Starting phenix.real_space_refine on Mon Jul 28 20:38:29 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6zzu_11587/07_2025/6zzu_11587.cif Found real_map, /net/cci-nas-00/data/ceres_data/6zzu_11587/07_2025/6zzu_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/6zzu_11587/07_2025/6zzu_11587.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6zzu_11587/07_2025/6zzu_11587.map" model { file = "/net/cci-nas-00/data/ceres_data/6zzu_11587/07_2025/6zzu_11587.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6zzu_11587/07_2025/6zzu_11587.cif" } resolution = 3.5 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.010 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): 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/modules/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: 7.14, per 1000 atoms: 0.66 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: 2.55 Conformation dependent library (CDL) restraints added in 1.6 seconds 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: 1.03 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: 3.25 Time building geometry restraints manager: 2.98 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: 0.03 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: 0.410 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.450 Check model and map are aligned: 0.100 Set scattering table: 0.110 Process input model: 27.420 Find NCS groups from input model: 0.510 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.960 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 32.020 ------------------------------------------------------------------------------- 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.89 (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 TRP 0.009 0.002 TRP A 165 HIS 0.007 0.002 HIS A 251 PHE 0.037 0.003 PHE B 285 TYR 0.013 0.002 TYR D 199 ARG 0.008 0.001 ARG D 168 Details of bonding type rmsd hydrogen bonds : bond 0.25181 ( 448) hydrogen bonds : angle 9.60086 ( 1308) covalent geometry : bond 0.00531 (11032) covalent geometry : angle 0.95944 (14968) *********************** 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 : 1.242 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: symmetry clash REVERT: B 174 ASP cc_start: 0.7459 (m-30) cc_final: 0.6935 (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: 0.8880 (mmt) REVERT: B 460 ASP cc_start: 0.8569 (t70) cc_final: 0.8185 (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: 0.8077 (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: 0.8254 (tp-100) REVERT: A 214 ARG cc_start: 0.7771 (mmm160) cc_final: 0.7420 (mmm160) REVERT: A 215 HIS cc_start: 0.8286 (t70) cc_final: 0.7803 (t70) REVERT: A 240 LYS cc_start: 0.8437 (tttp) cc_final: 0.8178 (tttm) REVERT: A 280 LYS cc_start: 0.8471 (mmmm) cc_final: 0.8033 (mmmm) REVERT: A 286 GLN cc_start: 0.7930 (pm20) cc_final: 0.7637 (pm20) REVERT: A 321 MET cc_start: 0.8974 (mmt) cc_final: 0.8690 (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: 0.7247 (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: 0.8785 (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: 0.7624 (ttt-90) REVERT: C 172 GLU cc_start: 0.7479 (mm-30) cc_final: 0.7055 (mm-30) REVERT: C 214 ARG cc_start: 0.8185 (tpp-160) cc_final: 0.7959 (tpp-160) REVERT: C 312 GLN cc_start: 0.8393 (mt0) cc_final: 0.8192 (mt0) REVERT: C 343 THR cc_start: 0.8596 (p) cc_final: 0.8353 (t) REVERT: C 443 LYS cc_start: 0.7902 (ttmm) cc_final: 0.7449 (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: 0.7107 (mp0) REVERT: D 172 GLU cc_start: 0.7539 (mm-30) cc_final: 0.6990 (mm-30) REVERT: D 197 GLN cc_start: 0.8763 (tp40) cc_final: 0.8392 (tp40) REVERT: D 224 TYR cc_start: 0.8682 (m-80) cc_final: 0.8434 (m-80) REVERT: D 243 TYR cc_start: 0.7608 (m-10) cc_final: 0.7342 (m-10) REVERT: D 268 ASN cc_start: 0.9218 (t0) cc_final: 0.8910 (t0) REVERT: D 278 PHE cc_start: 0.8013 (t80) cc_final: 0.7406 (t80) REVERT: D 286 GLN cc_start: 0.7853 (pm20) cc_final: 0.7524 (pm20) REVERT: D 321 MET cc_start: 0.9063 (mmt) cc_final: 0.8689 (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: 0.7542 (ptp90) REVERT: D 460 ASP cc_start: 0.8120 (t0) cc_final: 0.7836 (t0) outliers start: 2 outliers final: 0 residues processed: 449 average time/residue: 0.2834 time to fit residues: 168.6377 Evaluate side-chains 332 residues out of total 1152 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 331 time to evaluate : 1.295 ------------------------------------------------------------------------------- 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 111 optimal weight: 0.9990 chunk 100 optimal weight: 2.9990 chunk 55 optimal weight: 0.9980 chunk 34 optimal weight: 1.9990 chunk 67 optimal weight: 5.9990 chunk 53 optimal weight: 4.9990 chunk 103 optimal weight: 4.9990 chunk 40 optimal weight: 0.8980 chunk 62 optimal weight: 3.9990 chunk 77 optimal weight: 0.9990 chunk 119 optimal weight: 4.9990 overall best weight: 1.1786 ------------------------------------------------------------------------------- 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 ** both conformations clash, **PLEASE CHECK MANUALLY** C 425 GLN ** C 473 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 483 GLN D 178 HIS D 201 GLN D 246 HIS D 268 ASN 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 = 0.3574 r_free = 0.3574 target = 0.109751 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3407 r_free = 0.3407 target = 0.098700 restraints weight = 25537.100| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.3450 r_free = 0.3450 target = 0.101601 restraints weight = 13787.620| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3484 r_free = 0.3484 target = 0.103795 restraints weight = 8571.183| |-----------------------------------------------------------------------------| r_work (final): 0.3485 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7835 moved from start: 0.2396 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 11032 Z= 0.177 Angle : 0.695 7.278 14968 Z= 0.360 Chirality : 0.043 0.168 1600 Planarity : 0.005 0.072 1972 Dihedral : 5.909 51.148 1486 Min Nonbonded Distance : 2.086 Molprobity Statistics. All-atom Clashscore : 18.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.41 % Favored : 94.59 % Rotamer: Outliers : 2.86 % Allowed : 17.88 % Favored : 79.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.11 (0.20), residues: 1332 helix: -2.11 (0.16), residues: 664 sheet: -2.35 (0.41), residues: 136 loop : -1.64 (0.27), residues: 532 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.003 TRP B 371 HIS 0.008 0.001 HIS D 215 PHE 0.024 0.002 PHE C 344 TYR 0.017 0.002 TYR B 370 ARG 0.014 0.001 ARG C 168 Details of bonding type rmsd hydrogen bonds : bond 0.04867 ( 448) hydrogen bonds : angle 5.87748 ( 1308) covalent geometry : bond 0.00402 (11032) covalent geometry : angle 0.69535 (14968) *********************** 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 406 residues out of total 1152 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 373 time to evaluate : 1.288 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: B 172 GLU cc_start: 0.6766 (mt-10) cc_final: 0.6461 (mt-10) REVERT: B 177 HIS cc_start: 0.6728 (m90) cc_final: 0.6439 (m90) REVERT: B 178 HIS cc_start: 0.7425 (m-70) cc_final: 0.7214 (m-70) REVERT: B 331 GLU cc_start: 0.8677 (pt0) cc_final: 0.8416 (pt0) REVERT: B 447 TYR cc_start: 0.8127 (t80) cc_final: 0.7759 (t80) REVERT: B 460 ASP cc_start: 0.8497 (t70) cc_final: 0.8019 (t0) REVERT: B 464 LEU cc_start: 0.8909 (OUTLIER) cc_final: 0.8658 (tt) REVERT: B 485 GLU cc_start: 0.8309 (tm-30) cc_final: 0.8082 (tm-30) REVERT: A 169 LYS cc_start: 0.8182 (mmtm) cc_final: 0.7371 (mmtm) REVERT: A 214 ARG cc_start: 0.7767 (mmm160) cc_final: 0.7555 (mmm160) REVERT: A 257 LEU cc_start: 0.9075 (mp) cc_final: 0.8799 (mp) REVERT: A 280 LYS cc_start: 0.8467 (mmmm) cc_final: 0.7969 (mmmm) REVERT: A 286 GLN cc_start: 0.7803 (pm20) cc_final: 0.7231 (pm20) REVERT: A 447 TYR cc_start: 0.8311 (t80) cc_final: 0.7090 (t80) REVERT: A 460 ASP cc_start: 0.8229 (t0) cc_final: 0.7925 (t0) REVERT: A 477 ARG cc_start: 0.8068 (ptt-90) cc_final: 0.7710 (ptt-90) REVERT: C 172 GLU cc_start: 0.7354 (mm-30) cc_final: 0.7079 (mm-30) REVERT: C 224 TYR cc_start: 0.8163 (m-80) cc_final: 0.7848 (m-80) REVERT: C 312 GLN cc_start: 0.8558 (mt0) cc_final: 0.8258 (mt0) REVERT: C 343 THR cc_start: 0.8753 (p) cc_final: 0.8478 (t) REVERT: C 443 LYS cc_start: 0.8054 (ttmm) cc_final: 0.7523 (ttmm) REVERT: C 476 ARG cc_start: 0.7985 (ttt90) cc_final: 0.7484 (ttt90) REVERT: C 480 GLU cc_start: 0.7589 (OUTLIER) cc_final: 0.6889 (mp0) REVERT: D 214 ARG cc_start: 0.7433 (mmm160) cc_final: 0.7151 (mmp80) REVERT: D 280 LYS cc_start: 0.8368 (mmtt) cc_final: 0.8165 (mttt) REVERT: D 286 GLN cc_start: 0.7846 (pm20) cc_final: 0.7474 (pm20) REVERT: D 321 MET cc_start: 0.8933 (mmt) cc_final: 0.8713 (mmt) REVERT: D 346 GLN cc_start: 0.8397 (tp40) cc_final: 0.8187 (tp-100) REVERT: D 386 LYS cc_start: 0.7665 (mmtm) cc_final: 0.7441 (mmmm) REVERT: D 450 ARG cc_start: 0.8279 (ptp90) cc_final: 0.7713 (ptp90) REVERT: D 460 ASP cc_start: 0.8366 (t0) cc_final: 0.8019 (t0) REVERT: D 480 GLU cc_start: 0.7274 (OUTLIER) cc_final: 0.6505 (mp0) REVERT: D 486 LEU cc_start: 0.9120 (tp) cc_final: 0.8898 (tp) outliers start: 33 outliers final: 18 residues processed: 385 average time/residue: 0.2740 time to fit residues: 140.6038 Evaluate side-chains 324 residues out of total 1152 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 303 time to evaluate : 1.350 ------------------------------------------------------------------------------- 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 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 343 THR 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 14 optimal weight: 4.9990 chunk 61 optimal weight: 0.0670 chunk 97 optimal weight: 4.9990 chunk 71 optimal weight: 0.0470 chunk 43 optimal weight: 0.5980 chunk 113 optimal weight: 2.9990 chunk 78 optimal weight: 0.7980 chunk 4 optimal weight: 2.9990 chunk 60 optimal weight: 0.8980 chunk 103 optimal weight: 0.8980 chunk 55 optimal weight: 8.9990 overall best weight: 0.4816 ------------------------------------------------------------------------------- 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 ** B 483 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 201 GLN ** A 251 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 271 GLN A 483 GLN C 473 GLN C 483 GLN ** D 251 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 483 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3628 r_free = 0.3628 target = 0.113872 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3454 r_free = 0.3454 target = 0.102269 restraints weight = 25583.080| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.3496 r_free = 0.3496 target = 0.105243 restraints weight = 14114.864| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3533 r_free = 0.3533 target = 0.107645 restraints weight = 8879.242| |-----------------------------------------------------------------------------| r_work (final): 0.3537 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7792 moved from start: 0.3051 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 11032 Z= 0.132 Angle : 0.647 8.482 14968 Z= 0.334 Chirality : 0.043 0.206 1600 Planarity : 0.004 0.041 1972 Dihedral : 5.479 47.154 1486 Min Nonbonded Distance : 2.157 Molprobity Statistics. All-atom Clashscore : 17.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.88 % Favored : 95.12 % Rotamer: Outliers : 2.95 % Allowed : 21.53 % Favored : 75.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.30 (0.21), residues: 1332 helix: -1.25 (0.17), residues: 668 sheet: -2.34 (0.41), residues: 140 loop : -1.41 (0.27), residues: 524 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.003 TRP A 232 HIS 0.005 0.001 HIS B 177 PHE 0.024 0.002 PHE B 285 TYR 0.022 0.002 TYR D 447 ARG 0.006 0.001 ARG C 342 Details of bonding type rmsd hydrogen bonds : bond 0.04189 ( 448) hydrogen bonds : angle 5.47115 ( 1308) covalent geometry : bond 0.00300 (11032) covalent geometry : angle 0.64748 (14968) *********************** 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 392 residues out of total 1152 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 358 time to evaluate : 1.223 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: 0.6695 (mt-10) cc_final: 0.6490 (mt-10) REVERT: B 178 HIS cc_start: 0.7342 (m170) cc_final: 0.7118 (m170) REVERT: B 260 ARG cc_start: 0.8850 (ptp-110) cc_final: 0.8594 (ptp-110) REVERT: B 447 TYR cc_start: 0.8105 (t80) cc_final: 0.7738 (t80) REVERT: B 460 ASP cc_start: 0.8346 (t70) cc_final: 0.7877 (t0) REVERT: B 464 LEU cc_start: 0.8863 (OUTLIER) cc_final: 0.8662 (tt) REVERT: A 197 GLN cc_start: 0.8904 (tp40) cc_final: 0.8433 (tp40) REVERT: A 214 ARG cc_start: 0.7741 (mmm160) cc_final: 0.7448 (mmm160) REVERT: A 257 LEU cc_start: 0.9035 (mp) cc_final: 0.8823 (mp) REVERT: A 277 ARG cc_start: 0.8150 (ttm-80) cc_final: 0.7755 (ttm-80) REVERT: A 280 LYS cc_start: 0.8383 (mmmm) cc_final: 0.7871 (mmmm) REVERT: A 286 GLN cc_start: 0.7804 (pm20) cc_final: 0.7247 (pm20) REVERT: A 290 VAL cc_start: 0.8741 (p) cc_final: 0.8526 (m) REVERT: A 367 SER cc_start: 0.9306 (m) cc_final: 0.8960 (p) REVERT: A 447 TYR cc_start: 0.8075 (t80) cc_final: 0.6943 (t80) REVERT: A 460 ASP cc_start: 0.8256 (t0) cc_final: 0.7956 (t0) REVERT: A 476 ARG cc_start: 0.8280 (ttt-90) cc_final: 0.7940 (ttt-90) REVERT: A 484 ASP cc_start: 0.8010 (m-30) cc_final: 0.7747 (m-30) REVERT: C 172 GLU cc_start: 0.7165 (mm-30) cc_final: 0.6874 (mm-30) REVERT: C 224 TYR cc_start: 0.8041 (m-80) cc_final: 0.7779 (m-80) REVERT: C 312 GLN cc_start: 0.8528 (mt0) cc_final: 0.8322 (mt0) REVERT: C 473 GLN cc_start: 0.8343 (tp-100) cc_final: 0.8090 (tp40) REVERT: C 476 ARG cc_start: 0.8012 (ttt90) cc_final: 0.7486 (ttt90) REVERT: C 480 GLU cc_start: 0.7568 (OUTLIER) cc_final: 0.6878 (mp0) REVERT: D 172 GLU cc_start: 0.7035 (mm-30) cc_final: 0.6788 (mm-30) REVERT: D 197 GLN cc_start: 0.8755 (tp40) cc_final: 0.8365 (tp40) REVERT: D 214 ARG cc_start: 0.7467 (mmm160) cc_final: 0.7261 (mmp-170) REVERT: D 255 PHE cc_start: 0.7250 (t80) cc_final: 0.7035 (t80) REVERT: D 280 LYS cc_start: 0.8320 (mmtt) cc_final: 0.8090 (mttt) REVERT: D 286 GLN cc_start: 0.7732 (pm20) cc_final: 0.7327 (pm20) REVERT: D 308 PHE cc_start: 0.8146 (t80) cc_final: 0.7800 (t80) REVERT: D 450 ARG cc_start: 0.8357 (ptp90) cc_final: 0.7777 (ptp90) REVERT: D 460 ASP cc_start: 0.8490 (t0) cc_final: 0.8132 (t0) REVERT: D 476 ARG cc_start: 0.7753 (ttt90) cc_final: 0.7503 (ttt90) REVERT: D 480 GLU cc_start: 0.7237 (OUTLIER) cc_final: 0.6262 (mp0) outliers start: 34 outliers final: 21 residues processed: 372 average time/residue: 0.2744 time to fit residues: 135.8558 Evaluate side-chains 335 residues out of total 1152 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 311 time to evaluate : 1.307 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 234 GLU 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 A residue 173 LEU 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 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 C residue 480 GLU Chi-restraints excluded: chain D residue 234 GLU 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 82 optimal weight: 0.9980 chunk 17 optimal weight: 2.9990 chunk 92 optimal weight: 8.9990 chunk 5 optimal weight: 0.0970 chunk 15 optimal weight: 0.1980 chunk 113 optimal weight: 3.9990 chunk 117 optimal weight: 0.5980 chunk 71 optimal weight: 0.0870 chunk 60 optimal weight: 4.9990 chunk 70 optimal weight: 1.9990 chunk 3 optimal weight: 5.9990 overall best weight: 0.3956 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 483 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 178 HIS ** A 251 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 215 HIS C 246 HIS ** C 251 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 177 HIS ** D 251 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 346 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3661 r_free = 0.3661 target = 0.116134 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3482 r_free = 0.3482 target = 0.103857 restraints weight = 25575.292| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3527 r_free = 0.3527 target = 0.107094 restraints weight = 14263.915| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3561 r_free = 0.3561 target = 0.109362 restraints weight = 8974.770| |-----------------------------------------------------------------------------| r_work (final): 0.3569 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7773 moved from start: 0.3517 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.056 11032 Z= 0.129 Angle : 0.645 12.340 14968 Z= 0.329 Chirality : 0.042 0.152 1600 Planarity : 0.004 0.049 1972 Dihedral : 5.223 46.799 1486 Min Nonbonded Distance : 2.147 Molprobity Statistics. All-atom Clashscore : 16.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.56 % Favored : 94.44 % Rotamer: Outliers : 3.91 % Allowed : 23.52 % Favored : 72.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.67 (0.22), residues: 1332 helix: -0.67 (0.19), residues: 656 sheet: -2.08 (0.42), residues: 140 loop : -1.20 (0.27), residues: 536 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.035 0.003 TRP A 232 HIS 0.009 0.001 HIS C 215 PHE 0.035 0.002 PHE D 344 TYR 0.019 0.002 TYR A 264 ARG 0.005 0.000 ARG C 168 Details of bonding type rmsd hydrogen bonds : bond 0.03902 ( 448) hydrogen bonds : angle 5.21673 ( 1308) covalent geometry : bond 0.00299 (11032) covalent geometry : angle 0.64470 (14968) *********************** 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 397 residues out of total 1152 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 352 time to evaluate : 1.188 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: 0.6404 (mt-10) cc_final: 0.5683 (mt-10) REVERT: B 178 HIS cc_start: 0.7320 (m170) cc_final: 0.7085 (m170) REVERT: B 252 LEU cc_start: 0.7250 (mt) cc_final: 0.6963 (mm) REVERT: B 396 TYR cc_start: 0.7108 (t80) cc_final: 0.6827 (t80) REVERT: B 447 TYR cc_start: 0.8028 (t80) cc_final: 0.7800 (t80) REVERT: B 458 LYS cc_start: 0.8295 (ttpt) cc_final: 0.7545 (ttpt) REVERT: B 460 ASP cc_start: 0.8478 (t0) cc_final: 0.8055 (t0) REVERT: B 464 LEU cc_start: 0.8882 (OUTLIER) cc_final: 0.8681 (tt) REVERT: A 197 GLN cc_start: 0.8898 (tp40) cc_final: 0.8522 (tp40) REVERT: A 280 LYS cc_start: 0.8291 (mmmm) cc_final: 0.7816 (mmmm) REVERT: A 286 GLN cc_start: 0.7615 (pm20) cc_final: 0.7124 (pm20) REVERT: A 290 VAL cc_start: 0.8690 (p) cc_final: 0.8480 (m) REVERT: A 367 SER cc_start: 0.9324 (m) cc_final: 0.8916 (p) REVERT: A 447 TYR cc_start: 0.7995 (t80) cc_final: 0.6790 (t80) REVERT: A 460 ASP cc_start: 0.8262 (t0) cc_final: 0.7942 (t0) REVERT: A 484 ASP cc_start: 0.8034 (m-30) cc_final: 0.7781 (m-30) REVERT: C 172 GLU cc_start: 0.7111 (mm-30) cc_final: 0.6896 (mm-30) REVERT: C 274 ASP cc_start: 0.8295 (OUTLIER) cc_final: 0.7305 (t0) REVERT: C 321 MET cc_start: 0.8722 (mmm) cc_final: 0.8380 (mmm) REVERT: C 342 ARG cc_start: 0.8440 (mmm-85) cc_final: 0.8133 (mmm-85) REVERT: C 361 GLU cc_start: 0.8650 (pm20) cc_final: 0.8170 (pm20) REVERT: C 396 TYR cc_start: 0.5952 (t80) cc_final: 0.5665 (t80) REVERT: C 462 TYR cc_start: 0.7762 (m-10) cc_final: 0.7048 (m-10) REVERT: C 473 GLN cc_start: 0.8363 (tp-100) cc_final: 0.7993 (tp40) REVERT: C 476 ARG cc_start: 0.7977 (ttt90) cc_final: 0.7466 (ttt90) REVERT: C 480 GLU cc_start: 0.7506 (OUTLIER) cc_final: 0.6743 (mp0) REVERT: D 237 THR cc_start: 0.9110 (p) cc_final: 0.8886 (p) REVERT: D 274 ASP cc_start: 0.8463 (OUTLIER) cc_final: 0.7814 (t0) REVERT: D 280 LYS cc_start: 0.8335 (mmtt) cc_final: 0.8075 (mttt) REVERT: D 286 GLN cc_start: 0.7714 (pm20) cc_final: 0.7281 (pm20) REVERT: D 308 PHE cc_start: 0.8057 (t80) cc_final: 0.7836 (t80) REVERT: D 342 ARG cc_start: 0.8404 (mmm-85) cc_final: 0.8102 (mmm-85) REVERT: D 367 SER cc_start: 0.9308 (m) cc_final: 0.8939 (p) REVERT: D 450 ARG cc_start: 0.8394 (ptp90) cc_final: 0.7862 (ptp90) REVERT: D 460 ASP cc_start: 0.8376 (t0) cc_final: 0.7984 (t0) REVERT: D 480 GLU cc_start: 0.7181 (OUTLIER) cc_final: 0.6381 (mp0) outliers start: 45 outliers final: 25 residues processed: 371 average time/residue: 0.2702 time to fit residues: 134.9395 Evaluate side-chains 334 residues out of total 1152 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 304 time to evaluate : 1.256 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 234 GLU Chi-restraints excluded: chain B residue 269 ILE 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 A residue 225 THR Chi-restraints excluded: chain A residue 269 ILE Chi-restraints excluded: chain A residue 341 ASP 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 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 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 433 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 86 optimal weight: 7.9990 chunk 108 optimal weight: 2.9990 chunk 51 optimal weight: 1.9990 chunk 59 optimal weight: 0.9990 chunk 71 optimal weight: 0.4980 chunk 94 optimal weight: 2.9990 chunk 114 optimal weight: 0.9990 chunk 2 optimal weight: 5.9990 chunk 45 optimal weight: 0.9990 chunk 110 optimal weight: 0.6980 chunk 77 optimal weight: 2.9990 overall best weight: 0.8386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 483 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 251 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 483 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 251 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 = 0.3640 r_free = 0.3640 target = 0.114369 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3465 r_free = 0.3465 target = 0.102308 restraints weight = 25513.243| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3508 r_free = 0.3508 target = 0.105456 restraints weight = 14047.387| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3539 r_free = 0.3539 target = 0.107558 restraints weight = 8901.254| |-----------------------------------------------------------------------------| r_work (final): 0.3546 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7808 moved from start: 0.3695 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= 0.145 Angle : 0.663 12.940 14968 Z= 0.333 Chirality : 0.043 0.153 1600 Planarity : 0.004 0.039 1972 Dihedral : 5.101 44.886 1486 Min Nonbonded Distance : 2.143 Molprobity Statistics. All-atom Clashscore : 17.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.93 % Favored : 94.07 % Rotamer: Outliers : 3.73 % Allowed : 24.65 % Favored : 71.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.21 (0.22), residues: 1332 helix: -0.29 (0.19), residues: 636 sheet: -1.96 (0.42), residues: 140 loop : -0.92 (0.27), residues: 556 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.045 0.004 TRP A 232 HIS 0.008 0.001 HIS A 215 PHE 0.027 0.002 PHE D 344 TYR 0.023 0.002 TYR A 264 ARG 0.006 0.000 ARG C 260 Details of bonding type rmsd hydrogen bonds : bond 0.03929 ( 448) hydrogen bonds : angle 5.17343 ( 1308) covalent geometry : bond 0.00340 (11032) covalent geometry : angle 0.66327 (14968) *********************** 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 377 residues out of total 1152 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 334 time to evaluate : 1.318 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 172 GLU cc_start: 0.6360 (mt-10) cc_final: 0.5819 (mt-10) REVERT: B 217 ASP cc_start: 0.8018 (m-30) cc_final: 0.7716 (m-30) REVERT: B 252 LEU cc_start: 0.7248 (mt) cc_final: 0.7015 (mm) REVERT: B 260 ARG cc_start: 0.8854 (ptp-110) cc_final: 0.8462 (ptp-110) REVERT: B 280 LYS cc_start: 0.8372 (mmmm) cc_final: 0.7849 (mmmm) REVERT: B 281 GLU cc_start: 0.8003 (tt0) cc_final: 0.7618 (tt0) REVERT: B 460 ASP cc_start: 0.8436 (t0) cc_final: 0.7986 (t0) REVERT: A 197 GLN cc_start: 0.8948 (tp40) cc_final: 0.8598 (tp40) REVERT: A 280 LYS cc_start: 0.8272 (mmmm) cc_final: 0.7836 (mmmm) REVERT: A 286 GLN cc_start: 0.7708 (pm20) cc_final: 0.7300 (pm20) REVERT: A 346 GLN cc_start: 0.8300 (tp-100) cc_final: 0.8078 (tp40) REVERT: A 367 SER cc_start: 0.9313 (m) cc_final: 0.8971 (p) REVERT: A 447 TYR cc_start: 0.8220 (t80) cc_final: 0.7012 (t80) REVERT: A 460 ASP cc_start: 0.8243 (t0) cc_final: 0.7869 (t0) REVERT: A 476 ARG cc_start: 0.8417 (ttt90) cc_final: 0.8215 (ttt90) REVERT: C 172 GLU cc_start: 0.7248 (mm-30) cc_final: 0.6927 (mm-30) REVERT: C 274 ASP cc_start: 0.8332 (OUTLIER) cc_final: 0.7377 (t0) REVERT: C 286 GLN cc_start: 0.8011 (pm20) cc_final: 0.7662 (pm20) REVERT: C 361 GLU cc_start: 0.8613 (pm20) cc_final: 0.8123 (pm20) REVERT: C 462 TYR cc_start: 0.7759 (m-10) cc_final: 0.6962 (m-10) REVERT: C 473 GLN cc_start: 0.8360 (tp-100) cc_final: 0.7981 (tp40) REVERT: C 476 ARG cc_start: 0.7945 (ttt90) cc_final: 0.7545 (ttt90) REVERT: D 274 ASP cc_start: 0.8478 (OUTLIER) cc_final: 0.7854 (t0) REVERT: D 280 LYS cc_start: 0.8391 (mmtt) cc_final: 0.8118 (mttt) REVERT: D 286 GLN cc_start: 0.7830 (pm20) cc_final: 0.7367 (pm20) REVERT: D 308 PHE cc_start: 0.8181 (t80) cc_final: 0.7946 (t80) REVERT: D 342 ARG cc_start: 0.8453 (mmm-85) cc_final: 0.8184 (mmm-85) REVERT: D 367 SER cc_start: 0.9336 (m) cc_final: 0.8961 (p) REVERT: D 443 LYS cc_start: 0.7846 (ttmt) cc_final: 0.7643 (ttmt) REVERT: D 450 ARG cc_start: 0.8343 (ptp-170) cc_final: 0.7994 (ptp90) REVERT: D 460 ASP cc_start: 0.8316 (t0) cc_final: 0.7993 (t0) REVERT: D 466 ILE cc_start: 0.8676 (mt) cc_final: 0.8425 (mt) REVERT: D 476 ARG cc_start: 0.7911 (ttt90) cc_final: 0.7612 (ttt90) outliers start: 43 outliers final: 29 residues processed: 353 average time/residue: 0.2711 time to fit residues: 128.8697 Evaluate side-chains 334 residues out of total 1152 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 303 time to evaluate : 1.305 ------------------------------------------------------------------------------- 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 269 ILE Chi-restraints excluded: chain B residue 341 ASP Chi-restraints excluded: chain B residue 343 THR 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 239 LEU Chi-restraints excluded: chain A residue 269 ILE 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 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 466 ILE 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 433 VAL Chi-restraints excluded: chain D residue 444 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 29 optimal weight: 0.9980 chunk 46 optimal weight: 5.9990 chunk 15 optimal weight: 2.9990 chunk 79 optimal weight: 0.7980 chunk 16 optimal weight: 3.9990 chunk 78 optimal weight: 0.8980 chunk 90 optimal weight: 0.5980 chunk 65 optimal weight: 3.9990 chunk 87 optimal weight: 3.9990 chunk 19 optimal weight: 0.7980 chunk 112 optimal weight: 6.9990 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 483 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 191 HIS ** A 251 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 473 GLN ** A 483 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 483 GLN ** 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 = 0.3634 r_free = 0.3634 target = 0.114419 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3455 r_free = 0.3455 target = 0.102480 restraints weight = 25154.431| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3500 r_free = 0.3500 target = 0.105585 restraints weight = 13969.050| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3530 r_free = 0.3530 target = 0.107611 restraints weight = 8798.995| |-----------------------------------------------------------------------------| r_work (final): 0.3543 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7802 moved from start: 0.3960 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 11032 Z= 0.146 Angle : 0.686 11.248 14968 Z= 0.342 Chirality : 0.044 0.187 1600 Planarity : 0.004 0.039 1972 Dihedral : 4.960 18.747 1484 Min Nonbonded Distance : 2.166 Molprobity Statistics. All-atom Clashscore : 17.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.78 % Favored : 94.22 % Rotamer: Outliers : 4.60 % Allowed : 22.83 % Favored : 72.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.04 (0.23), residues: 1332 helix: -0.08 (0.20), residues: 636 sheet: -2.04 (0.41), residues: 140 loop : -0.86 (0.27), residues: 556 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.053 0.004 TRP B 232 HIS 0.011 0.001 HIS A 215 PHE 0.030 0.002 PHE D 344 TYR 0.025 0.002 TYR A 264 ARG 0.005 0.000 ARG C 260 Details of bonding type rmsd hydrogen bonds : bond 0.03937 ( 448) hydrogen bonds : angle 5.17812 ( 1308) covalent geometry : bond 0.00342 (11032) covalent geometry : angle 0.68616 (14968) *********************** 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 399 residues out of total 1152 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 346 time to evaluate : 1.324 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 217 ASP cc_start: 0.8039 (m-30) cc_final: 0.7740 (m-30) REVERT: B 280 LYS cc_start: 0.8393 (mmmm) cc_final: 0.7963 (mmmm) REVERT: B 281 GLU cc_start: 0.8073 (tt0) cc_final: 0.7714 (tt0) REVERT: B 447 TYR cc_start: 0.7938 (t80) cc_final: 0.7337 (t80) REVERT: B 460 ASP cc_start: 0.8275 (t0) cc_final: 0.7965 (t0) REVERT: A 178 HIS cc_start: 0.7670 (m170) cc_final: 0.7127 (m170) REVERT: A 197 GLN cc_start: 0.8965 (tp40) cc_final: 0.8619 (tp40) REVERT: A 280 LYS cc_start: 0.8252 (mmmm) cc_final: 0.7831 (mmmm) REVERT: A 286 GLN cc_start: 0.7771 (pm20) cc_final: 0.7294 (pm20) REVERT: A 346 GLN cc_start: 0.8228 (tp-100) cc_final: 0.8006 (tp-100) REVERT: A 367 SER cc_start: 0.9315 (m) cc_final: 0.9018 (p) REVERT: A 443 LYS cc_start: 0.7927 (ttmt) cc_final: 0.7491 (ttmt) REVERT: A 447 TYR cc_start: 0.8265 (t80) cc_final: 0.7171 (t80) REVERT: A 460 ASP cc_start: 0.8404 (t0) cc_final: 0.7966 (t0) REVERT: A 476 ARG cc_start: 0.8400 (ttt90) cc_final: 0.8166 (ttt90) REVERT: C 172 GLU cc_start: 0.7334 (mm-30) cc_final: 0.6912 (mm-30) REVERT: C 274 ASP cc_start: 0.8364 (OUTLIER) cc_final: 0.7372 (t0) REVERT: C 286 GLN cc_start: 0.8040 (pm20) cc_final: 0.7622 (pm20) REVERT: C 331 GLU cc_start: 0.8592 (pt0) cc_final: 0.8367 (pt0) REVERT: C 462 TYR cc_start: 0.7741 (m-10) cc_final: 0.7228 (m-10) REVERT: C 473 GLN cc_start: 0.8317 (tp-100) cc_final: 0.7941 (tp40) REVERT: C 476 ARG cc_start: 0.7886 (ttt90) cc_final: 0.7495 (ttt90) REVERT: C 480 GLU cc_start: 0.7579 (OUTLIER) cc_final: 0.6699 (mp0) REVERT: D 197 GLN cc_start: 0.8827 (tp40) cc_final: 0.8530 (tp40) REVERT: D 274 ASP cc_start: 0.8444 (OUTLIER) cc_final: 0.7892 (t0) REVERT: D 280 LYS cc_start: 0.8398 (mmtt) cc_final: 0.8078 (mttt) REVERT: D 286 GLN cc_start: 0.7904 (pm20) cc_final: 0.7390 (pm20) REVERT: D 342 ARG cc_start: 0.8464 (mmm-85) cc_final: 0.8187 (mmm-85) REVERT: D 367 SER cc_start: 0.9334 (m) cc_final: 0.8948 (p) REVERT: D 450 ARG cc_start: 0.8392 (ptp-170) cc_final: 0.7763 (ptp90) REVERT: D 460 ASP cc_start: 0.8439 (t0) cc_final: 0.8067 (t0) REVERT: D 467 ASP cc_start: 0.8035 (m-30) cc_final: 0.7814 (m-30) REVERT: D 476 ARG cc_start: 0.7809 (ttt90) cc_final: 0.7534 (ttt90) outliers start: 53 outliers final: 36 residues processed: 369 average time/residue: 0.3247 time to fit residues: 162.2722 Evaluate side-chains 340 residues out of total 1152 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 301 time to evaluate : 3.394 ------------------------------------------------------------------------------- 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 269 ILE 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 361 GLU Chi-restraints excluded: chain A residue 385 VAL Chi-restraints excluded: chain A residue 399 LEU 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 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 480 GLU Chi-restraints excluded: chain D residue 234 GLU Chi-restraints excluded: chain D residue 239 LEU 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 343 THR Chi-restraints excluded: chain D residue 351 ILE 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 Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 80 optimal weight: 3.9990 chunk 25 optimal weight: 1.9990 chunk 76 optimal weight: 2.9990 chunk 30 optimal weight: 0.7980 chunk 129 optimal weight: 7.9990 chunk 41 optimal weight: 2.9990 chunk 77 optimal weight: 0.8980 chunk 9 optimal weight: 0.9990 chunk 37 optimal weight: 5.9990 chunk 49 optimal weight: 0.8980 chunk 128 optimal weight: 0.7980 overall best weight: 0.8782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 178 HIS B 215 HIS B 268 ASN ** B 483 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 177 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 251 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 268 ASN ** A 483 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 251 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 420 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 428 GLN ** C 483 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3634 r_free = 0.3634 target = 0.114348 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3453 r_free = 0.3453 target = 0.102338 restraints weight = 25419.596| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3498 r_free = 0.3498 target = 0.105514 restraints weight = 14155.256| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3527 r_free = 0.3527 target = 0.107440 restraints weight = 8849.295| |-----------------------------------------------------------------------------| r_work (final): 0.3540 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7805 moved from start: 0.4145 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.066 11032 Z= 0.154 Angle : 0.714 14.011 14968 Z= 0.356 Chirality : 0.044 0.164 1600 Planarity : 0.004 0.038 1972 Dihedral : 5.018 18.825 1484 Min Nonbonded Distance : 2.151 Molprobity Statistics. All-atom Clashscore : 20.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.18 % Favored : 94.82 % Rotamer: Outliers : 3.99 % Allowed : 24.48 % Favored : 71.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.11 (0.22), residues: 1332 helix: -0.18 (0.20), residues: 660 sheet: -1.92 (0.42), residues: 140 loop : -0.93 (0.27), residues: 532 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.057 0.004 TRP B 232 HIS 0.012 0.001 HIS A 215 PHE 0.035 0.003 PHE D 344 TYR 0.023 0.002 TYR D 370 ARG 0.007 0.000 ARG A 282 Details of bonding type rmsd hydrogen bonds : bond 0.04086 ( 448) hydrogen bonds : angle 5.22481 ( 1308) covalent geometry : bond 0.00359 (11032) covalent geometry : angle 0.71401 (14968) *********************** 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 382 residues out of total 1152 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 336 time to evaluate : 1.393 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: B 217 ASP cc_start: 0.7853 (m-30) cc_final: 0.7520 (m-30) REVERT: B 260 ARG cc_start: 0.8887 (ptp-110) cc_final: 0.8487 (ptp-110) REVERT: B 280 LYS cc_start: 0.8347 (mmmm) cc_final: 0.7876 (mmmm) REVERT: B 447 TYR cc_start: 0.7893 (t80) cc_final: 0.7486 (t80) REVERT: B 455 PHE cc_start: 0.8426 (p90) cc_final: 0.7600 (p90) REVERT: B 458 LYS cc_start: 0.8025 (ttpt) cc_final: 0.7809 (ttpp) REVERT: B 460 ASP cc_start: 0.8325 (t0) cc_final: 0.7900 (t0) REVERT: B 476 ARG cc_start: 0.7795 (ttt-90) cc_final: 0.7337 (ttt-90) REVERT: A 197 GLN cc_start: 0.8970 (tp40) cc_final: 0.8652 (tp40) REVERT: A 214 ARG cc_start: 0.7644 (mmm160) cc_final: 0.7336 (mmm160) REVERT: A 280 LYS cc_start: 0.8175 (mmmm) cc_final: 0.7679 (mmmm) REVERT: A 286 GLN cc_start: 0.7808 (pm20) cc_final: 0.7340 (pm20) REVERT: A 367 SER cc_start: 0.9277 (m) cc_final: 0.8975 (p) REVERT: A 443 LYS cc_start: 0.7952 (ttmt) cc_final: 0.7510 (ttmt) REVERT: A 447 TYR cc_start: 0.8278 (t80) cc_final: 0.7353 (t80) REVERT: A 460 ASP cc_start: 0.8395 (t0) cc_final: 0.7966 (t0) REVERT: A 476 ARG cc_start: 0.8412 (ttt90) cc_final: 0.8028 (ttt90) REVERT: C 172 GLU cc_start: 0.7383 (mm-30) cc_final: 0.6937 (mm-30) REVERT: C 286 GLN cc_start: 0.8112 (pm20) cc_final: 0.7698 (pm20) REVERT: C 343 THR cc_start: 0.8795 (OUTLIER) cc_final: 0.8514 (t) REVERT: C 359 SER cc_start: 0.8462 (p) cc_final: 0.8195 (t) REVERT: C 361 GLU cc_start: 0.8661 (pm20) cc_final: 0.8385 (pm20) REVERT: C 473 GLN cc_start: 0.8309 (tp-100) cc_final: 0.7943 (tp40) REVERT: C 476 ARG cc_start: 0.7879 (ttt90) cc_final: 0.7412 (ttt90) REVERT: C 480 GLU cc_start: 0.7569 (OUTLIER) cc_final: 0.6670 (mp0) REVERT: D 178 HIS cc_start: 0.7312 (m170) cc_final: 0.7054 (m170) REVERT: D 274 ASP cc_start: 0.8387 (OUTLIER) cc_final: 0.7870 (t0) REVERT: D 280 LYS cc_start: 0.8417 (mmtt) cc_final: 0.8094 (mttt) REVERT: D 286 GLN cc_start: 0.7930 (pm20) cc_final: 0.7433 (pm20) REVERT: D 342 ARG cc_start: 0.8476 (mmm-85) cc_final: 0.8192 (mmm-85) REVERT: D 367 SER cc_start: 0.9354 (m) cc_final: 0.8985 (p) REVERT: D 460 ASP cc_start: 0.8481 (t0) cc_final: 0.8124 (t0) REVERT: D 467 ASP cc_start: 0.8049 (m-30) cc_final: 0.7788 (m-30) REVERT: D 476 ARG cc_start: 0.7875 (ttt90) cc_final: 0.7599 (ttt90) outliers start: 46 outliers final: 34 residues processed: 353 average time/residue: 0.4122 time to fit residues: 195.4637 Evaluate side-chains 348 residues out of total 1152 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 311 time to evaluate : 1.337 ------------------------------------------------------------------------------- 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 B residue 496 ILE Chi-restraints excluded: chain A residue 234 GLU Chi-restraints excluded: chain A residue 239 LEU Chi-restraints excluded: chain A residue 341 ASP Chi-restraints excluded: chain A residue 385 VAL Chi-restraints excluded: chain A residue 399 LEU 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 480 GLU Chi-restraints excluded: chain D residue 234 GLU Chi-restraints excluded: chain D residue 239 LEU 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 343 THR Chi-restraints excluded: chain D residue 351 ILE 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 Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 30 optimal weight: 4.9990 chunk 8 optimal weight: 2.9990 chunk 131 optimal weight: 0.6980 chunk 28 optimal weight: 0.5980 chunk 16 optimal weight: 0.6980 chunk 109 optimal weight: 0.5980 chunk 39 optimal weight: 0.9980 chunk 0 optimal weight: 5.9990 chunk 50 optimal weight: 0.0000 chunk 63 optimal weight: 0.8980 chunk 80 optimal weight: 1.9990 overall best weight: 0.5184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 177 HIS ** B 483 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 177 HIS A 178 HIS ** A 251 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 483 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 177 HIS C 215 HIS ** C 251 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 420 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 483 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 346 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3683 r_free = 0.3683 target = 0.117859 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3500 r_free = 0.3500 target = 0.105608 restraints weight = 24966.218| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3545 r_free = 0.3545 target = 0.108801 restraints weight = 14072.046| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3575 r_free = 0.3575 target = 0.110812 restraints weight = 8912.235| |-----------------------------------------------------------------------------| r_work (final): 0.3589 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7762 moved from start: 0.4432 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= 0.142 Angle : 0.733 14.580 14968 Z= 0.366 Chirality : 0.045 0.267 1600 Planarity : 0.004 0.039 1972 Dihedral : 5.001 18.641 1484 Min Nonbonded Distance : 2.182 Molprobity Statistics. All-atom Clashscore : 19.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.95 % Favored : 95.05 % Rotamer: Outliers : 3.56 % Allowed : 26.39 % Favored : 70.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.06 (0.23), residues: 1332 helix: -0.20 (0.20), residues: 660 sheet: -1.86 (0.42), residues: 140 loop : -0.82 (0.27), residues: 532 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.003 TRP B 232 HIS 0.013 0.001 HIS A 215 PHE 0.034 0.002 PHE D 344 TYR 0.022 0.002 TYR A 264 ARG 0.006 0.000 ARG A 282 Details of bonding type rmsd hydrogen bonds : bond 0.04048 ( 448) hydrogen bonds : angle 5.27164 ( 1308) covalent geometry : bond 0.00327 (11032) covalent geometry : angle 0.73326 (14968) *********************** 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 378 residues out of total 1152 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 337 time to evaluate : 2.523 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: B 217 ASP cc_start: 0.7428 (m-30) cc_final: 0.7223 (m-30) REVERT: B 280 LYS cc_start: 0.8338 (mmmm) cc_final: 0.7885 (mmmm) REVERT: B 281 GLU cc_start: 0.8081 (tt0) cc_final: 0.7857 (tt0) REVERT: B 447 TYR cc_start: 0.7878 (t80) cc_final: 0.7529 (t80) REVERT: B 458 LYS cc_start: 0.7933 (ttpt) cc_final: 0.7728 (ttpp) REVERT: B 460 ASP cc_start: 0.8383 (t0) cc_final: 0.7938 (t0) REVERT: B 476 ARG cc_start: 0.7788 (ttt-90) cc_final: 0.7308 (ttt-90) REVERT: A 178 HIS cc_start: 0.7603 (m170) cc_final: 0.7308 (m170) REVERT: A 197 GLN cc_start: 0.8964 (tp40) cc_final: 0.8671 (tp40) REVERT: A 280 LYS cc_start: 0.8251 (mmmm) cc_final: 0.7742 (mmmm) REVERT: A 286 GLN cc_start: 0.7886 (pm20) cc_final: 0.7348 (pm20) REVERT: A 367 SER cc_start: 0.9313 (m) cc_final: 0.8963 (p) REVERT: A 443 LYS cc_start: 0.7953 (ttmt) cc_final: 0.7512 (ttmt) REVERT: A 447 TYR cc_start: 0.8137 (t80) cc_final: 0.7147 (t80) REVERT: A 460 ASP cc_start: 0.8284 (t0) cc_final: 0.7958 (t0) REVERT: A 476 ARG cc_start: 0.8301 (ttt90) cc_final: 0.7921 (ttt90) REVERT: C 172 GLU cc_start: 0.7251 (mm-30) cc_final: 0.6830 (mm-30) REVERT: C 177 HIS cc_start: 0.6583 (m-70) cc_final: 0.6275 (m-70) REVERT: C 286 GLN cc_start: 0.8116 (pm20) cc_final: 0.7696 (pm20) REVERT: C 343 THR cc_start: 0.8776 (OUTLIER) cc_final: 0.8491 (t) REVERT: C 359 SER cc_start: 0.8316 (p) cc_final: 0.8020 (t) REVERT: C 361 GLU cc_start: 0.8585 (pm20) cc_final: 0.8383 (pm20) REVERT: C 367 SER cc_start: 0.9384 (m) cc_final: 0.9011 (p) REVERT: C 473 GLN cc_start: 0.8247 (tp-100) cc_final: 0.7821 (tp40) REVERT: C 476 ARG cc_start: 0.7798 (ttt90) cc_final: 0.7238 (ttt90) REVERT: C 480 GLU cc_start: 0.7527 (OUTLIER) cc_final: 0.6627 (mp0) REVERT: D 178 HIS cc_start: 0.7128 (m170) cc_final: 0.6831 (m170) REVERT: D 274 ASP cc_start: 0.8360 (OUTLIER) cc_final: 0.7946 (t0) REVERT: D 280 LYS cc_start: 0.8371 (mmtt) cc_final: 0.8074 (mttt) REVERT: D 286 GLN cc_start: 0.7897 (pm20) cc_final: 0.7358 (pm20) REVERT: D 342 ARG cc_start: 0.8459 (mmm-85) cc_final: 0.8202 (mmm-85) REVERT: D 367 SER cc_start: 0.9348 (m) cc_final: 0.8958 (p) REVERT: D 450 ARG cc_start: 0.8227 (ptp-170) cc_final: 0.7504 (ptp90) REVERT: D 460 ASP cc_start: 0.8482 (t0) cc_final: 0.8144 (t0) REVERT: D 476 ARG cc_start: 0.7688 (ttt90) cc_final: 0.7451 (ttt90) REVERT: D 477 ARG cc_start: 0.7722 (ptt-90) cc_final: 0.7125 (ptt-90) outliers start: 41 outliers final: 29 residues processed: 356 average time/residue: 0.4268 time to fit residues: 209.4676 Evaluate side-chains 340 residues out of total 1152 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 308 time to evaluate : 1.447 ------------------------------------------------------------------------------- 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 356 LEU Chi-restraints excluded: chain B residue 433 VAL Chi-restraints excluded: chain B residue 444 LEU Chi-restraints excluded: chain A residue 234 GLU 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 399 LEU 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 274 ASP Chi-restraints excluded: chain D residue 283 THR Chi-restraints excluded: chain D residue 302 SER 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 Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 59 optimal weight: 0.9990 chunk 109 optimal weight: 0.9980 chunk 17 optimal weight: 0.8980 chunk 126 optimal weight: 4.9990 chunk 92 optimal weight: 6.9990 chunk 51 optimal weight: 0.6980 chunk 40 optimal weight: 0.9980 chunk 23 optimal weight: 0.0970 chunk 78 optimal weight: 3.9990 chunk 53 optimal weight: 0.9990 chunk 79 optimal weight: 6.9990 overall best weight: 0.7378 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 177 HIS B 201 GLN ** B 483 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 251 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 483 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 251 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 420 GLN ** 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 = 0.3670 r_free = 0.3670 target = 0.117337 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3490 r_free = 0.3490 target = 0.105180 restraints weight = 25298.242| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3534 r_free = 0.3534 target = 0.108391 restraints weight = 14058.025| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3563 r_free = 0.3563 target = 0.110328 restraints weight = 8810.822| |-----------------------------------------------------------------------------| r_work (final): 0.3575 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7770 moved from start: 0.4581 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 11032 Z= 0.154 Angle : 0.766 13.969 14968 Z= 0.379 Chirality : 0.046 0.255 1600 Planarity : 0.005 0.060 1972 Dihedral : 5.069 19.443 1484 Min Nonbonded Distance : 2.150 Molprobity Statistics. All-atom Clashscore : 20.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.95 % Favored : 95.05 % Rotamer: Outliers : 3.56 % Allowed : 27.17 % Favored : 69.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.09 (0.22), residues: 1332 helix: -0.23 (0.20), residues: 660 sheet: -1.88 (0.41), residues: 140 loop : -0.81 (0.27), residues: 532 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.003 TRP A 232 HIS 0.013 0.001 HIS A 215 PHE 0.034 0.003 PHE D 344 TYR 0.022 0.002 TYR D 370 ARG 0.007 0.001 ARG A 265 Details of bonding type rmsd hydrogen bonds : bond 0.04157 ( 448) hydrogen bonds : angle 5.34494 ( 1308) covalent geometry : bond 0.00360 (11032) covalent geometry : angle 0.76590 (14968) *********************** 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 353 residues out of total 1152 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 312 time to evaluate : 1.317 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: B 217 ASP cc_start: 0.7744 (m-30) cc_final: 0.7438 (m-30) REVERT: B 260 ARG cc_start: 0.8830 (ptp-110) cc_final: 0.8556 (ptp-110) REVERT: B 280 LYS cc_start: 0.8318 (mmmm) cc_final: 0.7883 (mmmm) REVERT: B 447 TYR cc_start: 0.7971 (t80) cc_final: 0.7667 (t80) REVERT: B 458 LYS cc_start: 0.7953 (ttpt) cc_final: 0.7743 (ttpp) REVERT: B 460 ASP cc_start: 0.8369 (t0) cc_final: 0.7972 (t0) REVERT: B 476 ARG cc_start: 0.7795 (ttt-90) cc_final: 0.7340 (ttt-90) REVERT: A 177 HIS cc_start: 0.6713 (m-70) cc_final: 0.6173 (m-70) REVERT: A 197 GLN cc_start: 0.8968 (tp40) cc_final: 0.8657 (tp40) REVERT: A 271 GLN cc_start: 0.7264 (OUTLIER) cc_final: 0.7036 (tp40) REVERT: A 280 LYS cc_start: 0.8362 (mmmm) cc_final: 0.7951 (mmmm) REVERT: A 367 SER cc_start: 0.9341 (m) cc_final: 0.8971 (p) REVERT: A 443 LYS cc_start: 0.7971 (ttmt) cc_final: 0.7534 (ttmt) REVERT: A 447 TYR cc_start: 0.8159 (t80) cc_final: 0.7266 (t80) REVERT: A 460 ASP cc_start: 0.8283 (t0) cc_final: 0.7897 (t0) REVERT: A 476 ARG cc_start: 0.8284 (ttt90) cc_final: 0.7927 (ttt90) REVERT: C 172 GLU cc_start: 0.7294 (mm-30) cc_final: 0.6853 (mm-30) REVERT: C 274 ASP cc_start: 0.8402 (OUTLIER) cc_final: 0.8009 (t70) REVERT: C 286 GLN cc_start: 0.8144 (pm20) cc_final: 0.7719 (pm20) REVERT: C 343 THR cc_start: 0.8745 (OUTLIER) cc_final: 0.8481 (t) REVERT: C 359 SER cc_start: 0.8299 (p) cc_final: 0.7983 (t) REVERT: C 361 GLU cc_start: 0.8567 (pm20) cc_final: 0.8362 (pm20) REVERT: C 367 SER cc_start: 0.9382 (m) cc_final: 0.9023 (p) REVERT: C 473 GLN cc_start: 0.8240 (tp-100) cc_final: 0.7851 (tp40) REVERT: C 476 ARG cc_start: 0.7754 (ttt90) cc_final: 0.7249 (ttt90) REVERT: C 480 GLU cc_start: 0.7391 (OUTLIER) cc_final: 0.6520 (mp0) REVERT: D 178 HIS cc_start: 0.7096 (m170) cc_final: 0.6767 (m170) REVERT: D 274 ASP cc_start: 0.8424 (OUTLIER) cc_final: 0.8010 (t0) REVERT: D 280 LYS cc_start: 0.8377 (mmtt) cc_final: 0.8082 (mttt) REVERT: D 286 GLN cc_start: 0.7975 (pm20) cc_final: 0.7460 (pm20) REVERT: D 342 ARG cc_start: 0.8439 (mmm-85) cc_final: 0.8172 (mmm-85) REVERT: D 367 SER cc_start: 0.9360 (m) cc_final: 0.8991 (p) REVERT: D 450 ARG cc_start: 0.8212 (ptp-170) cc_final: 0.7481 (ptp90) REVERT: D 460 ASP cc_start: 0.8422 (t0) cc_final: 0.8110 (t0) REVERT: D 476 ARG cc_start: 0.7677 (ttt90) cc_final: 0.7458 (ttt90) REVERT: D 477 ARG cc_start: 0.7723 (ptt-90) cc_final: 0.7111 (ptt-90) outliers start: 41 outliers final: 28 residues processed: 333 average time/residue: 0.2682 time to fit residues: 120.1160 Evaluate side-chains 334 residues out of total 1152 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 301 time to evaluate : 1.209 ------------------------------------------------------------------------------- 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 356 LEU Chi-restraints excluded: chain B residue 433 VAL Chi-restraints excluded: chain B residue 444 LEU Chi-restraints excluded: chain A residue 234 GLU Chi-restraints excluded: chain A residue 271 GLN Chi-restraints excluded: chain A residue 341 ASP Chi-restraints excluded: chain A residue 385 VAL Chi-restraints excluded: chain A residue 399 LEU Chi-restraints excluded: chain A residue 433 VAL Chi-restraints excluded: chain A residue 444 LEU Chi-restraints excluded: chain A residue 488 THR 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 239 LEU Chi-restraints excluded: chain D residue 274 ASP Chi-restraints excluded: chain D residue 283 THR Chi-restraints excluded: chain D residue 302 SER 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 444 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 20 optimal weight: 2.9990 chunk 111 optimal weight: 0.7980 chunk 38 optimal weight: 3.9990 chunk 17 optimal weight: 5.9990 chunk 1 optimal weight: 1.9990 chunk 15 optimal weight: 0.8980 chunk 84 optimal weight: 3.9990 chunk 74 optimal weight: 0.9990 chunk 108 optimal weight: 0.7980 chunk 103 optimal weight: 0.8980 chunk 28 optimal weight: 0.6980 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 177 HIS B 201 GLN ** B 483 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 178 HIS ** A 251 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 483 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 177 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 251 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 420 GLN ** 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 = 0.3670 r_free = 0.3670 target = 0.117161 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3484 r_free = 0.3484 target = 0.104904 restraints weight = 25421.253| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3529 r_free = 0.3529 target = 0.108047 restraints weight = 14247.075| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3560 r_free = 0.3560 target = 0.110088 restraints weight = 9108.944| |-----------------------------------------------------------------------------| r_work (final): 0.3572 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7776 moved from start: 0.4718 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.069 11032 Z= 0.157 Angle : 0.781 13.717 14968 Z= 0.385 Chirality : 0.046 0.225 1600 Planarity : 0.005 0.056 1972 Dihedral : 5.114 25.069 1484 Min Nonbonded Distance : 2.167 Molprobity Statistics. All-atom Clashscore : 20.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.33 % Favored : 94.67 % Rotamer: Outliers : 3.21 % Allowed : 27.78 % Favored : 69.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.10 (0.22), residues: 1332 helix: -0.18 (0.20), residues: 656 sheet: -2.02 (0.41), residues: 140 loop : -0.86 (0.27), residues: 536 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.003 TRP B 371 HIS 0.009 0.001 HIS A 215 PHE 0.034 0.003 PHE D 344 TYR 0.027 0.002 TYR D 370 ARG 0.004 0.000 ARG B 265 Details of bonding type rmsd hydrogen bonds : bond 0.04170 ( 448) hydrogen bonds : angle 5.38371 ( 1308) covalent geometry : bond 0.00371 (11032) covalent geometry : angle 0.78100 (14968) ********************** 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 348 residues out of total 1152 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 311 time to evaluate : 1.355 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 217 ASP cc_start: 0.7816 (m-30) cc_final: 0.7517 (m-30) REVERT: B 260 ARG cc_start: 0.8766 (ptp-110) cc_final: 0.8442 (ptp-110) REVERT: B 280 LYS cc_start: 0.8340 (mmmm) cc_final: 0.7890 (mmmm) REVERT: B 450 ARG cc_start: 0.8918 (ptp-170) cc_final: 0.8173 (mtm180) REVERT: B 460 ASP cc_start: 0.8509 (t0) cc_final: 0.8139 (t0) REVERT: B 476 ARG cc_start: 0.7783 (ttt-90) cc_final: 0.7329 (ttt-90) REVERT: A 178 HIS cc_start: 0.7354 (m170) cc_final: 0.6975 (m170) REVERT: A 197 GLN cc_start: 0.8968 (tp40) cc_final: 0.8648 (tp40) REVERT: A 271 GLN cc_start: 0.6859 (OUTLIER) cc_final: 0.6646 (tp40) REVERT: A 280 LYS cc_start: 0.8420 (mmmm) cc_final: 0.7877 (mmmm) REVERT: A 286 GLN cc_start: 0.7955 (pm20) cc_final: 0.7380 (pm20) REVERT: A 367 SER cc_start: 0.9331 (m) cc_final: 0.8978 (p) REVERT: A 443 LYS cc_start: 0.7953 (ttmt) cc_final: 0.7529 (ttmt) REVERT: A 447 TYR cc_start: 0.8172 (t80) cc_final: 0.7177 (t80) REVERT: A 460 ASP cc_start: 0.8292 (t0) cc_final: 0.7919 (t0) REVERT: A 476 ARG cc_start: 0.8276 (ttt90) cc_final: 0.7926 (ttt90) REVERT: C 172 GLU cc_start: 0.7294 (mm-30) cc_final: 0.6904 (mm-30) REVERT: C 177 HIS cc_start: 0.6396 (m90) cc_final: 0.6171 (m90) REVERT: C 274 ASP cc_start: 0.8523 (OUTLIER) cc_final: 0.7547 (t0) REVERT: C 286 GLN cc_start: 0.8170 (pm20) cc_final: 0.7755 (pm20) REVERT: C 343 THR cc_start: 0.8740 (OUTLIER) cc_final: 0.8487 (t) REVERT: C 361 GLU cc_start: 0.8519 (pm20) cc_final: 0.8099 (pm20) REVERT: C 367 SER cc_start: 0.9404 (m) cc_final: 0.9096 (p) REVERT: C 473 GLN cc_start: 0.8233 (tp-100) cc_final: 0.7845 (tp40) REVERT: C 476 ARG cc_start: 0.7743 (ttt90) cc_final: 0.7269 (ttt90) REVERT: C 480 GLU cc_start: 0.7383 (OUTLIER) cc_final: 0.6479 (mp0) REVERT: D 178 HIS cc_start: 0.7088 (m170) cc_final: 0.6600 (m170) REVERT: D 223 GLU cc_start: 0.8694 (mp0) cc_final: 0.8361 (mp0) REVERT: D 274 ASP cc_start: 0.8252 (OUTLIER) cc_final: 0.7695 (t0) REVERT: D 280 LYS cc_start: 0.8389 (mmtt) cc_final: 0.8090 (mttt) REVERT: D 286 GLN cc_start: 0.7969 (pm20) cc_final: 0.7492 (pm20) REVERT: D 342 ARG cc_start: 0.8429 (mmm-85) cc_final: 0.8178 (mmm-85) REVERT: D 367 SER cc_start: 0.9401 (m) cc_final: 0.9087 (p) REVERT: D 450 ARG cc_start: 0.8189 (ptp-170) cc_final: 0.7473 (ptp90) REVERT: D 460 ASP cc_start: 0.8481 (t0) cc_final: 0.8137 (t0) REVERT: D 476 ARG cc_start: 0.7686 (ttt90) cc_final: 0.7448 (ttt90) REVERT: D 477 ARG cc_start: 0.7789 (ptt-90) cc_final: 0.7182 (ptt-90) outliers start: 37 outliers final: 30 residues processed: 328 average time/residue: 0.2723 time to fit residues: 120.1342 Evaluate side-chains 328 residues out of total 1152 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 293 time to evaluate : 1.363 ------------------------------------------------------------------------------- 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 356 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 234 GLU Chi-restraints excluded: chain A residue 271 GLN 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 399 LEU Chi-restraints excluded: chain A residue 433 VAL Chi-restraints excluded: chain A residue 444 LEU Chi-restraints excluded: chain A residue 488 THR 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 302 SER 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 444 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 23 optimal weight: 0.9980 chunk 60 optimal weight: 3.9990 chunk 56 optimal weight: 0.7980 chunk 110 optimal weight: 0.5980 chunk 107 optimal weight: 2.9990 chunk 21 optimal weight: 0.9980 chunk 78 optimal weight: 0.8980 chunk 62 optimal weight: 3.9990 chunk 121 optimal weight: 0.7980 chunk 74 optimal weight: 1.9990 chunk 81 optimal weight: 0.0370 overall best weight: 0.6258 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 177 HIS ** A 251 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 483 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 177 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 251 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 420 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 483 GLN D 177 HIS ** 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 = 0.3692 r_free = 0.3692 target = 0.118731 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3508 r_free = 0.3508 target = 0.106453 restraints weight = 25440.860| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3552 r_free = 0.3552 target = 0.109662 restraints weight = 14378.906| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3584 r_free = 0.3584 target = 0.111741 restraints weight = 9114.146| |-----------------------------------------------------------------------------| r_work (final): 0.3595 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7753 moved from start: 0.4839 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.072 11032 Z= 0.152 Angle : 0.797 13.489 14968 Z= 0.389 Chirality : 0.047 0.338 1600 Planarity : 0.005 0.051 1972 Dihedral : 5.136 25.445 1484 Min Nonbonded Distance : 2.188 Molprobity Statistics. All-atom Clashscore : 20.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.03 % Favored : 94.97 % Rotamer: Outliers : 2.95 % Allowed : 28.47 % Favored : 68.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.99 (0.22), residues: 1332 helix: -0.20 (0.20), residues: 656 sheet: -1.55 (0.54), residues: 88 loop : -0.90 (0.25), residues: 588 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.003 TRP A 371 HIS 0.009 0.001 HIS A 215 PHE 0.033 0.003 PHE B 261 TYR 0.031 0.002 TYR D 264 ARG 0.003 0.000 ARG C 260 Details of bonding type rmsd hydrogen bonds : bond 0.04174 ( 448) hydrogen bonds : angle 5.40364 ( 1308) covalent geometry : bond 0.00356 (11032) covalent geometry : angle 0.79665 (14968) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4031.17 seconds wall clock time: 74 minutes 42.66 seconds (4482.66 seconds total)