) Processing helix chain 'A' and resid 206 through 216 Processing helix chain 'A' and resid 223 through 239 removed outlier: 3.521A pdb=" N ILE A 234 " --> pdb=" O LEU A 230 " (cutoff:3.500A) Processing helix chain 'A' and resid 239 through 244 Processing helix chain 'A' and resid 251 through 260 removed outlier: 3.647A pdb=" N GLN A 256 " --> pdb=" O LEU A 252 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N ASN A 258 " --> pdb=" O GLU A 254 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N VAL A 260 " --> pdb=" O GLN A 256 " (cutoff:3.500A) Processing helix chain 'A' and resid 277 through 282 removed outlier: 3.805A pdb=" N TYR A 282 " --> pdb=" O ALA A 278 " (cutoff:3.500A) Processing helix chain 'A' and resid 287 through 297 removed outlier: 3.636A pdb=" N PHE A 296 " --> pdb=" O THR A 292 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N GLU A 297 " --> pdb=" O ASN A 293 " (cutoff:3.500A) Processing helix chain 'A' and resid 324 through 338 removed outlier: 3.517A pdb=" N VAL A 328 " --> pdb=" O VAL A 324 " (cutoff:3.500A) Processing helix chain 'A' and resid 384 through 401 removed outlier: 3.600A pdb=" N TRP A 388 " --> pdb=" O ILE A 384 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N ARG A 390 " --> pdb=" O GLU A 386 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N LEU A 391 " --> pdb=" O ALA A 387 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N LYS A 394 " --> pdb=" O ARG A 390 " (cutoff:3.500A) removed outlier: 3.793A pdb=" N LYS A 401 " --> pdb=" O LEU A 397 " (cutoff:3.500A) Processing helix chain 'A' and resid 404 through 411 removed outlier: 3.933A pdb=" N TYR A 408 " --> pdb=" O PHE A 404 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N GLU A 411 " --> pdb=" O TRP A 407 " (cutoff:3.500A) Processing helix chain 'A' and resid 414 through 437 removed outlier: 3.931A pdb=" N PHE A 418 " --> pdb=" O GLU A 414 " (cutoff:3.500A) removed outlier: 3.807A pdb=" N SER A 419 " --> pdb=" O GLU A 415 " (cutoff:3.500A) Processing helix chain 'C' and resid 10 through 29 Processing helix chain 'C' and resid 71 through 81 removed outlier: 4.271A pdb=" N ILE C 75 " --> pdb=" O GLU C 71 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N GLU C 77 " --> pdb=" O THR C 73 " (cutoff:3.500A) removed outlier: 3.724A pdb=" N VAL C 78 " --> pdb=" O VAL C 74 " (cutoff:3.500A) Processing helix chain 'C' and resid 82 through 85 removed outlier: 4.268A pdb=" N GLN C 85 " --> pdb=" O THR C 82 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 82 through 85' Processing helix chain 'C' and resid 110 through 129 removed outlier: 3.657A pdb=" N ILE C 114 " --> pdb=" O ILE C 110 " (cutoff:3.500A) removed outlier: 4.344A pdb=" N ASP C 116 " --> pdb=" O LYS C 112 " (cutoff:3.500A) removed outlier: 5.694A pdb=" N LEU C 117 " --> pdb=" O GLU C 113 " (cutoff:3.500A) removed outlier: 3.754A pdb=" N VAL C 118 " --> pdb=" O ILE C 114 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N GLN C 128 " --> pdb=" O LYS C 124 " (cutoff:3.500A) Processing helix chain 'C' and resid 143 through 161 removed outlier: 4.541A pdb=" N THR C 150 " --> pdb=" O GLY C 146 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N SER C 151 " --> pdb=" O SER C 147 " (cutoff:3.500A) Processing helix chain 'C' and resid 182 through 190 Processing helix chain 'C' and resid 190 through 198 removed outlier: 3.505A pdb=" N THR C 194 " --> pdb=" O THR C 190 " (cutoff:3.500A) Processing helix chain 'C' and resid 206 through 216 Processing helix chain 'C' and resid 223 through 239 removed outlier: 3.842A pdb=" N GLN C 233 " --> pdb=" O ARG C 229 " (cutoff:3.500A) removed outlier: 3.908A pdb=" N ILE C 234 " --> pdb=" O LEU C 230 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N VAL C 235 " --> pdb=" O ILE C 231 " (cutoff:3.500A) Processing helix chain 'C' and resid 239 through 244 removed outlier: 3.601A pdb=" N ARG C 243 " --> pdb=" O THR C 239 " (cutoff:3.500A) Processing helix chain 'C' and resid 253 through 258 removed outlier: 4.514A pdb=" N THR C 257 " --> pdb=" O THR C 253 " (cutoff:3.500A) Processing helix chain 'C' and resid 277 through 283 removed outlier: 3.504A pdb=" N TYR C 282 " --> pdb=" O ALA C 278 " (cutoff:3.500A) removed outlier: 3.893A pdb=" N HIS C 283 " --> pdb=" O GLU C 279 " (cutoff:3.500A) Processing helix chain 'C' and resid 287 through 297 Processing helix chain 'C' and resid 324 through 338 removed outlier: 3.553A pdb=" N VAL C 328 " --> pdb=" O VAL C 324 " (cutoff:3.500A) Processing helix chain 'C' and resid 384 through 402 removed outlier: 3.553A pdb=" N TRP C 388 " --> pdb=" O ILE C 384 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N LEU C 391 " --> pdb=" O ALA C 387 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N LYS C 401 " --> pdb=" O LEU C 397 " (cutoff:3.500A) Processing helix chain 'C' and resid 404 through 412 removed outlier: 3.914A pdb=" N TYR C 408 " --> pdb=" O PHE C 404 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N GLU C 411 " --> pdb=" O TRP C 407 " (cutoff:3.500A) Processing helix chain 'C' and resid 414 through 437 removed outlier: 3.867A pdb=" N PHE C 418 " --> pdb=" O GLU C 414 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'B' and resid 90 through 92 removed outlier: 8.013A pdb=" N ILE B 91 " --> pdb=" O ALA B 63 " (cutoff:3.500A) removed outlier: 5.695A pdb=" N LEU B 65 " --> pdb=" O ILE B 91 " (cutoff:3.500A) removed outlier: 8.770A pdb=" N ILE B 64 " --> pdb=" O ILE B 4 " (cutoff:3.500A) removed outlier: 6.981A pdb=" N HIS B 6 " --> pdb=" O ILE B 64 " (cutoff:3.500A) removed outlier: 8.014A pdb=" N VAL B 66 " --> pdb=" O HIS B 6 " (cutoff:3.500A) removed outlier: 6.224A pdb=" N GLN B 8 " --> pdb=" O VAL B 66 " (cutoff:3.500A) removed outlier: 7.371A pdb=" N GLU B 3 " --> pdb=" O GLN B 131 " (cutoff:3.500A) removed outlier: 6.184A pdb=" N PHE B 133 " --> pdb=" O GLU B 3 " (cutoff:3.500A) removed outlier: 6.476A pdb=" N VAL B 5 " --> pdb=" O PHE B 133 " (cutoff:3.500A) removed outlier: 5.664A pdb=" N LEU B 135 " --> pdb=" O VAL B 5 " (cutoff:3.500A) removed outlier: 6.764A pdb=" N ILE B 7 " --> pdb=" O LEU B 135 " (cutoff:3.500A) removed outlier: 5.928A pdb=" N HIS B 137 " --> pdb=" O ILE B 7 " (cutoff:3.500A) removed outlier: 7.391A pdb=" N ALA B 9 " --> pdb=" O HIS B 137 " (cutoff:3.500A) removed outlier: 7.290A pdb=" N GLN B 131 " --> pdb=" O ILE B 163 " (cutoff:3.500A) removed outlier: 8.205A pdb=" N ASN B 165 " --> pdb=" O GLN B 131 " (cutoff:3.500A) removed outlier: 6.302A pdb=" N PHE B 133 " --> pdb=" O ASN B 165 " (cutoff:3.500A) removed outlier: 7.770A pdb=" N PHE B 167 " --> pdb=" O PHE B 133 " (cutoff:3.500A) removed outlier: 6.677A pdb=" N LEU B 135 " --> pdb=" O PHE B 167 " (cutoff:3.500A) removed outlier: 7.696A pdb=" N VAL B 169 " --> pdb=" O LEU B 135 " (cutoff:3.500A) removed outlier: 7.381A pdb=" N HIS B 137 " --> pdb=" O VAL B 169 " (cutoff:3.500A) removed outlier: 6.454A pdb=" N MET B 164 " --> pdb=" O GLU B 198 " (cutoff:3.500A) removed outlier: 7.989A pdb=" N TYR B 200 " --> pdb=" O MET B 164 " (cutoff:3.500A) removed outlier: 6.835A pdb=" N THR B 166 " --> pdb=" O TYR B 200 " (cutoff:3.500A) removed outlier: 7.715A pdb=" N ILE B 202 " --> pdb=" O THR B 166 " (cutoff:3.500A) removed outlier: 7.139A pdb=" N SER B 168 " --> pdb=" O ILE B 202 " (cutoff:3.500A) removed outlier: 7.150A pdb=" N PHE B 265 " --> pdb=" O SER B 371 " (cutoff:3.500A) removed outlier: 4.799A pdb=" N SER B 371 " --> pdb=" O PHE B 265 " (cutoff:3.500A) removed outlier: 8.615A pdb=" N LYS B 350 " --> pdb=" O LEU B 311 " (cutoff:3.500A) removed outlier: 6.729A pdb=" N VAL B 313 " --> pdb=" O LYS B 350 " (cutoff:3.500A) removed outlier: 8.038A pdb=" N ALA B 352 " --> pdb=" O VAL B 313 " (cutoff:3.500A) removed outlier: 6.486A pdb=" N THR B 315 " --> pdb=" O ALA B 352 " (cutoff:3.500A) removed outlier: 7.869A pdb=" N CYS B 354 " --> pdb=" O THR B 315 " (cutoff:3.500A) removed outlier: 6.208A pdb=" N PHE B 317 " --> pdb=" O CYS B 354 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 51 through 53 Processing sheet with id=AA3, first strand: chain 'D' and resid 90 through 92 removed outlier: 8.399A pdb=" N ILE D 91 " --> pdb=" O ALA D 63 " (cutoff:3.500A) removed outlier: 6.097A pdb=" N LEU D 65 " --> pdb=" O ILE D 91 " (cutoff:3.500A) removed outlier: 5.927A pdb=" N GLU D 3 " --> pdb=" O LEU D 130 " (cutoff:3.500A) removed outlier: 4.136A pdb=" N GLY D 132 " --> pdb=" O GLU D 3 " (cutoff:3.500A) removed outlier: 10.375A pdb=" N ILE D 163 " --> pdb=" O CYS D 129 " (cutoff:3.500A) removed outlier: 7.222A pdb=" N GLN D 131 " --> pdb=" O ILE D 163 " (cutoff:3.500A) removed outlier: 8.144A pdb=" N ASN D 165 " --> pdb=" O GLN D 131 " (cutoff:3.500A) removed outlier: 6.103A pdb=" N PHE D 133 " --> pdb=" O ASN D 165 " (cutoff:3.500A) removed outlier: 7.423A pdb=" N PHE D 167 " --> pdb=" O PHE D 133 " (cutoff:3.500A) removed outlier: 6.500A pdb=" N LEU D 135 " --> pdb=" O PHE D 167 " (cutoff:3.500A) removed outlier: 7.648A pdb=" N VAL D 169 " --> pdb=" O LEU D 135 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N GLU D 198 " --> pdb=" O MET D 164 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N THR D 166 " --> pdb=" O GLU D 198 " (cutoff:3.500A) removed outlier: 6.455A pdb=" N THR D 199 " --> pdb=" O PHE D 266 " (cutoff:3.500A) removed outlier: 7.864A pdb=" N CYS D 201 " --> pdb=" O PRO D 268 " (cutoff:3.500A) removed outlier: 10.390A pdb=" N PHE D 270 " --> pdb=" O CYS D 201 " (cutoff:3.500A) removed outlier: 13.647A pdb=" N ASP D 203 " --> pdb=" O PHE D 270 " (cutoff:3.500A) removed outlier: 7.177A pdb=" N PHE D 265 " --> pdb=" O SER D 371 " (cutoff:3.500A) removed outlier: 5.074A pdb=" N SER D 371 " --> pdb=" O PHE D 265 " (cutoff:3.500A) removed outlier: 3.932A pdb=" N THR D 312 " --> pdb=" O ASN D 370 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'D' and resid 51 through 54 removed outlier: 3.784A pdb=" N LYS D 58 " --> pdb=" O ALA D 54 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 92 through 94 removed outlier: 8.177A pdb=" N ILE A 93 " --> pdb=" O ALA A 65 " (cutoff:3.500A) removed outlier: 6.302A pdb=" N PHE A 67 " --> pdb=" O ILE A 93 " (cutoff:3.500A) removed outlier: 8.781A pdb=" N VAL A 66 " --> pdb=" O CYS A 4 " (cutoff:3.500A) removed outlier: 7.020A pdb=" N SER A 6 " --> pdb=" O VAL A 66 " (cutoff:3.500A) removed outlier: 8.101A pdb=" N VAL A 68 " --> pdb=" O SER A 6 " (cutoff:3.500A) removed outlier: 6.209A pdb=" N HIS A 8 " --> pdb=" O VAL A 68 " (cutoff:3.500A) removed outlier: 6.338A pdb=" N GLU A 3 " --> pdb=" O LEU A 132 " (cutoff:3.500A) removed outlier: 4.391A pdb=" N GLY A 134 " --> pdb=" O GLU A 3 " (cutoff:3.500A) removed outlier: 4.929A pdb=" N SER A 140 " --> pdb=" O VAL A 9 " (cutoff:3.500A) removed outlier: 7.024A pdb=" N GLN A 133 " --> pdb=" O SER A 165 " (cutoff:3.500A) removed outlier: 7.845A pdb=" N LEU A 167 " --> pdb=" O GLN A 133 " (cutoff:3.500A) removed outlier: 6.297A pdb=" N PHE A 135 " --> pdb=" O LEU A 167 " (cutoff:3.500A) removed outlier: 7.635A pdb=" N PHE A 169 " --> pdb=" O PHE A 135 " (cutoff:3.500A) removed outlier: 6.334A pdb=" N VAL A 137 " --> pdb=" O PHE A 169 " (cutoff:3.500A) removed outlier: 8.171A pdb=" N ILE A 171 " --> pdb=" O VAL A 137 " (cutoff:3.500A) removed outlier: 8.076A pdb=" N HIS A 139 " --> pdb=" O ILE A 171 " (cutoff:3.500A) removed outlier: 3.714A pdb=" N CYS A 200 " --> pdb=" O LYS A 166 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 53 through 55 Processing sheet with id=AA7, first strand: chain 'A' and resid 269 through 273 Processing sheet with id=AA8, first strand: chain 'C' and resid 92 through 93 removed outlier: 7.747A pdb=" N ILE C 93 " --> pdb=" O ALA C 65 " (cutoff:3.500A) removed outlier: 5.976A pdb=" N PHE C 67 " --> pdb=" O ILE C 93 " (cutoff:3.500A) removed outlier: 6.422A pdb=" N GLU C 3 " --> pdb=" O LEU C 132 " (cutoff:3.500A) removed outlier: 4.193A pdb=" N GLY C 134 " --> pdb=" O GLU C 3 " (cutoff:3.500A) removed outlier: 5.039A pdb=" N SER C 140 " --> pdb=" O VAL C 9 " (cutoff:3.500A) removed outlier: 10.528A pdb=" N SER C 165 " --> pdb=" O GLY C 131 " (cutoff:3.500A) removed outlier: 7.182A pdb=" N GLN C 133 " --> pdb=" O SER C 165 " (cutoff:3.500A) removed outlier: 7.873A pdb=" N LEU C 167 " --> pdb=" O GLN C 133 " (cutoff:3.500A) removed outlier: 6.211A pdb=" N PHE C 135 " --> pdb=" O LEU C 167 " (cutoff:3.500A) removed outlier: 7.691A pdb=" N PHE C 169 " --> pdb=" O PHE C 135 " (cutoff:3.500A) removed outlier: 6.386A pdb=" N VAL C 137 " --> pdb=" O PHE C 169 " (cutoff:3.500A) removed outlier: 8.206A pdb=" N ILE C 171 " --> pdb=" O VAL C 137 " (cutoff:3.500A) removed outlier: 7.957A pdb=" N HIS C 139 " --> pdb=" O ILE C 171 " (cutoff:3.500A) removed outlier: 6.667A pdb=" N LYS C 166 " --> pdb=" O CYS C 200 " (cutoff:3.500A) removed outlier: 8.154A pdb=" N PHE C 202 " --> pdb=" O LYS C 166 " (cutoff:3.500A) removed outlier: 6.728A pdb=" N GLU C 168 " --> pdb=" O PHE C 202 " (cutoff:3.500A) removed outlier: 8.007A pdb=" N VAL C 204 " --> pdb=" O GLU C 168 " (cutoff:3.500A) removed outlier: 6.956A pdb=" N SER C 170 " --> pdb=" O VAL C 204 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'C' and resid 53 through 55 Processing sheet with id=AB1, first strand: chain 'C' and resid 269 through 273 removed outlier: 3.529A pdb=" N LYS C 352 " --> pdb=" O CYS C 315 " (cutoff:3.500A) 620 hydrogen bonds defined for protein. 1818 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 2.11 Time building geometry restraints manager: 1.59 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 3222 1.33 - 1.45: 3002 1.45 - 1.57: 7692 1.57 - 1.69: 16 1.69 - 1.82: 156 Bond restraints: 14088 Sorted by residual: bond pdb=" CA THR D 166 " pdb=" CB THR D 166 " ideal model delta sigma weight residual 1.524 1.541 -0.016 1.46e-02 4.69e+03 1.28e+00 bond pdb=" C5 GDP D 502 " pdb=" C4 GDP D 502 " ideal model delta sigma weight residual 1.490 1.470 0.020 2.00e-02 2.50e+03 1.03e+00 bond pdb=" CB ASP D 118 " pdb=" CG ASP D 118 " ideal model delta sigma weight residual 1.516 1.541 -0.025 2.50e-02 1.60e+03 1.01e+00 bond pdb=" CA ASP A 322 " pdb=" CB ASP A 322 " ideal model delta sigma weight residual 1.524 1.537 -0.013 1.31e-02 5.83e+03 9.98e-01 bond pdb=" CB ASN B 99 " pdb=" CG ASN B 99 " ideal model delta sigma weight residual 1.516 1.541 -0.025 2.50e-02 1.60e+03 9.92e-01 ... (remaining 14083 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.72: 18916 1.72 - 3.44: 181 3.44 - 5.16: 34 5.16 - 6.88: 7 6.88 - 8.60: 4 Bond angle restraints: 19142 Sorted by residual: angle pdb=" CB MET C 1 " pdb=" CG MET C 1 " pdb=" SD MET C 1 " ideal model delta sigma weight residual 112.70 121.30 -8.60 3.00e+00 1.11e-01 8.21e+00 angle pdb=" CB MET D 299 " pdb=" CG MET D 299 " pdb=" SD MET D 299 " ideal model delta sigma weight residual 112.70 120.13 -7.43 3.00e+00 1.11e-01 6.13e+00 angle pdb=" CB MET C 413 " pdb=" CG MET C 413 " pdb=" SD MET C 413 " ideal model delta sigma weight residual 112.70 119.80 -7.10 3.00e+00 1.11e-01 5.60e+00 angle pdb=" CB ARG A 339 " pdb=" CG ARG A 339 " pdb=" CD ARG A 339 " ideal model delta sigma weight residual 111.30 116.53 -5.23 2.30e+00 1.89e-01 5.16e+00 angle pdb=" CA LEU B 84 " pdb=" CB LEU B 84 " pdb=" CG LEU B 84 " ideal model delta sigma weight residual 116.30 124.09 -7.79 3.50e+00 8.16e-02 4.95e+00 ... (remaining 19137 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 25.53: 7890 25.53 - 51.05: 446 51.05 - 76.58: 83 76.58 - 102.10: 13 102.10 - 127.63: 6 Dihedral angle restraints: 8438 sinusoidal: 3436 harmonic: 5002 Sorted by residual: dihedral pdb=" C8 GTP C 501 " pdb=" C1' GTP C 501 " pdb=" N9 GTP C 501 " pdb=" O4' GTP C 501 " ideal model delta sinusoidal sigma weight residual 104.59 -23.04 127.63 1 2.00e+01 2.50e-03 3.87e+01 dihedral pdb=" C5' GTP A 501 " pdb=" O5' GTP A 501 " pdb=" PA GTP A 501 " pdb=" O3A GTP A 501 " ideal model delta sinusoidal sigma weight residual 69.27 -164.39 -126.34 1 2.00e+01 2.50e-03 3.82e+01 dihedral pdb=" C5' GTP C 501 " pdb=" O5' GTP C 501 " pdb=" PA GTP C 501 " pdb=" O3A GTP C 501 " ideal model delta sinusoidal sigma weight residual 69.27 -167.41 -123.32 1 2.00e+01 2.50e-03 3.72e+01 ... (remaining 8435 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.035: 1462 0.035 - 0.069: 440 0.069 - 0.104: 142 0.104 - 0.139: 46 0.139 - 0.174: 2 Chirality restraints: 2092 Sorted by residual: chirality pdb=" C2 EPB D 503 " pdb=" C20 EPB D 503 " pdb=" C3 EPB D 503 " pdb=" O1 EPB D 503 " both_signs ideal model delta sigma weight residual False 2.51 2.34 0.17 2.00e-01 2.50e+01 7.55e-01 chirality pdb=" CA ASN B 99 " pdb=" N ASN B 99 " pdb=" C ASN B 99 " pdb=" CB ASN B 99 " both_signs ideal model delta sigma weight residual False 2.51 2.37 0.14 2.00e-01 2.50e+01 4.89e-01 chirality pdb=" CA ILE B 368 " pdb=" N ILE B 368 " pdb=" C ILE B 368 " pdb=" CB ILE B 368 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.12 2.00e-01 2.50e+01 3.78e-01 ... (remaining 2089 not shown) Planarity restraints: 2486 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TRP D 344 " 0.011 2.00e-02 2.50e+03 1.06e-02 2.80e+00 pdb=" CG TRP D 344 " -0.029 2.00e-02 2.50e+03 pdb=" CD1 TRP D 344 " 0.013 2.00e-02 2.50e+03 pdb=" CD2 TRP D 344 " 0.001 2.00e-02 2.50e+03 pdb=" NE1 TRP D 344 " -0.001 2.00e-02 2.50e+03 pdb=" CE2 TRP D 344 " -0.000 2.00e-02 2.50e+03 pdb=" CE3 TRP D 344 " 0.003 2.00e-02 2.50e+03 pdb=" CZ2 TRP D 344 " 0.001 2.00e-02 2.50e+03 pdb=" CZ3 TRP D 344 " 0.000 2.00e-02 2.50e+03 pdb=" CH2 TRP D 344 " 0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C HIS A 88 " -0.022 5.00e-02 4.00e+02 3.36e-02 1.81e+00 pdb=" N PRO A 89 " 0.058 5.00e-02 4.00e+02 pdb=" CA PRO A 89 " -0.017 5.00e-02 4.00e+02 pdb=" CD PRO A 89 " -0.019 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA VAL A 275 " 0.006 2.00e-02 2.50e+03 1.26e-02 1.58e+00 pdb=" C VAL A 275 " -0.022 2.00e-02 2.50e+03 pdb=" O VAL A 275 " 0.008 2.00e-02 2.50e+03 pdb=" N ILE A 276 " 0.007 2.00e-02 2.50e+03 ... (remaining 2483 not shown) Histogram of nonbonded interaction distances: 2.16 - 2.71: 303 2.71 - 3.26: 13251 3.26 - 3.80: 21489 3.80 - 4.35: 27829 4.35 - 4.90: 46754 Nonbonded interactions: 109626 Sorted by model distance: nonbonded pdb=" O1B GTP A 501 " pdb="MG MG A 502 " model vdw 2.162 2.170 nonbonded pdb=" OE2 GLU A 71 " pdb="MG MG A 502 " model vdw 2.166 2.170 nonbonded pdb=" O1B GTP C 501 " pdb="MG MG C 502 " model vdw 2.175 2.170 nonbonded pdb=" OE2 GLU C 71 " pdb="MG MG C 502 " model vdw 2.179 2.170 nonbonded pdb="MG MG D 501 " pdb=" O2A GDP D 502 " model vdw 2.181 2.170 ... (remaining 109621 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: 0.01 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'C' } ncs_group { reference = chain 'B' selection = chain 'D' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 5.670 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: 0.180 Check model and map are aligned: 0.030 Set scattering table: 0.040 Process input model: 13.720 Find NCS groups from input model: 0.240 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.300 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 21.220 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8154 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 : 0.002 0.026 14088 Z= 0.081 Angle : 0.458 8.596 19142 Z= 0.220 Chirality : 0.039 0.174 2092 Planarity : 0.003 0.034 2486 Dihedral : 16.300 127.629 5234 Min Nonbonded Distance : 2.162 Molprobity Statistics. All-atom Clashscore : 5.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.16 % Favored : 98.84 % Rotamer: Outliers : 0.82 % Allowed : 14.88 % Favored : 84.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.13 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.12 (0.20), residues: 1726 helix: 1.56 (0.19), residues: 758 sheet: 1.75 (0.33), residues: 268 loop : -0.57 (0.23), residues: 700 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 64 TYR 0.005 0.000 TYR D 36 PHE 0.009 0.001 PHE D 92 TRP 0.029 0.001 TRP D 344 HIS 0.006 0.000 HIS D 6 Details of bonding type rmsd covalent geometry : bond 0.00158 (14088) covalent geometry : angle 0.45835 (19142) hydrogen bonds : bond 0.27980 ( 620) hydrogen bonds : angle 6.96532 ( 1818) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3452 Ramachandran restraints generated. 1726 Oldfield, 0 Emsley, 1726 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3452 Ramachandran restraints generated. 1726 Oldfield, 0 Emsley, 1726 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 151 residues out of total 1474 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 139 time to evaluate : 0.435 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 57 HIS cc_start: 0.8450 (m-70) cc_final: 0.8173 (m-70) REVERT: B 324 LYS cc_start: 0.5775 (mttp) cc_final: 0.5418 (mttt) REVERT: D 135 LEU cc_start: 0.9145 (tt) cc_final: 0.8882 (tt) REVERT: D 189 ILE cc_start: 0.9023 (mt) cc_final: 0.8794 (mt) REVERT: D 190 HIS cc_start: 0.8770 (t-90) cc_final: 0.8211 (t-170) REVERT: D 205 GLU cc_start: 0.8791 (tt0) cc_final: 0.8473 (tm-30) REVERT: D 211 CYS cc_start: 0.9120 (t) cc_final: 0.8842 (m) REVERT: D 257 MET cc_start: 0.8977 (mmp) cc_final: 0.8733 (mmp) REVERT: D 280 GLN cc_start: 0.8583 (mt0) cc_final: 0.8343 (mm-40) REVERT: D 297 LYS cc_start: 0.9029 (mttt) cc_final: 0.8671 (mtmm) REVERT: D 362 LYS cc_start: 0.8895 (mptt) cc_final: 0.8607 (ttpt) REVERT: D 403 MET cc_start: 0.8464 (tpp) cc_final: 0.8217 (mtp) REVERT: A 24 TYR cc_start: 0.8413 (m-10) cc_final: 0.8119 (m-10) REVERT: A 90 GLU cc_start: 0.8643 (tp30) cc_final: 0.7973 (tp30) REVERT: A 168 GLU cc_start: 0.8329 (mt-10) cc_final: 0.8008 (tt0) REVERT: A 203 MET cc_start: 0.9124 (mtt) cc_final: 0.8640 (mtp) REVERT: A 255 PHE cc_start: 0.7992 (m-80) cc_final: 0.7585 (m-80) REVERT: A 300 ASN cc_start: 0.8883 (t0) cc_final: 0.8542 (t0) REVERT: A 302 MET cc_start: 0.8360 (mmm) cc_final: 0.7890 (mtt) REVERT: A 377 MET cc_start: 0.7933 (tpp) cc_final: 0.7486 (tpt) REVERT: A 425 MET cc_start: 0.8565 (mmm) cc_final: 0.8104 (tpp) REVERT: C 36 MET cc_start: 0.9017 (ttm) cc_final: 0.8657 (ttt) REVERT: C 123 ARG cc_start: 0.8801 (ttp-170) cc_final: 0.7952 (tpm170) REVERT: C 205 ASP cc_start: 0.7088 (t0) cc_final: 0.6730 (t0) REVERT: C 217 LEU cc_start: 0.9180 (mt) cc_final: 0.8905 (mt) REVERT: C 300 ASN cc_start: 0.8902 (t0) cc_final: 0.8530 (t0) REVERT: C 425 MET cc_start: 0.9067 (tpt) cc_final: 0.8592 (tpp) outliers start: 12 outliers final: 11 residues processed: 148 average time/residue: 0.1232 time to fit residues: 26.8282 Evaluate side-chains 145 residues out of total 1474 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 134 time to evaluate : 0.559 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 84 LEU Chi-restraints excluded: chain B residue 149 THR Chi-restraints excluded: chain B residue 348 ASN Chi-restraints excluded: chain D residue 31 ASP Chi-restraints excluded: chain D residue 65 LEU Chi-restraints excluded: chain D residue 164 MET Chi-restraints excluded: chain D residue 178 THR Chi-restraints excluded: chain A residue 269 LEU Chi-restraints excluded: chain C residue 68 VAL Chi-restraints excluded: chain C residue 286 LEU Chi-restraints excluded: chain C residue 363 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 98 optimal weight: 3.9990 chunk 107 optimal weight: 0.9980 chunk 10 optimal weight: 9.9990 chunk 66 optimal weight: 6.9990 chunk 130 optimal weight: 0.0970 chunk 124 optimal weight: 6.9990 chunk 103 optimal weight: 0.0870 chunk 77 optimal weight: 4.9990 chunk 122 optimal weight: 4.9990 chunk 91 optimal weight: 0.9980 chunk 149 optimal weight: 30.0000 overall best weight: 1.2358 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 6 HIS B 15 GLN B 89 ASN B 94 GLN B 126 ASN B 131 GLN B 307 HIS B 423 GLN B 426 GLN D 15 GLN D 89 ASN D 99 ASN D 190 HIS D 191 GLN D 307 HIS D 348 ASN A 88 HIS A 101 ASN A 133 GLN A 256 GLN C 31 GLN C 101 ASN C 107 HIS C 249 ASN C 309 HIS ** C 329 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 25 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3803 r_free = 0.3803 target = 0.101551 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3441 r_free = 0.3441 target = 0.080850 restraints weight = 26260.508| |-----------------------------------------------------------------------------| r_work (start): 0.3428 rms_B_bonded: 3.40 r_work: 0.3273 rms_B_bonded: 3.93 restraints_weight: 0.5000 r_work (final): 0.3273 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8220 moved from start: 0.1539 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 14088 Z= 0.127 Angle : 0.501 5.590 19142 Z= 0.258 Chirality : 0.042 0.164 2092 Planarity : 0.003 0.032 2486 Dihedral : 10.031 127.650 2061 Min Nonbonded Distance : 1.928 Molprobity Statistics. All-atom Clashscore : 4.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.26 % Favored : 97.74 % Rotamer: Outliers : 1.02 % Allowed : 15.01 % Favored : 83.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.13 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.49 (0.21), residues: 1726 helix: 1.99 (0.19), residues: 768 sheet: 1.51 (0.30), residues: 298 loop : -0.46 (0.24), residues: 660 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 339 TYR 0.012 0.001 TYR A 172 PHE 0.012 0.001 PHE A 202 TRP 0.014 0.001 TRP A 388 HIS 0.006 0.001 HIS D 6 Details of bonding type rmsd covalent geometry : bond 0.00260 (14088) covalent geometry : angle 0.50115 (19142) hydrogen bonds : bond 0.05638 ( 620) hydrogen bonds : angle 4.56150 ( 1818) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3452 Ramachandran restraints generated. 1726 Oldfield, 0 Emsley, 1726 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3452 Ramachandran restraints generated. 1726 Oldfield, 0 Emsley, 1726 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 171 residues out of total 1474 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 156 time to evaluate : 0.530 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 57 HIS cc_start: 0.8685 (m-70) cc_final: 0.8434 (m-70) REVERT: B 324 LYS cc_start: 0.5620 (mttp) cc_final: 0.4852 (mttp) REVERT: D 88 ASP cc_start: 0.8446 (t0) cc_final: 0.8144 (t0) REVERT: D 135 LEU cc_start: 0.9307 (tt) cc_final: 0.9077 (tt) REVERT: D 280 GLN cc_start: 0.8625 (mt0) cc_final: 0.8384 (mm-40) REVERT: D 362 LYS cc_start: 0.8835 (mptt) cc_final: 0.8490 (ttpt) REVERT: D 403 MET cc_start: 0.8330 (tpp) cc_final: 0.7719 (tpp) REVERT: A 90 GLU cc_start: 0.8789 (tp30) cc_final: 0.8127 (tp30) REVERT: A 168 GLU cc_start: 0.8441 (mt-10) cc_final: 0.8149 (tt0) REVERT: A 300 ASN cc_start: 0.9032 (t0) cc_final: 0.8742 (t0) REVERT: A 302 MET cc_start: 0.8521 (mmm) cc_final: 0.7989 (mtt) REVERT: A 425 MET cc_start: 0.8627 (mmm) cc_final: 0.8286 (tpp) REVERT: C 36 MET cc_start: 0.8974 (ttm) cc_final: 0.8176 (ttt) REVERT: C 182 VAL cc_start: 0.8872 (m) cc_final: 0.8652 (m) REVERT: C 217 LEU cc_start: 0.9173 (mt) cc_final: 0.8922 (mt) REVERT: C 269 LEU cc_start: 0.8064 (OUTLIER) cc_final: 0.7556 (pp) REVERT: C 300 ASN cc_start: 0.8966 (t0) cc_final: 0.8566 (t0) REVERT: C 425 MET cc_start: 0.9203 (tpt) cc_final: 0.8832 (tpp) outliers start: 15 outliers final: 12 residues processed: 169 average time/residue: 0.1040 time to fit residues: 26.7355 Evaluate side-chains 140 residues out of total 1474 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 127 time to evaluate : 0.530 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 124 CYS Chi-restraints excluded: chain B residue 311 LEU Chi-restraints excluded: chain B residue 342 VAL Chi-restraints excluded: chain D residue 119 VAL Chi-restraints excluded: chain D residue 211 CYS Chi-restraints excluded: chain D residue 217 LEU Chi-restraints excluded: chain A residue 181 VAL Chi-restraints excluded: chain A residue 269 LEU Chi-restraints excluded: chain A residue 324 VAL Chi-restraints excluded: chain C residue 116 ASP Chi-restraints excluded: chain C residue 253 THR Chi-restraints excluded: chain C residue 269 LEU Chi-restraints excluded: chain C residue 363 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 137 optimal weight: 10.0000 chunk 109 optimal weight: 0.9990 chunk 14 optimal weight: 10.0000 chunk 70 optimal weight: 6.9990 chunk 83 optimal weight: 5.9990 chunk 9 optimal weight: 5.9990 chunk 5 optimal weight: 0.4980 chunk 122 optimal weight: 3.9990 chunk 100 optimal weight: 4.9990 chunk 165 optimal weight: 0.7980 chunk 102 optimal weight: 1.9990 overall best weight: 1.6586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 396 HIS D 35 ASN D 334 GLN ** C 329 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3724 r_free = 0.3724 target = 0.097089 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3351 r_free = 0.3351 target = 0.076587 restraints weight = 26692.308| |-----------------------------------------------------------------------------| r_work (start): 0.3345 rms_B_bonded: 3.35 r_work: 0.3195 rms_B_bonded: 3.83 restraints_weight: 0.5000 r_work (final): 0.3195 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8288 moved from start: 0.2297 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 14088 Z= 0.131 Angle : 0.496 8.603 19142 Z= 0.250 Chirality : 0.042 0.154 2092 Planarity : 0.003 0.042 2486 Dihedral : 9.737 129.751 2045 Min Nonbonded Distance : 1.969 Molprobity Statistics. All-atom Clashscore : 4.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.03 % Favored : 97.97 % Rotamer: Outliers : 2.11 % Allowed : 14.81 % Favored : 83.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.13 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.41 (0.21), residues: 1726 helix: 2.01 (0.19), residues: 776 sheet: 1.59 (0.32), residues: 268 loop : -0.62 (0.23), residues: 682 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG D 320 TYR 0.016 0.001 TYR A 24 PHE 0.012 0.001 PHE A 202 TRP 0.013 0.001 TRP A 388 HIS 0.005 0.001 HIS D 6 Details of bonding type rmsd covalent geometry : bond 0.00286 (14088) covalent geometry : angle 0.49566 (19142) hydrogen bonds : bond 0.05172 ( 620) hydrogen bonds : angle 4.09741 ( 1818) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3452 Ramachandran restraints generated. 1726 Oldfield, 0 Emsley, 1726 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3452 Ramachandran restraints generated. 1726 Oldfield, 0 Emsley, 1726 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 165 residues out of total 1474 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 134 time to evaluate : 0.529 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 57 HIS cc_start: 0.8715 (m-70) cc_final: 0.8470 (m-70) REVERT: B 124 CYS cc_start: 0.8977 (OUTLIER) cc_final: 0.8538 (p) REVERT: B 324 LYS cc_start: 0.5725 (mttp) cc_final: 0.5349 (mttt) REVERT: D 1 MET cc_start: 0.7535 (mmm) cc_final: 0.7188 (tpt) REVERT: D 88 ASP cc_start: 0.8534 (t0) cc_final: 0.8221 (t0) REVERT: D 135 LEU cc_start: 0.9330 (tt) cc_final: 0.9087 (tt) REVERT: D 362 LYS cc_start: 0.8866 (mptt) cc_final: 0.8540 (ttpt) REVERT: D 403 MET cc_start: 0.8395 (tpp) cc_final: 0.7688 (tpp) REVERT: A 90 GLU cc_start: 0.8887 (tp30) cc_final: 0.8263 (tp30) REVERT: A 269 LEU cc_start: 0.8360 (OUTLIER) cc_final: 0.8045 (pt) REVERT: A 302 MET cc_start: 0.8794 (mmm) cc_final: 0.8394 (mtp) REVERT: C 36 MET cc_start: 0.8902 (ttm) cc_final: 0.8115 (ttt) REVERT: C 217 LEU cc_start: 0.9178 (mt) cc_final: 0.8912 (mt) REVERT: C 269 LEU cc_start: 0.8244 (OUTLIER) cc_final: 0.7967 (pp) REVERT: C 300 ASN cc_start: 0.8931 (t0) cc_final: 0.8609 (t0) REVERT: C 425 MET cc_start: 0.9282 (tpt) cc_final: 0.9056 (tpp) outliers start: 31 outliers final: 23 residues processed: 160 average time/residue: 0.1146 time to fit residues: 27.6690 Evaluate side-chains 146 residues out of total 1474 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 120 time to evaluate : 0.546 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 69 GLU Chi-restraints excluded: chain B residue 84 LEU Chi-restraints excluded: chain B residue 124 CYS Chi-restraints excluded: chain B residue 149 THR Chi-restraints excluded: chain B residue 172 SER Chi-restraints excluded: chain B residue 196 THR Chi-restraints excluded: chain B residue 311 LEU Chi-restraints excluded: chain B residue 342 VAL Chi-restraints excluded: chain B residue 415 MET Chi-restraints excluded: chain D residue 35 ASN Chi-restraints excluded: chain D residue 65 LEU Chi-restraints excluded: chain D residue 119 VAL Chi-restraints excluded: chain D residue 178 THR Chi-restraints excluded: chain D residue 198 GLU Chi-restraints excluded: chain D residue 211 CYS Chi-restraints excluded: chain D residue 217 LEU Chi-restraints excluded: chain A residue 33 ASP Chi-restraints excluded: chain A residue 136 LEU Chi-restraints excluded: chain A residue 159 VAL Chi-restraints excluded: chain A residue 181 VAL Chi-restraints excluded: chain A residue 269 LEU Chi-restraints excluded: chain C residue 129 CYS Chi-restraints excluded: chain C residue 181 VAL Chi-restraints excluded: chain C residue 253 THR Chi-restraints excluded: chain C residue 269 LEU Chi-restraints excluded: chain C residue 363 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 4 optimal weight: 0.7980 chunk 124 optimal weight: 6.9990 chunk 25 optimal weight: 6.9990 chunk 126 optimal weight: 0.9990 chunk 60 optimal weight: 3.9990 chunk 101 optimal weight: 0.8980 chunk 24 optimal weight: 0.0470 chunk 94 optimal weight: 0.7980 chunk 105 optimal weight: 0.9990 chunk 114 optimal weight: 5.9990 chunk 16 optimal weight: 4.9990 overall best weight: 0.7080 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3751 r_free = 0.3751 target = 0.098665 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3381 r_free = 0.3381 target = 0.078102 restraints weight = 26547.393| |-----------------------------------------------------------------------------| r_work (start): 0.3368 rms_B_bonded: 3.36 r_work: 0.3218 rms_B_bonded: 3.85 restraints_weight: 0.5000 r_work (final): 0.3218 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8216 moved from start: 0.2496 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 14088 Z= 0.095 Angle : 0.478 8.523 19142 Z= 0.235 Chirality : 0.041 0.160 2092 Planarity : 0.003 0.030 2486 Dihedral : 9.611 131.333 2045 Min Nonbonded Distance : 1.958 Molprobity Statistics. All-atom Clashscore : 4.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.97 % Favored : 98.03 % Rotamer: Outliers : 1.83 % Allowed : 14.40 % Favored : 83.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.13 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.44 (0.21), residues: 1726 helix: 2.03 (0.19), residues: 778 sheet: 1.47 (0.31), residues: 280 loop : -0.59 (0.23), residues: 668 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG D 320 TYR 0.016 0.001 TYR A 24 PHE 0.008 0.001 PHE D 317 TRP 0.011 0.001 TRP C 346 HIS 0.003 0.000 HIS D 6 Details of bonding type rmsd covalent geometry : bond 0.00196 (14088) covalent geometry : angle 0.47787 (19142) hydrogen bonds : bond 0.04062 ( 620) hydrogen bonds : angle 3.85186 ( 1818) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3452 Ramachandran restraints generated. 1726 Oldfield, 0 Emsley, 1726 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3452 Ramachandran restraints generated. 1726 Oldfield, 0 Emsley, 1726 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 161 residues out of total 1474 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 134 time to evaluate : 0.610 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 57 HIS cc_start: 0.8772 (m-70) cc_final: 0.8492 (m-70) REVERT: B 124 CYS cc_start: 0.8956 (OUTLIER) cc_final: 0.8511 (p) REVERT: D 88 ASP cc_start: 0.8521 (t0) cc_final: 0.8211 (t0) REVERT: D 135 LEU cc_start: 0.9346 (OUTLIER) cc_final: 0.9114 (tt) REVERT: D 211 CYS cc_start: 0.9214 (t) cc_final: 0.8749 (m) REVERT: D 280 GLN cc_start: 0.8606 (mt0) cc_final: 0.8326 (mm-40) REVERT: D 297 LYS cc_start: 0.8665 (mtmm) cc_final: 0.8266 (pttm) REVERT: D 362 LYS cc_start: 0.8844 (mptt) cc_final: 0.8496 (ttpt) REVERT: A 90 GLU cc_start: 0.8917 (tp30) cc_final: 0.8256 (tp30) REVERT: A 302 MET cc_start: 0.8782 (mmm) cc_final: 0.8368 (mtp) REVERT: C 36 MET cc_start: 0.8889 (ttm) cc_final: 0.8092 (ttt) REVERT: C 129 CYS cc_start: 0.7853 (OUTLIER) cc_final: 0.7563 (p) REVERT: C 217 LEU cc_start: 0.9155 (mt) cc_final: 0.8892 (mt) REVERT: C 269 LEU cc_start: 0.8166 (OUTLIER) cc_final: 0.7903 (pp) REVERT: C 284 GLU cc_start: 0.7986 (tt0) cc_final: 0.7709 (tt0) REVERT: C 300 ASN cc_start: 0.8941 (t0) cc_final: 0.8618 (t0) REVERT: C 425 MET cc_start: 0.9326 (tpt) cc_final: 0.9083 (tpp) REVERT: C 432 TYR cc_start: 0.8096 (OUTLIER) cc_final: 0.7581 (t80) outliers start: 27 outliers final: 17 residues processed: 155 average time/residue: 0.1131 time to fit residues: 26.6569 Evaluate side-chains 150 residues out of total 1474 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 128 time to evaluate : 0.489 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 69 GLU Chi-restraints excluded: chain B residue 84 LEU Chi-restraints excluded: chain B residue 124 CYS Chi-restraints excluded: chain B residue 147 MET Chi-restraints excluded: chain B residue 149 THR Chi-restraints excluded: chain B residue 172 SER Chi-restraints excluded: chain B residue 311 LEU Chi-restraints excluded: chain B residue 342 VAL Chi-restraints excluded: chain D residue 35 ASN Chi-restraints excluded: chain D residue 65 LEU Chi-restraints excluded: chain D residue 119 VAL Chi-restraints excluded: chain D residue 135 LEU Chi-restraints excluded: chain D residue 178 THR Chi-restraints excluded: chain D residue 217 LEU Chi-restraints excluded: chain A residue 33 ASP Chi-restraints excluded: chain A residue 269 LEU Chi-restraints excluded: chain A residue 324 VAL Chi-restraints excluded: chain C residue 94 THR Chi-restraints excluded: chain C residue 129 CYS Chi-restraints excluded: chain C residue 269 LEU Chi-restraints excluded: chain C residue 363 VAL Chi-restraints excluded: chain C residue 432 TYR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 165 optimal weight: 6.9990 chunk 33 optimal weight: 4.9990 chunk 153 optimal weight: 0.8980 chunk 139 optimal weight: 9.9990 chunk 83 optimal weight: 8.9990 chunk 166 optimal weight: 5.9990 chunk 22 optimal weight: 3.9990 chunk 7 optimal weight: 4.9990 chunk 15 optimal weight: 2.9990 chunk 89 optimal weight: 5.9990 chunk 132 optimal weight: 10.0000 overall best weight: 3.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 8 GLN B 334 GLN ** D 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 100 ASN ** D 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 137 HIS A 107 HIS A 258 ASN C 8 HIS C 31 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3640 r_free = 0.3640 target = 0.091719 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3258 r_free = 0.3258 target = 0.071604 restraints weight = 27165.721| |-----------------------------------------------------------------------------| r_work (start): 0.3255 rms_B_bonded: 3.31 r_work: 0.3102 rms_B_bonded: 3.76 restraints_weight: 0.5000 r_work (final): 0.3102 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8396 moved from start: 0.2971 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.033 14088 Z= 0.226 Angle : 0.571 8.752 19142 Z= 0.293 Chirality : 0.045 0.154 2092 Planarity : 0.004 0.045 2486 Dihedral : 9.951 131.969 2045 Min Nonbonded Distance : 1.905 Molprobity Statistics. All-atom Clashscore : 5.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.43 % Favored : 97.57 % Rotamer: Outliers : 2.65 % Allowed : 14.13 % Favored : 83.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.13 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.10 (0.20), residues: 1726 helix: 1.71 (0.19), residues: 790 sheet: 1.12 (0.30), residues: 290 loop : -0.67 (0.23), residues: 646 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG D 320 TYR 0.021 0.001 TYR A 24 PHE 0.013 0.002 PHE A 202 TRP 0.017 0.002 TRP A 388 HIS 0.005 0.001 HIS D 6 Details of bonding type rmsd covalent geometry : bond 0.00526 (14088) covalent geometry : angle 0.57056 (19142) hydrogen bonds : bond 0.06113 ( 620) hydrogen bonds : angle 4.28373 ( 1818) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3452 Ramachandran restraints generated. 1726 Oldfield, 0 Emsley, 1726 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3452 Ramachandran restraints generated. 1726 Oldfield, 0 Emsley, 1726 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 160 residues out of total 1474 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 121 time to evaluate : 0.553 Fit side-chains revert: symmetry clash REVERT: B 324 LYS cc_start: 0.6135 (mttp) cc_final: 0.5876 (mttt) REVERT: D 88 ASP cc_start: 0.8652 (t0) cc_final: 0.8218 (t0) REVERT: D 135 LEU cc_start: 0.9414 (OUTLIER) cc_final: 0.9192 (tt) REVERT: D 211 CYS cc_start: 0.9199 (OUTLIER) cc_final: 0.8663 (m) REVERT: D 297 LYS cc_start: 0.8769 (mtmm) cc_final: 0.8393 (pttm) REVERT: D 342 VAL cc_start: 0.8246 (OUTLIER) cc_final: 0.7959 (p) REVERT: D 362 LYS cc_start: 0.8956 (mptt) cc_final: 0.8547 (ttpt) REVERT: A 90 GLU cc_start: 0.9058 (tp30) cc_final: 0.8446 (tp30) REVERT: A 168 GLU cc_start: 0.8792 (tt0) cc_final: 0.8516 (tt0) REVERT: A 302 MET cc_start: 0.9054 (mmm) cc_final: 0.8752 (mtp) REVERT: C 35 GLN cc_start: 0.8130 (tm-30) cc_final: 0.7713 (tm-30) REVERT: C 36 MET cc_start: 0.8901 (ttm) cc_final: 0.8221 (ttt) REVERT: C 217 LEU cc_start: 0.9214 (mt) cc_final: 0.8902 (mt) REVERT: C 269 LEU cc_start: 0.8486 (OUTLIER) cc_final: 0.8170 (pt) REVERT: C 284 GLU cc_start: 0.8282 (tt0) cc_final: 0.7962 (tt0) REVERT: C 302 MET cc_start: 0.9333 (ttm) cc_final: 0.9088 (ttm) REVERT: C 425 MET cc_start: 0.9341 (tpt) cc_final: 0.9044 (tpp) outliers start: 39 outliers final: 27 residues processed: 155 average time/residue: 0.1213 time to fit residues: 28.1417 Evaluate side-chains 147 residues out of total 1474 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 116 time to evaluate : 0.492 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 69 GLU Chi-restraints excluded: chain B residue 124 CYS Chi-restraints excluded: chain B residue 149 THR Chi-restraints excluded: chain B residue 169 VAL Chi-restraints excluded: chain B residue 172 SER Chi-restraints excluded: chain B residue 311 LEU Chi-restraints excluded: chain B residue 342 VAL Chi-restraints excluded: chain B residue 348 ASN Chi-restraints excluded: chain D residue 35 ASN Chi-restraints excluded: chain D residue 65 LEU Chi-restraints excluded: chain D residue 119 VAL Chi-restraints excluded: chain D residue 135 LEU Chi-restraints excluded: chain D residue 166 THR Chi-restraints excluded: chain D residue 178 THR Chi-restraints excluded: chain D residue 211 CYS Chi-restraints excluded: chain D residue 311 LEU Chi-restraints excluded: chain D residue 342 VAL Chi-restraints excluded: chain A residue 33 ASP Chi-restraints excluded: chain A residue 159 VAL Chi-restraints excluded: chain A residue 181 VAL Chi-restraints excluded: chain A residue 193 THR Chi-restraints excluded: chain A residue 217 LEU Chi-restraints excluded: chain A residue 286 LEU Chi-restraints excluded: chain A residue 324 VAL Chi-restraints excluded: chain A residue 377 MET Chi-restraints excluded: chain C residue 94 THR Chi-restraints excluded: chain C residue 129 CYS Chi-restraints excluded: chain C residue 181 VAL Chi-restraints excluded: chain C residue 269 LEU Chi-restraints excluded: chain C residue 363 VAL Chi-restraints excluded: chain C residue 432 TYR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 41 optimal weight: 4.9990 chunk 51 optimal weight: 8.9990 chunk 129 optimal weight: 1.9990 chunk 139 optimal weight: 5.9990 chunk 45 optimal weight: 4.9990 chunk 118 optimal weight: 0.5980 chunk 49 optimal weight: 3.9990 chunk 29 optimal weight: 6.9990 chunk 98 optimal weight: 0.8980 chunk 13 optimal weight: 0.9990 chunk 7 optimal weight: 3.9990 overall best weight: 1.6986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 165 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 258 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3679 r_free = 0.3679 target = 0.094094 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3306 r_free = 0.3306 target = 0.074045 restraints weight = 26548.248| |-----------------------------------------------------------------------------| r_work (start): 0.3313 rms_B_bonded: 3.30 r_work: 0.3160 rms_B_bonded: 3.76 restraints_weight: 0.5000 r_work (final): 0.3160 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8366 moved from start: 0.3124 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 14088 Z= 0.126 Angle : 0.497 9.703 19142 Z= 0.247 Chirality : 0.042 0.154 2092 Planarity : 0.003 0.031 2486 Dihedral : 9.762 132.173 2043 Min Nonbonded Distance : 1.934 Molprobity Statistics. All-atom Clashscore : 5.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.91 % Favored : 98.09 % Rotamer: Outliers : 2.65 % Allowed : 14.88 % Favored : 82.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.13 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.20 (0.21), residues: 1726 helix: 1.82 (0.19), residues: 790 sheet: 1.11 (0.31), residues: 290 loop : -0.64 (0.24), residues: 646 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG D 320 TYR 0.015 0.001 TYR A 24 PHE 0.009 0.001 PHE B 367 TRP 0.014 0.001 TRP A 388 HIS 0.003 0.001 HIS D 6 Details of bonding type rmsd covalent geometry : bond 0.00281 (14088) covalent geometry : angle 0.49652 (19142) hydrogen bonds : bond 0.04629 ( 620) hydrogen bonds : angle 3.93913 ( 1818) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3452 Ramachandran restraints generated. 1726 Oldfield, 0 Emsley, 1726 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3452 Ramachandran restraints generated. 1726 Oldfield, 0 Emsley, 1726 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 162 residues out of total 1474 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 123 time to evaluate : 0.574 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: D 88 ASP cc_start: 0.8662 (t0) cc_final: 0.8224 (t0) REVERT: D 211 CYS cc_start: 0.9158 (OUTLIER) cc_final: 0.8704 (m) REVERT: D 297 LYS cc_start: 0.8763 (mtmm) cc_final: 0.8419 (pttm) REVERT: D 362 LYS cc_start: 0.8911 (mptt) cc_final: 0.8542 (ttpt) REVERT: D 403 MET cc_start: 0.7973 (tpp) cc_final: 0.7555 (tpp) REVERT: A 90 GLU cc_start: 0.9036 (tp30) cc_final: 0.8395 (tp30) REVERT: A 168 GLU cc_start: 0.8814 (tt0) cc_final: 0.8557 (tt0) REVERT: A 302 MET cc_start: 0.9066 (mmm) cc_final: 0.8650 (mtp) REVERT: C 36 MET cc_start: 0.8970 (ttm) cc_final: 0.8194 (ttt) REVERT: C 182 VAL cc_start: 0.8856 (m) cc_final: 0.8633 (m) REVERT: C 217 LEU cc_start: 0.9188 (mt) cc_final: 0.8872 (mt) REVERT: C 269 LEU cc_start: 0.8432 (OUTLIER) cc_final: 0.8148 (pt) REVERT: C 284 GLU cc_start: 0.8144 (tt0) cc_final: 0.7867 (tt0) REVERT: C 425 MET cc_start: 0.9320 (tpt) cc_final: 0.8986 (tpp) outliers start: 39 outliers final: 27 residues processed: 154 average time/residue: 0.1145 time to fit residues: 26.7335 Evaluate side-chains 144 residues out of total 1474 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 115 time to evaluate : 0.503 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 69 GLU Chi-restraints excluded: chain B residue 84 LEU Chi-restraints excluded: chain B residue 124 CYS Chi-restraints excluded: chain B residue 147 MET Chi-restraints excluded: chain B residue 149 THR Chi-restraints excluded: chain B residue 172 SER Chi-restraints excluded: chain B residue 311 LEU Chi-restraints excluded: chain B residue 342 VAL Chi-restraints excluded: chain B residue 348 ASN Chi-restraints excluded: chain D residue 35 ASN Chi-restraints excluded: chain D residue 65 LEU Chi-restraints excluded: chain D residue 119 VAL Chi-restraints excluded: chain D residue 166 THR Chi-restraints excluded: chain D residue 169 VAL Chi-restraints excluded: chain D residue 178 THR Chi-restraints excluded: chain D residue 211 CYS Chi-restraints excluded: chain A residue 33 ASP Chi-restraints excluded: chain A residue 116 ASP Chi-restraints excluded: chain A residue 159 VAL Chi-restraints excluded: chain A residue 181 VAL Chi-restraints excluded: chain A residue 286 LEU Chi-restraints excluded: chain A residue 324 VAL Chi-restraints excluded: chain A residue 377 MET Chi-restraints excluded: chain C residue 94 THR Chi-restraints excluded: chain C residue 129 CYS Chi-restraints excluded: chain C residue 269 LEU Chi-restraints excluded: chain C residue 286 LEU Chi-restraints excluded: chain C residue 363 VAL Chi-restraints excluded: chain C residue 432 TYR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 21 optimal weight: 7.9990 chunk 19 optimal weight: 0.8980 chunk 169 optimal weight: 10.0000 chunk 47 optimal weight: 0.9990 chunk 15 optimal weight: 3.9990 chunk 60 optimal weight: 0.9990 chunk 9 optimal weight: 5.9990 chunk 69 optimal weight: 1.9990 chunk 49 optimal weight: 0.9990 chunk 124 optimal weight: 8.9990 chunk 110 optimal weight: 0.0470 overall best weight: 0.7884 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 258 ASN C 18 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3727 r_free = 0.3727 target = 0.097121 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3353 r_free = 0.3353 target = 0.076672 restraints weight = 26583.073| |-----------------------------------------------------------------------------| r_work (start): 0.3342 rms_B_bonded: 3.36 r_work: 0.3190 rms_B_bonded: 3.84 restraints_weight: 0.5000 r_work (final): 0.3190 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8327 moved from start: 0.3219 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.025 14088 Z= 0.093 Angle : 0.472 9.106 19142 Z= 0.231 Chirality : 0.041 0.159 2092 Planarity : 0.003 0.030 2486 Dihedral : 9.508 133.935 2043 Min Nonbonded Distance : 1.964 Molprobity Statistics. All-atom Clashscore : 5.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.97 % Favored : 98.03 % Rotamer: Outliers : 2.31 % Allowed : 15.29 % Favored : 82.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.13 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.33 (0.21), residues: 1726 helix: 1.97 (0.19), residues: 792 sheet: 1.15 (0.31), residues: 290 loop : -0.62 (0.24), residues: 644 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG D 320 TYR 0.013 0.001 TYR A 24 PHE 0.008 0.001 PHE B 367 TRP 0.016 0.001 TRP A 388 HIS 0.003 0.000 HIS D 6 Details of bonding type rmsd covalent geometry : bond 0.00195 (14088) covalent geometry : angle 0.47204 (19142) hydrogen bonds : bond 0.03684 ( 620) hydrogen bonds : angle 3.69336 ( 1818) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3452 Ramachandran restraints generated. 1726 Oldfield, 0 Emsley, 1726 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3452 Ramachandran restraints generated. 1726 Oldfield, 0 Emsley, 1726 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 163 residues out of total 1474 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 129 time to evaluate : 0.536 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 293 MET cc_start: 0.8097 (mmm) cc_final: 0.7793 (mmm) REVERT: D 88 ASP cc_start: 0.8629 (t0) cc_final: 0.8193 (t0) REVERT: D 211 CYS cc_start: 0.9148 (OUTLIER) cc_final: 0.8747 (m) REVERT: D 297 LYS cc_start: 0.8750 (mtmm) cc_final: 0.8432 (pttm) REVERT: D 362 LYS cc_start: 0.8901 (mptt) cc_final: 0.8545 (ttpt) REVERT: D 423 GLN cc_start: 0.9247 (tt0) cc_final: 0.8790 (tp40) REVERT: A 90 GLU cc_start: 0.9047 (tp30) cc_final: 0.8388 (tp30) REVERT: A 168 GLU cc_start: 0.8836 (tt0) cc_final: 0.8587 (tt0) REVERT: A 255 PHE cc_start: 0.8225 (m-10) cc_final: 0.7802 (m-80) REVERT: A 302 MET cc_start: 0.9086 (mmm) cc_final: 0.8508 (mtp) REVERT: A 432 TYR cc_start: 0.7922 (OUTLIER) cc_final: 0.6785 (t80) REVERT: C 36 MET cc_start: 0.8972 (ttm) cc_final: 0.8197 (ttt) REVERT: C 182 VAL cc_start: 0.8845 (m) cc_final: 0.8623 (m) REVERT: C 217 LEU cc_start: 0.9133 (mt) cc_final: 0.8816 (mt) REVERT: C 269 LEU cc_start: 0.8331 (OUTLIER) cc_final: 0.8032 (pt) REVERT: C 284 GLU cc_start: 0.8123 (tt0) cc_final: 0.7825 (tt0) REVERT: C 425 MET cc_start: 0.9322 (tpt) cc_final: 0.8974 (tpp) REVERT: C 432 TYR cc_start: 0.8412 (OUTLIER) cc_final: 0.7533 (t80) outliers start: 34 outliers final: 26 residues processed: 159 average time/residue: 0.1112 time to fit residues: 26.9584 Evaluate side-chains 154 residues out of total 1474 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 124 time to evaluate : 0.533 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 69 GLU Chi-restraints excluded: chain B residue 84 LEU Chi-restraints excluded: chain B residue 124 CYS Chi-restraints excluded: chain B residue 147 MET Chi-restraints excluded: chain B residue 149 THR Chi-restraints excluded: chain B residue 172 SER Chi-restraints excluded: chain B residue 188 SER Chi-restraints excluded: chain B residue 311 LEU Chi-restraints excluded: chain B residue 342 VAL Chi-restraints excluded: chain B residue 348 ASN Chi-restraints excluded: chain D residue 166 THR Chi-restraints excluded: chain D residue 178 THR Chi-restraints excluded: chain D residue 211 CYS Chi-restraints excluded: chain D residue 217 LEU Chi-restraints excluded: chain A residue 33 ASP Chi-restraints excluded: chain A residue 116 ASP Chi-restraints excluded: chain A residue 117 LEU Chi-restraints excluded: chain A residue 181 VAL Chi-restraints excluded: chain A residue 193 THR Chi-restraints excluded: chain A residue 286 LEU Chi-restraints excluded: chain A residue 324 VAL Chi-restraints excluded: chain A residue 377 MET Chi-restraints excluded: chain A residue 432 TYR Chi-restraints excluded: chain C residue 94 THR Chi-restraints excluded: chain C residue 129 CYS Chi-restraints excluded: chain C residue 181 VAL Chi-restraints excluded: chain C residue 269 LEU Chi-restraints excluded: chain C residue 286 LEU Chi-restraints excluded: chain C residue 363 VAL Chi-restraints excluded: chain C residue 432 TYR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 92 optimal weight: 7.9990 chunk 72 optimal weight: 0.0040 chunk 15 optimal weight: 4.9990 chunk 3 optimal weight: 8.9990 chunk 102 optimal weight: 0.7980 chunk 65 optimal weight: 4.9990 chunk 153 optimal weight: 0.9990 chunk 14 optimal weight: 0.8980 chunk 119 optimal weight: 0.8980 chunk 111 optimal weight: 4.9990 chunk 55 optimal weight: 5.9990 overall best weight: 0.7194 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 126 ASN D 35 ASN ** D 165 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 35 GLN C 18 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3735 r_free = 0.3735 target = 0.097635 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3363 r_free = 0.3363 target = 0.077155 restraints weight = 26461.193| |-----------------------------------------------------------------------------| r_work (start): 0.3350 rms_B_bonded: 3.36 r_work: 0.3198 rms_B_bonded: 3.84 restraints_weight: 0.5000 r_work (final): 0.3198 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8320 moved from start: 0.3302 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 14088 Z= 0.090 Angle : 0.469 12.284 19142 Z= 0.228 Chirality : 0.041 0.160 2092 Planarity : 0.003 0.030 2486 Dihedral : 9.367 134.810 2043 Min Nonbonded Distance : 1.972 Molprobity Statistics. All-atom Clashscore : 4.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.91 % Favored : 98.09 % Rotamer: Outliers : 2.45 % Allowed : 15.49 % Favored : 82.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.13 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.40 (0.21), residues: 1726 helix: 2.04 (0.19), residues: 792 sheet: 1.18 (0.31), residues: 290 loop : -0.61 (0.24), residues: 644 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG D 320 TYR 0.016 0.001 TYR A 24 PHE 0.008 0.001 PHE B 367 TRP 0.014 0.001 TRP A 388 HIS 0.003 0.000 HIS D 6 Details of bonding type rmsd covalent geometry : bond 0.00188 (14088) covalent geometry : angle 0.46875 (19142) hydrogen bonds : bond 0.03596 ( 620) hydrogen bonds : angle 3.57814 ( 1818) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3452 Ramachandran restraints generated. 1726 Oldfield, 0 Emsley, 1726 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3452 Ramachandran restraints generated. 1726 Oldfield, 0 Emsley, 1726 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 166 residues out of total 1474 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 130 time to evaluate : 0.552 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: D 88 ASP cc_start: 0.8631 (t0) cc_final: 0.8201 (t0) REVERT: D 211 CYS cc_start: 0.9122 (OUTLIER) cc_final: 0.8726 (m) REVERT: D 297 LYS cc_start: 0.8765 (mtmm) cc_final: 0.8476 (pttm) REVERT: D 362 LYS cc_start: 0.8891 (mptt) cc_final: 0.8544 (ttpt) REVERT: D 423 GLN cc_start: 0.9249 (tt0) cc_final: 0.8771 (tp40) REVERT: A 90 GLU cc_start: 0.9070 (tp30) cc_final: 0.8263 (tp30) REVERT: A 168 GLU cc_start: 0.8849 (tt0) cc_final: 0.8624 (tt0) REVERT: A 255 PHE cc_start: 0.8163 (m-10) cc_final: 0.7743 (m-80) REVERT: A 302 MET cc_start: 0.9104 (mmm) cc_final: 0.8361 (mtp) REVERT: A 432 TYR cc_start: 0.7901 (OUTLIER) cc_final: 0.6742 (t80) REVERT: C 36 MET cc_start: 0.8967 (ttm) cc_final: 0.8189 (ttt) REVERT: C 182 VAL cc_start: 0.8849 (m) cc_final: 0.8615 (m) REVERT: C 217 LEU cc_start: 0.9125 (mt) cc_final: 0.8808 (mt) REVERT: C 269 LEU cc_start: 0.8298 (OUTLIER) cc_final: 0.8039 (pp) REVERT: C 284 GLU cc_start: 0.8154 (tt0) cc_final: 0.7869 (tt0) REVERT: C 425 MET cc_start: 0.9327 (tpt) cc_final: 0.8982 (tpp) REVERT: C 432 TYR cc_start: 0.8417 (OUTLIER) cc_final: 0.7579 (t80) outliers start: 36 outliers final: 30 residues processed: 160 average time/residue: 0.1140 time to fit residues: 27.4209 Evaluate side-chains 154 residues out of total 1474 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 120 time to evaluate : 0.654 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 69 GLU Chi-restraints excluded: chain B residue 84 LEU Chi-restraints excluded: chain B residue 120 VAL Chi-restraints excluded: chain B residue 124 CYS Chi-restraints excluded: chain B residue 126 ASN Chi-restraints excluded: chain B residue 147 MET Chi-restraints excluded: chain B residue 149 THR Chi-restraints excluded: chain B residue 169 VAL Chi-restraints excluded: chain B residue 172 SER Chi-restraints excluded: chain B residue 188 SER Chi-restraints excluded: chain B residue 311 LEU Chi-restraints excluded: chain B residue 342 VAL Chi-restraints excluded: chain B residue 348 ASN Chi-restraints excluded: chain D residue 35 ASN Chi-restraints excluded: chain D residue 65 LEU Chi-restraints excluded: chain D residue 166 THR Chi-restraints excluded: chain D residue 178 THR Chi-restraints excluded: chain D residue 211 CYS Chi-restraints excluded: chain D residue 217 LEU Chi-restraints excluded: chain A residue 33 ASP Chi-restraints excluded: chain A residue 117 LEU Chi-restraints excluded: chain A residue 181 VAL Chi-restraints excluded: chain A residue 193 THR Chi-restraints excluded: chain A residue 286 LEU Chi-restraints excluded: chain A residue 324 VAL Chi-restraints excluded: chain A residue 377 MET Chi-restraints excluded: chain A residue 432 TYR Chi-restraints excluded: chain C residue 129 CYS Chi-restraints excluded: chain C residue 181 VAL Chi-restraints excluded: chain C residue 193 THR Chi-restraints excluded: chain C residue 269 LEU Chi-restraints excluded: chain C residue 286 LEU Chi-restraints excluded: chain C residue 363 VAL Chi-restraints excluded: chain C residue 432 TYR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 133 optimal weight: 4.9990 chunk 93 optimal weight: 8.9990 chunk 57 optimal weight: 3.9990 chunk 163 optimal weight: 0.3980 chunk 22 optimal weight: 3.9990 chunk 139 optimal weight: 9.9990 chunk 148 optimal weight: 1.9990 chunk 125 optimal weight: 0.9990 chunk 111 optimal weight: 8.9990 chunk 99 optimal weight: 2.9990 chunk 95 optimal weight: 1.9990 overall best weight: 1.6788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 35 ASN ** D 165 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 35 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3697 r_free = 0.3697 target = 0.095335 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3324 r_free = 0.3324 target = 0.075117 restraints weight = 26785.790| |-----------------------------------------------------------------------------| r_work (start): 0.3318 rms_B_bonded: 3.33 r_work: 0.3166 rms_B_bonded: 3.79 restraints_weight: 0.5000 r_work (final): 0.3166 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8338 moved from start: 0.3345 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 14088 Z= 0.123 Angle : 0.488 9.055 19142 Z= 0.239 Chirality : 0.042 0.157 2092 Planarity : 0.003 0.035 2486 Dihedral : 9.397 135.415 2043 Min Nonbonded Distance : 1.938 Molprobity Statistics. All-atom Clashscore : 4.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.38 % Favored : 97.62 % Rotamer: Outliers : 2.24 % Allowed : 15.69 % Favored : 82.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.13 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.40 (0.21), residues: 1726 helix: 2.06 (0.19), residues: 790 sheet: 1.22 (0.31), residues: 280 loop : -0.62 (0.23), residues: 656 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG D 320 TYR 0.015 0.001 TYR D 36 PHE 0.008 0.001 PHE D 408 TRP 0.014 0.001 TRP A 388 HIS 0.004 0.001 HIS D 6 Details of bonding type rmsd covalent geometry : bond 0.00280 (14088) covalent geometry : angle 0.48755 (19142) hydrogen bonds : bond 0.04105 ( 620) hydrogen bonds : angle 3.66366 ( 1818) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3452 Ramachandran restraints generated. 1726 Oldfield, 0 Emsley, 1726 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3452 Ramachandran restraints generated. 1726 Oldfield, 0 Emsley, 1726 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 154 residues out of total 1474 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 121 time to evaluate : 0.565 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: D 88 ASP cc_start: 0.8664 (t0) cc_final: 0.8226 (t0) REVERT: D 211 CYS cc_start: 0.9139 (OUTLIER) cc_final: 0.8711 (m) REVERT: D 297 LYS cc_start: 0.8791 (mtmm) cc_final: 0.8495 (pttm) REVERT: D 362 LYS cc_start: 0.8906 (mptt) cc_final: 0.8545 (ttpt) REVERT: D 423 GLN cc_start: 0.9247 (tt0) cc_final: 0.8768 (tp40) REVERT: A 90 GLU cc_start: 0.9111 (tp30) cc_final: 0.8436 (tp30) REVERT: A 168 GLU cc_start: 0.8861 (tt0) cc_final: 0.8641 (tt0) REVERT: A 302 MET cc_start: 0.9141 (mmm) cc_final: 0.8472 (mtp) REVERT: C 36 MET cc_start: 0.8956 (ttm) cc_final: 0.8181 (ttt) REVERT: C 182 VAL cc_start: 0.8852 (m) cc_final: 0.8631 (m) REVERT: C 217 LEU cc_start: 0.9126 (mt) cc_final: 0.8807 (mt) REVERT: C 269 LEU cc_start: 0.8319 (OUTLIER) cc_final: 0.8052 (pt) REVERT: C 284 GLU cc_start: 0.8127 (tt0) cc_final: 0.7821 (tt0) REVERT: C 425 MET cc_start: 0.9329 (tpt) cc_final: 0.9089 (tpp) REVERT: C 432 TYR cc_start: 0.8442 (OUTLIER) cc_final: 0.7579 (t80) outliers start: 33 outliers final: 30 residues processed: 150 average time/residue: 0.1074 time to fit residues: 24.6795 Evaluate side-chains 153 residues out of total 1474 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 120 time to evaluate : 0.461 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 69 GLU Chi-restraints excluded: chain B residue 84 LEU Chi-restraints excluded: chain B residue 120 VAL Chi-restraints excluded: chain B residue 124 CYS Chi-restraints excluded: chain B residue 147 MET Chi-restraints excluded: chain B residue 149 THR Chi-restraints excluded: chain B residue 169 VAL Chi-restraints excluded: chain B residue 172 SER Chi-restraints excluded: chain B residue 188 SER Chi-restraints excluded: chain B residue 311 LEU Chi-restraints excluded: chain B residue 342 VAL Chi-restraints excluded: chain B residue 348 ASN Chi-restraints excluded: chain D residue 35 ASN Chi-restraints excluded: chain D residue 65 LEU Chi-restraints excluded: chain D residue 166 THR Chi-restraints excluded: chain D residue 178 THR Chi-restraints excluded: chain D residue 211 CYS Chi-restraints excluded: chain D residue 217 LEU Chi-restraints excluded: chain A residue 33 ASP Chi-restraints excluded: chain A residue 117 LEU Chi-restraints excluded: chain A residue 181 VAL Chi-restraints excluded: chain A residue 193 THR Chi-restraints excluded: chain A residue 286 LEU Chi-restraints excluded: chain A residue 324 VAL Chi-restraints excluded: chain A residue 377 MET Chi-restraints excluded: chain C residue 94 THR Chi-restraints excluded: chain C residue 129 CYS Chi-restraints excluded: chain C residue 181 VAL Chi-restraints excluded: chain C residue 193 THR Chi-restraints excluded: chain C residue 269 LEU Chi-restraints excluded: chain C residue 286 LEU Chi-restraints excluded: chain C residue 363 VAL Chi-restraints excluded: chain C residue 432 TYR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 11 optimal weight: 0.5980 chunk 23 optimal weight: 6.9990 chunk 98 optimal weight: 0.6980 chunk 57 optimal weight: 2.9990 chunk 82 optimal weight: 1.9990 chunk 43 optimal weight: 5.9990 chunk 38 optimal weight: 0.9990 chunk 160 optimal weight: 10.0000 chunk 102 optimal weight: 0.6980 chunk 128 optimal weight: 9.9990 chunk 35 optimal weight: 1.9990 overall best weight: 0.9984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 165 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3722 r_free = 0.3722 target = 0.096859 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3351 r_free = 0.3351 target = 0.076499 restraints weight = 26438.662| |-----------------------------------------------------------------------------| r_work (start): 0.3335 rms_B_bonded: 3.34 r_work: 0.3183 rms_B_bonded: 3.82 restraints_weight: 0.5000 r_work (final): 0.3183 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8339 moved from start: 0.3410 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 14088 Z= 0.098 Angle : 0.481 9.620 19142 Z= 0.233 Chirality : 0.041 0.159 2092 Planarity : 0.003 0.031 2486 Dihedral : 9.325 136.038 2043 Min Nonbonded Distance : 1.966 Molprobity Statistics. All-atom Clashscore : 4.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.09 % Favored : 97.91 % Rotamer: Outliers : 2.31 % Allowed : 15.96 % Favored : 81.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.13 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.44 (0.21), residues: 1726 helix: 2.10 (0.19), residues: 790 sheet: 1.07 (0.30), residues: 302 loop : -0.57 (0.24), residues: 634 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG D 320 TYR 0.010 0.001 TYR A 172 PHE 0.015 0.001 PHE A 49 TRP 0.016 0.001 TRP A 388 HIS 0.003 0.000 HIS D 6 Details of bonding type rmsd covalent geometry : bond 0.00212 (14088) covalent geometry : angle 0.48060 (19142) hydrogen bonds : bond 0.03751 ( 620) hydrogen bonds : angle 3.59314 ( 1818) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3452 Ramachandran restraints generated. 1726 Oldfield, 0 Emsley, 1726 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3452 Ramachandran restraints generated. 1726 Oldfield, 0 Emsley, 1726 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 157 residues out of total 1474 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 123 time to evaluate : 0.601 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 88 ASP cc_start: 0.8650 (t0) cc_final: 0.8211 (t0) REVERT: D 211 CYS cc_start: 0.9124 (OUTLIER) cc_final: 0.8727 (m) REVERT: D 297 LYS cc_start: 0.8769 (mtmm) cc_final: 0.8486 (pttm) REVERT: D 362 LYS cc_start: 0.8899 (mptt) cc_final: 0.8544 (ttpt) REVERT: D 423 GLN cc_start: 0.9252 (tt0) cc_final: 0.8758 (tp40) REVERT: A 90 GLU cc_start: 0.9113 (tp30) cc_final: 0.8296 (tp30) REVERT: A 168 GLU cc_start: 0.8845 (tt0) cc_final: 0.8637 (tt0) REVERT: A 255 PHE cc_start: 0.8164 (m-10) cc_final: 0.7753 (m-80) REVERT: A 302 MET cc_start: 0.9140 (mmm) cc_final: 0.8530 (mtp) REVERT: A 388 TRP cc_start: 0.8439 (m100) cc_final: 0.8231 (m100) REVERT: A 432 TYR cc_start: 0.7916 (OUTLIER) cc_final: 0.6708 (t80) REVERT: C 36 MET cc_start: 0.8976 (ttm) cc_final: 0.8203 (ttt) REVERT: C 182 VAL cc_start: 0.8858 (m) cc_final: 0.8624 (m) REVERT: C 217 LEU cc_start: 0.9149 (mt) cc_final: 0.8839 (mt) REVERT: C 269 LEU cc_start: 0.8310 (OUTLIER) cc_final: 0.8046 (pt) REVERT: C 284 GLU cc_start: 0.8157 (tt0) cc_final: 0.7865 (tt0) REVERT: C 425 MET cc_start: 0.9330 (tpt) cc_final: 0.9088 (tpp) REVERT: C 432 TYR cc_start: 0.8434 (OUTLIER) cc_final: 0.7580 (t80) outliers start: 34 outliers final: 29 residues processed: 154 average time/residue: 0.1085 time to fit residues: 25.1826 Evaluate side-chains 154 residues out of total 1474 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 121 time to evaluate : 0.428 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 69 GLU Chi-restraints excluded: chain B residue 84 LEU Chi-restraints excluded: chain B residue 120 VAL Chi-restraints excluded: chain B residue 147 MET Chi-restraints excluded: chain B residue 149 THR Chi-restraints excluded: chain B residue 169 VAL Chi-restraints excluded: chain B residue 172 SER Chi-restraints excluded: chain B residue 188 SER Chi-restraints excluded: chain B residue 311 LEU Chi-restraints excluded: chain B residue 342 VAL Chi-restraints excluded: chain B residue 348 ASN Chi-restraints excluded: chain D residue 35 ASN Chi-restraints excluded: chain D residue 65 LEU Chi-restraints excluded: chain D residue 166 THR Chi-restraints excluded: chain D residue 178 THR Chi-restraints excluded: chain D residue 211 CYS Chi-restraints excluded: chain D residue 217 LEU Chi-restraints excluded: chain A residue 33 ASP Chi-restraints excluded: chain A residue 117 LEU Chi-restraints excluded: chain A residue 181 VAL Chi-restraints excluded: chain A residue 193 THR Chi-restraints excluded: chain A residue 286 LEU Chi-restraints excluded: chain A residue 324 VAL Chi-restraints excluded: chain A residue 377 MET Chi-restraints excluded: chain A residue 432 TYR Chi-restraints excluded: chain C residue 94 THR Chi-restraints excluded: chain C residue 129 CYS Chi-restraints excluded: chain C residue 181 VAL Chi-restraints excluded: chain C residue 193 THR Chi-restraints excluded: chain C residue 269 LEU Chi-restraints excluded: chain C residue 286 LEU Chi-restraints excluded: chain C residue 363 VAL Chi-restraints excluded: chain C residue 432 TYR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 53 optimal weight: 5.9990 chunk 20 optimal weight: 6.9990 chunk 169 optimal weight: 5.9990 chunk 137 optimal weight: 9.9990 chunk 96 optimal weight: 2.9990 chunk 132 optimal weight: 8.9990 chunk 147 optimal weight: 6.9990 chunk 34 optimal weight: 0.5980 chunk 40 optimal weight: 9.9990 chunk 10 optimal weight: 6.9990 chunk 67 optimal weight: 1.9990 overall best weight: 3.5188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 35 ASN ** D 165 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3632 r_free = 0.3632 target = 0.091252 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3247 r_free = 0.3247 target = 0.071217 restraints weight = 27320.315| |-----------------------------------------------------------------------------| r_work (start): 0.3242 rms_B_bonded: 3.32 r_work: 0.3088 rms_B_bonded: 3.76 restraints_weight: 0.5000 r_work (final): 0.3088 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8422 moved from start: 0.3516 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.033 14088 Z= 0.224 Angle : 0.571 8.797 19142 Z= 0.289 Chirality : 0.045 0.156 2092 Planarity : 0.004 0.050 2486 Dihedral : 9.705 131.083 2043 Min Nonbonded Distance : 1.907 Molprobity Statistics. All-atom Clashscore : 4.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.07 % Favored : 96.93 % Rotamer: Outliers : 2.11 % Allowed : 16.17 % Favored : 81.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.13 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.17 (0.21), residues: 1726 helix: 1.87 (0.19), residues: 788 sheet: 1.03 (0.31), residues: 290 loop : -0.72 (0.23), residues: 648 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG D 320 TYR 0.019 0.001 TYR A 24 PHE 0.011 0.002 PHE D 133 TRP 0.015 0.002 TRP A 388 HIS 0.004 0.001 HIS D 396 Details of bonding type rmsd covalent geometry : bond 0.00528 (14088) covalent geometry : angle 0.57107 (19142) hydrogen bonds : bond 0.05740 ( 620) hydrogen bonds : angle 4.08815 ( 1818) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2874.17 seconds wall clock time: 50 minutes 20.53 seconds (3020.53 seconds total)