Starting phenix.real_space_refine on Wed Jun 18 19:21:10 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8jgn_36240/06_2025/8jgn_36240.cif Found real_map, /net/cci-nas-00/data/ceres_data/8jgn_36240/06_2025/8jgn_36240.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.39 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8jgn_36240/06_2025/8jgn_36240.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8jgn_36240/06_2025/8jgn_36240.map" model { file = "/net/cci-nas-00/data/ceres_data/8jgn_36240/06_2025/8jgn_36240.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8jgn_36240/06_2025/8jgn_36240.cif" } resolution = 3.39 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.008 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: 4 Type Number sf(0) Gaussians S 90 5.16 5 C 13836 2.51 5 N 3576 2.21 5 O 3858 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 141 residue(s): 0.06s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/chem_data/mon_lib" Total number of atoms: 21360 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 3560 Number of conformers: 1 Conformer: "" Number of residues, atoms: 448, 3560 Classifications: {'peptide': 448} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 27, 'TRANS': 419} Chain: "B" Number of atoms: 3560 Number of conformers: 1 Conformer: "" Number of residues, atoms: 448, 3560 Classifications: {'peptide': 448} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 27, 'TRANS': 419} Chain: "C" Number of atoms: 3560 Number of conformers: 1 Conformer: "" Number of residues, atoms: 448, 3560 Classifications: {'peptide': 448} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 27, 'TRANS': 419} Chain: "D" Number of atoms: 3560 Number of conformers: 1 Conformer: "" Number of residues, atoms: 448, 3560 Classifications: {'peptide': 448} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 27, 'TRANS': 419} Chain: "E" Number of atoms: 3560 Number of conformers: 1 Conformer: "" Number of residues, atoms: 448, 3560 Classifications: {'peptide': 448} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 27, 'TRANS': 419} Chain: "F" Number of atoms: 3560 Number of conformers: 1 Conformer: "" Number of residues, atoms: 448, 3560 Classifications: {'peptide': 448} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 27, 'TRANS': 419} Time building chain proxies: 14.39, per 1000 atoms: 0.67 Number of scatterers: 21360 At special positions: 0 Unit cell: (130.568, 136.828, 128.779, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 90 16.00 O 3858 8.00 N 3576 7.00 C 13836 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: 4.95 Conformation dependent library (CDL) restraints added in 3.1 seconds 5352 Ramachandran restraints generated. 2676 Oldfield, 0 Emsley, 2676 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4944 Finding SS restraints... Secondary structure from input PDB file: 145 helices and 19 sheets defined 50.3% alpha, 14.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.51 Creating SS restraints... Processing helix chain 'A' and resid 138 through 146 removed outlier: 3.526A pdb=" N ARG A 143 " --> pdb=" O GLY A 139 " (cutoff:3.500A) Processing helix chain 'A' and resid 165 through 170 Processing helix chain 'A' and resid 174 through 183 Processing helix chain 'A' and resid 186 through 202 removed outlier: 3.526A pdb=" N VAL A 199 " --> pdb=" O GLU A 195 " (cutoff:3.500A) removed outlier: 4.152A pdb=" N ARG A 200 " --> pdb=" O PHE A 196 " (cutoff:3.500A) Processing helix chain 'A' and resid 203 through 206 Processing helix chain 'A' and resid 214 through 226 Processing helix chain 'A' and resid 227 through 229 No H-bonds generated for 'chain 'A' and resid 227 through 229' Processing helix chain 'A' and resid 248 through 271 removed outlier: 4.001A pdb=" N GLU A 258 " --> pdb=" O GLU A 254 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N GLN A 259 " --> pdb=" O ALA A 255 " (cutoff:3.500A) Processing helix chain 'A' and resid 273 through 287 removed outlier: 3.822A pdb=" N ILE A 277 " --> pdb=" O GLN A 273 " (cutoff:3.500A) Processing helix chain 'A' and resid 302 through 307 Processing helix chain 'A' and resid 309 through 314 Processing helix chain 'A' and resid 318 through 328 Processing helix chain 'A' and resid 344 through 354 Processing helix chain 'A' and resid 361 through 366 Processing helix chain 'A' and resid 367 through 372 removed outlier: 3.510A pdb=" N CYS A 372 " --> pdb=" O ALA A 369 " (cutoff:3.500A) Processing helix chain 'A' and resid 379 through 386 removed outlier: 4.237A pdb=" N ASP A 386 " --> pdb=" O HIS A 382 " (cutoff:3.500A) Processing helix chain 'A' and resid 388 through 393 Processing helix chain 'A' and resid 393 through 400 Processing helix chain 'A' and resid 414 through 419 removed outlier: 3.552A pdb=" N GLU A 418 " --> pdb=" O TRP A 414 " (cutoff:3.500A) Processing helix chain 'A' and resid 422 through 424 No H-bonds generated for 'chain 'A' and resid 422 through 424' Processing helix chain 'A' and resid 425 through 434 removed outlier: 3.683A pdb=" N ASP A 430 " --> pdb=" O LYS A 426 " (cutoff:3.500A) Processing helix chain 'A' and resid 443 through 448 Processing helix chain 'A' and resid 466 through 474 Processing helix chain 'A' and resid 496 through 509 removed outlier: 4.265A pdb=" N ILE A 500 " --> pdb=" O ALA A 496 " (cutoff:3.500A) Processing helix chain 'B' and resid 138 through 145 removed outlier: 3.605A pdb=" N ARG B 143 " --> pdb=" O GLY B 139 " (cutoff:3.500A) Processing helix chain 'B' and resid 165 through 170 Processing helix chain 'B' and resid 174 through 183 Processing helix chain 'B' and resid 187 through 202 removed outlier: 4.121A pdb=" N ASP B 193 " --> pdb=" O ASN B 189 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N VAL B 199 " --> pdb=" O GLU B 195 " (cutoff:3.500A) removed outlier: 4.079A pdb=" N ARG B 200 " --> pdb=" O PHE B 196 " (cutoff:3.500A) Processing helix chain 'B' and resid 203 through 206 Processing helix chain 'B' and resid 214 through 227 removed outlier: 3.587A pdb=" N PHE B 218 " --> pdb=" O SER B 214 " (cutoff:3.500A) Processing helix chain 'B' and resid 248 through 271 removed outlier: 3.503A pdb=" N GLU B 254 " --> pdb=" O ASP B 250 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N ARG B 262 " --> pdb=" O GLU B 258 " (cutoff:3.500A) Processing helix chain 'B' and resid 273 through 288 removed outlier: 3.790A pdb=" N ILE B 277 " --> pdb=" O GLN B 273 " (cutoff:3.500A) Processing helix chain 'B' and resid 302 through 308 removed outlier: 3.790A pdb=" N THR B 308 " --> pdb=" O LYS B 304 " (cutoff:3.500A) Processing helix chain 'B' and resid 309 through 315 removed outlier: 3.954A pdb=" N GLY B 315 " --> pdb=" O LEU B 311 " (cutoff:3.500A) Processing helix chain 'B' and resid 318 through 328 Processing helix chain 'B' and resid 344 through 353 Processing helix chain 'B' and resid 360 through 366 removed outlier: 4.078A pdb=" N ALA B 364 " --> pdb=" O ASN B 360 " (cutoff:3.500A) Processing helix chain 'B' and resid 367 through 372 removed outlier: 3.747A pdb=" N ILE B 370 " --> pdb=" O HIS B 367 " (cutoff:3.500A) removed outlier: 3.760A pdb=" N TYR B 371 " --> pdb=" O GLU B 368 " (cutoff:3.500A) Processing helix chain 'B' and resid 379 through 388 removed outlier: 3.869A pdb=" N ASP B 386 " --> pdb=" O HIS B 382 " (cutoff:3.500A) removed outlier: 4.074A pdb=" N LYS B 387 " --> pdb=" O ARG B 383 " (cutoff:3.500A) removed outlier: 3.763A pdb=" N TYR B 388 " --> pdb=" O LEU B 384 " (cutoff:3.500A) Processing helix chain 'B' and resid 388 through 393 Processing helix chain 'B' and resid 393 through 400 Processing helix chain 'B' and resid 414 through 419 Processing helix chain 'B' and resid 420 through 424 Proline residue: B 424 - end of helix Processing helix chain 'B' and resid 425 through 435 Processing helix chain 'B' and resid 443 through 448 Processing helix chain 'B' and resid 466 through 474 Processing helix chain 'B' and resid 491 through 496 Processing helix chain 'B' and resid 496 through 510 removed outlier: 3.723A pdb=" N ILE B 508 " --> pdb=" O LEU B 504 " (cutoff:3.500A) Processing helix chain 'C' and resid 139 through 145 removed outlier: 4.104A pdb=" N ARG C 143 " --> pdb=" O GLY C 139 " (cutoff:3.500A) Processing helix chain 'C' and resid 165 through 170 Processing helix chain 'C' and resid 174 through 183 removed outlier: 3.746A pdb=" N VAL C 183 " --> pdb=" O ALA C 179 " (cutoff:3.500A) Processing helix chain 'C' and resid 186 through 202 removed outlier: 4.207A pdb=" N LYS C 192 " --> pdb=" O ASP C 188 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N VAL C 199 " --> pdb=" O GLU C 195 " (cutoff:3.500A) removed outlier: 4.220A pdb=" N ARG C 200 " --> pdb=" O PHE C 196 " (cutoff:3.500A) Processing helix chain 'C' and resid 203 through 206 Processing helix chain 'C' and resid 214 through 226 removed outlier: 3.692A pdb=" N PHE C 218 " --> pdb=" O SER C 214 " (cutoff:3.500A) Processing helix chain 'C' and resid 227 through 229 No H-bonds generated for 'chain 'C' and resid 227 through 229' Processing helix chain 'C' and resid 248 through 271 removed outlier: 4.392A pdb=" N GLU C 258 " --> pdb=" O GLU C 254 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N GLN C 259 " --> pdb=" O ALA C 255 " (cutoff:3.500A) Processing helix chain 'C' and resid 273 through 288 removed outlier: 3.848A pdb=" N ILE C 277 " --> pdb=" O GLN C 273 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N ARG C 279 " --> pdb=" O ILE C 275 " (cutoff:3.500A) Processing helix chain 'C' and resid 302 through 308 removed outlier: 3.514A pdb=" N THR C 308 " --> pdb=" O LYS C 304 " (cutoff:3.500A) Processing helix chain 'C' and resid 309 through 314 removed outlier: 3.694A pdb=" N GLY C 313 " --> pdb=" O LEU C 309 " (cutoff:3.500A) Processing helix chain 'C' and resid 318 through 328 Processing helix chain 'C' and resid 344 through 355 removed outlier: 4.055A pdb=" N HIS C 355 " --> pdb=" O PHE C 351 " (cutoff:3.500A) Processing helix chain 'C' and resid 361 through 366 Processing helix chain 'C' and resid 367 through 372 removed outlier: 3.577A pdb=" N ILE C 370 " --> pdb=" O HIS C 367 " (cutoff:3.500A) removed outlier: 3.784A pdb=" N CYS C 372 " --> pdb=" O ALA C 369 " (cutoff:3.500A) Processing helix chain 'C' and resid 379 through 393 removed outlier: 3.924A pdb=" N ASP C 386 " --> pdb=" O HIS C 382 " (cutoff:3.500A) removed outlier: 4.165A pdb=" N LYS C 387 " --> pdb=" O ARG C 383 " (cutoff:3.500A) removed outlier: 3.765A pdb=" N TYR C 388 " --> pdb=" O LEU C 384 " (cutoff:3.500A) removed outlier: 5.254A pdb=" N TYR C 390 " --> pdb=" O ASP C 386 " (cutoff:3.500A) removed outlier: 6.773A pdb=" N LYS C 391 " --> pdb=" O LYS C 387 " (cutoff:3.500A) Processing helix chain 'C' and resid 393 through 400 removed outlier: 3.736A pdb=" N LYS C 399 " --> pdb=" O MET C 395 " (cutoff:3.500A) Processing helix chain 'C' and resid 414 through 419 Processing helix chain 'C' and resid 420 through 424 Proline residue: C 424 - end of helix Processing helix chain 'C' and resid 425 through 434 Processing helix chain 'C' and resid 443 through 448 Processing helix chain 'C' and resid 466 through 474 removed outlier: 3.626A pdb=" N GLU C 472 " --> pdb=" O LYS C 468 " (cutoff:3.500A) Processing helix chain 'C' and resid 491 through 495 Processing helix chain 'C' and resid 496 through 510 removed outlier: 3.762A pdb=" N ILE C 500 " --> pdb=" O ALA C 496 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N ILE C 508 " --> pdb=" O LEU C 504 " (cutoff:3.500A) Processing helix chain 'D' and resid 138 through 145 removed outlier: 3.509A pdb=" N GLN D 142 " --> pdb=" O SER D 138 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N ARG D 143 " --> pdb=" O GLY D 139 " (cutoff:3.500A) Processing helix chain 'D' and resid 167 through 172 removed outlier: 4.083A pdb=" N PHE D 172 " --> pdb=" O MET D 169 " (cutoff:3.500A) Processing helix chain 'D' and resid 174 through 183 Processing helix chain 'D' and resid 186 through 202 removed outlier: 3.550A pdb=" N VAL D 199 " --> pdb=" O GLU D 195 " (cutoff:3.500A) removed outlier: 4.304A pdb=" N ARG D 200 " --> pdb=" O PHE D 196 " (cutoff:3.500A) Processing helix chain 'D' and resid 203 through 206 Processing helix chain 'D' and resid 214 through 226 removed outlier: 3.644A pdb=" N PHE D 218 " --> pdb=" O SER D 214 " (cutoff:3.500A) Processing helix chain 'D' and resid 227 through 229 No H-bonds generated for 'chain 'D' and resid 227 through 229' Processing helix chain 'D' and resid 248 through 271 removed outlier: 4.353A pdb=" N GLU D 258 " --> pdb=" O GLU D 254 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N GLN D 259 " --> pdb=" O ALA D 255 " (cutoff:3.500A) Processing helix chain 'D' and resid 273 through 288 removed outlier: 3.958A pdb=" N ILE D 277 " --> pdb=" O GLN D 273 " (cutoff:3.500A) Processing helix chain 'D' and resid 302 through 307 Processing helix chain 'D' and resid 309 through 314 Processing helix chain 'D' and resid 318 through 329 removed outlier: 4.053A pdb=" N ARG D 329 " --> pdb=" O TYR D 325 " (cutoff:3.500A) Processing helix chain 'D' and resid 344 through 355 removed outlier: 4.173A pdb=" N HIS D 355 " --> pdb=" O PHE D 351 " (cutoff:3.500A) Processing helix chain 'D' and resid 361 through 366 Processing helix chain 'D' and resid 367 through 371 removed outlier: 3.573A pdb=" N ILE D 370 " --> pdb=" O HIS D 367 " (cutoff:3.500A) Processing helix chain 'D' and resid 379 through 393 removed outlier: 4.114A pdb=" N ASP D 386 " --> pdb=" O HIS D 382 " (cutoff:3.500A) removed outlier: 4.128A pdb=" N LYS D 387 " --> pdb=" O ARG D 383 " (cutoff:3.500A) removed outlier: 3.769A pdb=" N TYR D 388 " --> pdb=" O LEU D 384 " (cutoff:3.500A) removed outlier: 5.412A pdb=" N TYR D 390 " --> pdb=" O ASP D 386 " (cutoff:3.500A) removed outlier: 7.069A pdb=" N LYS D 391 " --> pdb=" O LYS D 387 " (cutoff:3.500A) Processing helix chain 'D' and resid 393 through 401 Processing helix chain 'D' and resid 414 through 419 Processing helix chain 'D' and resid 420 through 424 Proline residue: D 424 - end of helix Processing helix chain 'D' and resid 425 through 434 removed outlier: 3.788A pdb=" N ASP D 430 " --> pdb=" O LYS D 426 " (cutoff:3.500A) Processing helix chain 'D' and resid 443 through 448 Processing helix chain 'D' and resid 466 through 475 removed outlier: 3.617A pdb=" N SER D 475 " --> pdb=" O THR D 471 " (cutoff:3.500A) Processing helix chain 'D' and resid 496 through 509 removed outlier: 3.775A pdb=" N ILE D 500 " --> pdb=" O ALA D 496 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N MET D 507 " --> pdb=" O HIS D 503 " (cutoff:3.500A) removed outlier: 3.817A pdb=" N ILE D 508 " --> pdb=" O LEU D 504 " (cutoff:3.500A) Processing helix chain 'E' and resid 138 through 145 removed outlier: 3.503A pdb=" N ARG E 143 " --> pdb=" O GLY E 139 " (cutoff:3.500A) Processing helix chain 'E' and resid 167 through 172 removed outlier: 3.704A pdb=" N PHE E 172 " --> pdb=" O MET E 169 " (cutoff:3.500A) Processing helix chain 'E' and resid 174 through 183 Processing helix chain 'E' and resid 186 through 202 removed outlier: 3.549A pdb=" N VAL E 199 " --> pdb=" O GLU E 195 " (cutoff:3.500A) removed outlier: 4.108A pdb=" N ARG E 200 " --> pdb=" O PHE E 196 " (cutoff:3.500A) Processing helix chain 'E' and resid 203 through 206 Processing helix chain 'E' and resid 214 through 226 Processing helix chain 'E' and resid 227 through 229 No H-bonds generated for 'chain 'E' and resid 227 through 229' Processing helix chain 'E' and resid 248 through 271 removed outlier: 4.077A pdb=" N GLU E 258 " --> pdb=" O GLU E 254 " (cutoff:3.500A) Processing helix chain 'E' and resid 273 through 288 removed outlier: 3.815A pdb=" N ILE E 277 " --> pdb=" O GLN E 273 " (cutoff:3.500A) Processing helix chain 'E' and resid 289 through 292 Processing helix chain 'E' and resid 302 through 307 removed outlier: 3.577A pdb=" N GLN E 307 " --> pdb=" O PRO E 303 " (cutoff:3.500A) Processing helix chain 'E' and resid 309 through 316 removed outlier: 3.537A pdb=" N GLY E 315 " --> pdb=" O LEU E 311 " (cutoff:3.500A) removed outlier: 3.916A pdb=" N SER E 316 " --> pdb=" O SER E 312 " (cutoff:3.500A) Processing helix chain 'E' and resid 318 through 328 Processing helix chain 'E' and resid 344 through 355 removed outlier: 4.155A pdb=" N HIS E 355 " --> pdb=" O PHE E 351 " (cutoff:3.500A) Processing helix chain 'E' and resid 361 through 366 Processing helix chain 'E' and resid 367 through 372 Processing helix chain 'E' and resid 379 through 386 removed outlier: 3.892A pdb=" N ASP E 386 " --> pdb=" O HIS E 382 " (cutoff:3.500A) Processing helix chain 'E' and resid 388 through 393 Processing helix chain 'E' and resid 393 through 400 Processing helix chain 'E' and resid 414 through 419 Processing helix chain 'E' and resid 420 through 424 Proline residue: E 424 - end of helix Processing helix chain 'E' and resid 425 through 434 removed outlier: 3.521A pdb=" N ASP E 430 " --> pdb=" O LYS E 426 " (cutoff:3.500A) Processing helix chain 'E' and resid 443 through 448 Processing helix chain 'E' and resid 466 through 475 removed outlier: 3.744A pdb=" N SER E 475 " --> pdb=" O THR E 471 " (cutoff:3.500A) Processing helix chain 'E' and resid 496 through 510 removed outlier: 3.683A pdb=" N ILE E 500 " --> pdb=" O ALA E 496 " (cutoff:3.500A) removed outlier: 3.878A pdb=" N ILE E 508 " --> pdb=" O LEU E 504 " (cutoff:3.500A) Processing helix chain 'F' and resid 138 through 145 removed outlier: 3.752A pdb=" N GLN F 142 " --> pdb=" O SER F 138 " (cutoff:3.500A) removed outlier: 3.841A pdb=" N ARG F 143 " --> pdb=" O GLY F 139 " (cutoff:3.500A) Processing helix chain 'F' and resid 165 through 170 Processing helix chain 'F' and resid 174 through 183 Processing helix chain 'F' and resid 186 through 202 removed outlier: 3.633A pdb=" N ILE F 190 " --> pdb=" O ARG F 186 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N VAL F 199 " --> pdb=" O GLU F 195 " (cutoff:3.500A) removed outlier: 4.465A pdb=" N ARG F 200 " --> pdb=" O PHE F 196 " (cutoff:3.500A) Processing helix chain 'F' and resid 203 through 206 Processing helix chain 'F' and resid 214 through 227 removed outlier: 3.717A pdb=" N THR F 222 " --> pdb=" O PHE F 218 " (cutoff:3.500A) Processing helix chain 'F' and resid 248 through 271 removed outlier: 4.164A pdb=" N GLU F 258 " --> pdb=" O GLU F 254 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N GLN F 259 " --> pdb=" O ALA F 255 " (cutoff:3.500A) Processing helix chain 'F' and resid 273 through 288 removed outlier: 4.172A pdb=" N ILE F 277 " --> pdb=" O GLN F 273 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N ARG F 279 " --> pdb=" O ILE F 275 " (cutoff:3.500A) Processing helix chain 'F' and resid 289 through 292 removed outlier: 4.126A pdb=" N GLY F 292 " --> pdb=" O GLU F 289 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 289 through 292' Processing helix chain 'F' and resid 302 through 308 removed outlier: 3.750A pdb=" N THR F 308 " --> pdb=" O LYS F 304 " (cutoff:3.500A) Processing helix chain 'F' and resid 309 through 314 Processing helix chain 'F' and resid 318 through 328 Processing helix chain 'F' and resid 344 through 355 removed outlier: 3.960A pdb=" N HIS F 355 " --> pdb=" O PHE F 351 " (cutoff:3.500A) Processing helix chain 'F' and resid 361 through 366 Processing helix chain 'F' and resid 367 through 372 removed outlier: 3.557A pdb=" N CYS F 372 " --> pdb=" O ALA F 369 " (cutoff:3.500A) Processing helix chain 'F' and resid 379 through 386 removed outlier: 4.152A pdb=" N ASP F 386 " --> pdb=" O HIS F 382 " (cutoff:3.500A) Processing helix chain 'F' and resid 388 through 393 Processing helix chain 'F' and resid 393 through 401 Processing helix chain 'F' and resid 414 through 419 Processing helix chain 'F' and resid 420 through 424 Proline residue: F 424 - end of helix Processing helix chain 'F' and resid 425 through 434 Processing helix chain 'F' and resid 443 through 448 Processing helix chain 'F' and resid 466 through 474 Processing helix chain 'F' and resid 491 through 495 Processing helix chain 'F' and resid 496 through 509 removed outlier: 3.510A pdb=" N MET F 507 " --> pdb=" O HIS F 503 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N ILE F 508 " --> pdb=" O LEU F 504 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 69 through 71 Processing sheet with id=AA2, first strand: chain 'A' and resid 69 through 71 removed outlier: 4.440A pdb=" N PHE A 103 " --> pdb=" O ASP A 154 " (cutoff:3.500A) removed outlier: 6.643A pdb=" N LEU A 120 " --> pdb=" O VAL A 151 " (cutoff:3.500A) removed outlier: 7.299A pdb=" N LEU A 153 " --> pdb=" O LEU A 120 " (cutoff:3.500A) removed outlier: 6.869A pdb=" N TYR A 122 " --> pdb=" O LEU A 153 " (cutoff:3.500A) removed outlier: 7.086A pdb=" N TRP A 208 " --> pdb=" O GLN A 233 " (cutoff:3.500A) removed outlier: 8.337A pdb=" N LEU A 235 " --> pdb=" O TRP A 208 " (cutoff:3.500A) removed outlier: 6.352A pdb=" N ILE A 210 " --> pdb=" O LEU A 235 " (cutoff:3.500A) removed outlier: 8.052A pdb=" N THR A 237 " --> pdb=" O ILE A 210 " (cutoff:3.500A) removed outlier: 6.732A pdb=" N GLY A 212 " --> pdb=" O THR A 237 " (cutoff:3.500A) removed outlier: 9.112A pdb=" N ALA A 455 " --> pdb=" O LYS A 232 " (cutoff:3.500A) removed outlier: 6.465A pdb=" N VAL A 234 " --> pdb=" O ALA A 455 " (cutoff:3.500A) removed outlier: 8.129A pdb=" N ALA A 457 " --> pdb=" O VAL A 234 " (cutoff:3.500A) removed outlier: 6.731A pdb=" N ILE A 236 " --> pdb=" O ALA A 457 " (cutoff:3.500A) removed outlier: 8.280A pdb=" N TYR A 459 " --> pdb=" O ILE A 236 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 293 through 294 Processing sheet with id=AA4, first strand: chain 'B' and resid 69 through 71 Processing sheet with id=AA5, first strand: chain 'B' and resid 69 through 71 removed outlier: 6.351A pdb=" N LEU B 120 " --> pdb=" O VAL B 151 " (cutoff:3.500A) removed outlier: 7.585A pdb=" N LEU B 153 " --> pdb=" O LEU B 120 " (cutoff:3.500A) removed outlier: 7.070A pdb=" N TYR B 122 " --> pdb=" O LEU B 153 " (cutoff:3.500A) removed outlier: 7.062A pdb=" N TRP B 208 " --> pdb=" O GLN B 233 " (cutoff:3.500A) removed outlier: 8.322A pdb=" N LEU B 235 " --> pdb=" O TRP B 208 " (cutoff:3.500A) removed outlier: 6.275A pdb=" N ILE B 210 " --> pdb=" O LEU B 235 " (cutoff:3.500A) removed outlier: 7.972A pdb=" N THR B 237 " --> pdb=" O ILE B 210 " (cutoff:3.500A) removed outlier: 6.642A pdb=" N GLY B 212 " --> pdb=" O THR B 237 " (cutoff:3.500A) removed outlier: 9.073A pdb=" N ALA B 455 " --> pdb=" O LYS B 232 " (cutoff:3.500A) removed outlier: 6.538A pdb=" N VAL B 234 " --> pdb=" O ALA B 455 " (cutoff:3.500A) removed outlier: 8.055A pdb=" N ALA B 457 " --> pdb=" O VAL B 234 " (cutoff:3.500A) removed outlier: 6.765A pdb=" N ILE B 236 " --> pdb=" O ALA B 457 " (cutoff:3.500A) removed outlier: 8.347A pdb=" N TYR B 459 " --> pdb=" O ILE B 236 " (cutoff:3.500A) removed outlier: 6.344A pdb=" N VAL B 454 " --> pdb=" O ARG B 481 " (cutoff:3.500A) removed outlier: 8.022A pdb=" N TRP B 483 " --> pdb=" O VAL B 454 " (cutoff:3.500A) removed outlier: 6.843A pdb=" N ALA B 456 " --> pdb=" O TRP B 483 " (cutoff:3.500A) removed outlier: 7.603A pdb=" N THR B 485 " --> pdb=" O ALA B 456 " (cutoff:3.500A) removed outlier: 6.392A pdb=" N VAL B 458 " --> pdb=" O THR B 485 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 293 through 294 Processing sheet with id=AA7, first strand: chain 'C' and resid 69 through 71 Processing sheet with id=AA8, first strand: chain 'C' and resid 69 through 71 removed outlier: 4.589A pdb=" N PHE C 103 " --> pdb=" O ASP C 154 " (cutoff:3.500A) removed outlier: 6.576A pdb=" N LEU C 120 " --> pdb=" O VAL C 151 " (cutoff:3.500A) removed outlier: 7.638A pdb=" N LEU C 153 " --> pdb=" O LEU C 120 " (cutoff:3.500A) removed outlier: 7.225A pdb=" N TYR C 122 " --> pdb=" O LEU C 153 " (cutoff:3.500A) removed outlier: 6.482A pdb=" N LEU C 121 " --> pdb=" O LEU C 211 " (cutoff:3.500A) removed outlier: 7.876A pdb=" N GLN C 213 " --> pdb=" O LEU C 121 " (cutoff:3.500A) removed outlier: 6.834A pdb=" N LEU C 123 " --> pdb=" O GLN C 213 " (cutoff:3.500A) removed outlier: 7.049A pdb=" N TRP C 208 " --> pdb=" O GLN C 233 " (cutoff:3.500A) removed outlier: 8.333A pdb=" N LEU C 235 " --> pdb=" O TRP C 208 " (cutoff:3.500A) removed outlier: 6.216A pdb=" N ILE C 210 " --> pdb=" O LEU C 235 " (cutoff:3.500A) removed outlier: 7.977A pdb=" N THR C 237 " --> pdb=" O ILE C 210 " (cutoff:3.500A) removed outlier: 6.632A pdb=" N GLY C 212 " --> pdb=" O THR C 237 " (cutoff:3.500A) removed outlier: 9.209A pdb=" N ALA C 455 " --> pdb=" O LYS C 232 " (cutoff:3.500A) removed outlier: 6.525A pdb=" N VAL C 234 " --> pdb=" O ALA C 455 " (cutoff:3.500A) removed outlier: 8.117A pdb=" N ALA C 457 " --> pdb=" O VAL C 234 " (cutoff:3.500A) removed outlier: 6.802A pdb=" N ILE C 236 " --> pdb=" O ALA C 457 " (cutoff:3.500A) removed outlier: 8.236A pdb=" N TYR C 459 " --> pdb=" O ILE C 236 " (cutoff:3.500A) removed outlier: 6.276A pdb=" N VAL C 454 " --> pdb=" O ARG C 481 " (cutoff:3.500A) removed outlier: 8.001A pdb=" N TRP C 483 " --> pdb=" O VAL C 454 " (cutoff:3.500A) removed outlier: 7.078A pdb=" N ALA C 456 " --> pdb=" O TRP C 483 " (cutoff:3.500A) removed outlier: 7.584A pdb=" N THR C 485 " --> pdb=" O ALA C 456 " (cutoff:3.500A) removed outlier: 6.278A pdb=" N VAL C 458 " --> pdb=" O THR C 485 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'C' and resid 293 through 294 Processing sheet with id=AB1, first strand: chain 'D' and resid 69 through 71 Processing sheet with id=AB2, first strand: chain 'D' and resid 69 through 71 removed outlier: 4.529A pdb=" N PHE D 103 " --> pdb=" O ASP D 154 " (cutoff:3.500A) removed outlier: 6.582A pdb=" N LEU D 120 " --> pdb=" O VAL D 151 " (cutoff:3.500A) removed outlier: 7.602A pdb=" N LEU D 153 " --> pdb=" O LEU D 120 " (cutoff:3.500A) removed outlier: 7.214A pdb=" N TYR D 122 " --> pdb=" O LEU D 153 " (cutoff:3.500A) removed outlier: 7.000A pdb=" N TRP D 208 " --> pdb=" O GLN D 233 " (cutoff:3.500A) removed outlier: 8.343A pdb=" N LEU D 235 " --> pdb=" O TRP D 208 " (cutoff:3.500A) removed outlier: 6.284A pdb=" N ILE D 210 " --> pdb=" O LEU D 235 " (cutoff:3.500A) removed outlier: 7.926A pdb=" N THR D 237 " --> pdb=" O ILE D 210 " (cutoff:3.500A) removed outlier: 6.577A pdb=" N GLY D 212 " --> pdb=" O THR D 237 " (cutoff:3.500A) removed outlier: 9.232A pdb=" N ALA D 455 " --> pdb=" O LYS D 232 " (cutoff:3.500A) removed outlier: 6.508A pdb=" N VAL D 234 " --> pdb=" O ALA D 455 " (cutoff:3.500A) removed outlier: 8.208A pdb=" N ALA D 457 " --> pdb=" O VAL D 234 " (cutoff:3.500A) removed outlier: 6.832A pdb=" N ILE D 236 " --> pdb=" O ALA D 457 " (cutoff:3.500A) removed outlier: 8.268A pdb=" N TYR D 459 " --> pdb=" O ILE D 236 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'D' and resid 293 through 294 Processing sheet with id=AB4, first strand: chain 'D' and resid 331 through 332 removed outlier: 4.685A pdb=" N CYS D 342 " --> pdb=" O ASP D 332 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'E' and resid 69 through 71 Processing sheet with id=AB6, first strand: chain 'E' and resid 69 through 71 removed outlier: 4.555A pdb=" N PHE E 103 " --> pdb=" O ASP E 154 " (cutoff:3.500A) removed outlier: 6.526A pdb=" N LEU E 120 " --> pdb=" O VAL E 151 " (cutoff:3.500A) removed outlier: 7.663A pdb=" N LEU E 153 " --> pdb=" O LEU E 120 " (cutoff:3.500A) removed outlier: 7.195A pdb=" N TYR E 122 " --> pdb=" O LEU E 153 " (cutoff:3.500A) removed outlier: 3.724A pdb=" N GLN E 213 " --> pdb=" O LEU E 123 " (cutoff:3.500A) removed outlier: 7.053A pdb=" N TRP E 208 " --> pdb=" O GLN E 233 " (cutoff:3.500A) removed outlier: 8.288A pdb=" N LEU E 235 " --> pdb=" O TRP E 208 " (cutoff:3.500A) removed outlier: 6.281A pdb=" N ILE E 210 " --> pdb=" O LEU E 235 " (cutoff:3.500A) removed outlier: 8.064A pdb=" N THR E 237 " --> pdb=" O ILE E 210 " (cutoff:3.500A) removed outlier: 6.676A pdb=" N GLY E 212 " --> pdb=" O THR E 237 " (cutoff:3.500A) removed outlier: 9.231A pdb=" N ALA E 455 " --> pdb=" O LYS E 232 " (cutoff:3.500A) removed outlier: 6.501A pdb=" N VAL E 234 " --> pdb=" O ALA E 455 " (cutoff:3.500A) removed outlier: 8.242A pdb=" N ALA E 457 " --> pdb=" O VAL E 234 " (cutoff:3.500A) removed outlier: 6.887A pdb=" N ILE E 236 " --> pdb=" O ALA E 457 " (cutoff:3.500A) removed outlier: 8.708A pdb=" N TYR E 459 " --> pdb=" O ILE E 236 " (cutoff:3.500A) removed outlier: 7.060A pdb=" N VAL E 454 " --> pdb=" O ARG E 481 " (cutoff:3.500A) removed outlier: 7.920A pdb=" N TRP E 483 " --> pdb=" O VAL E 454 " (cutoff:3.500A) removed outlier: 6.751A pdb=" N ALA E 456 " --> pdb=" O TRP E 483 " (cutoff:3.500A) removed outlier: 7.596A pdb=" N THR E 485 " --> pdb=" O ALA E 456 " (cutoff:3.500A) removed outlier: 6.321A pdb=" N VAL E 458 " --> pdb=" O THR E 485 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'E' and resid 293 through 294 Processing sheet with id=AB8, first strand: chain 'F' and resid 69 through 71 Processing sheet with id=AB9, first strand: chain 'F' and resid 69 through 71 removed outlier: 4.640A pdb=" N PHE F 103 " --> pdb=" O ASP F 154 " (cutoff:3.500A) removed outlier: 6.528A pdb=" N LEU F 120 " --> pdb=" O VAL F 151 " (cutoff:3.500A) removed outlier: 7.544A pdb=" N LEU F 153 " --> pdb=" O LEU F 120 " (cutoff:3.500A) removed outlier: 7.081A pdb=" N TYR F 122 " --> pdb=" O LEU F 153 " (cutoff:3.500A) removed outlier: 6.719A pdb=" N TYR F 119 " --> pdb=" O THR F 209 " (cutoff:3.500A) removed outlier: 8.176A pdb=" N LEU F 211 " --> pdb=" O TYR F 119 " (cutoff:3.500A) removed outlier: 6.428A pdb=" N LEU F 121 " --> pdb=" O LEU F 211 " (cutoff:3.500A) removed outlier: 8.300A pdb=" N GLN F 213 " --> pdb=" O LEU F 121 " (cutoff:3.500A) removed outlier: 6.892A pdb=" N LEU F 123 " --> pdb=" O GLN F 213 " (cutoff:3.500A) removed outlier: 7.186A pdb=" N TRP F 208 " --> pdb=" O LYS F 232 " (cutoff:3.500A) removed outlier: 6.404A pdb=" N VAL F 234 " --> pdb=" O TRP F 208 " (cutoff:3.500A) removed outlier: 6.655A pdb=" N ILE F 210 " --> pdb=" O VAL F 234 " (cutoff:3.500A) removed outlier: 5.452A pdb=" N ILE F 236 " --> pdb=" O ILE F 210 " (cutoff:3.500A) removed outlier: 6.526A pdb=" N GLY F 212 " --> pdb=" O ILE F 236 " (cutoff:3.500A) removed outlier: 9.349A pdb=" N ALA F 455 " --> pdb=" O LYS F 232 " (cutoff:3.500A) removed outlier: 6.555A pdb=" N VAL F 234 " --> pdb=" O ALA F 455 " (cutoff:3.500A) removed outlier: 8.203A pdb=" N ALA F 457 " --> pdb=" O VAL F 234 " (cutoff:3.500A) removed outlier: 6.892A pdb=" N ILE F 236 " --> pdb=" O ALA F 457 " (cutoff:3.500A) removed outlier: 8.373A pdb=" N TYR F 459 " --> pdb=" O ILE F 236 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'F' and resid 293 through 294 868 hydrogen bonds defined for protein. 2451 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: 8.09 Time building geometry restraints manager: 5.85 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.32: 3870 1.32 - 1.45: 5654 1.45 - 1.57: 12287 1.57 - 1.70: 5 1.70 - 1.82: 144 Bond restraints: 21960 Sorted by residual: bond pdb=" C PRO F 132 " pdb=" O PRO F 132 " ideal model delta sigma weight residual 1.237 1.303 -0.066 1.29e-02 6.01e+03 2.61e+01 bond pdb=" CZ ARG F 83 " pdb=" NH2 ARG F 83 " ideal model delta sigma weight residual 1.330 1.271 0.059 1.30e-02 5.92e+03 2.05e+01 bond pdb=" CA CYS F 219 " pdb=" C CYS F 219 " ideal model delta sigma weight residual 1.524 1.582 -0.058 1.32e-02 5.74e+03 1.94e+01 bond pdb=" CA PRO B 439 " pdb=" C PRO B 439 " ideal model delta sigma weight residual 1.514 1.538 -0.023 5.50e-03 3.31e+04 1.82e+01 bond pdb=" CA ALA E 227 " pdb=" C ALA E 227 " ideal model delta sigma weight residual 1.532 1.559 -0.027 6.50e-03 2.37e+04 1.68e+01 ... (remaining 21955 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.19: 23481 2.19 - 4.39: 5776 4.39 - 6.58: 488 6.58 - 8.77: 38 8.77 - 10.96: 7 Bond angle restraints: 29790 Sorted by residual: angle pdb=" N GLU B 487 " pdb=" CA GLU B 487 " pdb=" C GLU B 487 " ideal model delta sigma weight residual 112.38 123.34 -10.96 1.22e+00 6.72e-01 8.08e+01 angle pdb=" CA PHE C 218 " pdb=" CB PHE C 218 " pdb=" CG PHE C 218 " ideal model delta sigma weight residual 113.80 121.45 -7.65 1.00e+00 1.00e+00 5.86e+01 angle pdb=" N VAL A 150 " pdb=" CA VAL A 150 " pdb=" C VAL A 150 " ideal model delta sigma weight residual 109.30 117.65 -8.35 1.25e+00 6.40e-01 4.46e+01 angle pdb=" CA VAL E 77 " pdb=" C VAL E 77 " pdb=" N PRO E 78 " ideal model delta sigma weight residual 116.57 123.03 -6.46 9.80e-01 1.04e+00 4.35e+01 angle pdb=" CA PHE F 515 " pdb=" CB PHE F 515 " pdb=" CG PHE F 515 " ideal model delta sigma weight residual 113.80 120.39 -6.59 1.00e+00 1.00e+00 4.34e+01 ... (remaining 29785 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.87: 11999 17.87 - 35.74: 755 35.74 - 53.61: 167 53.61 - 71.48: 50 71.48 - 89.35: 25 Dihedral angle restraints: 12996 sinusoidal: 5262 harmonic: 7734 Sorted by residual: dihedral pdb=" CA GLY F 125 " pdb=" C GLY F 125 " pdb=" N GLY F 126 " pdb=" CA GLY F 126 " ideal model delta harmonic sigma weight residual 180.00 150.02 29.98 0 5.00e+00 4.00e-02 3.60e+01 dihedral pdb=" CA SER B 316 " pdb=" C SER B 316 " pdb=" N SER B 317 " pdb=" CA SER B 317 " ideal model delta harmonic sigma weight residual -180.00 -150.45 -29.55 0 5.00e+00 4.00e-02 3.49e+01 dihedral pdb=" CA PHE D 148 " pdb=" C PHE D 148 " pdb=" N ARG D 149 " pdb=" CA ARG D 149 " ideal model delta harmonic sigma weight residual 180.00 151.03 28.97 0 5.00e+00 4.00e-02 3.36e+01 ... (remaining 12993 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.091: 2099 0.091 - 0.182: 871 0.182 - 0.272: 157 0.272 - 0.363: 40 0.363 - 0.454: 7 Chirality restraints: 3174 Sorted by residual: chirality pdb=" CA PRO F 132 " pdb=" N PRO F 132 " pdb=" C PRO F 132 " pdb=" CB PRO F 132 " both_signs ideal model delta sigma weight residual False 2.72 2.26 0.45 2.00e-01 2.50e+01 5.15e+00 chirality pdb=" CA GLU B 79 " pdb=" N GLU B 79 " pdb=" C GLU B 79 " pdb=" CB GLU B 79 " both_signs ideal model delta sigma weight residual False 2.51 2.11 0.40 2.00e-01 2.50e+01 4.03e+00 chirality pdb=" CA PRO C 163 " pdb=" N PRO C 163 " pdb=" C PRO C 163 " pdb=" CB PRO C 163 " both_signs ideal model delta sigma weight residual False 2.72 2.34 0.38 2.00e-01 2.50e+01 3.64e+00 ... (remaining 3171 not shown) Planarity restraints: 3840 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TRP A 331 " -0.125 2.00e-02 2.50e+03 6.74e-02 1.13e+02 pdb=" CG TRP A 331 " 0.003 2.00e-02 2.50e+03 pdb=" CD1 TRP A 331 " 0.060 2.00e-02 2.50e+03 pdb=" CD2 TRP A 331 " 0.043 2.00e-02 2.50e+03 pdb=" NE1 TRP A 331 " 0.047 2.00e-02 2.50e+03 pdb=" CE2 TRP A 331 " -0.012 2.00e-02 2.50e+03 pdb=" CE3 TRP A 331 " 0.091 2.00e-02 2.50e+03 pdb=" CZ2 TRP A 331 " -0.084 2.00e-02 2.50e+03 pdb=" CZ3 TRP A 331 " 0.044 2.00e-02 2.50e+03 pdb=" CH2 TRP A 331 " -0.067 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR E 119 " 0.107 2.00e-02 2.50e+03 6.55e-02 8.59e+01 pdb=" CG TYR E 119 " -0.017 2.00e-02 2.50e+03 pdb=" CD1 TYR E 119 " -0.042 2.00e-02 2.50e+03 pdb=" CD2 TYR E 119 " -0.048 2.00e-02 2.50e+03 pdb=" CE1 TYR E 119 " -0.049 2.00e-02 2.50e+03 pdb=" CE2 TYR E 119 " -0.047 2.00e-02 2.50e+03 pdb=" CZ TYR E 119 " -0.021 2.00e-02 2.50e+03 pdb=" OH TYR E 119 " 0.116 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE F 515 " 0.099 2.00e-02 2.50e+03 6.06e-02 6.42e+01 pdb=" CG PHE F 515 " -0.079 2.00e-02 2.50e+03 pdb=" CD1 PHE F 515 " -0.059 2.00e-02 2.50e+03 pdb=" CD2 PHE F 515 " -0.046 2.00e-02 2.50e+03 pdb=" CE1 PHE F 515 " 0.019 2.00e-02 2.50e+03 pdb=" CE2 PHE F 515 " 0.006 2.00e-02 2.50e+03 pdb=" CZ PHE F 515 " 0.060 2.00e-02 2.50e+03 ... (remaining 3837 not shown) Histogram of nonbonded interaction distances: 2.25 - 2.78: 1987 2.78 - 3.31: 20803 3.31 - 3.84: 31893 3.84 - 4.37: 42711 4.37 - 4.90: 70643 Nonbonded interactions: 168037 Sorted by model distance: nonbonded pdb=" OD2 ASP A 332 " pdb=" OG SER B 167 " model vdw 2.253 3.040 nonbonded pdb=" OG SER E 167 " pdb=" OD2 ASP F 332 " model vdw 2.284 3.040 nonbonded pdb=" NE ARG C 156 " pdb=" OD2 ASP C 193 " model vdw 2.319 3.120 nonbonded pdb=" O GLU B 113 " pdb=" NH1 ARG B 149 " model vdw 2.365 3.120 nonbonded pdb=" OD1 ASP B 417 " pdb=" NZ LYS B 426 " model vdw 2.372 3.120 ... (remaining 168032 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: 0.04 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' selection = chain 'F' } 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: 3.970 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.990 Check model and map are aligned: 0.150 Set scattering table: 0.200 Process input model: 50.670 Find NCS groups from input model: 0.880 Set up NCS constraints: 0.130 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:3.230 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 60.250 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6789 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 : 0.012 0.119 21960 Z= 0.746 Angle : 1.799 10.964 29790 Z= 1.224 Chirality : 0.099 0.454 3174 Planarity : 0.013 0.136 3840 Dihedral : 13.705 89.353 8052 Min Nonbonded Distance : 2.253 Molprobity Statistics. All-atom Clashscore : 1.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.58 % Favored : 97.42 % Rotamer: Outliers : 0.04 % Allowed : 6.10 % Favored : 93.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.57 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.77 (0.15), residues: 2676 helix: -2.08 (0.12), residues: 1080 sheet: 0.24 (0.26), residues: 348 loop : -0.54 (0.17), residues: 1248 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.125 0.019 TRP A 331 HIS 0.018 0.003 HIS B 184 PHE 0.099 0.012 PHE F 515 TYR 0.116 0.017 TYR E 119 ARG 0.011 0.001 ARG A 133 Details of bonding type rmsd hydrogen bonds : bond 0.21725 ( 856) hydrogen bonds : angle 7.73946 ( 2451) covalent geometry : bond 0.01225 (21960) covalent geometry : angle 1.79940 (29790) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5352 Ramachandran restraints generated. 2676 Oldfield, 0 Emsley, 2676 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5352 Ramachandran restraints generated. 2676 Oldfield, 0 Emsley, 2676 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 371 residues out of total 2262 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 370 time to evaluate : 2.535 Fit side-chains REVERT: A 204 LYS cc_start: 0.7913 (mtmt) cc_final: 0.7298 (tmtt) REVERT: A 341 LYS cc_start: 0.7473 (tttt) cc_final: 0.7045 (tppt) REVERT: A 352 GLU cc_start: 0.6988 (tt0) cc_final: 0.6375 (tt0) REVERT: A 419 ILE cc_start: 0.7419 (mt) cc_final: 0.7162 (mp) REVERT: A 511 LYS cc_start: 0.7102 (mttt) cc_final: 0.6763 (mtpp) REVERT: B 73 LYS cc_start: 0.8007 (mttt) cc_final: 0.7443 (mtmt) REVERT: B 88 ILE cc_start: 0.7790 (mt) cc_final: 0.7259 (tt) REVERT: B 114 GLU cc_start: 0.7483 (mm-30) cc_final: 0.6947 (tt0) REVERT: B 147 GLU cc_start: 0.5979 (tp30) cc_final: 0.5704 (tt0) REVERT: B 195 GLU cc_start: 0.7227 (tt0) cc_final: 0.6971 (mm-30) REVERT: B 265 GLU cc_start: 0.6497 (mm-30) cc_final: 0.5927 (mt-10) REVERT: B 336 VAL cc_start: 0.6483 (t) cc_final: 0.6115 (p) REVERT: B 436 GLU cc_start: 0.7125 (pt0) cc_final: 0.6320 (mt-10) REVERT: B 491 SER cc_start: 0.6605 (m) cc_final: 0.6293 (t) REVERT: B 512 LYS cc_start: 0.7177 (mttt) cc_final: 0.6701 (tptp) REVERT: C 92 ASP cc_start: 0.6805 (t0) cc_final: 0.5796 (p0) REVERT: C 114 GLU cc_start: 0.8072 (mm-30) cc_final: 0.7547 (mt-10) REVERT: C 117 MET cc_start: 0.7909 (mtm) cc_final: 0.7663 (mtp) REVERT: C 136 GLU cc_start: 0.7589 (mt-10) cc_final: 0.7094 (pt0) REVERT: C 177 GLU cc_start: 0.7098 (mm-30) cc_final: 0.6644 (mt-10) REVERT: C 206 ASP cc_start: 0.7846 (m-30) cc_final: 0.7499 (m-30) REVERT: C 389 GLU cc_start: 0.6844 (tt0) cc_final: 0.6413 (tp30) REVERT: C 451 LYS cc_start: 0.8139 (mmtt) cc_final: 0.7894 (mmtt) REVERT: C 495 ASP cc_start: 0.5781 (m-30) cc_final: 0.5457 (m-30) REVERT: D 73 LYS cc_start: 0.8452 (mttt) cc_final: 0.7891 (mtmt) REVERT: D 138 SER cc_start: 0.7910 (t) cc_final: 0.7435 (p) REVERT: D 173 LYS cc_start: 0.7813 (mttt) cc_final: 0.7415 (mmmt) REVERT: D 174 SER cc_start: 0.7371 (m) cc_final: 0.6683 (p) REVERT: D 177 GLU cc_start: 0.7152 (mm-30) cc_final: 0.6461 (mp0) REVERT: D 461 GLU cc_start: 0.7652 (mt-10) cc_final: 0.7169 (mm-30) REVERT: D 494 ARG cc_start: 0.6901 (mtp180) cc_final: 0.6430 (mtp180) REVERT: E 95 LYS cc_start: 0.6360 (mmtt) cc_final: 0.5938 (mptt) REVERT: E 136 GLU cc_start: 0.7326 (mt-10) cc_final: 0.6800 (pt0) REVERT: E 138 SER cc_start: 0.6867 (t) cc_final: 0.6482 (m) REVERT: E 161 SER cc_start: 0.7141 (m) cc_final: 0.5983 (p) REVERT: E 304 LYS cc_start: 0.6489 (mttt) cc_final: 0.6189 (mtmm) REVERT: E 489 MET cc_start: 0.6147 (mtt) cc_final: 0.5857 (mtp) REVERT: E 511 LYS cc_start: 0.7174 (tttt) cc_final: 0.6922 (mtpp) REVERT: F 147 GLU cc_start: 0.7067 (mt-10) cc_final: 0.6679 (mt-10) REVERT: F 265 GLU cc_start: 0.6591 (mm-30) cc_final: 0.6131 (pt0) REVERT: F 280 GLU cc_start: 0.6465 (mt-10) cc_final: 0.6121 (mp0) REVERT: F 288 SER cc_start: 0.5525 (t) cc_final: 0.4858 (p) REVERT: F 304 LYS cc_start: 0.6642 (mttt) cc_final: 0.6256 (mtmm) REVERT: F 345 GLN cc_start: 0.6450 (tp40) cc_final: 0.6020 (tm-30) REVERT: F 468 LYS cc_start: 0.7032 (ttpp) cc_final: 0.6531 (ttpt) REVERT: F 494 ARG cc_start: 0.7001 (mtm-85) cc_final: 0.6601 (ptt90) outliers start: 1 outliers final: 0 residues processed: 371 average time/residue: 0.3783 time to fit residues: 206.7557 Evaluate side-chains 196 residues out of total 2262 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 196 time to evaluate : 2.322 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 264 random chunks: chunk 222 optimal weight: 0.9990 chunk 200 optimal weight: 1.9990 chunk 111 optimal weight: 1.9990 chunk 68 optimal weight: 1.9990 chunk 134 optimal weight: 3.9990 chunk 106 optimal weight: 0.9990 chunk 206 optimal weight: 2.9990 chunk 80 optimal weight: 1.9990 chunk 125 optimal weight: 4.9990 chunk 154 optimal weight: 2.9990 chunk 239 optimal weight: 0.9990 overall best weight: 1.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 85 HIS A 142 GLN A 283 ASN A 448 GLN A 486 ASN A 503 HIS D 355 HIS E 486 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3015 r_free = 0.3015 target = 0.097278 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2868 r_free = 0.2868 target = 0.086837 restraints weight = 31392.461| |-----------------------------------------------------------------------------| r_work (start): 0.2844 rms_B_bonded: 1.29 r_work: 0.2762 rms_B_bonded: 1.65 restraints_weight: 0.5000 r_work: 0.2650 rms_B_bonded: 2.86 restraints_weight: 0.2500 r_work (final): 0.2650 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8658 moved from start: 0.1903 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.057 21960 Z= 0.146 Angle : 0.634 8.648 29790 Z= 0.346 Chirality : 0.047 0.196 3174 Planarity : 0.005 0.064 3840 Dihedral : 5.601 43.401 2928 Min Nonbonded Distance : 2.160 Molprobity Statistics. All-atom Clashscore : 1.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.20 % Favored : 97.80 % Rotamer: Outliers : 1.68 % Allowed : 9.77 % Favored : 88.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.57 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.65 (0.16), residues: 2676 helix: -0.60 (0.15), residues: 1098 sheet: 0.55 (0.26), residues: 366 loop : -0.41 (0.18), residues: 1212 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP A 483 HIS 0.006 0.001 HIS D 69 PHE 0.033 0.002 PHE F 515 TYR 0.013 0.001 TYR C 253 ARG 0.005 0.001 ARG F 198 Details of bonding type rmsd hydrogen bonds : bond 0.05455 ( 856) hydrogen bonds : angle 5.13128 ( 2451) covalent geometry : bond 0.00319 (21960) covalent geometry : angle 0.63450 (29790) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5352 Ramachandran restraints generated. 2676 Oldfield, 0 Emsley, 2676 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5352 Ramachandran restraints generated. 2676 Oldfield, 0 Emsley, 2676 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 260 residues out of total 2262 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 222 time to evaluate : 4.205 Fit side-chains REVERT: A 204 LYS cc_start: 0.8179 (mtmt) cc_final: 0.7868 (tmtt) REVERT: A 449 ASN cc_start: 0.8488 (p0) cc_final: 0.8273 (p0) REVERT: B 88 ILE cc_start: 0.9135 (mt) cc_final: 0.8716 (tt) REVERT: B 158 THR cc_start: 0.9275 (OUTLIER) cc_final: 0.9015 (p) REVERT: B 221 LEU cc_start: 0.8529 (OUTLIER) cc_final: 0.8214 (mp) REVERT: B 486 ASN cc_start: 0.8658 (t0) cc_final: 0.8424 (t0) REVERT: C 114 GLU cc_start: 0.8206 (mm-30) cc_final: 0.7983 (mt-10) REVERT: C 206 ASP cc_start: 0.8416 (m-30) cc_final: 0.8201 (m-30) REVERT: C 359 THR cc_start: 0.8151 (m) cc_final: 0.7885 (p) REVERT: D 329 ARG cc_start: 0.7436 (OUTLIER) cc_final: 0.7043 (mtm-85) REVERT: D 389 GLU cc_start: 0.7750 (pp20) cc_final: 0.7542 (pt0) REVERT: D 494 ARG cc_start: 0.8163 (mtp180) cc_final: 0.7740 (mtp180) REVERT: D 512 LYS cc_start: 0.8873 (tttp) cc_final: 0.8379 (mtpp) REVERT: E 95 LYS cc_start: 0.7209 (mmtt) cc_final: 0.6824 (mptt) REVERT: E 410 MET cc_start: 0.8955 (mtt) cc_final: 0.8649 (mtt) REVERT: E 511 LYS cc_start: 0.8862 (tttt) cc_final: 0.8588 (mtpp) REVERT: F 79 GLU cc_start: 0.8558 (mm-30) cc_final: 0.8272 (mm-30) REVERT: F 277 ILE cc_start: 0.8738 (mm) cc_final: 0.8524 (mt) REVERT: F 283 ASN cc_start: 0.7862 (m-40) cc_final: 0.7545 (t0) REVERT: F 287 GLU cc_start: 0.7963 (OUTLIER) cc_final: 0.7066 (mp0) REVERT: F 288 SER cc_start: 0.8055 (t) cc_final: 0.7480 (p) REVERT: F 494 ARG cc_start: 0.8038 (mtm-85) cc_final: 0.7743 (ptt90) outliers start: 38 outliers final: 19 residues processed: 251 average time/residue: 0.3833 time to fit residues: 148.8710 Evaluate side-chains 191 residues out of total 2262 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 168 time to evaluate : 2.357 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 71 THR Chi-restraints excluded: chain A residue 94 SER Chi-restraints excluded: chain A residue 209 THR Chi-restraints excluded: chain B residue 151 VAL Chi-restraints excluded: chain B residue 158 THR Chi-restraints excluded: chain B residue 221 LEU Chi-restraints excluded: chain B residue 471 THR Chi-restraints excluded: chain C residue 218 PHE Chi-restraints excluded: chain C residue 289 GLU Chi-restraints excluded: chain C residue 471 THR Chi-restraints excluded: chain D residue 218 PHE Chi-restraints excluded: chain D residue 329 ARG Chi-restraints excluded: chain E residue 71 THR Chi-restraints excluded: chain E residue 92 ASP Chi-restraints excluded: chain E residue 209 THR Chi-restraints excluded: chain E residue 221 LEU Chi-restraints excluded: chain E residue 243 ILE Chi-restraints excluded: chain E residue 431 LEU Chi-restraints excluded: chain E residue 486 ASN Chi-restraints excluded: chain F residue 209 THR Chi-restraints excluded: chain F residue 287 GLU Chi-restraints excluded: chain F residue 337 THR Chi-restraints excluded: chain F residue 423 LYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 264 random chunks: chunk 45 optimal weight: 2.9990 chunk 41 optimal weight: 7.9990 chunk 3 optimal weight: 4.9990 chunk 103 optimal weight: 5.9990 chunk 46 optimal weight: 0.9980 chunk 203 optimal weight: 20.0000 chunk 168 optimal weight: 9.9990 chunk 204 optimal weight: 1.9990 chunk 32 optimal weight: 2.9990 chunk 214 optimal weight: 10.0000 chunk 22 optimal weight: 3.9990 overall best weight: 2.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 283 ASN D 503 HIS F 466 ASN F 486 ASN F 503 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2935 r_free = 0.2935 target = 0.092142 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2762 r_free = 0.2762 target = 0.080302 restraints weight = 32414.008| |-----------------------------------------------------------------------------| r_work (start): 0.2768 rms_B_bonded: 1.60 r_work: 0.2669 rms_B_bonded: 2.02 restraints_weight: 0.5000 r_work: 0.2546 rms_B_bonded: 3.44 restraints_weight: 0.2500 r_work (final): 0.2546 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8690 moved from start: 0.2414 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.052 21960 Z= 0.183 Angle : 0.610 9.734 29790 Z= 0.324 Chirality : 0.047 0.241 3174 Planarity : 0.005 0.050 3840 Dihedral : 5.250 66.372 2928 Min Nonbonded Distance : 2.442 Molprobity Statistics. All-atom Clashscore : 2.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.88 % Favored : 97.12 % Rotamer: Outliers : 2.70 % Allowed : 11.32 % Favored : 85.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.57 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.46 (0.16), residues: 2676 helix: -0.14 (0.15), residues: 1098 sheet: 0.41 (0.26), residues: 378 loop : -0.55 (0.18), residues: 1200 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP A 483 HIS 0.006 0.001 HIS D 69 PHE 0.021 0.002 PHE F 515 TYR 0.014 0.001 TYR B 181 ARG 0.004 0.000 ARG F 105 Details of bonding type rmsd hydrogen bonds : bond 0.05118 ( 856) hydrogen bonds : angle 4.74869 ( 2451) covalent geometry : bond 0.00455 (21960) covalent geometry : angle 0.60997 (29790) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5352 Ramachandran restraints generated. 2676 Oldfield, 0 Emsley, 2676 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5352 Ramachandran restraints generated. 2676 Oldfield, 0 Emsley, 2676 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 227 residues out of total 2262 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 166 time to evaluate : 2.646 Fit side-chains REVERT: A 204 LYS cc_start: 0.8270 (mtmt) cc_final: 0.7764 (tmtt) REVERT: A 390 TYR cc_start: 0.8610 (p90) cc_final: 0.8368 (p90) REVERT: B 158 THR cc_start: 0.9212 (OUTLIER) cc_final: 0.8871 (p) REVERT: B 218 PHE cc_start: 0.8899 (OUTLIER) cc_final: 0.8449 (m-10) REVERT: B 277 ILE cc_start: 0.8530 (mm) cc_final: 0.8290 (mt) REVERT: B 356 SER cc_start: 0.9009 (m) cc_final: 0.8751 (p) REVERT: B 432 LEU cc_start: 0.8760 (OUTLIER) cc_final: 0.8331 (mp) REVERT: C 114 GLU cc_start: 0.8433 (mm-30) cc_final: 0.8140 (mp0) REVERT: C 206 ASP cc_start: 0.8497 (m-30) cc_final: 0.8272 (m-30) REVERT: C 359 THR cc_start: 0.8159 (m) cc_final: 0.7839 (p) REVERT: D 279 ARG cc_start: 0.8267 (OUTLIER) cc_final: 0.7688 (mtm-85) REVERT: D 329 ARG cc_start: 0.7882 (OUTLIER) cc_final: 0.7418 (mtm-85) REVERT: D 389 GLU cc_start: 0.7800 (pp20) cc_final: 0.7592 (pt0) REVERT: D 494 ARG cc_start: 0.8277 (mtp180) cc_final: 0.7762 (mtp180) REVERT: D 512 LYS cc_start: 0.8880 (tttp) cc_final: 0.8333 (mtpp) REVERT: E 95 LYS cc_start: 0.7097 (mmtt) cc_final: 0.6697 (mptt) REVERT: E 166 CYS cc_start: 0.8609 (m) cc_final: 0.8252 (m) REVERT: E 511 LYS cc_start: 0.8888 (tttt) cc_final: 0.8667 (mtpp) REVERT: F 79 GLU cc_start: 0.8673 (mm-30) cc_final: 0.8362 (mm-30) REVERT: F 280 GLU cc_start: 0.7995 (OUTLIER) cc_final: 0.7608 (mp0) REVERT: F 288 SER cc_start: 0.8072 (t) cc_final: 0.7433 (p) REVERT: F 494 ARG cc_start: 0.8188 (mtm-85) cc_final: 0.7620 (ptt90) outliers start: 61 outliers final: 28 residues processed: 218 average time/residue: 0.4084 time to fit residues: 139.9772 Evaluate side-chains 186 residues out of total 2262 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 152 time to evaluate : 3.367 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 94 SER Chi-restraints excluded: chain A residue 209 THR Chi-restraints excluded: chain A residue 404 VAL Chi-restraints excluded: chain A residue 410 MET Chi-restraints excluded: chain A residue 471 THR Chi-restraints excluded: chain B residue 151 VAL Chi-restraints excluded: chain B residue 158 THR Chi-restraints excluded: chain B residue 218 PHE Chi-restraints excluded: chain B residue 221 LEU Chi-restraints excluded: chain B residue 432 LEU Chi-restraints excluded: chain B residue 471 THR Chi-restraints excluded: chain C residue 209 THR Chi-restraints excluded: chain C residue 218 PHE Chi-restraints excluded: chain C residue 289 GLU Chi-restraints excluded: chain C residue 404 VAL Chi-restraints excluded: chain C residue 471 THR Chi-restraints excluded: chain D residue 218 PHE Chi-restraints excluded: chain D residue 279 ARG Chi-restraints excluded: chain D residue 329 ARG Chi-restraints excluded: chain E residue 92 ASP Chi-restraints excluded: chain E residue 101 THR Chi-restraints excluded: chain E residue 191 VAL Chi-restraints excluded: chain E residue 209 THR Chi-restraints excluded: chain E residue 221 LEU Chi-restraints excluded: chain E residue 243 ILE Chi-restraints excluded: chain E residue 431 LEU Chi-restraints excluded: chain F residue 158 THR Chi-restraints excluded: chain F residue 209 THR Chi-restraints excluded: chain F residue 222 THR Chi-restraints excluded: chain F residue 273 GLN Chi-restraints excluded: chain F residue 280 GLU Chi-restraints excluded: chain F residue 285 LEU Chi-restraints excluded: chain F residue 337 THR Chi-restraints excluded: chain F residue 404 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 264 random chunks: chunk 179 optimal weight: 0.9990 chunk 114 optimal weight: 0.9980 chunk 85 optimal weight: 4.9990 chunk 209 optimal weight: 3.9990 chunk 147 optimal weight: 0.7980 chunk 186 optimal weight: 2.9990 chunk 170 optimal weight: 6.9990 chunk 21 optimal weight: 2.9990 chunk 171 optimal weight: 6.9990 chunk 132 optimal weight: 10.0000 chunk 99 optimal weight: 3.9990 overall best weight: 1.7586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 85 HIS C 509 ASN D 85 HIS E 449 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2950 r_free = 0.2950 target = 0.093170 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2778 r_free = 0.2778 target = 0.081271 restraints weight = 32590.506| |-----------------------------------------------------------------------------| r_work (start): 0.2784 rms_B_bonded: 1.62 r_work: 0.2684 rms_B_bonded: 2.04 restraints_weight: 0.5000 r_work: 0.2560 rms_B_bonded: 3.47 restraints_weight: 0.2500 r_work (final): 0.2560 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8676 moved from start: 0.2681 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 21960 Z= 0.134 Angle : 0.538 9.474 29790 Z= 0.285 Chirality : 0.044 0.192 3174 Planarity : 0.005 0.044 3840 Dihedral : 4.956 68.654 2928 Min Nonbonded Distance : 2.398 Molprobity Statistics. All-atom Clashscore : 2.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.58 % Favored : 97.42 % Rotamer: Outliers : 2.25 % Allowed : 12.33 % Favored : 85.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.57 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.25 (0.16), residues: 2676 helix: 0.12 (0.16), residues: 1098 sheet: 0.62 (0.27), residues: 354 loop : -0.56 (0.18), residues: 1224 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP A 483 HIS 0.005 0.001 HIS D 85 PHE 0.018 0.001 PHE E 515 TYR 0.009 0.001 TYR D 388 ARG 0.003 0.000 ARG E 200 Details of bonding type rmsd hydrogen bonds : bond 0.04212 ( 856) hydrogen bonds : angle 4.50075 ( 2451) covalent geometry : bond 0.00324 (21960) covalent geometry : angle 0.53846 (29790) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5352 Ramachandran restraints generated. 2676 Oldfield, 0 Emsley, 2676 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5352 Ramachandran restraints generated. 2676 Oldfield, 0 Emsley, 2676 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 224 residues out of total 2262 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 173 time to evaluate : 2.642 Fit side-chains REVERT: A 204 LYS cc_start: 0.8255 (mtmt) cc_final: 0.7737 (tmtt) REVERT: A 300 ILE cc_start: 0.8981 (mt) cc_final: 0.8461 (tt) REVERT: A 390 TYR cc_start: 0.8614 (p90) cc_final: 0.8375 (p90) REVERT: A 395 MET cc_start: 0.8109 (mmm) cc_final: 0.7873 (mmm) REVERT: B 158 THR cc_start: 0.9183 (OUTLIER) cc_final: 0.8882 (p) REVERT: B 218 PHE cc_start: 0.8886 (OUTLIER) cc_final: 0.8480 (m-10) REVERT: B 356 SER cc_start: 0.9006 (m) cc_final: 0.8782 (p) REVERT: C 114 GLU cc_start: 0.8432 (mm-30) cc_final: 0.8122 (mp0) REVERT: C 147 GLU cc_start: 0.8376 (mt-10) cc_final: 0.7973 (tt0) REVERT: C 359 THR cc_start: 0.8205 (m) cc_final: 0.7889 (p) REVERT: D 279 ARG cc_start: 0.8281 (OUTLIER) cc_final: 0.7701 (mtm-85) REVERT: D 329 ARG cc_start: 0.7786 (OUTLIER) cc_final: 0.7341 (mtm-85) REVERT: D 389 GLU cc_start: 0.7781 (pp20) cc_final: 0.7553 (pt0) REVERT: D 494 ARG cc_start: 0.8251 (mtp180) cc_final: 0.7735 (mtp180) REVERT: D 512 LYS cc_start: 0.8831 (tttp) cc_final: 0.8309 (mtpp) REVERT: E 95 LYS cc_start: 0.7005 (mmtt) cc_final: 0.6609 (mptt) REVERT: E 511 LYS cc_start: 0.8895 (tttt) cc_final: 0.8677 (mtpp) REVERT: F 79 GLU cc_start: 0.8668 (mm-30) cc_final: 0.8359 (mm-30) REVERT: F 287 GLU cc_start: 0.8115 (OUTLIER) cc_final: 0.7332 (mp0) REVERT: F 288 SER cc_start: 0.8021 (t) cc_final: 0.7422 (p) REVERT: F 494 ARG cc_start: 0.8188 (mtm-85) cc_final: 0.7589 (ptt90) outliers start: 51 outliers final: 25 residues processed: 212 average time/residue: 0.3428 time to fit residues: 114.3998 Evaluate side-chains 183 residues out of total 2262 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 153 time to evaluate : 2.411 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 209 THR Chi-restraints excluded: chain A residue 404 VAL Chi-restraints excluded: chain A residue 410 MET Chi-restraints excluded: chain A residue 471 THR Chi-restraints excluded: chain B residue 151 VAL Chi-restraints excluded: chain B residue 158 THR Chi-restraints excluded: chain B residue 218 PHE Chi-restraints excluded: chain B residue 221 LEU Chi-restraints excluded: chain B residue 471 THR Chi-restraints excluded: chain C residue 218 PHE Chi-restraints excluded: chain C residue 289 GLU Chi-restraints excluded: chain C residue 471 THR Chi-restraints excluded: chain C residue 495 ASP Chi-restraints excluded: chain D residue 279 ARG Chi-restraints excluded: chain D residue 329 ARG Chi-restraints excluded: chain D residue 410 MET Chi-restraints excluded: chain E residue 71 THR Chi-restraints excluded: chain E residue 92 ASP Chi-restraints excluded: chain E residue 191 VAL Chi-restraints excluded: chain E residue 209 THR Chi-restraints excluded: chain E residue 221 LEU Chi-restraints excluded: chain E residue 243 ILE Chi-restraints excluded: chain F residue 209 THR Chi-restraints excluded: chain F residue 273 GLN Chi-restraints excluded: chain F residue 285 LEU Chi-restraints excluded: chain F residue 287 GLU Chi-restraints excluded: chain F residue 337 THR Chi-restraints excluded: chain F residue 404 VAL Chi-restraints excluded: chain F residue 512 LYS Chi-restraints excluded: chain F residue 515 PHE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 264 random chunks: chunk 83 optimal weight: 1.9990 chunk 230 optimal weight: 5.9990 chunk 86 optimal weight: 0.0670 chunk 123 optimal weight: 0.7980 chunk 108 optimal weight: 3.9990 chunk 41 optimal weight: 6.9990 chunk 257 optimal weight: 5.9990 chunk 156 optimal weight: 6.9990 chunk 26 optimal weight: 6.9990 chunk 28 optimal weight: 6.9990 chunk 256 optimal weight: 4.9990 overall best weight: 2.3724 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 283 ASN C 85 HIS C 486 ASN C 509 ASN D 360 ASN E 449 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2950 r_free = 0.2950 target = 0.092939 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2790 r_free = 0.2790 target = 0.081934 restraints weight = 32197.256| |-----------------------------------------------------------------------------| r_work (start): 0.2789 rms_B_bonded: 1.42 r_work: 0.2700 rms_B_bonded: 1.80 restraints_weight: 0.5000 r_work: 0.2583 rms_B_bonded: 3.09 restraints_weight: 0.2500 r_work (final): 0.2583 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8749 moved from start: 0.2852 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 21960 Z= 0.169 Angle : 0.562 9.697 29790 Z= 0.295 Chirality : 0.045 0.184 3174 Planarity : 0.005 0.045 3840 Dihedral : 4.927 67.831 2928 Min Nonbonded Distance : 2.383 Molprobity Statistics. All-atom Clashscore : 2.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.91 % Favored : 97.09 % Rotamer: Outliers : 2.61 % Allowed : 13.17 % Favored : 84.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.57 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.36 (0.16), residues: 2676 helix: 0.05 (0.15), residues: 1134 sheet: 0.64 (0.27), residues: 354 loop : -0.69 (0.18), residues: 1188 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP A 483 HIS 0.005 0.001 HIS D 69 PHE 0.018 0.002 PHE E 515 TYR 0.014 0.001 TYR D 388 ARG 0.003 0.000 ARG B 200 Details of bonding type rmsd hydrogen bonds : bond 0.04539 ( 856) hydrogen bonds : angle 4.47472 ( 2451) covalent geometry : bond 0.00419 (21960) covalent geometry : angle 0.56156 (29790) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5352 Ramachandran restraints generated. 2676 Oldfield, 0 Emsley, 2676 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5352 Ramachandran restraints generated. 2676 Oldfield, 0 Emsley, 2676 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 214 residues out of total 2262 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 155 time to evaluate : 2.887 Fit side-chains revert: symmetry clash REVERT: A 204 LYS cc_start: 0.8290 (mtmt) cc_final: 0.7866 (tmtt) REVERT: A 300 ILE cc_start: 0.9104 (mt) cc_final: 0.8605 (tt) REVERT: A 390 TYR cc_start: 0.8681 (p90) cc_final: 0.8458 (p90) REVERT: B 158 THR cc_start: 0.9267 (OUTLIER) cc_final: 0.8988 (p) REVERT: B 218 PHE cc_start: 0.9036 (OUTLIER) cc_final: 0.8691 (m-10) REVERT: B 432 LEU cc_start: 0.8933 (OUTLIER) cc_final: 0.8460 (mp) REVERT: C 147 GLU cc_start: 0.8449 (mt-10) cc_final: 0.8092 (tt0) REVERT: D 279 ARG cc_start: 0.8446 (OUTLIER) cc_final: 0.7849 (mtm-85) REVERT: D 329 ARG cc_start: 0.7940 (OUTLIER) cc_final: 0.7490 (mtm-85) REVERT: D 494 ARG cc_start: 0.8315 (mtp180) cc_final: 0.7846 (mtp180) REVERT: D 512 LYS cc_start: 0.8870 (tttp) cc_final: 0.8346 (mtpp) REVERT: E 95 LYS cc_start: 0.7110 (mmtt) cc_final: 0.6739 (mptt) REVERT: F 79 GLU cc_start: 0.8630 (mm-30) cc_final: 0.8372 (mm-30) REVERT: F 280 GLU cc_start: 0.7936 (OUTLIER) cc_final: 0.7526 (mp0) REVERT: F 287 GLU cc_start: 0.8208 (OUTLIER) cc_final: 0.7243 (mp0) REVERT: F 288 SER cc_start: 0.8253 (t) cc_final: 0.7732 (p) REVERT: F 494 ARG cc_start: 0.8194 (mtm-85) cc_final: 0.7644 (ptt90) outliers start: 59 outliers final: 35 residues processed: 200 average time/residue: 0.4339 time to fit residues: 136.7314 Evaluate side-chains 189 residues out of total 2262 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 147 time to evaluate : 2.511 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 209 THR Chi-restraints excluded: chain A residue 404 VAL Chi-restraints excluded: chain A residue 410 MET Chi-restraints excluded: chain A residue 471 THR Chi-restraints excluded: chain B residue 151 VAL Chi-restraints excluded: chain B residue 158 THR Chi-restraints excluded: chain B residue 218 PHE Chi-restraints excluded: chain B residue 221 LEU Chi-restraints excluded: chain B residue 336 VAL Chi-restraints excluded: chain B residue 432 LEU Chi-restraints excluded: chain B residue 471 THR Chi-restraints excluded: chain C residue 209 THR Chi-restraints excluded: chain C residue 218 PHE Chi-restraints excluded: chain C residue 289 GLU Chi-restraints excluded: chain C residue 404 VAL Chi-restraints excluded: chain C residue 471 THR Chi-restraints excluded: chain C residue 482 LEU Chi-restraints excluded: chain C residue 495 ASP Chi-restraints excluded: chain D residue 221 LEU Chi-restraints excluded: chain D residue 279 ARG Chi-restraints excluded: chain D residue 329 ARG Chi-restraints excluded: chain D residue 343 ILE Chi-restraints excluded: chain D residue 410 MET Chi-restraints excluded: chain E residue 71 THR Chi-restraints excluded: chain E residue 92 ASP Chi-restraints excluded: chain E residue 101 THR Chi-restraints excluded: chain E residue 136 GLU Chi-restraints excluded: chain E residue 191 VAL Chi-restraints excluded: chain E residue 209 THR Chi-restraints excluded: chain E residue 221 LEU Chi-restraints excluded: chain E residue 431 LEU Chi-restraints excluded: chain F residue 117 MET Chi-restraints excluded: chain F residue 209 THR Chi-restraints excluded: chain F residue 222 THR Chi-restraints excluded: chain F residue 273 GLN Chi-restraints excluded: chain F residue 280 GLU Chi-restraints excluded: chain F residue 285 LEU Chi-restraints excluded: chain F residue 287 GLU Chi-restraints excluded: chain F residue 337 THR Chi-restraints excluded: chain F residue 404 VAL Chi-restraints excluded: chain F residue 472 GLU Chi-restraints excluded: chain F residue 515 PHE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 264 random chunks: chunk 220 optimal weight: 9.9990 chunk 256 optimal weight: 5.9990 chunk 214 optimal weight: 3.9990 chunk 230 optimal weight: 2.9990 chunk 129 optimal weight: 5.9990 chunk 61 optimal weight: 4.9990 chunk 102 optimal weight: 4.9990 chunk 158 optimal weight: 0.2980 chunk 233 optimal weight: 5.9990 chunk 19 optimal weight: 3.9990 chunk 68 optimal weight: 7.9990 overall best weight: 3.2588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 283 ASN C 509 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2910 r_free = 0.2910 target = 0.090454 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2741 r_free = 0.2741 target = 0.078949 restraints weight = 32416.125| |-----------------------------------------------------------------------------| r_work (start): 0.2743 rms_B_bonded: 1.54 r_work: 0.2647 rms_B_bonded: 1.92 restraints_weight: 0.5000 r_work: 0.2526 rms_B_bonded: 3.28 restraints_weight: 0.2500 r_work (final): 0.2526 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8737 moved from start: 0.2970 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.038 21960 Z= 0.216 Angle : 0.601 10.057 29790 Z= 0.316 Chirality : 0.047 0.183 3174 Planarity : 0.005 0.047 3840 Dihedral : 5.071 67.777 2928 Min Nonbonded Distance : 2.472 Molprobity Statistics. All-atom Clashscore : 2.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.84 % Favored : 97.16 % Rotamer: Outliers : 2.92 % Allowed : 13.66 % Favored : 83.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.57 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.56 (0.16), residues: 2676 helix: -0.02 (0.15), residues: 1134 sheet: 0.60 (0.27), residues: 348 loop : -0.91 (0.18), residues: 1194 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP B 483 HIS 0.005 0.001 HIS C 85 PHE 0.022 0.002 PHE C 75 TYR 0.014 0.001 TYR D 388 ARG 0.004 0.000 ARG F 105 Details of bonding type rmsd hydrogen bonds : bond 0.05028 ( 856) hydrogen bonds : angle 4.57646 ( 2451) covalent geometry : bond 0.00543 (21960) covalent geometry : angle 0.60094 (29790) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5352 Ramachandran restraints generated. 2676 Oldfield, 0 Emsley, 2676 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5352 Ramachandran restraints generated. 2676 Oldfield, 0 Emsley, 2676 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 213 residues out of total 2262 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 147 time to evaluate : 2.343 Fit side-chains revert: symmetry clash REVERT: A 204 LYS cc_start: 0.8298 (mtmt) cc_final: 0.7758 (tmtt) REVERT: A 300 ILE cc_start: 0.9036 (mt) cc_final: 0.8498 (tt) REVERT: A 390 TYR cc_start: 0.8740 (p90) cc_final: 0.8481 (p90) REVERT: A 395 MET cc_start: 0.8138 (mmm) cc_final: 0.7879 (mmm) REVERT: B 158 THR cc_start: 0.9199 (OUTLIER) cc_final: 0.8825 (p) REVERT: B 245 LYS cc_start: 0.8064 (mtpt) cc_final: 0.7828 (mtmm) REVERT: C 147 GLU cc_start: 0.8410 (mt-10) cc_final: 0.8022 (tt0) REVERT: D 218 PHE cc_start: 0.8559 (OUTLIER) cc_final: 0.8250 (m-80) REVERT: D 259 GLN cc_start: 0.8921 (OUTLIER) cc_final: 0.8711 (tp-100) REVERT: D 279 ARG cc_start: 0.8352 (OUTLIER) cc_final: 0.7826 (mtm-85) REVERT: D 329 ARG cc_start: 0.8076 (OUTLIER) cc_final: 0.7569 (mtm-85) REVERT: D 494 ARG cc_start: 0.8300 (mtp180) cc_final: 0.7786 (mtp180) REVERT: D 512 LYS cc_start: 0.8911 (tttp) cc_final: 0.8391 (mtpp) REVERT: E 95 LYS cc_start: 0.7026 (mmtt) cc_final: 0.6644 (mptt) REVERT: F 280 GLU cc_start: 0.7821 (OUTLIER) cc_final: 0.7373 (mp0) REVERT: F 287 GLU cc_start: 0.8198 (OUTLIER) cc_final: 0.7324 (mp0) REVERT: F 288 SER cc_start: 0.8142 (t) cc_final: 0.7588 (p) REVERT: F 430 ASP cc_start: 0.7797 (OUTLIER) cc_final: 0.7415 (m-30) REVERT: F 494 ARG cc_start: 0.8177 (mtm-85) cc_final: 0.7550 (ptt90) outliers start: 66 outliers final: 41 residues processed: 196 average time/residue: 0.3267 time to fit residues: 99.9219 Evaluate side-chains 192 residues out of total 2262 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 143 time to evaluate : 2.292 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 94 SER Chi-restraints excluded: chain A residue 209 THR Chi-restraints excluded: chain A residue 247 CYS Chi-restraints excluded: chain A residue 343 ILE Chi-restraints excluded: chain A residue 384 LEU Chi-restraints excluded: chain A residue 404 VAL Chi-restraints excluded: chain A residue 471 THR Chi-restraints excluded: chain B residue 151 VAL Chi-restraints excluded: chain B residue 152 LEU Chi-restraints excluded: chain B residue 158 THR Chi-restraints excluded: chain B residue 221 LEU Chi-restraints excluded: chain B residue 336 VAL Chi-restraints excluded: chain B residue 410 MET Chi-restraints excluded: chain C residue 209 THR Chi-restraints excluded: chain C residue 218 PHE Chi-restraints excluded: chain C residue 285 LEU Chi-restraints excluded: chain C residue 289 GLU Chi-restraints excluded: chain C residue 359 THR Chi-restraints excluded: chain C residue 404 VAL Chi-restraints excluded: chain C residue 471 THR Chi-restraints excluded: chain C residue 482 LEU Chi-restraints excluded: chain C residue 495 ASP Chi-restraints excluded: chain D residue 218 PHE Chi-restraints excluded: chain D residue 221 LEU Chi-restraints excluded: chain D residue 259 GLN Chi-restraints excluded: chain D residue 279 ARG Chi-restraints excluded: chain D residue 329 ARG Chi-restraints excluded: chain D residue 415 MET Chi-restraints excluded: chain E residue 71 THR Chi-restraints excluded: chain E residue 92 ASP Chi-restraints excluded: chain E residue 101 THR Chi-restraints excluded: chain E residue 136 GLU Chi-restraints excluded: chain E residue 191 VAL Chi-restraints excluded: chain E residue 209 THR Chi-restraints excluded: chain E residue 221 LEU Chi-restraints excluded: chain E residue 431 LEU Chi-restraints excluded: chain F residue 117 MET Chi-restraints excluded: chain F residue 209 THR Chi-restraints excluded: chain F residue 222 THR Chi-restraints excluded: chain F residue 273 GLN Chi-restraints excluded: chain F residue 280 GLU Chi-restraints excluded: chain F residue 285 LEU Chi-restraints excluded: chain F residue 287 GLU Chi-restraints excluded: chain F residue 337 THR Chi-restraints excluded: chain F residue 404 VAL Chi-restraints excluded: chain F residue 411 ILE Chi-restraints excluded: chain F residue 430 ASP Chi-restraints excluded: chain F residue 472 GLU Chi-restraints excluded: chain F residue 515 PHE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 264 random chunks: chunk 164 optimal weight: 0.7980 chunk 233 optimal weight: 3.9990 chunk 98 optimal weight: 4.9990 chunk 13 optimal weight: 0.5980 chunk 102 optimal weight: 7.9990 chunk 46 optimal weight: 5.9990 chunk 155 optimal weight: 2.9990 chunk 218 optimal weight: 0.8980 chunk 146 optimal weight: 0.9990 chunk 11 optimal weight: 5.9990 chunk 3 optimal weight: 4.9990 overall best weight: 1.2584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 283 ASN C 466 ASN C 509 ASN F 486 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2978 r_free = 0.2978 target = 0.094719 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2820 r_free = 0.2820 target = 0.083746 restraints weight = 31612.822| |-----------------------------------------------------------------------------| r_work (start): 0.2795 rms_B_bonded: 1.41 r_work: 0.2708 rms_B_bonded: 1.77 restraints_weight: 0.5000 r_work: 0.2591 rms_B_bonded: 3.05 restraints_weight: 0.2500 r_work (final): 0.2591 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8697 moved from start: 0.3103 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 21960 Z= 0.111 Angle : 0.507 9.438 29790 Z= 0.267 Chirality : 0.043 0.186 3174 Planarity : 0.005 0.045 3840 Dihedral : 4.735 66.855 2928 Min Nonbonded Distance : 2.478 Molprobity Statistics. All-atom Clashscore : 2.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.88 % Favored : 97.12 % Rotamer: Outliers : 2.12 % Allowed : 14.54 % Favored : 83.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.57 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.32 (0.16), residues: 2676 helix: 0.19 (0.16), residues: 1134 sheet: 0.64 (0.27), residues: 354 loop : -0.78 (0.18), residues: 1188 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP A 483 HIS 0.003 0.001 HIS D 69 PHE 0.017 0.001 PHE E 515 TYR 0.011 0.001 TYR D 388 ARG 0.004 0.000 ARG B 200 Details of bonding type rmsd hydrogen bonds : bond 0.03808 ( 856) hydrogen bonds : angle 4.35857 ( 2451) covalent geometry : bond 0.00259 (21960) covalent geometry : angle 0.50735 (29790) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5352 Ramachandran restraints generated. 2676 Oldfield, 0 Emsley, 2676 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5352 Ramachandran restraints generated. 2676 Oldfield, 0 Emsley, 2676 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 205 residues out of total 2262 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 157 time to evaluate : 2.688 Fit side-chains revert: symmetry clash REVERT: A 124 GLN cc_start: 0.8884 (OUTLIER) cc_final: 0.7564 (tp40) REVERT: A 204 LYS cc_start: 0.8241 (mtmt) cc_final: 0.7540 (tptt) REVERT: A 214 SER cc_start: 0.8597 (OUTLIER) cc_final: 0.8346 (t) REVERT: A 300 ILE cc_start: 0.9020 (mt) cc_final: 0.8512 (tt) REVERT: A 390 TYR cc_start: 0.8702 (p90) cc_final: 0.8460 (p90) REVERT: A 395 MET cc_start: 0.8124 (mmm) cc_final: 0.7884 (mmm) REVERT: B 158 THR cc_start: 0.9176 (OUTLIER) cc_final: 0.8905 (p) REVERT: B 316 SER cc_start: 0.8392 (t) cc_final: 0.8035 (m) REVERT: C 147 GLU cc_start: 0.8363 (mt-10) cc_final: 0.7980 (tt0) REVERT: D 218 PHE cc_start: 0.8530 (OUTLIER) cc_final: 0.7949 (m-80) REVERT: D 329 ARG cc_start: 0.7805 (OUTLIER) cc_final: 0.7394 (mtm-85) REVERT: D 332 ASP cc_start: 0.8581 (OUTLIER) cc_final: 0.8346 (m-30) REVERT: D 494 ARG cc_start: 0.8279 (mtp180) cc_final: 0.7862 (mtp180) REVERT: D 512 LYS cc_start: 0.8827 (tttp) cc_final: 0.8300 (mtpp) REVERT: E 95 LYS cc_start: 0.7005 (mmtt) cc_final: 0.6716 (mptt) REVERT: F 79 GLU cc_start: 0.8638 (mm-30) cc_final: 0.8363 (mm-30) REVERT: F 280 GLU cc_start: 0.7768 (OUTLIER) cc_final: 0.7320 (mp0) REVERT: F 287 GLU cc_start: 0.8164 (OUTLIER) cc_final: 0.7236 (mp0) REVERT: F 288 SER cc_start: 0.8151 (t) cc_final: 0.7629 (p) REVERT: F 430 ASP cc_start: 0.7780 (OUTLIER) cc_final: 0.7426 (m-30) REVERT: F 494 ARG cc_start: 0.8123 (mtm-85) cc_final: 0.7489 (ptt90) outliers start: 48 outliers final: 26 residues processed: 199 average time/residue: 0.3254 time to fit residues: 103.8816 Evaluate side-chains 184 residues out of total 2262 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 149 time to evaluate : 2.498 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 94 SER Chi-restraints excluded: chain A residue 124 GLN Chi-restraints excluded: chain A residue 209 THR Chi-restraints excluded: chain A residue 214 SER Chi-restraints excluded: chain A residue 404 VAL Chi-restraints excluded: chain A residue 471 THR Chi-restraints excluded: chain B residue 152 LEU Chi-restraints excluded: chain B residue 158 THR Chi-restraints excluded: chain B residue 221 LEU Chi-restraints excluded: chain B residue 336 VAL Chi-restraints excluded: chain B residue 410 MET Chi-restraints excluded: chain C residue 289 GLU Chi-restraints excluded: chain C residue 404 VAL Chi-restraints excluded: chain D residue 218 PHE Chi-restraints excluded: chain D residue 221 LEU Chi-restraints excluded: chain D residue 329 ARG Chi-restraints excluded: chain D residue 332 ASP Chi-restraints excluded: chain D residue 482 LEU Chi-restraints excluded: chain E residue 71 THR Chi-restraints excluded: chain E residue 191 VAL Chi-restraints excluded: chain E residue 209 THR Chi-restraints excluded: chain E residue 221 LEU Chi-restraints excluded: chain E residue 431 LEU Chi-restraints excluded: chain F residue 117 MET Chi-restraints excluded: chain F residue 209 THR Chi-restraints excluded: chain F residue 273 GLN Chi-restraints excluded: chain F residue 280 GLU Chi-restraints excluded: chain F residue 285 LEU Chi-restraints excluded: chain F residue 287 GLU Chi-restraints excluded: chain F residue 337 THR Chi-restraints excluded: chain F residue 365 LEU Chi-restraints excluded: chain F residue 404 VAL Chi-restraints excluded: chain F residue 430 ASP Chi-restraints excluded: chain F residue 472 GLU Chi-restraints excluded: chain F residue 515 PHE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 264 random chunks: chunk 96 optimal weight: 6.9990 chunk 51 optimal weight: 5.9990 chunk 23 optimal weight: 0.8980 chunk 198 optimal weight: 0.0050 chunk 6 optimal weight: 6.9990 chunk 136 optimal weight: 2.9990 chunk 72 optimal weight: 6.9990 chunk 107 optimal weight: 6.9990 chunk 94 optimal weight: 3.9990 chunk 108 optimal weight: 3.9990 chunk 123 optimal weight: 0.3980 overall best weight: 1.6598 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 450 ASN C 509 ASN F 402 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2944 r_free = 0.2944 target = 0.092674 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.2771 r_free = 0.2771 target = 0.080765 restraints weight = 32252.325| |-----------------------------------------------------------------------------| r_work (start): 0.2784 rms_B_bonded: 1.62 r_work: 0.2685 rms_B_bonded: 2.02 restraints_weight: 0.5000 r_work: 0.2560 rms_B_bonded: 3.45 restraints_weight: 0.2500 r_work (final): 0.2560 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8690 moved from start: 0.3161 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 21960 Z= 0.129 Angle : 0.516 9.522 29790 Z= 0.269 Chirality : 0.043 0.186 3174 Planarity : 0.005 0.045 3840 Dihedral : 4.640 64.112 2928 Min Nonbonded Distance : 2.473 Molprobity Statistics. All-atom Clashscore : 2.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.91 % Favored : 97.09 % Rotamer: Outliers : 2.25 % Allowed : 14.77 % Favored : 82.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.57 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.21 (0.16), residues: 2676 helix: 0.29 (0.16), residues: 1140 sheet: 0.70 (0.27), residues: 354 loop : -0.75 (0.18), residues: 1182 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP B 483 HIS 0.003 0.001 HIS A 85 PHE 0.020 0.001 PHE E 515 TYR 0.013 0.001 TYR D 388 ARG 0.002 0.000 ARG B 200 Details of bonding type rmsd hydrogen bonds : bond 0.03905 ( 856) hydrogen bonds : angle 4.29626 ( 2451) covalent geometry : bond 0.00313 (21960) covalent geometry : angle 0.51592 (29790) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5352 Ramachandran restraints generated. 2676 Oldfield, 0 Emsley, 2676 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5352 Ramachandran restraints generated. 2676 Oldfield, 0 Emsley, 2676 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 202 residues out of total 2262 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 151 time to evaluate : 2.973 Fit side-chains revert: symmetry clash REVERT: A 204 LYS cc_start: 0.8234 (mtmt) cc_final: 0.7468 (tptt) REVERT: A 214 SER cc_start: 0.8627 (OUTLIER) cc_final: 0.8404 (t) REVERT: A 300 ILE cc_start: 0.8992 (mt) cc_final: 0.8467 (tt) REVERT: A 390 TYR cc_start: 0.8716 (p90) cc_final: 0.8469 (p90) REVERT: A 395 MET cc_start: 0.8094 (mmm) cc_final: 0.7880 (mmm) REVERT: A 495 ASP cc_start: 0.7552 (m-30) cc_final: 0.7304 (m-30) REVERT: B 158 THR cc_start: 0.9136 (OUTLIER) cc_final: 0.8766 (p) REVERT: B 316 SER cc_start: 0.8350 (t) cc_final: 0.8001 (m) REVERT: C 147 GLU cc_start: 0.8422 (mt-10) cc_final: 0.8009 (tt0) REVERT: D 218 PHE cc_start: 0.8465 (OUTLIER) cc_final: 0.7970 (m-80) REVERT: D 329 ARG cc_start: 0.7895 (OUTLIER) cc_final: 0.7469 (mtm-85) REVERT: D 332 ASP cc_start: 0.8632 (OUTLIER) cc_final: 0.8398 (m-30) REVERT: D 415 MET cc_start: 0.9004 (OUTLIER) cc_final: 0.8773 (mtm) REVERT: D 494 ARG cc_start: 0.8275 (mtp180) cc_final: 0.7819 (mtp180) REVERT: D 512 LYS cc_start: 0.8831 (tttp) cc_final: 0.8293 (mtpp) REVERT: E 95 LYS cc_start: 0.6909 (mmtt) cc_final: 0.6610 (mptt) REVERT: F 280 GLU cc_start: 0.7756 (OUTLIER) cc_final: 0.7285 (mp0) REVERT: F 287 GLU cc_start: 0.8177 (OUTLIER) cc_final: 0.7334 (mp0) REVERT: F 288 SER cc_start: 0.8074 (t) cc_final: 0.7525 (p) REVERT: F 494 ARG cc_start: 0.8167 (mtm-85) cc_final: 0.7410 (ptt90) outliers start: 51 outliers final: 33 residues processed: 190 average time/residue: 0.4436 time to fit residues: 134.3596 Evaluate side-chains 187 residues out of total 2262 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 146 time to evaluate : 2.705 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 136 GLU Chi-restraints excluded: chain A residue 209 THR Chi-restraints excluded: chain A residue 214 SER Chi-restraints excluded: chain A residue 283 ASN Chi-restraints excluded: chain A residue 404 VAL Chi-restraints excluded: chain A residue 471 THR Chi-restraints excluded: chain B residue 77 VAL Chi-restraints excluded: chain B residue 152 LEU Chi-restraints excluded: chain B residue 158 THR Chi-restraints excluded: chain B residue 180 ASP Chi-restraints excluded: chain B residue 221 LEU Chi-restraints excluded: chain B residue 336 VAL Chi-restraints excluded: chain B residue 410 MET Chi-restraints excluded: chain C residue 289 GLU Chi-restraints excluded: chain C residue 359 THR Chi-restraints excluded: chain C residue 404 VAL Chi-restraints excluded: chain C residue 482 LEU Chi-restraints excluded: chain D residue 218 PHE Chi-restraints excluded: chain D residue 221 LEU Chi-restraints excluded: chain D residue 329 ARG Chi-restraints excluded: chain D residue 332 ASP Chi-restraints excluded: chain D residue 343 ILE Chi-restraints excluded: chain D residue 415 MET Chi-restraints excluded: chain D residue 482 LEU Chi-restraints excluded: chain E residue 71 THR Chi-restraints excluded: chain E residue 191 VAL Chi-restraints excluded: chain E residue 209 THR Chi-restraints excluded: chain E residue 221 LEU Chi-restraints excluded: chain E residue 431 LEU Chi-restraints excluded: chain F residue 117 MET Chi-restraints excluded: chain F residue 209 THR Chi-restraints excluded: chain F residue 273 GLN Chi-restraints excluded: chain F residue 280 GLU Chi-restraints excluded: chain F residue 285 LEU Chi-restraints excluded: chain F residue 287 GLU Chi-restraints excluded: chain F residue 337 THR Chi-restraints excluded: chain F residue 365 LEU Chi-restraints excluded: chain F residue 404 VAL Chi-restraints excluded: chain F residue 410 MET Chi-restraints excluded: chain F residue 472 GLU Chi-restraints excluded: chain F residue 515 PHE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 264 random chunks: chunk 148 optimal weight: 3.9990 chunk 84 optimal weight: 0.9990 chunk 136 optimal weight: 4.9990 chunk 94 optimal weight: 0.6980 chunk 18 optimal weight: 5.9990 chunk 130 optimal weight: 2.9990 chunk 113 optimal weight: 4.9990 chunk 201 optimal weight: 6.9990 chunk 199 optimal weight: 1.9990 chunk 139 optimal weight: 0.3980 chunk 4 optimal weight: 4.9990 overall best weight: 1.4186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 509 ASN E 307 GLN F 402 GLN F 486 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2954 r_free = 0.2954 target = 0.093347 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2782 r_free = 0.2782 target = 0.081514 restraints weight = 31999.827| |-----------------------------------------------------------------------------| r_work (start): 0.2790 rms_B_bonded: 1.60 r_work: 0.2692 rms_B_bonded: 2.01 restraints_weight: 0.5000 r_work: 0.2568 rms_B_bonded: 3.43 restraints_weight: 0.2500 r_work (final): 0.2568 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8676 moved from start: 0.3238 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 21960 Z= 0.115 Angle : 0.499 8.893 29790 Z= 0.260 Chirality : 0.043 0.187 3174 Planarity : 0.005 0.044 3840 Dihedral : 4.534 61.979 2928 Min Nonbonded Distance : 2.480 Molprobity Statistics. All-atom Clashscore : 2.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.95 % Favored : 97.05 % Rotamer: Outliers : 1.99 % Allowed : 14.94 % Favored : 83.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.57 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.19 (0.16), residues: 2676 helix: 0.21 (0.16), residues: 1176 sheet: 0.79 (0.27), residues: 354 loop : -0.68 (0.18), residues: 1146 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP E 483 HIS 0.002 0.001 HIS D 69 PHE 0.020 0.001 PHE E 515 TYR 0.012 0.001 TYR D 388 ARG 0.003 0.000 ARG B 200 Details of bonding type rmsd hydrogen bonds : bond 0.03636 ( 856) hydrogen bonds : angle 4.23254 ( 2451) covalent geometry : bond 0.00277 (21960) covalent geometry : angle 0.49942 (29790) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5352 Ramachandran restraints generated. 2676 Oldfield, 0 Emsley, 2676 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5352 Ramachandran restraints generated. 2676 Oldfield, 0 Emsley, 2676 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 198 residues out of total 2262 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 153 time to evaluate : 2.897 Fit side-chains revert: symmetry clash REVERT: A 204 LYS cc_start: 0.8229 (mtmt) cc_final: 0.7460 (tptt) REVERT: A 214 SER cc_start: 0.8613 (OUTLIER) cc_final: 0.8352 (t) REVERT: A 300 ILE cc_start: 0.8984 (mt) cc_final: 0.8466 (tt) REVERT: A 390 TYR cc_start: 0.8712 (p90) cc_final: 0.8461 (p90) REVERT: A 495 ASP cc_start: 0.7557 (m-30) cc_final: 0.7250 (m-30) REVERT: B 158 THR cc_start: 0.9121 (OUTLIER) cc_final: 0.8757 (p) REVERT: B 316 SER cc_start: 0.8310 (t) cc_final: 0.7982 (m) REVERT: C 147 GLU cc_start: 0.8442 (mt-10) cc_final: 0.8037 (tt0) REVERT: C 342 CYS cc_start: 0.7970 (t) cc_final: 0.7762 (p) REVERT: D 174 SER cc_start: 0.8818 (m) cc_final: 0.8186 (p) REVERT: D 218 PHE cc_start: 0.8455 (OUTLIER) cc_final: 0.7776 (m-80) REVERT: D 329 ARG cc_start: 0.7853 (OUTLIER) cc_final: 0.7449 (mtm-85) REVERT: D 332 ASP cc_start: 0.8559 (OUTLIER) cc_final: 0.8307 (m-30) REVERT: D 415 MET cc_start: 0.8989 (OUTLIER) cc_final: 0.8761 (mtm) REVERT: D 494 ARG cc_start: 0.8235 (mtp180) cc_final: 0.7766 (mtp180) REVERT: D 512 LYS cc_start: 0.8797 (tttp) cc_final: 0.8265 (mtpp) REVERT: E 95 LYS cc_start: 0.6885 (mmtt) cc_final: 0.6541 (mptt) REVERT: F 280 GLU cc_start: 0.7738 (OUTLIER) cc_final: 0.7272 (mp0) REVERT: F 287 GLU cc_start: 0.8197 (OUTLIER) cc_final: 0.7400 (mp0) REVERT: F 288 SER cc_start: 0.8026 (t) cc_final: 0.7682 (t) REVERT: F 430 ASP cc_start: 0.7769 (OUTLIER) cc_final: 0.7445 (m-30) REVERT: F 494 ARG cc_start: 0.8148 (mtm-85) cc_final: 0.7401 (ptt90) outliers start: 45 outliers final: 33 residues processed: 186 average time/residue: 0.3759 time to fit residues: 112.3852 Evaluate side-chains 195 residues out of total 2262 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 153 time to evaluate : 2.605 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 94 SER Chi-restraints excluded: chain A residue 136 GLU Chi-restraints excluded: chain A residue 209 THR Chi-restraints excluded: chain A residue 214 SER Chi-restraints excluded: chain A residue 283 ASN Chi-restraints excluded: chain A residue 404 VAL Chi-restraints excluded: chain A residue 471 THR Chi-restraints excluded: chain B residue 77 VAL Chi-restraints excluded: chain B residue 158 THR Chi-restraints excluded: chain B residue 180 ASP Chi-restraints excluded: chain B residue 221 LEU Chi-restraints excluded: chain B residue 336 VAL Chi-restraints excluded: chain B residue 410 MET Chi-restraints excluded: chain C residue 289 GLU Chi-restraints excluded: chain C residue 404 VAL Chi-restraints excluded: chain C residue 471 THR Chi-restraints excluded: chain C residue 482 LEU Chi-restraints excluded: chain D residue 218 PHE Chi-restraints excluded: chain D residue 221 LEU Chi-restraints excluded: chain D residue 329 ARG Chi-restraints excluded: chain D residue 332 ASP Chi-restraints excluded: chain D residue 343 ILE Chi-restraints excluded: chain D residue 415 MET Chi-restraints excluded: chain D residue 482 LEU Chi-restraints excluded: chain E residue 71 THR Chi-restraints excluded: chain E residue 191 VAL Chi-restraints excluded: chain E residue 209 THR Chi-restraints excluded: chain E residue 221 LEU Chi-restraints excluded: chain E residue 431 LEU Chi-restraints excluded: chain F residue 209 THR Chi-restraints excluded: chain F residue 273 GLN Chi-restraints excluded: chain F residue 280 GLU Chi-restraints excluded: chain F residue 285 LEU Chi-restraints excluded: chain F residue 287 GLU Chi-restraints excluded: chain F residue 337 THR Chi-restraints excluded: chain F residue 365 LEU Chi-restraints excluded: chain F residue 404 VAL Chi-restraints excluded: chain F residue 410 MET Chi-restraints excluded: chain F residue 411 ILE Chi-restraints excluded: chain F residue 430 ASP Chi-restraints excluded: chain F residue 472 GLU Chi-restraints excluded: chain F residue 515 PHE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 264 random chunks: chunk 185 optimal weight: 0.0980 chunk 163 optimal weight: 5.9990 chunk 157 optimal weight: 7.9990 chunk 13 optimal weight: 0.0030 chunk 220 optimal weight: 0.9980 chunk 166 optimal weight: 0.9980 chunk 109 optimal weight: 0.9980 chunk 119 optimal weight: 0.8980 chunk 108 optimal weight: 5.9990 chunk 59 optimal weight: 0.9980 chunk 226 optimal weight: 3.9990 overall best weight: 0.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 466 ASN C 509 ASN E 466 ASN F 402 GLN F 486 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2999 r_free = 0.2999 target = 0.096284 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2835 r_free = 0.2835 target = 0.084747 restraints weight = 31774.799| |-----------------------------------------------------------------------------| r_work (start): 0.2836 rms_B_bonded: 1.53 r_work: 0.2745 rms_B_bonded: 1.91 restraints_weight: 0.5000 r_work: 0.2626 rms_B_bonded: 3.29 restraints_weight: 0.2500 r_work (final): 0.2626 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8638 moved from start: 0.3404 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 21960 Z= 0.089 Angle : 0.469 9.260 29790 Z= 0.242 Chirality : 0.041 0.185 3174 Planarity : 0.004 0.045 3840 Dihedral : 4.246 59.061 2928 Min Nonbonded Distance : 2.480 Molprobity Statistics. All-atom Clashscore : 2.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.80 % Favored : 97.20 % Rotamer: Outliers : 1.68 % Allowed : 15.34 % Favored : 82.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.57 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.13 (0.17), residues: 2676 helix: 0.50 (0.16), residues: 1140 sheet: 1.03 (0.27), residues: 366 loop : -0.55 (0.19), residues: 1170 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 483 HIS 0.002 0.000 HIS D 69 PHE 0.015 0.001 PHE E 515 TYR 0.011 0.001 TYR D 388 ARG 0.003 0.000 ARG B 200 Details of bonding type rmsd hydrogen bonds : bond 0.02924 ( 856) hydrogen bonds : angle 4.09190 ( 2451) covalent geometry : bond 0.00200 (21960) covalent geometry : angle 0.46856 (29790) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5352 Ramachandran restraints generated. 2676 Oldfield, 0 Emsley, 2676 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5352 Ramachandran restraints generated. 2676 Oldfield, 0 Emsley, 2676 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 208 residues out of total 2262 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 170 time to evaluate : 2.505 Fit side-chains revert: symmetry clash REVERT: A 204 LYS cc_start: 0.8210 (mtmt) cc_final: 0.7465 (tptt) REVERT: A 300 ILE cc_start: 0.8980 (mt) cc_final: 0.8536 (tt) REVERT: A 341 LYS cc_start: 0.7817 (tttt) cc_final: 0.7484 (tppt) REVERT: A 390 TYR cc_start: 0.8669 (p90) cc_final: 0.8440 (p90) REVERT: A 495 ASP cc_start: 0.7493 (m-30) cc_final: 0.7288 (m-30) REVERT: B 158 THR cc_start: 0.9109 (OUTLIER) cc_final: 0.8767 (p) REVERT: B 316 SER cc_start: 0.8078 (t) cc_final: 0.7819 (m) REVERT: C 147 GLU cc_start: 0.8380 (mt-10) cc_final: 0.7981 (tt0) REVERT: C 342 CYS cc_start: 0.7791 (t) cc_final: 0.7510 (p) REVERT: D 174 SER cc_start: 0.8792 (m) cc_final: 0.8166 (p) REVERT: D 218 PHE cc_start: 0.8376 (OUTLIER) cc_final: 0.7775 (m-80) REVERT: D 326 MET cc_start: 0.8630 (ttt) cc_final: 0.8362 (ttt) REVERT: D 332 ASP cc_start: 0.8463 (OUTLIER) cc_final: 0.8221 (m-30) REVERT: D 415 MET cc_start: 0.8943 (OUTLIER) cc_final: 0.8713 (mtm) REVERT: D 494 ARG cc_start: 0.8129 (mtp180) cc_final: 0.7679 (mtp180) REVERT: D 512 LYS cc_start: 0.8636 (tttp) cc_final: 0.7986 (mtmm) REVERT: E 95 LYS cc_start: 0.6866 (mmtt) cc_final: 0.6513 (mptt) REVERT: F 280 GLU cc_start: 0.7679 (OUTLIER) cc_final: 0.7230 (mp0) REVERT: F 287 GLU cc_start: 0.8195 (OUTLIER) cc_final: 0.7478 (mp0) REVERT: F 288 SER cc_start: 0.8020 (t) cc_final: 0.7683 (t) outliers start: 38 outliers final: 19 residues processed: 194 average time/residue: 0.3506 time to fit residues: 108.0641 Evaluate side-chains 182 residues out of total 2262 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 157 time to evaluate : 2.557 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 94 SER Chi-restraints excluded: chain A residue 214 SER Chi-restraints excluded: chain A residue 283 ASN Chi-restraints excluded: chain A residue 404 VAL Chi-restraints excluded: chain B residue 77 VAL Chi-restraints excluded: chain B residue 158 THR Chi-restraints excluded: chain B residue 180 ASP Chi-restraints excluded: chain B residue 410 MET Chi-restraints excluded: chain C residue 359 THR Chi-restraints excluded: chain C residue 404 VAL Chi-restraints excluded: chain C residue 471 THR Chi-restraints excluded: chain D residue 218 PHE Chi-restraints excluded: chain D residue 221 LEU Chi-restraints excluded: chain D residue 332 ASP Chi-restraints excluded: chain D residue 415 MET Chi-restraints excluded: chain E residue 71 THR Chi-restraints excluded: chain E residue 431 LEU Chi-restraints excluded: chain F residue 209 THR Chi-restraints excluded: chain F residue 280 GLU Chi-restraints excluded: chain F residue 285 LEU Chi-restraints excluded: chain F residue 287 GLU Chi-restraints excluded: chain F residue 337 THR Chi-restraints excluded: chain F residue 404 VAL Chi-restraints excluded: chain F residue 472 GLU Chi-restraints excluded: chain F residue 515 PHE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 264 random chunks: chunk 31 optimal weight: 9.9990 chunk 210 optimal weight: 1.9990 chunk 225 optimal weight: 1.9990 chunk 74 optimal weight: 10.0000 chunk 237 optimal weight: 8.9990 chunk 201 optimal weight: 6.9990 chunk 18 optimal weight: 3.9990 chunk 196 optimal weight: 3.9990 chunk 24 optimal weight: 9.9990 chunk 143 optimal weight: 5.9990 chunk 19 optimal weight: 2.9990 overall best weight: 2.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 486 ASN D 259 GLN E 466 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2934 r_free = 0.2934 target = 0.091987 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2753 r_free = 0.2753 target = 0.079706 restraints weight = 32236.319| |-----------------------------------------------------------------------------| r_work (start): 0.2757 rms_B_bonded: 1.69 r_work: 0.2651 rms_B_bonded: 2.17 restraints_weight: 0.5000 r_work: 0.2524 rms_B_bonded: 3.67 restraints_weight: 0.2500 r_work (final): 0.2524 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8783 moved from start: 0.3286 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.043 21960 Z= 0.202 Angle : 0.572 12.236 29790 Z= 0.296 Chirality : 0.046 0.189 3174 Planarity : 0.005 0.044 3840 Dihedral : 4.627 56.530 2928 Min Nonbonded Distance : 2.412 Molprobity Statistics. All-atom Clashscore : 2.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.10 % Favored : 96.90 % Rotamer: Outliers : 1.37 % Allowed : 15.30 % Favored : 83.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.57 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.12 (0.16), residues: 2676 helix: 0.37 (0.16), residues: 1140 sheet: 0.92 (0.28), residues: 348 loop : -0.76 (0.18), residues: 1188 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.040 0.002 TRP A 483 HIS 0.004 0.001 HIS E 85 PHE 0.022 0.002 PHE C 75 TYR 0.015 0.001 TYR E 390 ARG 0.003 0.000 ARG A 270 Details of bonding type rmsd hydrogen bonds : bond 0.04516 ( 856) hydrogen bonds : angle 4.31469 ( 2451) covalent geometry : bond 0.00503 (21960) covalent geometry : angle 0.57160 (29790) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 9803.57 seconds wall clock time: 174 minutes 17.08 seconds (10457.08 seconds total)