Starting phenix.real_space_refine on Wed Mar 4 17:33:58 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6lyp_30017/03_2026/6lyp_30017.cif Found real_map, /net/cci-nas-00/data/ceres_data/6lyp_30017/03_2026/6lyp_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 { model { file = "/net/cci-nas-00/data/ceres_data/6lyp_30017/03_2026/6lyp_30017.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6lyp_30017/03_2026/6lyp_30017.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/6lyp_30017/03_2026/6lyp_30017.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6lyp_30017/03_2026/6lyp_30017.map" } resolution = 3.3 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.011 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): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/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: B, C, D, E, F, G Time building chain proxies: 1.84, per 1000 atoms: 0.12 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: 1.15 Conformation dependent library (CDL) restraints added in 610.7 milliseconds 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: 0.48 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: 2.33 Time building geometry restraints manager: 1.56 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: 0.05 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: 1.140 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: 0.200 Check model and map are aligned: 0.050 Set scattering table: 0.040 Process input model: 12.430 Find NCS groups from input model: 0.130 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.330 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 15.350 ------------------------------------------------------------------------------- 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= 0.453 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -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 ARG 0.009 0.001 ARG F 398 TYR 0.033 0.005 TYR C 467 PHE 0.033 0.004 PHE A 323 TRP 0.037 0.005 TRP C 397 HIS 0.004 0.002 HIS E 484 Details of bonding type rmsd covalent geometry : bond 0.01107 (15407) covalent geometry : angle 1.34970 (20853) hydrogen bonds : bond 0.16299 ( 589) hydrogen bonds : angle 12.58424 ( 1743) *********************** 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 : 0.443 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: 0.7684 (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: 0.8566 (t) cc_final: 0.8203 (p) REVERT: E 346 MET cc_start: 0.7996 (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: 0.6392 (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: 0.8150 (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: 0.1272 time to fit residues: 57.7675 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 : 0.508 ------------------------------------------------------------------------------- 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 98 optimal weight: 1.9990 chunk 194 optimal weight: 0.9990 chunk 107 optimal weight: 6.9990 chunk 10 optimal weight: 0.7980 chunk 66 optimal weight: 0.7980 chunk 130 optimal weight: 1.9990 chunk 124 optimal weight: 0.7980 chunk 103 optimal weight: 3.9990 chunk 77 optimal weight: 3.9990 chunk 122 optimal weight: 5.9990 chunk 91 optimal weight: 5.9990 overall best weight: 1.0784 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4209 r_free = 0.4209 target = 0.204130 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3808 r_free = 0.3808 target = 0.160905 restraints weight = 13966.537| |-----------------------------------------------------------------------------| r_work (start): 0.3787 rms_B_bonded: 2.66 r_work: 0.3426 rms_B_bonded: 3.65 restraints_weight: 0.5000 r_work (final): 0.3426 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6904 moved from start: 0.2083 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.029 15407 Z= 0.166 Angle : 0.725 9.541 20853 Z= 0.381 Chirality : 0.048 0.158 2527 Planarity : 0.005 0.038 2604 Dihedral : 6.733 43.976 2118 Min Nonbonded Distance : 2.505 Molprobity Statistics. All-atom Clashscore : 10.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.92 % Favored : 92.08 % Rotamer: Outliers : 4.09 % Allowed : 13.25 % Favored : 82.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -5.18 (0.15), residues: 1995 helix: -3.07 (0.13), residues: 973 sheet: -1.84 (0.32), residues: 238 loop : -4.37 (0.17), residues: 784 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG D 398 TYR 0.010 0.001 TYR G 467 PHE 0.013 0.002 PHE G 323 TRP 0.018 0.002 TRP G 397 HIS 0.003 0.001 HIS C 484 Details of bonding type rmsd covalent geometry : bond 0.00376 (15407) covalent geometry : angle 0.72458 (20853) hydrogen bonds : bond 0.03225 ( 589) hydrogen bonds : angle 7.15612 ( 1743) *********************** 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 318 residues out of total 1659 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 251 time to evaluate : 0.546 Fit side-chains revert: symmetry clash REVERT: A 250 SER cc_start: 0.7575 (m) cc_final: 0.7146 (t) REVERT: A 253 TRP cc_start: 0.7332 (m-90) cc_final: 0.6313 (m100) REVERT: A 287 SER cc_start: 0.8572 (t) cc_final: 0.7974 (p) REVERT: A 308 GLN cc_start: 0.8213 (pm20) cc_final: 0.7942 (pm20) REVERT: A 474 LEU cc_start: 0.5937 (OUTLIER) cc_final: 0.5634 (tt) REVERT: A 484 HIS cc_start: 0.7024 (m-70) cc_final: 0.6480 (m90) REVERT: B 266 MET cc_start: 0.4994 (ttm) cc_final: 0.4701 (ttp) REVERT: B 278 GLU cc_start: 0.6751 (mt-10) cc_final: 0.6395 (tp30) REVERT: B 285 LYS cc_start: 0.8083 (ttmp) cc_final: 0.7600 (tttp) REVERT: B 287 SER cc_start: 0.8367 (t) cc_final: 0.7829 (p) REVERT: B 296 LEU cc_start: 0.8218 (OUTLIER) cc_final: 0.7953 (tp) REVERT: B 378 LEU cc_start: 0.8532 (tt) cc_final: 0.8329 (mp) REVERT: B 429 THR cc_start: 0.7126 (p) cc_final: 0.6926 (p) REVERT: B 432 PHE cc_start: 0.6433 (t80) cc_final: 0.5982 (t80) REVERT: B 436 GLU cc_start: 0.7871 (mp0) cc_final: 0.7560 (mt-10) REVERT: B 474 LEU cc_start: 0.5678 (OUTLIER) cc_final: 0.5381 (tt) REVERT: C 287 SER cc_start: 0.8412 (t) cc_final: 0.7874 (p) REVERT: C 308 GLN cc_start: 0.8187 (pm20) cc_final: 0.7948 (pm20) REVERT: C 447 LYS cc_start: 0.7156 (tppt) cc_final: 0.6827 (tptm) REVERT: C 474 LEU cc_start: 0.5727 (OUTLIER) cc_final: 0.5238 (tt) REVERT: D 278 GLU cc_start: 0.7172 (tp30) cc_final: 0.6365 (tt0) REVERT: D 287 SER cc_start: 0.8580 (t) cc_final: 0.8077 (p) REVERT: D 474 LEU cc_start: 0.6085 (OUTLIER) cc_final: 0.5815 (tp) REVERT: E 250 SER cc_start: 0.7112 (m) cc_final: 0.6736 (t) REVERT: E 278 GLU cc_start: 0.7206 (mt-10) cc_final: 0.6862 (tt0) REVERT: E 285 LYS cc_start: 0.7977 (ttmp) cc_final: 0.7478 (ttmt) REVERT: E 287 SER cc_start: 0.8491 (t) cc_final: 0.7953 (p) REVERT: E 338 MET cc_start: 0.7810 (mmp) cc_final: 0.7386 (mmp) REVERT: E 413 MET cc_start: 0.5105 (tpp) cc_final: 0.4860 (mpp) REVERT: E 479 LYS cc_start: 0.5475 (mtpt) cc_final: 0.4845 (mttp) REVERT: F 287 SER cc_start: 0.8427 (t) cc_final: 0.7847 (p) REVERT: F 292 PHE cc_start: 0.7146 (t80) cc_final: 0.6854 (t80) REVERT: F 346 MET cc_start: 0.7969 (mmt) cc_final: 0.7601 (mmm) REVERT: F 484 HIS cc_start: 0.6814 (m-70) cc_final: 0.6261 (m90) REVERT: G 266 MET cc_start: 0.5564 (ttm) cc_final: 0.5309 (ttp) REVERT: G 278 GLU cc_start: 0.7088 (mt-10) cc_final: 0.6709 (tt0) REVERT: G 285 LYS cc_start: 0.8107 (ttmp) cc_final: 0.7617 (tttp) REVERT: G 287 SER cc_start: 0.8567 (t) cc_final: 0.7996 (p) REVERT: G 338 MET cc_start: 0.7804 (mmp) cc_final: 0.7512 (mmp) REVERT: G 378 LEU cc_start: 0.8449 (tt) cc_final: 0.8247 (mp) REVERT: G 413 MET cc_start: 0.5203 (mpp) cc_final: 0.4782 (mpp) REVERT: G 436 GLU cc_start: 0.7813 (mp0) cc_final: 0.7413 (mt-10) REVERT: G 460 ARG cc_start: 0.7188 (tpt170) cc_final: 0.6896 (tpm170) outliers start: 67 outliers final: 37 residues processed: 301 average time/residue: 0.1072 time to fit residues: 49.0593 Evaluate side-chains 271 residues out of total 1659 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 229 time to evaluate : 0.462 ------------------------------------------------------------------------------- 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 433 LEU 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 C residue 474 LEU 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 378 LEU Chi-restraints excluded: chain D residue 408 ILE Chi-restraints excluded: chain D residue 436 GLU Chi-restraints excluded: chain D residue 474 LEU 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 229 VAL Chi-restraints excluded: chain G residue 316 VAL 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 2 optimal weight: 2.9990 chunk 106 optimal weight: 4.9990 chunk 103 optimal weight: 0.9980 chunk 121 optimal weight: 0.9990 chunk 42 optimal weight: 1.9990 chunk 150 optimal weight: 0.9990 chunk 146 optimal weight: 4.9990 chunk 110 optimal weight: 6.9990 chunk 161 optimal weight: 2.9990 chunk 36 optimal weight: 0.9980 chunk 156 optimal weight: 0.9980 overall best weight: 0.9984 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4211 r_free = 0.4211 target = 0.203909 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3801 r_free = 0.3801 target = 0.160169 restraints weight = 14084.345| |-----------------------------------------------------------------------------| r_work (start): 0.3791 rms_B_bonded: 2.65 r_work: 0.3425 rms_B_bonded: 3.70 restraints_weight: 0.5000 r_work (final): 0.3425 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6915 moved from start: 0.2731 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 15407 Z= 0.153 Angle : 0.670 7.578 20853 Z= 0.347 Chirality : 0.047 0.153 2527 Planarity : 0.004 0.033 2604 Dihedral : 6.080 37.664 2116 Min Nonbonded Distance : 2.498 Molprobity Statistics. All-atom Clashscore : 10.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.47 % Favored : 91.53 % Rotamer: Outliers : 6.35 % Allowed : 12.70 % Favored : 80.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -4.62 (0.16), residues: 1995 helix: -2.34 (0.15), residues: 938 sheet: -1.79 (0.32), residues: 238 loop : -4.36 (0.16), residues: 819 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG E 426 TYR 0.007 0.001 TYR E 441 PHE 0.011 0.001 PHE G 323 TRP 0.016 0.002 TRP B 397 HIS 0.003 0.001 HIS A 484 Details of bonding type rmsd covalent geometry : bond 0.00357 (15407) covalent geometry : angle 0.66976 (20853) hydrogen bonds : bond 0.02675 ( 589) hydrogen bonds : angle 6.31580 ( 1743) *********************** 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 344 residues out of total 1659 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 104 poor density : 240 time to evaluate : 0.546 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 253 TRP cc_start: 0.7213 (m-90) cc_final: 0.6213 (m100) REVERT: A 278 GLU cc_start: 0.6649 (tp30) cc_final: 0.5952 (mt-10) REVERT: A 287 SER cc_start: 0.8568 (t) cc_final: 0.7951 (p) REVERT: A 413 MET cc_start: 0.5296 (tpp) cc_final: 0.4837 (mpp) REVERT: A 474 LEU cc_start: 0.6011 (OUTLIER) cc_final: 0.5657 (tt) REVERT: B 270 LYS cc_start: 0.5696 (OUTLIER) cc_final: 0.5303 (tmtt) REVERT: B 287 SER cc_start: 0.8399 (t) cc_final: 0.7853 (p) REVERT: B 296 LEU cc_start: 0.8223 (OUTLIER) cc_final: 0.7939 (tp) REVERT: B 361 GLU cc_start: 0.8027 (mt-10) cc_final: 0.7743 (mt-10) REVERT: B 436 GLU cc_start: 0.7893 (mp0) cc_final: 0.7665 (mt-10) REVERT: C 287 SER cc_start: 0.8367 (t) cc_final: 0.7857 (p) REVERT: C 297 MET cc_start: 0.8844 (ttp) cc_final: 0.8600 (mtp) REVERT: C 308 GLN cc_start: 0.8287 (pm20) cc_final: 0.8050 (pm20) REVERT: C 413 MET cc_start: 0.4965 (mpp) cc_final: 0.4636 (mpp) REVERT: C 474 LEU cc_start: 0.5777 (OUTLIER) cc_final: 0.5221 (tt) REVERT: D 287 SER cc_start: 0.8598 (t) cc_final: 0.8060 (p) REVERT: D 296 LEU cc_start: 0.8145 (OUTLIER) cc_final: 0.7871 (tp) REVERT: D 446 GLU cc_start: 0.6608 (OUTLIER) cc_final: 0.5992 (mm-30) REVERT: D 474 LEU cc_start: 0.5971 (OUTLIER) cc_final: 0.5715 (tp) REVERT: D 484 HIS cc_start: 0.6819 (m-70) cc_final: 0.6225 (m90) REVERT: E 278 GLU cc_start: 0.7211 (mt-10) cc_final: 0.6857 (tt0) REVERT: E 287 SER cc_start: 0.8365 (t) cc_final: 0.7805 (p) REVERT: E 479 LYS cc_start: 0.5438 (mtpt) cc_final: 0.4856 (mttp) REVERT: F 287 SER cc_start: 0.8496 (t) cc_final: 0.7899 (p) REVERT: F 292 PHE cc_start: 0.7198 (t80) cc_final: 0.6929 (t80) REVERT: F 338 MET cc_start: 0.7803 (mmp) cc_final: 0.7495 (mmp) REVERT: F 361 GLU cc_start: 0.7855 (mt-10) cc_final: 0.7643 (mt-10) REVERT: F 446 GLU cc_start: 0.6585 (tt0) cc_final: 0.6327 (tt0) REVERT: G 266 MET cc_start: 0.5387 (ttm) cc_final: 0.5183 (ttp) REVERT: G 270 LYS cc_start: 0.5856 (OUTLIER) cc_final: 0.5543 (tmtt) REVERT: G 285 LYS cc_start: 0.8047 (ttmp) cc_final: 0.7526 (tttp) REVERT: G 287 SER cc_start: 0.8625 (t) cc_final: 0.8024 (p) REVERT: G 406 LEU cc_start: 0.6580 (OUTLIER) cc_final: 0.6314 (pp) REVERT: G 413 MET cc_start: 0.5276 (mpp) cc_final: 0.4871 (mpp) REVERT: G 436 GLU cc_start: 0.7759 (mp0) cc_final: 0.7391 (mt-10) REVERT: G 460 ARG cc_start: 0.7236 (tpt170) cc_final: 0.6910 (tpm170) outliers start: 104 outliers final: 65 residues processed: 326 average time/residue: 0.1003 time to fit residues: 50.5335 Evaluate side-chains 282 residues out of total 1659 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 74 poor density : 208 time to evaluate : 0.516 ------------------------------------------------------------------------------- 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 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 408 ILE Chi-restraints excluded: chain C residue 433 LEU Chi-restraints excluded: chain C residue 474 LEU Chi-restraints excluded: chain D residue 229 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 369 LEU Chi-restraints excluded: chain D residue 408 ILE Chi-restraints excluded: chain D residue 446 GLU Chi-restraints excluded: chain D residue 474 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 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 F residue 483 LYS 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 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 53 optimal weight: 0.9980 chunk 57 optimal weight: 5.9990 chunk 193 optimal weight: 0.9990 chunk 21 optimal weight: 0.6980 chunk 163 optimal weight: 2.9990 chunk 11 optimal weight: 3.9990 chunk 158 optimal weight: 0.6980 chunk 3 optimal weight: 0.0070 chunk 51 optimal weight: 5.9990 chunk 65 optimal weight: 0.8980 chunk 5 optimal weight: 3.9990 overall best weight: 0.6598 ------------------------------------------------------------------------------- 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 470 GLN C 484 HIS E 358 GLN F 470 GLN G 358 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4226 r_free = 0.4226 target = 0.206247 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3820 r_free = 0.3820 target = 0.162290 restraints weight = 13973.630| |-----------------------------------------------------------------------------| r_work (start): 0.3823 rms_B_bonded: 2.45 r_work: 0.3467 rms_B_bonded: 3.67 restraints_weight: 0.5000 r_work (final): 0.3467 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6921 moved from start: 0.3182 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 15407 Z= 0.124 Angle : 0.621 8.152 20853 Z= 0.324 Chirality : 0.045 0.138 2527 Planarity : 0.003 0.033 2604 Dihedral : 5.716 35.891 2116 Min Nonbonded Distance : 2.497 Molprobity Statistics. All-atom Clashscore : 10.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.92 % Favored : 92.08 % Rotamer: Outliers : 6.23 % Allowed : 15.63 % Favored : 78.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -4.19 (0.17), residues: 1995 helix: -1.80 (0.16), residues: 938 sheet: -2.38 (0.30), residues: 266 loop : -4.13 (0.16), residues: 791 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 426 TYR 0.005 0.001 TYR B 467 PHE 0.013 0.001 PHE E 432 TRP 0.011 0.001 TRP D 397 HIS 0.002 0.001 HIS B 484 Details of bonding type rmsd covalent geometry : bond 0.00277 (15407) covalent geometry : angle 0.62093 (20853) hydrogen bonds : bond 0.02342 ( 589) hydrogen bonds : angle 5.83644 ( 1743) *********************** 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 329 residues out of total 1659 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 102 poor density : 227 time to evaluate : 0.409 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: 0.6722 (tp30) cc_final: 0.6055 (mt-10) REVERT: A 287 SER cc_start: 0.8580 (t) cc_final: 0.7976 (p) REVERT: A 413 MET cc_start: 0.5208 (tpp) cc_final: 0.4808 (mpp) REVERT: A 474 LEU cc_start: 0.5796 (OUTLIER) cc_final: 0.5592 (tp) REVERT: B 270 LYS cc_start: 0.5491 (OUTLIER) cc_final: 0.5217 (tmtt) REVERT: B 285 LYS cc_start: 0.8147 (ttmp) cc_final: 0.7537 (tttp) REVERT: B 287 SER cc_start: 0.8410 (t) cc_final: 0.7842 (p) REVERT: B 296 LEU cc_start: 0.8221 (OUTLIER) cc_final: 0.7977 (tp) REVERT: B 368 SER cc_start: 0.8897 (OUTLIER) cc_final: 0.8695 (m) REVERT: B 413 MET cc_start: 0.5275 (tpp) cc_final: 0.4825 (mpp) REVERT: C 287 SER cc_start: 0.8483 (t) cc_final: 0.7946 (p) REVERT: C 308 GLN cc_start: 0.8175 (pm20) cc_final: 0.7973 (pm20) REVERT: C 447 LYS cc_start: 0.6974 (tptm) cc_final: 0.6719 (tppt) REVERT: C 474 LEU cc_start: 0.5845 (OUTLIER) cc_final: 0.5280 (tt) REVERT: D 270 LYS cc_start: 0.5841 (OUTLIER) cc_final: 0.5496 (tmtt) REVERT: D 287 SER cc_start: 0.8566 (t) cc_final: 0.8054 (p) REVERT: D 296 LEU cc_start: 0.8109 (OUTLIER) cc_final: 0.7884 (tp) REVERT: D 368 SER cc_start: 0.8904 (OUTLIER) cc_final: 0.8626 (m) REVERT: D 446 GLU cc_start: 0.6514 (OUTLIER) cc_final: 0.5948 (mm-30) REVERT: D 474 LEU cc_start: 0.6004 (OUTLIER) cc_final: 0.5770 (tp) REVERT: E 278 GLU cc_start: 0.7292 (mt-10) cc_final: 0.6973 (tt0) REVERT: E 287 SER cc_start: 0.8455 (t) cc_final: 0.7873 (p) REVERT: E 378 LEU cc_start: 0.8360 (OUTLIER) cc_final: 0.8133 (mp) REVERT: E 479 LYS cc_start: 0.5567 (mtpt) cc_final: 0.4975 (mttp) REVERT: F 287 SER cc_start: 0.8428 (t) cc_final: 0.7921 (p) REVERT: F 292 PHE cc_start: 0.7268 (t80) cc_final: 0.6992 (t80) REVERT: F 413 MET cc_start: 0.5332 (ptp) cc_final: 0.4732 (tpt) REVERT: G 270 LYS cc_start: 0.5795 (OUTLIER) cc_final: 0.5491 (tmtt) REVERT: G 285 LYS cc_start: 0.8022 (ttmp) cc_final: 0.7506 (tttp) REVERT: G 287 SER cc_start: 0.8487 (t) cc_final: 0.7921 (p) REVERT: G 368 SER cc_start: 0.8927 (OUTLIER) cc_final: 0.8706 (m) REVERT: G 436 GLU cc_start: 0.7704 (mp0) cc_final: 0.7289 (mt-10) outliers start: 102 outliers final: 74 residues processed: 303 average time/residue: 0.1103 time to fit residues: 50.1845 Evaluate side-chains 299 residues out of total 1659 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 87 poor density : 212 time to evaluate : 0.505 ------------------------------------------------------------------------------- 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 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 406 LEU Chi-restraints excluded: chain B residue 408 ILE Chi-restraints excluded: chain C residue 217 VAL 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 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 474 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 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 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 D residue 474 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 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 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 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 F residue 483 LYS Chi-restraints excluded: chain G residue 217 VAL Chi-restraints excluded: chain G residue 229 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 369 LEU Chi-restraints excluded: chain G residue 406 LEU Chi-restraints excluded: chain G residue 408 ILE Chi-restraints excluded: chain G residue 433 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 196 random chunks: chunk 33 optimal weight: 4.9990 chunk 176 optimal weight: 1.9990 chunk 115 optimal weight: 0.9980 chunk 106 optimal weight: 0.9990 chunk 47 optimal weight: 6.9990 chunk 182 optimal weight: 2.9990 chunk 138 optimal weight: 0.9980 chunk 45 optimal weight: 0.5980 chunk 101 optimal weight: 0.9990 chunk 118 optimal weight: 0.0670 chunk 110 optimal weight: 0.9990 overall best weight: 0.7320 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 484 HIS C 484 HIS D 484 HIS F 470 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4224 r_free = 0.4224 target = 0.206397 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3814 r_free = 0.3814 target = 0.162040 restraints weight = 13868.180| |-----------------------------------------------------------------------------| r_work (start): 0.3802 rms_B_bonded: 2.45 r_work: 0.3460 rms_B_bonded: 3.57 restraints_weight: 0.5000 r_work (final): 0.3460 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6921 moved from start: 0.3464 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 15407 Z= 0.126 Angle : 0.612 7.370 20853 Z= 0.317 Chirality : 0.045 0.158 2527 Planarity : 0.003 0.031 2604 Dihedral : 5.486 18.053 2114 Min Nonbonded Distance : 2.513 Molprobity Statistics. All-atom Clashscore : 10.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.32 % Favored : 91.68 % Rotamer: Outliers : 6.90 % Allowed : 16.24 % Favored : 76.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.90 (0.17), residues: 1995 helix: -1.57 (0.16), residues: 973 sheet: -2.33 (0.31), residues: 266 loop : -4.01 (0.17), residues: 756 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 426 TYR 0.006 0.001 TYR A 467 PHE 0.014 0.001 PHE D 432 TRP 0.012 0.001 TRP D 397 HIS 0.002 0.000 HIS C 484 Details of bonding type rmsd covalent geometry : bond 0.00288 (15407) covalent geometry : angle 0.61217 (20853) hydrogen bonds : bond 0.02306 ( 589) hydrogen bonds : angle 5.59782 ( 1743) *********************** 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 326 residues out of total 1659 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 113 poor density : 213 time to evaluate : 0.454 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: 0.6710 (tp30) cc_final: 0.6087 (mt-10) REVERT: A 287 SER cc_start: 0.8553 (t) cc_final: 0.7964 (p) REVERT: A 474 LEU cc_start: 0.5925 (OUTLIER) cc_final: 0.5711 (tp) REVERT: A 484 HIS cc_start: 0.6995 (m-70) cc_final: 0.6729 (m90) REVERT: B 285 LYS cc_start: 0.8116 (ttmp) cc_final: 0.7520 (tttp) REVERT: B 287 SER cc_start: 0.8548 (t) cc_final: 0.7952 (p) REVERT: B 296 LEU cc_start: 0.8180 (OUTLIER) cc_final: 0.7941 (tp) REVERT: B 368 SER cc_start: 0.8881 (OUTLIER) cc_final: 0.8663 (m) REVERT: B 413 MET cc_start: 0.5122 (tpp) cc_final: 0.4778 (mpp) REVERT: B 459 ILE cc_start: 0.7099 (tp) cc_final: 0.6859 (tp) REVERT: B 479 LYS cc_start: 0.5611 (mtpt) cc_final: 0.5089 (mttp) REVERT: C 287 SER cc_start: 0.8447 (t) cc_final: 0.7949 (p) REVERT: C 297 MET cc_start: 0.9069 (mtp) cc_final: 0.8770 (mtp) REVERT: C 447 LYS cc_start: 0.6962 (tptm) cc_final: 0.6734 (tppt) REVERT: C 474 LEU cc_start: 0.5839 (OUTLIER) cc_final: 0.5259 (tt) REVERT: D 270 LYS cc_start: 0.5823 (OUTLIER) cc_final: 0.5482 (tmtt) REVERT: D 287 SER cc_start: 0.8606 (t) cc_final: 0.8096 (p) REVERT: D 446 GLU cc_start: 0.6494 (OUTLIER) cc_final: 0.5917 (mm-30) REVERT: D 474 LEU cc_start: 0.6085 (OUTLIER) cc_final: 0.5821 (tp) REVERT: E 278 GLU cc_start: 0.7326 (mt-10) cc_final: 0.7075 (tt0) REVERT: E 285 LYS cc_start: 0.7937 (ttmp) cc_final: 0.7374 (ttmt) REVERT: E 287 SER cc_start: 0.8409 (t) cc_final: 0.7831 (p) REVERT: E 368 SER cc_start: 0.8846 (p) cc_final: 0.8583 (m) REVERT: E 378 LEU cc_start: 0.8325 (OUTLIER) cc_final: 0.8107 (mp) REVERT: E 479 LYS cc_start: 0.5686 (mtpt) cc_final: 0.4988 (mttm) REVERT: F 287 SER cc_start: 0.8484 (t) cc_final: 0.7991 (p) REVERT: F 413 MET cc_start: 0.5211 (OUTLIER) cc_final: 0.4592 (tpt) REVERT: F 459 ILE cc_start: 0.7255 (tp) cc_final: 0.6945 (tp) REVERT: G 270 LYS cc_start: 0.5641 (OUTLIER) cc_final: 0.5394 (tmtt) REVERT: G 285 LYS cc_start: 0.7980 (ttmp) cc_final: 0.7440 (tttp) REVERT: G 287 SER cc_start: 0.8583 (t) cc_final: 0.8027 (p) REVERT: G 436 GLU cc_start: 0.7799 (mp0) cc_final: 0.7430 (mt-10) outliers start: 113 outliers final: 81 residues processed: 303 average time/residue: 0.1062 time to fit residues: 48.7141 Evaluate side-chains 293 residues out of total 1659 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 91 poor density : 202 time to evaluate : 0.489 ------------------------------------------------------------------------------- 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 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 311 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 406 LEU Chi-restraints excluded: chain B residue 408 ILE Chi-restraints excluded: chain B residue 436 GLU Chi-restraints excluded: chain B residue 469 THR 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 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 474 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 406 LEU Chi-restraints excluded: chain D residue 408 ILE Chi-restraints excluded: chain D residue 442 LEU Chi-restraints excluded: chain D residue 446 GLU Chi-restraints excluded: chain D residue 474 LEU Chi-restraints excluded: chain E residue 216 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 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 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 369 LEU 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 F residue 483 LYS Chi-restraints excluded: chain G residue 217 VAL Chi-restraints excluded: chain G residue 229 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 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 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 122 optimal weight: 0.8980 chunk 25 optimal weight: 10.0000 chunk 93 optimal weight: 0.6980 chunk 139 optimal weight: 2.9990 chunk 153 optimal weight: 0.2980 chunk 26 optimal weight: 0.8980 chunk 168 optimal weight: 10.0000 chunk 140 optimal weight: 9.9990 chunk 133 optimal weight: 0.8980 chunk 88 optimal weight: 2.9990 chunk 108 optimal weight: 0.8980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 484 HIS D 484 HIS F 471 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4228 r_free = 0.4228 target = 0.207168 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3822 r_free = 0.3822 target = 0.163447 restraints weight = 13692.982| |-----------------------------------------------------------------------------| r_work (start): 0.3801 rms_B_bonded: 2.66 r_work: 0.3450 rms_B_bonded: 3.59 restraints_weight: 0.5000 r_work (final): 0.3450 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6885 moved from start: 0.3682 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= 0.124 Angle : 0.608 8.008 20853 Z= 0.312 Chirality : 0.045 0.137 2527 Planarity : 0.003 0.032 2604 Dihedral : 5.391 17.346 2114 Min Nonbonded Distance : 2.529 Molprobity Statistics. All-atom Clashscore : 10.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.17 % Favored : 91.83 % Rotamer: Outliers : 5.98 % Allowed : 16.97 % Favored : 77.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.64 (0.17), residues: 1995 helix: -1.28 (0.16), residues: 952 sheet: -1.83 (0.33), residues: 238 loop : -4.05 (0.16), residues: 805 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG G 326 TYR 0.005 0.001 TYR E 441 PHE 0.014 0.001 PHE E 432 TRP 0.011 0.001 TRP C 397 HIS 0.003 0.001 HIS C 484 Details of bonding type rmsd covalent geometry : bond 0.00282 (15407) covalent geometry : angle 0.60777 (20853) hydrogen bonds : bond 0.02228 ( 589) hydrogen bonds : angle 5.47288 ( 1743) *********************** 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 303 residues out of total 1659 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 98 poor density : 205 time to evaluate : 0.543 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: 0.6627 (tp30) cc_final: 0.6047 (mt-10) REVERT: A 287 SER cc_start: 0.8543 (t) cc_final: 0.7915 (p) REVERT: A 474 LEU cc_start: 0.5912 (OUTLIER) cc_final: 0.5701 (tp) REVERT: B 284 ASP cc_start: 0.6177 (m-30) cc_final: 0.5970 (m-30) REVERT: B 285 LYS cc_start: 0.8133 (ttmp) cc_final: 0.7459 (tttp) REVERT: B 287 SER cc_start: 0.8540 (t) cc_final: 0.7913 (p) REVERT: B 296 LEU cc_start: 0.8175 (OUTLIER) cc_final: 0.7942 (tp) REVERT: B 368 SER cc_start: 0.8897 (OUTLIER) cc_final: 0.8694 (m) REVERT: B 413 MET cc_start: 0.5028 (tpp) cc_final: 0.4643 (mpp) REVERT: B 459 ILE cc_start: 0.7148 (tp) cc_final: 0.6863 (tp) REVERT: B 479 LYS cc_start: 0.5545 (mtpt) cc_final: 0.5029 (mttp) REVERT: C 287 SER cc_start: 0.8468 (t) cc_final: 0.7951 (p) REVERT: C 447 LYS cc_start: 0.7102 (tptm) cc_final: 0.6871 (tppt) REVERT: C 474 LEU cc_start: 0.5645 (OUTLIER) cc_final: 0.5049 (tt) REVERT: D 270 LYS cc_start: 0.5809 (OUTLIER) cc_final: 0.5441 (tmtt) REVERT: D 278 GLU cc_start: 0.7125 (tp30) cc_final: 0.6321 (tt0) REVERT: D 287 SER cc_start: 0.8612 (t) cc_final: 0.8014 (p) REVERT: D 446 GLU cc_start: 0.6468 (OUTLIER) cc_final: 0.5873 (mm-30) REVERT: D 474 LEU cc_start: 0.5873 (OUTLIER) cc_final: 0.5636 (tp) REVERT: E 278 GLU cc_start: 0.7406 (mt-10) cc_final: 0.7139 (tt0) REVERT: E 285 LYS cc_start: 0.7926 (ttmp) cc_final: 0.7338 (ttmt) REVERT: E 287 SER cc_start: 0.8294 (t) cc_final: 0.7695 (p) REVERT: E 368 SER cc_start: 0.8851 (p) cc_final: 0.8624 (m) REVERT: E 378 LEU cc_start: 0.8323 (OUTLIER) cc_final: 0.8118 (mp) REVERT: E 479 LYS cc_start: 0.5668 (mtpt) cc_final: 0.4963 (mttm) REVERT: F 287 SER cc_start: 0.8493 (t) cc_final: 0.7951 (p) REVERT: F 413 MET cc_start: 0.5219 (ptp) cc_final: 0.4579 (tpt) REVERT: F 459 ILE cc_start: 0.7220 (tp) cc_final: 0.6898 (tp) REVERT: G 270 LYS cc_start: 0.5757 (OUTLIER) cc_final: 0.5391 (tmtt) REVERT: G 285 LYS cc_start: 0.7961 (ttmp) cc_final: 0.7404 (tttp) REVERT: G 287 SER cc_start: 0.8538 (t) cc_final: 0.7924 (p) REVERT: G 413 MET cc_start: 0.5637 (ptt) cc_final: 0.4943 (tpp) REVERT: G 432 PHE cc_start: 0.6611 (t80) cc_final: 0.6194 (t80) REVERT: G 436 GLU cc_start: 0.7878 (mp0) cc_final: 0.7640 (mt-10) outliers start: 98 outliers final: 81 residues processed: 282 average time/residue: 0.1088 time to fit residues: 46.0588 Evaluate side-chains 287 residues out of total 1659 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 90 poor density : 197 time to evaluate : 0.436 ------------------------------------------------------------------------------- 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 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 296 LEU Chi-restraints excluded: chain B residue 311 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 406 LEU Chi-restraints excluded: chain B residue 408 ILE Chi-restraints excluded: chain B residue 436 GLU 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 474 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 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 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 D residue 446 GLU Chi-restraints excluded: chain D residue 474 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 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 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 369 LEU 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 433 LEU Chi-restraints excluded: chain F residue 442 LEU Chi-restraints excluded: chain F residue 483 LYS 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 369 LEU Chi-restraints excluded: chain G residue 408 ILE 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 40 optimal weight: 0.0770 chunk 98 optimal weight: 1.9990 chunk 114 optimal weight: 6.9990 chunk 73 optimal weight: 0.6980 chunk 29 optimal weight: 0.9980 chunk 113 optimal weight: 4.9990 chunk 85 optimal weight: 0.9990 chunk 93 optimal weight: 3.9990 chunk 101 optimal weight: 0.5980 chunk 175 optimal weight: 0.6980 chunk 53 optimal weight: 7.9990 overall best weight: 0.6138 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 484 HIS D 484 HIS E 470 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4231 r_free = 0.4231 target = 0.208705 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3838 r_free = 0.3838 target = 0.166871 restraints weight = 13840.632| |-----------------------------------------------------------------------------| r_work (start): 0.3827 rms_B_bonded: 2.12 r_work: 0.3474 rms_B_bonded: 3.39 restraints_weight: 0.5000 r_work (final): 0.3474 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6953 moved from start: 0.3926 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= 0.115 Angle : 0.601 8.696 20853 Z= 0.306 Chirality : 0.045 0.136 2527 Planarity : 0.003 0.032 2604 Dihedral : 5.235 17.590 2114 Min Nonbonded Distance : 2.542 Molprobity Statistics. All-atom Clashscore : 10.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.92 % Favored : 92.08 % Rotamer: Outliers : 5.80 % Allowed : 17.83 % Favored : 76.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.44 (0.17), residues: 1995 helix: -1.03 (0.17), residues: 952 sheet: -2.24 (0.31), residues: 266 loop : -3.91 (0.17), residues: 777 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG D 426 TYR 0.005 0.001 TYR E 441 PHE 0.010 0.001 PHE E 432 TRP 0.011 0.001 TRP C 397 HIS 0.003 0.000 HIS C 484 Details of bonding type rmsd covalent geometry : bond 0.00260 (15407) covalent geometry : angle 0.60066 (20853) hydrogen bonds : bond 0.02139 ( 589) hydrogen bonds : angle 5.28352 ( 1743) *********************** 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 294 residues out of total 1659 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 95 poor density : 199 time to evaluate : 0.559 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: 0.6536 (tp30) cc_final: 0.6087 (mt-10) REVERT: A 287 SER cc_start: 0.8576 (t) cc_final: 0.7971 (p) REVERT: A 370 LEU cc_start: 0.8762 (tp) cc_final: 0.8529 (mt) REVERT: A 413 MET cc_start: 0.4982 (tpp) cc_final: 0.4528 (mpp) REVERT: A 424 MET cc_start: 0.7562 (tmm) cc_final: 0.7336 (ppp) REVERT: A 446 GLU cc_start: 0.6532 (tt0) cc_final: 0.6322 (mm-30) REVERT: A 461 MET cc_start: 0.7492 (mtp) cc_final: 0.6953 (mtp) REVERT: B 285 LYS cc_start: 0.8167 (ttmp) cc_final: 0.7482 (tttp) REVERT: B 287 SER cc_start: 0.8531 (t) cc_final: 0.7935 (p) REVERT: B 413 MET cc_start: 0.5052 (tpp) cc_final: 0.4640 (mpp) REVERT: B 459 ILE cc_start: 0.7224 (tp) cc_final: 0.6950 (tp) REVERT: B 479 LYS cc_start: 0.5643 (mtpt) cc_final: 0.5121 (mttp) REVERT: C 287 SER cc_start: 0.8605 (t) cc_final: 0.8122 (p) REVERT: C 368 SER cc_start: 0.8937 (OUTLIER) cc_final: 0.8669 (m) REVERT: C 474 LEU cc_start: 0.5878 (OUTLIER) cc_final: 0.5267 (tt) REVERT: D 270 LYS cc_start: 0.5748 (OUTLIER) cc_final: 0.5444 (tmtt) REVERT: D 278 GLU cc_start: 0.7064 (tp30) cc_final: 0.6388 (tt0) REVERT: D 287 SER cc_start: 0.8638 (t) cc_final: 0.8073 (p) REVERT: D 446 GLU cc_start: 0.6515 (OUTLIER) cc_final: 0.5943 (mm-30) REVERT: D 474 LEU cc_start: 0.6103 (OUTLIER) cc_final: 0.5512 (tt) REVERT: E 278 GLU cc_start: 0.7393 (mt-10) cc_final: 0.7169 (tt0) REVERT: E 285 LYS cc_start: 0.7976 (ttmp) cc_final: 0.7425 (tttt) REVERT: E 287 SER cc_start: 0.8275 (t) cc_final: 0.7699 (p) REVERT: E 479 LYS cc_start: 0.5777 (mtpt) cc_final: 0.5080 (mttm) REVERT: F 287 SER cc_start: 0.8519 (t) cc_final: 0.8038 (p) REVERT: F 413 MET cc_start: 0.5350 (ptp) cc_final: 0.4735 (tpt) REVERT: F 459 ILE cc_start: 0.7226 (tp) cc_final: 0.6921 (tp) REVERT: G 285 LYS cc_start: 0.8020 (ttmp) cc_final: 0.7460 (tttp) REVERT: G 287 SER cc_start: 0.8569 (t) cc_final: 0.7996 (p) REVERT: G 368 SER cc_start: 0.8612 (OUTLIER) cc_final: 0.8386 (m) REVERT: G 413 MET cc_start: 0.5588 (ptt) cc_final: 0.4971 (tpp) REVERT: G 432 PHE cc_start: 0.6569 (t80) cc_final: 0.6231 (t80) REVERT: G 436 GLU cc_start: 0.7753 (mp0) cc_final: 0.7546 (mt-10) outliers start: 95 outliers final: 80 residues processed: 275 average time/residue: 0.1056 time to fit residues: 44.3075 Evaluate side-chains 280 residues out of total 1659 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 86 poor density : 194 time to evaluate : 0.463 ------------------------------------------------------------------------------- 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 311 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 369 LEU Chi-restraints excluded: chain B residue 406 LEU Chi-restraints excluded: chain B residue 408 ILE Chi-restraints excluded: chain B residue 436 GLU 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 474 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 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 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 D residue 446 GLU Chi-restraints excluded: chain D residue 474 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 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 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 F residue 483 LYS 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 355 VAL Chi-restraints excluded: chain G residue 368 SER Chi-restraints excluded: chain G residue 369 LEU Chi-restraints excluded: chain G residue 406 LEU Chi-restraints excluded: chain G residue 408 ILE 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 163 optimal weight: 5.9990 chunk 145 optimal weight: 0.9990 chunk 152 optimal weight: 1.9990 chunk 2 optimal weight: 0.3980 chunk 13 optimal weight: 0.4980 chunk 187 optimal weight: 3.9990 chunk 85 optimal weight: 1.9990 chunk 71 optimal weight: 2.9990 chunk 47 optimal weight: 6.9990 chunk 36 optimal weight: 0.6980 chunk 162 optimal weight: 5.9990 overall best weight: 0.9184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 339 GLN C 484 HIS F 471 GLN G 407 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4213 r_free = 0.4213 target = 0.206867 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3815 r_free = 0.3815 target = 0.164652 restraints weight = 14068.064| |-----------------------------------------------------------------------------| r_work (start): 0.3805 rms_B_bonded: 2.16 r_work: 0.3454 rms_B_bonded: 3.33 restraints_weight: 0.5000 r_work (final): 0.3454 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6970 moved from start: 0.4004 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 15407 Z= 0.134 Angle : 0.618 10.810 20853 Z= 0.314 Chirality : 0.045 0.138 2527 Planarity : 0.003 0.033 2604 Dihedral : 5.288 16.997 2114 Min Nonbonded Distance : 2.552 Molprobity Statistics. All-atom Clashscore : 10.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.47 % Favored : 91.53 % Rotamer: Outliers : 5.86 % Allowed : 18.07 % Favored : 76.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.29 (0.17), residues: 1995 helix: -0.91 (0.17), residues: 938 sheet: -2.18 (0.32), residues: 266 loop : -3.79 (0.17), residues: 791 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG D 426 TYR 0.005 0.001 TYR E 441 PHE 0.010 0.001 PHE A 432 TRP 0.012 0.001 TRP C 397 HIS 0.002 0.000 HIS C 484 Details of bonding type rmsd covalent geometry : bond 0.00313 (15407) covalent geometry : angle 0.61759 (20853) hydrogen bonds : bond 0.02254 ( 589) hydrogen bonds : angle 5.33803 ( 1743) *********************** 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 295 residues out of total 1659 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 96 poor density : 199 time to evaluate : 0.567 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 278 GLU cc_start: 0.6531 (tp30) cc_final: 0.6091 (mt-10) REVERT: A 287 SER cc_start: 0.8495 (t) cc_final: 0.7896 (p) REVERT: A 413 MET cc_start: 0.4855 (tpp) cc_final: 0.4525 (mpp) REVERT: A 424 MET cc_start: 0.7619 (tmm) cc_final: 0.7360 (ppp) REVERT: A 446 GLU cc_start: 0.6532 (tt0) cc_final: 0.6300 (mm-30) REVERT: A 484 HIS cc_start: 0.6970 (m-70) cc_final: 0.6652 (m90) REVERT: B 285 LYS cc_start: 0.8184 (ttmp) cc_final: 0.7506 (tttp) REVERT: B 287 SER cc_start: 0.8478 (t) cc_final: 0.7891 (p) REVERT: B 296 LEU cc_start: 0.8178 (OUTLIER) cc_final: 0.7947 (tp) REVERT: B 413 MET cc_start: 0.4898 (tpp) cc_final: 0.4669 (tpt) REVERT: B 432 PHE cc_start: 0.6490 (t80) cc_final: 0.6268 (t80) REVERT: B 459 ILE cc_start: 0.7267 (tp) cc_final: 0.6969 (tp) REVERT: B 479 LYS cc_start: 0.5658 (mtpt) cc_final: 0.5134 (mttp) REVERT: C 285 LYS cc_start: 0.8097 (ttmp) cc_final: 0.7407 (tttp) REVERT: C 287 SER cc_start: 0.8613 (t) cc_final: 0.8096 (p) REVERT: C 413 MET cc_start: 0.5457 (tpt) cc_final: 0.4836 (mpp) REVERT: C 474 LEU cc_start: 0.5927 (OUTLIER) cc_final: 0.5304 (tt) REVERT: D 270 LYS cc_start: 0.5775 (OUTLIER) cc_final: 0.5438 (tmtt) REVERT: D 278 GLU cc_start: 0.7077 (tp30) cc_final: 0.6389 (tt0) REVERT: D 285 LYS cc_start: 0.7894 (ttmp) cc_final: 0.7276 (tttp) REVERT: D 287 SER cc_start: 0.8617 (t) cc_final: 0.8049 (p) REVERT: D 338 MET cc_start: 0.7838 (mmp) cc_final: 0.7487 (mmp) REVERT: D 413 MET cc_start: 0.5221 (ptp) cc_final: 0.4945 (tpp) REVERT: D 474 LEU cc_start: 0.6072 (OUTLIER) cc_final: 0.5466 (tt) REVERT: E 285 LYS cc_start: 0.7943 (ttmp) cc_final: 0.7403 (tttt) REVERT: E 287 SER cc_start: 0.8275 (t) cc_final: 0.7684 (p) REVERT: E 479 LYS cc_start: 0.5694 (mtpt) cc_final: 0.5006 (mttm) REVERT: F 287 SER cc_start: 0.8545 (t) cc_final: 0.8035 (p) REVERT: F 413 MET cc_start: 0.5354 (ptp) cc_final: 0.4707 (tpt) REVERT: F 432 PHE cc_start: 0.6497 (t80) cc_final: 0.6086 (t80) REVERT: F 459 ILE cc_start: 0.7289 (tp) cc_final: 0.6851 (tp) REVERT: F 466 LEU cc_start: 0.6893 (tt) cc_final: 0.6263 (tp) REVERT: G 285 LYS cc_start: 0.8050 (ttmp) cc_final: 0.7457 (tttp) REVERT: G 287 SER cc_start: 0.8586 (t) cc_final: 0.8004 (p) REVERT: G 413 MET cc_start: 0.5590 (ptt) cc_final: 0.4940 (tpp) outliers start: 96 outliers final: 80 residues processed: 279 average time/residue: 0.1090 time to fit residues: 45.5115 Evaluate side-chains 275 residues out of total 1659 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 84 poor density : 191 time to evaluate : 0.457 ------------------------------------------------------------------------------- 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 296 LEU Chi-restraints excluded: chain B residue 311 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 369 LEU 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 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 474 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 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 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 D residue 474 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 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 408 ILE Chi-restraints excluded: chain F residue 433 LEU Chi-restraints excluded: chain F residue 442 LEU Chi-restraints excluded: chain F residue 483 LYS 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 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 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 117 optimal weight: 0.8980 chunk 7 optimal weight: 6.9990 chunk 132 optimal weight: 2.9990 chunk 48 optimal weight: 4.9990 chunk 79 optimal weight: 1.9990 chunk 172 optimal weight: 0.7980 chunk 47 optimal weight: 4.9990 chunk 49 optimal weight: 1.9990 chunk 133 optimal weight: 0.9990 chunk 183 optimal weight: 3.9990 chunk 192 optimal weight: 0.9980 overall best weight: 1.1384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 339 GLN ** C 484 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 471 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4228 r_free = 0.4228 target = 0.205444 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3780 r_free = 0.3780 target = 0.157902 restraints weight = 13903.696| |-----------------------------------------------------------------------------| r_work (start): 0.3774 rms_B_bonded: 2.55 r_work: 0.3436 rms_B_bonded: 3.65 restraints_weight: 0.5000 r_work (final): 0.3436 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6955 moved from start: 0.4123 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 15407 Z= 0.152 Angle : 0.636 11.918 20853 Z= 0.323 Chirality : 0.046 0.194 2527 Planarity : 0.003 0.033 2604 Dihedral : 5.369 20.485 2114 Min Nonbonded Distance : 2.557 Molprobity Statistics. All-atom Clashscore : 10.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.12 % Favored : 90.88 % Rotamer: Outliers : 5.49 % Allowed : 18.62 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.25 (0.17), residues: 1995 helix: -0.93 (0.17), residues: 952 sheet: -2.14 (0.32), residues: 266 loop : -3.74 (0.17), residues: 777 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG D 426 TYR 0.006 0.001 TYR F 467 PHE 0.010 0.001 PHE A 432 TRP 0.013 0.001 TRP C 397 HIS 0.004 0.001 HIS C 484 Details of bonding type rmsd covalent geometry : bond 0.00359 (15407) covalent geometry : angle 0.63642 (20853) hydrogen bonds : bond 0.02323 ( 589) hydrogen bonds : angle 5.40707 ( 1743) *********************** 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 284 residues out of total 1659 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 90 poor density : 194 time to evaluate : 0.529 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 278 GLU cc_start: 0.6655 (tp30) cc_final: 0.6080 (mt-10) REVERT: A 287 SER cc_start: 0.8481 (t) cc_final: 0.7854 (p) REVERT: A 413 MET cc_start: 0.4788 (tpp) cc_final: 0.4459 (mpp) REVERT: A 484 HIS cc_start: 0.6890 (m-70) cc_final: 0.6559 (m90) REVERT: B 285 LYS cc_start: 0.8180 (ttmp) cc_final: 0.7477 (tttp) REVERT: B 287 SER cc_start: 0.8488 (t) cc_final: 0.7881 (p) REVERT: B 296 LEU cc_start: 0.8204 (OUTLIER) cc_final: 0.7950 (tp) REVERT: B 413 MET cc_start: 0.4905 (tpp) cc_final: 0.4615 (mpp) REVERT: B 459 ILE cc_start: 0.7189 (tp) cc_final: 0.6882 (tp) REVERT: B 479 LYS cc_start: 0.5460 (mtpt) cc_final: 0.4950 (mttp) REVERT: C 285 LYS cc_start: 0.8020 (ttmp) cc_final: 0.7340 (tttp) REVERT: C 287 SER cc_start: 0.8654 (t) cc_final: 0.8096 (p) REVERT: C 447 LYS cc_start: 0.6703 (tptm) cc_final: 0.5286 (ttpp) REVERT: C 474 LEU cc_start: 0.5642 (OUTLIER) cc_final: 0.5029 (tt) REVERT: D 270 LYS cc_start: 0.5762 (OUTLIER) cc_final: 0.5387 (tmtt) REVERT: D 278 GLU cc_start: 0.7143 (tp30) cc_final: 0.6358 (tt0) REVERT: D 287 SER cc_start: 0.8625 (t) cc_final: 0.8048 (p) REVERT: D 338 MET cc_start: 0.7837 (mmp) cc_final: 0.7464 (mmp) REVERT: D 413 MET cc_start: 0.5325 (ptp) cc_final: 0.4840 (tpt) REVERT: D 474 LEU cc_start: 0.5907 (OUTLIER) cc_final: 0.5334 (tt) REVERT: E 285 LYS cc_start: 0.7897 (ttmp) cc_final: 0.7223 (tttt) REVERT: E 287 SER cc_start: 0.8261 (t) cc_final: 0.7615 (p) REVERT: E 346 MET cc_start: 0.6730 (tpt) cc_final: 0.6324 (tpt) REVERT: E 413 MET cc_start: 0.4857 (ptp) cc_final: 0.4540 (tpp) REVERT: E 479 LYS cc_start: 0.5556 (mtpt) cc_final: 0.4901 (mttm) REVERT: F 287 SER cc_start: 0.8451 (t) cc_final: 0.7849 (p) REVERT: F 338 MET cc_start: 0.7926 (mmp) cc_final: 0.7517 (mmp) REVERT: F 413 MET cc_start: 0.5492 (ptp) cc_final: 0.4700 (tpt) REVERT: F 466 LEU cc_start: 0.6852 (tt) cc_final: 0.6619 (tp) REVERT: G 285 LYS cc_start: 0.8047 (ttmp) cc_final: 0.7445 (tttp) REVERT: G 287 SER cc_start: 0.8640 (t) cc_final: 0.8059 (p) REVERT: G 413 MET cc_start: 0.5699 (ptt) cc_final: 0.4959 (tpp) REVERT: G 436 GLU cc_start: 0.7869 (mp0) cc_final: 0.7515 (mt-10) REVERT: G 460 ARG cc_start: 0.7330 (tpt170) cc_final: 0.7120 (tpm170) outliers start: 90 outliers final: 81 residues processed: 271 average time/residue: 0.1093 time to fit residues: 44.5466 Evaluate side-chains 273 residues out of total 1659 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 85 poor density : 188 time to evaluate : 0.427 ------------------------------------------------------------------------------- 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 296 LEU Chi-restraints excluded: chain B residue 311 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 369 LEU 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 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 474 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 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 406 LEU Chi-restraints excluded: chain D residue 408 ILE Chi-restraints excluded: chain D residue 442 LEU Chi-restraints excluded: chain D residue 474 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 355 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 249 LEU 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 408 ILE Chi-restraints excluded: chain F residue 433 LEU Chi-restraints excluded: chain F residue 442 LEU Chi-restraints excluded: chain F residue 483 LYS 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 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 Chi-restraints excluded: chain G residue 433 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 196 random chunks: chunk 23 optimal weight: 1.9990 chunk 10 optimal weight: 0.9990 chunk 33 optimal weight: 3.9990 chunk 72 optimal weight: 1.9990 chunk 60 optimal weight: 0.9980 chunk 99 optimal weight: 0.9990 chunk 181 optimal weight: 0.9990 chunk 11 optimal weight: 0.8980 chunk 132 optimal weight: 1.9990 chunk 78 optimal weight: 0.6980 chunk 154 optimal weight: 3.9990 overall best weight: 0.9184 ------------------------------------------------------------------------------- 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 ** C 484 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4210 r_free = 0.4210 target = 0.206333 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.3817 r_free = 0.3817 target = 0.164505 restraints weight = 13990.208| |-----------------------------------------------------------------------------| r_work (start): 0.3807 rms_B_bonded: 2.25 r_work: 0.3435 rms_B_bonded: 3.42 restraints_weight: 0.5000 r_work (final): 0.3435 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6968 moved from start: 0.4224 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 15407 Z= 0.137 Angle : 0.626 12.295 20853 Z= 0.318 Chirality : 0.045 0.171 2527 Planarity : 0.003 0.033 2604 Dihedral : 5.289 19.321 2114 Min Nonbonded Distance : 2.567 Molprobity Statistics. All-atom Clashscore : 10.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.37 % Favored : 91.63 % Rotamer: Outliers : 5.31 % Allowed : 18.86 % Favored : 75.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.15 (0.18), residues: 1995 helix: -0.91 (0.17), residues: 980 sheet: -2.15 (0.31), residues: 266 loop : -3.65 (0.18), residues: 749 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG D 426 TYR 0.006 0.001 TYR E 441 PHE 0.013 0.001 PHE G 432 TRP 0.013 0.001 TRP C 397 HIS 0.003 0.001 HIS C 484 Details of bonding type rmsd covalent geometry : bond 0.00320 (15407) covalent geometry : angle 0.62592 (20853) hydrogen bonds : bond 0.02245 ( 589) hydrogen bonds : angle 5.31687 ( 1743) ********************** 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 276 residues out of total 1659 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 87 poor density : 189 time to evaluate : 0.463 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 278 GLU cc_start: 0.6530 (tp30) cc_final: 0.6070 (mt-10) REVERT: A 287 SER cc_start: 0.8469 (t) cc_final: 0.7836 (p) REVERT: A 413 MET cc_start: 0.4993 (tpp) cc_final: 0.4628 (mpp) REVERT: A 484 HIS cc_start: 0.6927 (m-70) cc_final: 0.6589 (m90) REVERT: B 285 LYS cc_start: 0.8183 (ttmp) cc_final: 0.7485 (tttp) REVERT: B 287 SER cc_start: 0.8482 (t) cc_final: 0.7875 (p) REVERT: B 296 LEU cc_start: 0.8196 (OUTLIER) cc_final: 0.7940 (tp) REVERT: B 459 ILE cc_start: 0.7191 (tp) cc_final: 0.6880 (tp) REVERT: B 479 LYS cc_start: 0.5588 (mtpt) cc_final: 0.5080 (mttp) REVERT: C 285 LYS cc_start: 0.8073 (ttmp) cc_final: 0.7384 (tttp) REVERT: C 287 SER cc_start: 0.8650 (t) cc_final: 0.8106 (p) REVERT: C 338 MET cc_start: 0.7816 (mmp) cc_final: 0.7382 (mmp) REVERT: C 474 LEU cc_start: 0.5769 (OUTLIER) cc_final: 0.5117 (tt) REVERT: D 270 LYS cc_start: 0.5734 (OUTLIER) cc_final: 0.5387 (tmtt) REVERT: D 278 GLU cc_start: 0.7116 (tp30) cc_final: 0.6408 (tt0) REVERT: D 287 SER cc_start: 0.8625 (t) cc_final: 0.8038 (p) REVERT: D 338 MET cc_start: 0.7844 (mmp) cc_final: 0.7483 (mmp) REVERT: D 413 MET cc_start: 0.5456 (ptp) cc_final: 0.4878 (tpt) REVERT: D 474 LEU cc_start: 0.5918 (OUTLIER) cc_final: 0.5268 (tt) REVERT: E 285 LYS cc_start: 0.8043 (ttmp) cc_final: 0.7368 (tttt) REVERT: E 287 SER cc_start: 0.8260 (t) cc_final: 0.7656 (p) REVERT: E 346 MET cc_start: 0.6398 (tpt) cc_final: 0.5882 (tpt) REVERT: E 413 MET cc_start: 0.4964 (ptp) cc_final: 0.4720 (tpp) REVERT: E 479 LYS cc_start: 0.5593 (mtpt) cc_final: 0.4930 (mttm) REVERT: F 287 SER cc_start: 0.8396 (t) cc_final: 0.7868 (p) REVERT: F 338 MET cc_start: 0.7962 (mmp) cc_final: 0.7570 (mmp) REVERT: F 447 LYS cc_start: 0.6884 (tptt) cc_final: 0.6679 (tptm) REVERT: F 459 ILE cc_start: 0.7282 (tp) cc_final: 0.6870 (tp) REVERT: G 285 LYS cc_start: 0.8054 (ttmp) cc_final: 0.7457 (tttp) REVERT: G 287 SER cc_start: 0.8643 (t) cc_final: 0.8062 (p) REVERT: G 413 MET cc_start: 0.5691 (ptt) cc_final: 0.4974 (tpp) REVERT: G 460 ARG cc_start: 0.7390 (tpt170) cc_final: 0.7184 (tpm170) outliers start: 87 outliers final: 80 residues processed: 260 average time/residue: 0.1064 time to fit residues: 41.9358 Evaluate side-chains 271 residues out of total 1659 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 84 poor density : 187 time to evaluate : 0.365 ------------------------------------------------------------------------------- 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 296 LEU Chi-restraints excluded: chain B residue 311 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 369 LEU 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 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 474 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 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 406 LEU Chi-restraints excluded: chain D residue 408 ILE Chi-restraints excluded: chain D residue 442 LEU Chi-restraints excluded: chain D residue 474 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 249 LEU 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 369 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 F residue 483 LYS 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 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 Chi-restraints excluded: chain G residue 433 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 196 random chunks: chunk 54 optimal weight: 0.7980 chunk 129 optimal weight: 0.1980 chunk 181 optimal weight: 1.9990 chunk 56 optimal weight: 9.9990 chunk 172 optimal weight: 0.8980 chunk 127 optimal weight: 0.8980 chunk 174 optimal weight: 10.0000 chunk 163 optimal weight: 3.9990 chunk 11 optimal weight: 3.9990 chunk 30 optimal weight: 0.6980 chunk 15 optimal weight: 0.7980 overall best weight: 0.6780 ------------------------------------------------------------------------------- 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 C 484 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4225 r_free = 0.4225 target = 0.208041 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3824 r_free = 0.3824 target = 0.165332 restraints weight = 13900.341| |-----------------------------------------------------------------------------| r_work (start): 0.3814 rms_B_bonded: 2.07 r_work: 0.3473 rms_B_bonded: 3.27 restraints_weight: 0.5000 r_work (final): 0.3473 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6933 moved from start: 0.4358 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= 0.121 Angle : 0.610 12.312 20853 Z= 0.308 Chirality : 0.045 0.167 2527 Planarity : 0.003 0.034 2604 Dihedral : 5.151 19.323 2114 Min Nonbonded Distance : 2.579 Molprobity Statistics. All-atom Clashscore : 10.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.17 % Favored : 91.83 % Rotamer: Outliers : 5.19 % Allowed : 19.05 % Favored : 75.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.00 (0.18), residues: 1995 helix: -0.77 (0.17), residues: 980 sheet: -2.15 (0.31), residues: 266 loop : -3.58 (0.18), residues: 749 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG D 426 TYR 0.006 0.001 TYR E 441 PHE 0.013 0.001 PHE G 432 TRP 0.012 0.001 TRP C 397 HIS 0.002 0.000 HIS C 484 Details of bonding type rmsd covalent geometry : bond 0.00278 (15407) covalent geometry : angle 0.61039 (20853) hydrogen bonds : bond 0.02145 ( 589) hydrogen bonds : angle 5.16738 ( 1743) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3014.02 seconds wall clock time: 52 minutes 36.44 seconds (3156.44 seconds total)