Starting phenix.real_space_refine on Tue Dec 31 08:06:46 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6lyp_30017/12_2024/6lyp_30017.cif Found real_map, /net/cci-nas-00/data/ceres_data/6lyp_30017/12_2024/6lyp_30017.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/6lyp_30017/12_2024/6lyp_30017.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6lyp_30017/12_2024/6lyp_30017.map" model { file = "/net/cci-nas-00/data/ceres_data/6lyp_30017/12_2024/6lyp_30017.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6lyp_30017/12_2024/6lyp_30017.cif" } resolution = 3.3 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.011 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 84 5.16 5 C 9744 2.51 5 N 2548 2.21 5 O 2793 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 42 residue(s): 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5532/modules/chem_data/mon_lib" Total number of atoms: 15169 Number of models: 1 Model: "" Number of chains: 1 Chain: "A" Number of atoms: 2167 Number of conformers: 1 Conformer: "" Number of residues, atoms: 287, 2167 Classifications: {'peptide': 287} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 9, 'TRANS': 277} Unresolved non-hydrogen bonds: 19 Unresolved non-hydrogen angles: 26 Unresolved non-hydrogen dihedrals: 21 Planarities with less than four sites: {'PHE:plan': 1, 'TRP:plan': 1} Unresolved non-hydrogen planarities: 15 Restraints were copied for chains: C, B, E, D, G, F Time building chain proxies: 5.30, per 1000 atoms: 0.35 Number of scatterers: 15169 At special positions: 0 Unit cell: (102.96, 100.88, 123.76, 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 84 16.00 O 2793 8.00 N 2548 7.00 C 9744 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: 3.42 Conformation dependent library (CDL) restraints added in 2.1 seconds 3990 Ramachandran restraints generated. 1995 Oldfield, 0 Emsley, 1995 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3710 Finding SS restraints... Secondary structure from input PDB file: 84 helices and 21 sheets defined 48.4% alpha, 11.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.92 Creating SS restraints... Processing helix chain 'A' and resid 209 through 223 removed outlier: 3.641A pdb=" N ALA A 213 " --> pdb=" O LEU A 209 " (cutoff:3.500A) removed outlier: 4.047A pdb=" N LEU A 216 " --> pdb=" O PRO A 212 " (cutoff:3.500A) removed outlier: 3.791A pdb=" N VAL A 217 " --> pdb=" O ALA A 213 " (cutoff:3.500A) removed outlier: 3.737A pdb=" N ILE A 220 " --> pdb=" O LEU A 216 " (cutoff:3.500A) Processing helix chain 'A' and resid 243 through 248 Processing helix chain 'A' and resid 251 through 266 removed outlier: 4.494A pdb=" N ARG A 257 " --> pdb=" O TRP A 253 " (cutoff:3.500A) removed outlier: 3.972A pdb=" N VAL A 262 " --> pdb=" O TRP A 258 " (cutoff:3.500A) removed outlier: 3.952A pdb=" N ILE A 263 " --> pdb=" O LYS A 259 " (cutoff:3.500A) removed outlier: 3.796A pdb=" N THR A 264 " --> pdb=" O THR A 260 " (cutoff:3.500A) Processing helix chain 'A' and resid 276 through 282 removed outlier: 3.779A pdb=" N THR A 282 " --> pdb=" O GLU A 278 " (cutoff:3.500A) Processing helix chain 'A' and resid 282 through 287 Processing helix chain 'A' and resid 289 through 303 removed outlier: 3.535A pdb=" N ILE A 294 " --> pdb=" O GLY A 290 " (cutoff:3.500A) removed outlier: 3.770A pdb=" N GLU A 301 " --> pdb=" O MET A 297 " (cutoff:3.500A) Processing helix chain 'A' and resid 306 through 315 removed outlier: 3.645A pdb=" N ILE A 310 " --> pdb=" O ALA A 306 " (cutoff:3.500A) removed outlier: 3.928A pdb=" N THR A 312 " --> pdb=" O GLN A 308 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N VAL A 313 " --> pdb=" O SER A 309 " (cutoff:3.500A) Processing helix chain 'A' and resid 319 through 324 Processing helix chain 'A' and resid 327 through 342 removed outlier: 4.063A pdb=" N GLN A 339 " --> pdb=" O GLY A 335 " (cutoff:3.500A) removed outlier: 4.168A pdb=" N PHE A 340 " --> pdb=" O LEU A 336 " (cutoff:3.500A) Processing helix chain 'A' and resid 381 through 386 removed outlier: 3.698A pdb=" N SER A 385 " --> pdb=" O ASN A 381 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N SER A 386 " --> pdb=" O SER A 382 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 381 through 386' Processing helix chain 'A' and resid 413 through 427 removed outlier: 3.676A pdb=" N LYS A 422 " --> pdb=" O SER A 418 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N SER A 427 " --> pdb=" O GLU A 423 " (cutoff:3.500A) Processing helix chain 'A' and resid 464 through 484 removed outlier: 4.025A pdb=" N ASN A 468 " --> pdb=" O GLU A 464 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N THR A 469 " --> pdb=" O GLU A 465 " (cutoff:3.500A) removed outlier: 3.928A pdb=" N LEU A 474 " --> pdb=" O GLN A 470 " (cutoff:3.500A) Processing helix chain 'B' and resid 209 through 223 removed outlier: 3.639A pdb=" N ALA B 213 " --> pdb=" O LEU B 209 " (cutoff:3.500A) removed outlier: 4.046A pdb=" N LEU B 216 " --> pdb=" O PRO B 212 " (cutoff:3.500A) removed outlier: 3.791A pdb=" N VAL B 217 " --> pdb=" O ALA B 213 " (cutoff:3.500A) removed outlier: 3.737A pdb=" N ILE B 220 " --> pdb=" O LEU B 216 " (cutoff:3.500A) Processing helix chain 'B' and resid 243 through 248 Processing helix chain 'B' and resid 251 through 266 removed outlier: 4.494A pdb=" N ARG B 257 " --> pdb=" O TRP B 253 " (cutoff:3.500A) removed outlier: 3.972A pdb=" N VAL B 262 " --> pdb=" O TRP B 258 " (cutoff:3.500A) removed outlier: 3.952A pdb=" N ILE B 263 " --> pdb=" O LYS B 259 " (cutoff:3.500A) removed outlier: 3.796A pdb=" N THR B 264 " --> pdb=" O THR B 260 " (cutoff:3.500A) Processing helix chain 'B' and resid 276 through 282 removed outlier: 3.780A pdb=" N THR B 282 " --> pdb=" O GLU B 278 " (cutoff:3.500A) Processing helix chain 'B' and resid 282 through 287 Processing helix chain 'B' and resid 289 through 303 removed outlier: 3.535A pdb=" N ILE B 294 " --> pdb=" O GLY B 290 " (cutoff:3.500A) removed outlier: 3.769A pdb=" N GLU B 301 " --> pdb=" O MET B 297 " (cutoff:3.500A) Processing helix chain 'B' and resid 306 through 315 removed outlier: 3.644A pdb=" N ILE B 310 " --> pdb=" O ALA B 306 " (cutoff:3.500A) removed outlier: 3.927A pdb=" N THR B 312 " --> pdb=" O GLN B 308 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N VAL B 313 " --> pdb=" O SER B 309 " (cutoff:3.500A) Processing helix chain 'B' and resid 319 through 324 Processing helix chain 'B' and resid 327 through 342 removed outlier: 4.062A pdb=" N GLN B 339 " --> pdb=" O GLY B 335 " (cutoff:3.500A) removed outlier: 4.168A pdb=" N PHE B 340 " --> pdb=" O LEU B 336 " (cutoff:3.500A) Processing helix chain 'B' and resid 381 through 386 removed outlier: 3.700A pdb=" N SER B 385 " --> pdb=" O ASN B 381 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N SER B 386 " --> pdb=" O SER B 382 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 381 through 386' Processing helix chain 'B' and resid 413 through 427 removed outlier: 3.677A pdb=" N LYS B 422 " --> pdb=" O SER B 418 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N SER B 427 " --> pdb=" O GLU B 423 " (cutoff:3.500A) Processing helix chain 'B' and resid 464 through 484 removed outlier: 4.025A pdb=" N ASN B 468 " --> pdb=" O GLU B 464 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N THR B 469 " --> pdb=" O GLU B 465 " (cutoff:3.500A) removed outlier: 3.928A pdb=" N LEU B 474 " --> pdb=" O GLN B 470 " (cutoff:3.500A) Processing helix chain 'C' and resid 209 through 223 removed outlier: 3.641A pdb=" N ALA C 213 " --> pdb=" O LEU C 209 " (cutoff:3.500A) removed outlier: 4.046A pdb=" N LEU C 216 " --> pdb=" O PRO C 212 " (cutoff:3.500A) removed outlier: 3.791A pdb=" N VAL C 217 " --> pdb=" O ALA C 213 " (cutoff:3.500A) removed outlier: 3.737A pdb=" N ILE C 220 " --> pdb=" O LEU C 216 " (cutoff:3.500A) Processing helix chain 'C' and resid 243 through 248 Processing helix chain 'C' and resid 251 through 266 removed outlier: 4.493A pdb=" N ARG C 257 " --> pdb=" O TRP C 253 " (cutoff:3.500A) removed outlier: 3.972A pdb=" N VAL C 262 " --> pdb=" O TRP C 258 " (cutoff:3.500A) removed outlier: 3.953A pdb=" N ILE C 263 " --> pdb=" O LYS C 259 " (cutoff:3.500A) removed outlier: 3.794A pdb=" N THR C 264 " --> pdb=" O THR C 260 " (cutoff:3.500A) Processing helix chain 'C' and resid 276 through 282 removed outlier: 3.780A pdb=" N THR C 282 " --> pdb=" O GLU C 278 " (cutoff:3.500A) Processing helix chain 'C' and resid 282 through 287 Processing helix chain 'C' and resid 289 through 303 removed outlier: 3.535A pdb=" N ILE C 294 " --> pdb=" O GLY C 290 " (cutoff:3.500A) removed outlier: 3.769A pdb=" N GLU C 301 " --> pdb=" O MET C 297 " (cutoff:3.500A) Processing helix chain 'C' and resid 306 through 315 removed outlier: 3.643A pdb=" N ILE C 310 " --> pdb=" O ALA C 306 " (cutoff:3.500A) removed outlier: 3.928A pdb=" N THR C 312 " --> pdb=" O GLN C 308 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N VAL C 313 " --> pdb=" O SER C 309 " (cutoff:3.500A) Processing helix chain 'C' and resid 319 through 324 Processing helix chain 'C' and resid 327 through 342 removed outlier: 4.062A pdb=" N GLN C 339 " --> pdb=" O GLY C 335 " (cutoff:3.500A) removed outlier: 4.170A pdb=" N PHE C 340 " --> pdb=" O LEU C 336 " (cutoff:3.500A) Processing helix chain 'C' and resid 381 through 386 removed outlier: 3.699A pdb=" N SER C 385 " --> pdb=" O ASN C 381 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N SER C 386 " --> pdb=" O SER C 382 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 381 through 386' Processing helix chain 'C' and resid 413 through 427 removed outlier: 3.677A pdb=" N LYS C 422 " --> pdb=" O SER C 418 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N SER C 427 " --> pdb=" O GLU C 423 " (cutoff:3.500A) Processing helix chain 'C' and resid 464 through 484 removed outlier: 4.025A pdb=" N ASN C 468 " --> pdb=" O GLU C 464 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N THR C 469 " --> pdb=" O GLU C 465 " (cutoff:3.500A) removed outlier: 3.928A pdb=" N LEU C 474 " --> pdb=" O GLN C 470 " (cutoff:3.500A) Processing helix chain 'D' and resid 209 through 223 removed outlier: 3.640A pdb=" N ALA D 213 " --> pdb=" O LEU D 209 " (cutoff:3.500A) removed outlier: 4.046A pdb=" N LEU D 216 " --> pdb=" O PRO D 212 " (cutoff:3.500A) removed outlier: 3.791A pdb=" N VAL D 217 " --> pdb=" O ALA D 213 " (cutoff:3.500A) removed outlier: 3.737A pdb=" N ILE D 220 " --> pdb=" O LEU D 216 " (cutoff:3.500A) Processing helix chain 'D' and resid 243 through 248 Processing helix chain 'D' and resid 251 through 266 removed outlier: 4.494A pdb=" N ARG D 257 " --> pdb=" O TRP D 253 " (cutoff:3.500A) removed outlier: 3.973A pdb=" N VAL D 262 " --> pdb=" O TRP D 258 " (cutoff:3.500A) removed outlier: 3.953A pdb=" N ILE D 263 " --> pdb=" O LYS D 259 " (cutoff:3.500A) removed outlier: 3.795A pdb=" N THR D 264 " --> pdb=" O THR D 260 " (cutoff:3.500A) Processing helix chain 'D' and resid 276 through 282 removed outlier: 3.779A pdb=" N THR D 282 " --> pdb=" O GLU D 278 " (cutoff:3.500A) Processing helix chain 'D' and resid 282 through 287 Processing helix chain 'D' and resid 289 through 303 removed outlier: 3.535A pdb=" N ILE D 294 " --> pdb=" O GLY D 290 " (cutoff:3.500A) removed outlier: 3.768A pdb=" N GLU D 301 " --> pdb=" O MET D 297 " (cutoff:3.500A) Processing helix chain 'D' and resid 306 through 315 removed outlier: 3.645A pdb=" N ILE D 310 " --> pdb=" O ALA D 306 " (cutoff:3.500A) removed outlier: 3.928A pdb=" N THR D 312 " --> pdb=" O GLN D 308 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N VAL D 313 " --> pdb=" O SER D 309 " (cutoff:3.500A) Processing helix chain 'D' and resid 319 through 324 Processing helix chain 'D' and resid 327 through 342 removed outlier: 4.062A pdb=" N GLN D 339 " --> pdb=" O GLY D 335 " (cutoff:3.500A) removed outlier: 4.168A pdb=" N PHE D 340 " --> pdb=" O LEU D 336 " (cutoff:3.500A) Processing helix chain 'D' and resid 381 through 386 removed outlier: 3.699A pdb=" N SER D 385 " --> pdb=" O ASN D 381 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N SER D 386 " --> pdb=" O SER D 382 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 381 through 386' Processing helix chain 'D' and resid 413 through 427 removed outlier: 3.677A pdb=" N LYS D 422 " --> pdb=" O SER D 418 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N SER D 427 " --> pdb=" O GLU D 423 " (cutoff:3.500A) Processing helix chain 'D' and resid 464 through 484 removed outlier: 4.025A pdb=" N ASN D 468 " --> pdb=" O GLU D 464 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N THR D 469 " --> pdb=" O GLU D 465 " (cutoff:3.500A) removed outlier: 3.928A pdb=" N LEU D 474 " --> pdb=" O GLN D 470 " (cutoff:3.500A) Processing helix chain 'E' and resid 209 through 223 removed outlier: 3.640A pdb=" N ALA E 213 " --> pdb=" O LEU E 209 " (cutoff:3.500A) removed outlier: 4.047A pdb=" N LEU E 216 " --> pdb=" O PRO E 212 " (cutoff:3.500A) removed outlier: 3.792A pdb=" N VAL E 217 " --> pdb=" O ALA E 213 " (cutoff:3.500A) removed outlier: 3.736A pdb=" N ILE E 220 " --> pdb=" O LEU E 216 " (cutoff:3.500A) Processing helix chain 'E' and resid 243 through 248 Processing helix chain 'E' and resid 251 through 266 removed outlier: 4.494A pdb=" N ARG E 257 " --> pdb=" O TRP E 253 " (cutoff:3.500A) removed outlier: 3.973A pdb=" N VAL E 262 " --> pdb=" O TRP E 258 " (cutoff:3.500A) removed outlier: 3.953A pdb=" N ILE E 263 " --> pdb=" O LYS E 259 " (cutoff:3.500A) removed outlier: 3.797A pdb=" N THR E 264 " --> pdb=" O THR E 260 " (cutoff:3.500A) Processing helix chain 'E' and resid 276 through 282 removed outlier: 3.779A pdb=" N THR E 282 " --> pdb=" O GLU E 278 " (cutoff:3.500A) Processing helix chain 'E' and resid 282 through 287 Processing helix chain 'E' and resid 289 through 303 removed outlier: 3.535A pdb=" N ILE E 294 " --> pdb=" O GLY E 290 " (cutoff:3.500A) removed outlier: 3.768A pdb=" N GLU E 301 " --> pdb=" O MET E 297 " (cutoff:3.500A) Processing helix chain 'E' and resid 306 through 315 removed outlier: 3.645A pdb=" N ILE E 310 " --> pdb=" O ALA E 306 " (cutoff:3.500A) removed outlier: 3.928A pdb=" N THR E 312 " --> pdb=" O GLN E 308 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N VAL E 313 " --> pdb=" O SER E 309 " (cutoff:3.500A) Processing helix chain 'E' and resid 319 through 324 Processing helix chain 'E' and resid 327 through 342 removed outlier: 4.062A pdb=" N GLN E 339 " --> pdb=" O GLY E 335 " (cutoff:3.500A) removed outlier: 4.169A pdb=" N PHE E 340 " --> pdb=" O LEU E 336 " (cutoff:3.500A) Processing helix chain 'E' and resid 381 through 386 removed outlier: 3.699A pdb=" N SER E 385 " --> pdb=" O ASN E 381 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N SER E 386 " --> pdb=" O SER E 382 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 381 through 386' Processing helix chain 'E' and resid 413 through 427 removed outlier: 3.677A pdb=" N LYS E 422 " --> pdb=" O SER E 418 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N SER E 427 " --> pdb=" O GLU E 423 " (cutoff:3.500A) Processing helix chain 'E' and resid 464 through 484 removed outlier: 4.025A pdb=" N ASN E 468 " --> pdb=" O GLU E 464 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N THR E 469 " --> pdb=" O GLU E 465 " (cutoff:3.500A) removed outlier: 3.928A pdb=" N LEU E 474 " --> pdb=" O GLN E 470 " (cutoff:3.500A) Processing helix chain 'F' and resid 209 through 223 removed outlier: 3.641A pdb=" N ALA F 213 " --> pdb=" O LEU F 209 " (cutoff:3.500A) removed outlier: 4.047A pdb=" N LEU F 216 " --> pdb=" O PRO F 212 " (cutoff:3.500A) removed outlier: 3.793A pdb=" N VAL F 217 " --> pdb=" O ALA F 213 " (cutoff:3.500A) removed outlier: 3.737A pdb=" N ILE F 220 " --> pdb=" O LEU F 216 " (cutoff:3.500A) Processing helix chain 'F' and resid 243 through 248 Processing helix chain 'F' and resid 251 through 266 removed outlier: 4.493A pdb=" N ARG F 257 " --> pdb=" O TRP F 253 " (cutoff:3.500A) removed outlier: 3.971A pdb=" N VAL F 262 " --> pdb=" O TRP F 258 " (cutoff:3.500A) removed outlier: 3.953A pdb=" N ILE F 263 " --> pdb=" O LYS F 259 " (cutoff:3.500A) removed outlier: 3.795A pdb=" N THR F 264 " --> pdb=" O THR F 260 " (cutoff:3.500A) Processing helix chain 'F' and resid 276 through 282 removed outlier: 3.780A pdb=" N THR F 282 " --> pdb=" O GLU F 278 " (cutoff:3.500A) Processing helix chain 'F' and resid 282 through 287 Processing helix chain 'F' and resid 289 through 303 removed outlier: 3.535A pdb=" N ILE F 294 " --> pdb=" O GLY F 290 " (cutoff:3.500A) removed outlier: 3.769A pdb=" N GLU F 301 " --> pdb=" O MET F 297 " (cutoff:3.500A) Processing helix chain 'F' and resid 306 through 315 removed outlier: 3.645A pdb=" N ILE F 310 " --> pdb=" O ALA F 306 " (cutoff:3.500A) removed outlier: 3.928A pdb=" N THR F 312 " --> pdb=" O GLN F 308 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N VAL F 313 " --> pdb=" O SER F 309 " (cutoff:3.500A) Processing helix chain 'F' and resid 319 through 324 Processing helix chain 'F' and resid 327 through 342 removed outlier: 4.063A pdb=" N GLN F 339 " --> pdb=" O GLY F 335 " (cutoff:3.500A) removed outlier: 4.169A pdb=" N PHE F 340 " --> pdb=" O LEU F 336 " (cutoff:3.500A) Processing helix chain 'F' and resid 381 through 386 removed outlier: 3.699A pdb=" N SER F 385 " --> pdb=" O ASN F 381 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N SER F 386 " --> pdb=" O SER F 382 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 381 through 386' Processing helix chain 'F' and resid 413 through 427 removed outlier: 3.677A pdb=" N LYS F 422 " --> pdb=" O SER F 418 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N SER F 427 " --> pdb=" O GLU F 423 " (cutoff:3.500A) Processing helix chain 'F' and resid 464 through 484 removed outlier: 4.025A pdb=" N ASN F 468 " --> pdb=" O GLU F 464 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N THR F 469 " --> pdb=" O GLU F 465 " (cutoff:3.500A) removed outlier: 3.929A pdb=" N LEU F 474 " --> pdb=" O GLN F 470 " (cutoff:3.500A) Processing helix chain 'G' and resid 209 through 223 removed outlier: 3.640A pdb=" N ALA G 213 " --> pdb=" O LEU G 209 " (cutoff:3.500A) removed outlier: 4.047A pdb=" N LEU G 216 " --> pdb=" O PRO G 212 " (cutoff:3.500A) removed outlier: 3.791A pdb=" N VAL G 217 " --> pdb=" O ALA G 213 " (cutoff:3.500A) removed outlier: 3.737A pdb=" N ILE G 220 " --> pdb=" O LEU G 216 " (cutoff:3.500A) Processing helix chain 'G' and resid 243 through 248 Processing helix chain 'G' and resid 251 through 266 removed outlier: 4.494A pdb=" N ARG G 257 " --> pdb=" O TRP G 253 " (cutoff:3.500A) removed outlier: 3.971A pdb=" N VAL G 262 " --> pdb=" O TRP G 258 " (cutoff:3.500A) removed outlier: 3.952A pdb=" N ILE G 263 " --> pdb=" O LYS G 259 " (cutoff:3.500A) removed outlier: 3.796A pdb=" N THR G 264 " --> pdb=" O THR G 260 " (cutoff:3.500A) Processing helix chain 'G' and resid 276 through 282 removed outlier: 3.780A pdb=" N THR G 282 " --> pdb=" O GLU G 278 " (cutoff:3.500A) Processing helix chain 'G' and resid 282 through 287 Processing helix chain 'G' and resid 289 through 303 removed outlier: 3.537A pdb=" N ILE G 294 " --> pdb=" O GLY G 290 " (cutoff:3.500A) removed outlier: 3.769A pdb=" N GLU G 301 " --> pdb=" O MET G 297 " (cutoff:3.500A) Processing helix chain 'G' and resid 306 through 315 removed outlier: 3.644A pdb=" N ILE G 310 " --> pdb=" O ALA G 306 " (cutoff:3.500A) removed outlier: 3.927A pdb=" N THR G 312 " --> pdb=" O GLN G 308 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N VAL G 313 " --> pdb=" O SER G 309 " (cutoff:3.500A) Processing helix chain 'G' and resid 319 through 324 Processing helix chain 'G' and resid 327 through 342 removed outlier: 4.063A pdb=" N GLN G 339 " --> pdb=" O GLY G 335 " (cutoff:3.500A) removed outlier: 4.169A pdb=" N PHE G 340 " --> pdb=" O LEU G 336 " (cutoff:3.500A) Processing helix chain 'G' and resid 381 through 386 removed outlier: 3.699A pdb=" N SER G 385 " --> pdb=" O ASN G 381 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N SER G 386 " --> pdb=" O SER G 382 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 381 through 386' Processing helix chain 'G' and resid 413 through 427 removed outlier: 3.677A pdb=" N LYS G 422 " --> pdb=" O SER G 418 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N SER G 427 " --> pdb=" O GLU G 423 " (cutoff:3.500A) Processing helix chain 'G' and resid 464 through 484 removed outlier: 4.025A pdb=" N ASN G 468 " --> pdb=" O GLU G 464 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N THR G 469 " --> pdb=" O GLU G 465 " (cutoff:3.500A) removed outlier: 3.928A pdb=" N LEU G 474 " --> pdb=" O GLN G 470 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 349 through 350 removed outlier: 6.682A pdb=" N SER A 368 " --> pdb=" O ILE A 360 " (cutoff:3.500A) removed outlier: 5.428A pdb=" N MET A 362 " --> pdb=" O THR A 366 " (cutoff:3.500A) removed outlier: 7.203A pdb=" N THR A 366 " --> pdb=" O MET A 362 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N ILE G 389 " --> pdb=" O LEU A 378 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 389 through 390 removed outlier: 3.650A pdb=" N ILE A 389 " --> pdb=" O LEU B 378 " (cutoff:3.500A) removed outlier: 7.201A pdb=" N THR B 366 " --> pdb=" O MET B 362 " (cutoff:3.500A) removed outlier: 5.428A pdb=" N MET B 362 " --> pdb=" O THR B 366 " (cutoff:3.500A) removed outlier: 6.681A pdb=" N SER B 368 " --> pdb=" O ILE B 360 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 399 through 401 removed outlier: 3.860A pdb=" N TYR A 441 " --> pdb=" O THR A 453 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 406 through 407 removed outlier: 3.747A pdb=" N SER A 487 " --> pdb=" O GLN A 407 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 389 through 390 removed outlier: 3.648A pdb=" N ILE B 389 " --> pdb=" O LEU C 378 " (cutoff:3.500A) removed outlier: 7.202A pdb=" N THR C 366 " --> pdb=" O MET C 362 " (cutoff:3.500A) removed outlier: 5.429A pdb=" N MET C 362 " --> pdb=" O THR C 366 " (cutoff:3.500A) removed outlier: 6.682A pdb=" N SER C 368 " --> pdb=" O ILE C 360 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 399 through 401 removed outlier: 3.861A pdb=" N TYR B 441 " --> pdb=" O THR B 453 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 406 through 407 removed outlier: 3.747A pdb=" N SER B 487 " --> pdb=" O GLN B 407 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'C' and resid 389 through 390 removed outlier: 3.626A pdb=" N ILE C 389 " --> pdb=" O LEU D 378 " (cutoff:3.500A) removed outlier: 7.202A pdb=" N THR D 366 " --> pdb=" O MET D 362 " (cutoff:3.500A) removed outlier: 5.428A pdb=" N MET D 362 " --> pdb=" O THR D 366 " (cutoff:3.500A) removed outlier: 6.682A pdb=" N SER D 368 " --> pdb=" O ILE D 360 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'C' and resid 399 through 401 removed outlier: 3.860A pdb=" N TYR C 441 " --> pdb=" O THR C 453 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'C' and resid 406 through 407 removed outlier: 3.747A pdb=" N SER C 487 " --> pdb=" O GLN C 407 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'D' and resid 389 through 390 removed outlier: 3.637A pdb=" N ILE D 389 " --> pdb=" O LEU E 378 " (cutoff:3.500A) removed outlier: 7.202A pdb=" N THR E 366 " --> pdb=" O MET E 362 " (cutoff:3.500A) removed outlier: 5.428A pdb=" N MET E 362 " --> pdb=" O THR E 366 " (cutoff:3.500A) removed outlier: 6.682A pdb=" N SER E 368 " --> pdb=" O ILE E 360 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'D' and resid 399 through 401 removed outlier: 3.861A pdb=" N TYR D 441 " --> pdb=" O THR D 453 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'D' and resid 406 through 407 removed outlier: 3.748A pdb=" N SER D 487 " --> pdb=" O GLN D 407 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'E' and resid 389 through 390 removed outlier: 7.202A pdb=" N THR F 366 " --> pdb=" O MET F 362 " (cutoff:3.500A) removed outlier: 5.429A pdb=" N MET F 362 " --> pdb=" O THR F 366 " (cutoff:3.500A) removed outlier: 6.682A pdb=" N SER F 368 " --> pdb=" O ILE F 360 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'E' and resid 399 through 401 removed outlier: 3.860A pdb=" N TYR E 441 " --> pdb=" O THR E 453 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'E' and resid 406 through 407 removed outlier: 3.746A pdb=" N SER E 487 " --> pdb=" O GLN E 407 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'F' and resid 389 through 390 removed outlier: 3.561A pdb=" N ILE F 389 " --> pdb=" O LEU G 378 " (cutoff:3.500A) removed outlier: 7.203A pdb=" N THR G 366 " --> pdb=" O MET G 362 " (cutoff:3.500A) removed outlier: 5.429A pdb=" N MET G 362 " --> pdb=" O THR G 366 " (cutoff:3.500A) removed outlier: 6.682A pdb=" N SER G 368 " --> pdb=" O ILE G 360 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'F' and resid 399 through 401 removed outlier: 3.861A pdb=" N TYR F 441 " --> pdb=" O THR F 453 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'F' and resid 406 through 407 removed outlier: 3.747A pdb=" N SER F 487 " --> pdb=" O GLN F 407 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'G' and resid 399 through 401 removed outlier: 3.860A pdb=" N TYR G 441 " --> pdb=" O THR G 453 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'G' and resid 406 through 407 removed outlier: 3.747A pdb=" N SER G 487 " --> pdb=" O GLN G 407 " (cutoff:3.500A) 589 hydrogen bonds defined for protein. 1743 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 4.24 Time building geometry restraints manager: 3.97 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.33: 2973 1.33 - 1.45: 3346 1.45 - 1.57: 8941 1.57 - 1.69: 0 1.69 - 1.81: 147 Bond restraints: 15407 Sorted by residual: bond pdb=" C PHE B 375 " pdb=" N PRO B 376 " ideal model delta sigma weight residual 1.334 1.205 0.129 2.34e-02 1.83e+03 3.05e+01 bond pdb=" C PHE A 375 " pdb=" N PRO A 376 " ideal model delta sigma weight residual 1.334 1.205 0.129 2.34e-02 1.83e+03 3.02e+01 bond pdb=" C PHE E 375 " pdb=" N PRO E 376 " ideal model delta sigma weight residual 1.334 1.206 0.128 2.34e-02 1.83e+03 3.01e+01 bond pdb=" C PHE C 375 " pdb=" N PRO C 376 " ideal model delta sigma weight residual 1.334 1.206 0.128 2.34e-02 1.83e+03 3.00e+01 bond pdb=" C PHE F 375 " pdb=" N PRO F 376 " ideal model delta sigma weight residual 1.334 1.206 0.128 2.34e-02 1.83e+03 3.00e+01 ... (remaining 15402 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.69: 19771 2.69 - 5.38: 880 5.38 - 8.07: 146 8.07 - 10.76: 49 10.76 - 13.45: 7 Bond angle restraints: 20853 Sorted by residual: angle pdb=" C LYS C 374 " pdb=" N PHE C 375 " pdb=" CA PHE C 375 " ideal model delta sigma weight residual 121.83 135.28 -13.45 1.56e+00 4.11e-01 7.43e+01 angle pdb=" C LYS D 374 " pdb=" N PHE D 375 " pdb=" CA PHE D 375 " ideal model delta sigma weight residual 121.83 135.26 -13.43 1.56e+00 4.11e-01 7.41e+01 angle pdb=" C LYS F 374 " pdb=" N PHE F 375 " pdb=" CA PHE F 375 " ideal model delta sigma weight residual 121.83 135.25 -13.42 1.56e+00 4.11e-01 7.40e+01 angle pdb=" C LYS E 374 " pdb=" N PHE E 375 " pdb=" CA PHE E 375 " ideal model delta sigma weight residual 121.83 135.23 -13.40 1.56e+00 4.11e-01 7.38e+01 angle pdb=" C LYS G 374 " pdb=" N PHE G 375 " pdb=" CA PHE G 375 " ideal model delta sigma weight residual 121.83 135.20 -13.37 1.56e+00 4.11e-01 7.35e+01 ... (remaining 20848 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 10.59: 7795 10.59 - 21.17: 1081 21.17 - 31.76: 287 31.76 - 42.34: 105 42.34 - 52.93: 42 Dihedral angle restraints: 9310 sinusoidal: 3563 harmonic: 5747 Sorted by residual: dihedral pdb=" CA TRP E 253 " pdb=" C TRP E 253 " pdb=" N PHE E 254 " pdb=" CA PHE E 254 " ideal model delta harmonic sigma weight residual 180.00 149.23 30.77 0 5.00e+00 4.00e-02 3.79e+01 dihedral pdb=" CA TRP B 253 " pdb=" C TRP B 253 " pdb=" N PHE B 254 " pdb=" CA PHE B 254 " ideal model delta harmonic sigma weight residual 180.00 149.31 30.69 0 5.00e+00 4.00e-02 3.77e+01 dihedral pdb=" CA TRP G 253 " pdb=" C TRP G 253 " pdb=" N PHE G 254 " pdb=" CA PHE G 254 " ideal model delta harmonic sigma weight residual 180.00 149.33 30.67 0 5.00e+00 4.00e-02 3.76e+01 ... (remaining 9307 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.059: 1556 0.059 - 0.117: 621 0.117 - 0.176: 283 0.176 - 0.234: 53 0.234 - 0.293: 14 Chirality restraints: 2527 Sorted by residual: chirality pdb=" CB ILE G 459 " pdb=" CA ILE G 459 " pdb=" CG1 ILE G 459 " pdb=" CG2 ILE G 459 " both_signs ideal model delta sigma weight residual False 2.64 2.35 0.29 2.00e-01 2.50e+01 2.15e+00 chirality pdb=" CB ILE F 459 " pdb=" CA ILE F 459 " pdb=" CG1 ILE F 459 " pdb=" CG2 ILE F 459 " both_signs ideal model delta sigma weight residual False 2.64 2.35 0.29 2.00e-01 2.50e+01 2.14e+00 chirality pdb=" CB ILE A 459 " pdb=" CA ILE A 459 " pdb=" CG1 ILE A 459 " pdb=" CG2 ILE A 459 " both_signs ideal model delta sigma weight residual False 2.64 2.35 0.29 2.00e-01 2.50e+01 2.14e+00 ... (remaining 2524 not shown) Planarity restraints: 2604 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA VAL F 355 " -0.016 2.00e-02 2.50e+03 3.14e-02 9.84e+00 pdb=" C VAL F 355 " 0.054 2.00e-02 2.50e+03 pdb=" O VAL F 355 " -0.021 2.00e-02 2.50e+03 pdb=" N GLU F 356 " -0.018 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA VAL B 355 " 0.016 2.00e-02 2.50e+03 3.13e-02 9.81e+00 pdb=" C VAL B 355 " -0.054 2.00e-02 2.50e+03 pdb=" O VAL B 355 " 0.020 2.00e-02 2.50e+03 pdb=" N GLU B 356 " 0.018 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA VAL A 355 " 0.016 2.00e-02 2.50e+03 3.13e-02 9.78e+00 pdb=" C VAL A 355 " -0.054 2.00e-02 2.50e+03 pdb=" O VAL A 355 " 0.020 2.00e-02 2.50e+03 pdb=" N GLU A 356 " 0.018 2.00e-02 2.50e+03 ... (remaining 2601 not shown) Histogram of nonbonded interaction distances: 2.15 - 2.70: 587 2.70 - 3.25: 14426 3.25 - 3.80: 23785 3.80 - 4.35: 31622 4.35 - 4.90: 51212 Nonbonded interactions: 121632 Sorted by model distance: nonbonded pdb=" OG1 THR A 491 " pdb=" OE2 GLU G 446 " model vdw 2.148 3.040 nonbonded pdb=" OE2 GLU C 446 " pdb=" OG1 THR D 491 " model vdw 2.215 3.040 nonbonded pdb=" OE2 GLU B 446 " pdb=" OG1 THR C 491 " model vdw 2.234 3.040 nonbonded pdb=" OE2 GLU F 446 " pdb=" OG1 THR G 491 " model vdw 2.249 3.040 nonbonded pdb=" OE2 GLU E 446 " pdb=" OG1 THR F 491 " model vdw 2.253 3.040 ... (remaining 121627 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' selection = chain 'F' selection = chain 'G' } 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: 0.700 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: 0.630 Check model and map are aligned: 0.110 Set scattering table: 0.130 Process input model: 30.680 Find NCS groups from input model: 0.520 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.490 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 35.310 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6646 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 : 0.011 0.129 15407 Z= 0.719 Angle : 1.350 13.450 20853 Z= 0.725 Chirality : 0.076 0.293 2527 Planarity : 0.007 0.046 2604 Dihedral : 11.789 52.927 5600 Min Nonbonded Distance : 2.148 Molprobity Statistics. All-atom Clashscore : 8.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.77 % Favored : 90.23 % Rotamer: Outliers : 1.40 % Allowed : 11.54 % Favored : 87.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.36 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -6.19 (0.13), residues: 1995 helix: -4.35 (0.08), residues: 973 sheet: -2.72 (0.30), residues: 224 loop : -4.01 (0.18), residues: 798 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.037 0.005 TRP C 397 HIS 0.004 0.002 HIS E 484 PHE 0.033 0.004 PHE A 323 TYR 0.033 0.005 TYR C 467 ARG 0.009 0.001 ARG F 398 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3990 Ramachandran restraints generated. 1995 Oldfield, 0 Emsley, 1995 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3990 Ramachandran restraints generated. 1995 Oldfield, 0 Emsley, 1995 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 321 residues out of total 1659 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 298 time to evaluate : 1.544 Fit side-chains REVERT: A 285 LYS cc_start: 0.7561 (ttmp) cc_final: 0.7151 (ttmm) REVERT: A 287 SER cc_start: 0.8504 (t) cc_final: 0.8234 (p) REVERT: B 266 MET cc_start: 0.5081 (ttm) cc_final: 0.4845 (ttp) REVERT: B 278 GLU cc_start: 0.6243 (mt-10) cc_final: 0.6039 (tt0) REVERT: B 285 LYS cc_start: 0.7731 (ttmp) cc_final: 0.7232 (tttp) REVERT: B 287 SER cc_start: 0.8719 (t) cc_final: 0.8355 (p) REVERT: B 428 ASN cc_start: 0.7766 (t160) cc_final: 0.7544 (t0) REVERT: B 432 PHE cc_start: 0.6563 (t80) cc_final: 0.6113 (t80) REVERT: B 436 GLU cc_start: 0.7900 (mp0) cc_final: 0.7685 (mt-10) REVERT: C 266 MET cc_start: 0.5471 (ttm) cc_final: 0.5221 (ttp) REVERT: C 287 SER cc_start: 0.8635 (t) cc_final: 0.8251 (p) REVERT: D 287 SER cc_start: 0.8700 (t) cc_final: 0.8351 (p) REVERT: D 346 MET cc_start: 0.8005 (mmt) cc_final: 0.7769 (mmm) REVERT: D 360 ILE cc_start: 0.7778 (mt) cc_final: 0.7061 (mt) REVERT: D 432 PHE cc_start: 0.6604 (t80) cc_final: 0.6046 (t80) REVERT: E 266 MET cc_start: 0.5433 (ttm) cc_final: 0.5159 (ttp) REVERT: E 278 GLU cc_start: 0.6805 (mt-10) cc_final: 0.6472 (tt0) REVERT: E 285 LYS cc_start: 0.7733 (ttmp) cc_final: 0.7282 (ttmt) REVERT: E 287 SER cc_start: 0.8567 (t) cc_final: 0.8203 (p) REVERT: E 346 MET cc_start: 0.7997 (mmt) cc_final: 0.7742 (mmm) REVERT: E 360 ILE cc_start: 0.8039 (mt) cc_final: 0.7673 (mt) REVERT: E 406 LEU cc_start: 0.6624 (OUTLIER) cc_final: 0.6391 (pp) REVERT: E 429 THR cc_start: 0.7346 (p) cc_final: 0.7142 (p) REVERT: E 460 ARG cc_start: 0.7117 (tpt170) cc_final: 0.6885 (tpt90) REVERT: E 467 TYR cc_start: 0.8143 (m-80) cc_final: 0.7792 (m-80) REVERT: F 266 MET cc_start: 0.5665 (ttm) cc_final: 0.5406 (ttp) REVERT: F 287 SER cc_start: 0.8537 (t) cc_final: 0.7907 (p) REVERT: F 346 MET cc_start: 0.7964 (mmt) cc_final: 0.7499 (mmm) REVERT: F 428 ASN cc_start: 0.7763 (t160) cc_final: 0.7466 (t0) REVERT: F 429 THR cc_start: 0.7074 (p) cc_final: 0.6774 (p) REVERT: F 446 GLU cc_start: 0.7117 (tt0) cc_final: 0.6873 (tt0) REVERT: F 474 LEU cc_start: 0.5140 (OUTLIER) cc_final: 0.4909 (tp) REVERT: F 484 HIS cc_start: 0.7273 (m-70) cc_final: 0.6889 (m-70) REVERT: G 266 MET cc_start: 0.5724 (ttm) cc_final: 0.5471 (ttp) REVERT: G 278 GLU cc_start: 0.6768 (mt-10) cc_final: 0.6328 (tp30) REVERT: G 285 LYS cc_start: 0.7752 (ttmp) cc_final: 0.7297 (tttp) REVERT: G 287 SER cc_start: 0.8673 (t) cc_final: 0.8151 (p) REVERT: G 346 MET cc_start: 0.7907 (mmt) cc_final: 0.7535 (mmm) REVERT: G 428 ASN cc_start: 0.7595 (t160) cc_final: 0.7385 (t0) REVERT: G 429 THR cc_start: 0.7283 (p) cc_final: 0.7013 (p) REVERT: G 436 GLU cc_start: 0.7708 (mp0) cc_final: 0.7345 (mt-10) REVERT: G 460 ARG cc_start: 0.6887 (tpt170) cc_final: 0.6673 (tpt90) outliers start: 23 outliers final: 0 residues processed: 316 average time/residue: 0.3017 time to fit residues: 135.7512 Evaluate side-chains 209 residues out of total 1659 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 207 time to evaluate : 2.010 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 406 LEU Chi-restraints excluded: chain F residue 474 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 196 random chunks: chunk 165 optimal weight: 1.9990 chunk 148 optimal weight: 0.8980 chunk 82 optimal weight: 1.9990 chunk 50 optimal weight: 0.9990 chunk 100 optimal weight: 0.9980 chunk 79 optimal weight: 1.9990 chunk 153 optimal weight: 0.7980 chunk 59 optimal weight: 4.9990 chunk 93 optimal weight: 0.8980 chunk 114 optimal weight: 7.9990 chunk 177 optimal weight: 1.9990 overall best weight: 0.9182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 358 GLN A 407 GLN A 457 ASN B 358 GLN B 407 GLN B 428 ASN B 457 ASN B 470 GLN C 358 GLN C 407 GLN C 457 ASN C 470 GLN D 358 GLN D 457 ASN D 470 GLN E 358 GLN E 407 GLN E 457 ASN F 358 GLN F 407 GLN F 428 ASN F 457 ASN G 358 GLN G 407 GLN G 428 ASN G 457 ASN Total number of N/Q/H flips: 26 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6584 moved from start: 0.2003 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 15407 Z= 0.226 Angle : 0.722 9.612 20853 Z= 0.379 Chirality : 0.047 0.153 2527 Planarity : 0.005 0.039 2604 Dihedral : 6.734 43.753 2118 Min Nonbonded Distance : 2.507 Molprobity Statistics. All-atom Clashscore : 10.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.62 % Favored : 92.38 % Rotamer: Outliers : 3.85 % Allowed : 13.13 % Favored : 83.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -5.20 (0.15), residues: 1995 helix: -3.09 (0.13), residues: 973 sheet: -1.84 (0.32), residues: 238 loop : -4.36 (0.17), residues: 784 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP G 397 HIS 0.002 0.001 HIS C 484 PHE 0.012 0.002 PHE G 323 TYR 0.009 0.001 TYR G 467 ARG 0.004 0.000 ARG F 398 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3990 Ramachandran restraints generated. 1995 Oldfield, 0 Emsley, 1995 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3990 Ramachandran restraints generated. 1995 Oldfield, 0 Emsley, 1995 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 314 residues out of total 1659 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 251 time to evaluate : 1.679 Fit side-chains revert: symmetry clash REVERT: A 250 SER cc_start: 0.7241 (m) cc_final: 0.6795 (t) REVERT: A 253 TRP cc_start: 0.6923 (m-90) cc_final: 0.6012 (m100) REVERT: A 287 SER cc_start: 0.8411 (t) cc_final: 0.7736 (p) REVERT: A 308 GLN cc_start: 0.8002 (pm20) cc_final: 0.7727 (pm20) REVERT: A 474 LEU cc_start: 0.5140 (OUTLIER) cc_final: 0.4905 (tt) REVERT: A 484 HIS cc_start: 0.6973 (m-70) cc_final: 0.6406 (m90) REVERT: B 250 SER cc_start: 0.7268 (m) cc_final: 0.6905 (t) REVERT: B 266 MET cc_start: 0.4849 (ttm) cc_final: 0.4499 (ttp) REVERT: B 285 LYS cc_start: 0.7806 (ttmp) cc_final: 0.7288 (tttp) REVERT: B 287 SER cc_start: 0.8295 (t) cc_final: 0.7707 (p) REVERT: B 296 LEU cc_start: 0.7902 (OUTLIER) cc_final: 0.7682 (tp) REVERT: B 378 LEU cc_start: 0.8301 (tt) cc_final: 0.8048 (mp) REVERT: B 413 MET cc_start: 0.5430 (tpp) cc_final: 0.5161 (mpp) REVERT: B 432 PHE cc_start: 0.6314 (t80) cc_final: 0.5803 (t80) REVERT: B 436 GLU cc_start: 0.7844 (mp0) cc_final: 0.7546 (mt-10) REVERT: B 474 LEU cc_start: 0.5235 (OUTLIER) cc_final: 0.4977 (tt) REVERT: C 287 SER cc_start: 0.8298 (t) cc_final: 0.7701 (p) REVERT: C 308 GLN cc_start: 0.7969 (pm20) cc_final: 0.7711 (pm20) REVERT: D 278 GLU cc_start: 0.6911 (tp30) cc_final: 0.6160 (tt0) REVERT: D 287 SER cc_start: 0.8444 (t) cc_final: 0.7897 (p) REVERT: D 460 ARG cc_start: 0.7088 (tpt170) cc_final: 0.6719 (tpm170) REVERT: E 250 SER cc_start: 0.6737 (m) cc_final: 0.6404 (t) REVERT: E 278 GLU cc_start: 0.6958 (mt-10) cc_final: 0.6620 (tt0) REVERT: E 285 LYS cc_start: 0.7624 (ttmp) cc_final: 0.7087 (ttmt) REVERT: E 287 SER cc_start: 0.8359 (t) cc_final: 0.7769 (p) REVERT: E 338 MET cc_start: 0.7366 (mmp) cc_final: 0.6864 (mmp) REVERT: E 413 MET cc_start: 0.5103 (tpp) cc_final: 0.4868 (mpp) REVERT: E 479 LYS cc_start: 0.5227 (mtpt) cc_final: 0.4657 (mttp) REVERT: E 484 HIS cc_start: 0.6741 (m-70) cc_final: 0.6326 (m90) REVERT: F 287 SER cc_start: 0.8236 (t) cc_final: 0.7617 (p) REVERT: F 292 PHE cc_start: 0.6744 (t80) cc_final: 0.6454 (t80) REVERT: F 346 MET cc_start: 0.7626 (mmt) cc_final: 0.7368 (mmm) REVERT: F 484 HIS cc_start: 0.6811 (m-70) cc_final: 0.6224 (m90) REVERT: G 266 MET cc_start: 0.5366 (ttm) cc_final: 0.5123 (ttp) REVERT: G 278 GLU cc_start: 0.6817 (mt-10) cc_final: 0.6439 (tt0) REVERT: G 285 LYS cc_start: 0.7718 (ttmp) cc_final: 0.7177 (tttp) REVERT: G 287 SER cc_start: 0.8450 (t) cc_final: 0.7826 (p) REVERT: G 338 MET cc_start: 0.7395 (mmp) cc_final: 0.7120 (mmp) REVERT: G 378 LEU cc_start: 0.8135 (tt) cc_final: 0.7910 (mp) REVERT: G 413 MET cc_start: 0.5180 (mpp) cc_final: 0.4712 (mpp) REVERT: G 436 GLU cc_start: 0.7765 (mp0) cc_final: 0.7347 (mt-10) REVERT: G 460 ARG cc_start: 0.6908 (tpt170) cc_final: 0.6612 (tpm170) outliers start: 63 outliers final: 32 residues processed: 297 average time/residue: 0.2754 time to fit residues: 123.7456 Evaluate side-chains 265 residues out of total 1659 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 230 time to evaluate : 1.788 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 281 LEU Chi-restraints excluded: chain A residue 319 VAL Chi-restraints excluded: chain A residue 368 SER Chi-restraints excluded: chain A residue 408 ILE Chi-restraints excluded: chain A residue 474 LEU Chi-restraints excluded: chain B residue 296 LEU Chi-restraints excluded: chain B residue 319 VAL Chi-restraints excluded: chain B residue 368 SER Chi-restraints excluded: chain B residue 408 ILE Chi-restraints excluded: chain B residue 474 LEU Chi-restraints excluded: chain C residue 281 LEU Chi-restraints excluded: chain C residue 296 LEU Chi-restraints excluded: chain C residue 319 VAL Chi-restraints excluded: chain C residue 368 SER Chi-restraints excluded: chain C residue 388 VAL Chi-restraints excluded: chain C residue 408 ILE Chi-restraints excluded: chain D residue 281 LEU Chi-restraints excluded: chain D residue 296 LEU Chi-restraints excluded: chain D residue 319 VAL Chi-restraints excluded: chain D residue 368 SER Chi-restraints excluded: chain D residue 408 ILE Chi-restraints excluded: chain E residue 229 VAL Chi-restraints excluded: chain E residue 296 LEU Chi-restraints excluded: chain E residue 313 VAL Chi-restraints excluded: chain E residue 319 VAL Chi-restraints excluded: chain E residue 378 LEU Chi-restraints excluded: chain E residue 406 LEU Chi-restraints excluded: chain E residue 408 ILE Chi-restraints excluded: chain F residue 281 LEU Chi-restraints excluded: chain F residue 319 VAL Chi-restraints excluded: chain F residue 368 SER Chi-restraints excluded: chain F residue 378 LEU Chi-restraints excluded: chain F residue 388 VAL Chi-restraints excluded: chain F residue 408 ILE Chi-restraints excluded: chain G residue 319 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 196 random chunks: chunk 98 optimal weight: 1.9990 chunk 55 optimal weight: 6.9990 chunk 148 optimal weight: 0.7980 chunk 121 optimal weight: 1.9990 chunk 49 optimal weight: 1.9990 chunk 178 optimal weight: 0.8980 chunk 192 optimal weight: 3.9990 chunk 158 optimal weight: 1.9990 chunk 176 optimal weight: 0.9980 chunk 60 optimal weight: 0.0770 chunk 143 optimal weight: 6.9990 overall best weight: 0.9540 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 470 GLN B 358 GLN B 470 GLN C 358 GLN C 470 GLN D 339 GLN D 358 GLN D 484 HIS F 358 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6583 moved from start: 0.2687 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 15407 Z= 0.222 Angle : 0.672 7.550 20853 Z= 0.348 Chirality : 0.046 0.157 2527 Planarity : 0.004 0.032 2604 Dihedral : 6.089 37.915 2116 Min Nonbonded Distance : 2.496 Molprobity Statistics. All-atom Clashscore : 10.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.67 % Favored : 91.33 % Rotamer: Outliers : 6.41 % Allowed : 11.84 % Favored : 81.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.62 (0.16), residues: 1995 helix: -2.34 (0.15), residues: 938 sheet: -1.78 (0.32), residues: 238 loop : -4.35 (0.16), residues: 819 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP D 397 HIS 0.003 0.001 HIS E 484 PHE 0.011 0.001 PHE G 323 TYR 0.007 0.001 TYR E 441 ARG 0.005 0.001 ARG E 426 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3990 Ramachandran restraints generated. 1995 Oldfield, 0 Emsley, 1995 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3990 Ramachandran restraints generated. 1995 Oldfield, 0 Emsley, 1995 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 343 residues out of total 1659 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 105 poor density : 238 time to evaluate : 1.682 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 253 TRP cc_start: 0.6787 (m-90) cc_final: 0.5853 (m100) REVERT: A 278 GLU cc_start: 0.6393 (tp30) cc_final: 0.5688 (mt-10) REVERT: A 287 SER cc_start: 0.8388 (t) cc_final: 0.7667 (p) REVERT: A 413 MET cc_start: 0.5163 (tpp) cc_final: 0.4830 (mpp) REVERT: A 474 LEU cc_start: 0.5236 (OUTLIER) cc_final: 0.4938 (tt) REVERT: B 270 LYS cc_start: 0.5734 (OUTLIER) cc_final: 0.5388 (tmtt) REVERT: B 278 GLU cc_start: 0.6818 (tp30) cc_final: 0.6377 (mt-10) REVERT: B 287 SER cc_start: 0.8305 (t) cc_final: 0.7719 (p) REVERT: B 296 LEU cc_start: 0.7833 (OUTLIER) cc_final: 0.7604 (tp) REVERT: C 287 SER cc_start: 0.8301 (t) cc_final: 0.7698 (p) REVERT: C 297 MET cc_start: 0.8603 (ttp) cc_final: 0.8400 (mtp) REVERT: C 308 GLN cc_start: 0.7963 (pm20) cc_final: 0.7683 (pm20) REVERT: C 447 LYS cc_start: 0.6794 (tptt) cc_final: 0.5283 (tttm) REVERT: D 270 LYS cc_start: 0.5990 (OUTLIER) cc_final: 0.5508 (tmtt) REVERT: D 287 SER cc_start: 0.8464 (t) cc_final: 0.7872 (p) REVERT: D 296 LEU cc_start: 0.7770 (OUTLIER) cc_final: 0.7533 (tp) REVERT: D 484 HIS cc_start: 0.6922 (m-70) cc_final: 0.6355 (m90) REVERT: E 278 GLU cc_start: 0.6961 (mt-10) cc_final: 0.6615 (tt0) REVERT: E 287 SER cc_start: 0.8215 (t) cc_final: 0.7584 (p) REVERT: E 479 LYS cc_start: 0.5306 (mtpt) cc_final: 0.4783 (mttp) REVERT: F 287 SER cc_start: 0.8305 (t) cc_final: 0.7647 (p) REVERT: F 292 PHE cc_start: 0.6835 (t80) cc_final: 0.6559 (t80) REVERT: F 338 MET cc_start: 0.7411 (mmp) cc_final: 0.7061 (mmp) REVERT: F 446 GLU cc_start: 0.6369 (tt0) cc_final: 0.6128 (tt0) REVERT: G 270 LYS cc_start: 0.5788 (OUTLIER) cc_final: 0.5476 (tmtt) REVERT: G 285 LYS cc_start: 0.7660 (ttmp) cc_final: 0.7058 (tttp) REVERT: G 287 SER cc_start: 0.8461 (t) cc_final: 0.7775 (p) REVERT: G 406 LEU cc_start: 0.6050 (OUTLIER) cc_final: 0.5836 (pp) REVERT: G 413 MET cc_start: 0.5256 (mpp) cc_final: 0.4822 (mpp) REVERT: G 436 GLU cc_start: 0.7792 (mp0) cc_final: 0.7345 (mt-10) outliers start: 105 outliers final: 68 residues processed: 322 average time/residue: 0.2527 time to fit residues: 124.0028 Evaluate side-chains 280 residues out of total 1659 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 75 poor density : 205 time to evaluate : 1.755 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 270 LYS Chi-restraints excluded: chain A residue 281 LEU Chi-restraints excluded: chain A residue 313 VAL Chi-restraints excluded: chain A residue 319 VAL Chi-restraints excluded: chain A residue 355 VAL Chi-restraints excluded: chain A residue 368 SER Chi-restraints excluded: chain A residue 369 LEU Chi-restraints excluded: chain A residue 406 LEU Chi-restraints excluded: chain A residue 408 ILE Chi-restraints excluded: chain A residue 433 LEU Chi-restraints excluded: chain A residue 474 LEU Chi-restraints excluded: chain B residue 270 LYS Chi-restraints excluded: chain B residue 281 LEU Chi-restraints excluded: chain B residue 296 LEU Chi-restraints excluded: chain B residue 313 VAL Chi-restraints excluded: chain B residue 319 VAL Chi-restraints excluded: chain B residue 355 VAL Chi-restraints excluded: chain B residue 368 SER Chi-restraints excluded: chain B residue 369 LEU Chi-restraints excluded: chain B residue 408 ILE Chi-restraints excluded: chain B residue 442 LEU Chi-restraints excluded: chain C residue 270 LYS Chi-restraints excluded: chain C residue 281 LEU Chi-restraints excluded: chain C residue 313 VAL Chi-restraints excluded: chain C residue 319 VAL Chi-restraints excluded: chain C residue 355 VAL Chi-restraints excluded: chain C residue 368 SER Chi-restraints excluded: chain C residue 369 LEU Chi-restraints excluded: chain C residue 388 VAL Chi-restraints excluded: chain C residue 408 ILE Chi-restraints excluded: chain C residue 433 LEU Chi-restraints excluded: chain C residue 442 LEU Chi-restraints excluded: chain D residue 270 LYS Chi-restraints excluded: chain D residue 281 LEU Chi-restraints excluded: chain D residue 296 LEU Chi-restraints excluded: chain D residue 313 VAL Chi-restraints excluded: chain D residue 319 VAL Chi-restraints excluded: chain D residue 355 VAL Chi-restraints excluded: chain D residue 368 SER Chi-restraints excluded: chain D residue 369 LEU Chi-restraints excluded: chain D residue 378 LEU Chi-restraints excluded: chain D residue 408 ILE Chi-restraints excluded: chain D residue 446 GLU Chi-restraints excluded: chain E residue 270 LYS Chi-restraints excluded: chain E residue 281 LEU Chi-restraints excluded: chain E residue 296 LEU Chi-restraints excluded: chain E residue 313 VAL Chi-restraints excluded: chain E residue 319 VAL Chi-restraints excluded: chain E residue 355 VAL Chi-restraints excluded: chain E residue 369 LEU Chi-restraints excluded: chain E residue 378 LEU Chi-restraints excluded: chain E residue 406 LEU Chi-restraints excluded: chain E residue 408 ILE Chi-restraints excluded: chain E residue 433 LEU Chi-restraints excluded: chain F residue 270 LYS Chi-restraints excluded: chain F residue 281 LEU Chi-restraints excluded: chain F residue 313 VAL Chi-restraints excluded: chain F residue 319 VAL Chi-restraints excluded: chain F residue 355 VAL Chi-restraints excluded: chain F residue 368 SER Chi-restraints excluded: chain F residue 369 LEU Chi-restraints excluded: chain F residue 378 LEU Chi-restraints excluded: chain F residue 408 ILE Chi-restraints excluded: chain F residue 442 LEU Chi-restraints excluded: chain G residue 229 VAL Chi-restraints excluded: chain G residue 249 LEU Chi-restraints excluded: chain G residue 270 LYS Chi-restraints excluded: chain G residue 281 LEU Chi-restraints excluded: chain G residue 313 VAL Chi-restraints excluded: chain G residue 316 VAL Chi-restraints excluded: chain G residue 319 VAL Chi-restraints excluded: chain G residue 355 VAL Chi-restraints excluded: chain G residue 369 LEU Chi-restraints excluded: chain G residue 406 LEU Chi-restraints excluded: chain G residue 408 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 196 random chunks: chunk 176 optimal weight: 2.9990 chunk 134 optimal weight: 0.7980 chunk 92 optimal weight: 1.9990 chunk 19 optimal weight: 10.0000 chunk 85 optimal weight: 5.9990 chunk 119 optimal weight: 4.9990 chunk 178 optimal weight: 1.9990 chunk 189 optimal weight: 9.9990 chunk 93 optimal weight: 3.9990 chunk 169 optimal weight: 5.9990 chunk 51 optimal weight: 7.9990 overall best weight: 2.3588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 358 GLN B 470 GLN C 484 HIS E 358 GLN G 358 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6700 moved from start: 0.3115 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.059 15407 Z= 0.394 Angle : 0.751 8.943 20853 Z= 0.388 Chirality : 0.050 0.150 2527 Planarity : 0.004 0.039 2604 Dihedral : 6.401 38.707 2116 Min Nonbonded Distance : 2.460 Molprobity Statistics. All-atom Clashscore : 11.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.78 % Favored : 89.22 % Rotamer: Outliers : 6.84 % Allowed : 15.45 % Favored : 77.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.51 (0.16), residues: 1995 helix: -2.19 (0.15), residues: 980 sheet: -1.84 (0.32), residues: 238 loop : -4.42 (0.17), residues: 777 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP C 397 HIS 0.004 0.001 HIS D 484 PHE 0.014 0.002 PHE C 323 TYR 0.008 0.001 TYR D 467 ARG 0.004 0.001 ARG D 426 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3990 Ramachandran restraints generated. 1995 Oldfield, 0 Emsley, 1995 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3990 Ramachandran restraints generated. 1995 Oldfield, 0 Emsley, 1995 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 341 residues out of total 1659 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 112 poor density : 229 time to evaluate : 1.747 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 278 GLU cc_start: 0.6554 (tp30) cc_final: 0.5815 (mt-10) REVERT: A 287 SER cc_start: 0.8420 (t) cc_final: 0.7688 (p) REVERT: A 308 GLN cc_start: 0.8036 (pm20) cc_final: 0.7657 (pm20) REVERT: A 474 LEU cc_start: 0.5867 (OUTLIER) cc_final: 0.5303 (tt) REVERT: B 270 LYS cc_start: 0.5739 (OUTLIER) cc_final: 0.5424 (tmtt) REVERT: B 285 LYS cc_start: 0.7864 (ttmp) cc_final: 0.7158 (tttp) REVERT: B 287 SER cc_start: 0.8379 (t) cc_final: 0.7732 (p) REVERT: B 296 LEU cc_start: 0.7967 (OUTLIER) cc_final: 0.7680 (tp) REVERT: B 432 PHE cc_start: 0.6919 (t80) cc_final: 0.6688 (t80) REVERT: B 436 GLU cc_start: 0.7699 (mt-10) cc_final: 0.7433 (mt-10) REVERT: C 270 LYS cc_start: 0.5606 (OUTLIER) cc_final: 0.5347 (tmtt) REVERT: C 287 SER cc_start: 0.8443 (t) cc_final: 0.7817 (p) REVERT: C 297 MET cc_start: 0.8708 (ttp) cc_final: 0.8368 (mtp) REVERT: C 338 MET cc_start: 0.7474 (mmp) cc_final: 0.7188 (mmp) REVERT: C 361 GLU cc_start: 0.7394 (mt-10) cc_final: 0.7175 (mt-10) REVERT: C 447 LYS cc_start: 0.6652 (tptt) cc_final: 0.5191 (tttm) REVERT: D 270 LYS cc_start: 0.5987 (OUTLIER) cc_final: 0.5523 (tmtt) REVERT: D 285 LYS cc_start: 0.7611 (ttmp) cc_final: 0.6929 (tttp) REVERT: D 287 SER cc_start: 0.8560 (t) cc_final: 0.7866 (p) REVERT: D 338 MET cc_start: 0.7688 (mmp) cc_final: 0.7269 (mmp) REVERT: D 356 GLU cc_start: 0.7849 (tm-30) cc_final: 0.7442 (tm-30) REVERT: D 459 ILE cc_start: 0.7108 (tp) cc_final: 0.6836 (tp) REVERT: E 278 GLU cc_start: 0.7012 (mt-10) cc_final: 0.6705 (tt0) REVERT: E 285 LYS cc_start: 0.7643 (ttmp) cc_final: 0.7033 (ttmt) REVERT: E 287 SER cc_start: 0.8280 (t) cc_final: 0.7581 (p) REVERT: F 287 SER cc_start: 0.8398 (t) cc_final: 0.7738 (p) REVERT: F 413 MET cc_start: 0.5429 (ptp) cc_final: 0.5057 (tpp) REVERT: G 270 LYS cc_start: 0.5710 (OUTLIER) cc_final: 0.5410 (tmtt) REVERT: G 285 LYS cc_start: 0.7564 (ttmp) cc_final: 0.6936 (tttp) REVERT: G 287 SER cc_start: 0.8596 (t) cc_final: 0.7927 (p) REVERT: G 406 LEU cc_start: 0.5935 (OUTLIER) cc_final: 0.5714 (pp) REVERT: G 436 GLU cc_start: 0.7888 (mp0) cc_final: 0.7466 (mt-10) REVERT: G 463 LYS cc_start: 0.6128 (tptm) cc_final: 0.5753 (tptm) outliers start: 112 outliers final: 81 residues processed: 320 average time/residue: 0.2733 time to fit residues: 132.7369 Evaluate side-chains 300 residues out of total 1659 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 88 poor density : 212 time to evaluate : 1.893 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 217 VAL Chi-restraints excluded: chain A residue 270 LYS Chi-restraints excluded: chain A residue 281 LEU Chi-restraints excluded: chain A residue 313 VAL Chi-restraints excluded: chain A residue 319 VAL Chi-restraints excluded: chain A residue 355 VAL Chi-restraints excluded: chain A residue 368 SER Chi-restraints excluded: chain A residue 369 LEU Chi-restraints excluded: chain A residue 408 ILE Chi-restraints excluded: chain A residue 433 LEU Chi-restraints excluded: chain A residue 442 LEU Chi-restraints excluded: chain A residue 474 LEU Chi-restraints excluded: chain B residue 217 VAL Chi-restraints excluded: chain B residue 270 LYS Chi-restraints excluded: chain B residue 280 VAL Chi-restraints excluded: chain B residue 281 LEU Chi-restraints excluded: chain B residue 296 LEU Chi-restraints excluded: chain B residue 313 VAL Chi-restraints excluded: chain B residue 319 VAL Chi-restraints excluded: chain B residue 355 VAL Chi-restraints excluded: chain B residue 368 SER Chi-restraints excluded: chain B residue 408 ILE Chi-restraints excluded: chain B residue 433 LEU Chi-restraints excluded: chain B residue 442 LEU Chi-restraints excluded: chain C residue 217 VAL Chi-restraints excluded: chain C residue 249 LEU Chi-restraints excluded: chain C residue 270 LYS Chi-restraints excluded: chain C residue 280 VAL Chi-restraints excluded: chain C residue 281 LEU Chi-restraints excluded: chain C residue 313 VAL Chi-restraints excluded: chain C residue 319 VAL Chi-restraints excluded: chain C residue 355 VAL Chi-restraints excluded: chain C residue 368 SER Chi-restraints excluded: chain C residue 369 LEU Chi-restraints excluded: chain C residue 370 LEU Chi-restraints excluded: chain C residue 388 VAL Chi-restraints excluded: chain C residue 406 LEU Chi-restraints excluded: chain C residue 408 ILE Chi-restraints excluded: chain C residue 433 LEU Chi-restraints excluded: chain C residue 442 LEU Chi-restraints excluded: chain D residue 217 VAL Chi-restraints excluded: chain D residue 249 LEU Chi-restraints excluded: chain D residue 270 LYS Chi-restraints excluded: chain D residue 281 LEU Chi-restraints excluded: chain D residue 296 LEU Chi-restraints excluded: chain D residue 313 VAL Chi-restraints excluded: chain D residue 319 VAL Chi-restraints excluded: chain D residue 368 SER Chi-restraints excluded: chain D residue 442 LEU Chi-restraints excluded: chain E residue 217 VAL Chi-restraints excluded: chain E residue 229 VAL Chi-restraints excluded: chain E residue 270 LYS Chi-restraints excluded: chain E residue 280 VAL Chi-restraints excluded: chain E residue 281 LEU Chi-restraints excluded: chain E residue 296 LEU Chi-restraints excluded: chain E residue 313 VAL Chi-restraints excluded: chain E residue 319 VAL Chi-restraints excluded: chain E residue 355 VAL Chi-restraints excluded: chain E residue 369 LEU Chi-restraints excluded: chain E residue 378 LEU Chi-restraints excluded: chain E residue 408 ILE Chi-restraints excluded: chain F residue 217 VAL Chi-restraints excluded: chain F residue 270 LYS Chi-restraints excluded: chain F residue 280 VAL Chi-restraints excluded: chain F residue 281 LEU Chi-restraints excluded: chain F residue 313 VAL Chi-restraints excluded: chain F residue 319 VAL Chi-restraints excluded: chain F residue 355 VAL Chi-restraints excluded: chain F residue 368 SER Chi-restraints excluded: chain F residue 370 LEU Chi-restraints excluded: chain F residue 378 LEU Chi-restraints excluded: chain F residue 408 ILE Chi-restraints excluded: chain F residue 433 LEU Chi-restraints excluded: chain F residue 442 LEU Chi-restraints excluded: chain G residue 217 VAL Chi-restraints excluded: chain G residue 229 VAL Chi-restraints excluded: chain G residue 249 LEU Chi-restraints excluded: chain G residue 270 LYS Chi-restraints excluded: chain G residue 281 LEU Chi-restraints excluded: chain G residue 313 VAL Chi-restraints excluded: chain G residue 316 VAL Chi-restraints excluded: chain G residue 319 VAL Chi-restraints excluded: chain G residue 355 VAL Chi-restraints excluded: chain G residue 406 LEU Chi-restraints excluded: chain G residue 408 ILE Chi-restraints excluded: chain G residue 433 LEU Chi-restraints excluded: chain G residue 442 LEU Chi-restraints excluded: chain G residue 469 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 196 random chunks: chunk 157 optimal weight: 0.9990 chunk 107 optimal weight: 8.9990 chunk 2 optimal weight: 6.9990 chunk 141 optimal weight: 4.9990 chunk 78 optimal weight: 7.9990 chunk 161 optimal weight: 0.9990 chunk 130 optimal weight: 0.7980 chunk 0 optimal weight: 9.9990 chunk 96 optimal weight: 0.6980 chunk 170 optimal weight: 1.9990 chunk 47 optimal weight: 3.9990 overall best weight: 1.0986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 470 GLN B 470 GLN C 470 GLN C 484 HIS D 484 HIS F 470 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6633 moved from start: 0.3446 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 15407 Z= 0.232 Angle : 0.663 8.212 20853 Z= 0.340 Chirality : 0.046 0.152 2527 Planarity : 0.003 0.037 2604 Dihedral : 5.810 18.713 2114 Min Nonbonded Distance : 2.486 Molprobity Statistics. All-atom Clashscore : 10.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.32 % Favored : 91.68 % Rotamer: Outliers : 6.47 % Allowed : 17.40 % Favored : 76.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.18 (0.16), residues: 1995 helix: -1.85 (0.16), residues: 980 sheet: -1.66 (0.32), residues: 231 loop : -4.34 (0.16), residues: 784 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP D 397 HIS 0.002 0.001 HIS A 484 PHE 0.012 0.001 PHE F 432 TYR 0.005 0.001 TYR D 467 ARG 0.004 0.000 ARG E 426 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3990 Ramachandran restraints generated. 1995 Oldfield, 0 Emsley, 1995 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3990 Ramachandran restraints generated. 1995 Oldfield, 0 Emsley, 1995 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 323 residues out of total 1659 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 106 poor density : 217 time to evaluate : 1.698 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 278 GLU cc_start: 0.6492 (tp30) cc_final: 0.5780 (mt-10) REVERT: A 287 SER cc_start: 0.8294 (t) cc_final: 0.7563 (p) REVERT: A 474 LEU cc_start: 0.5605 (OUTLIER) cc_final: 0.5031 (tt) REVERT: B 285 LYS cc_start: 0.7928 (ttmp) cc_final: 0.7159 (tttp) REVERT: B 287 SER cc_start: 0.8425 (t) cc_final: 0.7754 (p) REVERT: B 432 PHE cc_start: 0.6588 (t80) cc_final: 0.6383 (t80) REVERT: C 270 LYS cc_start: 0.5534 (OUTLIER) cc_final: 0.5287 (tmtt) REVERT: C 287 SER cc_start: 0.8446 (t) cc_final: 0.7785 (p) REVERT: C 297 MET cc_start: 0.8727 (ttp) cc_final: 0.8309 (mtp) REVERT: C 338 MET cc_start: 0.7389 (mmp) cc_final: 0.6987 (mmp) REVERT: C 413 MET cc_start: 0.5180 (tpp) cc_final: 0.4593 (mpp) REVERT: C 447 LYS cc_start: 0.6622 (tptt) cc_final: 0.5194 (tttm) REVERT: D 285 LYS cc_start: 0.7558 (ttmp) cc_final: 0.6876 (tttp) REVERT: D 287 SER cc_start: 0.8498 (t) cc_final: 0.7810 (p) REVERT: D 296 LEU cc_start: 0.7726 (OUTLIER) cc_final: 0.7483 (tp) REVERT: D 338 MET cc_start: 0.7641 (mmp) cc_final: 0.7135 (mmp) REVERT: D 459 ILE cc_start: 0.7094 (tp) cc_final: 0.6852 (tp) REVERT: E 278 GLU cc_start: 0.7013 (mt-10) cc_final: 0.6670 (tt0) REVERT: E 285 LYS cc_start: 0.7536 (ttmp) cc_final: 0.6857 (ttmt) REVERT: E 287 SER cc_start: 0.8076 (t) cc_final: 0.7348 (p) REVERT: E 368 SER cc_start: 0.8748 (OUTLIER) cc_final: 0.8463 (m) REVERT: E 479 LYS cc_start: 0.5393 (mtpt) cc_final: 0.4755 (mttm) REVERT: F 287 SER cc_start: 0.8363 (t) cc_final: 0.7755 (p) REVERT: F 338 MET cc_start: 0.7670 (mmp) cc_final: 0.7172 (mmp) REVERT: F 413 MET cc_start: 0.5405 (OUTLIER) cc_final: 0.4851 (tpt) REVERT: G 270 LYS cc_start: 0.5686 (OUTLIER) cc_final: 0.5384 (tmtt) REVERT: G 285 LYS cc_start: 0.7622 (ttmp) cc_final: 0.7002 (tttp) REVERT: G 287 SER cc_start: 0.8402 (t) cc_final: 0.7707 (p) REVERT: G 406 LEU cc_start: 0.6003 (OUTLIER) cc_final: 0.5611 (pp) REVERT: G 432 PHE cc_start: 0.6568 (t80) cc_final: 0.6153 (t80) outliers start: 106 outliers final: 87 residues processed: 298 average time/residue: 0.2750 time to fit residues: 120.9939 Evaluate side-chains 295 residues out of total 1659 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 94 poor density : 201 time to evaluate : 1.694 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 217 VAL Chi-restraints excluded: chain A residue 270 LYS Chi-restraints excluded: chain A residue 281 LEU Chi-restraints excluded: chain A residue 313 VAL Chi-restraints excluded: chain A residue 319 VAL Chi-restraints excluded: chain A residue 355 VAL Chi-restraints excluded: chain A residue 368 SER Chi-restraints excluded: chain A residue 369 LEU Chi-restraints excluded: chain A residue 396 GLN Chi-restraints excluded: chain A residue 406 LEU Chi-restraints excluded: chain A residue 408 ILE Chi-restraints excluded: chain A residue 433 LEU Chi-restraints excluded: chain A residue 442 LEU Chi-restraints excluded: chain A residue 474 LEU Chi-restraints excluded: chain B residue 270 LYS Chi-restraints excluded: chain B residue 281 LEU Chi-restraints excluded: chain B residue 313 VAL Chi-restraints excluded: chain B residue 319 VAL Chi-restraints excluded: chain B residue 355 VAL Chi-restraints excluded: chain B residue 368 SER Chi-restraints excluded: chain B residue 406 LEU Chi-restraints excluded: chain B residue 408 ILE Chi-restraints excluded: chain B residue 442 LEU Chi-restraints excluded: chain C residue 217 VAL Chi-restraints excluded: chain C residue 229 VAL Chi-restraints excluded: chain C residue 249 LEU Chi-restraints excluded: chain C residue 270 LYS Chi-restraints excluded: chain C residue 280 VAL Chi-restraints excluded: chain C residue 281 LEU Chi-restraints excluded: chain C residue 313 VAL Chi-restraints excluded: chain C residue 319 VAL Chi-restraints excluded: chain C residue 355 VAL Chi-restraints excluded: chain C residue 368 SER Chi-restraints excluded: chain C residue 369 LEU Chi-restraints excluded: chain C residue 388 VAL Chi-restraints excluded: chain C residue 396 GLN Chi-restraints excluded: chain C residue 406 LEU Chi-restraints excluded: chain C residue 408 ILE Chi-restraints excluded: chain C residue 433 LEU Chi-restraints excluded: chain C residue 442 LEU Chi-restraints excluded: chain D residue 217 VAL Chi-restraints excluded: chain D residue 229 VAL Chi-restraints excluded: chain D residue 262 VAL Chi-restraints excluded: chain D residue 270 LYS Chi-restraints excluded: chain D residue 281 LEU Chi-restraints excluded: chain D residue 296 LEU Chi-restraints excluded: chain D residue 313 VAL Chi-restraints excluded: chain D residue 319 VAL Chi-restraints excluded: chain D residue 355 VAL Chi-restraints excluded: chain D residue 368 SER Chi-restraints excluded: chain D residue 406 LEU Chi-restraints excluded: chain D residue 408 ILE Chi-restraints excluded: chain D residue 433 LEU Chi-restraints excluded: chain D residue 442 LEU Chi-restraints excluded: chain E residue 217 VAL Chi-restraints excluded: chain E residue 270 LYS Chi-restraints excluded: chain E residue 280 VAL Chi-restraints excluded: chain E residue 281 LEU Chi-restraints excluded: chain E residue 296 LEU Chi-restraints excluded: chain E residue 313 VAL Chi-restraints excluded: chain E residue 319 VAL Chi-restraints excluded: chain E residue 368 SER Chi-restraints excluded: chain E residue 369 LEU Chi-restraints excluded: chain E residue 378 LEU Chi-restraints excluded: chain E residue 408 ILE Chi-restraints excluded: chain E residue 433 LEU Chi-restraints excluded: chain F residue 217 VAL Chi-restraints excluded: chain F residue 249 LEU Chi-restraints excluded: chain F residue 270 LYS Chi-restraints excluded: chain F residue 281 LEU Chi-restraints excluded: chain F residue 313 VAL Chi-restraints excluded: chain F residue 316 VAL Chi-restraints excluded: chain F residue 319 VAL Chi-restraints excluded: chain F residue 355 VAL Chi-restraints excluded: chain F residue 368 SER Chi-restraints excluded: chain F residue 378 LEU Chi-restraints excluded: chain F residue 406 LEU Chi-restraints excluded: chain F residue 408 ILE Chi-restraints excluded: chain F residue 413 MET Chi-restraints excluded: chain F residue 433 LEU Chi-restraints excluded: chain F residue 442 LEU Chi-restraints excluded: chain G residue 217 VAL Chi-restraints excluded: chain G residue 229 VAL Chi-restraints excluded: chain G residue 249 LEU Chi-restraints excluded: chain G residue 262 VAL Chi-restraints excluded: chain G residue 270 LYS Chi-restraints excluded: chain G residue 281 LEU Chi-restraints excluded: chain G residue 313 VAL Chi-restraints excluded: chain G residue 316 VAL Chi-restraints excluded: chain G residue 319 VAL Chi-restraints excluded: chain G residue 355 VAL Chi-restraints excluded: chain G residue 368 SER Chi-restraints excluded: chain G residue 406 LEU Chi-restraints excluded: chain G residue 433 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 196 random chunks: chunk 63 optimal weight: 1.9990 chunk 170 optimal weight: 1.9990 chunk 37 optimal weight: 1.9990 chunk 111 optimal weight: 0.9990 chunk 46 optimal weight: 0.9990 chunk 189 optimal weight: 0.9990 chunk 157 optimal weight: 0.9980 chunk 87 optimal weight: 0.2980 chunk 15 optimal weight: 0.9980 chunk 62 optimal weight: 6.9990 chunk 99 optimal weight: 0.9990 overall best weight: 0.8584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 470 GLN B 470 GLN C 484 HIS D 470 GLN D 484 HIS G 484 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6608 moved from start: 0.3712 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 15407 Z= 0.208 Angle : 0.638 8.019 20853 Z= 0.327 Chirality : 0.045 0.152 2527 Planarity : 0.003 0.035 2604 Dihedral : 5.580 17.639 2114 Min Nonbonded Distance : 2.485 Molprobity Statistics. All-atom Clashscore : 10.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.72 % Favored : 91.28 % Rotamer: Outliers : 6.29 % Allowed : 17.83 % Favored : 75.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.92 (0.17), residues: 1995 helix: -1.62 (0.16), residues: 980 sheet: -1.85 (0.33), residues: 238 loop : -4.13 (0.16), residues: 777 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP C 397 HIS 0.003 0.001 HIS C 484 PHE 0.011 0.001 PHE D 432 TYR 0.005 0.001 TYR E 441 ARG 0.007 0.000 ARG D 426 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3990 Ramachandran restraints generated. 1995 Oldfield, 0 Emsley, 1995 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3990 Ramachandran restraints generated. 1995 Oldfield, 0 Emsley, 1995 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 317 residues out of total 1659 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 103 poor density : 214 time to evaluate : 1.687 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 278 GLU cc_start: 0.6458 (tp30) cc_final: 0.5749 (mt-10) REVERT: A 287 SER cc_start: 0.8281 (t) cc_final: 0.7554 (p) REVERT: A 308 GLN cc_start: 0.7926 (pm20) cc_final: 0.7589 (pm20) REVERT: A 413 MET cc_start: 0.5107 (tpp) cc_final: 0.4736 (mpp) REVERT: A 474 LEU cc_start: 0.5584 (OUTLIER) cc_final: 0.5050 (tt) REVERT: B 285 LYS cc_start: 0.7938 (ttmp) cc_final: 0.7193 (tttp) REVERT: B 287 SER cc_start: 0.8443 (t) cc_final: 0.7766 (p) REVERT: B 368 SER cc_start: 0.8769 (OUTLIER) cc_final: 0.8502 (m) REVERT: B 432 PHE cc_start: 0.6437 (t80) cc_final: 0.6237 (t80) REVERT: B 479 LYS cc_start: 0.5522 (mtpt) cc_final: 0.4999 (mttp) REVERT: C 287 SER cc_start: 0.8503 (t) cc_final: 0.7863 (p) REVERT: C 297 MET cc_start: 0.8702 (ttp) cc_final: 0.8342 (mtp) REVERT: C 447 LYS cc_start: 0.6648 (tptt) cc_final: 0.5189 (tttm) REVERT: D 285 LYS cc_start: 0.7455 (ttmp) cc_final: 0.6796 (tttp) REVERT: D 287 SER cc_start: 0.8503 (t) cc_final: 0.7815 (p) REVERT: D 296 LEU cc_start: 0.7763 (OUTLIER) cc_final: 0.7536 (tp) REVERT: D 446 GLU cc_start: 0.6425 (OUTLIER) cc_final: 0.5846 (mm-30) REVERT: E 249 LEU cc_start: 0.7633 (OUTLIER) cc_final: 0.7194 (tt) REVERT: E 278 GLU cc_start: 0.7052 (mt-10) cc_final: 0.6767 (tt0) REVERT: E 285 LYS cc_start: 0.7602 (ttmp) cc_final: 0.6818 (ttmt) REVERT: E 287 SER cc_start: 0.8094 (t) cc_final: 0.7400 (p) REVERT: E 368 SER cc_start: 0.8727 (OUTLIER) cc_final: 0.8456 (m) REVERT: E 378 LEU cc_start: 0.8080 (OUTLIER) cc_final: 0.7832 (mp) REVERT: E 479 LYS cc_start: 0.5288 (mtpt) cc_final: 0.4702 (mttm) REVERT: F 287 SER cc_start: 0.8370 (t) cc_final: 0.7771 (p) REVERT: F 413 MET cc_start: 0.5399 (OUTLIER) cc_final: 0.4872 (tpt) REVERT: G 270 LYS cc_start: 0.5771 (OUTLIER) cc_final: 0.5461 (tmtt) REVERT: G 285 LYS cc_start: 0.7591 (ttmp) cc_final: 0.6969 (tttp) REVERT: G 287 SER cc_start: 0.8362 (t) cc_final: 0.7711 (p) REVERT: G 368 SER cc_start: 0.8632 (OUTLIER) cc_final: 0.8378 (m) REVERT: G 432 PHE cc_start: 0.6531 (t80) cc_final: 0.6066 (t80) outliers start: 103 outliers final: 81 residues processed: 294 average time/residue: 0.2794 time to fit residues: 121.1598 Evaluate side-chains 297 residues out of total 1659 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 91 poor density : 206 time to evaluate : 1.848 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 217 VAL Chi-restraints excluded: chain A residue 270 LYS Chi-restraints excluded: chain A residue 281 LEU Chi-restraints excluded: chain A residue 313 VAL Chi-restraints excluded: chain A residue 319 VAL Chi-restraints excluded: chain A residue 355 VAL Chi-restraints excluded: chain A residue 369 LEU Chi-restraints excluded: chain A residue 396 GLN Chi-restraints excluded: chain A residue 406 LEU Chi-restraints excluded: chain A residue 408 ILE Chi-restraints excluded: chain A residue 433 LEU Chi-restraints excluded: chain A residue 442 LEU Chi-restraints excluded: chain A residue 474 LEU Chi-restraints excluded: chain B residue 217 VAL Chi-restraints excluded: chain B residue 270 LYS Chi-restraints excluded: chain B residue 281 LEU Chi-restraints excluded: chain B residue 313 VAL Chi-restraints excluded: chain B residue 319 VAL Chi-restraints excluded: chain B residue 355 VAL Chi-restraints excluded: chain B residue 368 SER Chi-restraints excluded: chain B residue 406 LEU Chi-restraints excluded: chain B residue 442 LEU Chi-restraints excluded: chain C residue 217 VAL Chi-restraints excluded: chain C residue 229 VAL Chi-restraints excluded: chain C residue 270 LYS Chi-restraints excluded: chain C residue 280 VAL Chi-restraints excluded: chain C residue 281 LEU Chi-restraints excluded: chain C residue 313 VAL Chi-restraints excluded: chain C residue 319 VAL Chi-restraints excluded: chain C residue 355 VAL Chi-restraints excluded: chain C residue 368 SER Chi-restraints excluded: chain C residue 369 LEU Chi-restraints excluded: chain C residue 370 LEU Chi-restraints excluded: chain C residue 388 VAL Chi-restraints excluded: chain C residue 396 GLN Chi-restraints excluded: chain C residue 406 LEU Chi-restraints excluded: chain C residue 408 ILE Chi-restraints excluded: chain C residue 433 LEU Chi-restraints excluded: chain C residue 442 LEU Chi-restraints excluded: chain D residue 217 VAL Chi-restraints excluded: chain D residue 229 VAL Chi-restraints excluded: chain D residue 270 LYS Chi-restraints excluded: chain D residue 296 LEU Chi-restraints excluded: chain D residue 313 VAL Chi-restraints excluded: chain D residue 319 VAL Chi-restraints excluded: chain D residue 355 VAL Chi-restraints excluded: chain D residue 368 SER Chi-restraints excluded: chain D residue 369 LEU Chi-restraints excluded: chain D residue 378 LEU Chi-restraints excluded: chain D residue 408 ILE Chi-restraints excluded: chain D residue 433 LEU Chi-restraints excluded: chain D residue 442 LEU Chi-restraints excluded: chain D residue 446 GLU Chi-restraints excluded: chain E residue 217 VAL Chi-restraints excluded: chain E residue 249 LEU Chi-restraints excluded: chain E residue 270 LYS Chi-restraints excluded: chain E residue 281 LEU Chi-restraints excluded: chain E residue 296 LEU Chi-restraints excluded: chain E residue 313 VAL Chi-restraints excluded: chain E residue 319 VAL Chi-restraints excluded: chain E residue 368 SER Chi-restraints excluded: chain E residue 369 LEU Chi-restraints excluded: chain E residue 378 LEU Chi-restraints excluded: chain E residue 408 ILE Chi-restraints excluded: chain E residue 433 LEU Chi-restraints excluded: chain F residue 217 VAL Chi-restraints excluded: chain F residue 270 LYS Chi-restraints excluded: chain F residue 281 LEU Chi-restraints excluded: chain F residue 313 VAL Chi-restraints excluded: chain F residue 319 VAL Chi-restraints excluded: chain F residue 355 VAL Chi-restraints excluded: chain F residue 368 SER Chi-restraints excluded: chain F residue 378 LEU Chi-restraints excluded: chain F residue 406 LEU Chi-restraints excluded: chain F residue 408 ILE Chi-restraints excluded: chain F residue 413 MET Chi-restraints excluded: chain F residue 433 LEU Chi-restraints excluded: chain F residue 442 LEU Chi-restraints excluded: chain G residue 217 VAL Chi-restraints excluded: chain G residue 229 VAL Chi-restraints excluded: chain G residue 249 LEU Chi-restraints excluded: chain G residue 270 LYS Chi-restraints excluded: chain G residue 281 LEU Chi-restraints excluded: chain G residue 311 LEU Chi-restraints excluded: chain G residue 313 VAL Chi-restraints excluded: chain G residue 316 VAL Chi-restraints excluded: chain G residue 319 VAL Chi-restraints excluded: chain G residue 355 VAL Chi-restraints excluded: chain G residue 368 SER Chi-restraints excluded: chain G residue 396 GLN Chi-restraints excluded: chain G residue 433 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 196 random chunks: chunk 182 optimal weight: 2.9990 chunk 21 optimal weight: 0.9990 chunk 108 optimal weight: 0.0770 chunk 138 optimal weight: 2.9990 chunk 107 optimal weight: 0.5980 chunk 159 optimal weight: 3.9990 chunk 105 optimal weight: 1.9990 chunk 188 optimal weight: 3.9990 chunk 118 optimal weight: 0.3980 chunk 115 optimal weight: 2.9990 chunk 87 optimal weight: 0.0030 overall best weight: 0.4150 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 484 HIS B 470 GLN C 484 HIS D 470 GLN D 484 HIS F 470 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6553 moved from start: 0.3991 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.041 15407 Z= 0.164 Angle : 0.617 7.650 20853 Z= 0.314 Chirality : 0.044 0.160 2527 Planarity : 0.003 0.034 2604 Dihedral : 5.284 16.171 2114 Min Nonbonded Distance : 2.493 Molprobity Statistics. All-atom Clashscore : 10.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.67 % Favored : 92.33 % Rotamer: Outliers : 5.74 % Allowed : 19.05 % Favored : 75.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.60 (0.17), residues: 1995 helix: -1.34 (0.16), residues: 973 sheet: -1.85 (0.33), residues: 238 loop : -3.94 (0.16), residues: 784 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP G 397 HIS 0.003 0.001 HIS C 484 PHE 0.018 0.001 PHE D 432 TYR 0.005 0.001 TYR E 441 ARG 0.007 0.000 ARG D 426 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3990 Ramachandran restraints generated. 1995 Oldfield, 0 Emsley, 1995 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3990 Ramachandran restraints generated. 1995 Oldfield, 0 Emsley, 1995 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 314 residues out of total 1659 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 94 poor density : 220 time to evaluate : 1.476 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 278 GLU cc_start: 0.6383 (tp30) cc_final: 0.5777 (mt-10) REVERT: A 287 SER cc_start: 0.8278 (t) cc_final: 0.7575 (p) REVERT: A 308 GLN cc_start: 0.7799 (pm20) cc_final: 0.7538 (pm20) REVERT: A 370 LEU cc_start: 0.8444 (tp) cc_final: 0.8156 (mt) REVERT: A 413 MET cc_start: 0.4952 (tpp) cc_final: 0.4595 (mpp) REVERT: B 285 LYS cc_start: 0.7868 (ttmp) cc_final: 0.7123 (tttp) REVERT: B 287 SER cc_start: 0.8443 (t) cc_final: 0.7791 (p) REVERT: B 459 ILE cc_start: 0.7024 (tp) cc_final: 0.6739 (tp) REVERT: B 479 LYS cc_start: 0.5569 (mtpt) cc_final: 0.5052 (mttp) REVERT: C 287 SER cc_start: 0.8444 (t) cc_final: 0.7818 (p) REVERT: C 297 MET cc_start: 0.8634 (ttp) cc_final: 0.8257 (mtp) REVERT: C 368 SER cc_start: 0.8625 (OUTLIER) cc_final: 0.8346 (m) REVERT: C 413 MET cc_start: 0.5326 (ptp) cc_final: 0.4734 (tpt) REVERT: C 447 LYS cc_start: 0.6587 (tptt) cc_final: 0.5159 (tttm) REVERT: C 459 ILE cc_start: 0.6947 (tp) cc_final: 0.6658 (tp) REVERT: C 484 HIS cc_start: 0.6553 (m-70) cc_final: 0.6351 (m90) REVERT: D 287 SER cc_start: 0.8480 (t) cc_final: 0.7830 (p) REVERT: D 446 GLU cc_start: 0.6354 (OUTLIER) cc_final: 0.5782 (mm-30) REVERT: E 278 GLU cc_start: 0.7018 (mt-10) cc_final: 0.6809 (tt0) REVERT: E 287 SER cc_start: 0.8083 (t) cc_final: 0.7404 (p) REVERT: E 370 LEU cc_start: 0.8433 (tp) cc_final: 0.8177 (mt) REVERT: E 479 LYS cc_start: 0.5290 (mtpt) cc_final: 0.4671 (mttm) REVERT: F 287 SER cc_start: 0.8230 (t) cc_final: 0.7601 (p) REVERT: F 308 GLN cc_start: 0.7922 (pm20) cc_final: 0.7713 (pm20) REVERT: F 413 MET cc_start: 0.5316 (ptp) cc_final: 0.4814 (tpt) REVERT: F 459 ILE cc_start: 0.7044 (tp) cc_final: 0.6720 (tp) REVERT: G 270 LYS cc_start: 0.5747 (OUTLIER) cc_final: 0.5340 (tmtt) REVERT: G 285 LYS cc_start: 0.7570 (ttmp) cc_final: 0.6945 (tttp) REVERT: G 287 SER cc_start: 0.8426 (t) cc_final: 0.7738 (p) REVERT: G 308 GLN cc_start: 0.7623 (pm20) cc_final: 0.7365 (pm20) REVERT: G 326 ARG cc_start: 0.7392 (ptt-90) cc_final: 0.7180 (ptt-90) REVERT: G 436 GLU cc_start: 0.7919 (mp0) cc_final: 0.7396 (mt-10) outliers start: 94 outliers final: 69 residues processed: 292 average time/residue: 0.2711 time to fit residues: 116.7310 Evaluate side-chains 275 residues out of total 1659 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 72 poor density : 203 time to evaluate : 1.689 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 270 LYS Chi-restraints excluded: chain A residue 281 LEU Chi-restraints excluded: chain A residue 313 VAL Chi-restraints excluded: chain A residue 319 VAL Chi-restraints excluded: chain A residue 355 VAL Chi-restraints excluded: chain A residue 369 LEU Chi-restraints excluded: chain A residue 396 GLN Chi-restraints excluded: chain A residue 406 LEU Chi-restraints excluded: chain A residue 408 ILE Chi-restraints excluded: chain A residue 433 LEU Chi-restraints excluded: chain A residue 442 LEU Chi-restraints excluded: chain B residue 217 VAL Chi-restraints excluded: chain B residue 270 LYS Chi-restraints excluded: chain B residue 313 VAL Chi-restraints excluded: chain B residue 319 VAL Chi-restraints excluded: chain B residue 355 VAL Chi-restraints excluded: chain B residue 406 LEU Chi-restraints excluded: chain B residue 442 LEU Chi-restraints excluded: chain C residue 229 VAL Chi-restraints excluded: chain C residue 270 LYS Chi-restraints excluded: chain C residue 281 LEU Chi-restraints excluded: chain C residue 311 LEU Chi-restraints excluded: chain C residue 313 VAL Chi-restraints excluded: chain C residue 319 VAL Chi-restraints excluded: chain C residue 355 VAL Chi-restraints excluded: chain C residue 368 SER Chi-restraints excluded: chain C residue 369 LEU Chi-restraints excluded: chain C residue 388 VAL Chi-restraints excluded: chain C residue 396 GLN Chi-restraints excluded: chain C residue 406 LEU Chi-restraints excluded: chain C residue 408 ILE Chi-restraints excluded: chain C residue 442 LEU Chi-restraints excluded: chain D residue 229 VAL Chi-restraints excluded: chain D residue 270 LYS Chi-restraints excluded: chain D residue 313 VAL Chi-restraints excluded: chain D residue 319 VAL Chi-restraints excluded: chain D residue 355 VAL Chi-restraints excluded: chain D residue 368 SER Chi-restraints excluded: chain D residue 378 LEU Chi-restraints excluded: chain D residue 406 LEU Chi-restraints excluded: chain D residue 433 LEU Chi-restraints excluded: chain D residue 442 LEU Chi-restraints excluded: chain D residue 446 GLU Chi-restraints excluded: chain E residue 270 LYS Chi-restraints excluded: chain E residue 281 LEU Chi-restraints excluded: chain E residue 296 LEU Chi-restraints excluded: chain E residue 313 VAL Chi-restraints excluded: chain E residue 319 VAL Chi-restraints excluded: chain E residue 369 LEU Chi-restraints excluded: chain E residue 406 LEU Chi-restraints excluded: chain E residue 408 ILE Chi-restraints excluded: chain E residue 433 LEU Chi-restraints excluded: chain F residue 217 VAL Chi-restraints excluded: chain F residue 270 LYS Chi-restraints excluded: chain F residue 281 LEU Chi-restraints excluded: chain F residue 313 VAL Chi-restraints excluded: chain F residue 319 VAL Chi-restraints excluded: chain F residue 355 VAL Chi-restraints excluded: chain F residue 406 LEU Chi-restraints excluded: chain F residue 408 ILE Chi-restraints excluded: chain F residue 433 LEU Chi-restraints excluded: chain F residue 442 LEU Chi-restraints excluded: chain G residue 217 VAL Chi-restraints excluded: chain G residue 229 VAL Chi-restraints excluded: chain G residue 249 LEU Chi-restraints excluded: chain G residue 270 LYS Chi-restraints excluded: chain G residue 281 LEU Chi-restraints excluded: chain G residue 311 LEU Chi-restraints excluded: chain G residue 313 VAL Chi-restraints excluded: chain G residue 316 VAL Chi-restraints excluded: chain G residue 396 GLN Chi-restraints excluded: chain G residue 433 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 196 random chunks: chunk 116 optimal weight: 0.6980 chunk 75 optimal weight: 3.9990 chunk 112 optimal weight: 9.9990 chunk 56 optimal weight: 9.9990 chunk 37 optimal weight: 0.8980 chunk 36 optimal weight: 0.9990 chunk 120 optimal weight: 0.4980 chunk 128 optimal weight: 2.9990 chunk 93 optimal weight: 0.8980 chunk 17 optimal weight: 0.9990 chunk 148 optimal weight: 0.0970 overall best weight: 0.6178 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 470 GLN C 339 GLN D 484 HIS F 470 GLN G 407 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6562 moved from start: 0.4138 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 15407 Z= 0.178 Angle : 0.619 11.110 20853 Z= 0.314 Chirality : 0.045 0.163 2527 Planarity : 0.003 0.033 2604 Dihedral : 5.235 16.714 2114 Min Nonbonded Distance : 2.511 Molprobity Statistics. All-atom Clashscore : 10.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.72 % Favored : 92.28 % Rotamer: Outliers : 5.31 % Allowed : 19.60 % Favored : 75.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.37 (0.17), residues: 1995 helix: -1.15 (0.16), residues: 973 sheet: -1.79 (0.33), residues: 238 loop : -3.80 (0.17), residues: 784 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP C 397 HIS 0.002 0.000 HIS D 484 PHE 0.012 0.001 PHE D 432 TYR 0.005 0.001 TYR E 467 ARG 0.007 0.000 ARG D 426 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3990 Ramachandran restraints generated. 1995 Oldfield, 0 Emsley, 1995 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3990 Ramachandran restraints generated. 1995 Oldfield, 0 Emsley, 1995 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 293 residues out of total 1659 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 87 poor density : 206 time to evaluate : 1.626 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 278 GLU cc_start: 0.6341 (tp30) cc_final: 0.5788 (mt-10) REVERT: A 287 SER cc_start: 0.8303 (t) cc_final: 0.7587 (p) REVERT: A 370 LEU cc_start: 0.8445 (tp) cc_final: 0.8170 (mt) REVERT: A 413 MET cc_start: 0.5000 (tpp) cc_final: 0.4665 (mpp) REVERT: A 424 MET cc_start: 0.7567 (tmm) cc_final: 0.7308 (ppp) REVERT: A 484 HIS cc_start: 0.6944 (m-70) cc_final: 0.6642 (m90) REVERT: B 285 LYS cc_start: 0.7912 (ttmp) cc_final: 0.7110 (tttp) REVERT: B 287 SER cc_start: 0.8365 (t) cc_final: 0.7732 (p) REVERT: B 459 ILE cc_start: 0.7079 (tp) cc_final: 0.6780 (tp) REVERT: B 479 LYS cc_start: 0.5645 (mtpt) cc_final: 0.5130 (mttp) REVERT: C 287 SER cc_start: 0.8509 (t) cc_final: 0.7879 (p) REVERT: C 368 SER cc_start: 0.8636 (OUTLIER) cc_final: 0.8349 (m) REVERT: C 413 MET cc_start: 0.5203 (ptp) cc_final: 0.4670 (ttp) REVERT: C 447 LYS cc_start: 0.6513 (tptt) cc_final: 0.5139 (tttm) REVERT: C 459 ILE cc_start: 0.6862 (tp) cc_final: 0.6573 (tp) REVERT: D 278 GLU cc_start: 0.6824 (tp30) cc_final: 0.6063 (tt0) REVERT: D 287 SER cc_start: 0.8442 (t) cc_final: 0.7857 (p) REVERT: E 278 GLU cc_start: 0.7027 (mt-10) cc_final: 0.6813 (tt0) REVERT: E 285 LYS cc_start: 0.7675 (ttmp) cc_final: 0.6851 (ttmt) REVERT: E 287 SER cc_start: 0.8070 (t) cc_final: 0.7397 (p) REVERT: E 346 MET cc_start: 0.7483 (tpp) cc_final: 0.6882 (tpp) REVERT: E 370 LEU cc_start: 0.8456 (tp) cc_final: 0.8184 (mt) REVERT: E 413 MET cc_start: 0.5092 (tpp) cc_final: 0.4710 (mpp) REVERT: E 479 LYS cc_start: 0.5373 (mtpt) cc_final: 0.4766 (mttm) REVERT: F 287 SER cc_start: 0.8287 (t) cc_final: 0.7647 (p) REVERT: F 413 MET cc_start: 0.5379 (ptp) cc_final: 0.4805 (tpt) REVERT: F 459 ILE cc_start: 0.7052 (tp) cc_final: 0.6741 (tp) REVERT: G 285 LYS cc_start: 0.7631 (ttmp) cc_final: 0.6962 (tttp) REVERT: G 287 SER cc_start: 0.8444 (t) cc_final: 0.7753 (p) REVERT: G 413 MET cc_start: 0.5268 (ptp) cc_final: 0.4787 (tpt) REVERT: G 436 GLU cc_start: 0.7934 (mp0) cc_final: 0.7433 (mt-10) REVERT: G 461 MET cc_start: 0.7418 (mtp) cc_final: 0.7013 (mtt) outliers start: 87 outliers final: 73 residues processed: 281 average time/residue: 0.2779 time to fit residues: 114.3871 Evaluate side-chains 269 residues out of total 1659 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 74 poor density : 195 time to evaluate : 1.772 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 270 LYS Chi-restraints excluded: chain A residue 313 VAL Chi-restraints excluded: chain A residue 319 VAL Chi-restraints excluded: chain A residue 355 VAL Chi-restraints excluded: chain A residue 369 LEU Chi-restraints excluded: chain A residue 396 GLN Chi-restraints excluded: chain A residue 406 LEU Chi-restraints excluded: chain A residue 408 ILE Chi-restraints excluded: chain A residue 433 LEU Chi-restraints excluded: chain A residue 442 LEU Chi-restraints excluded: chain B residue 217 VAL Chi-restraints excluded: chain B residue 270 LYS Chi-restraints excluded: chain B residue 281 LEU Chi-restraints excluded: chain B residue 313 VAL Chi-restraints excluded: chain B residue 319 VAL Chi-restraints excluded: chain B residue 355 VAL Chi-restraints excluded: chain B residue 406 LEU Chi-restraints excluded: chain B residue 442 LEU Chi-restraints excluded: chain C residue 229 VAL Chi-restraints excluded: chain C residue 270 LYS Chi-restraints excluded: chain C residue 281 LEU Chi-restraints excluded: chain C residue 311 LEU Chi-restraints excluded: chain C residue 313 VAL Chi-restraints excluded: chain C residue 319 VAL Chi-restraints excluded: chain C residue 355 VAL Chi-restraints excluded: chain C residue 368 SER Chi-restraints excluded: chain C residue 369 LEU Chi-restraints excluded: chain C residue 388 VAL Chi-restraints excluded: chain C residue 396 GLN Chi-restraints excluded: chain C residue 406 LEU Chi-restraints excluded: chain C residue 408 ILE Chi-restraints excluded: chain C residue 433 LEU Chi-restraints excluded: chain C residue 442 LEU Chi-restraints excluded: chain D residue 217 VAL Chi-restraints excluded: chain D residue 229 VAL Chi-restraints excluded: chain D residue 262 VAL Chi-restraints excluded: chain D residue 270 LYS Chi-restraints excluded: chain D residue 281 LEU Chi-restraints excluded: chain D residue 313 VAL Chi-restraints excluded: chain D residue 319 VAL Chi-restraints excluded: chain D residue 355 VAL Chi-restraints excluded: chain D residue 368 SER Chi-restraints excluded: chain D residue 378 LEU Chi-restraints excluded: chain D residue 406 LEU Chi-restraints excluded: chain D residue 433 LEU Chi-restraints excluded: chain D residue 442 LEU Chi-restraints excluded: chain E residue 270 LYS Chi-restraints excluded: chain E residue 281 LEU Chi-restraints excluded: chain E residue 296 LEU Chi-restraints excluded: chain E residue 313 VAL Chi-restraints excluded: chain E residue 319 VAL Chi-restraints excluded: chain E residue 408 ILE Chi-restraints excluded: chain F residue 217 VAL Chi-restraints excluded: chain F residue 270 LYS Chi-restraints excluded: chain F residue 280 VAL Chi-restraints excluded: chain F residue 281 LEU Chi-restraints excluded: chain F residue 313 VAL Chi-restraints excluded: chain F residue 316 VAL Chi-restraints excluded: chain F residue 355 VAL Chi-restraints excluded: chain F residue 369 LEU Chi-restraints excluded: chain F residue 406 LEU Chi-restraints excluded: chain F residue 408 ILE Chi-restraints excluded: chain F residue 433 LEU Chi-restraints excluded: chain F residue 442 LEU Chi-restraints excluded: chain G residue 217 VAL Chi-restraints excluded: chain G residue 249 LEU Chi-restraints excluded: chain G residue 270 LYS Chi-restraints excluded: chain G residue 281 LEU Chi-restraints excluded: chain G residue 311 LEU Chi-restraints excluded: chain G residue 313 VAL Chi-restraints excluded: chain G residue 316 VAL Chi-restraints excluded: chain G residue 319 VAL Chi-restraints excluded: chain G residue 396 GLN Chi-restraints excluded: chain G residue 433 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 196 random chunks: chunk 171 optimal weight: 0.0870 chunk 180 optimal weight: 1.9990 chunk 165 optimal weight: 8.9990 chunk 176 optimal weight: 1.9990 chunk 105 optimal weight: 1.9990 chunk 76 optimal weight: 4.9990 chunk 138 optimal weight: 8.9990 chunk 54 optimal weight: 0.9990 chunk 159 optimal weight: 5.9990 chunk 166 optimal weight: 6.9990 chunk 175 optimal weight: 0.9980 overall best weight: 1.2164 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 407 GLN B 470 GLN C 339 GLN C 484 HIS ** D 484 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 470 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6623 moved from start: 0.4179 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 15407 Z= 0.245 Angle : 0.659 12.035 20853 Z= 0.332 Chirality : 0.047 0.173 2527 Planarity : 0.003 0.033 2604 Dihedral : 5.434 17.796 2114 Min Nonbonded Distance : 2.521 Molprobity Statistics. All-atom Clashscore : 10.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.02 % Favored : 90.98 % Rotamer: Outliers : 5.43 % Allowed : 19.54 % Favored : 75.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.39 (0.17), residues: 1995 helix: -1.18 (0.16), residues: 980 sheet: -2.20 (0.31), residues: 266 loop : -3.68 (0.18), residues: 749 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 397 HIS 0.006 0.001 HIS B 484 PHE 0.011 0.001 PHE G 432 TYR 0.005 0.001 TYR E 441 ARG 0.008 0.000 ARG D 426 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3990 Ramachandran restraints generated. 1995 Oldfield, 0 Emsley, 1995 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3990 Ramachandran restraints generated. 1995 Oldfield, 0 Emsley, 1995 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 283 residues out of total 1659 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 89 poor density : 194 time to evaluate : 1.728 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 278 GLU cc_start: 0.6349 (tp30) cc_final: 0.5768 (mt-10) REVERT: A 287 SER cc_start: 0.8331 (t) cc_final: 0.7593 (p) REVERT: A 413 MET cc_start: 0.5211 (tpp) cc_final: 0.4776 (mpp) REVERT: A 484 HIS cc_start: 0.6989 (m-70) cc_final: 0.6662 (m90) REVERT: B 285 LYS cc_start: 0.7900 (ttmp) cc_final: 0.7111 (tttp) REVERT: B 287 SER cc_start: 0.8386 (t) cc_final: 0.7728 (p) REVERT: B 432 PHE cc_start: 0.6617 (t80) cc_final: 0.6410 (t80) REVERT: B 479 LYS cc_start: 0.5572 (mtpt) cc_final: 0.5052 (mttp) REVERT: C 287 SER cc_start: 0.8525 (t) cc_final: 0.7891 (p) REVERT: C 338 MET cc_start: 0.7346 (mmp) cc_final: 0.6873 (mmp) REVERT: C 346 MET cc_start: 0.7406 (tpp) cc_final: 0.7181 (tpp) REVERT: C 413 MET cc_start: 0.5323 (ptp) cc_final: 0.4832 (ttp) REVERT: C 447 LYS cc_start: 0.6451 (tptt) cc_final: 0.5064 (tttm) REVERT: D 278 GLU cc_start: 0.6821 (tp30) cc_final: 0.6038 (tt0) REVERT: D 287 SER cc_start: 0.8516 (t) cc_final: 0.7841 (p) REVERT: D 369 LEU cc_start: 0.8418 (OUTLIER) cc_final: 0.7912 (pt) REVERT: D 446 GLU cc_start: 0.6573 (mm-30) cc_final: 0.6302 (tp30) REVERT: E 285 LYS cc_start: 0.7717 (ttmp) cc_final: 0.6908 (ttmt) REVERT: E 287 SER cc_start: 0.8059 (t) cc_final: 0.7367 (p) REVERT: E 413 MET cc_start: 0.4852 (tpp) cc_final: 0.4589 (mpp) REVERT: E 479 LYS cc_start: 0.5249 (mtpt) cc_final: 0.4651 (mttm) REVERT: F 287 SER cc_start: 0.8119 (t) cc_final: 0.7452 (p) REVERT: F 338 MET cc_start: 0.7737 (mmp) cc_final: 0.7230 (mmp) REVERT: G 285 LYS cc_start: 0.7608 (ttmp) cc_final: 0.6940 (tttp) REVERT: G 287 SER cc_start: 0.8457 (t) cc_final: 0.7769 (p) REVERT: G 461 MET cc_start: 0.7565 (mtp) cc_final: 0.7047 (mtt) outliers start: 89 outliers final: 79 residues processed: 268 average time/residue: 0.2672 time to fit residues: 106.9629 Evaluate side-chains 274 residues out of total 1659 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 80 poor density : 194 time to evaluate : 1.779 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 217 VAL Chi-restraints excluded: chain A residue 270 LYS Chi-restraints excluded: chain A residue 281 LEU Chi-restraints excluded: chain A residue 313 VAL Chi-restraints excluded: chain A residue 319 VAL Chi-restraints excluded: chain A residue 355 VAL Chi-restraints excluded: chain A residue 369 LEU Chi-restraints excluded: chain A residue 406 LEU Chi-restraints excluded: chain A residue 408 ILE Chi-restraints excluded: chain A residue 433 LEU Chi-restraints excluded: chain A residue 442 LEU Chi-restraints excluded: chain B residue 217 VAL Chi-restraints excluded: chain B residue 270 LYS Chi-restraints excluded: chain B residue 281 LEU Chi-restraints excluded: chain B residue 313 VAL Chi-restraints excluded: chain B residue 319 VAL Chi-restraints excluded: chain B residue 355 VAL Chi-restraints excluded: chain B residue 406 LEU Chi-restraints excluded: chain B residue 442 LEU Chi-restraints excluded: chain C residue 217 VAL Chi-restraints excluded: chain C residue 229 VAL Chi-restraints excluded: chain C residue 238 TYR Chi-restraints excluded: chain C residue 249 LEU Chi-restraints excluded: chain C residue 270 LYS Chi-restraints excluded: chain C residue 281 LEU Chi-restraints excluded: chain C residue 311 LEU Chi-restraints excluded: chain C residue 313 VAL Chi-restraints excluded: chain C residue 319 VAL Chi-restraints excluded: chain C residue 355 VAL Chi-restraints excluded: chain C residue 368 SER Chi-restraints excluded: chain C residue 369 LEU Chi-restraints excluded: chain C residue 388 VAL Chi-restraints excluded: chain C residue 396 GLN Chi-restraints excluded: chain C residue 406 LEU Chi-restraints excluded: chain C residue 408 ILE Chi-restraints excluded: chain C residue 433 LEU Chi-restraints excluded: chain C residue 442 LEU Chi-restraints excluded: chain D residue 217 VAL Chi-restraints excluded: chain D residue 229 VAL Chi-restraints excluded: chain D residue 262 VAL Chi-restraints excluded: chain D residue 270 LYS Chi-restraints excluded: chain D residue 281 LEU Chi-restraints excluded: chain D residue 313 VAL Chi-restraints excluded: chain D residue 319 VAL Chi-restraints excluded: chain D residue 355 VAL Chi-restraints excluded: chain D residue 368 SER Chi-restraints excluded: chain D residue 369 LEU Chi-restraints excluded: chain D residue 378 LEU Chi-restraints excluded: chain D residue 406 LEU Chi-restraints excluded: chain D residue 433 LEU Chi-restraints excluded: chain D residue 442 LEU Chi-restraints excluded: chain E residue 217 VAL Chi-restraints excluded: chain E residue 270 LYS Chi-restraints excluded: chain E residue 281 LEU Chi-restraints excluded: chain E residue 296 LEU Chi-restraints excluded: chain E residue 313 VAL Chi-restraints excluded: chain E residue 319 VAL Chi-restraints excluded: chain E residue 369 LEU Chi-restraints excluded: chain E residue 408 ILE Chi-restraints excluded: chain F residue 217 VAL Chi-restraints excluded: chain F residue 270 LYS Chi-restraints excluded: chain F residue 280 VAL Chi-restraints excluded: chain F residue 281 LEU Chi-restraints excluded: chain F residue 313 VAL Chi-restraints excluded: chain F residue 316 VAL Chi-restraints excluded: chain F residue 319 VAL Chi-restraints excluded: chain F residue 355 VAL Chi-restraints excluded: chain F residue 369 LEU Chi-restraints excluded: chain F residue 406 LEU Chi-restraints excluded: chain F residue 408 ILE Chi-restraints excluded: chain F residue 433 LEU Chi-restraints excluded: chain F residue 442 LEU Chi-restraints excluded: chain G residue 217 VAL Chi-restraints excluded: chain G residue 249 LEU Chi-restraints excluded: chain G residue 270 LYS Chi-restraints excluded: chain G residue 281 LEU Chi-restraints excluded: chain G residue 311 LEU Chi-restraints excluded: chain G residue 313 VAL Chi-restraints excluded: chain G residue 316 VAL Chi-restraints excluded: chain G residue 319 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 196 random chunks: chunk 115 optimal weight: 4.9990 chunk 186 optimal weight: 0.9980 chunk 113 optimal weight: 4.9990 chunk 88 optimal weight: 0.8980 chunk 129 optimal weight: 0.3980 chunk 195 optimal weight: 0.9980 chunk 179 optimal weight: 0.0170 chunk 155 optimal weight: 0.8980 chunk 16 optimal weight: 0.8980 chunk 120 optimal weight: 3.9990 chunk 95 optimal weight: 3.9990 overall best weight: 0.6218 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 381 ASN B 470 GLN C 484 HIS D 470 GLN ** D 484 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 470 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6567 moved from start: 0.4387 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 15407 Z= 0.179 Angle : 0.635 12.543 20853 Z= 0.318 Chirality : 0.045 0.166 2527 Planarity : 0.003 0.035 2604 Dihedral : 5.189 16.744 2114 Min Nonbonded Distance : 2.543 Molprobity Statistics. All-atom Clashscore : 10.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.47 % Favored : 92.53 % Rotamer: Outliers : 4.95 % Allowed : 20.33 % Favored : 74.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.17 (0.17), residues: 1995 helix: -1.10 (0.16), residues: 1029 sheet: -1.79 (0.33), residues: 238 loop : -3.63 (0.18), residues: 728 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP A 397 HIS 0.006 0.001 HIS B 484 PHE 0.013 0.001 PHE G 432 TYR 0.005 0.001 TYR F 467 ARG 0.008 0.000 ARG D 426 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3990 Ramachandran restraints generated. 1995 Oldfield, 0 Emsley, 1995 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3990 Ramachandran restraints generated. 1995 Oldfield, 0 Emsley, 1995 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 272 residues out of total 1659 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 81 poor density : 191 time to evaluate : 1.760 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 278 GLU cc_start: 0.6316 (tp30) cc_final: 0.5805 (mt-10) REVERT: A 287 SER cc_start: 0.8260 (t) cc_final: 0.7527 (p) REVERT: A 370 LEU cc_start: 0.8432 (tp) cc_final: 0.8184 (mt) REVERT: A 413 MET cc_start: 0.5167 (tpp) cc_final: 0.4738 (mpp) REVERT: A 484 HIS cc_start: 0.6967 (m-70) cc_final: 0.6614 (m90) REVERT: B 278 GLU cc_start: 0.6611 (tp30) cc_final: 0.5849 (tt0) REVERT: B 285 LYS cc_start: 0.7879 (ttmp) cc_final: 0.7102 (tttp) REVERT: B 287 SER cc_start: 0.8365 (t) cc_final: 0.7720 (p) REVERT: B 432 PHE cc_start: 0.6409 (t80) cc_final: 0.6123 (t80) REVERT: B 479 LYS cc_start: 0.5573 (mtpt) cc_final: 0.5035 (mttp) REVERT: C 287 SER cc_start: 0.8484 (t) cc_final: 0.7846 (p) REVERT: C 368 SER cc_start: 0.8678 (OUTLIER) cc_final: 0.8398 (m) REVERT: C 413 MET cc_start: 0.5278 (ptp) cc_final: 0.4692 (ttp) REVERT: C 447 LYS cc_start: 0.6487 (tptt) cc_final: 0.5089 (tttm) REVERT: C 459 ILE cc_start: 0.6904 (tp) cc_final: 0.6605 (tp) REVERT: D 278 GLU cc_start: 0.6758 (tp30) cc_final: 0.6067 (tt0) REVERT: D 287 SER cc_start: 0.8451 (t) cc_final: 0.7795 (p) REVERT: D 446 GLU cc_start: 0.6536 (mm-30) cc_final: 0.6290 (tp30) REVERT: E 249 LEU cc_start: 0.7394 (OUTLIER) cc_final: 0.6869 (tt) REVERT: E 285 LYS cc_start: 0.7712 (ttmp) cc_final: 0.6896 (ttmt) REVERT: E 287 SER cc_start: 0.8052 (t) cc_final: 0.7372 (p) REVERT: E 346 MET cc_start: 0.7363 (tpp) cc_final: 0.6849 (tpp) REVERT: E 370 LEU cc_start: 0.8505 (tp) cc_final: 0.8209 (mt) REVERT: E 413 MET cc_start: 0.4997 (tpp) cc_final: 0.4654 (mpp) REVERT: E 479 LYS cc_start: 0.5202 (mtpt) cc_final: 0.4633 (mttm) REVERT: F 287 SER cc_start: 0.8094 (t) cc_final: 0.7446 (p) REVERT: F 346 MET cc_start: 0.7049 (tpp) cc_final: 0.6521 (tpp) REVERT: F 459 ILE cc_start: 0.7069 (tp) cc_final: 0.6742 (tp) REVERT: G 285 LYS cc_start: 0.7585 (ttmp) cc_final: 0.6927 (tttp) REVERT: G 287 SER cc_start: 0.8437 (t) cc_final: 0.7735 (p) REVERT: G 413 MET cc_start: 0.4984 (ptp) cc_final: 0.4601 (tpp) REVERT: G 461 MET cc_start: 0.7664 (mtp) cc_final: 0.7280 (mtt) outliers start: 81 outliers final: 76 residues processed: 258 average time/residue: 0.2646 time to fit residues: 101.8215 Evaluate side-chains 262 residues out of total 1659 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 78 poor density : 184 time to evaluate : 1.637 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 217 VAL Chi-restraints excluded: chain A residue 270 LYS Chi-restraints excluded: chain A residue 281 LEU Chi-restraints excluded: chain A residue 313 VAL Chi-restraints excluded: chain A residue 319 VAL Chi-restraints excluded: chain A residue 355 VAL Chi-restraints excluded: chain A residue 369 LEU Chi-restraints excluded: chain A residue 396 GLN Chi-restraints excluded: chain A residue 406 LEU Chi-restraints excluded: chain A residue 408 ILE Chi-restraints excluded: chain A residue 433 LEU Chi-restraints excluded: chain A residue 442 LEU Chi-restraints excluded: chain B residue 217 VAL Chi-restraints excluded: chain B residue 281 LEU Chi-restraints excluded: chain B residue 313 VAL Chi-restraints excluded: chain B residue 355 VAL Chi-restraints excluded: chain B residue 406 LEU Chi-restraints excluded: chain B residue 442 LEU Chi-restraints excluded: chain C residue 217 VAL Chi-restraints excluded: chain C residue 229 VAL Chi-restraints excluded: chain C residue 270 LYS Chi-restraints excluded: chain C residue 281 LEU Chi-restraints excluded: chain C residue 311 LEU Chi-restraints excluded: chain C residue 313 VAL Chi-restraints excluded: chain C residue 319 VAL Chi-restraints excluded: chain C residue 355 VAL Chi-restraints excluded: chain C residue 368 SER Chi-restraints excluded: chain C residue 369 LEU Chi-restraints excluded: chain C residue 388 VAL Chi-restraints excluded: chain C residue 396 GLN Chi-restraints excluded: chain C residue 406 LEU Chi-restraints excluded: chain C residue 408 ILE Chi-restraints excluded: chain C residue 433 LEU Chi-restraints excluded: chain C residue 442 LEU Chi-restraints excluded: chain D residue 217 VAL Chi-restraints excluded: chain D residue 229 VAL Chi-restraints excluded: chain D residue 262 VAL Chi-restraints excluded: chain D residue 270 LYS Chi-restraints excluded: chain D residue 281 LEU Chi-restraints excluded: chain D residue 313 VAL Chi-restraints excluded: chain D residue 319 VAL Chi-restraints excluded: chain D residue 355 VAL Chi-restraints excluded: chain D residue 368 SER Chi-restraints excluded: chain D residue 378 LEU Chi-restraints excluded: chain D residue 406 LEU Chi-restraints excluded: chain D residue 433 LEU Chi-restraints excluded: chain D residue 442 LEU Chi-restraints excluded: chain E residue 217 VAL Chi-restraints excluded: chain E residue 249 LEU Chi-restraints excluded: chain E residue 270 LYS Chi-restraints excluded: chain E residue 281 LEU Chi-restraints excluded: chain E residue 296 LEU Chi-restraints excluded: chain E residue 311 LEU Chi-restraints excluded: chain E residue 313 VAL Chi-restraints excluded: chain E residue 319 VAL Chi-restraints excluded: chain E residue 369 LEU Chi-restraints excluded: chain E residue 406 LEU Chi-restraints excluded: chain E residue 408 ILE Chi-restraints excluded: chain F residue 217 VAL Chi-restraints excluded: chain F residue 270 LYS Chi-restraints excluded: chain F residue 281 LEU Chi-restraints excluded: chain F residue 313 VAL Chi-restraints excluded: chain F residue 316 VAL Chi-restraints excluded: chain F residue 319 VAL Chi-restraints excluded: chain F residue 369 LEU Chi-restraints excluded: chain F residue 406 LEU Chi-restraints excluded: chain F residue 408 ILE Chi-restraints excluded: chain F residue 433 LEU Chi-restraints excluded: chain F residue 442 LEU Chi-restraints excluded: chain G residue 217 VAL Chi-restraints excluded: chain G residue 249 LEU Chi-restraints excluded: chain G residue 270 LYS Chi-restraints excluded: chain G residue 281 LEU Chi-restraints excluded: chain G residue 311 LEU Chi-restraints excluded: chain G residue 313 VAL Chi-restraints excluded: chain G residue 316 VAL Chi-restraints excluded: chain G residue 319 VAL Chi-restraints excluded: chain G residue 396 GLN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 196 random chunks: chunk 123 optimal weight: 3.9990 chunk 165 optimal weight: 3.9990 chunk 47 optimal weight: 4.9990 chunk 143 optimal weight: 0.2980 chunk 22 optimal weight: 0.9990 chunk 43 optimal weight: 2.9990 chunk 155 optimal weight: 2.9990 chunk 65 optimal weight: 0.8980 chunk 159 optimal weight: 5.9990 chunk 19 optimal weight: 5.9990 chunk 28 optimal weight: 9.9990 overall best weight: 1.6386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 407 GLN B 470 GLN C 339 GLN C 484 HIS E 470 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4201 r_free = 0.4201 target = 0.201566 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3749 r_free = 0.3749 target = 0.155097 restraints weight = 14075.555| |-----------------------------------------------------------------------------| r_work (start): 0.3721 rms_B_bonded: 2.52 r_work: 0.3403 rms_B_bonded: 3.35 restraints_weight: 0.5000 r_work (final): 0.3403 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6974 moved from start: 0.4324 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.045 15407 Z= 0.301 Angle : 0.704 12.460 20853 Z= 0.352 Chirality : 0.048 0.185 2527 Planarity : 0.003 0.031 2604 Dihedral : 5.548 18.515 2114 Min Nonbonded Distance : 2.536 Molprobity Statistics. All-atom Clashscore : 11.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.03 % Favored : 89.97 % Rotamer: Outliers : 5.13 % Allowed : 20.39 % Favored : 74.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.32 (0.17), residues: 1995 helix: -1.21 (0.16), residues: 1022 sheet: -2.18 (0.31), residues: 266 loop : -3.61 (0.19), residues: 707 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 397 HIS 0.003 0.001 HIS C 484 PHE 0.011 0.001 PHE D 432 TYR 0.005 0.001 TYR C 238 ARG 0.009 0.000 ARG D 426 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3098.54 seconds wall clock time: 57 minutes 34.09 seconds (3454.09 seconds total)