Starting phenix.real_space_refine on Wed Mar 4 03:59:28 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6zzu_11587/03_2026/6zzu_11587.cif Found real_map, /net/cci-nas-00/data/ceres_data/6zzu_11587/03_2026/6zzu_11587.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.5 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/6zzu_11587/03_2026/6zzu_11587.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6zzu_11587/03_2026/6zzu_11587.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/6zzu_11587/03_2026/6zzu_11587.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6zzu_11587/03_2026/6zzu_11587.map" } resolution = 3.5 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= 0.010 sd= 0.096 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: 5 Type Number sf(0) Gaussians Fe 4 7.16 5 S 36 5.16 5 C 6848 2.51 5 N 1828 2.21 5 O 2044 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 85 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 10760 Number of models: 1 Model: "" Number of chains: 12 Chain: "B" Number of atoms: 2688 Number of conformers: 1 Conformer: "" Number of residues, atoms: 335, 2688 Classifications: {'peptide': 335} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 18, 'TRANS': 316} Chain: "A" Number of atoms: 2688 Number of conformers: 1 Conformer: "" Number of residues, atoms: 335, 2688 Classifications: {'peptide': 335} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 18, 'TRANS': 316} Chain: "C" Number of atoms: 2688 Number of conformers: 1 Conformer: "" Number of residues, atoms: 335, 2688 Classifications: {'peptide': 335} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 18, 'TRANS': 316} Chain: "D" Number of atoms: 2688 Number of conformers: 1 Conformer: "" Number of residues, atoms: 335, 2688 Classifications: {'peptide': 335} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 18, 'TRANS': 316} Chain: "B" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' FE': 1} Classifications: {'undetermined': 1} Chain: "A" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' FE': 1} Classifications: {'undetermined': 1} Chain: "C" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' FE': 1} Classifications: {'undetermined': 1} Chain: "D" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' FE': 1} Classifications: {'undetermined': 1} Chain: "B" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "A" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "C" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "D" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Time building chain proxies: 2.66, per 1000 atoms: 0.25 Number of scatterers: 10760 At special positions: 0 Unit cell: (99.75, 66.15, 119.7, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) Fe 4 26.01 S 36 16.00 O 2044 8.00 N 1828 7.00 C 6848 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.85 Conformation dependent library (CDL) restraints added in 525.2 milliseconds 2664 Ramachandran restraints generated. 1332 Oldfield, 0 Emsley, 1332 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2544 Finding SS restraints... Secondary structure from input PDB file: 56 helices and 14 sheets defined 51.3% alpha, 7.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.33 Creating SS restraints... Processing helix chain 'B' and resid 170 through 173 Processing helix chain 'B' and resid 174 through 182 removed outlier: 4.507A pdb=" N VAL B 180 " --> pdb=" O CYS B 176 " (cutoff:3.500A) Processing helix chain 'B' and resid 196 through 208 Processing helix chain 'B' and resid 225 through 242 removed outlier: 3.751A pdb=" N GLY B 241 " --> pdb=" O THR B 237 " (cutoff:3.500A) Processing helix chain 'B' and resid 248 through 261 Processing helix chain 'B' and resid 271 through 283 removed outlier: 3.769A pdb=" N VAL B 275 " --> pdb=" O GLN B 271 " (cutoff:3.500A) Processing helix chain 'B' and resid 295 through 305 removed outlier: 3.744A pdb=" N LEU B 300 " --> pdb=" O ALA B 296 " (cutoff:3.500A) removed outlier: 3.894A pdb=" N PHE B 305 " --> pdb=" O ALA B 301 " (cutoff:3.500A) Processing helix chain 'B' and resid 327 through 335 removed outlier: 4.059A pdb=" N LEU B 333 " --> pdb=" O CYS B 329 " (cutoff:3.500A) Processing helix chain 'B' and resid 335 through 340 Processing helix chain 'B' and resid 341 through 355 removed outlier: 3.734A pdb=" N GLY B 352 " --> pdb=" O SER B 348 " (cutoff:3.500A) Processing helix chain 'B' and resid 359 through 374 removed outlier: 3.514A pdb=" N PHE B 372 " --> pdb=" O THR B 368 " (cutoff:3.500A) Processing helix chain 'B' and resid 395 through 402 removed outlier: 3.884A pdb=" N LEU B 399 " --> pdb=" O SER B 395 " (cutoff:3.500A) removed outlier: 4.032A pdb=" N LEU B 400 " --> pdb=" O TYR B 396 " (cutoff:3.500A) Processing helix chain 'B' and resid 436 through 451 removed outlier: 3.770A pdb=" N ARG B 450 " --> pdb=" O SER B 446 " (cutoff:3.500A) Processing helix chain 'B' and resid 471 through 496 removed outlier: 4.091A pdb=" N GLY B 481 " --> pdb=" O ARG B 477 " (cutoff:3.500A) Processing helix chain 'A' and resid 171 through 176 removed outlier: 4.459A pdb=" N LYS A 175 " --> pdb=" O SER A 171 " (cutoff:3.500A) removed outlier: 4.034A pdb=" N CYS A 176 " --> pdb=" O GLU A 172 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 171 through 176' Processing helix chain 'A' and resid 196 through 209 Processing helix chain 'A' and resid 225 through 240 removed outlier: 3.709A pdb=" N THR A 231 " --> pdb=" O GLU A 227 " (cutoff:3.500A) Processing helix chain 'A' and resid 241 through 244 removed outlier: 3.936A pdb=" N ALA A 244 " --> pdb=" O GLY A 241 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 241 through 244' Processing helix chain 'A' and resid 248 through 261 Processing helix chain 'A' and resid 271 through 283 removed outlier: 3.547A pdb=" N VAL A 275 " --> pdb=" O GLN A 271 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N GLU A 281 " --> pdb=" O ARG A 277 " (cutoff:3.500A) Processing helix chain 'A' and resid 295 through 304 removed outlier: 3.745A pdb=" N PHE A 299 " --> pdb=" O SER A 295 " (cutoff:3.500A) removed outlier: 3.802A pdb=" N LEU A 300 " --> pdb=" O ALA A 296 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N ALA A 304 " --> pdb=" O LEU A 300 " (cutoff:3.500A) Processing helix chain 'A' and resid 327 through 335 removed outlier: 4.399A pdb=" N LEU A 333 " --> pdb=" O CYS A 329 " (cutoff:3.500A) Processing helix chain 'A' and resid 335 through 340 Processing helix chain 'A' and resid 341 through 354 Processing helix chain 'A' and resid 359 through 374 removed outlier: 3.557A pdb=" N PHE A 372 " --> pdb=" O THR A 368 " (cutoff:3.500A) Processing helix chain 'A' and resid 391 through 395 removed outlier: 4.158A pdb=" N SER A 395 " --> pdb=" O LEU A 392 " (cutoff:3.500A) Processing helix chain 'A' and resid 397 through 403 removed outlier: 4.499A pdb=" N LEU A 403 " --> pdb=" O LEU A 399 " (cutoff:3.500A) Processing helix chain 'A' and resid 436 through 450 removed outlier: 3.735A pdb=" N ARG A 450 " --> pdb=" O SER A 446 " (cutoff:3.500A) Processing helix chain 'A' and resid 471 through 496 removed outlier: 3.506A pdb=" N VAL A 475 " --> pdb=" O SER A 471 " (cutoff:3.500A) removed outlier: 3.904A pdb=" N GLY A 481 " --> pdb=" O ARG A 477 " (cutoff:3.500A) Processing helix chain 'C' and resid 171 through 176 removed outlier: 4.041A pdb=" N LYS C 175 " --> pdb=" O SER C 171 " (cutoff:3.500A) removed outlier: 3.915A pdb=" N CYS C 176 " --> pdb=" O GLU C 172 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 171 through 176' Processing helix chain 'C' and resid 196 through 208 Processing helix chain 'C' and resid 225 through 242 removed outlier: 3.511A pdb=" N GLY C 241 " --> pdb=" O THR C 237 " (cutoff:3.500A) Processing helix chain 'C' and resid 248 through 261 Processing helix chain 'C' and resid 271 through 283 removed outlier: 3.782A pdb=" N VAL C 275 " --> pdb=" O GLN C 271 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N PHE C 278 " --> pdb=" O ASP C 274 " (cutoff:3.500A) Processing helix chain 'C' and resid 295 through 304 removed outlier: 3.538A pdb=" N LEU C 300 " --> pdb=" O ALA C 296 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N ALA C 304 " --> pdb=" O LEU C 300 " (cutoff:3.500A) Processing helix chain 'C' and resid 327 through 332 Processing helix chain 'C' and resid 335 through 340 Processing helix chain 'C' and resid 341 through 354 Processing helix chain 'C' and resid 359 through 374 removed outlier: 3.582A pdb=" N PHE C 372 " --> pdb=" O THR C 368 " (cutoff:3.500A) Processing helix chain 'C' and resid 395 through 403 removed outlier: 4.024A pdb=" N LEU C 399 " --> pdb=" O SER C 395 " (cutoff:3.500A) removed outlier: 4.122A pdb=" N LEU C 400 " --> pdb=" O TYR C 396 " (cutoff:3.500A) removed outlier: 4.419A pdb=" N LEU C 403 " --> pdb=" O LEU C 399 " (cutoff:3.500A) Processing helix chain 'C' and resid 436 through 448 Processing helix chain 'C' and resid 471 through 496 removed outlier: 3.835A pdb=" N GLY C 481 " --> pdb=" O ARG C 477 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N GLU C 485 " --> pdb=" O GLY C 481 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N SER C 494 " --> pdb=" O ALA C 490 " (cutoff:3.500A) Processing helix chain 'D' and resid 171 through 176 removed outlier: 4.242A pdb=" N LYS D 175 " --> pdb=" O SER D 171 " (cutoff:3.500A) removed outlier: 4.080A pdb=" N CYS D 176 " --> pdb=" O GLU D 172 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 171 through 176' Processing helix chain 'D' and resid 196 through 209 removed outlier: 3.587A pdb=" N ALA D 207 " --> pdb=" O ARG D 203 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N ILE D 209 " --> pdb=" O LEU D 205 " (cutoff:3.500A) Processing helix chain 'D' and resid 225 through 242 removed outlier: 3.736A pdb=" N THR D 231 " --> pdb=" O GLU D 227 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N GLY D 241 " --> pdb=" O THR D 237 " (cutoff:3.500A) Processing helix chain 'D' and resid 248 through 261 Processing helix chain 'D' and resid 271 through 283 removed outlier: 3.730A pdb=" N VAL D 275 " --> pdb=" O GLN D 271 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N GLU D 281 " --> pdb=" O ARG D 277 " (cutoff:3.500A) Processing helix chain 'D' and resid 295 through 304 removed outlier: 3.555A pdb=" N PHE D 299 " --> pdb=" O SER D 295 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N LEU D 300 " --> pdb=" O ALA D 296 " (cutoff:3.500A) Processing helix chain 'D' and resid 327 through 332 Processing helix chain 'D' and resid 335 through 340 Processing helix chain 'D' and resid 341 through 354 Processing helix chain 'D' and resid 359 through 374 removed outlier: 3.727A pdb=" N PHE D 372 " --> pdb=" O THR D 368 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N VAL D 374 " --> pdb=" O TYR D 370 " (cutoff:3.500A) Processing helix chain 'D' and resid 391 through 395 removed outlier: 4.198A pdb=" N SER D 395 " --> pdb=" O LEU D 392 " (cutoff:3.500A) Processing helix chain 'D' and resid 397 through 403 removed outlier: 4.507A pdb=" N LEU D 403 " --> pdb=" O LEU D 399 " (cutoff:3.500A) Processing helix chain 'D' and resid 436 through 451 removed outlier: 3.528A pdb=" N SER D 449 " --> pdb=" O ARG D 445 " (cutoff:3.500A) removed outlier: 3.751A pdb=" N ARG D 450 " --> pdb=" O SER D 446 " (cutoff:3.500A) Processing helix chain 'D' and resid 471 through 496 removed outlier: 3.984A pdb=" N GLY D 481 " --> pdb=" O ARG D 477 " (cutoff:3.500A) removed outlier: 4.073A pdb=" N GLU D 485 " --> pdb=" O GLY D 481 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N THR D 488 " --> pdb=" O ASP D 484 " (cutoff:3.500A) removed outlier: 3.775A pdb=" N SER D 494 " --> pdb=" O ALA D 490 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'B' and resid 286 through 289 removed outlier: 6.372A pdb=" N GLN B 286 " --> pdb=" O PHE B 308 " (cutoff:3.500A) removed outlier: 6.989A pdb=" N CYS B 310 " --> pdb=" O GLN B 286 " (cutoff:3.500A) removed outlier: 5.586A pdb=" N ARG B 288 " --> pdb=" O CYS B 310 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA1 Processing sheet with id=AA2, first strand: chain 'B' and resid 384 through 387 removed outlier: 6.464A pdb=" N LEU B 378 " --> pdb=" O SER B 434 " (cutoff:3.500A) removed outlier: 6.776A pdb=" N GLU B 408 " --> pdb=" O TYR B 431 " (cutoff:3.500A) removed outlier: 7.450A pdb=" N VAL B 433 " --> pdb=" O GLU B 408 " (cutoff:3.500A) removed outlier: 7.128A pdb=" N ARG B 410 " --> pdb=" O VAL B 433 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 456 through 460 Processing sheet with id=AA4, first strand: chain 'A' and resid 286 through 289 removed outlier: 6.427A pdb=" N GLN A 286 " --> pdb=" O PHE A 308 " (cutoff:3.500A) removed outlier: 6.981A pdb=" N CYS A 310 " --> pdb=" O GLN A 286 " (cutoff:3.500A) removed outlier: 5.597A pdb=" N ARG A 288 " --> pdb=" O CYS A 310 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA4 Processing sheet with id=AA5, first strand: chain 'A' and resid 378 through 380 Processing sheet with id=AA6, first strand: chain 'A' and resid 408 through 411 removed outlier: 6.828A pdb=" N GLU A 408 " --> pdb=" O TYR A 431 " (cutoff:3.500A) removed outlier: 7.481A pdb=" N VAL A 433 " --> pdb=" O GLU A 408 " (cutoff:3.500A) removed outlier: 7.069A pdb=" N ARG A 410 " --> pdb=" O VAL A 433 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA6 Processing sheet with id=AA7, first strand: chain 'A' and resid 456 through 460 removed outlier: 3.544A pdb=" N SER A 456 " --> pdb=" O LEU A 469 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'C' and resid 286 through 289 Processing sheet with id=AA9, first strand: chain 'C' and resid 384 through 387 removed outlier: 6.589A pdb=" N LEU C 378 " --> pdb=" O SER C 434 " (cutoff:3.500A) removed outlier: 6.829A pdb=" N GLU C 408 " --> pdb=" O TYR C 431 " (cutoff:3.500A) removed outlier: 7.501A pdb=" N VAL C 433 " --> pdb=" O GLU C 408 " (cutoff:3.500A) removed outlier: 7.114A pdb=" N ARG C 410 " --> pdb=" O VAL C 433 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'C' and resid 456 through 460 Processing sheet with id=AB2, first strand: chain 'D' and resid 286 through 289 removed outlier: 6.461A pdb=" N GLN D 286 " --> pdb=" O PHE D 308 " (cutoff:3.500A) removed outlier: 6.971A pdb=" N CYS D 310 " --> pdb=" O GLN D 286 " (cutoff:3.500A) removed outlier: 5.470A pdb=" N ARG D 288 " --> pdb=" O CYS D 310 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB2 Processing sheet with id=AB3, first strand: chain 'D' and resid 378 through 381 Processing sheet with id=AB4, first strand: chain 'D' and resid 408 through 411 Processing sheet with id=AB5, first strand: chain 'D' and resid 456 through 460 removed outlier: 3.567A pdb=" N SER D 456 " --> pdb=" O LEU D 469 " (cutoff:3.500A) 448 hydrogen bonds defined for protein. 1308 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: 1.60 Time building geometry restraints manager: 1.17 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 3572 1.34 - 1.46: 2610 1.46 - 1.58: 4806 1.58 - 1.70: 0 1.70 - 1.81: 44 Bond restraints: 11032 Sorted by residual: bond pdb=" CA VAL A 336 " pdb=" C VAL A 336 " ideal model delta sigma weight residual 1.520 1.537 -0.017 8.80e-03 1.29e+04 3.89e+00 bond pdb=" C VAL C 336 " pdb=" N PRO C 337 " ideal model delta sigma weight residual 1.337 1.354 -0.018 1.06e-02 8.90e+03 2.86e+00 bond pdb=" C VAL B 336 " pdb=" N PRO B 337 " ideal model delta sigma weight residual 1.337 1.354 -0.018 1.06e-02 8.90e+03 2.81e+00 bond pdb=" C VAL A 336 " pdb=" N PRO A 337 " ideal model delta sigma weight residual 1.337 1.355 -0.019 1.11e-02 8.12e+03 2.78e+00 bond pdb=" C LEU D 287 " pdb=" N ARG D 288 " ideal model delta sigma weight residual 1.331 1.316 0.016 1.05e-02 9.07e+03 2.30e+00 ... (remaining 11027 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.21: 14780 3.21 - 6.43: 156 6.43 - 9.64: 23 9.64 - 12.86: 7 12.86 - 16.07: 2 Bond angle restraints: 14968 Sorted by residual: angle pdb=" C LEU B 293 " pdb=" N LEU B 294 " pdb=" CA LEU B 294 " ideal model delta sigma weight residual 120.38 128.27 -7.89 1.46e+00 4.69e-01 2.92e+01 angle pdb=" C LEU C 293 " pdb=" N LEU C 294 " pdb=" CA LEU C 294 " ideal model delta sigma weight residual 120.38 127.73 -7.35 1.46e+00 4.69e-01 2.53e+01 angle pdb=" CA LEU A 464 " pdb=" CB LEU A 464 " pdb=" CG LEU A 464 " ideal model delta sigma weight residual 116.30 132.37 -16.07 3.50e+00 8.16e-02 2.11e+01 angle pdb=" CA LEU C 464 " pdb=" CB LEU C 464 " pdb=" CG LEU C 464 " ideal model delta sigma weight residual 116.30 130.94 -14.64 3.50e+00 8.16e-02 1.75e+01 angle pdb=" CA PRO A 337 " pdb=" N PRO A 337 " pdb=" CD PRO A 337 " ideal model delta sigma weight residual 112.00 106.28 5.72 1.40e+00 5.10e-01 1.67e+01 ... (remaining 14963 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.97: 5786 17.97 - 35.93: 654 35.93 - 53.90: 114 53.90 - 71.86: 18 71.86 - 89.83: 24 Dihedral angle restraints: 6596 sinusoidal: 2656 harmonic: 3940 Sorted by residual: dihedral pdb=" CA LYS A 182 " pdb=" C LYS A 182 " pdb=" N PHE A 183 " pdb=" CA PHE A 183 " ideal model delta harmonic sigma weight residual -180.00 -153.30 -26.70 0 5.00e+00 4.00e-02 2.85e+01 dihedral pdb=" CA GLU A 406 " pdb=" C GLU A 406 " pdb=" N PRO A 407 " pdb=" CA PRO A 407 " ideal model delta harmonic sigma weight residual 180.00 155.10 24.90 0 5.00e+00 4.00e-02 2.48e+01 dihedral pdb=" CA LYS B 182 " pdb=" C LYS B 182 " pdb=" N PHE B 183 " pdb=" CA PHE B 183 " ideal model delta harmonic sigma weight residual -180.00 -156.00 -24.00 0 5.00e+00 4.00e-02 2.30e+01 ... (remaining 6593 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.050: 1099 0.050 - 0.100: 390 0.100 - 0.150: 84 0.150 - 0.200: 24 0.200 - 0.250: 3 Chirality restraints: 1600 Sorted by residual: chirality pdb=" CB ILE B 269 " pdb=" CA ILE B 269 " pdb=" CG1 ILE B 269 " pdb=" CG2 ILE B 269 " both_signs ideal model delta sigma weight residual False 2.64 2.39 0.25 2.00e-01 2.50e+01 1.56e+00 chirality pdb=" CG LEU A 339 " pdb=" CB LEU A 339 " pdb=" CD1 LEU A 339 " pdb=" CD2 LEU A 339 " both_signs ideal model delta sigma weight residual False -2.59 -2.35 -0.24 2.00e-01 2.50e+01 1.46e+00 chirality pdb=" CA GLU B 406 " pdb=" N GLU B 406 " pdb=" C GLU B 406 " pdb=" CB GLU B 406 " both_signs ideal model delta sigma weight residual False 2.51 2.31 0.20 2.00e-01 2.50e+01 1.01e+00 ... (remaining 1597 not shown) Planarity restraints: 1972 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB PHE B 285 " 0.020 2.00e-02 2.50e+03 1.74e-02 5.33e+00 pdb=" CG PHE B 285 " -0.037 2.00e-02 2.50e+03 pdb=" CD1 PHE B 285 " 0.011 2.00e-02 2.50e+03 pdb=" CD2 PHE B 285 " -0.001 2.00e-02 2.50e+03 pdb=" CE1 PHE B 285 " -0.008 2.00e-02 2.50e+03 pdb=" CE2 PHE B 285 " 0.003 2.00e-02 2.50e+03 pdb=" CZ PHE B 285 " 0.012 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C GLU A 406 " -0.037 5.00e-02 4.00e+02 5.47e-02 4.78e+00 pdb=" N PRO A 407 " 0.094 5.00e-02 4.00e+02 pdb=" CA PRO A 407 " -0.027 5.00e-02 4.00e+02 pdb=" CD PRO A 407 " -0.031 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA VAL A 468 " 0.011 2.00e-02 2.50e+03 2.15e-02 4.64e+00 pdb=" C VAL A 468 " -0.037 2.00e-02 2.50e+03 pdb=" O VAL A 468 " 0.014 2.00e-02 2.50e+03 pdb=" N LEU A 469 " 0.012 2.00e-02 2.50e+03 ... (remaining 1969 not shown) Histogram of nonbonded interaction distances: 2.12 - 2.68: 370 2.68 - 3.23: 10474 3.23 - 3.79: 20139 3.79 - 4.34: 25679 4.34 - 4.90: 39044 Nonbonded interactions: 95706 Sorted by model distance: nonbonded pdb=" OE2 GLU C 375 " pdb="FE FE C 500 " model vdw 2.125 2.260 nonbonded pdb=" NE2 HIS A 330 " pdb="FE FE A 500 " model vdw 2.175 2.340 nonbonded pdb=" NE2 HIS C 330 " pdb="FE FE C 500 " model vdw 2.185 2.340 nonbonded pdb=" NE2 HIS D 330 " pdb="FE FE D 500 " model vdw 2.189 2.340 nonbonded pdb=" NE2 HIS C 335 " pdb="FE FE C 500 " model vdw 2.189 2.340 ... (remaining 95701 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.01 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' } 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 group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.420 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: 0.140 Check model and map are aligned: 0.030 Set scattering table: 0.040 Process input model: 10.870 Find NCS groups from input model: 0.110 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.240 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 12.880 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7758 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 : 0.005 0.069 11032 Z= 0.238 Angle : 0.959 16.071 14968 Z= 0.518 Chirality : 0.054 0.250 1600 Planarity : 0.006 0.055 1972 Dihedral : 16.185 89.827 4052 Min Nonbonded Distance : 2.125 Molprobity Statistics. All-atom Clashscore : 10.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.88 % Favored : 95.12 % Rotamer: Outliers : 0.17 % Allowed : 7.99 % Favored : 91.84 % 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: -4.89 (0.18), residues: 1332 helix: -3.89 (0.10), residues: 688 sheet: -2.07 (0.45), residues: 128 loop : -2.28 (0.25), residues: 516 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG D 168 TYR 0.013 0.002 TYR D 199 PHE 0.037 0.003 PHE B 285 TRP 0.009 0.002 TRP A 165 HIS 0.007 0.002 HIS A 251 Details of bonding type rmsd covalent geometry : bond 0.00531 (11032) covalent geometry : angle 0.95944 (14968) hydrogen bonds : bond 0.25181 ( 448) hydrogen bonds : angle 9.60086 ( 1308) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2664 Ramachandran restraints generated. 1332 Oldfield, 0 Emsley, 1332 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2664 Ramachandran restraints generated. 1332 Oldfield, 0 Emsley, 1332 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 451 residues out of total 1152 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 449 time to evaluate : 0.398 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 174 ASP cc_start: 0.7459 (m-30) cc_final: 0.6936 (m-30) REVERT: B 178 HIS cc_start: 0.7540 (m-70) cc_final: 0.7142 (m-70) REVERT: B 321 MET cc_start: 0.9082 (mmt) cc_final: 0.8881 (mmt) REVERT: B 460 ASP cc_start: 0.8569 (t70) cc_final: 0.8183 (t0) REVERT: B 464 LEU cc_start: 0.8888 (OUTLIER) cc_final: 0.8676 (tt) REVERT: B 487 ASP cc_start: 0.8355 (t70) cc_final: 0.8075 (t70) REVERT: A 178 HIS cc_start: 0.7679 (m170) cc_final: 0.7371 (m170) REVERT: A 197 GLN cc_start: 0.8796 (tp40) cc_final: 0.8253 (tp-100) REVERT: A 214 ARG cc_start: 0.7771 (mmm160) cc_final: 0.7421 (mmm160) REVERT: A 215 HIS cc_start: 0.8286 (t70) cc_final: 0.7802 (t70) REVERT: A 240 LYS cc_start: 0.8437 (tttp) cc_final: 0.8181 (tttm) REVERT: A 280 LYS cc_start: 0.8471 (mmmm) cc_final: 0.8032 (mmmm) REVERT: A 286 GLN cc_start: 0.7930 (pm20) cc_final: 0.7639 (pm20) REVERT: A 321 MET cc_start: 0.8974 (mmt) cc_final: 0.8689 (mmt) REVERT: A 370 TYR cc_start: 0.9061 (t80) cc_final: 0.8827 (t80) REVERT: A 447 TYR cc_start: 0.8361 (t80) cc_final: 0.7246 (t80) REVERT: A 460 ASP cc_start: 0.8453 (t0) cc_final: 0.7942 (t0) REVERT: A 464 LEU cc_start: 0.9034 (tp) cc_final: 0.8786 (tp) REVERT: A 473 GLN cc_start: 0.8537 (tp40) cc_final: 0.8324 (tp40) REVERT: A 476 ARG cc_start: 0.7896 (ttt90) cc_final: 0.7625 (ttt-90) REVERT: C 172 GLU cc_start: 0.7479 (mm-30) cc_final: 0.7056 (mm-30) REVERT: C 214 ARG cc_start: 0.8185 (tpp-160) cc_final: 0.7958 (tpp-160) REVERT: C 343 THR cc_start: 0.8596 (p) cc_final: 0.8354 (t) REVERT: C 443 LYS cc_start: 0.7902 (ttmm) cc_final: 0.7450 (ttmm) REVERT: C 466 ILE cc_start: 0.8394 (mm) cc_final: 0.7873 (mt) REVERT: C 480 GLU cc_start: 0.7680 (mp0) cc_final: 0.7106 (mp0) REVERT: D 172 GLU cc_start: 0.7539 (mm-30) cc_final: 0.6990 (mm-30) REVERT: D 197 GLN cc_start: 0.8764 (tp40) cc_final: 0.8395 (tp40) REVERT: D 224 TYR cc_start: 0.8682 (m-80) cc_final: 0.8407 (m-80) REVERT: D 243 TYR cc_start: 0.7608 (m-10) cc_final: 0.7343 (m-10) REVERT: D 268 ASN cc_start: 0.9218 (t0) cc_final: 0.8934 (t0) REVERT: D 278 PHE cc_start: 0.8013 (t80) cc_final: 0.7407 (t80) REVERT: D 286 GLN cc_start: 0.7853 (pm20) cc_final: 0.7528 (pm20) REVERT: D 321 MET cc_start: 0.9063 (mmt) cc_final: 0.8690 (mmt) REVERT: D 346 GLN cc_start: 0.8579 (tp-100) cc_final: 0.8125 (tp40) REVERT: D 450 ARG cc_start: 0.8069 (ptp90) cc_final: 0.7543 (ptp90) REVERT: D 460 ASP cc_start: 0.8120 (t0) cc_final: 0.7835 (t0) outliers start: 2 outliers final: 0 residues processed: 449 average time/residue: 0.1222 time to fit residues: 73.6729 Evaluate side-chains 331 residues out of total 1152 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 330 time to evaluate : 0.408 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 464 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 98 optimal weight: 0.9990 chunk 107 optimal weight: 2.9990 chunk 10 optimal weight: 0.8980 chunk 66 optimal weight: 0.9990 chunk 130 optimal weight: 1.9990 chunk 124 optimal weight: 1.9990 chunk 103 optimal weight: 5.9990 chunk 77 optimal weight: 0.8980 chunk 122 optimal weight: 2.9990 chunk 91 optimal weight: 5.9990 chunk 55 optimal weight: 0.9980 overall best weight: 0.9584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 177 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 312 GLN B 349 GLN B 425 GLN ** B 483 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 246 HIS ** A 251 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 312 GLN A 401 HIS A 425 GLN A 473 GLN C 425 GLN C 483 GLN D 178 HIS D 201 GLN D 246 HIS D 346 GLN D 420 GLN D 425 GLN ** D 483 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3591 r_free = 0.3591 target = 0.111111 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3419 r_free = 0.3419 target = 0.099704 restraints weight = 25803.819| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3463 r_free = 0.3463 target = 0.102696 restraints weight = 14093.049| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3498 r_free = 0.3498 target = 0.104947 restraints weight = 8790.944| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3518 r_free = 0.3518 target = 0.106279 restraints weight = 5914.717| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.3538 r_free = 0.3538 target = 0.107550 restraints weight = 4363.093| |-----------------------------------------------------------------------------| r_work (final): 0.3539 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7791 moved from start: 0.2461 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 11032 Z= 0.165 Angle : 0.689 7.252 14968 Z= 0.357 Chirality : 0.043 0.174 1600 Planarity : 0.005 0.064 1972 Dihedral : 5.857 50.806 1486 Min Nonbonded Distance : 2.093 Molprobity Statistics. All-atom Clashscore : 18.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.26 % Favored : 94.74 % Rotamer: Outliers : 2.86 % Allowed : 18.06 % Favored : 79.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.09 (0.20), residues: 1332 helix: -2.09 (0.16), residues: 668 sheet: -2.35 (0.41), residues: 136 loop : -1.63 (0.27), residues: 528 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.001 ARG C 168 TYR 0.017 0.002 TYR B 370 PHE 0.022 0.002 PHE C 344 TRP 0.017 0.003 TRP B 371 HIS 0.008 0.001 HIS D 215 Details of bonding type rmsd covalent geometry : bond 0.00376 (11032) covalent geometry : angle 0.68889 (14968) hydrogen bonds : bond 0.04731 ( 448) hydrogen bonds : angle 5.81369 ( 1308) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2664 Ramachandran restraints generated. 1332 Oldfield, 0 Emsley, 1332 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2664 Ramachandran restraints generated. 1332 Oldfield, 0 Emsley, 1332 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 398 residues out of total 1152 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 365 time to evaluate : 0.385 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 172 GLU cc_start: 0.6725 (mt-10) cc_final: 0.6211 (mt-10) REVERT: B 177 HIS cc_start: 0.6602 (m90) cc_final: 0.6292 (m-70) REVERT: B 331 GLU cc_start: 0.8687 (pt0) cc_final: 0.8417 (pt0) REVERT: B 447 TYR cc_start: 0.8116 (t80) cc_final: 0.7736 (t80) REVERT: B 460 ASP cc_start: 0.8456 (t70) cc_final: 0.7974 (t0) REVERT: B 464 LEU cc_start: 0.8876 (OUTLIER) cc_final: 0.8638 (tt) REVERT: B 485 GLU cc_start: 0.8220 (tm-30) cc_final: 0.8019 (tm-30) REVERT: A 169 LYS cc_start: 0.8156 (mmtm) cc_final: 0.7335 (mmtm) REVERT: A 214 ARG cc_start: 0.7749 (mmm160) cc_final: 0.7545 (mmm160) REVERT: A 280 LYS cc_start: 0.8461 (mmmm) cc_final: 0.8000 (mmmm) REVERT: A 286 GLN cc_start: 0.7768 (pm20) cc_final: 0.7267 (pm20) REVERT: A 290 VAL cc_start: 0.8760 (p) cc_final: 0.8458 (m) REVERT: A 447 TYR cc_start: 0.8240 (t80) cc_final: 0.6967 (t80) REVERT: A 460 ASP cc_start: 0.8206 (t0) cc_final: 0.7885 (t0) REVERT: A 466 ILE cc_start: 0.8646 (OUTLIER) cc_final: 0.8444 (mt) REVERT: A 476 ARG cc_start: 0.8005 (ttt90) cc_final: 0.7792 (ttt-90) REVERT: C 172 GLU cc_start: 0.7325 (mm-30) cc_final: 0.7039 (mm-30) REVERT: C 343 THR cc_start: 0.8745 (p) cc_final: 0.8441 (t) REVERT: C 364 GLU cc_start: 0.8739 (tm-30) cc_final: 0.8533 (tm-30) REVERT: C 443 LYS cc_start: 0.8023 (ttmm) cc_final: 0.7494 (ttmm) REVERT: C 476 ARG cc_start: 0.7992 (ttt90) cc_final: 0.7512 (ttt90) REVERT: C 480 GLU cc_start: 0.7594 (OUTLIER) cc_final: 0.6862 (mp0) REVERT: D 172 GLU cc_start: 0.7367 (mm-30) cc_final: 0.7150 (mm-30) REVERT: D 214 ARG cc_start: 0.7449 (mmm160) cc_final: 0.7160 (mmp-170) REVERT: D 280 LYS cc_start: 0.8332 (mmtt) cc_final: 0.8089 (mttt) REVERT: D 286 GLN cc_start: 0.7810 (pm20) cc_final: 0.7432 (pm20) REVERT: D 321 MET cc_start: 0.8981 (mmt) cc_final: 0.8765 (mmt) REVERT: D 346 GLN cc_start: 0.8364 (tp40) cc_final: 0.8116 (tp40) REVERT: D 386 LYS cc_start: 0.7637 (mmtm) cc_final: 0.7392 (mmmm) REVERT: D 450 ARG cc_start: 0.8246 (ptp90) cc_final: 0.7671 (ptp90) REVERT: D 460 ASP cc_start: 0.8331 (t0) cc_final: 0.7963 (t0) REVERT: D 476 ARG cc_start: 0.7828 (ttt90) cc_final: 0.7515 (ttt90) REVERT: D 480 GLU cc_start: 0.7232 (OUTLIER) cc_final: 0.6336 (mp0) outliers start: 33 outliers final: 17 residues processed: 376 average time/residue: 0.1163 time to fit residues: 58.8530 Evaluate side-chains 322 residues out of total 1152 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 301 time to evaluate : 0.416 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 300 LEU Chi-restraints excluded: chain B residue 444 LEU Chi-restraints excluded: chain B residue 464 LEU Chi-restraints excluded: chain A residue 170 VAL Chi-restraints excluded: chain A residue 225 THR Chi-restraints excluded: chain A residue 234 GLU Chi-restraints excluded: chain A residue 269 ILE Chi-restraints excluded: chain A residue 287 LEU Chi-restraints excluded: chain A residue 444 LEU Chi-restraints excluded: chain A residue 466 ILE Chi-restraints excluded: chain A residue 488 THR Chi-restraints excluded: chain C residue 234 GLU Chi-restraints excluded: chain C residue 287 LEU Chi-restraints excluded: chain C residue 385 VAL Chi-restraints excluded: chain C residue 444 LEU Chi-restraints excluded: chain C residue 452 GLN Chi-restraints excluded: chain C residue 480 GLU Chi-restraints excluded: chain D residue 225 THR Chi-restraints excluded: chain D residue 234 GLU Chi-restraints excluded: chain D residue 444 LEU Chi-restraints excluded: chain D residue 480 GLU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 124 optimal weight: 4.9990 chunk 128 optimal weight: 0.0570 chunk 61 optimal weight: 0.9990 chunk 15 optimal weight: 0.0050 chunk 56 optimal weight: 0.5980 chunk 113 optimal weight: 1.9990 chunk 2 optimal weight: 6.9990 chunk 32 optimal weight: 0.8980 chunk 11 optimal weight: 0.8980 chunk 43 optimal weight: 0.0670 chunk 115 optimal weight: 5.9990 overall best weight: 0.3250 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 177 HIS B 178 HIS ** A 251 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 473 GLN C 483 GLN D 197 GLN ** D 251 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 268 ASN D 483 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3643 r_free = 0.3643 target = 0.114905 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3465 r_free = 0.3465 target = 0.102710 restraints weight = 25575.276| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3509 r_free = 0.3509 target = 0.105821 restraints weight = 14128.330| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3543 r_free = 0.3543 target = 0.108124 restraints weight = 8995.751| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3563 r_free = 0.3563 target = 0.109552 restraints weight = 6091.167| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3580 r_free = 0.3580 target = 0.110759 restraints weight = 4504.355| |-----------------------------------------------------------------------------| r_work (final): 0.3589 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7753 moved from start: 0.3048 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 11032 Z= 0.128 Angle : 0.654 12.420 14968 Z= 0.333 Chirality : 0.043 0.174 1600 Planarity : 0.004 0.041 1972 Dihedral : 5.456 46.844 1486 Min Nonbonded Distance : 2.141 Molprobity Statistics. All-atom Clashscore : 16.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.33 % Favored : 94.67 % Rotamer: Outliers : 3.12 % Allowed : 20.75 % Favored : 76.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: -2.22 (0.21), residues: 1332 helix: -1.28 (0.18), residues: 668 sheet: -2.00 (0.42), residues: 132 loop : -1.33 (0.27), residues: 532 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG C 342 TYR 0.022 0.002 TYR D 447 PHE 0.025 0.002 PHE B 285 TRP 0.028 0.003 TRP A 232 HIS 0.004 0.001 HIS A 251 Details of bonding type rmsd covalent geometry : bond 0.00289 (11032) covalent geometry : angle 0.65354 (14968) hydrogen bonds : bond 0.04150 ( 448) hydrogen bonds : angle 5.46011 ( 1308) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2664 Ramachandran restraints generated. 1332 Oldfield, 0 Emsley, 1332 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2664 Ramachandran restraints generated. 1332 Oldfield, 0 Emsley, 1332 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 388 residues out of total 1152 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 352 time to evaluate : 0.332 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 260 ARG cc_start: 0.8844 (ptp-110) cc_final: 0.8580 (ptp-110) REVERT: B 281 GLU cc_start: 0.7829 (tt0) cc_final: 0.7505 (tt0) REVERT: B 447 TYR cc_start: 0.8095 (t80) cc_final: 0.7847 (t80) REVERT: B 460 ASP cc_start: 0.8342 (t70) cc_final: 0.8068 (t0) REVERT: B 464 LEU cc_start: 0.8889 (OUTLIER) cc_final: 0.8670 (tt) REVERT: A 197 GLN cc_start: 0.8867 (tp40) cc_final: 0.8110 (tp40) REVERT: A 214 ARG cc_start: 0.7722 (mmm160) cc_final: 0.7512 (mmm160) REVERT: A 277 ARG cc_start: 0.8224 (ttm-80) cc_final: 0.7923 (ttm-80) REVERT: A 280 LYS cc_start: 0.8375 (mmmm) cc_final: 0.7829 (mmmm) REVERT: A 286 GLN cc_start: 0.7657 (pm20) cc_final: 0.7219 (pm20) REVERT: A 290 VAL cc_start: 0.8722 (p) cc_final: 0.8515 (m) REVERT: A 367 SER cc_start: 0.9278 (m) cc_final: 0.8903 (p) REVERT: A 447 TYR cc_start: 0.8010 (t80) cc_final: 0.6954 (t80) REVERT: A 460 ASP cc_start: 0.8255 (t0) cc_final: 0.7924 (t0) REVERT: A 476 ARG cc_start: 0.8016 (ttt90) cc_final: 0.7734 (ttt-90) REVERT: A 484 ASP cc_start: 0.8034 (m-30) cc_final: 0.7774 (m-30) REVERT: C 172 GLU cc_start: 0.7107 (mm-30) cc_final: 0.6804 (mm-30) REVERT: C 274 ASP cc_start: 0.8570 (OUTLIER) cc_final: 0.7808 (t70) REVERT: C 367 SER cc_start: 0.9246 (m) cc_final: 0.8793 (p) REVERT: C 462 TYR cc_start: 0.8122 (m-80) cc_final: 0.7754 (m-10) REVERT: C 476 ARG cc_start: 0.7999 (ttt90) cc_final: 0.7400 (ttt90) REVERT: C 480 GLU cc_start: 0.7500 (mp0) cc_final: 0.6753 (mp0) REVERT: D 172 GLU cc_start: 0.7003 (mm-30) cc_final: 0.6541 (mm-30) REVERT: D 280 LYS cc_start: 0.8308 (mmtt) cc_final: 0.8069 (mttt) REVERT: D 286 GLN cc_start: 0.7701 (pm20) cc_final: 0.7311 (pm20) REVERT: D 308 PHE cc_start: 0.8170 (t80) cc_final: 0.7939 (t80) REVERT: D 450 ARG cc_start: 0.8348 (ptp90) cc_final: 0.7761 (mtm180) REVERT: D 460 ASP cc_start: 0.8398 (t0) cc_final: 0.7985 (t0) REVERT: D 476 ARG cc_start: 0.7716 (ttt90) cc_final: 0.7440 (ttt90) REVERT: D 480 GLU cc_start: 0.7209 (OUTLIER) cc_final: 0.6431 (mp0) outliers start: 36 outliers final: 23 residues processed: 368 average time/residue: 0.1181 time to fit residues: 58.9749 Evaluate side-chains 333 residues out of total 1152 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 307 time to evaluate : 0.405 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 234 GLU Chi-restraints excluded: chain B residue 343 THR Chi-restraints excluded: chain B residue 444 LEU Chi-restraints excluded: chain B residue 464 LEU Chi-restraints excluded: chain B residue 488 THR Chi-restraints excluded: chain A residue 170 VAL Chi-restraints excluded: chain A residue 225 THR Chi-restraints excluded: chain A residue 234 GLU Chi-restraints excluded: chain A residue 269 ILE Chi-restraints excluded: chain A residue 287 LEU Chi-restraints excluded: chain A residue 444 LEU Chi-restraints excluded: chain A residue 485 GLU Chi-restraints excluded: chain A residue 488 THR Chi-restraints excluded: chain C residue 234 GLU Chi-restraints excluded: chain C residue 274 ASP Chi-restraints excluded: chain C residue 300 LEU Chi-restraints excluded: chain C residue 385 VAL Chi-restraints excluded: chain C residue 444 LEU Chi-restraints excluded: chain C residue 452 GLN Chi-restraints excluded: chain D residue 234 GLU Chi-restraints excluded: chain D residue 272 LEU Chi-restraints excluded: chain D residue 310 CYS Chi-restraints excluded: chain D residue 311 THR Chi-restraints excluded: chain D residue 343 THR Chi-restraints excluded: chain D residue 444 LEU Chi-restraints excluded: chain D residue 480 GLU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 40 optimal weight: 4.9990 chunk 18 optimal weight: 4.9990 chunk 21 optimal weight: 1.9990 chunk 114 optimal weight: 8.9990 chunk 85 optimal weight: 3.9990 chunk 93 optimal weight: 7.9990 chunk 99 optimal weight: 2.9990 chunk 61 optimal weight: 0.0980 chunk 63 optimal weight: 0.5980 chunk 89 optimal weight: 0.8980 chunk 111 optimal weight: 0.2980 overall best weight: 0.7782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 178 HIS A 177 HIS ** A 251 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 246 HIS ** C 251 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 177 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 251 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3633 r_free = 0.3633 target = 0.114057 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3453 r_free = 0.3453 target = 0.102065 restraints weight = 26010.505| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3498 r_free = 0.3498 target = 0.105212 restraints weight = 14559.456| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3531 r_free = 0.3531 target = 0.107387 restraints weight = 9213.384| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3550 r_free = 0.3550 target = 0.108729 restraints weight = 6289.595| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3569 r_free = 0.3569 target = 0.109999 restraints weight = 4702.064| |-----------------------------------------------------------------------------| r_work (final): 0.3575 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7774 moved from start: 0.3460 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 11032 Z= 0.142 Angle : 0.651 9.761 14968 Z= 0.331 Chirality : 0.042 0.143 1600 Planarity : 0.004 0.040 1972 Dihedral : 5.271 46.902 1486 Min Nonbonded Distance : 2.126 Molprobity Statistics. All-atom Clashscore : 16.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.18 % Favored : 94.82 % Rotamer: Outliers : 4.17 % Allowed : 22.14 % Favored : 73.70 % 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: -1.65 (0.22), residues: 1332 helix: -0.74 (0.19), residues: 668 sheet: -1.95 (0.42), residues: 132 loop : -1.12 (0.27), residues: 532 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG C 168 TYR 0.021 0.002 TYR A 264 PHE 0.035 0.002 PHE D 344 TRP 0.037 0.003 TRP B 232 HIS 0.009 0.001 HIS C 215 Details of bonding type rmsd covalent geometry : bond 0.00331 (11032) covalent geometry : angle 0.65100 (14968) hydrogen bonds : bond 0.04005 ( 448) hydrogen bonds : angle 5.28968 ( 1308) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2664 Ramachandran restraints generated. 1332 Oldfield, 0 Emsley, 1332 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2664 Ramachandran restraints generated. 1332 Oldfield, 0 Emsley, 1332 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 391 residues out of total 1152 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 343 time to evaluate : 0.282 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 178 HIS cc_start: 0.7065 (m170) cc_final: 0.6830 (m170) REVERT: B 252 LEU cc_start: 0.7239 (mt) cc_final: 0.6988 (mm) REVERT: B 460 ASP cc_start: 0.8518 (t0) cc_final: 0.8118 (t0) REVERT: B 464 LEU cc_start: 0.8870 (OUTLIER) cc_final: 0.8665 (tt) REVERT: A 197 GLN cc_start: 0.8837 (tp40) cc_final: 0.8502 (tp40) REVERT: A 280 LYS cc_start: 0.8309 (mmmm) cc_final: 0.7795 (mmmm) REVERT: A 286 GLN cc_start: 0.7756 (pm20) cc_final: 0.7205 (pm20) REVERT: A 290 VAL cc_start: 0.8723 (p) cc_final: 0.8502 (m) REVERT: A 346 GLN cc_start: 0.8371 (tp-100) cc_final: 0.8091 (tp40) REVERT: A 367 SER cc_start: 0.9310 (m) cc_final: 0.8910 (p) REVERT: A 447 TYR cc_start: 0.8103 (t80) cc_final: 0.6833 (t80) REVERT: A 460 ASP cc_start: 0.8253 (t0) cc_final: 0.7981 (t0) REVERT: A 476 ARG cc_start: 0.8059 (ttt90) cc_final: 0.7628 (ttt-90) REVERT: A 484 ASP cc_start: 0.8078 (m-30) cc_final: 0.7812 (m-30) REVERT: C 172 GLU cc_start: 0.7020 (mm-30) cc_final: 0.6785 (mm-30) REVERT: C 274 ASP cc_start: 0.8323 (OUTLIER) cc_final: 0.7361 (t0) REVERT: C 342 ARG cc_start: 0.8489 (mmm-85) cc_final: 0.8177 (mmm-85) REVERT: C 361 GLU cc_start: 0.8662 (pm20) cc_final: 0.8215 (pm20) REVERT: C 458 LYS cc_start: 0.8294 (ttpt) cc_final: 0.8067 (ttpp) REVERT: C 462 TYR cc_start: 0.8027 (m-80) cc_final: 0.7388 (m-10) REVERT: C 473 GLN cc_start: 0.8346 (tp-100) cc_final: 0.7961 (tp40) REVERT: C 476 ARG cc_start: 0.8005 (ttt90) cc_final: 0.7571 (ttt90) REVERT: C 480 GLU cc_start: 0.7535 (OUTLIER) cc_final: 0.6739 (mp0) REVERT: D 237 THR cc_start: 0.9138 (p) cc_final: 0.8925 (p) REVERT: D 274 ASP cc_start: 0.8600 (OUTLIER) cc_final: 0.8080 (t0) REVERT: D 280 LYS cc_start: 0.8367 (mmtt) cc_final: 0.8119 (mttt) REVERT: D 286 GLN cc_start: 0.7798 (pm20) cc_final: 0.7360 (pm20) REVERT: D 308 PHE cc_start: 0.8162 (t80) cc_final: 0.7875 (t80) REVERT: D 367 SER cc_start: 0.9302 (m) cc_final: 0.8946 (p) REVERT: D 410 ARG cc_start: 0.8472 (ptp-170) cc_final: 0.8236 (ptp-170) REVERT: D 450 ARG cc_start: 0.8254 (ptp-170) cc_final: 0.7673 (mtm180) REVERT: D 460 ASP cc_start: 0.8342 (t0) cc_final: 0.7927 (t0) REVERT: D 476 ARG cc_start: 0.7728 (ttt90) cc_final: 0.7466 (ttt90) REVERT: D 480 GLU cc_start: 0.7171 (OUTLIER) cc_final: 0.6257 (mp0) outliers start: 48 outliers final: 29 residues processed: 364 average time/residue: 0.1159 time to fit residues: 56.8809 Evaluate side-chains 329 residues out of total 1152 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 295 time to evaluate : 0.390 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 170 VAL Chi-restraints excluded: chain B residue 234 GLU Chi-restraints excluded: chain B residue 343 THR Chi-restraints excluded: chain B residue 385 VAL Chi-restraints excluded: chain B residue 444 LEU Chi-restraints excluded: chain B residue 464 LEU Chi-restraints excluded: chain B residue 488 THR Chi-restraints excluded: chain A residue 170 VAL Chi-restraints excluded: chain A residue 225 THR Chi-restraints excluded: chain A residue 234 GLU Chi-restraints excluded: chain A residue 341 ASP Chi-restraints excluded: chain A residue 444 LEU Chi-restraints excluded: chain A residue 485 GLU Chi-restraints excluded: chain A residue 488 THR Chi-restraints excluded: chain C residue 234 GLU Chi-restraints excluded: chain C residue 274 ASP Chi-restraints excluded: chain C residue 300 LEU Chi-restraints excluded: chain C residue 343 THR Chi-restraints excluded: chain C residue 385 VAL Chi-restraints excluded: chain C residue 444 LEU Chi-restraints excluded: chain C residue 452 GLN Chi-restraints excluded: chain C residue 466 ILE Chi-restraints excluded: chain C residue 480 GLU Chi-restraints excluded: chain D residue 179 LEU Chi-restraints excluded: chain D residue 234 GLU Chi-restraints excluded: chain D residue 272 LEU Chi-restraints excluded: chain D residue 274 ASP Chi-restraints excluded: chain D residue 310 CYS Chi-restraints excluded: chain D residue 311 THR Chi-restraints excluded: chain D residue 343 THR Chi-restraints excluded: chain D residue 351 ILE Chi-restraints excluded: chain D residue 385 VAL Chi-restraints excluded: chain D residue 444 LEU Chi-restraints excluded: chain D residue 480 GLU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 67 optimal weight: 3.9990 chunk 124 optimal weight: 0.0770 chunk 31 optimal weight: 0.6980 chunk 128 optimal weight: 0.7980 chunk 93 optimal weight: 0.8980 chunk 28 optimal weight: 5.9990 chunk 81 optimal weight: 4.9990 chunk 43 optimal weight: 3.9990 chunk 63 optimal weight: 5.9990 chunk 33 optimal weight: 5.9990 chunk 102 optimal weight: 0.1980 overall best weight: 0.5338 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 251 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 401 HIS C 215 HIS ** C 251 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 483 GLN ** D 177 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3660 r_free = 0.3660 target = 0.116085 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 25)----------------| | r_work = 0.3481 r_free = 0.3481 target = 0.104094 restraints weight = 24914.217| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3525 r_free = 0.3525 target = 0.107193 restraints weight = 13908.517| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3559 r_free = 0.3559 target = 0.109420 restraints weight = 8835.886| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 41)----------------| | r_work = 0.3581 r_free = 0.3581 target = 0.110887 restraints weight = 6019.401| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3598 r_free = 0.3598 target = 0.112048 restraints weight = 4379.187| |-----------------------------------------------------------------------------| r_work (final): 0.3603 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7743 moved from start: 0.3792 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 11032 Z= 0.133 Angle : 0.676 13.474 14968 Z= 0.338 Chirality : 0.043 0.160 1600 Planarity : 0.004 0.044 1972 Dihedral : 5.122 44.993 1486 Min Nonbonded Distance : 2.169 Molprobity Statistics. All-atom Clashscore : 17.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.41 % Favored : 94.59 % Rotamer: Outliers : 4.34 % Allowed : 22.74 % Favored : 72.92 % 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: -1.42 (0.22), residues: 1332 helix: -0.52 (0.19), residues: 692 sheet: -1.67 (0.44), residues: 132 loop : -1.10 (0.28), residues: 508 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG C 260 TYR 0.025 0.002 TYR A 264 PHE 0.027 0.002 PHE D 344 TRP 0.044 0.003 TRP A 232 HIS 0.010 0.001 HIS A 215 Details of bonding type rmsd covalent geometry : bond 0.00307 (11032) covalent geometry : angle 0.67633 (14968) hydrogen bonds : bond 0.03862 ( 448) hydrogen bonds : angle 5.20463 ( 1308) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2664 Ramachandran restraints generated. 1332 Oldfield, 0 Emsley, 1332 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2664 Ramachandran restraints generated. 1332 Oldfield, 0 Emsley, 1332 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 381 residues out of total 1152 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 331 time to evaluate : 0.374 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 178 HIS cc_start: 0.7120 (m170) cc_final: 0.6874 (m170) REVERT: B 217 ASP cc_start: 0.7966 (m-30) cc_final: 0.7678 (m-30) REVERT: B 260 ARG cc_start: 0.8977 (ptp-110) cc_final: 0.8581 (ptp-110) REVERT: B 280 LYS cc_start: 0.8368 (mmmm) cc_final: 0.7852 (mmmm) REVERT: B 281 GLU cc_start: 0.8034 (tt0) cc_final: 0.7708 (tt0) REVERT: B 364 GLU cc_start: 0.8665 (tm-30) cc_final: 0.8439 (tm-30) REVERT: B 396 TYR cc_start: 0.7070 (t80) cc_final: 0.6768 (t80) REVERT: B 447 TYR cc_start: 0.7958 (t80) cc_final: 0.7380 (t80) REVERT: B 460 ASP cc_start: 0.8469 (t0) cc_final: 0.8028 (t0) REVERT: A 197 GLN cc_start: 0.8881 (tp40) cc_final: 0.8629 (tp40) REVERT: A 280 LYS cc_start: 0.8261 (mmmm) cc_final: 0.7780 (mmmm) REVERT: A 290 VAL cc_start: 0.8560 (p) cc_final: 0.8359 (m) REVERT: A 346 GLN cc_start: 0.8321 (tp-100) cc_final: 0.8043 (tp40) REVERT: A 367 SER cc_start: 0.9298 (m) cc_final: 0.8955 (p) REVERT: A 447 TYR cc_start: 0.8140 (t80) cc_final: 0.6888 (t80) REVERT: A 460 ASP cc_start: 0.8217 (t0) cc_final: 0.7919 (t0) REVERT: A 476 ARG cc_start: 0.8046 (ttt90) cc_final: 0.7581 (ttt-90) REVERT: A 484 ASP cc_start: 0.7922 (m-30) cc_final: 0.7594 (m-30) REVERT: C 172 GLU cc_start: 0.6992 (mm-30) cc_final: 0.6713 (mm-30) REVERT: C 274 ASP cc_start: 0.8262 (OUTLIER) cc_final: 0.7342 (t0) REVERT: C 286 GLN cc_start: 0.7926 (pm20) cc_final: 0.7636 (pm20) REVERT: C 361 GLU cc_start: 0.8588 (pm20) cc_final: 0.8088 (pm20) REVERT: C 462 TYR cc_start: 0.7758 (m-80) cc_final: 0.7342 (m-10) REVERT: C 473 GLN cc_start: 0.8332 (tp-100) cc_final: 0.7958 (tp40) REVERT: C 476 ARG cc_start: 0.7949 (ttt90) cc_final: 0.7548 (ttt90) REVERT: C 480 GLU cc_start: 0.7556 (OUTLIER) cc_final: 0.6772 (mp0) REVERT: D 274 ASP cc_start: 0.8556 (OUTLIER) cc_final: 0.8094 (t0) REVERT: D 280 LYS cc_start: 0.8333 (mmtt) cc_final: 0.8065 (mttt) REVERT: D 286 GLN cc_start: 0.7813 (pm20) cc_final: 0.7351 (pm20) REVERT: D 308 PHE cc_start: 0.8160 (t80) cc_final: 0.7909 (t80) REVERT: D 342 ARG cc_start: 0.8467 (mmm-85) cc_final: 0.8192 (mmm-85) REVERT: D 367 SER cc_start: 0.9282 (m) cc_final: 0.8917 (p) REVERT: D 443 LYS cc_start: 0.7858 (ttmt) cc_final: 0.7652 (ttmt) REVERT: D 450 ARG cc_start: 0.8304 (ptp-170) cc_final: 0.8025 (ptp90) REVERT: D 460 ASP cc_start: 0.8230 (t0) cc_final: 0.7945 (t0) REVERT: D 476 ARG cc_start: 0.7668 (ttt90) cc_final: 0.7079 (ttt90) REVERT: D 480 GLU cc_start: 0.7191 (OUTLIER) cc_final: 0.6346 (mp0) outliers start: 50 outliers final: 30 residues processed: 352 average time/residue: 0.1131 time to fit residues: 54.1374 Evaluate side-chains 322 residues out of total 1152 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 288 time to evaluate : 0.417 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 170 VAL Chi-restraints excluded: chain B residue 198 VAL Chi-restraints excluded: chain B residue 234 GLU Chi-restraints excluded: chain B residue 343 THR Chi-restraints excluded: chain B residue 356 LEU Chi-restraints excluded: chain B residue 444 LEU Chi-restraints excluded: chain A residue 209 ILE Chi-restraints excluded: chain A residue 225 THR Chi-restraints excluded: chain A residue 234 GLU Chi-restraints excluded: chain A residue 269 ILE Chi-restraints excluded: chain A residue 287 LEU Chi-restraints excluded: chain A residue 361 GLU Chi-restraints excluded: chain A residue 444 LEU Chi-restraints excluded: chain A residue 485 GLU Chi-restraints excluded: chain A residue 488 THR Chi-restraints excluded: chain C residue 234 GLU Chi-restraints excluded: chain C residue 274 ASP Chi-restraints excluded: chain C residue 300 LEU Chi-restraints excluded: chain C residue 343 THR Chi-restraints excluded: chain C residue 385 VAL Chi-restraints excluded: chain C residue 433 VAL Chi-restraints excluded: chain C residue 444 LEU Chi-restraints excluded: chain C residue 452 GLN Chi-restraints excluded: chain C residue 468 VAL Chi-restraints excluded: chain C residue 480 GLU Chi-restraints excluded: chain D residue 234 GLU Chi-restraints excluded: chain D residue 274 ASP Chi-restraints excluded: chain D residue 310 CYS Chi-restraints excluded: chain D residue 311 THR Chi-restraints excluded: chain D residue 341 ASP Chi-restraints excluded: chain D residue 343 THR Chi-restraints excluded: chain D residue 433 VAL Chi-restraints excluded: chain D residue 444 LEU Chi-restraints excluded: chain D residue 480 GLU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 6 optimal weight: 0.8980 chunk 15 optimal weight: 1.9990 chunk 93 optimal weight: 0.8980 chunk 126 optimal weight: 0.9980 chunk 18 optimal weight: 0.9980 chunk 131 optimal weight: 0.7980 chunk 86 optimal weight: 6.9990 chunk 57 optimal weight: 0.0470 chunk 48 optimal weight: 4.9990 chunk 88 optimal weight: 3.9990 chunk 34 optimal weight: 0.1980 overall best weight: 0.5678 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 286 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 177 HIS A 191 HIS ** A 251 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 251 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 428 GLN ** D 177 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3667 r_free = 0.3667 target = 0.116696 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3491 r_free = 0.3491 target = 0.104804 restraints weight = 25106.774| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3536 r_free = 0.3536 target = 0.107966 restraints weight = 13954.534| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3566 r_free = 0.3566 target = 0.109993 restraints weight = 8799.545| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3590 r_free = 0.3590 target = 0.111551 restraints weight = 6145.599| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3606 r_free = 0.3606 target = 0.112643 restraints weight = 4417.054| |-----------------------------------------------------------------------------| r_work (final): 0.3611 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7740 moved from start: 0.4022 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.055 11032 Z= 0.136 Angle : 0.691 11.801 14968 Z= 0.342 Chirality : 0.044 0.201 1600 Planarity : 0.004 0.040 1972 Dihedral : 4.886 18.825 1484 Min Nonbonded Distance : 2.170 Molprobity Statistics. All-atom Clashscore : 18.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.33 % Favored : 94.67 % Rotamer: Outliers : 4.69 % Allowed : 21.53 % Favored : 73.78 % 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: -1.10 (0.22), residues: 1332 helix: -0.09 (0.20), residues: 636 sheet: -1.99 (0.42), residues: 140 loop : -0.98 (0.26), residues: 556 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG C 260 TYR 0.025 0.002 TYR A 264 PHE 0.026 0.002 PHE D 344 TRP 0.050 0.003 TRP A 232 HIS 0.011 0.001 HIS A 215 Details of bonding type rmsd covalent geometry : bond 0.00317 (11032) covalent geometry : angle 0.69054 (14968) hydrogen bonds : bond 0.03902 ( 448) hydrogen bonds : angle 5.15676 ( 1308) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2664 Ramachandran restraints generated. 1332 Oldfield, 0 Emsley, 1332 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2664 Ramachandran restraints generated. 1332 Oldfield, 0 Emsley, 1332 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 382 residues out of total 1152 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 328 time to evaluate : 0.401 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 178 HIS cc_start: 0.7147 (m170) cc_final: 0.6858 (m170) REVERT: B 217 ASP cc_start: 0.7963 (m-30) cc_final: 0.7667 (m-30) REVERT: B 280 LYS cc_start: 0.8374 (mmmm) cc_final: 0.7862 (mmmm) REVERT: B 281 GLU cc_start: 0.8069 (tt0) cc_final: 0.7743 (tt0) REVERT: B 364 GLU cc_start: 0.8663 (tm-30) cc_final: 0.8448 (tm-30) REVERT: B 447 TYR cc_start: 0.7983 (t80) cc_final: 0.7548 (t80) REVERT: B 460 ASP cc_start: 0.8339 (t0) cc_final: 0.8010 (t0) REVERT: A 176 CYS cc_start: 0.6803 (t) cc_final: 0.6554 (t) REVERT: A 280 LYS cc_start: 0.8283 (mmmm) cc_final: 0.7828 (mmmm) REVERT: A 286 GLN cc_start: 0.7667 (pm20) cc_final: 0.7194 (pm20) REVERT: A 346 GLN cc_start: 0.8249 (tp-100) cc_final: 0.7972 (tp-100) REVERT: A 367 SER cc_start: 0.9321 (m) cc_final: 0.9007 (p) REVERT: A 447 TYR cc_start: 0.8211 (t80) cc_final: 0.7159 (t80) REVERT: A 460 ASP cc_start: 0.8351 (t0) cc_final: 0.7965 (t0) REVERT: A 476 ARG cc_start: 0.8031 (ttt90) cc_final: 0.7634 (ttt-90) REVERT: C 172 GLU cc_start: 0.7048 (mm-30) cc_final: 0.6701 (mm-30) REVERT: C 274 ASP cc_start: 0.8297 (OUTLIER) cc_final: 0.7327 (t0) REVERT: C 361 GLU cc_start: 0.8588 (pm20) cc_final: 0.8088 (pm20) REVERT: C 462 TYR cc_start: 0.7675 (m-80) cc_final: 0.7379 (m-10) REVERT: C 473 GLN cc_start: 0.8249 (tp-100) cc_final: 0.7835 (tp40) REVERT: C 476 ARG cc_start: 0.7934 (ttt90) cc_final: 0.7527 (ttt90) REVERT: C 480 GLU cc_start: 0.7528 (OUTLIER) cc_final: 0.6668 (mp0) REVERT: D 178 HIS cc_start: 0.7212 (m170) cc_final: 0.6910 (m170) REVERT: D 274 ASP cc_start: 0.8505 (OUTLIER) cc_final: 0.8098 (t0) REVERT: D 280 LYS cc_start: 0.8379 (mmtt) cc_final: 0.8108 (mttt) REVERT: D 286 GLN cc_start: 0.7858 (pm20) cc_final: 0.7329 (pm20) REVERT: D 342 ARG cc_start: 0.8490 (mmm-85) cc_final: 0.8198 (mmm-85) REVERT: D 367 SER cc_start: 0.9313 (m) cc_final: 0.8898 (p) REVERT: D 380 LYS cc_start: 0.8897 (mmmm) cc_final: 0.8694 (mmmt) REVERT: D 408 GLU cc_start: 0.8071 (OUTLIER) cc_final: 0.7651 (pp20) REVERT: D 410 ARG cc_start: 0.8118 (ptp90) cc_final: 0.7595 (ptp-170) REVERT: D 450 ARG cc_start: 0.8334 (ptp-170) cc_final: 0.8103 (ptp90) REVERT: D 460 ASP cc_start: 0.8330 (t0) cc_final: 0.8036 (t0) REVERT: D 476 ARG cc_start: 0.7537 (ttt90) cc_final: 0.6978 (ttt90) REVERT: D 480 GLU cc_start: 0.7190 (OUTLIER) cc_final: 0.6315 (mp0) outliers start: 54 outliers final: 36 residues processed: 352 average time/residue: 0.1154 time to fit residues: 55.5554 Evaluate side-chains 339 residues out of total 1152 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 298 time to evaluate : 0.428 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 170 VAL Chi-restraints excluded: chain B residue 198 VAL Chi-restraints excluded: chain B residue 234 GLU Chi-restraints excluded: chain B residue 341 ASP Chi-restraints excluded: chain B residue 343 THR Chi-restraints excluded: chain B residue 356 LEU Chi-restraints excluded: chain B residue 444 LEU Chi-restraints excluded: chain A residue 209 ILE Chi-restraints excluded: chain A residue 225 THR Chi-restraints excluded: chain A residue 234 GLU Chi-restraints excluded: chain A residue 269 ILE Chi-restraints excluded: chain A residue 287 LEU Chi-restraints excluded: chain A residue 341 ASP Chi-restraints excluded: chain A residue 361 GLU Chi-restraints excluded: chain A residue 385 VAL Chi-restraints excluded: chain A residue 444 LEU Chi-restraints excluded: chain A residue 488 THR Chi-restraints excluded: chain C residue 219 ILE Chi-restraints excluded: chain C residue 234 GLU Chi-restraints excluded: chain C residue 274 ASP Chi-restraints excluded: chain C residue 300 LEU Chi-restraints excluded: chain C residue 341 ASP Chi-restraints excluded: chain C residue 343 THR Chi-restraints excluded: chain C residue 385 VAL Chi-restraints excluded: chain C residue 433 VAL Chi-restraints excluded: chain C residue 444 LEU Chi-restraints excluded: chain C residue 452 GLN Chi-restraints excluded: chain C residue 468 VAL Chi-restraints excluded: chain C residue 480 GLU Chi-restraints excluded: chain D residue 234 GLU Chi-restraints excluded: chain D residue 272 LEU Chi-restraints excluded: chain D residue 274 ASP Chi-restraints excluded: chain D residue 310 CYS Chi-restraints excluded: chain D residue 311 THR Chi-restraints excluded: chain D residue 343 THR Chi-restraints excluded: chain D residue 385 VAL Chi-restraints excluded: chain D residue 399 LEU Chi-restraints excluded: chain D residue 408 GLU Chi-restraints excluded: chain D residue 433 VAL Chi-restraints excluded: chain D residue 444 LEU Chi-restraints excluded: chain D residue 480 GLU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 118 optimal weight: 0.8980 chunk 70 optimal weight: 3.9990 chunk 7 optimal weight: 0.9990 chunk 40 optimal weight: 7.9990 chunk 55 optimal weight: 4.9990 chunk 17 optimal weight: 3.9990 chunk 4 optimal weight: 7.9990 chunk 41 optimal weight: 3.9990 chunk 90 optimal weight: 0.0040 chunk 12 optimal weight: 0.4980 chunk 39 optimal weight: 0.7980 overall best weight: 0.6394 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 251 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 251 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 177 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 251 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3670 r_free = 0.3670 target = 0.116726 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3491 r_free = 0.3491 target = 0.104844 restraints weight = 24967.657| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3537 r_free = 0.3537 target = 0.107989 restraints weight = 13916.355| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3567 r_free = 0.3567 target = 0.110038 restraints weight = 8790.253| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3594 r_free = 0.3594 target = 0.111745 restraints weight = 6118.691| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3610 r_free = 0.3610 target = 0.112863 restraints weight = 4316.599| |-----------------------------------------------------------------------------| r_work (final): 0.3625 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7736 moved from start: 0.4213 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 11032 Z= 0.140 Angle : 0.718 14.763 14968 Z= 0.353 Chirality : 0.044 0.183 1600 Planarity : 0.004 0.039 1972 Dihedral : 4.925 18.710 1484 Min Nonbonded Distance : 2.179 Molprobity Statistics. All-atom Clashscore : 17.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.33 % Favored : 94.67 % Rotamer: Outliers : 3.99 % Allowed : 23.87 % Favored : 72.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.04 (0.22), residues: 1332 helix: -0.05 (0.20), residues: 636 sheet: -1.94 (0.43), residues: 140 loop : -0.95 (0.26), residues: 556 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 260 TYR 0.026 0.002 TYR A 264 PHE 0.029 0.002 PHE B 261 TRP 0.047 0.003 TRP A 232 HIS 0.012 0.001 HIS A 215 Details of bonding type rmsd covalent geometry : bond 0.00329 (11032) covalent geometry : angle 0.71808 (14968) hydrogen bonds : bond 0.03865 ( 448) hydrogen bonds : angle 5.17817 ( 1308) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2664 Ramachandran restraints generated. 1332 Oldfield, 0 Emsley, 1332 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2664 Ramachandran restraints generated. 1332 Oldfield, 0 Emsley, 1332 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 369 residues out of total 1152 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 323 time to evaluate : 0.290 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 178 HIS cc_start: 0.7215 (m170) cc_final: 0.6943 (m170) REVERT: B 217 ASP cc_start: 0.7927 (m-30) cc_final: 0.7637 (m-30) REVERT: B 260 ARG cc_start: 0.8914 (ptp-110) cc_final: 0.8576 (ptp-110) REVERT: B 280 LYS cc_start: 0.8379 (mmmm) cc_final: 0.8009 (mmmm) REVERT: B 447 TYR cc_start: 0.7931 (t80) cc_final: 0.7517 (t80) REVERT: B 458 LYS cc_start: 0.7895 (ttpt) cc_final: 0.7688 (ttpp) REVERT: B 460 ASP cc_start: 0.8270 (t0) cc_final: 0.8035 (t0) REVERT: B 476 ARG cc_start: 0.7757 (ttt-90) cc_final: 0.7314 (ttt-90) REVERT: A 197 GLN cc_start: 0.8719 (tp40) cc_final: 0.8513 (tp40) REVERT: A 274 ASP cc_start: 0.8819 (OUTLIER) cc_final: 0.8137 (t0) REVERT: A 280 LYS cc_start: 0.8303 (mmmm) cc_final: 0.7828 (mmmm) REVERT: A 286 GLN cc_start: 0.7694 (pm20) cc_final: 0.7176 (pm20) REVERT: A 346 GLN cc_start: 0.8125 (tp-100) cc_final: 0.7911 (tp-100) REVERT: A 367 SER cc_start: 0.9287 (m) cc_final: 0.8976 (p) REVERT: A 443 LYS cc_start: 0.7914 (ttmt) cc_final: 0.7574 (ttmt) REVERT: A 447 TYR cc_start: 0.8215 (t80) cc_final: 0.7345 (t80) REVERT: A 450 ARG cc_start: 0.8414 (ptt90) cc_final: 0.8207 (ptt90) REVERT: A 460 ASP cc_start: 0.8241 (t0) cc_final: 0.7945 (t0) REVERT: A 476 ARG cc_start: 0.8047 (ttt90) cc_final: 0.7843 (ttt-90) REVERT: C 172 GLU cc_start: 0.7054 (mm-30) cc_final: 0.6626 (mm-30) REVERT: C 274 ASP cc_start: 0.8278 (OUTLIER) cc_final: 0.7315 (t0) REVERT: C 286 GLN cc_start: 0.8009 (pm20) cc_final: 0.7646 (pm20) REVERT: C 361 GLU cc_start: 0.8563 (pm20) cc_final: 0.8085 (pm20) REVERT: C 473 GLN cc_start: 0.8238 (tp-100) cc_final: 0.7820 (tp40) REVERT: C 476 ARG cc_start: 0.7870 (ttt90) cc_final: 0.7363 (ttt90) REVERT: C 480 GLU cc_start: 0.7510 (OUTLIER) cc_final: 0.6634 (mp0) REVERT: D 178 HIS cc_start: 0.7250 (m170) cc_final: 0.6879 (m170) REVERT: D 197 GLN cc_start: 0.8742 (tp40) cc_final: 0.8342 (tp40) REVERT: D 274 ASP cc_start: 0.8487 (OUTLIER) cc_final: 0.8108 (t0) REVERT: D 280 LYS cc_start: 0.8383 (mmtt) cc_final: 0.8102 (mtmt) REVERT: D 286 GLN cc_start: 0.7841 (pm20) cc_final: 0.7327 (pm20) REVERT: D 342 ARG cc_start: 0.8511 (mmm-85) cc_final: 0.8218 (mmm-85) REVERT: D 367 SER cc_start: 0.9328 (m) cc_final: 0.8926 (p) REVERT: D 443 LYS cc_start: 0.7835 (ttmt) cc_final: 0.7594 (ttmt) REVERT: D 450 ARG cc_start: 0.8306 (ptp-170) cc_final: 0.8024 (ptp-170) REVERT: D 460 ASP cc_start: 0.8353 (t0) cc_final: 0.8024 (t0) REVERT: D 476 ARG cc_start: 0.7397 (ttt90) cc_final: 0.6861 (ttt90) REVERT: D 480 GLU cc_start: 0.7202 (OUTLIER) cc_final: 0.6322 (mp0) outliers start: 46 outliers final: 31 residues processed: 340 average time/residue: 0.1110 time to fit residues: 51.7924 Evaluate side-chains 330 residues out of total 1152 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 294 time to evaluate : 0.387 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 170 VAL Chi-restraints excluded: chain B residue 198 VAL Chi-restraints excluded: chain B residue 234 GLU Chi-restraints excluded: chain B residue 341 ASP Chi-restraints excluded: chain B residue 343 THR Chi-restraints excluded: chain B residue 356 LEU Chi-restraints excluded: chain B residue 444 LEU Chi-restraints excluded: chain A residue 209 ILE Chi-restraints excluded: chain A residue 274 ASP Chi-restraints excluded: chain A residue 287 LEU Chi-restraints excluded: chain A residue 341 ASP Chi-restraints excluded: chain A residue 361 GLU Chi-restraints excluded: chain A residue 385 VAL Chi-restraints excluded: chain A residue 444 LEU Chi-restraints excluded: chain A residue 488 THR Chi-restraints excluded: chain C residue 219 ILE Chi-restraints excluded: chain C residue 274 ASP Chi-restraints excluded: chain C residue 300 LEU Chi-restraints excluded: chain C residue 343 THR Chi-restraints excluded: chain C residue 385 VAL Chi-restraints excluded: chain C residue 433 VAL Chi-restraints excluded: chain C residue 444 LEU Chi-restraints excluded: chain C residue 452 GLN Chi-restraints excluded: chain C residue 468 VAL Chi-restraints excluded: chain C residue 480 GLU Chi-restraints excluded: chain D residue 272 LEU Chi-restraints excluded: chain D residue 274 ASP Chi-restraints excluded: chain D residue 283 THR Chi-restraints excluded: chain D residue 310 CYS Chi-restraints excluded: chain D residue 311 THR Chi-restraints excluded: chain D residue 341 ASP Chi-restraints excluded: chain D residue 343 THR Chi-restraints excluded: chain D residue 385 VAL Chi-restraints excluded: chain D residue 433 VAL Chi-restraints excluded: chain D residue 444 LEU Chi-restraints excluded: chain D residue 480 GLU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 71 optimal weight: 0.9980 chunk 131 optimal weight: 4.9990 chunk 120 optimal weight: 6.9990 chunk 108 optimal weight: 1.9990 chunk 87 optimal weight: 0.9990 chunk 49 optimal weight: 0.0970 chunk 51 optimal weight: 1.9990 chunk 68 optimal weight: 6.9990 chunk 103 optimal weight: 4.9990 chunk 30 optimal weight: 4.9990 chunk 58 optimal weight: 0.9980 overall best weight: 1.0182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 215 HIS ** B 286 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 178 HIS ** A 251 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 251 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 177 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 251 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3635 r_free = 0.3635 target = 0.114227 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3453 r_free = 0.3453 target = 0.102448 restraints weight = 25206.256| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3500 r_free = 0.3500 target = 0.105590 restraints weight = 14005.401| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3529 r_free = 0.3529 target = 0.107503 restraints weight = 8768.362| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3556 r_free = 0.3556 target = 0.109190 restraints weight = 6190.646| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3572 r_free = 0.3572 target = 0.110299 restraints weight = 4382.641| |-----------------------------------------------------------------------------| r_work (final): 0.3586 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7771 moved from start: 0.4346 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.060 11032 Z= 0.162 Angle : 0.748 14.094 14968 Z= 0.367 Chirality : 0.046 0.263 1600 Planarity : 0.004 0.039 1972 Dihedral : 4.985 18.512 1484 Min Nonbonded Distance : 2.152 Molprobity Statistics. All-atom Clashscore : 19.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.11 % Favored : 94.89 % Rotamer: Outliers : 3.91 % Allowed : 25.78 % Favored : 70.31 % 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: -0.98 (0.22), residues: 1332 helix: -0.11 (0.20), residues: 640 sheet: -1.58 (0.44), residues: 132 loop : -0.88 (0.26), residues: 560 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 214 TYR 0.027 0.002 TYR D 213 PHE 0.027 0.002 PHE B 261 TRP 0.034 0.003 TRP B 232 HIS 0.011 0.001 HIS A 215 Details of bonding type rmsd covalent geometry : bond 0.00385 (11032) covalent geometry : angle 0.74841 (14968) hydrogen bonds : bond 0.03985 ( 448) hydrogen bonds : angle 5.25469 ( 1308) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2664 Ramachandran restraints generated. 1332 Oldfield, 0 Emsley, 1332 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2664 Ramachandran restraints generated. 1332 Oldfield, 0 Emsley, 1332 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 354 residues out of total 1152 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 309 time to evaluate : 0.315 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 178 HIS cc_start: 0.7257 (m170) cc_final: 0.7032 (m170) REVERT: B 217 ASP cc_start: 0.7939 (m-30) cc_final: 0.7661 (m-30) REVERT: B 280 LYS cc_start: 0.8338 (mmmm) cc_final: 0.7845 (mmmm) REVERT: B 447 TYR cc_start: 0.7982 (t80) cc_final: 0.7631 (t80) REVERT: B 458 LYS cc_start: 0.7968 (ttpt) cc_final: 0.7696 (ttpp) REVERT: B 460 ASP cc_start: 0.8285 (t0) cc_final: 0.8031 (t0) REVERT: B 476 ARG cc_start: 0.7752 (ttt-90) cc_final: 0.7335 (ttt-90) REVERT: A 178 HIS cc_start: 0.7554 (m170) cc_final: 0.7176 (m170) REVERT: A 274 ASP cc_start: 0.8783 (OUTLIER) cc_final: 0.8101 (t0) REVERT: A 280 LYS cc_start: 0.8319 (mmmm) cc_final: 0.7851 (mmmm) REVERT: A 286 GLN cc_start: 0.7786 (pm20) cc_final: 0.7272 (pm20) REVERT: A 367 SER cc_start: 0.9292 (m) cc_final: 0.8964 (p) REVERT: A 443 LYS cc_start: 0.7944 (ttmt) cc_final: 0.7611 (ttmt) REVERT: A 447 TYR cc_start: 0.8230 (t80) cc_final: 0.7366 (t80) REVERT: A 450 ARG cc_start: 0.8421 (ptt90) cc_final: 0.8207 (ptt90) REVERT: A 460 ASP cc_start: 0.8278 (t0) cc_final: 0.7866 (t0) REVERT: C 172 GLU cc_start: 0.7092 (mm-30) cc_final: 0.6718 (mm-30) REVERT: C 274 ASP cc_start: 0.8290 (OUTLIER) cc_final: 0.7291 (t0) REVERT: C 286 GLN cc_start: 0.8184 (pm20) cc_final: 0.7853 (pm20) REVERT: C 343 THR cc_start: 0.8795 (OUTLIER) cc_final: 0.8550 (t) REVERT: C 361 GLU cc_start: 0.8534 (pm20) cc_final: 0.8070 (pm20) REVERT: C 473 GLN cc_start: 0.8266 (tp-100) cc_final: 0.7893 (tp40) REVERT: C 476 ARG cc_start: 0.7823 (ttt90) cc_final: 0.7341 (ttt90) REVERT: C 480 GLU cc_start: 0.7476 (OUTLIER) cc_final: 0.6607 (mp0) REVERT: D 197 GLN cc_start: 0.8737 (tp40) cc_final: 0.8525 (tp40) REVERT: D 274 ASP cc_start: 0.8328 (OUTLIER) cc_final: 0.7783 (t0) REVERT: D 280 LYS cc_start: 0.8412 (mmtt) cc_final: 0.8124 (mtmt) REVERT: D 286 GLN cc_start: 0.7940 (pm20) cc_final: 0.7427 (pm20) REVERT: D 342 ARG cc_start: 0.8503 (mmm-85) cc_final: 0.8205 (mmm160) REVERT: D 367 SER cc_start: 0.9345 (m) cc_final: 0.8980 (p) REVERT: D 450 ARG cc_start: 0.8266 (ptp-170) cc_final: 0.8038 (ptp90) REVERT: D 460 ASP cc_start: 0.8395 (t0) cc_final: 0.8119 (t0) REVERT: D 476 ARG cc_start: 0.7408 (ttt90) cc_final: 0.6877 (ttt90) REVERT: D 480 GLU cc_start: 0.7199 (OUTLIER) cc_final: 0.6341 (mp0) outliers start: 45 outliers final: 31 residues processed: 327 average time/residue: 0.1167 time to fit residues: 51.6264 Evaluate side-chains 327 residues out of total 1152 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 290 time to evaluate : 0.326 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 170 VAL Chi-restraints excluded: chain B residue 198 VAL Chi-restraints excluded: chain B residue 234 GLU Chi-restraints excluded: chain B residue 341 ASP Chi-restraints excluded: chain B residue 343 THR Chi-restraints excluded: chain B residue 356 LEU Chi-restraints excluded: chain B residue 399 LEU Chi-restraints excluded: chain B residue 433 VAL Chi-restraints excluded: chain B residue 444 LEU Chi-restraints excluded: chain A residue 274 ASP Chi-restraints excluded: chain A residue 287 LEU Chi-restraints excluded: chain A residue 341 ASP Chi-restraints excluded: chain A residue 361 GLU Chi-restraints excluded: chain A residue 385 VAL Chi-restraints excluded: chain A residue 444 LEU Chi-restraints excluded: chain A residue 488 THR Chi-restraints excluded: chain C residue 219 ILE Chi-restraints excluded: chain C residue 274 ASP Chi-restraints excluded: chain C residue 300 LEU Chi-restraints excluded: chain C residue 343 THR Chi-restraints excluded: chain C residue 385 VAL Chi-restraints excluded: chain C residue 433 VAL Chi-restraints excluded: chain C residue 444 LEU Chi-restraints excluded: chain C residue 452 GLN Chi-restraints excluded: chain C residue 468 VAL Chi-restraints excluded: chain C residue 480 GLU Chi-restraints excluded: chain D residue 234 GLU Chi-restraints excluded: chain D residue 272 LEU Chi-restraints excluded: chain D residue 274 ASP Chi-restraints excluded: chain D residue 283 THR Chi-restraints excluded: chain D residue 310 CYS Chi-restraints excluded: chain D residue 311 THR Chi-restraints excluded: chain D residue 341 ASP Chi-restraints excluded: chain D residue 343 THR Chi-restraints excluded: chain D residue 433 VAL Chi-restraints excluded: chain D residue 444 LEU Chi-restraints excluded: chain D residue 480 GLU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 48 optimal weight: 0.9990 chunk 83 optimal weight: 0.5980 chunk 58 optimal weight: 0.9980 chunk 46 optimal weight: 2.9990 chunk 63 optimal weight: 4.9990 chunk 47 optimal weight: 0.9980 chunk 32 optimal weight: 0.6980 chunk 102 optimal weight: 0.6980 chunk 71 optimal weight: 1.9990 chunk 73 optimal weight: 0.9980 chunk 110 optimal weight: 0.7980 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 251 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 251 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 177 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 251 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3650 r_free = 0.3650 target = 0.115393 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3472 r_free = 0.3472 target = 0.103623 restraints weight = 25139.845| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3517 r_free = 0.3517 target = 0.106714 restraints weight = 13992.983| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3546 r_free = 0.3546 target = 0.108686 restraints weight = 8746.919| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3571 r_free = 0.3571 target = 0.110357 restraints weight = 6161.532| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3588 r_free = 0.3588 target = 0.111463 restraints weight = 4375.454| |-----------------------------------------------------------------------------| r_work (final): 0.3603 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7753 moved from start: 0.4499 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 11032 Z= 0.154 Angle : 0.774 13.670 14968 Z= 0.380 Chirality : 0.046 0.234 1600 Planarity : 0.004 0.040 1972 Dihedral : 5.035 20.400 1484 Min Nonbonded Distance : 2.179 Molprobity Statistics. All-atom Clashscore : 18.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.80 % Favored : 95.20 % Rotamer: Outliers : 3.65 % Allowed : 26.65 % Favored : 69.70 % 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: -1.06 (0.23), residues: 1332 helix: -0.13 (0.20), residues: 636 sheet: -1.98 (0.42), residues: 140 loop : -0.87 (0.27), residues: 556 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 202 TYR 0.025 0.002 TYR A 264 PHE 0.028 0.003 PHE C 255 TRP 0.039 0.003 TRP A 232 HIS 0.010 0.001 HIS A 215 Details of bonding type rmsd covalent geometry : bond 0.00362 (11032) covalent geometry : angle 0.77442 (14968) hydrogen bonds : bond 0.04043 ( 448) hydrogen bonds : angle 5.28753 ( 1308) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2664 Ramachandran restraints generated. 1332 Oldfield, 0 Emsley, 1332 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2664 Ramachandran restraints generated. 1332 Oldfield, 0 Emsley, 1332 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 344 residues out of total 1152 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 302 time to evaluate : 0.321 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 178 HIS cc_start: 0.7275 (m170) cc_final: 0.7040 (m170) REVERT: B 217 ASP cc_start: 0.7906 (m-30) cc_final: 0.7634 (m-30) REVERT: B 260 ARG cc_start: 0.8891 (ptp-110) cc_final: 0.8602 (ptp-110) REVERT: B 280 LYS cc_start: 0.8316 (mmmm) cc_final: 0.7807 (mmmm) REVERT: B 447 TYR cc_start: 0.7924 (t80) cc_final: 0.7593 (t80) REVERT: B 458 LYS cc_start: 0.7870 (ttpt) cc_final: 0.7594 (ttpp) REVERT: B 460 ASP cc_start: 0.8280 (t0) cc_final: 0.8004 (t0) REVERT: B 476 ARG cc_start: 0.7820 (ttt-90) cc_final: 0.7366 (ttt-90) REVERT: A 280 LYS cc_start: 0.8301 (mmmm) cc_final: 0.7866 (mmmm) REVERT: A 286 GLN cc_start: 0.7921 (pm20) cc_final: 0.7401 (pm20) REVERT: A 367 SER cc_start: 0.9323 (m) cc_final: 0.8971 (p) REVERT: A 443 LYS cc_start: 0.7948 (ttmt) cc_final: 0.7519 (ttmt) REVERT: A 447 TYR cc_start: 0.8185 (t80) cc_final: 0.7285 (t80) REVERT: A 450 ARG cc_start: 0.8428 (ptt90) cc_final: 0.8200 (ptt90) REVERT: A 460 ASP cc_start: 0.8253 (t0) cc_final: 0.7873 (t0) REVERT: A 484 ASP cc_start: 0.7936 (m-30) cc_final: 0.7583 (m-30) REVERT: C 172 GLU cc_start: 0.7080 (mm-30) cc_final: 0.6674 (mm-30) REVERT: C 274 ASP cc_start: 0.8310 (OUTLIER) cc_final: 0.7334 (t0) REVERT: C 286 GLN cc_start: 0.8265 (pm20) cc_final: 0.7850 (pm20) REVERT: C 343 THR cc_start: 0.8762 (OUTLIER) cc_final: 0.8528 (t) REVERT: C 361 GLU cc_start: 0.8545 (pm20) cc_final: 0.8068 (pm20) REVERT: C 473 GLN cc_start: 0.8269 (tp-100) cc_final: 0.7890 (tp40) REVERT: C 476 ARG cc_start: 0.7797 (ttt90) cc_final: 0.7315 (ttt90) REVERT: C 480 GLU cc_start: 0.7464 (OUTLIER) cc_final: 0.6569 (mp0) REVERT: D 274 ASP cc_start: 0.8310 (OUTLIER) cc_final: 0.7712 (t0) REVERT: D 280 LYS cc_start: 0.8380 (mmtt) cc_final: 0.8060 (mtmt) REVERT: D 286 GLN cc_start: 0.7911 (pm20) cc_final: 0.7392 (pm20) REVERT: D 342 ARG cc_start: 0.8486 (mmm-85) cc_final: 0.8195 (mmm-85) REVERT: D 367 SER cc_start: 0.9342 (m) cc_final: 0.8975 (p) REVERT: D 450 ARG cc_start: 0.8266 (ptp-170) cc_final: 0.8039 (ptp90) REVERT: D 460 ASP cc_start: 0.8411 (t0) cc_final: 0.8133 (t0) REVERT: D 476 ARG cc_start: 0.7434 (ttt90) cc_final: 0.6749 (ttt90) REVERT: D 480 GLU cc_start: 0.7204 (OUTLIER) cc_final: 0.6318 (mp0) outliers start: 42 outliers final: 35 residues processed: 315 average time/residue: 0.1117 time to fit residues: 47.9265 Evaluate side-chains 332 residues out of total 1152 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 292 time to evaluate : 0.388 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 170 VAL Chi-restraints excluded: chain B residue 234 GLU Chi-restraints excluded: chain B residue 341 ASP Chi-restraints excluded: chain B residue 343 THR Chi-restraints excluded: chain B residue 356 LEU Chi-restraints excluded: chain B residue 399 LEU Chi-restraints excluded: chain B residue 433 VAL Chi-restraints excluded: chain B residue 444 LEU Chi-restraints excluded: chain A residue 215 HIS Chi-restraints excluded: chain A residue 222 VAL Chi-restraints excluded: chain A residue 274 ASP Chi-restraints excluded: chain A residue 287 LEU Chi-restraints excluded: chain A residue 341 ASP Chi-restraints excluded: chain A residue 361 GLU Chi-restraints excluded: chain A residue 385 VAL Chi-restraints excluded: chain A residue 444 LEU Chi-restraints excluded: chain A residue 488 THR Chi-restraints excluded: chain C residue 219 ILE Chi-restraints excluded: chain C residue 274 ASP Chi-restraints excluded: chain C residue 300 LEU Chi-restraints excluded: chain C residue 343 THR Chi-restraints excluded: chain C residue 385 VAL Chi-restraints excluded: chain C residue 399 LEU Chi-restraints excluded: chain C residue 433 VAL Chi-restraints excluded: chain C residue 444 LEU Chi-restraints excluded: chain C residue 452 GLN Chi-restraints excluded: chain C residue 468 VAL Chi-restraints excluded: chain C residue 480 GLU Chi-restraints excluded: chain D residue 234 GLU Chi-restraints excluded: chain D residue 274 ASP Chi-restraints excluded: chain D residue 283 THR Chi-restraints excluded: chain D residue 310 CYS Chi-restraints excluded: chain D residue 311 THR Chi-restraints excluded: chain D residue 343 THR Chi-restraints excluded: chain D residue 385 VAL Chi-restraints excluded: chain D residue 399 LEU Chi-restraints excluded: chain D residue 433 VAL Chi-restraints excluded: chain D residue 444 LEU Chi-restraints excluded: chain D residue 451 ILE Chi-restraints excluded: chain D residue 480 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 113 optimal weight: 3.9990 chunk 59 optimal weight: 1.9990 chunk 75 optimal weight: 0.8980 chunk 87 optimal weight: 2.9990 chunk 93 optimal weight: 0.4980 chunk 115 optimal weight: 1.9990 chunk 61 optimal weight: 5.9990 chunk 124 optimal weight: 0.9980 chunk 62 optimal weight: 0.8980 chunk 37 optimal weight: 0.9980 chunk 94 optimal weight: 0.9990 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 177 HIS B 268 ASN A 178 HIS ** A 251 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 191 HIS ** C 251 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 177 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 251 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 286 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3647 r_free = 0.3647 target = 0.114832 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3468 r_free = 0.3468 target = 0.103044 restraints weight = 25171.878| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3513 r_free = 0.3513 target = 0.106057 restraints weight = 14058.572| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3544 r_free = 0.3544 target = 0.108114 restraints weight = 8971.004| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3566 r_free = 0.3566 target = 0.109609 restraints weight = 6226.544| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3583 r_free = 0.3583 target = 0.110741 restraints weight = 4544.091| |-----------------------------------------------------------------------------| r_work (final): 0.3596 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7763 moved from start: 0.4634 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 11032 Z= 0.158 Angle : 0.773 15.650 14968 Z= 0.379 Chirality : 0.046 0.242 1600 Planarity : 0.004 0.042 1972 Dihedral : 5.037 22.461 1484 Min Nonbonded Distance : 2.161 Molprobity Statistics. All-atom Clashscore : 19.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.63 % Favored : 94.37 % Rotamer: Outliers : 3.91 % Allowed : 26.91 % Favored : 69.18 % 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: -1.08 (0.23), residues: 1332 helix: -0.17 (0.20), residues: 636 sheet: -2.02 (0.42), residues: 140 loop : -0.83 (0.27), residues: 556 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG C 260 TYR 0.026 0.002 TYR A 264 PHE 0.028 0.003 PHE C 308 TRP 0.040 0.004 TRP A 232 HIS 0.009 0.001 HIS A 215 Details of bonding type rmsd covalent geometry : bond 0.00373 (11032) covalent geometry : angle 0.77259 (14968) hydrogen bonds : bond 0.04048 ( 448) hydrogen bonds : angle 5.25302 ( 1308) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2664 Ramachandran restraints generated. 1332 Oldfield, 0 Emsley, 1332 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2664 Ramachandran restraints generated. 1332 Oldfield, 0 Emsley, 1332 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 355 residues out of total 1152 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 310 time to evaluate : 0.379 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 178 HIS cc_start: 0.7310 (m170) cc_final: 0.7077 (m170) REVERT: B 217 ASP cc_start: 0.7896 (m-30) cc_final: 0.7614 (m-30) REVERT: B 260 ARG cc_start: 0.8896 (ptp-110) cc_final: 0.8579 (ptp-110) REVERT: B 280 LYS cc_start: 0.8395 (mmmm) cc_final: 0.7904 (mmmm) REVERT: B 447 TYR cc_start: 0.7937 (t80) cc_final: 0.7669 (t80) REVERT: B 458 LYS cc_start: 0.7877 (ttpt) cc_final: 0.7597 (ttpp) REVERT: B 460 ASP cc_start: 0.8287 (t0) cc_final: 0.8043 (t0) REVERT: B 476 ARG cc_start: 0.7811 (ttt-90) cc_final: 0.7374 (ttt-90) REVERT: A 274 ASP cc_start: 0.8473 (OUTLIER) cc_final: 0.7829 (t0) REVERT: A 280 LYS cc_start: 0.8304 (mmmm) cc_final: 0.7847 (mmmm) REVERT: A 286 GLN cc_start: 0.7988 (pm20) cc_final: 0.7438 (pm20) REVERT: A 367 SER cc_start: 0.9296 (m) cc_final: 0.8928 (p) REVERT: A 443 LYS cc_start: 0.7966 (ttmt) cc_final: 0.7531 (ttmt) REVERT: A 447 TYR cc_start: 0.8222 (t80) cc_final: 0.7171 (t80) REVERT: A 460 ASP cc_start: 0.8238 (t0) cc_final: 0.7896 (t0) REVERT: A 484 ASP cc_start: 0.7867 (m-30) cc_final: 0.7521 (m-30) REVERT: C 172 GLU cc_start: 0.7153 (mm-30) cc_final: 0.6783 (mm-30) REVERT: C 274 ASP cc_start: 0.8387 (OUTLIER) cc_final: 0.7443 (t0) REVERT: C 286 GLN cc_start: 0.8336 (pm20) cc_final: 0.7922 (pm20) REVERT: C 343 THR cc_start: 0.8745 (OUTLIER) cc_final: 0.8501 (t) REVERT: C 361 GLU cc_start: 0.8504 (pm20) cc_final: 0.8042 (pm20) REVERT: C 473 GLN cc_start: 0.8245 (tp-100) cc_final: 0.7861 (tp40) REVERT: C 476 ARG cc_start: 0.7788 (ttt90) cc_final: 0.7293 (ttt90) REVERT: C 480 GLU cc_start: 0.7476 (OUTLIER) cc_final: 0.6543 (mp0) REVERT: D 177 HIS cc_start: 0.6172 (m90) cc_final: 0.5972 (m-70) REVERT: D 178 HIS cc_start: 0.7177 (m170) cc_final: 0.6657 (m170) REVERT: D 223 GLU cc_start: 0.8670 (mp0) cc_final: 0.8274 (mp0) REVERT: D 274 ASP cc_start: 0.8284 (OUTLIER) cc_final: 0.7699 (t0) REVERT: D 280 LYS cc_start: 0.8358 (mmtt) cc_final: 0.8045 (mttt) REVERT: D 286 GLN cc_start: 0.7932 (pm20) cc_final: 0.7426 (pm20) REVERT: D 342 ARG cc_start: 0.8467 (mmm-85) cc_final: 0.8220 (mmm-85) REVERT: D 367 SER cc_start: 0.9359 (m) cc_final: 0.9026 (p) REVERT: D 450 ARG cc_start: 0.8265 (ptp-170) cc_final: 0.8002 (ptp-170) REVERT: D 460 ASP cc_start: 0.8419 (t0) cc_final: 0.8108 (t0) REVERT: D 476 ARG cc_start: 0.7423 (ttt90) cc_final: 0.6782 (ttt90) REVERT: D 480 GLU cc_start: 0.7183 (OUTLIER) cc_final: 0.6311 (mp0) outliers start: 45 outliers final: 33 residues processed: 326 average time/residue: 0.1132 time to fit residues: 50.5691 Evaluate side-chains 332 residues out of total 1152 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 293 time to evaluate : 0.332 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 170 VAL Chi-restraints excluded: chain B residue 173 LEU Chi-restraints excluded: chain B residue 234 GLU Chi-restraints excluded: chain B residue 341 ASP Chi-restraints excluded: chain B residue 343 THR Chi-restraints excluded: chain B residue 356 LEU Chi-restraints excluded: chain B residue 399 LEU Chi-restraints excluded: chain B residue 433 VAL Chi-restraints excluded: chain B residue 444 LEU Chi-restraints excluded: chain A residue 215 HIS Chi-restraints excluded: chain A residue 274 ASP Chi-restraints excluded: chain A residue 287 LEU Chi-restraints excluded: chain A residue 341 ASP Chi-restraints excluded: chain A residue 361 GLU Chi-restraints excluded: chain A residue 385 VAL Chi-restraints excluded: chain A residue 444 LEU Chi-restraints excluded: chain A residue 488 THR Chi-restraints excluded: chain C residue 219 ILE Chi-restraints excluded: chain C residue 274 ASP Chi-restraints excluded: chain C residue 300 LEU Chi-restraints excluded: chain C residue 343 THR Chi-restraints excluded: chain C residue 385 VAL Chi-restraints excluded: chain C residue 399 LEU Chi-restraints excluded: chain C residue 433 VAL Chi-restraints excluded: chain C residue 444 LEU Chi-restraints excluded: chain C residue 452 GLN Chi-restraints excluded: chain C residue 468 VAL Chi-restraints excluded: chain C residue 480 GLU Chi-restraints excluded: chain D residue 234 GLU Chi-restraints excluded: chain D residue 274 ASP Chi-restraints excluded: chain D residue 283 THR Chi-restraints excluded: chain D residue 311 THR Chi-restraints excluded: chain D residue 343 THR Chi-restraints excluded: chain D residue 385 VAL Chi-restraints excluded: chain D residue 399 LEU Chi-restraints excluded: chain D residue 433 VAL Chi-restraints excluded: chain D residue 444 LEU Chi-restraints excluded: chain D residue 451 ILE Chi-restraints excluded: chain D residue 480 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 78 optimal weight: 0.9980 chunk 54 optimal weight: 5.9990 chunk 114 optimal weight: 0.2980 chunk 99 optimal weight: 4.9990 chunk 107 optimal weight: 1.9990 chunk 110 optimal weight: 0.6980 chunk 60 optimal weight: 2.9990 chunk 67 optimal weight: 7.9990 chunk 51 optimal weight: 0.5980 chunk 65 optimal weight: 0.9990 chunk 124 optimal weight: 0.8980 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 177 HIS A 178 HIS ** A 251 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 251 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 483 GLN ** D 177 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 251 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 286 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3661 r_free = 0.3661 target = 0.116224 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3482 r_free = 0.3482 target = 0.104418 restraints weight = 25513.990| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3527 r_free = 0.3527 target = 0.107453 restraints weight = 14198.398| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3556 r_free = 0.3556 target = 0.109403 restraints weight = 9014.871| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3583 r_free = 0.3583 target = 0.111157 restraints weight = 6340.215| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3595 r_free = 0.3595 target = 0.111996 restraints weight = 4487.942| |-----------------------------------------------------------------------------| r_work (final): 0.3608 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7746 moved from start: 0.4781 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 11032 Z= 0.153 Angle : 0.785 15.336 14968 Z= 0.385 Chirality : 0.046 0.234 1600 Planarity : 0.004 0.049 1972 Dihedral : 5.067 22.387 1484 Min Nonbonded Distance : 2.181 Molprobity Statistics. All-atom Clashscore : 19.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.71 % Favored : 94.29 % Rotamer: Outliers : 3.56 % Allowed : 27.26 % Favored : 69.18 % 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: -1.19 (0.23), residues: 1332 helix: -0.29 (0.19), residues: 660 sheet: -2.08 (0.42), residues: 140 loop : -0.85 (0.27), residues: 532 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 260 TYR 0.036 0.002 TYR A 264 PHE 0.028 0.003 PHE C 308 TRP 0.040 0.004 TRP A 232 HIS 0.008 0.001 HIS A 215 Details of bonding type rmsd covalent geometry : bond 0.00362 (11032) covalent geometry : angle 0.78467 (14968) hydrogen bonds : bond 0.04076 ( 448) hydrogen bonds : angle 5.25776 ( 1308) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1681.11 seconds wall clock time: 30 minutes 1.67 seconds (1801.67 seconds total)