Starting phenix.real_space_refine on Thu Feb 5 22:36:00 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9uo5_64373/02_2026/9uo5_64373.cif Found real_map, /net/cci-nas-00/data/ceres_data/9uo5_64373/02_2026/9uo5_64373.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.75 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9uo5_64373/02_2026/9uo5_64373.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9uo5_64373/02_2026/9uo5_64373.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9uo5_64373/02_2026/9uo5_64373.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9uo5_64373/02_2026/9uo5_64373.map" } resolution = 2.75 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= 0.012 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 72 5.16 5 C 12864 2.51 5 N 3424 2.21 5 O 3896 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 4 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 20256 Number of models: 1 Model: "" Number of chains: 12 Chain: "E" Number of atoms: 1691 Number of conformers: 1 Conformer: "" Number of residues, atoms: 212, 1691 Classifications: {'peptide': 212} Link IDs: {'PTRANS': 17, 'TRANS': 194} Chain: "F" Number of atoms: 1691 Number of conformers: 1 Conformer: "" Number of residues, atoms: 212, 1691 Classifications: {'peptide': 212} Link IDs: {'PTRANS': 17, 'TRANS': 194} Chain: "G" Number of atoms: 1691 Number of conformers: 1 Conformer: "" Number of residues, atoms: 212, 1691 Classifications: {'peptide': 212} Link IDs: {'PTRANS': 17, 'TRANS': 194} Chain: "H" Number of atoms: 1682 Number of conformers: 1 Conformer: "" Number of residues, atoms: 211, 1682 Classifications: {'peptide': 211} Link IDs: {'PTRANS': 17, 'TRANS': 193} Chain: "I" Number of atoms: 1682 Number of conformers: 1 Conformer: "" Number of residues, atoms: 211, 1682 Classifications: {'peptide': 211} Link IDs: {'PTRANS': 17, 'TRANS': 193} Chain: "J" Number of atoms: 1682 Number of conformers: 1 Conformer: "" Number of residues, atoms: 211, 1682 Classifications: {'peptide': 211} Link IDs: {'PTRANS': 17, 'TRANS': 193} Chain: "B" Number of atoms: 1691 Number of conformers: 1 Conformer: "" Number of residues, atoms: 212, 1691 Classifications: {'peptide': 212} Link IDs: {'PTRANS': 17, 'TRANS': 194} Chain: "K" Number of atoms: 1691 Number of conformers: 1 Conformer: "" Number of residues, atoms: 212, 1691 Classifications: {'peptide': 212} Link IDs: {'PTRANS': 17, 'TRANS': 194} Chain: "L" Number of atoms: 1691 Number of conformers: 1 Conformer: "" Number of residues, atoms: 212, 1691 Classifications: {'peptide': 212} Link IDs: {'PTRANS': 17, 'TRANS': 194} Chain: "A" Number of atoms: 1682 Number of conformers: 1 Conformer: "" Number of residues, atoms: 211, 1682 Classifications: {'peptide': 211} Link IDs: {'PTRANS': 17, 'TRANS': 193} Chain: "D" Number of atoms: 1691 Number of conformers: 1 Conformer: "" Number of residues, atoms: 212, 1691 Classifications: {'peptide': 212} Link IDs: {'PTRANS': 17, 'TRANS': 194} Chain: "C" Number of atoms: 1691 Number of conformers: 1 Conformer: "" Number of residues, atoms: 212, 1691 Classifications: {'peptide': 212} Link IDs: {'PTRANS': 17, 'TRANS': 194} Time building chain proxies: 4.72, per 1000 atoms: 0.23 Number of scatterers: 20256 At special positions: 0 Unit cell: (56.56, 188.72, 188.72, 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 72 16.00 O 3896 8.00 N 3424 7.00 C 12864 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=22, symmetry=0 Simple disulfide: pdb=" SG CYS E 261 " - pdb=" SG CYS E 321 " distance=2.03 Simple disulfide: pdb=" SG CYS E 367 " - pdb=" SG CYS E 425 " distance=2.03 Simple disulfide: pdb=" SG CYS F 261 " - pdb=" SG CYS F 321 " distance=2.03 Simple disulfide: pdb=" SG CYS F 367 " - pdb=" SG CYS F 425 " distance=2.03 Simple disulfide: pdb=" SG CYS G 367 " - pdb=" SG CYS G 425 " distance=2.03 Simple disulfide: pdb=" SG CYS H 261 " - pdb=" SG CYS H 321 " distance=2.03 Simple disulfide: pdb=" SG CYS H 367 " - pdb=" SG CYS H 425 " distance=2.03 Simple disulfide: pdb=" SG CYS I 261 " - pdb=" SG CYS I 321 " distance=2.03 Simple disulfide: pdb=" SG CYS I 367 " - pdb=" SG CYS I 425 " distance=2.03 Simple disulfide: pdb=" SG CYS J 261 " - pdb=" SG CYS J 321 " distance=2.03 Simple disulfide: pdb=" SG CYS J 367 " - pdb=" SG CYS J 425 " distance=2.03 Simple disulfide: pdb=" SG CYS B 261 " - pdb=" SG CYS B 321 " distance=2.03 Simple disulfide: pdb=" SG CYS B 367 " - pdb=" SG CYS B 425 " distance=2.03 Simple disulfide: pdb=" SG CYS K 261 " - pdb=" SG CYS K 321 " distance=2.03 Simple disulfide: pdb=" SG CYS K 367 " - pdb=" SG CYS K 425 " distance=2.03 Simple disulfide: pdb=" SG CYS L 261 " - pdb=" SG CYS L 321 " distance=2.03 Simple disulfide: pdb=" SG CYS L 367 " - pdb=" SG CYS L 425 " distance=2.03 Simple disulfide: pdb=" SG CYS A 261 " - pdb=" SG CYS A 321 " distance=2.08 Simple disulfide: pdb=" SG CYS A 367 " - pdb=" SG CYS A 425 " distance=2.03 Simple disulfide: pdb=" SG CYS D 367 " - pdb=" SG CYS D 425 " distance=2.03 Simple disulfide: pdb=" SG CYS C 261 " - pdb=" SG CYS C 321 " distance=2.03 Simple disulfide: pdb=" SG CYS C 367 " - pdb=" SG CYS C 425 " distance=2.03 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: 1.61 Conformation dependent library (CDL) restraints added in 754.3 milliseconds 5032 Ramachandran restraints generated. 2516 Oldfield, 0 Emsley, 2516 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4840 Finding SS restraints... Secondary structure from input PDB file: 58 helices and 70 sheets defined 14.1% alpha, 42.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.14 Creating SS restraints... Processing helix chain 'E' and resid 246 through 252 Processing helix chain 'E' and resid 309 through 315 Processing helix chain 'E' and resid 354 through 360 removed outlier: 3.639A pdb=" N THR E 359 " --> pdb=" O ASP E 356 " (cutoff:3.500A) Processing helix chain 'E' and resid 414 through 419 Processing helix chain 'E' and resid 432 through 436 Processing helix chain 'F' and resid 246 through 252 Processing helix chain 'F' and resid 309 through 315 Processing helix chain 'F' and resid 356 through 360 removed outlier: 3.675A pdb=" N THR F 359 " --> pdb=" O ASP F 356 " (cutoff:3.500A) Processing helix chain 'F' and resid 414 through 420 removed outlier: 3.606A pdb=" N GLY F 420 " --> pdb=" O ARG F 416 " (cutoff:3.500A) Processing helix chain 'F' and resid 432 through 436 Processing helix chain 'G' and resid 246 through 252 Processing helix chain 'G' and resid 309 through 316 removed outlier: 3.720A pdb=" N TRP G 313 " --> pdb=" O LEU G 309 " (cutoff:3.500A) Processing helix chain 'G' and resid 356 through 360 removed outlier: 3.573A pdb=" N THR G 359 " --> pdb=" O ASP G 356 " (cutoff:3.500A) Processing helix chain 'G' and resid 414 through 419 Processing helix chain 'G' and resid 432 through 436 Processing helix chain 'H' and resid 246 through 252 Processing helix chain 'H' and resid 309 through 316 removed outlier: 3.738A pdb=" N TRP H 313 " --> pdb=" O LEU H 309 " (cutoff:3.500A) Processing helix chain 'H' and resid 356 through 360 removed outlier: 3.844A pdb=" N THR H 359 " --> pdb=" O ASP H 356 " (cutoff:3.500A) Processing helix chain 'H' and resid 414 through 419 Processing helix chain 'H' and resid 432 through 436 removed outlier: 3.503A pdb=" N TYR H 436 " --> pdb=" O HIS H 433 " (cutoff:3.500A) Processing helix chain 'I' and resid 309 through 315 Processing helix chain 'I' and resid 356 through 360 removed outlier: 3.671A pdb=" N THR I 359 " --> pdb=" O ASP I 356 " (cutoff:3.500A) Processing helix chain 'I' and resid 414 through 419 Processing helix chain 'I' and resid 432 through 436 Processing helix chain 'J' and resid 246 through 252 removed outlier: 3.937A pdb=" N MET J 252 " --> pdb=" O LYS J 248 " (cutoff:3.500A) Processing helix chain 'J' and resid 309 through 316 removed outlier: 3.715A pdb=" N TRP J 313 " --> pdb=" O LEU J 309 " (cutoff:3.500A) removed outlier: 3.873A pdb=" N LEU J 314 " --> pdb=" O HIS J 310 " (cutoff:3.500A) Processing helix chain 'J' and resid 354 through 359 removed outlier: 3.544A pdb=" N THR J 359 " --> pdb=" O ASP J 356 " (cutoff:3.500A) Processing helix chain 'J' and resid 414 through 419 Processing helix chain 'J' and resid 432 through 436 Processing helix chain 'B' and resid 246 through 252 Processing helix chain 'B' and resid 309 through 316 Processing helix chain 'B' and resid 354 through 360 Processing helix chain 'B' and resid 414 through 419 removed outlier: 3.694A pdb=" N GLN B 419 " --> pdb=" O SER B 415 " (cutoff:3.500A) Processing helix chain 'B' and resid 432 through 436 Processing helix chain 'K' and resid 246 through 252 removed outlier: 3.912A pdb=" N LEU K 251 " --> pdb=" O PRO K 247 " (cutoff:3.500A) Processing helix chain 'K' and resid 309 through 316 removed outlier: 3.514A pdb=" N TRP K 313 " --> pdb=" O LEU K 309 " (cutoff:3.500A) Processing helix chain 'K' and resid 354 through 358 Processing helix chain 'K' and resid 414 through 419 Processing helix chain 'K' and resid 432 through 436 removed outlier: 3.539A pdb=" N TYR K 436 " --> pdb=" O HIS K 433 " (cutoff:3.500A) Processing helix chain 'L' and resid 246 through 251 Processing helix chain 'L' and resid 309 through 315 removed outlier: 3.795A pdb=" N TRP L 313 " --> pdb=" O LEU L 309 " (cutoff:3.500A) Processing helix chain 'L' and resid 356 through 360 removed outlier: 3.741A pdb=" N THR L 359 " --> pdb=" O ASP L 356 " (cutoff:3.500A) Processing helix chain 'L' and resid 414 through 419 Processing helix chain 'L' and resid 432 through 436 removed outlier: 3.514A pdb=" N TYR L 436 " --> pdb=" O HIS L 433 " (cutoff:3.500A) Processing helix chain 'A' and resid 246 through 251 Processing helix chain 'A' and resid 309 through 316 removed outlier: 3.872A pdb=" N TRP A 313 " --> pdb=" O LEU A 309 " (cutoff:3.500A) removed outlier: 3.895A pdb=" N LEU A 314 " --> pdb=" O HIS A 310 " (cutoff:3.500A) Processing helix chain 'A' and resid 354 through 358 removed outlier: 3.532A pdb=" N LEU A 358 " --> pdb=" O ARG A 355 " (cutoff:3.500A) Processing helix chain 'A' and resid 414 through 419 Processing helix chain 'A' and resid 432 through 436 Processing helix chain 'D' and resid 309 through 315 removed outlier: 3.623A pdb=" N TRP D 313 " --> pdb=" O LEU D 309 " (cutoff:3.500A) Processing helix chain 'D' and resid 356 through 360 removed outlier: 3.648A pdb=" N THR D 359 " --> pdb=" O ASP D 356 " (cutoff:3.500A) Processing helix chain 'D' and resid 414 through 420 removed outlier: 3.911A pdb=" N GLY D 420 " --> pdb=" O ARG D 416 " (cutoff:3.500A) Processing helix chain 'D' and resid 432 through 436 Processing helix chain 'C' and resid 246 through 251 removed outlier: 3.531A pdb=" N LEU C 251 " --> pdb=" O PRO C 247 " (cutoff:3.500A) Processing helix chain 'C' and resid 309 through 314 removed outlier: 3.612A pdb=" N LEU C 314 " --> pdb=" O HIS C 310 " (cutoff:3.500A) Processing helix chain 'C' and resid 354 through 360 removed outlier: 3.836A pdb=" N THR C 359 " --> pdb=" O ASP C 356 " (cutoff:3.500A) Processing helix chain 'C' and resid 414 through 419 Processing helix chain 'C' and resid 432 through 436 Processing sheet with id=AA1, first strand: chain 'E' and resid 239 through 243 removed outlier: 3.505A pdb=" N VAL E 262 " --> pdb=" O PHE E 241 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N VAL E 302 " --> pdb=" O VAL E 263 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'E' and resid 282 through 283 Processing sheet with id=AA3, first strand: chain 'E' and resid 347 through 351 removed outlier: 5.360A pdb=" N PHE E 404 " --> pdb=" O GLY E 371 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'E' and resid 347 through 351 removed outlier: 5.360A pdb=" N PHE E 404 " --> pdb=" O GLY E 371 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'E' and resid 386 through 388 removed outlier: 4.458A pdb=" N TRP E 381 " --> pdb=" O GLU E 388 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'F' and resid 240 through 243 removed outlier: 3.791A pdb=" N THR F 260 " --> pdb=" O PHE F 243 " (cutoff:3.500A) removed outlier: 3.776A pdb=" N SER F 304 " --> pdb=" O CYS F 261 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N VAL F 263 " --> pdb=" O VAL F 302 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N VAL F 302 " --> pdb=" O VAL F 263 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N VAL F 305 " --> pdb=" O LYS F 288 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'F' and resid 278 through 279 removed outlier: 3.669A pdb=" N VAL F 279 " --> pdb=" O VAL F 282 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'F' and resid 319 through 322 Processing sheet with id=AA9, first strand: chain 'F' and resid 347 through 351 removed outlier: 5.734A pdb=" N PHE F 404 " --> pdb=" O GLY F 371 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'F' and resid 347 through 351 removed outlier: 5.734A pdb=" N PHE F 404 " --> pdb=" O GLY F 371 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'F' and resid 386 through 388 removed outlier: 4.435A pdb=" N TRP F 381 " --> pdb=" O GLU F 388 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'G' and resid 239 through 243 removed outlier: 3.934A pdb=" N THR G 260 " --> pdb=" O PHE G 243 " (cutoff:3.500A) removed outlier: 3.915A pdb=" N SER G 304 " --> pdb=" O CYS G 261 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'G' and resid 282 through 283 removed outlier: 3.822A pdb=" N ASN G 276 " --> pdb=" O LYS G 322 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N LYS G 322 " --> pdb=" O ASN G 276 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N TYR G 278 " --> pdb=" O LYS G 320 " (cutoff:3.500A) removed outlier: 3.753A pdb=" N ILE G 332 " --> pdb=" O VAL G 323 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'G' and resid 293 through 294 Processing sheet with id=AB6, first strand: chain 'G' and resid 347 through 351 removed outlier: 5.678A pdb=" N PHE G 404 " --> pdb=" O GLY G 371 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'G' and resid 347 through 351 removed outlier: 5.678A pdb=" N PHE G 404 " --> pdb=" O GLY G 371 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'G' and resid 386 through 387 Processing sheet with id=AB9, first strand: chain 'H' and resid 239 through 243 removed outlier: 3.637A pdb=" N THR H 260 " --> pdb=" O PHE H 243 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'H' and resid 276 through 279 removed outlier: 3.734A pdb=" N VAL H 323 " --> pdb=" O ILE H 332 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N ILE H 332 " --> pdb=" O VAL H 323 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'H' and resid 347 through 351 removed outlier: 4.911A pdb=" N PHE H 404 " --> pdb=" O GLY H 371 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'H' and resid 347 through 351 removed outlier: 4.911A pdb=" N PHE H 404 " --> pdb=" O GLY H 371 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'H' and resid 386 through 388 removed outlier: 4.512A pdb=" N TRP H 381 " --> pdb=" O GLU H 388 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'I' and resid 239 through 243 removed outlier: 3.700A pdb=" N THR I 260 " --> pdb=" O PHE I 243 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N VAL I 259 " --> pdb=" O LEU I 306 " (cutoff:3.500A) removed outlier: 4.089A pdb=" N SER I 304 " --> pdb=" O CYS I 261 " (cutoff:3.500A) removed outlier: 4.307A pdb=" N VAL I 263 " --> pdb=" O VAL I 302 " (cutoff:3.500A) removed outlier: 5.240A pdb=" N VAL I 302 " --> pdb=" O VAL I 263 " (cutoff:3.500A) removed outlier: 4.750A pdb=" N VAL I 303 " --> pdb=" O PRO I 291 " (cutoff:3.500A) removed outlier: 7.117A pdb=" N VAL I 305 " --> pdb=" O THR I 289 " (cutoff:3.500A) removed outlier: 4.977A pdb=" N THR I 289 " --> pdb=" O VAL I 305 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'I' and resid 282 through 283 removed outlier: 3.561A pdb=" N VAL I 279 " --> pdb=" O VAL I 282 " (cutoff:3.500A) removed outlier: 4.929A pdb=" N LYS I 320 " --> pdb=" O TYR I 278 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N CYS I 321 " --> pdb=" O LYS I 334 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'I' and resid 347 through 351 removed outlier: 4.974A pdb=" N PHE I 404 " --> pdb=" O GLY I 371 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'I' and resid 347 through 351 removed outlier: 4.974A pdb=" N PHE I 404 " --> pdb=" O GLY I 371 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'I' and resid 386 through 387 Processing sheet with id=AD1, first strand: chain 'J' and resid 258 through 259 Processing sheet with id=AD2, first strand: chain 'J' and resid 266 through 267 Processing sheet with id=AD3, first strand: chain 'J' and resid 273 through 274 Processing sheet with id=AD4, first strand: chain 'J' and resid 278 through 279 Processing sheet with id=AD5, first strand: chain 'J' and resid 347 through 351 removed outlier: 5.072A pdb=" N PHE J 404 " --> pdb=" O GLY J 371 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'J' and resid 347 through 351 removed outlier: 5.072A pdb=" N PHE J 404 " --> pdb=" O GLY J 371 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'J' and resid 386 through 388 removed outlier: 4.377A pdb=" N TRP J 381 " --> pdb=" O GLU J 388 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'B' and resid 239 through 243 Processing sheet with id=AD9, first strand: chain 'B' and resid 282 through 284 removed outlier: 4.692A pdb=" N TRP B 277 " --> pdb=" O VAL B 284 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'B' and resid 347 through 351 removed outlier: 5.018A pdb=" N PHE B 404 " --> pdb=" O GLY B 371 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'B' and resid 347 through 351 removed outlier: 5.018A pdb=" N PHE B 404 " --> pdb=" O GLY B 371 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'B' and resid 386 through 388 removed outlier: 4.516A pdb=" N TRP B 381 " --> pdb=" O GLU B 388 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'K' and resid 239 through 240 Processing sheet with id=AE5, first strand: chain 'K' and resid 258 through 260 removed outlier: 3.812A pdb=" N VAL K 259 " --> pdb=" O LEU K 306 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'K' and resid 282 through 283 removed outlier: 3.525A pdb=" N LYS K 274 " --> pdb=" O SER K 324 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'K' and resid 293 through 295 removed outlier: 3.710A pdb=" N THR K 299 " --> pdb=" O GLN K 295 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'K' and resid 347 through 351 removed outlier: 3.501A pdb=" N THR K 366 " --> pdb=" O LEU K 351 " (cutoff:3.500A) removed outlier: 5.550A pdb=" N PHE K 404 " --> pdb=" O GLY K 371 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'K' and resid 347 through 351 removed outlier: 3.501A pdb=" N THR K 366 " --> pdb=" O LEU K 351 " (cutoff:3.500A) removed outlier: 5.550A pdb=" N PHE K 404 " --> pdb=" O GLY K 371 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'K' and resid 386 through 388 removed outlier: 4.654A pdb=" N TRP K 381 " --> pdb=" O GLU K 388 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'L' and resid 239 through 243 removed outlier: 3.516A pdb=" N PHE L 241 " --> pdb=" O VAL L 262 " (cutoff:3.500A) removed outlier: 4.153A pdb=" N VAL L 262 " --> pdb=" O PHE L 241 " (cutoff:3.500A) removed outlier: 4.257A pdb=" N PHE L 243 " --> pdb=" O THR L 260 " (cutoff:3.500A) removed outlier: 3.869A pdb=" N THR L 260 " --> pdb=" O PHE L 243 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N VAL L 259 " --> pdb=" O LEU L 306 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N LEU L 306 " --> pdb=" O VAL L 259 " (cutoff:3.500A) removed outlier: 3.748A pdb=" N VAL L 263 " --> pdb=" O VAL L 302 " (cutoff:3.500A) removed outlier: 4.701A pdb=" N VAL L 302 " --> pdb=" O VAL L 263 " (cutoff:3.500A) removed outlier: 4.021A pdb=" N VAL L 303 " --> pdb=" O LYS L 290 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'L' and resid 282 through 283 removed outlier: 3.564A pdb=" N ASN L 276 " --> pdb=" O LYS L 322 " (cutoff:3.500A) Processing sheet with id=AF4, first strand: chain 'L' and resid 347 through 351 Processing sheet with id=AF5, first strand: chain 'L' and resid 347 through 351 Processing sheet with id=AF6, first strand: chain 'L' and resid 386 through 388 removed outlier: 4.255A pdb=" N TRP L 381 " --> pdb=" O GLU L 388 " (cutoff:3.500A) Processing sheet with id=AF7, first strand: chain 'A' and resid 239 through 240 Processing sheet with id=AF8, first strand: chain 'A' and resid 282 through 283 removed outlier: 3.641A pdb=" N VAL A 323 " --> pdb=" O ILE A 332 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N ILE A 332 " --> pdb=" O VAL A 323 " (cutoff:3.500A) Processing sheet with id=AF9, first strand: chain 'A' and resid 288 through 289 removed outlier: 3.572A pdb=" N LYS A 288 " --> pdb=" O VAL A 305 " (cutoff:3.500A) Processing sheet with id=AG1, first strand: chain 'A' and resid 293 through 294 Processing sheet with id=AG2, first strand: chain 'A' and resid 347 through 351 removed outlier: 4.999A pdb=" N PHE A 404 " --> pdb=" O GLY A 371 " (cutoff:3.500A) Processing sheet with id=AG3, first strand: chain 'A' and resid 347 through 351 removed outlier: 4.999A pdb=" N PHE A 404 " --> pdb=" O GLY A 371 " (cutoff:3.500A) Processing sheet with id=AG4, first strand: chain 'A' and resid 386 through 388 removed outlier: 4.216A pdb=" N TRP A 381 " --> pdb=" O GLU A 388 " (cutoff:3.500A) Processing sheet with id=AG5, first strand: chain 'D' and resid 239 through 243 removed outlier: 3.681A pdb=" N ASP D 265 " --> pdb=" O TYR D 300 " (cutoff:3.500A) removed outlier: 6.200A pdb=" N TYR D 300 " --> pdb=" O ASP D 265 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N VAL D 305 " --> pdb=" O LYS D 288 " (cutoff:3.500A) Processing sheet with id=AG6, first strand: chain 'D' and resid 239 through 243 removed outlier: 3.681A pdb=" N ASP D 265 " --> pdb=" O TYR D 300 " (cutoff:3.500A) removed outlier: 6.200A pdb=" N TYR D 300 " --> pdb=" O ASP D 265 " (cutoff:3.500A) Processing sheet with id=AG7, first strand: chain 'D' and resid 282 through 283 removed outlier: 3.577A pdb=" N ASN D 276 " --> pdb=" O LYS D 322 " (cutoff:3.500A) Processing sheet with id=AG8, first strand: chain 'D' and resid 347 through 351 removed outlier: 5.741A pdb=" N PHE D 404 " --> pdb=" O GLY D 371 " (cutoff:3.500A) Processing sheet with id=AG9, first strand: chain 'D' and resid 347 through 351 removed outlier: 5.741A pdb=" N PHE D 404 " --> pdb=" O GLY D 371 " (cutoff:3.500A) Processing sheet with id=AH1, first strand: chain 'D' and resid 378 through 382 Processing sheet with id=AH2, first strand: chain 'C' and resid 258 through 260 removed outlier: 3.717A pdb=" N VAL C 259 " --> pdb=" O LEU C 306 " (cutoff:3.500A) removed outlier: 3.865A pdb=" N LEU C 306 " --> pdb=" O VAL C 259 " (cutoff:3.500A) No H-bonds generated for sheet with id=AH2 Processing sheet with id=AH3, first strand: chain 'C' and resid 263 through 266 removed outlier: 5.741A pdb=" N VAL C 264 " --> pdb=" O VAL C 302 " (cutoff:3.500A) removed outlier: 6.478A pdb=" N VAL C 302 " --> pdb=" O VAL C 264 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N TYR C 300 " --> pdb=" O VAL C 266 " (cutoff:3.500A) Processing sheet with id=AH4, first strand: chain 'C' and resid 273 through 274 removed outlier: 3.772A pdb=" N SER C 324 " --> pdb=" O LYS C 274 " (cutoff:3.500A) Processing sheet with id=AH5, first strand: chain 'C' and resid 347 through 351 removed outlier: 5.805A pdb=" N PHE C 404 " --> pdb=" O GLY C 371 " (cutoff:3.500A) Processing sheet with id=AH6, first strand: chain 'C' and resid 347 through 351 removed outlier: 5.805A pdb=" N PHE C 404 " --> pdb=" O GLY C 371 " (cutoff:3.500A) Processing sheet with id=AH7, first strand: chain 'C' and resid 386 through 388 removed outlier: 4.395A pdb=" N TRP C 381 " --> pdb=" O GLU C 388 " (cutoff:3.500A) 875 hydrogen bonds defined for protein. 2136 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 3.68 Time building geometry restraints manager: 2.19 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.35: 6502 1.35 - 1.46: 4715 1.46 - 1.58: 9495 1.58 - 1.70: 0 1.70 - 1.82: 96 Bond restraints: 20808 Sorted by residual: bond pdb=" N ILE D 253 " pdb=" CA ILE D 253 " ideal model delta sigma weight residual 1.460 1.496 -0.036 1.21e-02 6.83e+03 8.82e+00 bond pdb=" N LEU K 251 " pdb=" CA LEU K 251 " ideal model delta sigma weight residual 1.455 1.493 -0.039 1.38e-02 5.25e+03 7.82e+00 bond pdb=" N SER D 254 " pdb=" CA SER D 254 " ideal model delta sigma weight residual 1.458 1.492 -0.034 1.30e-02 5.92e+03 6.79e+00 bond pdb=" N ASN K 315 " pdb=" CA ASN K 315 " ideal model delta sigma weight residual 1.459 1.490 -0.031 1.20e-02 6.94e+03 6.56e+00 bond pdb=" N ASP K 312 " pdb=" CA ASP K 312 " ideal model delta sigma weight residual 1.457 1.489 -0.031 1.29e-02 6.01e+03 5.88e+00 ... (remaining 20803 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.96: 27765 1.96 - 3.91: 497 3.91 - 5.87: 32 5.87 - 7.83: 27 7.83 - 9.78: 3 Bond angle restraints: 28324 Sorted by residual: angle pdb=" C PRO B 329 " pdb=" N ALA B 330 " pdb=" CA ALA B 330 " ideal model delta sigma weight residual 120.51 126.87 -6.36 1.45e+00 4.76e-01 1.93e+01 angle pdb=" C PRO B 291 " pdb=" N ARG B 292 " pdb=" CA ARG B 292 " ideal model delta sigma weight residual 122.82 127.88 -5.06 1.42e+00 4.96e-01 1.27e+01 angle pdb=" N LYS C 370 " pdb=" CA LYS C 370 " pdb=" CB LYS C 370 " ideal model delta sigma weight residual 111.00 104.96 6.04 1.81e+00 3.05e-01 1.11e+01 angle pdb=" C PRO G 291 " pdb=" N ARG G 292 " pdb=" CA ARG G 292 " ideal model delta sigma weight residual 121.54 127.74 -6.20 1.91e+00 2.74e-01 1.06e+01 angle pdb=" C GLU C 333 " pdb=" CA GLU C 333 " pdb=" CB GLU C 333 " ideal model delta sigma weight residual 110.79 105.59 5.20 1.63e+00 3.76e-01 1.02e+01 ... (remaining 28319 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.90: 10720 17.90 - 35.79: 1417 35.79 - 53.69: 418 53.69 - 71.59: 97 71.59 - 89.48: 46 Dihedral angle restraints: 12698 sinusoidal: 5222 harmonic: 7476 Sorted by residual: dihedral pdb=" CB CYS J 261 " pdb=" SG CYS J 261 " pdb=" SG CYS J 321 " pdb=" CB CYS J 321 " ideal model delta sinusoidal sigma weight residual 93.00 151.85 -58.85 1 1.00e+01 1.00e-02 4.63e+01 dihedral pdb=" CB CYS C 261 " pdb=" SG CYS C 261 " pdb=" SG CYS C 321 " pdb=" CB CYS C 321 " ideal model delta sinusoidal sigma weight residual 93.00 150.13 -57.13 1 1.00e+01 1.00e-02 4.39e+01 dihedral pdb=" CA MET A 252 " pdb=" C MET A 252 " pdb=" N ILE A 253 " pdb=" CA ILE A 253 " ideal model delta harmonic sigma weight residual 180.00 -156.79 -23.21 0 5.00e+00 4.00e-02 2.15e+01 ... (remaining 12695 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.056: 2531 0.056 - 0.111: 502 0.111 - 0.167: 65 0.167 - 0.223: 4 0.223 - 0.278: 2 Chirality restraints: 3104 Sorted by residual: chirality pdb=" CA VAL C 369 " pdb=" N VAL C 369 " pdb=" C VAL C 369 " pdb=" CB VAL C 369 " both_signs ideal model delta sigma weight residual False 2.44 2.72 -0.28 2.00e-01 2.50e+01 1.94e+00 chirality pdb=" CA LYS C 370 " pdb=" N LYS C 370 " pdb=" C LYS C 370 " pdb=" CB LYS C 370 " both_signs ideal model delta sigma weight residual False 2.51 2.74 -0.23 2.00e-01 2.50e+01 1.32e+00 chirality pdb=" CB THR I 260 " pdb=" CA THR I 260 " pdb=" OG1 THR I 260 " pdb=" CG2 THR I 260 " both_signs ideal model delta sigma weight residual False 2.55 2.35 0.20 2.00e-01 2.50e+01 1.04e+00 ... (remaining 3101 not shown) Planarity restraints: 3656 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA LEU K 251 " 0.010 2.00e-02 2.50e+03 2.12e-02 4.51e+00 pdb=" C LEU K 251 " -0.037 2.00e-02 2.50e+03 pdb=" O LEU K 251 " 0.013 2.00e-02 2.50e+03 pdb=" N MET K 252 " 0.013 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C GLY E 237 " -0.035 5.00e-02 4.00e+02 5.28e-02 4.46e+00 pdb=" N PRO E 238 " 0.091 5.00e-02 4.00e+02 pdb=" CA PRO E 238 " -0.027 5.00e-02 4.00e+02 pdb=" CD PRO E 238 " -0.030 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LEU B 328 " 0.031 5.00e-02 4.00e+02 4.66e-02 3.47e+00 pdb=" N PRO B 329 " -0.081 5.00e-02 4.00e+02 pdb=" CA PRO B 329 " 0.024 5.00e-02 4.00e+02 pdb=" CD PRO B 329 " 0.026 5.00e-02 4.00e+02 ... (remaining 3653 not shown) Histogram of nonbonded interaction distances: 2.27 - 2.79: 4582 2.79 - 3.32: 17119 3.32 - 3.85: 34731 3.85 - 4.37: 39842 4.37 - 4.90: 69338 Nonbonded interactions: 165612 Sorted by model distance: nonbonded pdb=" O MET K 252 " pdb=" OG1 THR K 256 " model vdw 2.268 3.040 nonbonded pdb=" OD1 ASP H 312 " pdb=" OH TYR H 319 " model vdw 2.275 3.040 nonbonded pdb=" OE2 GLU L 357 " pdb=" OG SER L 364 " model vdw 2.286 3.040 nonbonded pdb=" O SER F 324 " pdb=" OG SER F 324 " model vdw 2.302 3.040 nonbonded pdb=" O SER D 298 " pdb=" OG SER D 298 " model vdw 2.305 3.040 ... (remaining 165607 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.01 Found NCS groups: ncs_group { reference = chain 'A' selection = (chain 'B' and resid 236 through 446) selection = (chain 'C' and resid 236 through 446) selection = (chain 'D' and resid 236 through 446) selection = (chain 'E' and resid 236 through 446) selection = (chain 'F' and resid 236 through 446) selection = (chain 'G' and resid 236 through 446) selection = chain 'H' selection = chain 'I' selection = chain 'J' selection = (chain 'K' and resid 236 through 446) selection = (chain 'L' and resid 236 through 446) } 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: 10.710 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.580 Check model and map are aligned: 0.060 Set scattering table: 0.080 Process input model: 18.870 Find NCS groups from input model: 0.350 Set up NCS constraints: 0.040 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:6.010 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 36.720 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7816 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 : 0.003 0.052 20830 Z= 0.150 Angle : 0.626 24.500 28368 Z= 0.323 Chirality : 0.046 0.278 3104 Planarity : 0.005 0.053 3656 Dihedral : 18.280 89.485 7792 Min Nonbonded Distance : 2.268 Molprobity Statistics. All-atom Clashscore : 9.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.82 % Favored : 96.18 % Rotamer: Outliers : 0.00 % Allowed : 32.67 % Favored : 67.33 % 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: -0.67 (0.17), residues: 2516 helix: -1.64 (0.30), residues: 222 sheet: -0.51 (0.16), residues: 993 loop : 0.02 (0.18), residues: 1301 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG H 292 TYR 0.015 0.002 TYR E 407 PHE 0.017 0.002 PHE I 405 TRP 0.008 0.001 TRP B 417 HIS 0.007 0.001 HIS I 310 Details of bonding type rmsd covalent geometry : bond 0.00312 (20808) covalent geometry : angle 0.59660 (28324) SS BOND : bond 0.01129 ( 22) SS BOND : angle 4.82111 ( 44) hydrogen bonds : bond 0.25308 ( 685) hydrogen bonds : angle 8.95852 ( 2136) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5032 Ramachandran restraints generated. 2516 Oldfield, 0 Emsley, 2516 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5032 Ramachandran restraints generated. 2516 Oldfield, 0 Emsley, 2516 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 241 residues out of total 2348 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 241 time to evaluate : 0.868 Fit side-chains revert: symmetry clash REVERT: E 310 HIS cc_start: 0.7275 (m90) cc_final: 0.7059 (m170) REVERT: E 315 ASN cc_start: 0.7393 (m-40) cc_final: 0.7155 (m110) REVERT: E 443 LYS cc_start: 0.8500 (tmtt) cc_final: 0.7853 (ttpt) REVERT: F 246 LYS cc_start: 0.7836 (ttpt) cc_final: 0.7232 (tmtm) REVERT: F 340 LYS cc_start: 0.7862 (tppt) cc_final: 0.7493 (tppt) REVERT: G 311 GLN cc_start: 0.7716 (mt0) cc_final: 0.7436 (mt0) REVERT: G 315 ASN cc_start: 0.7910 (m-40) cc_final: 0.7282 (m110) REVERT: G 444 SER cc_start: 0.8482 (p) cc_final: 0.8173 (m) REVERT: H 250 THR cc_start: 0.8594 (t) cc_final: 0.8303 (p) REVERT: I 419 GLN cc_start: 0.7498 (tt0) cc_final: 0.7269 (tt0) REVERT: B 310 HIS cc_start: 0.8242 (m-70) cc_final: 0.7997 (m-70) REVERT: B 347 GLN cc_start: 0.8392 (mt0) cc_final: 0.7996 (mt0) REVERT: B 428 MET cc_start: 0.8400 (mtp) cc_final: 0.8063 (mtm) REVERT: K 390 ASN cc_start: 0.7544 (t0) cc_final: 0.7191 (t0) REVERT: K 443 LYS cc_start: 0.8245 (tptp) cc_final: 0.7515 (pttt) REVERT: L 361 ASN cc_start: 0.7550 (p0) cc_final: 0.7231 (t160) REVERT: L 413 ASP cc_start: 0.7553 (p0) cc_final: 0.7283 (m-30) REVERT: A 345 GLU cc_start: 0.8180 (tt0) cc_final: 0.7942 (tt0) REVERT: C 340 LYS cc_start: 0.8185 (mmtt) cc_final: 0.7836 (mmtt) REVERT: C 347 GLN cc_start: 0.8081 (mt0) cc_final: 0.7724 (mt0) outliers start: 0 outliers final: 0 residues processed: 241 average time/residue: 0.5382 time to fit residues: 147.9372 Evaluate side-chains 185 residues out of total 2348 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 185 time to evaluate : 0.733 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 252 random chunks: chunk 216 optimal weight: 8.9990 chunk 98 optimal weight: 5.9990 chunk 194 optimal weight: 1.9990 chunk 227 optimal weight: 1.9990 chunk 107 optimal weight: 10.0000 chunk 10 optimal weight: 6.9990 chunk 66 optimal weight: 20.0000 chunk 247 optimal weight: 0.7980 chunk 130 optimal weight: 20.0000 chunk 124 optimal weight: 5.9990 chunk 103 optimal weight: 0.9990 overall best weight: 2.3588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 429 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 362 GLN H 361 ASN J 418 GLN ** J 429 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 438 GLN ** L 311 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 315 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 418 GLN L 435 HIS A 434 ASN D 315 ASN C 389 ASN C 418 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4534 r_free = 0.4534 target = 0.231385 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3854 r_free = 0.3854 target = 0.159009 restraints weight = 22809.256| |-----------------------------------------------------------------------------| r_work (start): 0.3802 rms_B_bonded: 3.28 r_work: 0.3473 rms_B_bonded: 2.91 restraints_weight: 0.5000 r_work: 0.3351 rms_B_bonded: 4.37 restraints_weight: 0.2500 r_work (final): 0.3351 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8215 moved from start: 0.1214 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.058 20830 Z= 0.243 Angle : 0.639 8.282 28368 Z= 0.328 Chirality : 0.046 0.158 3104 Planarity : 0.005 0.053 3656 Dihedral : 4.343 21.021 2708 Min Nonbonded Distance : 2.508 Molprobity Statistics. All-atom Clashscore : 9.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.25 % Favored : 95.75 % Rotamer: Outliers : 7.16 % Allowed : 26.11 % Favored : 66.74 % 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: -0.45 (0.17), residues: 2516 helix: -0.91 (0.32), residues: 244 sheet: -0.48 (0.16), residues: 1013 loop : 0.20 (0.19), residues: 1259 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 301 TYR 0.019 0.002 TYR B 436 PHE 0.016 0.002 PHE L 372 TRP 0.014 0.002 TRP B 313 HIS 0.005 0.001 HIS I 310 Details of bonding type rmsd covalent geometry : bond 0.00575 (20808) covalent geometry : angle 0.63872 (28324) SS BOND : bond 0.00307 ( 22) SS BOND : angle 0.85063 ( 44) hydrogen bonds : bond 0.04859 ( 685) hydrogen bonds : angle 6.45477 ( 2136) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5032 Ramachandran restraints generated. 2516 Oldfield, 0 Emsley, 2516 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5032 Ramachandran restraints generated. 2516 Oldfield, 0 Emsley, 2516 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 348 residues out of total 2348 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 168 poor density : 180 time to evaluate : 0.637 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: E 252 MET cc_start: 0.5819 (OUTLIER) cc_final: 0.4502 (mpt) REVERT: E 315 ASN cc_start: 0.7357 (m-40) cc_final: 0.6972 (m110) REVERT: E 409 LYS cc_start: 0.9151 (OUTLIER) cc_final: 0.8515 (ttpt) REVERT: E 443 LYS cc_start: 0.8564 (tmtt) cc_final: 0.7816 (ttpt) REVERT: F 246 LYS cc_start: 0.7662 (ttpt) cc_final: 0.6953 (tmtm) REVERT: F 289 THR cc_start: 0.5291 (OUTLIER) cc_final: 0.5007 (p) REVERT: F 340 LYS cc_start: 0.7983 (tppt) cc_final: 0.7480 (tppt) REVERT: G 248 LYS cc_start: 0.7460 (tptp) cc_final: 0.6892 (tptp) REVERT: G 426 SER cc_start: 0.8825 (OUTLIER) cc_final: 0.8589 (p) REVERT: G 444 SER cc_start: 0.8463 (p) cc_final: 0.8239 (m) REVERT: G 447 LYS cc_start: 0.3732 (OUTLIER) cc_final: 0.3479 (tppt) REVERT: H 250 THR cc_start: 0.8560 (t) cc_final: 0.8257 (p) REVERT: H 312 ASP cc_start: 0.6881 (OUTLIER) cc_final: 0.6523 (p0) REVERT: H 386 GLN cc_start: 0.8528 (OUTLIER) cc_final: 0.8053 (mp10) REVERT: I 422 VAL cc_start: 0.8141 (OUTLIER) cc_final: 0.7679 (t) REVERT: I 441 LEU cc_start: 0.8968 (OUTLIER) cc_final: 0.8750 (pt) REVERT: J 318 GLU cc_start: 0.6011 (mp0) cc_final: 0.5766 (mp0) REVERT: B 347 GLN cc_start: 0.8713 (mt0) cc_final: 0.8262 (mt0) REVERT: B 421 ASN cc_start: 0.7478 (OUTLIER) cc_final: 0.7191 (t0) REVERT: B 428 MET cc_start: 0.8814 (mtp) cc_final: 0.8449 (mtm) REVERT: B 439 LYS cc_start: 0.8831 (OUTLIER) cc_final: 0.8365 (mptm) REVERT: K 241 PHE cc_start: 0.1472 (OUTLIER) cc_final: 0.0721 (m-80) REVERT: K 292 ARG cc_start: 0.2770 (OUTLIER) cc_final: 0.2485 (ttp-110) REVERT: K 443 LYS cc_start: 0.8288 (tptp) cc_final: 0.7518 (pttt) REVERT: L 361 ASN cc_start: 0.7692 (p0) cc_final: 0.7281 (t160) REVERT: L 413 ASP cc_start: 0.7721 (p0) cc_final: 0.7341 (m-30) REVERT: L 439 LYS cc_start: 0.8497 (OUTLIER) cc_final: 0.7676 (mptm) REVERT: A 345 GLU cc_start: 0.8445 (tt0) cc_final: 0.8208 (tt0) REVERT: D 276 ASN cc_start: 0.6435 (OUTLIER) cc_final: 0.5917 (m-40) REVERT: D 312 ASP cc_start: 0.7315 (t70) cc_final: 0.6597 (t70) REVERT: C 252 MET cc_start: 0.6410 (OUTLIER) cc_final: 0.5879 (ttt) REVERT: C 340 LYS cc_start: 0.8307 (mmtt) cc_final: 0.7909 (mmtt) outliers start: 168 outliers final: 83 residues processed: 323 average time/residue: 0.4482 time to fit residues: 169.0331 Evaluate side-chains 261 residues out of total 2348 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 99 poor density : 162 time to evaluate : 0.804 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 252 MET Chi-restraints excluded: chain E residue 305 VAL Chi-restraints excluded: chain E residue 359 THR Chi-restraints excluded: chain E residue 382 GLU Chi-restraints excluded: chain E residue 409 LYS Chi-restraints excluded: chain E residue 412 VAL Chi-restraints excluded: chain E residue 427 VAL Chi-restraints excluded: chain F residue 279 VAL Chi-restraints excluded: chain F residue 289 THR Chi-restraints excluded: chain F residue 302 VAL Chi-restraints excluded: chain F residue 308 VAL Chi-restraints excluded: chain F residue 427 VAL Chi-restraints excluded: chain G residue 264 VAL Chi-restraints excluded: chain G residue 321 CYS Chi-restraints excluded: chain G residue 355 ARG Chi-restraints excluded: chain G residue 360 LYS Chi-restraints excluded: chain G residue 375 SER Chi-restraints excluded: chain G residue 426 SER Chi-restraints excluded: chain G residue 447 LYS Chi-restraints excluded: chain H residue 240 VAL Chi-restraints excluded: chain H residue 263 VAL Chi-restraints excluded: chain H residue 279 VAL Chi-restraints excluded: chain H residue 312 ASP Chi-restraints excluded: chain H residue 357 GLU Chi-restraints excluded: chain H residue 369 VAL Chi-restraints excluded: chain H residue 375 SER Chi-restraints excluded: chain H residue 386 GLN Chi-restraints excluded: chain H residue 415 SER Chi-restraints excluded: chain H residue 427 VAL Chi-restraints excluded: chain I residue 240 VAL Chi-restraints excluded: chain I residue 266 VAL Chi-restraints excluded: chain I residue 279 VAL Chi-restraints excluded: chain I residue 305 VAL Chi-restraints excluded: chain I residue 324 SER Chi-restraints excluded: chain I residue 397 VAL Chi-restraints excluded: chain I residue 411 THR Chi-restraints excluded: chain I residue 422 VAL Chi-restraints excluded: chain I residue 426 SER Chi-restraints excluded: chain I residue 430 GLU Chi-restraints excluded: chain I residue 441 LEU Chi-restraints excluded: chain J residue 259 VAL Chi-restraints excluded: chain J residue 282 VAL Chi-restraints excluded: chain J residue 284 VAL Chi-restraints excluded: chain J residue 335 THR Chi-restraints excluded: chain J residue 363 VAL Chi-restraints excluded: chain J residue 375 SER Chi-restraints excluded: chain J residue 401 ASP Chi-restraints excluded: chain J residue 411 THR Chi-restraints excluded: chain J residue 422 VAL Chi-restraints excluded: chain J residue 427 VAL Chi-restraints excluded: chain B residue 261 CYS Chi-restraints excluded: chain B residue 308 VAL Chi-restraints excluded: chain B residue 356 ASP Chi-restraints excluded: chain B residue 358 LEU Chi-restraints excluded: chain B residue 421 ASN Chi-restraints excluded: chain B residue 426 SER Chi-restraints excluded: chain B residue 439 LYS Chi-restraints excluded: chain K residue 241 PHE Chi-restraints excluded: chain K residue 253 ILE Chi-restraints excluded: chain K residue 260 THR Chi-restraints excluded: chain K residue 266 VAL Chi-restraints excluded: chain K residue 292 ARG Chi-restraints excluded: chain K residue 335 THR Chi-restraints excluded: chain K residue 366 THR Chi-restraints excluded: chain K residue 375 SER Chi-restraints excluded: chain K residue 411 THR Chi-restraints excluded: chain L residue 239 SER Chi-restraints excluded: chain L residue 289 THR Chi-restraints excluded: chain L residue 307 THR Chi-restraints excluded: chain L residue 359 THR Chi-restraints excluded: chain L residue 375 SER Chi-restraints excluded: chain L residue 426 SER Chi-restraints excluded: chain L residue 439 LYS Chi-restraints excluded: chain A residue 282 VAL Chi-restraints excluded: chain A residue 307 THR Chi-restraints excluded: chain A residue 308 VAL Chi-restraints excluded: chain A residue 375 SER Chi-restraints excluded: chain D residue 261 CYS Chi-restraints excluded: chain D residue 273 VAL Chi-restraints excluded: chain D residue 276 ASN Chi-restraints excluded: chain D residue 284 VAL Chi-restraints excluded: chain D residue 292 ARG Chi-restraints excluded: chain D residue 350 THR Chi-restraints excluded: chain D residue 375 SER Chi-restraints excluded: chain D residue 439 LYS Chi-restraints excluded: chain D residue 440 SER Chi-restraints excluded: chain C residue 252 MET Chi-restraints excluded: chain C residue 256 THR Chi-restraints excluded: chain C residue 258 GLU Chi-restraints excluded: chain C residue 306 LEU Chi-restraints excluded: chain C residue 307 THR Chi-restraints excluded: chain C residue 337 SER Chi-restraints excluded: chain C residue 359 THR Chi-restraints excluded: chain C residue 365 LEU Chi-restraints excluded: chain C residue 366 THR Chi-restraints excluded: chain C residue 375 SER Chi-restraints excluded: chain C residue 427 VAL Chi-restraints excluded: chain C residue 440 SER Chi-restraints excluded: chain C residue 443 LYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 252 random chunks: chunk 121 optimal weight: 3.9990 chunk 86 optimal weight: 8.9990 chunk 13 optimal weight: 0.6980 chunk 162 optimal weight: 1.9990 chunk 102 optimal weight: 2.9990 chunk 236 optimal weight: 10.0000 chunk 3 optimal weight: 6.9990 chunk 11 optimal weight: 1.9990 chunk 18 optimal weight: 0.8980 chunk 23 optimal weight: 10.0000 chunk 184 optimal weight: 3.9990 overall best weight: 1.7186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 429 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 285 HIS G 362 GLN H 361 ASN I 295 GLN I 310 HIS I 418 GLN J 390 ASN ** J 429 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 438 GLN A 434 ASN C 389 ASN C 418 GLN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4538 r_free = 0.4538 target = 0.232093 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3814 r_free = 0.3814 target = 0.154814 restraints weight = 22623.653| |-----------------------------------------------------------------------------| r_work (start): 0.3761 rms_B_bonded: 2.78 r_work: 0.3493 rms_B_bonded: 2.87 restraints_weight: 0.5000 r_work: 0.3372 rms_B_bonded: 4.26 restraints_weight: 0.2500 r_work (final): 0.3372 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8202 moved from start: 0.1441 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.045 20830 Z= 0.192 Angle : 0.598 7.662 28368 Z= 0.302 Chirality : 0.045 0.146 3104 Planarity : 0.004 0.052 3656 Dihedral : 4.273 20.838 2708 Min Nonbonded Distance : 2.434 Molprobity Statistics. All-atom Clashscore : 10.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.93 % Favored : 96.07 % Rotamer: Outliers : 7.03 % Allowed : 26.96 % Favored : 66.01 % 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: -0.28 (0.17), residues: 2516 helix: -0.47 (0.34), residues: 231 sheet: -0.43 (0.16), residues: 1003 loop : 0.28 (0.19), residues: 1282 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG H 355 TYR 0.018 0.002 TYR H 407 PHE 0.015 0.001 PHE L 372 TRP 0.014 0.001 TRP B 313 HIS 0.007 0.001 HIS I 310 Details of bonding type rmsd covalent geometry : bond 0.00453 (20808) covalent geometry : angle 0.59750 (28324) SS BOND : bond 0.00268 ( 22) SS BOND : angle 0.68128 ( 44) hydrogen bonds : bond 0.04182 ( 685) hydrogen bonds : angle 6.08634 ( 2136) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5032 Ramachandran restraints generated. 2516 Oldfield, 0 Emsley, 2516 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5032 Ramachandran restraints generated. 2516 Oldfield, 0 Emsley, 2516 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 341 residues out of total 2348 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 165 poor density : 176 time to evaluate : 0.812 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: E 315 ASN cc_start: 0.7304 (m-40) cc_final: 0.6909 (m110) REVERT: F 246 LYS cc_start: 0.7641 (ttpt) cc_final: 0.7005 (tmtm) REVERT: F 264 VAL cc_start: 0.1436 (OUTLIER) cc_final: 0.1107 (t) REVERT: F 289 THR cc_start: 0.5238 (OUTLIER) cc_final: 0.5007 (p) REVERT: F 340 LYS cc_start: 0.8037 (tppt) cc_final: 0.7533 (tppt) REVERT: G 426 SER cc_start: 0.8806 (OUTLIER) cc_final: 0.8591 (p) REVERT: G 444 SER cc_start: 0.8479 (p) cc_final: 0.8228 (m) REVERT: H 312 ASP cc_start: 0.6867 (OUTLIER) cc_final: 0.6554 (p0) REVERT: H 386 GLN cc_start: 0.8545 (OUTLIER) cc_final: 0.8053 (mp10) REVERT: I 276 ASN cc_start: 0.4408 (OUTLIER) cc_final: 0.3943 (p0) REVERT: I 419 GLN cc_start: 0.7591 (tt0) cc_final: 0.7341 (tt0) REVERT: J 318 GLU cc_start: 0.6008 (mp0) cc_final: 0.5760 (mp0) REVERT: B 347 GLN cc_start: 0.8707 (mt0) cc_final: 0.8274 (mt0) REVERT: B 428 MET cc_start: 0.8777 (mtp) cc_final: 0.8507 (mtm) REVERT: B 439 LYS cc_start: 0.8860 (OUTLIER) cc_final: 0.8628 (mptm) REVERT: K 241 PHE cc_start: 0.1521 (OUTLIER) cc_final: 0.0778 (m-80) REVERT: K 390 ASN cc_start: 0.7630 (t0) cc_final: 0.7283 (t0) REVERT: K 443 LYS cc_start: 0.8283 (tptp) cc_final: 0.7517 (pttt) REVERT: L 248 LYS cc_start: 0.5454 (OUTLIER) cc_final: 0.5104 (tptp) REVERT: L 361 ASN cc_start: 0.7684 (p0) cc_final: 0.7295 (t160) REVERT: L 413 ASP cc_start: 0.7733 (p0) cc_final: 0.7377 (m-30) REVERT: L 439 LYS cc_start: 0.8489 (OUTLIER) cc_final: 0.7714 (mptm) REVERT: A 345 GLU cc_start: 0.8483 (tt0) cc_final: 0.8255 (tt0) REVERT: D 276 ASN cc_start: 0.6502 (OUTLIER) cc_final: 0.5980 (m-40) REVERT: D 312 ASP cc_start: 0.7345 (t70) cc_final: 0.6579 (t70) REVERT: D 357 GLU cc_start: 0.8730 (OUTLIER) cc_final: 0.8487 (tp30) REVERT: C 340 LYS cc_start: 0.8290 (mmtt) cc_final: 0.7897 (mmtt) outliers start: 165 outliers final: 94 residues processed: 318 average time/residue: 0.4171 time to fit residues: 155.7020 Evaluate side-chains 272 residues out of total 2348 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 106 poor density : 166 time to evaluate : 0.771 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 240 VAL Chi-restraints excluded: chain E residue 258 GLU Chi-restraints excluded: chain E residue 306 LEU Chi-restraints excluded: chain E residue 314 LEU Chi-restraints excluded: chain E residue 359 THR Chi-restraints excluded: chain E residue 382 GLU Chi-restraints excluded: chain E residue 412 VAL Chi-restraints excluded: chain E residue 426 SER Chi-restraints excluded: chain E residue 427 VAL Chi-restraints excluded: chain F residue 264 VAL Chi-restraints excluded: chain F residue 279 VAL Chi-restraints excluded: chain F residue 289 THR Chi-restraints excluded: chain F residue 299 THR Chi-restraints excluded: chain F residue 302 VAL Chi-restraints excluded: chain F residue 308 VAL Chi-restraints excluded: chain F residue 345 GLU Chi-restraints excluded: chain F residue 363 VAL Chi-restraints excluded: chain F residue 427 VAL Chi-restraints excluded: chain F residue 442 ASP Chi-restraints excluded: chain G residue 264 VAL Chi-restraints excluded: chain G residue 314 LEU Chi-restraints excluded: chain G residue 321 CYS Chi-restraints excluded: chain G residue 355 ARG Chi-restraints excluded: chain G residue 375 SER Chi-restraints excluded: chain G residue 426 SER Chi-restraints excluded: chain H residue 240 VAL Chi-restraints excluded: chain H residue 263 VAL Chi-restraints excluded: chain H residue 279 VAL Chi-restraints excluded: chain H residue 312 ASP Chi-restraints excluded: chain H residue 357 GLU Chi-restraints excluded: chain H residue 369 VAL Chi-restraints excluded: chain H residue 375 SER Chi-restraints excluded: chain H residue 386 GLN Chi-restraints excluded: chain H residue 415 SER Chi-restraints excluded: chain H residue 427 VAL Chi-restraints excluded: chain I residue 240 VAL Chi-restraints excluded: chain I residue 266 VAL Chi-restraints excluded: chain I residue 276 ASN Chi-restraints excluded: chain I residue 279 VAL Chi-restraints excluded: chain I residue 305 VAL Chi-restraints excluded: chain I residue 314 LEU Chi-restraints excluded: chain I residue 324 SER Chi-restraints excluded: chain I residue 397 VAL Chi-restraints excluded: chain I residue 411 THR Chi-restraints excluded: chain I residue 426 SER Chi-restraints excluded: chain J residue 259 VAL Chi-restraints excluded: chain J residue 282 VAL Chi-restraints excluded: chain J residue 284 VAL Chi-restraints excluded: chain J residue 335 THR Chi-restraints excluded: chain J residue 363 VAL Chi-restraints excluded: chain J residue 375 SER Chi-restraints excluded: chain J residue 401 ASP Chi-restraints excluded: chain J residue 411 THR Chi-restraints excluded: chain J residue 427 VAL Chi-restraints excluded: chain B residue 261 CYS Chi-restraints excluded: chain B residue 308 VAL Chi-restraints excluded: chain B residue 358 LEU Chi-restraints excluded: chain B residue 376 ASP Chi-restraints excluded: chain B residue 426 SER Chi-restraints excluded: chain B residue 439 LYS Chi-restraints excluded: chain K residue 241 PHE Chi-restraints excluded: chain K residue 260 THR Chi-restraints excluded: chain K residue 266 VAL Chi-restraints excluded: chain K residue 335 THR Chi-restraints excluded: chain K residue 366 THR Chi-restraints excluded: chain K residue 375 SER Chi-restraints excluded: chain K residue 411 THR Chi-restraints excluded: chain K residue 437 THR Chi-restraints excluded: chain L residue 239 SER Chi-restraints excluded: chain L residue 242 LEU Chi-restraints excluded: chain L residue 248 LYS Chi-restraints excluded: chain L residue 262 VAL Chi-restraints excluded: chain L residue 289 THR Chi-restraints excluded: chain L residue 307 THR Chi-restraints excluded: chain L residue 359 THR Chi-restraints excluded: chain L residue 375 SER Chi-restraints excluded: chain L residue 398 LEU Chi-restraints excluded: chain L residue 426 SER Chi-restraints excluded: chain L residue 439 LYS Chi-restraints excluded: chain A residue 282 VAL Chi-restraints excluded: chain A residue 308 VAL Chi-restraints excluded: chain A residue 375 SER Chi-restraints excluded: chain A residue 408 SER Chi-restraints excluded: chain D residue 261 CYS Chi-restraints excluded: chain D residue 273 VAL Chi-restraints excluded: chain D residue 276 ASN Chi-restraints excluded: chain D residue 284 VAL Chi-restraints excluded: chain D residue 292 ARG Chi-restraints excluded: chain D residue 350 THR Chi-restraints excluded: chain D residue 357 GLU Chi-restraints excluded: chain D residue 375 SER Chi-restraints excluded: chain D residue 439 LYS Chi-restraints excluded: chain D residue 440 SER Chi-restraints excluded: chain C residue 256 THR Chi-restraints excluded: chain C residue 258 GLU Chi-restraints excluded: chain C residue 264 VAL Chi-restraints excluded: chain C residue 306 LEU Chi-restraints excluded: chain C residue 307 THR Chi-restraints excluded: chain C residue 337 SER Chi-restraints excluded: chain C residue 359 THR Chi-restraints excluded: chain C residue 365 LEU Chi-restraints excluded: chain C residue 366 THR Chi-restraints excluded: chain C residue 375 SER Chi-restraints excluded: chain C residue 427 VAL Chi-restraints excluded: chain C residue 440 SER Chi-restraints excluded: chain C residue 443 LYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 252 random chunks: chunk 120 optimal weight: 0.7980 chunk 116 optimal weight: 2.9990 chunk 74 optimal weight: 3.9990 chunk 103 optimal weight: 0.9980 chunk 149 optimal weight: 1.9990 chunk 161 optimal weight: 4.9990 chunk 136 optimal weight: 8.9990 chunk 155 optimal weight: 5.9990 chunk 153 optimal weight: 5.9990 chunk 101 optimal weight: 0.7980 chunk 251 optimal weight: 0.9980 overall best weight: 1.1182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 362 GLN H 361 ASN I 418 GLN J 418 GLN ** J 429 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 421 ASN K 438 GLN L 418 GLN A 433 HIS A 434 ASN A 435 HIS C 389 ASN C 418 GLN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4547 r_free = 0.4547 target = 0.230270 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.4025 r_free = 0.4025 target = 0.170203 restraints weight = 22725.586| |-----------------------------------------------------------------------------| r_work (start): 0.3966 rms_B_bonded: 2.27 r_work: 0.3532 rms_B_bonded: 2.93 restraints_weight: 0.5000 r_work: 0.3413 rms_B_bonded: 4.44 restraints_weight: 0.2500 r_work (final): 0.3413 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8216 moved from start: 0.1597 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 20830 Z= 0.145 Angle : 0.555 6.992 28368 Z= 0.278 Chirality : 0.044 0.177 3104 Planarity : 0.004 0.051 3656 Dihedral : 4.100 19.974 2708 Min Nonbonded Distance : 2.538 Molprobity Statistics. All-atom Clashscore : 10.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.09 % Favored : 95.91 % Rotamer: Outliers : 6.30 % Allowed : 27.73 % Favored : 65.97 % 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: -0.13 (0.18), residues: 2516 helix: -0.31 (0.35), residues: 232 sheet: -0.32 (0.16), residues: 988 loop : 0.36 (0.19), residues: 1296 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG H 355 TYR 0.016 0.002 TYR H 407 PHE 0.013 0.001 PHE I 405 TRP 0.013 0.001 TRP B 313 HIS 0.005 0.001 HIS G 268 Details of bonding type rmsd covalent geometry : bond 0.00342 (20808) covalent geometry : angle 0.55527 (28324) SS BOND : bond 0.00219 ( 22) SS BOND : angle 0.57383 ( 44) hydrogen bonds : bond 0.03517 ( 685) hydrogen bonds : angle 5.75441 ( 2136) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5032 Ramachandran restraints generated. 2516 Oldfield, 0 Emsley, 2516 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5032 Ramachandran restraints generated. 2516 Oldfield, 0 Emsley, 2516 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 327 residues out of total 2348 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 148 poor density : 179 time to evaluate : 0.816 Fit side-chains revert: symmetry clash REVERT: E 285 HIS cc_start: 0.6140 (OUTLIER) cc_final: 0.5814 (m-70) REVERT: E 315 ASN cc_start: 0.7351 (m-40) cc_final: 0.6968 (m110) REVERT: E 409 LYS cc_start: 0.9136 (OUTLIER) cc_final: 0.8424 (ttpp) REVERT: F 246 LYS cc_start: 0.7703 (ttpt) cc_final: 0.7063 (tmtm) REVERT: F 340 LYS cc_start: 0.8057 (tppt) cc_final: 0.7592 (tppt) REVERT: G 315 ASN cc_start: 0.7620 (m-40) cc_final: 0.7058 (m110) REVERT: G 444 SER cc_start: 0.8491 (p) cc_final: 0.8221 (m) REVERT: H 250 THR cc_start: 0.8651 (t) cc_final: 0.8407 (p) REVERT: H 312 ASP cc_start: 0.6803 (OUTLIER) cc_final: 0.6470 (p0) REVERT: H 347 GLN cc_start: 0.8210 (mt0) cc_final: 0.7906 (mt0) REVERT: H 386 GLN cc_start: 0.8535 (OUTLIER) cc_final: 0.8042 (mp10) REVERT: I 419 GLN cc_start: 0.7615 (tt0) cc_final: 0.7395 (tt0) REVERT: J 267 SER cc_start: 0.2429 (OUTLIER) cc_final: 0.1961 (p) REVERT: J 436 TYR cc_start: 0.8394 (t80) cc_final: 0.8172 (t80) REVERT: B 310 HIS cc_start: 0.8338 (m-70) cc_final: 0.8039 (m-70) REVERT: B 315 ASN cc_start: 0.8194 (m-40) cc_final: 0.7993 (m-40) REVERT: B 347 GLN cc_start: 0.8719 (mt0) cc_final: 0.8318 (mt0) REVERT: B 439 LYS cc_start: 0.8875 (OUTLIER) cc_final: 0.8662 (mptm) REVERT: K 241 PHE cc_start: 0.1511 (OUTLIER) cc_final: 0.0687 (m-80) REVERT: K 390 ASN cc_start: 0.7690 (t0) cc_final: 0.7363 (t0) REVERT: K 443 LYS cc_start: 0.8263 (tptp) cc_final: 0.7537 (pttt) REVERT: L 252 MET cc_start: 0.5617 (OUTLIER) cc_final: 0.5386 (mtp) REVERT: L 361 ASN cc_start: 0.7743 (p0) cc_final: 0.7508 (t0) REVERT: L 380 GLU cc_start: 0.8522 (mt-10) cc_final: 0.8294 (mt-10) REVERT: L 439 LYS cc_start: 0.8437 (OUTLIER) cc_final: 0.7669 (mptm) REVERT: A 345 GLU cc_start: 0.8428 (tt0) cc_final: 0.8221 (tt0) REVERT: D 276 ASN cc_start: 0.6431 (OUTLIER) cc_final: 0.5884 (m-40) REVERT: D 309 LEU cc_start: 0.7644 (OUTLIER) cc_final: 0.6554 (tm) REVERT: D 312 ASP cc_start: 0.7312 (t70) cc_final: 0.6500 (t70) REVERT: C 340 LYS cc_start: 0.8279 (mmtt) cc_final: 0.7938 (mmtt) outliers start: 148 outliers final: 95 residues processed: 307 average time/residue: 0.4852 time to fit residues: 174.2460 Evaluate side-chains 276 residues out of total 2348 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 106 poor density : 170 time to evaluate : 0.777 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 240 VAL Chi-restraints excluded: chain E residue 258 GLU Chi-restraints excluded: chain E residue 285 HIS Chi-restraints excluded: chain E residue 345 GLU Chi-restraints excluded: chain E residue 359 THR Chi-restraints excluded: chain E residue 382 GLU Chi-restraints excluded: chain E residue 409 LYS Chi-restraints excluded: chain E residue 412 VAL Chi-restraints excluded: chain E residue 424 SER Chi-restraints excluded: chain E residue 426 SER Chi-restraints excluded: chain E residue 427 VAL Chi-restraints excluded: chain F residue 256 THR Chi-restraints excluded: chain F residue 279 VAL Chi-restraints excluded: chain F residue 299 THR Chi-restraints excluded: chain F residue 302 VAL Chi-restraints excluded: chain F residue 308 VAL Chi-restraints excluded: chain F residue 345 GLU Chi-restraints excluded: chain F residue 363 VAL Chi-restraints excluded: chain F residue 376 ASP Chi-restraints excluded: chain F residue 427 VAL Chi-restraints excluded: chain F residue 442 ASP Chi-restraints excluded: chain G residue 264 VAL Chi-restraints excluded: chain G residue 308 VAL Chi-restraints excluded: chain G residue 314 LEU Chi-restraints excluded: chain G residue 321 CYS Chi-restraints excluded: chain G residue 347 GLN Chi-restraints excluded: chain G residue 355 ARG Chi-restraints excluded: chain G residue 375 SER Chi-restraints excluded: chain H residue 240 VAL Chi-restraints excluded: chain H residue 241 PHE Chi-restraints excluded: chain H residue 263 VAL Chi-restraints excluded: chain H residue 279 VAL Chi-restraints excluded: chain H residue 280 ASP Chi-restraints excluded: chain H residue 312 ASP Chi-restraints excluded: chain H residue 357 GLU Chi-restraints excluded: chain H residue 360 LYS Chi-restraints excluded: chain H residue 369 VAL Chi-restraints excluded: chain H residue 375 SER Chi-restraints excluded: chain H residue 386 GLN Chi-restraints excluded: chain H residue 415 SER Chi-restraints excluded: chain H residue 424 SER Chi-restraints excluded: chain H residue 427 VAL Chi-restraints excluded: chain I residue 266 VAL Chi-restraints excluded: chain I residue 279 VAL Chi-restraints excluded: chain I residue 305 VAL Chi-restraints excluded: chain I residue 308 VAL Chi-restraints excluded: chain I residue 324 SER Chi-restraints excluded: chain I residue 397 VAL Chi-restraints excluded: chain I residue 411 THR Chi-restraints excluded: chain I residue 426 SER Chi-restraints excluded: chain J residue 267 SER Chi-restraints excluded: chain J residue 282 VAL Chi-restraints excluded: chain J residue 284 VAL Chi-restraints excluded: chain J residue 335 THR Chi-restraints excluded: chain J residue 363 VAL Chi-restraints excluded: chain J residue 375 SER Chi-restraints excluded: chain J residue 401 ASP Chi-restraints excluded: chain J residue 411 THR Chi-restraints excluded: chain J residue 427 VAL Chi-restraints excluded: chain B residue 261 CYS Chi-restraints excluded: chain B residue 263 VAL Chi-restraints excluded: chain B residue 308 VAL Chi-restraints excluded: chain B residue 358 LEU Chi-restraints excluded: chain B residue 376 ASP Chi-restraints excluded: chain B residue 411 THR Chi-restraints excluded: chain B residue 426 SER Chi-restraints excluded: chain B residue 439 LYS Chi-restraints excluded: chain K residue 241 PHE Chi-restraints excluded: chain K residue 260 THR Chi-restraints excluded: chain K residue 266 VAL Chi-restraints excluded: chain K residue 335 THR Chi-restraints excluded: chain K residue 366 THR Chi-restraints excluded: chain K residue 411 THR Chi-restraints excluded: chain L residue 239 SER Chi-restraints excluded: chain L residue 242 LEU Chi-restraints excluded: chain L residue 252 MET Chi-restraints excluded: chain L residue 289 THR Chi-restraints excluded: chain L residue 315 ASN Chi-restraints excluded: chain L residue 375 SER Chi-restraints excluded: chain L residue 398 LEU Chi-restraints excluded: chain L residue 426 SER Chi-restraints excluded: chain L residue 439 LYS Chi-restraints excluded: chain A residue 307 THR Chi-restraints excluded: chain A residue 308 VAL Chi-restraints excluded: chain A residue 375 SER Chi-restraints excluded: chain D residue 261 CYS Chi-restraints excluded: chain D residue 273 VAL Chi-restraints excluded: chain D residue 276 ASN Chi-restraints excluded: chain D residue 284 VAL Chi-restraints excluded: chain D residue 292 ARG Chi-restraints excluded: chain D residue 309 LEU Chi-restraints excluded: chain D residue 350 THR Chi-restraints excluded: chain D residue 439 LYS Chi-restraints excluded: chain C residue 258 GLU Chi-restraints excluded: chain C residue 264 VAL Chi-restraints excluded: chain C residue 306 LEU Chi-restraints excluded: chain C residue 307 THR Chi-restraints excluded: chain C residue 337 SER Chi-restraints excluded: chain C residue 359 THR Chi-restraints excluded: chain C residue 365 LEU Chi-restraints excluded: chain C residue 366 THR Chi-restraints excluded: chain C residue 375 SER Chi-restraints excluded: chain C residue 427 VAL Chi-restraints excluded: chain C residue 437 THR Chi-restraints excluded: chain C residue 440 SER Chi-restraints excluded: chain C residue 443 LYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 252 random chunks: chunk 98 optimal weight: 1.9990 chunk 10 optimal weight: 0.5980 chunk 95 optimal weight: 0.9980 chunk 116 optimal weight: 0.9990 chunk 55 optimal weight: 2.9990 chunk 243 optimal weight: 0.5980 chunk 136 optimal weight: 7.9990 chunk 228 optimal weight: 3.9990 chunk 187 optimal weight: 4.9990 chunk 112 optimal weight: 6.9990 chunk 121 optimal weight: 2.9990 overall best weight: 1.0384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 362 GLN H 361 ASN J 418 GLN ** J 429 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 421 ASN K 438 GLN L 418 GLN A 434 ASN C 389 ASN C 418 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4546 r_free = 0.4546 target = 0.230018 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.4015 r_free = 0.4015 target = 0.168961 restraints weight = 22590.162| |-----------------------------------------------------------------------------| r_work (start): 0.3944 rms_B_bonded: 2.27 r_work: 0.3524 rms_B_bonded: 2.95 restraints_weight: 0.5000 r_work: 0.3406 rms_B_bonded: 4.43 restraints_weight: 0.2500 r_work (final): 0.3406 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8212 moved from start: 0.1714 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 20830 Z= 0.139 Angle : 0.549 6.958 28368 Z= 0.275 Chirality : 0.044 0.140 3104 Planarity : 0.004 0.049 3656 Dihedral : 4.064 19.981 2708 Min Nonbonded Distance : 2.545 Molprobity Statistics. All-atom Clashscore : 10.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.01 % Favored : 95.99 % Rotamer: Outliers : 6.39 % Allowed : 27.34 % Favored : 66.27 % 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: -0.04 (0.18), residues: 2516 helix: -0.33 (0.35), residues: 225 sheet: -0.25 (0.17), residues: 991 loop : 0.42 (0.19), residues: 1300 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG H 355 TYR 0.016 0.002 TYR A 407 PHE 0.013 0.001 PHE I 405 TRP 0.014 0.001 TRP B 313 HIS 0.008 0.001 HIS G 268 Details of bonding type rmsd covalent geometry : bond 0.00328 (20808) covalent geometry : angle 0.54935 (28324) SS BOND : bond 0.00225 ( 22) SS BOND : angle 0.60504 ( 44) hydrogen bonds : bond 0.03378 ( 685) hydrogen bonds : angle 5.59017 ( 2136) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5032 Ramachandran restraints generated. 2516 Oldfield, 0 Emsley, 2516 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5032 Ramachandran restraints generated. 2516 Oldfield, 0 Emsley, 2516 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 324 residues out of total 2348 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 150 poor density : 174 time to evaluate : 0.833 Fit side-chains revert: symmetry clash REVERT: E 285 HIS cc_start: 0.6162 (OUTLIER) cc_final: 0.5811 (m-70) REVERT: E 315 ASN cc_start: 0.7346 (m-40) cc_final: 0.6965 (m110) REVERT: E 409 LYS cc_start: 0.9129 (OUTLIER) cc_final: 0.8428 (ttpp) REVERT: F 246 LYS cc_start: 0.7689 (ttpt) cc_final: 0.7055 (tmtm) REVERT: G 315 ASN cc_start: 0.7615 (m-40) cc_final: 0.7030 (m110) REVERT: G 444 SER cc_start: 0.8477 (p) cc_final: 0.8221 (m) REVERT: H 250 THR cc_start: 0.8655 (t) cc_final: 0.8396 (p) REVERT: H 312 ASP cc_start: 0.6821 (OUTLIER) cc_final: 0.6506 (p0) REVERT: H 347 GLN cc_start: 0.8206 (mt0) cc_final: 0.7914 (mt0) REVERT: H 386 GLN cc_start: 0.8526 (OUTLIER) cc_final: 0.8047 (mp10) REVERT: I 419 GLN cc_start: 0.7610 (tt0) cc_final: 0.7380 (tt0) REVERT: J 267 SER cc_start: 0.2404 (OUTLIER) cc_final: 0.1936 (p) REVERT: J 290 LYS cc_start: 0.0122 (OUTLIER) cc_final: -0.0087 (mtpt) REVERT: J 436 TYR cc_start: 0.8422 (t80) cc_final: 0.8200 (t80) REVERT: B 310 HIS cc_start: 0.8284 (m-70) cc_final: 0.7998 (m-70) REVERT: B 347 GLN cc_start: 0.8727 (mt0) cc_final: 0.8322 (mt0) REVERT: B 447 LYS cc_start: 0.4654 (OUTLIER) cc_final: 0.4176 (mttp) REVERT: K 241 PHE cc_start: 0.1495 (OUTLIER) cc_final: 0.0670 (m-80) REVERT: K 390 ASN cc_start: 0.7689 (t0) cc_final: 0.7356 (t0) REVERT: K 443 LYS cc_start: 0.8181 (tptp) cc_final: 0.7461 (pttt) REVERT: L 361 ASN cc_start: 0.7760 (p0) cc_final: 0.7495 (t0) REVERT: L 424 SER cc_start: 0.8784 (OUTLIER) cc_final: 0.8405 (p) REVERT: L 439 LYS cc_start: 0.8426 (OUTLIER) cc_final: 0.7654 (mptm) REVERT: D 276 ASN cc_start: 0.6496 (OUTLIER) cc_final: 0.5999 (m-40) REVERT: D 309 LEU cc_start: 0.7638 (OUTLIER) cc_final: 0.6549 (tm) REVERT: D 312 ASP cc_start: 0.7273 (t70) cc_final: 0.6441 (t70) REVERT: C 340 LYS cc_start: 0.8277 (mmtt) cc_final: 0.7948 (mmtt) outliers start: 150 outliers final: 98 residues processed: 305 average time/residue: 0.4389 time to fit residues: 157.5268 Evaluate side-chains 274 residues out of total 2348 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 110 poor density : 164 time to evaluate : 0.495 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 240 VAL Chi-restraints excluded: chain E residue 258 GLU Chi-restraints excluded: chain E residue 285 HIS Chi-restraints excluded: chain E residue 306 LEU Chi-restraints excluded: chain E residue 345 GLU Chi-restraints excluded: chain E residue 359 THR Chi-restraints excluded: chain E residue 382 GLU Chi-restraints excluded: chain E residue 409 LYS Chi-restraints excluded: chain E residue 412 VAL Chi-restraints excluded: chain E residue 424 SER Chi-restraints excluded: chain E residue 426 SER Chi-restraints excluded: chain E residue 427 VAL Chi-restraints excluded: chain F residue 256 THR Chi-restraints excluded: chain F residue 279 VAL Chi-restraints excluded: chain F residue 299 THR Chi-restraints excluded: chain F residue 302 VAL Chi-restraints excluded: chain F residue 308 VAL Chi-restraints excluded: chain F residue 345 GLU Chi-restraints excluded: chain F residue 347 GLN Chi-restraints excluded: chain F residue 363 VAL Chi-restraints excluded: chain F residue 427 VAL Chi-restraints excluded: chain F residue 442 ASP Chi-restraints excluded: chain F residue 443 LYS Chi-restraints excluded: chain G residue 264 VAL Chi-restraints excluded: chain G residue 308 VAL Chi-restraints excluded: chain G residue 314 LEU Chi-restraints excluded: chain G residue 321 CYS Chi-restraints excluded: chain G residue 347 GLN Chi-restraints excluded: chain G residue 355 ARG Chi-restraints excluded: chain G residue 375 SER Chi-restraints excluded: chain G residue 426 SER Chi-restraints excluded: chain H residue 240 VAL Chi-restraints excluded: chain H residue 241 PHE Chi-restraints excluded: chain H residue 263 VAL Chi-restraints excluded: chain H residue 279 VAL Chi-restraints excluded: chain H residue 280 ASP Chi-restraints excluded: chain H residue 312 ASP Chi-restraints excluded: chain H residue 336 ILE Chi-restraints excluded: chain H residue 357 GLU Chi-restraints excluded: chain H residue 360 LYS Chi-restraints excluded: chain H residue 369 VAL Chi-restraints excluded: chain H residue 375 SER Chi-restraints excluded: chain H residue 386 GLN Chi-restraints excluded: chain H residue 415 SER Chi-restraints excluded: chain H residue 424 SER Chi-restraints excluded: chain H residue 427 VAL Chi-restraints excluded: chain I residue 266 VAL Chi-restraints excluded: chain I residue 279 VAL Chi-restraints excluded: chain I residue 305 VAL Chi-restraints excluded: chain I residue 308 VAL Chi-restraints excluded: chain I residue 324 SER Chi-restraints excluded: chain I residue 397 VAL Chi-restraints excluded: chain I residue 411 THR Chi-restraints excluded: chain I residue 426 SER Chi-restraints excluded: chain J residue 259 VAL Chi-restraints excluded: chain J residue 267 SER Chi-restraints excluded: chain J residue 282 VAL Chi-restraints excluded: chain J residue 284 VAL Chi-restraints excluded: chain J residue 290 LYS Chi-restraints excluded: chain J residue 363 VAL Chi-restraints excluded: chain J residue 375 SER Chi-restraints excluded: chain J residue 401 ASP Chi-restraints excluded: chain J residue 411 THR Chi-restraints excluded: chain J residue 427 VAL Chi-restraints excluded: chain B residue 263 VAL Chi-restraints excluded: chain B residue 308 VAL Chi-restraints excluded: chain B residue 358 LEU Chi-restraints excluded: chain B residue 411 THR Chi-restraints excluded: chain B residue 426 SER Chi-restraints excluded: chain B residue 447 LYS Chi-restraints excluded: chain K residue 241 PHE Chi-restraints excluded: chain K residue 260 THR Chi-restraints excluded: chain K residue 266 VAL Chi-restraints excluded: chain K residue 335 THR Chi-restraints excluded: chain K residue 366 THR Chi-restraints excluded: chain K residue 411 THR Chi-restraints excluded: chain L residue 242 LEU Chi-restraints excluded: chain L residue 289 THR Chi-restraints excluded: chain L residue 307 THR Chi-restraints excluded: chain L residue 315 ASN Chi-restraints excluded: chain L residue 375 SER Chi-restraints excluded: chain L residue 398 LEU Chi-restraints excluded: chain L residue 424 SER Chi-restraints excluded: chain L residue 426 SER Chi-restraints excluded: chain L residue 439 LYS Chi-restraints excluded: chain A residue 308 VAL Chi-restraints excluded: chain A residue 350 THR Chi-restraints excluded: chain D residue 261 CYS Chi-restraints excluded: chain D residue 273 VAL Chi-restraints excluded: chain D residue 276 ASN Chi-restraints excluded: chain D residue 284 VAL Chi-restraints excluded: chain D residue 292 ARG Chi-restraints excluded: chain D residue 309 LEU Chi-restraints excluded: chain D residue 350 THR Chi-restraints excluded: chain D residue 375 SER Chi-restraints excluded: chain D residue 439 LYS Chi-restraints excluded: chain D residue 440 SER Chi-restraints excluded: chain C residue 258 GLU Chi-restraints excluded: chain C residue 264 VAL Chi-restraints excluded: chain C residue 306 LEU Chi-restraints excluded: chain C residue 307 THR Chi-restraints excluded: chain C residue 337 SER Chi-restraints excluded: chain C residue 359 THR Chi-restraints excluded: chain C residue 365 LEU Chi-restraints excluded: chain C residue 366 THR Chi-restraints excluded: chain C residue 375 SER Chi-restraints excluded: chain C residue 427 VAL Chi-restraints excluded: chain C residue 437 THR Chi-restraints excluded: chain C residue 440 SER Chi-restraints excluded: chain C residue 443 LYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 252 random chunks: chunk 144 optimal weight: 4.9990 chunk 239 optimal weight: 5.9990 chunk 66 optimal weight: 0.5980 chunk 7 optimal weight: 8.9990 chunk 112 optimal weight: 2.9990 chunk 43 optimal weight: 5.9990 chunk 138 optimal weight: 0.9990 chunk 118 optimal weight: 3.9990 chunk 220 optimal weight: 6.9990 chunk 175 optimal weight: 0.9990 chunk 139 optimal weight: 0.9990 overall best weight: 1.3188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 362 GLN H 361 ASN ** J 429 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 421 ASN K 438 GLN A 434 ASN C 389 ASN C 418 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4549 r_free = 0.4549 target = 0.233205 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3905 r_free = 0.3905 target = 0.163524 restraints weight = 22418.043| |-----------------------------------------------------------------------------| r_work (start): 0.3840 rms_B_bonded: 2.77 r_work: 0.3488 rms_B_bonded: 2.91 restraints_weight: 0.5000 r_work: 0.3374 rms_B_bonded: 4.18 restraints_weight: 0.2500 r_work (final): 0.3374 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8194 moved from start: 0.1843 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 20830 Z= 0.158 Angle : 0.563 7.271 28368 Z= 0.281 Chirality : 0.044 0.140 3104 Planarity : 0.004 0.050 3656 Dihedral : 4.107 19.052 2708 Min Nonbonded Distance : 2.552 Molprobity Statistics. All-atom Clashscore : 10.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.25 % Favored : 95.75 % Rotamer: Outliers : 7.11 % Allowed : 26.96 % Favored : 65.93 % 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: 0.00 (0.18), residues: 2516 helix: -0.36 (0.35), residues: 225 sheet: -0.18 (0.16), residues: 998 loop : 0.42 (0.19), residues: 1293 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG H 355 TYR 0.016 0.002 TYR H 407 PHE 0.013 0.001 PHE I 405 TRP 0.014 0.001 TRP B 313 HIS 0.003 0.001 HIS I 310 Details of bonding type rmsd covalent geometry : bond 0.00376 (20808) covalent geometry : angle 0.56316 (28324) SS BOND : bond 0.00232 ( 22) SS BOND : angle 0.62642 ( 44) hydrogen bonds : bond 0.03419 ( 685) hydrogen bonds : angle 5.54210 ( 2136) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5032 Ramachandran restraints generated. 2516 Oldfield, 0 Emsley, 2516 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5032 Ramachandran restraints generated. 2516 Oldfield, 0 Emsley, 2516 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 336 residues out of total 2348 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 167 poor density : 169 time to evaluate : 0.854 Fit side-chains revert: symmetry clash REVERT: E 285 HIS cc_start: 0.6177 (OUTLIER) cc_final: 0.5798 (m-70) REVERT: E 315 ASN cc_start: 0.7305 (m-40) cc_final: 0.6879 (m110) REVERT: E 409 LYS cc_start: 0.9138 (OUTLIER) cc_final: 0.8487 (tttm) REVERT: F 246 LYS cc_start: 0.7684 (ttpt) cc_final: 0.7058 (tmtm) REVERT: F 299 THR cc_start: 0.1254 (OUTLIER) cc_final: 0.1007 (m) REVERT: G 315 ASN cc_start: 0.7574 (m-40) cc_final: 0.6970 (m110) REVERT: G 321 CYS cc_start: 0.1098 (OUTLIER) cc_final: -0.0004 (t) REVERT: G 444 SER cc_start: 0.8501 (p) cc_final: 0.8241 (m) REVERT: H 250 THR cc_start: 0.8634 (t) cc_final: 0.8376 (p) REVERT: H 312 ASP cc_start: 0.6857 (OUTLIER) cc_final: 0.6550 (p0) REVERT: H 347 GLN cc_start: 0.8175 (mt0) cc_final: 0.7871 (mt0) REVERT: H 386 GLN cc_start: 0.8524 (OUTLIER) cc_final: 0.8027 (mp10) REVERT: I 419 GLN cc_start: 0.7590 (tt0) cc_final: 0.7355 (tt0) REVERT: J 267 SER cc_start: 0.2524 (OUTLIER) cc_final: 0.2079 (p) REVERT: J 290 LYS cc_start: 0.0051 (OUTLIER) cc_final: -0.0151 (mtpt) REVERT: J 436 TYR cc_start: 0.8415 (t80) cc_final: 0.8156 (t80) REVERT: B 310 HIS cc_start: 0.8172 (m-70) cc_final: 0.7904 (m-70) REVERT: B 347 GLN cc_start: 0.8685 (mt0) cc_final: 0.8278 (mt0) REVERT: B 447 LYS cc_start: 0.4720 (OUTLIER) cc_final: 0.4194 (mttp) REVERT: K 241 PHE cc_start: 0.1377 (OUTLIER) cc_final: 0.0648 (m-80) REVERT: K 390 ASN cc_start: 0.7662 (t0) cc_final: 0.7324 (t0) REVERT: K 413 ASP cc_start: 0.7492 (m-30) cc_final: 0.7227 (t0) REVERT: K 443 LYS cc_start: 0.8153 (tptp) cc_final: 0.7417 (pttt) REVERT: L 361 ASN cc_start: 0.7766 (p0) cc_final: 0.7483 (t0) REVERT: L 424 SER cc_start: 0.8789 (OUTLIER) cc_final: 0.8351 (p) REVERT: L 439 LYS cc_start: 0.8412 (OUTLIER) cc_final: 0.7594 (mptm) REVERT: D 309 LEU cc_start: 0.7630 (OUTLIER) cc_final: 0.6580 (tm) REVERT: D 340 LYS cc_start: 0.8443 (OUTLIER) cc_final: 0.8196 (ptmm) REVERT: D 361 ASN cc_start: 0.7081 (p0) cc_final: 0.6811 (t0) REVERT: C 340 LYS cc_start: 0.8211 (mmtt) cc_final: 0.7825 (mmtt) outliers start: 167 outliers final: 103 residues processed: 316 average time/residue: 0.4718 time to fit residues: 174.3863 Evaluate side-chains 280 residues out of total 2348 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 117 poor density : 163 time to evaluate : 0.802 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 240 VAL Chi-restraints excluded: chain E residue 258 GLU Chi-restraints excluded: chain E residue 285 HIS Chi-restraints excluded: chain E residue 306 LEU Chi-restraints excluded: chain E residue 345 GLU Chi-restraints excluded: chain E residue 359 THR Chi-restraints excluded: chain E residue 382 GLU Chi-restraints excluded: chain E residue 409 LYS Chi-restraints excluded: chain E residue 412 VAL Chi-restraints excluded: chain E residue 424 SER Chi-restraints excluded: chain E residue 426 SER Chi-restraints excluded: chain E residue 427 VAL Chi-restraints excluded: chain F residue 256 THR Chi-restraints excluded: chain F residue 279 VAL Chi-restraints excluded: chain F residue 299 THR Chi-restraints excluded: chain F residue 302 VAL Chi-restraints excluded: chain F residue 308 VAL Chi-restraints excluded: chain F residue 345 GLU Chi-restraints excluded: chain F residue 347 GLN Chi-restraints excluded: chain F residue 363 VAL Chi-restraints excluded: chain F residue 427 VAL Chi-restraints excluded: chain F residue 442 ASP Chi-restraints excluded: chain F residue 443 LYS Chi-restraints excluded: chain G residue 264 VAL Chi-restraints excluded: chain G residue 308 VAL Chi-restraints excluded: chain G residue 314 LEU Chi-restraints excluded: chain G residue 321 CYS Chi-restraints excluded: chain G residue 347 GLN Chi-restraints excluded: chain G residue 355 ARG Chi-restraints excluded: chain G residue 375 SER Chi-restraints excluded: chain G residue 426 SER Chi-restraints excluded: chain H residue 240 VAL Chi-restraints excluded: chain H residue 241 PHE Chi-restraints excluded: chain H residue 263 VAL Chi-restraints excluded: chain H residue 279 VAL Chi-restraints excluded: chain H residue 280 ASP Chi-restraints excluded: chain H residue 312 ASP Chi-restraints excluded: chain H residue 336 ILE Chi-restraints excluded: chain H residue 357 GLU Chi-restraints excluded: chain H residue 360 LYS Chi-restraints excluded: chain H residue 369 VAL Chi-restraints excluded: chain H residue 375 SER Chi-restraints excluded: chain H residue 386 GLN Chi-restraints excluded: chain H residue 415 SER Chi-restraints excluded: chain H residue 424 SER Chi-restraints excluded: chain H residue 427 VAL Chi-restraints excluded: chain I residue 279 VAL Chi-restraints excluded: chain I residue 284 VAL Chi-restraints excluded: chain I residue 305 VAL Chi-restraints excluded: chain I residue 361 ASN Chi-restraints excluded: chain I residue 397 VAL Chi-restraints excluded: chain I residue 411 THR Chi-restraints excluded: chain I residue 438 GLN Chi-restraints excluded: chain J residue 259 VAL Chi-restraints excluded: chain J residue 267 SER Chi-restraints excluded: chain J residue 282 VAL Chi-restraints excluded: chain J residue 284 VAL Chi-restraints excluded: chain J residue 290 LYS Chi-restraints excluded: chain J residue 363 VAL Chi-restraints excluded: chain J residue 365 LEU Chi-restraints excluded: chain J residue 375 SER Chi-restraints excluded: chain J residue 401 ASP Chi-restraints excluded: chain J residue 411 THR Chi-restraints excluded: chain J residue 427 VAL Chi-restraints excluded: chain B residue 263 VAL Chi-restraints excluded: chain B residue 308 VAL Chi-restraints excluded: chain B residue 358 LEU Chi-restraints excluded: chain B residue 376 ASP Chi-restraints excluded: chain B residue 411 THR Chi-restraints excluded: chain B residue 426 SER Chi-restraints excluded: chain B residue 447 LYS Chi-restraints excluded: chain K residue 241 PHE Chi-restraints excluded: chain K residue 253 ILE Chi-restraints excluded: chain K residue 260 THR Chi-restraints excluded: chain K residue 266 VAL Chi-restraints excluded: chain K residue 335 THR Chi-restraints excluded: chain K residue 366 THR Chi-restraints excluded: chain K residue 411 THR Chi-restraints excluded: chain L residue 242 LEU Chi-restraints excluded: chain L residue 289 THR Chi-restraints excluded: chain L residue 307 THR Chi-restraints excluded: chain L residue 315 ASN Chi-restraints excluded: chain L residue 375 SER Chi-restraints excluded: chain L residue 398 LEU Chi-restraints excluded: chain L residue 424 SER Chi-restraints excluded: chain L residue 426 SER Chi-restraints excluded: chain L residue 439 LYS Chi-restraints excluded: chain A residue 307 THR Chi-restraints excluded: chain A residue 308 VAL Chi-restraints excluded: chain A residue 345 GLU Chi-restraints excluded: chain A residue 375 SER Chi-restraints excluded: chain A residue 424 SER Chi-restraints excluded: chain D residue 261 CYS Chi-restraints excluded: chain D residue 273 VAL Chi-restraints excluded: chain D residue 276 ASN Chi-restraints excluded: chain D residue 284 VAL Chi-restraints excluded: chain D residue 292 ARG Chi-restraints excluded: chain D residue 309 LEU Chi-restraints excluded: chain D residue 340 LYS Chi-restraints excluded: chain D residue 350 THR Chi-restraints excluded: chain D residue 375 SER Chi-restraints excluded: chain D residue 439 LYS Chi-restraints excluded: chain D residue 440 SER Chi-restraints excluded: chain C residue 256 THR Chi-restraints excluded: chain C residue 258 GLU Chi-restraints excluded: chain C residue 264 VAL Chi-restraints excluded: chain C residue 306 LEU Chi-restraints excluded: chain C residue 307 THR Chi-restraints excluded: chain C residue 337 SER Chi-restraints excluded: chain C residue 359 THR Chi-restraints excluded: chain C residue 365 LEU Chi-restraints excluded: chain C residue 366 THR Chi-restraints excluded: chain C residue 375 SER Chi-restraints excluded: chain C residue 427 VAL Chi-restraints excluded: chain C residue 437 THR Chi-restraints excluded: chain C residue 440 SER Chi-restraints excluded: chain C residue 443 LYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 252 random chunks: chunk 117 optimal weight: 2.9990 chunk 146 optimal weight: 3.9990 chunk 158 optimal weight: 0.0270 chunk 104 optimal weight: 2.9990 chunk 211 optimal weight: 0.4980 chunk 225 optimal weight: 1.9990 chunk 13 optimal weight: 0.6980 chunk 70 optimal weight: 10.0000 chunk 118 optimal weight: 0.8980 chunk 107 optimal weight: 9.9990 chunk 50 optimal weight: 2.9990 overall best weight: 0.8240 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 362 GLN H 361 ASN ** J 429 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 421 ASN K 438 GLN L 295 GLN A 419 GLN A 434 ASN C 418 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4562 r_free = 0.4562 target = 0.234660 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3921 r_free = 0.3921 target = 0.164977 restraints weight = 22551.141| |-----------------------------------------------------------------------------| r_work (start): 0.3853 rms_B_bonded: 2.74 r_work: 0.3510 rms_B_bonded: 2.90 restraints_weight: 0.5000 r_work: 0.3390 rms_B_bonded: 4.32 restraints_weight: 0.2500 r_work (final): 0.3390 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8206 moved from start: 0.1896 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 20830 Z= 0.122 Angle : 0.535 6.586 28368 Z= 0.266 Chirality : 0.043 0.136 3104 Planarity : 0.004 0.049 3656 Dihedral : 3.995 19.519 2708 Min Nonbonded Distance : 2.553 Molprobity Statistics. All-atom Clashscore : 10.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.90 % Favored : 96.10 % Rotamer: Outliers : 5.88 % Allowed : 28.15 % Favored : 65.97 % 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: 0.09 (0.18), residues: 2516 helix: -0.29 (0.35), residues: 226 sheet: -0.10 (0.17), residues: 987 loop : 0.46 (0.19), residues: 1303 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG H 355 TYR 0.015 0.002 TYR H 407 PHE 0.015 0.001 PHE I 405 TRP 0.015 0.001 TRP B 313 HIS 0.006 0.001 HIS G 268 Details of bonding type rmsd covalent geometry : bond 0.00290 (20808) covalent geometry : angle 0.53528 (28324) SS BOND : bond 0.00203 ( 22) SS BOND : angle 0.53158 ( 44) hydrogen bonds : bond 0.03141 ( 685) hydrogen bonds : angle 5.38058 ( 2136) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5032 Ramachandran restraints generated. 2516 Oldfield, 0 Emsley, 2516 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5032 Ramachandran restraints generated. 2516 Oldfield, 0 Emsley, 2516 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 313 residues out of total 2348 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 138 poor density : 175 time to evaluate : 0.665 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: E 285 HIS cc_start: 0.6115 (OUTLIER) cc_final: 0.5790 (m-70) REVERT: E 315 ASN cc_start: 0.7362 (m-40) cc_final: 0.6966 (m110) REVERT: F 246 LYS cc_start: 0.7657 (ttpt) cc_final: 0.6982 (tmtm) REVERT: F 264 VAL cc_start: 0.1303 (OUTLIER) cc_final: 0.1016 (t) REVERT: F 299 THR cc_start: 0.1385 (OUTLIER) cc_final: 0.1037 (m) REVERT: G 315 ASN cc_start: 0.7578 (m-40) cc_final: 0.7010 (m110) REVERT: G 321 CYS cc_start: 0.1106 (OUTLIER) cc_final: 0.0134 (t) REVERT: G 444 SER cc_start: 0.8472 (p) cc_final: 0.8209 (m) REVERT: H 250 THR cc_start: 0.8617 (t) cc_final: 0.8364 (p) REVERT: H 312 ASP cc_start: 0.6870 (OUTLIER) cc_final: 0.6573 (p0) REVERT: H 347 GLN cc_start: 0.8186 (mt0) cc_final: 0.7911 (mt0) REVERT: H 357 GLU cc_start: 0.8399 (OUTLIER) cc_final: 0.7627 (tp30) REVERT: H 386 GLN cc_start: 0.8548 (OUTLIER) cc_final: 0.8071 (mp10) REVERT: I 248 LYS cc_start: 0.7498 (tptp) cc_final: 0.5785 (mtpt) REVERT: I 419 GLN cc_start: 0.7600 (tt0) cc_final: 0.7357 (tt0) REVERT: J 267 SER cc_start: 0.2202 (OUTLIER) cc_final: 0.1761 (p) REVERT: J 290 LYS cc_start: 0.0140 (OUTLIER) cc_final: -0.0069 (mtpt) REVERT: J 436 TYR cc_start: 0.8374 (t80) cc_final: 0.8106 (t80) REVERT: B 310 HIS cc_start: 0.8197 (m-70) cc_final: 0.7941 (m-70) REVERT: B 347 GLN cc_start: 0.8697 (mt0) cc_final: 0.8328 (mt0) REVERT: B 447 LYS cc_start: 0.4611 (OUTLIER) cc_final: 0.4139 (mttp) REVERT: K 241 PHE cc_start: 0.1395 (OUTLIER) cc_final: 0.0593 (m-80) REVERT: K 390 ASN cc_start: 0.7684 (t0) cc_final: 0.7358 (t0) REVERT: K 413 ASP cc_start: 0.7453 (m-30) cc_final: 0.7231 (t0) REVERT: K 443 LYS cc_start: 0.8116 (tptp) cc_final: 0.7370 (ptpt) REVERT: L 361 ASN cc_start: 0.7758 (p0) cc_final: 0.7523 (t0) REVERT: L 424 SER cc_start: 0.8703 (OUTLIER) cc_final: 0.8366 (p) REVERT: D 309 LEU cc_start: 0.7655 (OUTLIER) cc_final: 0.6566 (tm) REVERT: D 312 ASP cc_start: 0.7188 (OUTLIER) cc_final: 0.6381 (t70) REVERT: D 340 LYS cc_start: 0.8402 (OUTLIER) cc_final: 0.8187 (ptmm) REVERT: D 361 ASN cc_start: 0.7077 (p0) cc_final: 0.6830 (t0) REVERT: C 252 MET cc_start: 0.6480 (ttt) cc_final: 0.6104 (mtp) REVERT: C 317 LYS cc_start: 0.6773 (OUTLIER) cc_final: 0.6164 (mmmt) REVERT: C 340 LYS cc_start: 0.8232 (mmtt) cc_final: 0.7889 (mmtt) outliers start: 138 outliers final: 91 residues processed: 292 average time/residue: 0.4359 time to fit residues: 149.4331 Evaluate side-chains 273 residues out of total 2348 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 107 poor density : 166 time to evaluate : 0.710 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 240 VAL Chi-restraints excluded: chain E residue 258 GLU Chi-restraints excluded: chain E residue 285 HIS Chi-restraints excluded: chain E residue 306 LEU Chi-restraints excluded: chain E residue 345 GLU Chi-restraints excluded: chain E residue 382 GLU Chi-restraints excluded: chain E residue 412 VAL Chi-restraints excluded: chain E residue 424 SER Chi-restraints excluded: chain E residue 426 SER Chi-restraints excluded: chain E residue 427 VAL Chi-restraints excluded: chain F residue 256 THR Chi-restraints excluded: chain F residue 264 VAL Chi-restraints excluded: chain F residue 279 VAL Chi-restraints excluded: chain F residue 299 THR Chi-restraints excluded: chain F residue 302 VAL Chi-restraints excluded: chain F residue 308 VAL Chi-restraints excluded: chain F residue 345 GLU Chi-restraints excluded: chain F residue 363 VAL Chi-restraints excluded: chain F residue 427 VAL Chi-restraints excluded: chain F residue 442 ASP Chi-restraints excluded: chain F residue 443 LYS Chi-restraints excluded: chain G residue 264 VAL Chi-restraints excluded: chain G residue 308 VAL Chi-restraints excluded: chain G residue 314 LEU Chi-restraints excluded: chain G residue 321 CYS Chi-restraints excluded: chain G residue 355 ARG Chi-restraints excluded: chain G residue 375 SER Chi-restraints excluded: chain G residue 413 ASP Chi-restraints excluded: chain G residue 426 SER Chi-restraints excluded: chain H residue 240 VAL Chi-restraints excluded: chain H residue 241 PHE Chi-restraints excluded: chain H residue 279 VAL Chi-restraints excluded: chain H residue 280 ASP Chi-restraints excluded: chain H residue 312 ASP Chi-restraints excluded: chain H residue 336 ILE Chi-restraints excluded: chain H residue 357 GLU Chi-restraints excluded: chain H residue 360 LYS Chi-restraints excluded: chain H residue 369 VAL Chi-restraints excluded: chain H residue 375 SER Chi-restraints excluded: chain H residue 386 GLN Chi-restraints excluded: chain H residue 427 VAL Chi-restraints excluded: chain I residue 279 VAL Chi-restraints excluded: chain I residue 284 VAL Chi-restraints excluded: chain I residue 305 VAL Chi-restraints excluded: chain I residue 361 ASN Chi-restraints excluded: chain I residue 397 VAL Chi-restraints excluded: chain I residue 411 THR Chi-restraints excluded: chain I residue 426 SER Chi-restraints excluded: chain J residue 267 SER Chi-restraints excluded: chain J residue 282 VAL Chi-restraints excluded: chain J residue 284 VAL Chi-restraints excluded: chain J residue 290 LYS Chi-restraints excluded: chain J residue 363 VAL Chi-restraints excluded: chain J residue 365 LEU Chi-restraints excluded: chain J residue 375 SER Chi-restraints excluded: chain J residue 401 ASP Chi-restraints excluded: chain J residue 411 THR Chi-restraints excluded: chain J residue 427 VAL Chi-restraints excluded: chain B residue 263 VAL Chi-restraints excluded: chain B residue 308 VAL Chi-restraints excluded: chain B residue 358 LEU Chi-restraints excluded: chain B residue 376 ASP Chi-restraints excluded: chain B residue 411 THR Chi-restraints excluded: chain B residue 426 SER Chi-restraints excluded: chain B residue 447 LYS Chi-restraints excluded: chain K residue 241 PHE Chi-restraints excluded: chain K residue 253 ILE Chi-restraints excluded: chain K residue 260 THR Chi-restraints excluded: chain K residue 266 VAL Chi-restraints excluded: chain K residue 335 THR Chi-restraints excluded: chain K residue 366 THR Chi-restraints excluded: chain K residue 411 THR Chi-restraints excluded: chain L residue 289 THR Chi-restraints excluded: chain L residue 307 THR Chi-restraints excluded: chain L residue 315 ASN Chi-restraints excluded: chain L residue 375 SER Chi-restraints excluded: chain L residue 398 LEU Chi-restraints excluded: chain L residue 411 THR Chi-restraints excluded: chain L residue 424 SER Chi-restraints excluded: chain L residue 426 SER Chi-restraints excluded: chain A residue 307 THR Chi-restraints excluded: chain A residue 308 VAL Chi-restraints excluded: chain A residue 375 SER Chi-restraints excluded: chain A residue 424 SER Chi-restraints excluded: chain D residue 253 ILE Chi-restraints excluded: chain D residue 261 CYS Chi-restraints excluded: chain D residue 273 VAL Chi-restraints excluded: chain D residue 276 ASN Chi-restraints excluded: chain D residue 284 VAL Chi-restraints excluded: chain D residue 292 ARG Chi-restraints excluded: chain D residue 309 LEU Chi-restraints excluded: chain D residue 312 ASP Chi-restraints excluded: chain D residue 340 LYS Chi-restraints excluded: chain D residue 350 THR Chi-restraints excluded: chain D residue 439 LYS Chi-restraints excluded: chain C residue 258 GLU Chi-restraints excluded: chain C residue 264 VAL Chi-restraints excluded: chain C residue 306 LEU Chi-restraints excluded: chain C residue 317 LYS Chi-restraints excluded: chain C residue 337 SER Chi-restraints excluded: chain C residue 359 THR Chi-restraints excluded: chain C residue 365 LEU Chi-restraints excluded: chain C residue 375 SER Chi-restraints excluded: chain C residue 427 VAL Chi-restraints excluded: chain C residue 437 THR Chi-restraints excluded: chain C residue 440 SER Chi-restraints excluded: chain C residue 443 LYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 252 random chunks: chunk 239 optimal weight: 6.9990 chunk 51 optimal weight: 0.9990 chunk 214 optimal weight: 10.0000 chunk 245 optimal weight: 1.9990 chunk 74 optimal weight: 3.9990 chunk 167 optimal weight: 6.9990 chunk 113 optimal weight: 5.9990 chunk 204 optimal weight: 0.6980 chunk 141 optimal weight: 3.9990 chunk 105 optimal weight: 20.0000 chunk 160 optimal weight: 2.9990 overall best weight: 2.1388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 389 ASN ** E 429 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 362 GLN H 361 ASN I 310 HIS I 418 GLN ** J 429 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 421 ASN K 438 GLN L 418 GLN A 419 GLN C 418 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4521 r_free = 0.4521 target = 0.227672 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3825 r_free = 0.3825 target = 0.153602 restraints weight = 22555.296| |-----------------------------------------------------------------------------| r_work (start): 0.3780 rms_B_bonded: 3.33 r_work: 0.3473 rms_B_bonded: 2.89 restraints_weight: 0.5000 r_work: 0.3348 rms_B_bonded: 4.32 restraints_weight: 0.2500 r_work (final): 0.3348 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8189 moved from start: 0.2026 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.040 20830 Z= 0.219 Angle : 0.606 8.040 28368 Z= 0.302 Chirality : 0.046 0.154 3104 Planarity : 0.004 0.049 3656 Dihedral : 4.253 19.868 2708 Min Nonbonded Distance : 2.555 Molprobity Statistics. All-atom Clashscore : 10.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.41 % Favored : 95.59 % Rotamer: Outliers : 6.18 % Allowed : 27.85 % Favored : 65.97 % 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: -0.02 (0.18), residues: 2516 helix: -0.46 (0.35), residues: 230 sheet: -0.21 (0.16), residues: 1014 loop : 0.45 (0.19), residues: 1272 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG H 355 TYR 0.019 0.002 TYR C 373 PHE 0.014 0.002 PHE L 372 TRP 0.015 0.002 TRP B 313 HIS 0.004 0.001 HIS I 310 Details of bonding type rmsd covalent geometry : bond 0.00527 (20808) covalent geometry : angle 0.60628 (28324) SS BOND : bond 0.00296 ( 22) SS BOND : angle 0.72224 ( 44) hydrogen bonds : bond 0.03598 ( 685) hydrogen bonds : angle 5.54735 ( 2136) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5032 Ramachandran restraints generated. 2516 Oldfield, 0 Emsley, 2516 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5032 Ramachandran restraints generated. 2516 Oldfield, 0 Emsley, 2516 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 316 residues out of total 2348 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 145 poor density : 171 time to evaluate : 0.863 Fit side-chains revert: symmetry clash REVERT: E 285 HIS cc_start: 0.6227 (OUTLIER) cc_final: 0.5802 (m-70) REVERT: E 315 ASN cc_start: 0.7312 (m-40) cc_final: 0.6893 (m110) REVERT: E 409 LYS cc_start: 0.9151 (OUTLIER) cc_final: 0.8502 (tttm) REVERT: F 246 LYS cc_start: 0.7548 (ttpt) cc_final: 0.6901 (tmtm) REVERT: F 299 THR cc_start: 0.1420 (OUTLIER) cc_final: 0.1132 (m) REVERT: G 315 ASN cc_start: 0.7535 (m-40) cc_final: 0.6919 (m110) REVERT: G 321 CYS cc_start: 0.1027 (OUTLIER) cc_final: 0.0010 (t) REVERT: G 444 SER cc_start: 0.8450 (p) cc_final: 0.8230 (m) REVERT: H 250 THR cc_start: 0.8506 (t) cc_final: 0.8258 (p) REVERT: H 312 ASP cc_start: 0.6856 (OUTLIER) cc_final: 0.6527 (p0) REVERT: H 347 GLN cc_start: 0.8176 (mt0) cc_final: 0.7843 (mt0) REVERT: H 386 GLN cc_start: 0.8512 (OUTLIER) cc_final: 0.7981 (mp10) REVERT: I 386 GLN cc_start: 0.8829 (OUTLIER) cc_final: 0.7846 (mp10) REVERT: I 419 GLN cc_start: 0.7579 (tt0) cc_final: 0.7343 (tt0) REVERT: J 267 SER cc_start: 0.2272 (OUTLIER) cc_final: 0.1861 (p) REVERT: J 436 TYR cc_start: 0.8394 (t80) cc_final: 0.8161 (t80) REVERT: B 310 HIS cc_start: 0.8106 (m-70) cc_final: 0.7783 (m-70) REVERT: B 347 GLN cc_start: 0.8711 (mt0) cc_final: 0.8297 (mt0) REVERT: B 439 LYS cc_start: 0.8886 (OUTLIER) cc_final: 0.8226 (mptm) REVERT: B 447 LYS cc_start: 0.4601 (OUTLIER) cc_final: 0.4096 (mttp) REVERT: K 241 PHE cc_start: 0.1366 (OUTLIER) cc_final: 0.0707 (m-80) REVERT: K 390 ASN cc_start: 0.7670 (t0) cc_final: 0.7341 (t0) REVERT: K 443 LYS cc_start: 0.8069 (tptp) cc_final: 0.7311 (pttt) REVERT: L 361 ASN cc_start: 0.7727 (p0) cc_final: 0.7383 (t0) REVERT: D 309 LEU cc_start: 0.7612 (OUTLIER) cc_final: 0.6455 (tm) REVERT: D 312 ASP cc_start: 0.7228 (OUTLIER) cc_final: 0.6377 (t70) REVERT: D 340 LYS cc_start: 0.8443 (OUTLIER) cc_final: 0.8218 (ptmm) REVERT: D 361 ASN cc_start: 0.7062 (p0) cc_final: 0.6777 (t0) REVERT: C 317 LYS cc_start: 0.6744 (OUTLIER) cc_final: 0.6011 (mmmt) REVERT: C 340 LYS cc_start: 0.8246 (mmtt) cc_final: 0.7854 (mmtt) outliers start: 145 outliers final: 95 residues processed: 295 average time/residue: 0.5125 time to fit residues: 175.8621 Evaluate side-chains 274 residues out of total 2348 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 110 poor density : 164 time to evaluate : 0.823 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 240 VAL Chi-restraints excluded: chain E residue 258 GLU Chi-restraints excluded: chain E residue 285 HIS Chi-restraints excluded: chain E residue 306 LEU Chi-restraints excluded: chain E residue 359 THR Chi-restraints excluded: chain E residue 409 LYS Chi-restraints excluded: chain E residue 412 VAL Chi-restraints excluded: chain E residue 424 SER Chi-restraints excluded: chain E residue 426 SER Chi-restraints excluded: chain E residue 427 VAL Chi-restraints excluded: chain F residue 256 THR Chi-restraints excluded: chain F residue 264 VAL Chi-restraints excluded: chain F residue 279 VAL Chi-restraints excluded: chain F residue 299 THR Chi-restraints excluded: chain F residue 302 VAL Chi-restraints excluded: chain F residue 308 VAL Chi-restraints excluded: chain F residue 345 GLU Chi-restraints excluded: chain F residue 363 VAL Chi-restraints excluded: chain F residue 427 VAL Chi-restraints excluded: chain F residue 442 ASP Chi-restraints excluded: chain G residue 264 VAL Chi-restraints excluded: chain G residue 308 VAL Chi-restraints excluded: chain G residue 314 LEU Chi-restraints excluded: chain G residue 321 CYS Chi-restraints excluded: chain G residue 347 GLN Chi-restraints excluded: chain G residue 355 ARG Chi-restraints excluded: chain G residue 375 SER Chi-restraints excluded: chain G residue 413 ASP Chi-restraints excluded: chain G residue 426 SER Chi-restraints excluded: chain H residue 240 VAL Chi-restraints excluded: chain H residue 241 PHE Chi-restraints excluded: chain H residue 279 VAL Chi-restraints excluded: chain H residue 280 ASP Chi-restraints excluded: chain H residue 312 ASP Chi-restraints excluded: chain H residue 336 ILE Chi-restraints excluded: chain H residue 357 GLU Chi-restraints excluded: chain H residue 360 LYS Chi-restraints excluded: chain H residue 369 VAL Chi-restraints excluded: chain H residue 375 SER Chi-restraints excluded: chain H residue 386 GLN Chi-restraints excluded: chain H residue 427 VAL Chi-restraints excluded: chain I residue 240 VAL Chi-restraints excluded: chain I residue 279 VAL Chi-restraints excluded: chain I residue 284 VAL Chi-restraints excluded: chain I residue 314 LEU Chi-restraints excluded: chain I residue 324 SER Chi-restraints excluded: chain I residue 361 ASN Chi-restraints excluded: chain I residue 386 GLN Chi-restraints excluded: chain I residue 397 VAL Chi-restraints excluded: chain I residue 411 THR Chi-restraints excluded: chain I residue 426 SER Chi-restraints excluded: chain J residue 267 SER Chi-restraints excluded: chain J residue 282 VAL Chi-restraints excluded: chain J residue 284 VAL Chi-restraints excluded: chain J residue 363 VAL Chi-restraints excluded: chain J residue 365 LEU Chi-restraints excluded: chain J residue 375 SER Chi-restraints excluded: chain J residue 401 ASP Chi-restraints excluded: chain J residue 411 THR Chi-restraints excluded: chain J residue 427 VAL Chi-restraints excluded: chain B residue 263 VAL Chi-restraints excluded: chain B residue 308 VAL Chi-restraints excluded: chain B residue 358 LEU Chi-restraints excluded: chain B residue 411 THR Chi-restraints excluded: chain B residue 426 SER Chi-restraints excluded: chain B residue 439 LYS Chi-restraints excluded: chain B residue 447 LYS Chi-restraints excluded: chain K residue 241 PHE Chi-restraints excluded: chain K residue 253 ILE Chi-restraints excluded: chain K residue 260 THR Chi-restraints excluded: chain K residue 266 VAL Chi-restraints excluded: chain K residue 335 THR Chi-restraints excluded: chain K residue 366 THR Chi-restraints excluded: chain K residue 411 THR Chi-restraints excluded: chain L residue 239 SER Chi-restraints excluded: chain L residue 289 THR Chi-restraints excluded: chain L residue 307 THR Chi-restraints excluded: chain L residue 375 SER Chi-restraints excluded: chain L residue 398 LEU Chi-restraints excluded: chain L residue 411 THR Chi-restraints excluded: chain L residue 424 SER Chi-restraints excluded: chain L residue 426 SER Chi-restraints excluded: chain A residue 307 THR Chi-restraints excluded: chain A residue 308 VAL Chi-restraints excluded: chain A residue 375 SER Chi-restraints excluded: chain D residue 253 ILE Chi-restraints excluded: chain D residue 261 CYS Chi-restraints excluded: chain D residue 273 VAL Chi-restraints excluded: chain D residue 276 ASN Chi-restraints excluded: chain D residue 284 VAL Chi-restraints excluded: chain D residue 292 ARG Chi-restraints excluded: chain D residue 309 LEU Chi-restraints excluded: chain D residue 312 ASP Chi-restraints excluded: chain D residue 340 LYS Chi-restraints excluded: chain D residue 350 THR Chi-restraints excluded: chain D residue 439 LYS Chi-restraints excluded: chain D residue 440 SER Chi-restraints excluded: chain C residue 256 THR Chi-restraints excluded: chain C residue 258 GLU Chi-restraints excluded: chain C residue 264 VAL Chi-restraints excluded: chain C residue 306 LEU Chi-restraints excluded: chain C residue 307 THR Chi-restraints excluded: chain C residue 317 LYS Chi-restraints excluded: chain C residue 337 SER Chi-restraints excluded: chain C residue 359 THR Chi-restraints excluded: chain C residue 375 SER Chi-restraints excluded: chain C residue 427 VAL Chi-restraints excluded: chain C residue 437 THR Chi-restraints excluded: chain C residue 440 SER Chi-restraints excluded: chain C residue 443 LYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 252 random chunks: chunk 247 optimal weight: 0.5980 chunk 40 optimal weight: 0.9990 chunk 80 optimal weight: 2.9990 chunk 41 optimal weight: 0.9990 chunk 68 optimal weight: 0.0370 chunk 27 optimal weight: 20.0000 chunk 131 optimal weight: 6.9990 chunk 215 optimal weight: 10.0000 chunk 226 optimal weight: 0.9990 chunk 174 optimal weight: 30.0000 chunk 238 optimal weight: 3.9990 overall best weight: 0.7264 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 362 GLN H 361 ASN ** J 429 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 421 ASN K 438 GLN L 315 ASN A 419 GLN A 434 ASN D 435 HIS C 418 GLN C 419 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4546 r_free = 0.4546 target = 0.230453 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3905 r_free = 0.3905 target = 0.160141 restraints weight = 22665.672| |-----------------------------------------------------------------------------| r_work (start): 0.3857 rms_B_bonded: 3.08 r_work: 0.3522 rms_B_bonded: 2.92 restraints_weight: 0.5000 r_work: 0.3402 rms_B_bonded: 4.34 restraints_weight: 0.2500 r_work (final): 0.3402 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8126 moved from start: 0.2045 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.058 20830 Z= 0.119 Angle : 0.543 7.403 28368 Z= 0.269 Chirality : 0.043 0.136 3104 Planarity : 0.004 0.049 3656 Dihedral : 4.037 20.514 2708 Min Nonbonded Distance : 2.557 Molprobity Statistics. All-atom Clashscore : 10.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.97 % Favored : 96.03 % Rotamer: Outliers : 4.94 % Allowed : 29.22 % Favored : 65.84 % 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: 0.12 (0.18), residues: 2516 helix: -0.30 (0.35), residues: 226 sheet: -0.08 (0.17), residues: 986 loop : 0.49 (0.19), residues: 1304 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG H 355 TYR 0.017 0.002 TYR D 436 PHE 0.016 0.001 PHE I 405 TRP 0.015 0.001 TRP B 313 HIS 0.006 0.001 HIS I 310 Details of bonding type rmsd covalent geometry : bond 0.00283 (20808) covalent geometry : angle 0.54282 (28324) SS BOND : bond 0.00205 ( 22) SS BOND : angle 0.51856 ( 44) hydrogen bonds : bond 0.03095 ( 685) hydrogen bonds : angle 5.34825 ( 2136) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5032 Ramachandran restraints generated. 2516 Oldfield, 0 Emsley, 2516 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5032 Ramachandran restraints generated. 2516 Oldfield, 0 Emsley, 2516 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 287 residues out of total 2348 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 116 poor density : 171 time to evaluate : 0.837 Fit side-chains revert: symmetry clash REVERT: E 285 HIS cc_start: 0.6142 (OUTLIER) cc_final: 0.5782 (m-70) REVERT: E 315 ASN cc_start: 0.7405 (m-40) cc_final: 0.7002 (m110) REVERT: F 246 LYS cc_start: 0.7586 (ttpt) cc_final: 0.6950 (tmtm) REVERT: F 264 VAL cc_start: 0.1257 (OUTLIER) cc_final: 0.0974 (t) REVERT: F 299 THR cc_start: 0.1433 (OUTLIER) cc_final: 0.1151 (m) REVERT: G 246 LYS cc_start: 0.7748 (ttmp) cc_final: 0.6708 (tttp) REVERT: G 249 ASP cc_start: 0.7611 (m-30) cc_final: 0.7339 (m-30) REVERT: G 252 MET cc_start: 0.5868 (tpt) cc_final: 0.5660 (tpt) REVERT: G 315 ASN cc_start: 0.7548 (m-40) cc_final: 0.6959 (m110) REVERT: G 321 CYS cc_start: 0.1026 (OUTLIER) cc_final: 0.0067 (t) REVERT: G 444 SER cc_start: 0.8409 (p) cc_final: 0.8184 (m) REVERT: H 250 THR cc_start: 0.8523 (t) cc_final: 0.8290 (p) REVERT: H 312 ASP cc_start: 0.6895 (OUTLIER) cc_final: 0.6579 (p0) REVERT: H 347 GLN cc_start: 0.8200 (mt0) cc_final: 0.7868 (mt0) REVERT: H 357 GLU cc_start: 0.8440 (OUTLIER) cc_final: 0.7659 (tp30) REVERT: H 386 GLN cc_start: 0.8478 (OUTLIER) cc_final: 0.7964 (mp10) REVERT: I 419 GLN cc_start: 0.7558 (tt0) cc_final: 0.7352 (tt0) REVERT: J 267 SER cc_start: 0.2254 (OUTLIER) cc_final: 0.1831 (p) REVERT: J 436 TYR cc_start: 0.8320 (t80) cc_final: 0.8056 (t80) REVERT: B 310 HIS cc_start: 0.8137 (m-70) cc_final: 0.7887 (m-70) REVERT: B 347 GLN cc_start: 0.8690 (mt0) cc_final: 0.8272 (mt0) REVERT: B 447 LYS cc_start: 0.4560 (OUTLIER) cc_final: 0.4083 (mttp) REVERT: K 241 PHE cc_start: 0.1376 (OUTLIER) cc_final: 0.0631 (m-80) REVERT: K 390 ASN cc_start: 0.7676 (t0) cc_final: 0.7276 (t0) REVERT: K 413 ASP cc_start: 0.7487 (m-30) cc_final: 0.7172 (t0) REVERT: K 443 LYS cc_start: 0.7999 (tptp) cc_final: 0.7219 (ptpt) REVERT: L 361 ASN cc_start: 0.7724 (p0) cc_final: 0.7402 (t0) REVERT: L 424 SER cc_start: 0.8732 (OUTLIER) cc_final: 0.8399 (p) REVERT: A 338 LYS cc_start: 0.7121 (ptmm) cc_final: 0.6857 (mtmm) REVERT: D 309 LEU cc_start: 0.7492 (OUTLIER) cc_final: 0.6401 (tm) REVERT: D 312 ASP cc_start: 0.7211 (OUTLIER) cc_final: 0.6393 (t70) REVERT: D 340 LYS cc_start: 0.8390 (OUTLIER) cc_final: 0.8179 (ptmm) REVERT: D 361 ASN cc_start: 0.7008 (p0) cc_final: 0.6754 (t0) REVERT: C 252 MET cc_start: 0.5885 (ttt) cc_final: 0.5474 (mmm) REVERT: C 317 LYS cc_start: 0.6773 (mmmm) cc_final: 0.6079 (mmmt) REVERT: C 340 LYS cc_start: 0.8157 (mmtt) cc_final: 0.7780 (mmtt) outliers start: 116 outliers final: 82 residues processed: 273 average time/residue: 0.4831 time to fit residues: 154.0562 Evaluate side-chains 263 residues out of total 2348 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 96 poor density : 167 time to evaluate : 0.806 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 240 VAL Chi-restraints excluded: chain E residue 258 GLU Chi-restraints excluded: chain E residue 285 HIS Chi-restraints excluded: chain E residue 306 LEU Chi-restraints excluded: chain E residue 345 GLU Chi-restraints excluded: chain E residue 359 THR Chi-restraints excluded: chain E residue 412 VAL Chi-restraints excluded: chain E residue 424 SER Chi-restraints excluded: chain E residue 426 SER Chi-restraints excluded: chain E residue 427 VAL Chi-restraints excluded: chain F residue 256 THR Chi-restraints excluded: chain F residue 264 VAL Chi-restraints excluded: chain F residue 279 VAL Chi-restraints excluded: chain F residue 299 THR Chi-restraints excluded: chain F residue 302 VAL Chi-restraints excluded: chain F residue 308 VAL Chi-restraints excluded: chain F residue 345 GLU Chi-restraints excluded: chain F residue 363 VAL Chi-restraints excluded: chain F residue 427 VAL Chi-restraints excluded: chain G residue 264 VAL Chi-restraints excluded: chain G residue 308 VAL Chi-restraints excluded: chain G residue 314 LEU Chi-restraints excluded: chain G residue 321 CYS Chi-restraints excluded: chain G residue 347 GLN Chi-restraints excluded: chain G residue 355 ARG Chi-restraints excluded: chain G residue 375 SER Chi-restraints excluded: chain G residue 426 SER Chi-restraints excluded: chain H residue 240 VAL Chi-restraints excluded: chain H residue 241 PHE Chi-restraints excluded: chain H residue 279 VAL Chi-restraints excluded: chain H residue 280 ASP Chi-restraints excluded: chain H residue 312 ASP Chi-restraints excluded: chain H residue 357 GLU Chi-restraints excluded: chain H residue 360 LYS Chi-restraints excluded: chain H residue 369 VAL Chi-restraints excluded: chain H residue 375 SER Chi-restraints excluded: chain H residue 386 GLN Chi-restraints excluded: chain H residue 427 VAL Chi-restraints excluded: chain I residue 240 VAL Chi-restraints excluded: chain I residue 279 VAL Chi-restraints excluded: chain I residue 284 VAL Chi-restraints excluded: chain I residue 324 SER Chi-restraints excluded: chain I residue 397 VAL Chi-restraints excluded: chain I residue 411 THR Chi-restraints excluded: chain I residue 426 SER Chi-restraints excluded: chain J residue 267 SER Chi-restraints excluded: chain J residue 282 VAL Chi-restraints excluded: chain J residue 284 VAL Chi-restraints excluded: chain J residue 363 VAL Chi-restraints excluded: chain J residue 365 LEU Chi-restraints excluded: chain J residue 375 SER Chi-restraints excluded: chain J residue 401 ASP Chi-restraints excluded: chain J residue 411 THR Chi-restraints excluded: chain J residue 427 VAL Chi-restraints excluded: chain B residue 263 VAL Chi-restraints excluded: chain B residue 308 VAL Chi-restraints excluded: chain B residue 358 LEU Chi-restraints excluded: chain B residue 376 ASP Chi-restraints excluded: chain B residue 426 SER Chi-restraints excluded: chain B residue 447 LYS Chi-restraints excluded: chain K residue 241 PHE Chi-restraints excluded: chain K residue 253 ILE Chi-restraints excluded: chain K residue 260 THR Chi-restraints excluded: chain K residue 266 VAL Chi-restraints excluded: chain K residue 335 THR Chi-restraints excluded: chain K residue 366 THR Chi-restraints excluded: chain K residue 411 THR Chi-restraints excluded: chain L residue 289 THR Chi-restraints excluded: chain L residue 375 SER Chi-restraints excluded: chain L residue 398 LEU Chi-restraints excluded: chain L residue 411 THR Chi-restraints excluded: chain L residue 424 SER Chi-restraints excluded: chain L residue 426 SER Chi-restraints excluded: chain A residue 307 THR Chi-restraints excluded: chain A residue 308 VAL Chi-restraints excluded: chain D residue 253 ILE Chi-restraints excluded: chain D residue 261 CYS Chi-restraints excluded: chain D residue 273 VAL Chi-restraints excluded: chain D residue 276 ASN Chi-restraints excluded: chain D residue 284 VAL Chi-restraints excluded: chain D residue 292 ARG Chi-restraints excluded: chain D residue 309 LEU Chi-restraints excluded: chain D residue 312 ASP Chi-restraints excluded: chain D residue 340 LYS Chi-restraints excluded: chain D residue 350 THR Chi-restraints excluded: chain D residue 375 SER Chi-restraints excluded: chain D residue 439 LYS Chi-restraints excluded: chain C residue 256 THR Chi-restraints excluded: chain C residue 258 GLU Chi-restraints excluded: chain C residue 306 LEU Chi-restraints excluded: chain C residue 307 THR Chi-restraints excluded: chain C residue 337 SER Chi-restraints excluded: chain C residue 375 SER Chi-restraints excluded: chain C residue 427 VAL Chi-restraints excluded: chain C residue 437 THR Chi-restraints excluded: chain C residue 443 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 252 random chunks: chunk 12 optimal weight: 1.9990 chunk 169 optimal weight: 0.5980 chunk 130 optimal weight: 20.0000 chunk 82 optimal weight: 2.9990 chunk 183 optimal weight: 2.9990 chunk 25 optimal weight: 0.8980 chunk 199 optimal weight: 0.0980 chunk 186 optimal weight: 3.9990 chunk 27 optimal weight: 20.0000 chunk 99 optimal weight: 2.9990 chunk 207 optimal weight: 0.5980 overall best weight: 0.8382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 389 ASN G 362 GLN H 361 ASN ** J 429 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 421 ASN K 390 ASN K 438 GLN L 418 GLN A 419 GLN C 418 GLN C 419 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4542 r_free = 0.4542 target = 0.229845 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 80)----------------| | r_work = 0.3696 r_free = 0.3696 target = 0.149543 restraints weight = 22132.343| |-----------------------------------------------------------------------------| r_work (start): 0.3645 rms_B_bonded: 3.27 r_work: 0.3372 rms_B_bonded: 3.35 restraints_weight: 0.5000 r_work (final): 0.3372 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8221 moved from start: 0.2096 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 20830 Z= 0.125 Angle : 0.546 9.123 28368 Z= 0.270 Chirality : 0.043 0.143 3104 Planarity : 0.004 0.049 3656 Dihedral : 3.994 19.753 2708 Min Nonbonded Distance : 2.557 Molprobity Statistics. All-atom Clashscore : 10.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.05 % Favored : 95.95 % Rotamer: Outliers : 4.73 % Allowed : 29.56 % Favored : 65.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.17 (0.18), residues: 2516 helix: -0.27 (0.35), residues: 224 sheet: -0.05 (0.17), residues: 981 loop : 0.51 (0.19), residues: 1311 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG H 355 TYR 0.016 0.002 TYR H 407 PHE 0.014 0.001 PHE I 405 TRP 0.017 0.001 TRP B 313 HIS 0.006 0.001 HIS I 310 Details of bonding type rmsd covalent geometry : bond 0.00298 (20808) covalent geometry : angle 0.54559 (28324) SS BOND : bond 0.00215 ( 22) SS BOND : angle 0.54359 ( 44) hydrogen bonds : bond 0.03088 ( 685) hydrogen bonds : angle 5.26395 ( 2136) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5032 Ramachandran restraints generated. 2516 Oldfield, 0 Emsley, 2516 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5032 Ramachandran restraints generated. 2516 Oldfield, 0 Emsley, 2516 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 284 residues out of total 2348 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 111 poor density : 173 time to evaluate : 0.781 Fit side-chains revert: symmetry clash REVERT: E 285 HIS cc_start: 0.6113 (OUTLIER) cc_final: 0.5775 (m-70) REVERT: E 315 ASN cc_start: 0.7383 (m-40) cc_final: 0.6979 (m110) REVERT: F 246 LYS cc_start: 0.7709 (ttpt) cc_final: 0.7135 (tmtm) REVERT: F 264 VAL cc_start: 0.1276 (OUTLIER) cc_final: 0.0993 (t) REVERT: F 299 THR cc_start: 0.1445 (OUTLIER) cc_final: 0.1167 (m) REVERT: G 246 LYS cc_start: 0.7831 (ttmp) cc_final: 0.6852 (tttp) REVERT: G 315 ASN cc_start: 0.7590 (m-40) cc_final: 0.7059 (m110) REVERT: G 321 CYS cc_start: 0.0930 (OUTLIER) cc_final: 0.0012 (t) REVERT: G 444 SER cc_start: 0.8528 (p) cc_final: 0.8250 (m) REVERT: H 250 THR cc_start: 0.8537 (t) cc_final: 0.8333 (p) REVERT: H 312 ASP cc_start: 0.6858 (OUTLIER) cc_final: 0.6556 (p0) REVERT: H 357 GLU cc_start: 0.8214 (OUTLIER) cc_final: 0.7489 (tp30) REVERT: H 386 GLN cc_start: 0.8514 (OUTLIER) cc_final: 0.8079 (mp10) REVERT: I 419 GLN cc_start: 0.7609 (tt0) cc_final: 0.7370 (tt0) REVERT: J 267 SER cc_start: 0.2192 (OUTLIER) cc_final: 0.1780 (p) REVERT: J 308 VAL cc_start: 0.7317 (t) cc_final: 0.7083 (m) REVERT: B 347 GLN cc_start: 0.8504 (mt0) cc_final: 0.8224 (mt0) REVERT: B 447 LYS cc_start: 0.4730 (OUTLIER) cc_final: 0.4070 (mttp) REVERT: K 241 PHE cc_start: 0.1345 (OUTLIER) cc_final: 0.0638 (m-80) REVERT: K 390 ASN cc_start: 0.7686 (t0) cc_final: 0.7408 (t0) REVERT: K 443 LYS cc_start: 0.8083 (tptp) cc_final: 0.7423 (ptpt) REVERT: L 424 SER cc_start: 0.8522 (OUTLIER) cc_final: 0.8239 (p) REVERT: D 312 ASP cc_start: 0.7180 (OUTLIER) cc_final: 0.6385 (t70) REVERT: C 252 MET cc_start: 0.5996 (ttt) cc_final: 0.5728 (mmm) REVERT: C 317 LYS cc_start: 0.6818 (mmmm) cc_final: 0.6179 (mmmt) REVERT: C 340 LYS cc_start: 0.8261 (mmtt) cc_final: 0.7956 (mmtt) outliers start: 111 outliers final: 86 residues processed: 270 average time/residue: 0.4581 time to fit residues: 144.9175 Evaluate side-chains 265 residues out of total 2348 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 98 poor density : 167 time to evaluate : 0.816 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 240 VAL Chi-restraints excluded: chain E residue 258 GLU Chi-restraints excluded: chain E residue 285 HIS Chi-restraints excluded: chain E residue 306 LEU Chi-restraints excluded: chain E residue 345 GLU Chi-restraints excluded: chain E residue 359 THR Chi-restraints excluded: chain E residue 412 VAL Chi-restraints excluded: chain E residue 424 SER Chi-restraints excluded: chain E residue 426 SER Chi-restraints excluded: chain E residue 427 VAL Chi-restraints excluded: chain F residue 256 THR Chi-restraints excluded: chain F residue 264 VAL Chi-restraints excluded: chain F residue 279 VAL Chi-restraints excluded: chain F residue 299 THR Chi-restraints excluded: chain F residue 302 VAL Chi-restraints excluded: chain F residue 308 VAL Chi-restraints excluded: chain F residue 345 GLU Chi-restraints excluded: chain F residue 363 VAL Chi-restraints excluded: chain F residue 427 VAL Chi-restraints excluded: chain G residue 264 VAL Chi-restraints excluded: chain G residue 308 VAL Chi-restraints excluded: chain G residue 314 LEU Chi-restraints excluded: chain G residue 321 CYS Chi-restraints excluded: chain G residue 347 GLN Chi-restraints excluded: chain G residue 355 ARG Chi-restraints excluded: chain G residue 375 SER Chi-restraints excluded: chain G residue 413 ASP Chi-restraints excluded: chain G residue 426 SER Chi-restraints excluded: chain H residue 240 VAL Chi-restraints excluded: chain H residue 241 PHE Chi-restraints excluded: chain H residue 263 VAL Chi-restraints excluded: chain H residue 279 VAL Chi-restraints excluded: chain H residue 280 ASP Chi-restraints excluded: chain H residue 312 ASP Chi-restraints excluded: chain H residue 357 GLU Chi-restraints excluded: chain H residue 369 VAL Chi-restraints excluded: chain H residue 375 SER Chi-restraints excluded: chain H residue 386 GLN Chi-restraints excluded: chain H residue 427 VAL Chi-restraints excluded: chain I residue 240 VAL Chi-restraints excluded: chain I residue 279 VAL Chi-restraints excluded: chain I residue 284 VAL Chi-restraints excluded: chain I residue 324 SER Chi-restraints excluded: chain I residue 361 ASN Chi-restraints excluded: chain I residue 411 THR Chi-restraints excluded: chain I residue 426 SER Chi-restraints excluded: chain J residue 267 SER Chi-restraints excluded: chain J residue 282 VAL Chi-restraints excluded: chain J residue 284 VAL Chi-restraints excluded: chain J residue 363 VAL Chi-restraints excluded: chain J residue 365 LEU Chi-restraints excluded: chain J residue 375 SER Chi-restraints excluded: chain J residue 401 ASP Chi-restraints excluded: chain J residue 411 THR Chi-restraints excluded: chain J residue 427 VAL Chi-restraints excluded: chain B residue 263 VAL Chi-restraints excluded: chain B residue 308 VAL Chi-restraints excluded: chain B residue 358 LEU Chi-restraints excluded: chain B residue 376 ASP Chi-restraints excluded: chain B residue 411 THR Chi-restraints excluded: chain B residue 426 SER Chi-restraints excluded: chain B residue 447 LYS Chi-restraints excluded: chain K residue 241 PHE Chi-restraints excluded: chain K residue 253 ILE Chi-restraints excluded: chain K residue 260 THR Chi-restraints excluded: chain K residue 266 VAL Chi-restraints excluded: chain K residue 292 ARG Chi-restraints excluded: chain K residue 335 THR Chi-restraints excluded: chain K residue 366 THR Chi-restraints excluded: chain K residue 411 THR Chi-restraints excluded: chain L residue 289 THR Chi-restraints excluded: chain L residue 315 ASN Chi-restraints excluded: chain L residue 375 SER Chi-restraints excluded: chain L residue 411 THR Chi-restraints excluded: chain L residue 424 SER Chi-restraints excluded: chain L residue 426 SER Chi-restraints excluded: chain A residue 307 THR Chi-restraints excluded: chain A residue 308 VAL Chi-restraints excluded: chain D residue 253 ILE Chi-restraints excluded: chain D residue 261 CYS Chi-restraints excluded: chain D residue 273 VAL Chi-restraints excluded: chain D residue 276 ASN Chi-restraints excluded: chain D residue 284 VAL Chi-restraints excluded: chain D residue 292 ARG Chi-restraints excluded: chain D residue 312 ASP Chi-restraints excluded: chain D residue 350 THR Chi-restraints excluded: chain D residue 375 SER Chi-restraints excluded: chain D residue 439 LYS Chi-restraints excluded: chain C residue 256 THR Chi-restraints excluded: chain C residue 258 GLU Chi-restraints excluded: chain C residue 306 LEU Chi-restraints excluded: chain C residue 307 THR Chi-restraints excluded: chain C residue 337 SER Chi-restraints excluded: chain C residue 359 THR Chi-restraints excluded: chain C residue 375 SER Chi-restraints excluded: chain C residue 427 VAL Chi-restraints excluded: chain C residue 437 THR Chi-restraints excluded: chain C residue 443 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 252 random chunks: chunk 112 optimal weight: 7.9990 chunk 225 optimal weight: 1.9990 chunk 150 optimal weight: 0.9990 chunk 78 optimal weight: 0.5980 chunk 192 optimal weight: 2.9990 chunk 21 optimal weight: 10.0000 chunk 197 optimal weight: 7.9990 chunk 250 optimal weight: 3.9990 chunk 68 optimal weight: 0.6980 chunk 210 optimal weight: 30.0000 chunk 67 optimal weight: 0.0000 overall best weight: 0.8588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 389 ASN G 362 GLN H 361 ASN ** J 429 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 421 ASN K 438 GLN L 361 ASN L 418 GLN A 419 GLN A 434 ASN D 389 ASN C 418 GLN C 419 GLN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4539 r_free = 0.4539 target = 0.229550 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 79)----------------| | r_work = 0.3685 r_free = 0.3685 target = 0.146274 restraints weight = 22143.671| |-----------------------------------------------------------------------------| r_work (start): 0.3656 rms_B_bonded: 2.63 r_work: 0.3369 rms_B_bonded: 3.38 restraints_weight: 0.5000 r_work: 0.3230 rms_B_bonded: 4.95 restraints_weight: 0.2500 r_work (final): 0.3230 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8344 moved from start: 0.2139 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 20830 Z= 0.125 Angle : 0.546 9.059 28368 Z= 0.270 Chirality : 0.043 0.140 3104 Planarity : 0.004 0.049 3656 Dihedral : 3.977 20.403 2708 Min Nonbonded Distance : 2.539 Molprobity Statistics. All-atom Clashscore : 10.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.01 % Favored : 95.99 % Rotamer: Outliers : 4.64 % Allowed : 29.81 % Favored : 65.55 % 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: 0.18 (0.18), residues: 2516 helix: -0.34 (0.35), residues: 226 sheet: -0.02 (0.17), residues: 973 loop : 0.52 (0.19), residues: 1317 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG H 355 TYR 0.015 0.002 TYR E 436 PHE 0.014 0.001 PHE I 405 TRP 0.021 0.001 TRP G 313 HIS 0.007 0.001 HIS I 310 Details of bonding type rmsd covalent geometry : bond 0.00299 (20808) covalent geometry : angle 0.54610 (28324) SS BOND : bond 0.00206 ( 22) SS BOND : angle 0.51026 ( 44) hydrogen bonds : bond 0.03054 ( 685) hydrogen bonds : angle 5.21619 ( 2136) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 10839.65 seconds wall clock time: 184 minutes 46.23 seconds (11086.23 seconds total)