Starting phenix.real_space_refine on Fri Feb 6 00:21:09 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8jgn_36240/02_2026/8jgn_36240.cif Found real_map, /net/cci-nas-00/data/ceres_data/8jgn_36240/02_2026/8jgn_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_36240/02_2026/8jgn_36240.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8jgn_36240/02_2026/8jgn_36240.map" model { file = "/net/cci-nas-00/data/ceres_data/8jgn_36240/02_2026/8jgn_36240.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8jgn_36240/02_2026/8jgn_36240.cif" } resolution = 3.39 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.008 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): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 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: 4.54, per 1000 atoms: 0.21 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: 1.37 Conformation dependent library (CDL) restraints added in 920.9 milliseconds 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: 0.88 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: 3.54 Time building geometry restraints manager: 1.86 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: 0.01 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: 2.930 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.330 Check model and map are aligned: 0.060 Set scattering table: 0.050 Process input model: 18.580 Find NCS groups from input model: 0.370 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.320 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 23.700 ------------------------------------------------------------------------------- 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.77 (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 ARG 0.011 0.001 ARG A 133 TYR 0.116 0.017 TYR E 119 PHE 0.099 0.012 PHE F 515 TRP 0.125 0.019 TRP A 331 HIS 0.018 0.003 HIS B 184 Details of bonding type rmsd covalent geometry : bond 0.01225 (21960) covalent geometry : angle 1.79940 (29790) hydrogen bonds : bond 0.21725 ( 856) hydrogen bonds : angle 7.73946 ( 2451) *********************** 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 : 0.554 Fit side-chains REVERT: A 204 LYS cc_start: 0.7913 (mtmt) cc_final: 0.7297 (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: 0.5982 (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: 0.1677 time to fit residues: 91.9846 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 : 0.520 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 264 random chunks: chunk 197 optimal weight: 0.6980 chunk 215 optimal weight: 0.9990 chunk 20 optimal weight: 0.9980 chunk 132 optimal weight: 4.9990 chunk 261 optimal weight: 0.9990 chunk 248 optimal weight: 0.9990 chunk 207 optimal weight: 2.9990 chunk 155 optimal weight: 2.9990 chunk 244 optimal weight: 1.9990 chunk 183 optimal weight: 1.9990 chunk 111 optimal weight: 1.9990 overall best weight: 0.9386 ------------------------------------------------------------------------------- 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 = 0.3031 r_free = 0.3031 target = 0.098290 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2884 r_free = 0.2884 target = 0.087836 restraints weight = 31456.195| |-----------------------------------------------------------------------------| r_work (start): 0.2867 rms_B_bonded: 1.29 r_work: 0.2785 rms_B_bonded: 1.65 restraints_weight: 0.5000 r_work: 0.2673 rms_B_bonded: 2.87 restraints_weight: 0.2500 r_work (final): 0.2673 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8630 moved from start: 0.1942 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.060 21960 Z= 0.136 Angle : 0.619 8.885 29790 Z= 0.339 Chirality : 0.046 0.200 3174 Planarity : 0.005 0.064 3840 Dihedral : 5.527 42.935 2928 Min Nonbonded Distance : 2.151 Molprobity Statistics. All-atom Clashscore : 1.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.13 % Favored : 97.87 % Rotamer: Outliers : 1.46 % Allowed : 9.90 % Favored : 88.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.57 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.58 (0.16), residues: 2676 helix: -0.54 (0.15), residues: 1098 sheet: 0.57 (0.26), residues: 366 loop : -0.36 (0.18), residues: 1212 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG F 262 TYR 0.014 0.001 TYR E 119 PHE 0.033 0.002 PHE F 515 TRP 0.023 0.001 TRP A 483 HIS 0.005 0.001 HIS D 69 Details of bonding type rmsd covalent geometry : bond 0.00276 (21960) covalent geometry : angle 0.61893 (29790) hydrogen bonds : bond 0.05193 ( 856) hydrogen bonds : angle 5.08604 ( 2451) *********************** 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 258 residues out of total 2262 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 225 time to evaluate : 0.863 Fit side-chains REVERT: A 204 LYS cc_start: 0.8156 (mtmt) cc_final: 0.7834 (tmtt) REVERT: A 390 TYR cc_start: 0.8544 (p90) cc_final: 0.8311 (p90) REVERT: B 158 THR cc_start: 0.9254 (OUTLIER) cc_final: 0.8985 (p) REVERT: B 221 LEU cc_start: 0.8474 (OUTLIER) cc_final: 0.8143 (mp) REVERT: B 486 ASN cc_start: 0.8615 (t0) cc_final: 0.8393 (t0) REVERT: C 114 GLU cc_start: 0.8214 (mm-30) cc_final: 0.7971 (mt-10) REVERT: C 206 ASP cc_start: 0.8448 (m-30) cc_final: 0.8218 (m-30) REVERT: C 359 THR cc_start: 0.8119 (m) cc_final: 0.7835 (p) REVERT: D 494 ARG cc_start: 0.8155 (mtp180) cc_final: 0.7721 (mtp180) REVERT: D 512 LYS cc_start: 0.8843 (tttp) cc_final: 0.8348 (mtpp) REVERT: E 95 LYS cc_start: 0.7166 (mmtt) cc_final: 0.6770 (mptt) REVERT: E 410 MET cc_start: 0.8936 (mtt) cc_final: 0.8617 (mtt) REVERT: E 489 MET cc_start: 0.8201 (mtt) cc_final: 0.7930 (mtp) REVERT: E 511 LYS cc_start: 0.8852 (tttt) cc_final: 0.8576 (mtpp) REVERT: F 79 GLU cc_start: 0.8555 (mm-30) cc_final: 0.8245 (mm-30) REVERT: F 277 ILE cc_start: 0.8707 (mm) cc_final: 0.8507 (mt) REVERT: F 283 ASN cc_start: 0.7823 (m-40) cc_final: 0.7591 (t0) REVERT: F 287 GLU cc_start: 0.8015 (OUTLIER) cc_final: 0.7294 (mp0) REVERT: F 288 SER cc_start: 0.8000 (t) cc_final: 0.7407 (p) REVERT: F 494 ARG cc_start: 0.7994 (mtm-85) cc_final: 0.7715 (ptt90) outliers start: 33 outliers final: 18 residues processed: 250 average time/residue: 0.1588 time to fit residues: 61.2163 Evaluate side-chains 190 residues out of total 2262 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 169 time to evaluate : 0.802 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 71 THR 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 71 THR 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 166 optimal weight: 6.9990 chunk 254 optimal weight: 7.9990 chunk 259 optimal weight: 8.9990 chunk 255 optimal weight: 0.6980 chunk 169 optimal weight: 7.9990 chunk 97 optimal weight: 0.3980 chunk 11 optimal weight: 9.9990 chunk 24 optimal weight: 8.9990 chunk 114 optimal weight: 2.9990 chunk 238 optimal weight: 0.9990 chunk 198 optimal weight: 3.9990 overall best weight: 1.8186 ------------------------------------------------------------------------------- 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 Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2972 r_free = 0.2972 target = 0.094318 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2803 r_free = 0.2803 target = 0.082650 restraints weight = 32199.510| |-----------------------------------------------------------------------------| r_work (start): 0.2805 rms_B_bonded: 1.54 r_work: 0.2710 rms_B_bonded: 1.95 restraints_weight: 0.5000 r_work: 0.2587 rms_B_bonded: 3.36 restraints_weight: 0.2500 r_work (final): 0.2587 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8671 moved from start: 0.2413 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 21960 Z= 0.143 Angle : 0.571 9.680 29790 Z= 0.304 Chirality : 0.045 0.249 3174 Planarity : 0.005 0.046 3840 Dihedral : 4.981 41.964 2928 Min Nonbonded Distance : 2.488 Molprobity Statistics. All-atom Clashscore : 1.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.54 % Favored : 97.46 % Rotamer: Outliers : 2.17 % Allowed : 11.32 % Favored : 86.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.57 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.29 (0.16), residues: 2676 helix: -0.02 (0.16), residues: 1098 sheet: 0.46 (0.26), residues: 378 loop : -0.44 (0.18), residues: 1200 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG F 262 TYR 0.011 0.001 TYR C 253 PHE 0.020 0.002 PHE F 515 TRP 0.019 0.001 TRP A 483 HIS 0.005 0.001 HIS D 69 Details of bonding type rmsd covalent geometry : bond 0.00343 (21960) covalent geometry : angle 0.57147 (29790) hydrogen bonds : bond 0.04640 ( 856) hydrogen bonds : angle 4.63272 ( 2451) *********************** 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 218 residues out of total 2262 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 169 time to evaluate : 0.626 Fit side-chains REVERT: A 204 LYS cc_start: 0.8252 (mtmt) cc_final: 0.7789 (tmtt) REVERT: A 390 TYR cc_start: 0.8590 (p90) cc_final: 0.8370 (p90) REVERT: B 147 GLU cc_start: 0.8104 (tt0) cc_final: 0.7654 (tt0) REVERT: B 158 THR cc_start: 0.9235 (OUTLIER) cc_final: 0.8860 (p) REVERT: B 218 PHE cc_start: 0.8908 (OUTLIER) cc_final: 0.8497 (m-10) REVERT: B 221 LEU cc_start: 0.8514 (OUTLIER) cc_final: 0.8263 (mp) REVERT: B 277 ILE cc_start: 0.8574 (mm) cc_final: 0.8320 (mt) REVERT: B 356 SER cc_start: 0.9004 (m) cc_final: 0.8802 (p) REVERT: B 432 LEU cc_start: 0.8770 (OUTLIER) cc_final: 0.8385 (mp) REVERT: C 114 GLU cc_start: 0.8418 (mm-30) cc_final: 0.8138 (mp0) REVERT: C 206 ASP cc_start: 0.8475 (m-30) cc_final: 0.8243 (m-30) REVERT: C 359 THR cc_start: 0.8108 (m) cc_final: 0.7784 (p) REVERT: D 329 ARG cc_start: 0.7724 (OUTLIER) cc_final: 0.7259 (mtm-85) REVERT: D 389 GLU cc_start: 0.7738 (pp20) cc_final: 0.7500 (pt0) REVERT: D 494 ARG cc_start: 0.8263 (mtp180) cc_final: 0.7782 (mtp180) REVERT: D 512 LYS cc_start: 0.8846 (tttp) cc_final: 0.8298 (mtpp) REVERT: E 95 LYS cc_start: 0.7058 (mmtt) cc_final: 0.6655 (mptt) REVERT: E 511 LYS cc_start: 0.8864 (tttt) cc_final: 0.8643 (mtpp) REVERT: F 79 GLU cc_start: 0.8598 (mm-30) cc_final: 0.8295 (mm-30) REVERT: F 280 GLU cc_start: 0.7951 (OUTLIER) cc_final: 0.7588 (mp0) REVERT: F 288 SER cc_start: 0.8028 (t) cc_final: 0.7407 (p) REVERT: F 494 ARG cc_start: 0.8148 (mtm-85) cc_final: 0.7637 (ptt90) outliers start: 49 outliers final: 22 residues processed: 211 average time/residue: 0.1426 time to fit residues: 46.9446 Evaluate side-chains 182 residues out of total 2262 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 154 time to evaluate : 0.822 ------------------------------------------------------------------------------- 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 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 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 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 273 GLN Chi-restraints excluded: chain F residue 280 GLU 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 144 optimal weight: 1.9990 chunk 103 optimal weight: 5.9990 chunk 229 optimal weight: 0.8980 chunk 135 optimal weight: 1.9990 chunk 5 optimal weight: 1.9990 chunk 182 optimal weight: 8.9990 chunk 191 optimal weight: 4.9990 chunk 48 optimal weight: 5.9990 chunk 18 optimal weight: 7.9990 chunk 194 optimal weight: 0.9990 chunk 51 optimal weight: 7.9990 overall best weight: 1.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 85 HIS B 466 ASN C 486 ASN E 449 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 = 0.2968 r_free = 0.2968 target = 0.094207 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.2798 r_free = 0.2798 target = 0.082294 restraints weight = 32245.262| |-----------------------------------------------------------------------------| r_work (start): 0.2801 rms_B_bonded: 1.60 r_work: 0.2707 rms_B_bonded: 1.99 restraints_weight: 0.5000 r_work: 0.2585 rms_B_bonded: 3.41 restraints_weight: 0.2500 r_work (final): 0.2585 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8653 moved from start: 0.2657 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 21960 Z= 0.126 Angle : 0.530 9.395 29790 Z= 0.279 Chirality : 0.044 0.187 3174 Planarity : 0.005 0.043 3840 Dihedral : 4.825 62.057 2928 Min Nonbonded Distance : 2.409 Molprobity Statistics. All-atom Clashscore : 2.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.35 % Favored : 97.65 % Rotamer: Outliers : 2.43 % Allowed : 11.89 % Favored : 85.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.57 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.11 (0.16), residues: 2676 helix: 0.23 (0.16), residues: 1098 sheet: 0.75 (0.27), residues: 354 loop : -0.49 (0.18), residues: 1224 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG E 200 TYR 0.009 0.001 TYR D 388 PHE 0.015 0.001 PHE C 75 TRP 0.017 0.001 TRP A 483 HIS 0.005 0.001 HIS D 69 Details of bonding type rmsd covalent geometry : bond 0.00300 (21960) covalent geometry : angle 0.52988 (29790) hydrogen bonds : bond 0.04068 ( 856) hydrogen bonds : angle 4.44259 ( 2451) *********************** 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 230 residues out of total 2262 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 175 time to evaluate : 0.756 Fit side-chains REVERT: A 204 LYS cc_start: 0.8245 (mtmt) cc_final: 0.7755 (tmtt) REVERT: A 300 ILE cc_start: 0.8942 (mt) cc_final: 0.8428 (tt) REVERT: A 341 LYS cc_start: 0.7997 (tttt) cc_final: 0.7660 (tppt) REVERT: A 390 TYR cc_start: 0.8592 (p90) cc_final: 0.8389 (p90) REVERT: B 147 GLU cc_start: 0.8052 (tt0) cc_final: 0.7546 (tt0) REVERT: B 158 THR cc_start: 0.9166 (OUTLIER) cc_final: 0.8803 (p) REVERT: B 218 PHE cc_start: 0.8846 (OUTLIER) cc_final: 0.8508 (m-10) REVERT: B 221 LEU cc_start: 0.8440 (OUTLIER) cc_final: 0.8177 (mp) REVERT: B 410 MET cc_start: 0.9199 (ptp) cc_final: 0.8968 (ptp) REVERT: C 114 GLU cc_start: 0.8405 (mm-30) cc_final: 0.8101 (mp0) REVERT: C 147 GLU cc_start: 0.8327 (mt-10) cc_final: 0.7938 (tt0) REVERT: C 359 THR cc_start: 0.8119 (m) cc_final: 0.7804 (p) REVERT: D 279 ARG cc_start: 0.8237 (OUTLIER) cc_final: 0.7688 (mtm-85) REVERT: D 329 ARG cc_start: 0.7752 (OUTLIER) cc_final: 0.7292 (mtm-85) REVERT: D 389 GLU cc_start: 0.7731 (pp20) cc_final: 0.7511 (pt0) REVERT: D 494 ARG cc_start: 0.8247 (mtp180) cc_final: 0.7752 (mtp180) REVERT: D 512 LYS cc_start: 0.8797 (tttp) cc_final: 0.8214 (mtpp) REVERT: E 95 LYS cc_start: 0.7000 (mmtt) cc_final: 0.6614 (mptt) REVERT: E 511 LYS cc_start: 0.8857 (tttt) cc_final: 0.8626 (mtpp) REVERT: F 79 GLU cc_start: 0.8615 (mm-30) cc_final: 0.8291 (mm-30) REVERT: F 280 GLU cc_start: 0.7824 (OUTLIER) cc_final: 0.7303 (mp0) REVERT: F 287 GLU cc_start: 0.8068 (OUTLIER) cc_final: 0.7340 (mp0) REVERT: F 288 SER cc_start: 0.7943 (t) cc_final: 0.7355 (p) REVERT: F 494 ARG cc_start: 0.8155 (mtm-85) cc_final: 0.7570 (ptt90) outliers start: 55 outliers final: 26 residues processed: 219 average time/residue: 0.1456 time to fit residues: 49.6081 Evaluate side-chains 191 residues out of total 2262 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 158 time to evaluate : 0.719 ------------------------------------------------------------------------------- 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 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 495 ASP Chi-restraints excluded: chain D residue 279 ARG Chi-restraints excluded: chain D residue 329 ARG Chi-restraints excluded: chain D residue 332 ASP 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 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 404 VAL Chi-restraints excluded: chain F residue 512 LYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 264 random chunks: chunk 78 optimal weight: 5.9990 chunk 50 optimal weight: 0.0270 chunk 111 optimal weight: 6.9990 chunk 89 optimal weight: 0.9980 chunk 137 optimal weight: 4.9990 chunk 90 optimal weight: 0.0370 chunk 248 optimal weight: 5.9990 chunk 69 optimal weight: 6.9990 chunk 75 optimal weight: 8.9990 chunk 163 optimal weight: 0.0980 chunk 16 optimal weight: 1.9990 overall best weight: 0.6318 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 283 ASN B 503 HIS 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 = 0.3123 r_free = 0.3123 target = 0.104621 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2974 r_free = 0.2974 target = 0.093839 restraints weight = 30480.494| |-----------------------------------------------------------------------------| r_work (start): 0.2870 rms_B_bonded: 1.35 r_work: 0.2785 rms_B_bonded: 1.72 restraints_weight: 0.5000 r_work: 0.2672 rms_B_bonded: 3.01 restraints_weight: 0.2500 r_work (final): 0.2672 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8656 moved from start: 0.2965 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.039 21960 Z= 0.089 Angle : 0.482 9.134 29790 Z= 0.251 Chirality : 0.042 0.183 3174 Planarity : 0.004 0.043 3840 Dihedral : 4.450 60.933 2928 Min Nonbonded Distance : 2.413 Molprobity Statistics. All-atom Clashscore : 2.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.39 % Favored : 97.61 % Rotamer: Outliers : 1.86 % Allowed : 12.69 % Favored : 85.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.57 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.17 (0.16), residues: 2676 helix: 0.50 (0.16), residues: 1104 sheet: 0.92 (0.27), residues: 366 loop : -0.40 (0.18), residues: 1206 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 200 TYR 0.008 0.001 TYR D 388 PHE 0.013 0.001 PHE E 515 TRP 0.013 0.001 TRP A 483 HIS 0.004 0.001 HIS D 85 Details of bonding type rmsd covalent geometry : bond 0.00194 (21960) covalent geometry : angle 0.48237 (29790) hydrogen bonds : bond 0.03218 ( 856) hydrogen bonds : angle 4.22199 ( 2451) *********************** 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 219 residues out of total 2262 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 177 time to evaluate : 0.567 Fit side-chains revert: symmetry clash REVERT: A 204 LYS cc_start: 0.8229 (mtmt) cc_final: 0.7843 (tmtt) REVERT: A 300 ILE cc_start: 0.9051 (mt) cc_final: 0.8585 (tt) REVERT: A 341 LYS cc_start: 0.7890 (tttt) cc_final: 0.7609 (tppt) REVERT: B 158 THR cc_start: 0.9217 (OUTLIER) cc_final: 0.8881 (p) REVERT: B 432 LEU cc_start: 0.8786 (OUTLIER) cc_final: 0.8401 (mp) REVERT: C 147 GLU cc_start: 0.8355 (mt-10) cc_final: 0.7983 (tt0) REVERT: C 359 THR cc_start: 0.8229 (m) cc_final: 0.7929 (p) REVERT: C 404 VAL cc_start: 0.7974 (OUTLIER) cc_final: 0.7591 (m) REVERT: D 388 TYR cc_start: 0.8747 (m-80) cc_final: 0.8447 (m-80) REVERT: D 494 ARG cc_start: 0.8287 (mtp180) cc_final: 0.7839 (mtp180) REVERT: D 512 LYS cc_start: 0.8672 (tttp) cc_final: 0.8086 (mtmm) REVERT: E 95 LYS cc_start: 0.6989 (mmtt) cc_final: 0.6761 (mptt) REVERT: E 511 LYS cc_start: 0.8848 (tttt) cc_final: 0.8625 (mtpp) REVERT: F 280 GLU cc_start: 0.7891 (OUTLIER) cc_final: 0.7583 (mp0) REVERT: F 287 GLU cc_start: 0.8096 (OUTLIER) cc_final: 0.7225 (mp0) REVERT: F 288 SER cc_start: 0.8107 (t) cc_final: 0.7595 (p) REVERT: F 494 ARG cc_start: 0.8120 (mtm-85) cc_final: 0.7612 (ptt90) outliers start: 42 outliers final: 19 residues processed: 208 average time/residue: 0.1353 time to fit residues: 44.3721 Evaluate side-chains 183 residues out of total 2262 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 159 time to evaluate : 0.668 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 404 VAL Chi-restraints excluded: chain A residue 410 MET Chi-restraints excluded: chain B residue 77 VAL Chi-restraints excluded: chain B residue 158 THR Chi-restraints excluded: chain B residue 432 LEU Chi-restraints excluded: chain C residue 285 LEU Chi-restraints excluded: chain C residue 404 VAL Chi-restraints excluded: chain D residue 169 MET Chi-restraints excluded: chain D residue 221 LEU Chi-restraints excluded: chain D residue 332 ASP Chi-restraints excluded: chain D residue 410 MET Chi-restraints excluded: chain E residue 243 ILE 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 404 VAL Chi-restraints excluded: chain F residue 472 GLU Chi-restraints excluded: chain F residue 512 LYS 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 164 optimal weight: 5.9990 chunk 237 optimal weight: 5.9990 chunk 45 optimal weight: 5.9990 chunk 240 optimal weight: 4.9990 chunk 152 optimal weight: 6.9990 chunk 195 optimal weight: 7.9990 chunk 12 optimal weight: 7.9990 chunk 192 optimal weight: 5.9990 chunk 151 optimal weight: 0.8980 chunk 115 optimal weight: 2.9990 chunk 121 optimal weight: 4.9990 overall best weight: 3.9788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 283 ASN A 486 ASN B 466 ASN C 85 HIS D 360 ASN E 450 ASN F 402 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3000 r_free = 0.3000 target = 0.096047 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2844 r_free = 0.2844 target = 0.085269 restraints weight = 31455.369| |-----------------------------------------------------------------------------| r_work (start): 0.2753 rms_B_bonded: 1.37 r_work: 0.2666 rms_B_bonded: 1.72 restraints_weight: 0.5000 r_work: 0.2551 rms_B_bonded: 2.97 restraints_weight: 0.2500 r_work (final): 0.2551 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8748 moved from start: 0.2928 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.039 21960 Z= 0.263 Angle : 0.638 10.081 29790 Z= 0.333 Chirality : 0.048 0.182 3174 Planarity : 0.005 0.045 3840 Dihedral : 4.959 61.065 2928 Min Nonbonded Distance : 2.466 Molprobity Statistics. All-atom Clashscore : 2.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.14 % Favored : 96.86 % Rotamer: Outliers : 2.52 % Allowed : 12.82 % Favored : 84.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.57 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.24 (0.16), residues: 2676 helix: 0.22 (0.16), residues: 1116 sheet: 0.80 (0.27), residues: 348 loop : -0.72 (0.18), residues: 1212 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG B 143 TYR 0.017 0.002 TYR B 181 PHE 0.025 0.002 PHE C 75 TRP 0.019 0.002 TRP E 354 HIS 0.006 0.001 HIS D 367 Details of bonding type rmsd covalent geometry : bond 0.00665 (21960) covalent geometry : angle 0.63814 (29790) hydrogen bonds : bond 0.05299 ( 856) hydrogen bonds : angle 4.52184 ( 2451) *********************** 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 210 residues out of total 2262 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 153 time to evaluate : 0.885 Fit side-chains REVERT: A 204 LYS cc_start: 0.8270 (mtmt) cc_final: 0.7794 (tmtt) REVERT: A 300 ILE cc_start: 0.9078 (mt) cc_final: 0.8565 (tt) REVERT: B 158 THR cc_start: 0.9222 (OUTLIER) cc_final: 0.8910 (p) REVERT: B 218 PHE cc_start: 0.8992 (OUTLIER) cc_final: 0.8604 (m-10) REVERT: C 147 GLU cc_start: 0.8440 (mt-10) cc_final: 0.8061 (tt0) REVERT: D 279 ARG cc_start: 0.8413 (OUTLIER) cc_final: 0.7877 (mtm-85) REVERT: D 332 ASP cc_start: 0.8586 (OUTLIER) cc_final: 0.8266 (m-30) REVERT: D 494 ARG cc_start: 0.8318 (mtp180) cc_final: 0.7834 (mtp180) REVERT: D 512 LYS cc_start: 0.8891 (tttp) cc_final: 0.8288 (mtpp) REVERT: E 95 LYS cc_start: 0.7059 (mmtt) cc_final: 0.6759 (mptt) REVERT: F 287 GLU cc_start: 0.8136 (OUTLIER) cc_final: 0.7245 (mp0) REVERT: F 288 SER cc_start: 0.8200 (t) cc_final: 0.7684 (p) REVERT: F 494 ARG cc_start: 0.8164 (mtm-85) cc_final: 0.7629 (ptt90) outliers start: 57 outliers final: 31 residues processed: 196 average time/residue: 0.1446 time to fit residues: 44.9673 Evaluate side-chains 180 residues out of total 2262 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 144 time to evaluate : 0.701 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 166 CYS Chi-restraints excluded: chain A residue 209 THR Chi-restraints excluded: chain A residue 404 VAL Chi-restraints excluded: chain A residue 471 THR 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 471 THR Chi-restraints excluded: chain C residue 114 GLU Chi-restraints excluded: chain C residue 209 THR Chi-restraints excluded: chain C residue 285 LEU Chi-restraints excluded: chain C residue 380 SER 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 229 GLU Chi-restraints excluded: chain D residue 279 ARG Chi-restraints excluded: chain D residue 332 ASP Chi-restraints excluded: chain D residue 410 MET Chi-restraints excluded: chain D residue 463 MET Chi-restraints excluded: chain E residue 71 THR 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 411 ILE 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 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 515 PHE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 264 random chunks: chunk 73 optimal weight: 4.9990 chunk 13 optimal weight: 1.9990 chunk 37 optimal weight: 2.9990 chunk 19 optimal weight: 2.9990 chunk 175 optimal weight: 4.9990 chunk 212 optimal weight: 4.9990 chunk 10 optimal weight: 3.9990 chunk 245 optimal weight: 3.9990 chunk 258 optimal weight: 2.9990 chunk 190 optimal weight: 3.9990 chunk 44 optimal weight: 2.9990 overall best weight: 2.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 509 ASN F 402 GLN F 486 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2925 r_free = 0.2925 target = 0.091327 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2757 r_free = 0.2757 target = 0.079883 restraints weight = 32325.208| |-----------------------------------------------------------------------------| r_work (start): 0.2752 rms_B_bonded: 1.53 r_work: 0.2660 rms_B_bonded: 1.91 restraints_weight: 0.5000 r_work: 0.2540 rms_B_bonded: 3.28 restraints_weight: 0.2500 r_work (final): 0.2540 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8736 moved from start: 0.3052 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.039 21960 Z= 0.188 Angle : 0.564 9.954 29790 Z= 0.297 Chirality : 0.045 0.186 3174 Planarity : 0.005 0.045 3840 Dihedral : 4.894 64.359 2928 Min Nonbonded Distance : 2.473 Molprobity Statistics. All-atom Clashscore : 2.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.73 % Favored : 97.27 % Rotamer: Outliers : 2.39 % Allowed : 13.40 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.35 (0.16), residues: 2676 helix: 0.08 (0.15), residues: 1152 sheet: 0.75 (0.27), residues: 348 loop : -0.75 (0.18), residues: 1176 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG D 149 TYR 0.014 0.001 TYR D 388 PHE 0.022 0.002 PHE E 515 TRP 0.019 0.002 TRP A 483 HIS 0.004 0.001 HIS D 69 Details of bonding type rmsd covalent geometry : bond 0.00468 (21960) covalent geometry : angle 0.56447 (29790) hydrogen bonds : bond 0.04570 ( 856) hydrogen bonds : angle 4.45104 ( 2451) *********************** 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: 54 poor density : 151 time to evaluate : 0.845 Fit side-chains revert: symmetry clash REVERT: A 204 LYS cc_start: 0.8245 (mtmt) cc_final: 0.7712 (tmtt) REVERT: A 300 ILE cc_start: 0.9049 (mt) cc_final: 0.8533 (tt) REVERT: B 158 THR cc_start: 0.9182 (OUTLIER) cc_final: 0.8857 (p) REVERT: B 316 SER cc_start: 0.8505 (t) cc_final: 0.8149 (m) REVERT: C 147 GLU cc_start: 0.8504 (mt-10) cc_final: 0.8108 (tt0) REVERT: D 279 ARG cc_start: 0.8390 (OUTLIER) cc_final: 0.7883 (mtm-85) REVERT: D 332 ASP cc_start: 0.8599 (OUTLIER) cc_final: 0.8236 (m-30) REVERT: D 494 ARG cc_start: 0.8338 (mtp180) cc_final: 0.7858 (mtp180) REVERT: D 512 LYS cc_start: 0.8881 (tttp) cc_final: 0.8375 (mtpp) REVERT: E 95 LYS cc_start: 0.6985 (mmtt) cc_final: 0.6682 (mptt) REVERT: F 280 GLU cc_start: 0.7771 (OUTLIER) cc_final: 0.7307 (mp0) REVERT: F 287 GLU cc_start: 0.8206 (OUTLIER) cc_final: 0.7324 (mp0) REVERT: F 288 SER cc_start: 0.8188 (t) cc_final: 0.7648 (p) REVERT: F 494 ARG cc_start: 0.8169 (mtm-85) cc_final: 0.7590 (ptt90) outliers start: 54 outliers final: 33 residues processed: 190 average time/residue: 0.1465 time to fit residues: 43.7932 Evaluate side-chains 185 residues out of total 2262 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 147 time to evaluate : 0.821 ------------------------------------------------------------------------------- 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 404 VAL Chi-restraints excluded: chain A residue 471 THR 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 B residue 471 THR Chi-restraints excluded: chain C residue 209 THR Chi-restraints excluded: chain C residue 285 LEU 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 221 LEU Chi-restraints excluded: chain D residue 229 GLU Chi-restraints excluded: chain D residue 279 ARG Chi-restraints excluded: chain D residue 332 ASP Chi-restraints excluded: chain D residue 343 ILE 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 243 ILE Chi-restraints excluded: chain E residue 431 LEU Chi-restraints excluded: chain F residue 88 ILE 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 404 VAL 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 56 optimal weight: 0.6980 chunk 65 optimal weight: 4.9990 chunk 229 optimal weight: 0.3980 chunk 20 optimal weight: 6.9990 chunk 239 optimal weight: 0.9980 chunk 187 optimal weight: 6.9990 chunk 219 optimal weight: 4.9990 chunk 117 optimal weight: 0.6980 chunk 47 optimal weight: 2.9990 chunk 104 optimal weight: 0.0270 chunk 91 optimal weight: 1.9990 overall best weight: 0.5638 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 283 ASN B 466 ASN C 450 ASN C 466 ASN C 509 ASN F 402 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3010 r_free = 0.3010 target = 0.096690 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2862 r_free = 0.2862 target = 0.086285 restraints weight = 31501.278| |-----------------------------------------------------------------------------| r_work (start): 0.2840 rms_B_bonded: 1.31 r_work: 0.2758 rms_B_bonded: 1.66 restraints_weight: 0.5000 r_work: 0.2645 rms_B_bonded: 2.90 restraints_weight: 0.2500 r_work (final): 0.2645 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8675 moved from start: 0.3252 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 21960 Z= 0.092 Angle : 0.486 11.847 29790 Z= 0.252 Chirality : 0.041 0.192 3174 Planarity : 0.004 0.044 3840 Dihedral : 4.471 63.597 2928 Min Nonbonded Distance : 2.478 Molprobity Statistics. All-atom Clashscore : 2.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.54 % Favored : 97.46 % Rotamer: Outliers : 1.37 % Allowed : 14.32 % Favored : 84.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.57 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.06 (0.16), residues: 2676 helix: 0.49 (0.16), residues: 1116 sheet: 0.71 (0.26), residues: 378 loop : -0.53 (0.18), residues: 1182 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 200 TYR 0.010 0.001 TYR D 388 PHE 0.016 0.001 PHE E 515 TRP 0.014 0.001 TRP A 483 HIS 0.005 0.001 HIS A 490 Details of bonding type rmsd covalent geometry : bond 0.00206 (21960) covalent geometry : angle 0.48563 (29790) hydrogen bonds : bond 0.03167 ( 856) hydrogen bonds : angle 4.20180 ( 2451) *********************** 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 190 residues out of total 2262 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 159 time to evaluate : 0.704 Fit side-chains revert: symmetry clash REVERT: A 204 LYS cc_start: 0.8182 (mtmt) cc_final: 0.7731 (tmtt) REVERT: A 214 SER cc_start: 0.8572 (OUTLIER) cc_final: 0.8301 (t) REVERT: A 300 ILE cc_start: 0.9042 (mt) cc_final: 0.8553 (tt) REVERT: A 341 LYS cc_start: 0.7751 (tttt) cc_final: 0.7471 (tppt) REVERT: B 158 THR cc_start: 0.9195 (OUTLIER) cc_final: 0.8840 (p) REVERT: B 316 SER cc_start: 0.8207 (t) cc_final: 0.7887 (m) REVERT: C 147 GLU cc_start: 0.8398 (mt-10) cc_final: 0.8003 (tt0) REVERT: D 332 ASP cc_start: 0.8508 (OUTLIER) cc_final: 0.8148 (m-30) REVERT: D 494 ARG cc_start: 0.8253 (mtp180) cc_final: 0.7890 (mtp180) REVERT: D 512 LYS cc_start: 0.8713 (tttp) cc_final: 0.8125 (mtmm) REVERT: E 95 LYS cc_start: 0.6971 (mmtt) cc_final: 0.6666 (mptt) REVERT: F 280 GLU cc_start: 0.7744 (OUTLIER) cc_final: 0.7306 (mp0) REVERT: F 287 GLU cc_start: 0.8197 (OUTLIER) cc_final: 0.7299 (mp0) REVERT: F 288 SER cc_start: 0.8116 (t) cc_final: 0.7608 (p) REVERT: F 494 ARG cc_start: 0.8083 (mtm-85) cc_final: 0.7527 (ptt90) outliers start: 31 outliers final: 18 residues processed: 181 average time/residue: 0.1333 time to fit residues: 38.6088 Evaluate side-chains 174 residues out of total 2262 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 151 time to evaluate : 0.783 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 214 SER Chi-restraints excluded: chain A residue 404 VAL Chi-restraints excluded: chain B residue 158 THR Chi-restraints excluded: chain B residue 221 LEU 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 D residue 221 LEU 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 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 404 VAL Chi-restraints excluded: chain F residue 472 GLU Chi-restraints excluded: chain F residue 512 LYS 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 180 optimal weight: 7.9990 chunk 173 optimal weight: 6.9990 chunk 209 optimal weight: 2.9990 chunk 113 optimal weight: 6.9990 chunk 81 optimal weight: 3.9990 chunk 82 optimal weight: 0.7980 chunk 157 optimal weight: 8.9990 chunk 252 optimal weight: 5.9990 chunk 19 optimal weight: 4.9990 chunk 169 optimal weight: 2.9990 chunk 62 optimal weight: 6.9990 overall best weight: 3.1588 ------------------------------------------------------------------------------- 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 Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2921 r_free = 0.2921 target = 0.091114 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2753 r_free = 0.2753 target = 0.079674 restraints weight = 32385.918| |-----------------------------------------------------------------------------| r_work (start): 0.2757 rms_B_bonded: 1.53 r_work: 0.2665 rms_B_bonded: 1.90 restraints_weight: 0.5000 r_work: 0.2544 rms_B_bonded: 3.27 restraints_weight: 0.2500 r_work (final): 0.2544 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8727 moved from start: 0.3165 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.033 21960 Z= 0.206 Angle : 0.579 9.653 29790 Z= 0.302 Chirality : 0.046 0.188 3174 Planarity : 0.005 0.044 3840 Dihedral : 4.784 62.113 2928 Min Nonbonded Distance : 2.467 Molprobity Statistics. All-atom Clashscore : 2.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.06 % Favored : 96.94 % Rotamer: Outliers : 1.64 % Allowed : 14.19 % Favored : 84.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.57 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.15 (0.16), residues: 2676 helix: 0.38 (0.16), residues: 1116 sheet: 0.87 (0.28), residues: 348 loop : -0.77 (0.18), residues: 1212 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG D 149 TYR 0.014 0.001 TYR D 388 PHE 0.023 0.002 PHE E 515 TRP 0.017 0.002 TRP B 483 HIS 0.005 0.001 HIS D 367 Details of bonding type rmsd covalent geometry : bond 0.00515 (21960) covalent geometry : angle 0.57932 (29790) hydrogen bonds : bond 0.04702 ( 856) hydrogen bonds : angle 4.38238 ( 2451) *********************** 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 181 residues out of total 2262 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 144 time to evaluate : 0.901 Fit side-chains revert: symmetry clash REVERT: A 204 LYS cc_start: 0.8241 (mtmt) cc_final: 0.7679 (tmtt) REVERT: A 300 ILE cc_start: 0.9048 (mt) cc_final: 0.8524 (tt) REVERT: B 158 THR cc_start: 0.9163 (OUTLIER) cc_final: 0.8850 (p) REVERT: B 316 SER cc_start: 0.8483 (t) cc_final: 0.8141 (m) REVERT: C 147 GLU cc_start: 0.8509 (mt-10) cc_final: 0.8107 (tt0) REVERT: D 218 PHE cc_start: 0.8531 (OUTLIER) cc_final: 0.7911 (m-80) REVERT: D 332 ASP cc_start: 0.8624 (OUTLIER) cc_final: 0.8267 (m-30) REVERT: D 494 ARG cc_start: 0.8309 (mtp180) cc_final: 0.7882 (mtp180) REVERT: D 512 LYS cc_start: 0.8846 (tttp) cc_final: 0.8327 (mtpp) REVERT: E 95 LYS cc_start: 0.6956 (mmtt) cc_final: 0.6611 (mptt) REVERT: F 280 GLU cc_start: 0.7756 (OUTLIER) cc_final: 0.7267 (mp0) REVERT: F 287 GLU cc_start: 0.8184 (OUTLIER) cc_final: 0.7294 (mp0) REVERT: F 288 SER cc_start: 0.8114 (t) cc_final: 0.7586 (p) REVERT: F 430 ASP cc_start: 0.7836 (OUTLIER) cc_final: 0.7463 (m-30) REVERT: F 494 ARG cc_start: 0.8180 (mtm-85) cc_final: 0.7469 (ptt90) outliers start: 37 outliers final: 29 residues processed: 170 average time/residue: 0.1492 time to fit residues: 40.2548 Evaluate side-chains 179 residues out of total 2262 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 144 time to evaluate : 0.926 ------------------------------------------------------------------------------- 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 312 SER Chi-restraints excluded: chain A residue 404 VAL 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 359 THR Chi-restraints excluded: chain C residue 380 SER Chi-restraints excluded: chain C residue 404 VAL 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 332 ASP Chi-restraints excluded: chain D residue 463 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 431 LEU Chi-restraints excluded: chain F residue 117 MET Chi-restraints excluded: chain F residue 170 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 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 512 LYS 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 161 optimal weight: 2.9990 chunk 77 optimal weight: 1.9990 chunk 172 optimal weight: 4.9990 chunk 262 optimal weight: 0.7980 chunk 53 optimal weight: 5.9990 chunk 164 optimal weight: 0.0670 chunk 121 optimal weight: 5.9990 chunk 139 optimal weight: 7.9990 chunk 232 optimal weight: 4.9990 chunk 11 optimal weight: 1.9990 chunk 65 optimal weight: 1.9990 overall best weight: 1.3724 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 449 ASN F 486 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2959 r_free = 0.2959 target = 0.093523 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2794 r_free = 0.2794 target = 0.082083 restraints weight = 32060.328| |-----------------------------------------------------------------------------| r_work (start): 0.2788 rms_B_bonded: 1.52 r_work: 0.2696 rms_B_bonded: 1.90 restraints_weight: 0.5000 r_work: 0.2577 rms_B_bonded: 3.27 restraints_weight: 0.2500 r_work (final): 0.2577 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8701 moved from start: 0.3261 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= 0.118 Angle : 0.509 12.641 29790 Z= 0.264 Chirality : 0.043 0.190 3174 Planarity : 0.005 0.044 3840 Dihedral : 4.575 62.552 2928 Min Nonbonded Distance : 2.480 Molprobity Statistics. All-atom Clashscore : 2.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.77 % Favored : 97.23 % Rotamer: Outliers : 1.41 % Allowed : 14.54 % Favored : 84.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.57 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.02 (0.16), residues: 2676 helix: 0.49 (0.16), residues: 1116 sheet: 0.72 (0.27), residues: 378 loop : -0.67 (0.18), residues: 1182 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 200 TYR 0.012 0.001 TYR D 388 PHE 0.019 0.001 PHE E 515 TRP 0.016 0.001 TRP A 483 HIS 0.004 0.001 HIS D 69 Details of bonding type rmsd covalent geometry : bond 0.00283 (21960) covalent geometry : angle 0.50889 (29790) hydrogen bonds : bond 0.03683 ( 856) hydrogen bonds : angle 4.24944 ( 2451) ********************** 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 182 residues out of total 2262 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 150 time to evaluate : 0.917 Fit side-chains revert: symmetry clash REVERT: A 204 LYS cc_start: 0.8213 (mtmt) cc_final: 0.7660 (tmtt) REVERT: A 300 ILE cc_start: 0.9029 (mt) cc_final: 0.8527 (tt) REVERT: B 158 THR cc_start: 0.9167 (OUTLIER) cc_final: 0.8903 (p) REVERT: B 316 SER cc_start: 0.8346 (t) cc_final: 0.8016 (m) REVERT: C 147 GLU cc_start: 0.8501 (mt-10) cc_final: 0.8110 (tt0) REVERT: D 174 SER cc_start: 0.8847 (m) cc_final: 0.8224 (p) REVERT: D 218 PHE cc_start: 0.8504 (OUTLIER) cc_final: 0.7917 (m-80) REVERT: D 332 ASP cc_start: 0.8580 (OUTLIER) cc_final: 0.8230 (m-30) REVERT: D 494 ARG cc_start: 0.8255 (mtp180) cc_final: 0.7796 (mtp180) REVERT: D 512 LYS cc_start: 0.8793 (tttp) cc_final: 0.8274 (mtpp) REVERT: E 95 LYS cc_start: 0.6931 (mmtt) cc_final: 0.6613 (mptt) REVERT: F 280 GLU cc_start: 0.7700 (OUTLIER) cc_final: 0.7256 (mp0) REVERT: F 287 GLU cc_start: 0.8214 (OUTLIER) cc_final: 0.7387 (mp0) REVERT: F 288 SER cc_start: 0.8085 (t) cc_final: 0.7574 (p) REVERT: F 430 ASP cc_start: 0.7833 (OUTLIER) cc_final: 0.7519 (m-30) REVERT: F 494 ARG cc_start: 0.8149 (mtm-85) cc_final: 0.7479 (ptt90) outliers start: 32 outliers final: 20 residues processed: 174 average time/residue: 0.1483 time to fit residues: 41.1024 Evaluate side-chains 176 residues out of total 2262 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 150 time to evaluate : 0.878 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 209 THR Chi-restraints excluded: chain A residue 404 VAL Chi-restraints excluded: chain B residue 158 THR Chi-restraints excluded: chain B residue 221 LEU 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 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 482 LEU Chi-restraints excluded: chain E residue 71 THR Chi-restraints excluded: chain E residue 191 VAL 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 404 VAL Chi-restraints excluded: chain F residue 430 ASP Chi-restraints excluded: chain F residue 472 GLU Chi-restraints excluded: chain F residue 512 LYS 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 232 optimal weight: 8.9990 chunk 40 optimal weight: 2.9990 chunk 180 optimal weight: 7.9990 chunk 106 optimal weight: 1.9990 chunk 169 optimal weight: 1.9990 chunk 158 optimal weight: 7.9990 chunk 32 optimal weight: 1.9990 chunk 7 optimal weight: 3.9990 chunk 110 optimal weight: 7.9990 chunk 260 optimal weight: 7.9990 chunk 236 optimal weight: 2.9990 overall best weight: 2.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 449 ASN F 486 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2938 r_free = 0.2938 target = 0.092109 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.2771 r_free = 0.2771 target = 0.080705 restraints weight = 32271.259| |-----------------------------------------------------------------------------| r_work (start): 0.2764 rms_B_bonded: 1.51 r_work: 0.2673 rms_B_bonded: 1.88 restraints_weight: 0.5000 r_work: 0.2553 rms_B_bonded: 3.25 restraints_weight: 0.2500 r_work (final): 0.2553 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8726 moved from start: 0.3243 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 21960 Z= 0.165 Angle : 0.547 12.387 29790 Z= 0.284 Chirality : 0.044 0.190 3174 Planarity : 0.005 0.044 3840 Dihedral : 4.679 60.473 2928 Min Nonbonded Distance : 2.478 Molprobity Statistics. All-atom Clashscore : 2.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.03 % Favored : 96.97 % Rotamer: Outliers : 1.50 % Allowed : 14.59 % Favored : 83.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.57 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.11 (0.16), residues: 2676 helix: 0.43 (0.16), residues: 1116 sheet: 0.89 (0.28), residues: 348 loop : -0.79 (0.18), residues: 1212 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D 149 TYR 0.013 0.001 TYR D 388 PHE 0.022 0.002 PHE E 515 TRP 0.017 0.001 TRP B 483 HIS 0.004 0.001 HIS D 69 Details of bonding type rmsd covalent geometry : bond 0.00409 (21960) covalent geometry : angle 0.54702 (29790) hydrogen bonds : bond 0.04269 ( 856) hydrogen bonds : angle 4.31580 ( 2451) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3961.85 seconds wall clock time: 68 minutes 50.43 seconds (4130.43 seconds total)