Starting phenix.real_space_refine on Fri Jul 3 07:09:54 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/7x05_32917/07_2026/7x05_32917.cif Found real_map, /net/cci-nas-00/data/ceres_data/7x05_32917/07_2026/7x05_32917.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7x05_32917/07_2026/7x05_32917.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7x05_32917/07_2026/7x05_32917.map" model { file = "/net/cci-nas-00/data/ceres_data/7x05_32917/07_2026/7x05_32917.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7x05_32917/07_2026/7x05_32917.cif" restraint_files = "/net/cci-nas-00/data/ceres_data/7x05_32917/07_2026/7x05_32917.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/7x05_32917/07_2026/7x05_32917.cif" } resolution = 3.9 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.003 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: 6 Type Number sf(0) Gaussians Mn 2 7.51 5 P 4 5.49 5 S 72 5.16 5 C 8420 2.51 5 N 2156 2.21 5 O 2346 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 2 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 13000 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 6431 Number of conformers: 1 Conformer: "" Number of residues, atoms: 801, 6431 Classifications: {'peptide': 801} Link IDs: {'PTRANS': 30, 'TRANS': 770} Chain breaks: 1 Chain: "C" Number of atoms: 43 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 43 Unusual residues: {'NAG': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "A" Number of atoms: 25 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 25 Unusual residues: {'UDP': 1} Classifications: {'undetermined': 1} Chain: "A" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MN': 1} Classifications: {'undetermined': 1} Restraints were copied for chains: B, D Time building chain proxies: 6.91, per 1000 atoms: 0.53 Number of scatterers: 13000 At special positions: 0 Unit cell: (118.77, 114.49, 127.33, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) Mn 2 24.99 S 72 16.00 P 4 15.00 O 2346 8.00 N 2156 7.00 C 8420 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 Links applied BETA1-4 " NAG C 1 " - " NAG C 2 " " NAG C 2 " - " NAG C 3 " " NAG D 1 " - " NAG D 2 " " NAG D 2 " - " NAG D 3 " Time building additional restraints: 1.14 Conformation dependent library (CDL) restraints added in 643.8 milliseconds 3188 Ramachandran restraints generated. 1594 Oldfield, 0 Emsley, 1594 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3012 Finding SS restraints... Secondary structure from input PDB file: 62 helices and 6 sheets defined 66.3% alpha, 7.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.38 Creating SS restraints... Processing helix chain 'A' and resid 64 through 74 Processing helix chain 'A' and resid 76 through 89 removed outlier: 4.374A pdb=" N SER A 80 " --> pdb=" O LYS A 76 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N ALA A 81 " --> pdb=" O SER A 77 " (cutoff:3.500A) Processing helix chain 'A' and resid 93 through 110 Processing helix chain 'A' and resid 113 through 132 removed outlier: 4.347A pdb=" N GLU A 132 " --> pdb=" O ALA A 128 " (cutoff:3.500A) Processing helix chain 'A' and resid 136 through 162 Processing helix chain 'A' and resid 194 through 199 Processing helix chain 'A' and resid 210 through 215 removed outlier: 4.433A pdb=" N SER A 215 " --> pdb=" O ILE A 212 " (cutoff:3.500A) Processing helix chain 'A' and resid 221 through 227 Processing helix chain 'A' and resid 242 through 263 removed outlier: 3.875A pdb=" N LEU A 246 " --> pdb=" O GLY A 242 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N GLN A 263 " --> pdb=" O TYR A 259 " (cutoff:3.500A) Processing helix chain 'A' and resid 279 through 282 Processing helix chain 'A' and resid 297 through 307 Processing helix chain 'A' and resid 311 through 319 Processing helix chain 'A' and resid 357 through 374 Processing helix chain 'A' and resid 390 through 403 removed outlier: 3.888A pdb=" N HIS A 394 " --> pdb=" O SER A 390 " (cutoff:3.500A) Processing helix chain 'A' and resid 423 through 447 removed outlier: 4.233A pdb=" N SER A 427 " --> pdb=" O ASN A 423 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N PHE A 447 " --> pdb=" O LEU A 443 " (cutoff:3.500A) Processing helix chain 'A' and resid 467 through 474 Processing helix chain 'A' and resid 474 through 479 removed outlier: 3.755A pdb=" N ASN A 478 " --> pdb=" O PHE A 474 " (cutoff:3.500A) Processing helix chain 'A' and resid 480 through 485 removed outlier: 3.524A pdb=" N LEU A 484 " --> pdb=" O GLU A 480 " (cutoff:3.500A) Processing helix chain 'A' and resid 485 through 490 Processing helix chain 'A' and resid 494 through 505 removed outlier: 3.644A pdb=" N ILE A 498 " --> pdb=" O ALA A 494 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N VAL A 504 " --> pdb=" O SER A 500 " (cutoff:3.500A) Processing helix chain 'A' and resid 528 through 554 removed outlier: 3.574A pdb=" N LEU A 532 " --> pdb=" O ASP A 528 " (cutoff:3.500A) Processing helix chain 'A' and resid 555 through 560 Processing helix chain 'A' and resid 564 through 587 removed outlier: 3.710A pdb=" N PHE A 587 " --> pdb=" O ALA A 583 " (cutoff:3.500A) Processing helix chain 'A' and resid 587 through 605 Processing helix chain 'A' and resid 619 through 647 removed outlier: 4.079A pdb=" N ASP A 623 " --> pdb=" O GLN A 619 " (cutoff:3.500A) removed outlier: 4.064A pdb=" N VAL A 626 " --> pdb=" O LEU A 622 " (cutoff:3.500A) Processing helix chain 'A' and resid 652 through 681 Processing helix chain 'A' and resid 684 through 706 removed outlier: 5.329A pdb=" N VAL A 697 " --> pdb=" O LEU A 693 " (cutoff:3.500A) removed outlier: 5.941A pdb=" N TYR A 698 " --> pdb=" O THR A 694 " (cutoff:3.500A) removed outlier: 4.506A pdb=" N PHE A 699 " --> pdb=" O VAL A 695 " (cutoff:3.500A) Processing helix chain 'A' and resid 708 through 720 removed outlier: 5.051A pdb=" N THR A 716 " --> pdb=" O PHE A 712 " (cutoff:3.500A) removed outlier: 4.989A pdb=" N HIS A 717 " --> pdb=" O MET A 713 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N ALA A 720 " --> pdb=" O THR A 716 " (cutoff:3.500A) Processing helix chain 'A' and resid 721 through 736 Processing helix chain 'A' and resid 764 through 819 Processing helix chain 'A' and resid 820 through 857 Proline residue: A 826 - end of helix removed outlier: 4.998A pdb=" N GLY A 854 " --> pdb=" O ILE A 850 " (cutoff:3.500A) removed outlier: 5.214A pdb=" N LEU A 855 " --> pdb=" O HIS A 851 " (cutoff:3.500A) Processing helix chain 'B' and resid 64 through 74 Processing helix chain 'B' and resid 76 through 89 removed outlier: 4.374A pdb=" N SER B 80 " --> pdb=" O LYS B 76 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N ALA B 81 " --> pdb=" O SER B 77 " (cutoff:3.500A) Processing helix chain 'B' and resid 93 through 110 Processing helix chain 'B' and resid 113 through 132 removed outlier: 4.349A pdb=" N GLU B 132 " --> pdb=" O ALA B 128 " (cutoff:3.500A) Processing helix chain 'B' and resid 136 through 162 Processing helix chain 'B' and resid 194 through 199 Processing helix chain 'B' and resid 210 through 215 removed outlier: 4.434A pdb=" N SER B 215 " --> pdb=" O ILE B 212 " (cutoff:3.500A) Processing helix chain 'B' and resid 221 through 227 Processing helix chain 'B' and resid 242 through 263 removed outlier: 3.874A pdb=" N LEU B 246 " --> pdb=" O GLY B 242 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N GLN B 263 " --> pdb=" O TYR B 259 " (cutoff:3.500A) Processing helix chain 'B' and resid 279 through 282 Processing helix chain 'B' and resid 297 through 307 Processing helix chain 'B' and resid 311 through 319 Processing helix chain 'B' and resid 357 through 374 Processing helix chain 'B' and resid 390 through 403 removed outlier: 3.888A pdb=" N HIS B 394 " --> pdb=" O SER B 390 " (cutoff:3.500A) Processing helix chain 'B' and resid 423 through 447 removed outlier: 4.231A pdb=" N SER B 427 " --> pdb=" O ASN B 423 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N PHE B 447 " --> pdb=" O LEU B 443 " (cutoff:3.500A) Processing helix chain 'B' and resid 467 through 474 Processing helix chain 'B' and resid 474 through 479 removed outlier: 3.756A pdb=" N ASN B 478 " --> pdb=" O PHE B 474 " (cutoff:3.500A) Processing helix chain 'B' and resid 480 through 485 removed outlier: 3.524A pdb=" N LEU B 484 " --> pdb=" O GLU B 480 " (cutoff:3.500A) Processing helix chain 'B' and resid 485 through 490 Processing helix chain 'B' and resid 494 through 505 removed outlier: 3.644A pdb=" N ILE B 498 " --> pdb=" O ALA B 494 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N VAL B 504 " --> pdb=" O SER B 500 " (cutoff:3.500A) Processing helix chain 'B' and resid 528 through 554 removed outlier: 3.574A pdb=" N LEU B 532 " --> pdb=" O ASP B 528 " (cutoff:3.500A) Processing helix chain 'B' and resid 555 through 560 Processing helix chain 'B' and resid 564 through 587 removed outlier: 3.710A pdb=" N PHE B 587 " --> pdb=" O ALA B 583 " (cutoff:3.500A) Processing helix chain 'B' and resid 587 through 605 Processing helix chain 'B' and resid 619 through 647 removed outlier: 4.079A pdb=" N ASP B 623 " --> pdb=" O GLN B 619 " (cutoff:3.500A) removed outlier: 4.064A pdb=" N VAL B 626 " --> pdb=" O LEU B 622 " (cutoff:3.500A) Processing helix chain 'B' and resid 652 through 681 Processing helix chain 'B' and resid 684 through 706 removed outlier: 5.329A pdb=" N VAL B 697 " --> pdb=" O LEU B 693 " (cutoff:3.500A) removed outlier: 5.941A pdb=" N TYR B 698 " --> pdb=" O THR B 694 " (cutoff:3.500A) removed outlier: 4.506A pdb=" N PHE B 699 " --> pdb=" O VAL B 695 " (cutoff:3.500A) Processing helix chain 'B' and resid 708 through 720 removed outlier: 5.051A pdb=" N THR B 716 " --> pdb=" O PHE B 712 " (cutoff:3.500A) removed outlier: 4.988A pdb=" N HIS B 717 " --> pdb=" O MET B 713 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N ALA B 720 " --> pdb=" O THR B 716 " (cutoff:3.500A) Processing helix chain 'B' and resid 721 through 736 Processing helix chain 'B' and resid 764 through 819 Processing helix chain 'B' and resid 820 through 857 Proline residue: B 826 - end of helix removed outlier: 4.998A pdb=" N GLY B 854 " --> pdb=" O ILE B 850 " (cutoff:3.500A) removed outlier: 5.213A pdb=" N LEU B 855 " --> pdb=" O HIS B 851 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 52 through 56 removed outlier: 6.268A pdb=" N HIS B 175 " --> pdb=" O PRO B 205 " (cutoff:3.500A) removed outlier: 7.773A pdb=" N ARG B 200 " --> pdb=" O THR B 332 " (cutoff:3.500A) removed outlier: 5.628A pdb=" N THR B 332 " --> pdb=" O ARG B 200 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N CYS B 326 " --> pdb=" O VAL B 206 " (cutoff:3.500A) removed outlier: 7.114A pdb=" N VAL B 284 " --> pdb=" O GLN B 346 " (cutoff:3.500A) removed outlier: 8.377A pdb=" N VAL B 348 " --> pdb=" O VAL B 284 " (cutoff:3.500A) removed outlier: 6.452A pdb=" N VAL B 286 " --> pdb=" O VAL B 348 " (cutoff:3.500A) removed outlier: 7.408A pdb=" N ALA B 350 " --> pdb=" O VAL B 286 " (cutoff:3.500A) removed outlier: 6.283A pdb=" N ILE B 288 " --> pdb=" O ALA B 350 " (cutoff:3.500A) removed outlier: 7.580A pdb=" N LYS B 352 " --> pdb=" O ILE B 288 " (cutoff:3.500A) removed outlier: 6.579A pdb=" N LEU B 232 " --> pdb=" O LEU B 285 " (cutoff:3.500A) removed outlier: 7.737A pdb=" N CYS B 287 " --> pdb=" O LEU B 232 " (cutoff:3.500A) removed outlier: 6.375A pdb=" N ILE B 234 " --> pdb=" O CYS B 287 " (cutoff:3.500A) removed outlier: 7.357A pdb=" N VAL B 289 " --> pdb=" O ILE B 234 " (cutoff:3.500A) removed outlier: 6.440A pdb=" N ILE B 236 " --> pdb=" O VAL B 289 " (cutoff:3.500A) removed outlier: 6.148A pdb=" N MET B 233 " --> pdb=" O ALA B 379 " (cutoff:3.500A) removed outlier: 7.609A pdb=" N MET B 381 " --> pdb=" O MET B 233 " (cutoff:3.500A) removed outlier: 5.694A pdb=" N CYS B 235 " --> pdb=" O MET B 381 " (cutoff:3.500A) removed outlier: 4.289A pdb=" N ARG B 461 " --> pdb=" O GLY B 406 " (cutoff:3.500A) removed outlier: 7.243A pdb=" N GLY B 406 " --> pdb=" O ARG B 461 " (cutoff:3.500A) removed outlier: 4.204A pdb=" N ILE B 405 " --> pdb=" O THR B 512 " (cutoff:3.500A) removed outlier: 7.006A pdb=" N HIS B 514 " --> pdb=" O ILE B 405 " (cutoff:3.500A) removed outlier: 6.286A pdb=" N GLY B 407 " --> pdb=" O HIS B 514 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 512 through 515 removed outlier: 4.205A pdb=" N ILE A 405 " --> pdb=" O THR A 512 " (cutoff:3.500A) removed outlier: 7.007A pdb=" N HIS A 514 " --> pdb=" O ILE A 405 " (cutoff:3.500A) removed outlier: 6.286A pdb=" N GLY A 407 " --> pdb=" O HIS A 514 " (cutoff:3.500A) removed outlier: 7.243A pdb=" N GLY A 406 " --> pdb=" O ARG A 461 " (cutoff:3.500A) removed outlier: 4.289A pdb=" N ARG A 461 " --> pdb=" O GLY A 406 " (cutoff:3.500A) removed outlier: 6.148A pdb=" N MET A 233 " --> pdb=" O ALA A 379 " (cutoff:3.500A) removed outlier: 7.610A pdb=" N MET A 381 " --> pdb=" O MET A 233 " (cutoff:3.500A) removed outlier: 5.694A pdb=" N CYS A 235 " --> pdb=" O MET A 381 " (cutoff:3.500A) removed outlier: 6.579A pdb=" N LEU A 232 " --> pdb=" O LEU A 285 " (cutoff:3.500A) removed outlier: 7.735A pdb=" N CYS A 287 " --> pdb=" O LEU A 232 " (cutoff:3.500A) removed outlier: 6.375A pdb=" N ILE A 234 " --> pdb=" O CYS A 287 " (cutoff:3.500A) removed outlier: 7.358A pdb=" N VAL A 289 " --> pdb=" O ILE A 234 " (cutoff:3.500A) removed outlier: 6.440A pdb=" N ILE A 236 " --> pdb=" O VAL A 289 " (cutoff:3.500A) removed outlier: 7.114A pdb=" N VAL A 284 " --> pdb=" O GLN A 346 " (cutoff:3.500A) removed outlier: 8.375A pdb=" N VAL A 348 " --> pdb=" O VAL A 284 " (cutoff:3.500A) removed outlier: 6.450A pdb=" N VAL A 286 " --> pdb=" O VAL A 348 " (cutoff:3.500A) removed outlier: 7.408A pdb=" N ALA A 350 " --> pdb=" O VAL A 286 " (cutoff:3.500A) removed outlier: 6.282A pdb=" N ILE A 288 " --> pdb=" O ALA A 350 " (cutoff:3.500A) removed outlier: 7.580A pdb=" N LYS A 352 " --> pdb=" O ILE A 288 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N CYS A 326 " --> pdb=" O VAL A 206 " (cutoff:3.500A) removed outlier: 5.629A pdb=" N THR A 332 " --> pdb=" O ARG A 200 " (cutoff:3.500A) removed outlier: 7.773A pdb=" N ARG A 200 " --> pdb=" O THR A 332 " (cutoff:3.500A) removed outlier: 6.268A pdb=" N HIS A 175 " --> pdb=" O PRO A 205 " (cutoff:3.500A) removed outlier: 6.333A pdb=" N VAL A 174 " --> pdb=" O VAL B 53 " (cutoff:3.500A) removed outlier: 7.598A pdb=" N SER B 55 " --> pdb=" O VAL A 174 " (cutoff:3.500A) removed outlier: 6.300A pdb=" N LYS A 176 " --> pdb=" O SER B 55 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 336 through 337 Processing sheet with id=AA4, first strand: chain 'A' and resid 412 through 414 removed outlier: 6.754A pdb=" N THR A 413 " --> pdb=" O THR A 523 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA4 Processing sheet with id=AA5, first strand: chain 'B' and resid 336 through 337 Processing sheet with id=AA6, first strand: chain 'B' and resid 412 through 414 removed outlier: 6.754A pdb=" N THR B 413 " --> pdb=" O THR B 523 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA6 816 hydrogen bonds defined for protein. 2412 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 2.36 Time building geometry restraints manager: 1.53 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.31: 2032 1.31 - 1.43: 3909 1.43 - 1.56: 7289 1.56 - 1.68: 6 1.68 - 1.81: 112 Bond restraints: 13348 Sorted by residual: bond pdb=" C7 NAG D 1 " pdb=" N2 NAG D 1 " ideal model delta sigma weight residual 1.346 1.451 -0.105 2.00e-02 2.50e+03 2.77e+01 bond pdb=" C7 NAG C 1 " pdb=" N2 NAG C 1 " ideal model delta sigma weight residual 1.346 1.451 -0.105 2.00e-02 2.50e+03 2.74e+01 bond pdb=" C7 NAG C 3 " pdb=" N2 NAG C 3 " ideal model delta sigma weight residual 1.346 1.451 -0.105 2.00e-02 2.50e+03 2.73e+01 bond pdb=" C7 NAG D 3 " pdb=" N2 NAG D 3 " ideal model delta sigma weight residual 1.346 1.450 -0.104 2.00e-02 2.50e+03 2.73e+01 bond pdb=" C7 NAG D 2 " pdb=" N2 NAG D 2 " ideal model delta sigma weight residual 1.346 1.449 -0.103 2.00e-02 2.50e+03 2.66e+01 ... (remaining 13343 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.84: 17899 1.84 - 3.67: 167 3.67 - 5.51: 58 5.51 - 7.34: 4 7.34 - 9.18: 4 Bond angle restraints: 18132 Sorted by residual: angle pdb=" O1B UDP A1001 " pdb=" PB UDP A1001 " pdb=" O3A UDP A1001 " ideal model delta sigma weight residual 102.95 112.13 -9.18 1.00e+00 1.00e+00 8.42e+01 angle pdb=" O1B UDP B1001 " pdb=" PB UDP B1001 " pdb=" O3A UDP B1001 " ideal model delta sigma weight residual 102.95 112.12 -9.17 1.00e+00 1.00e+00 8.41e+01 angle pdb=" O3A UDP A1001 " pdb=" PB UDP A1001 " pdb=" O3B UDP A1001 " ideal model delta sigma weight residual 112.01 103.03 8.98 1.00e+00 1.00e+00 8.07e+01 angle pdb=" O3A UDP B1001 " pdb=" PB UDP B1001 " pdb=" O3B UDP B1001 " ideal model delta sigma weight residual 112.01 103.08 8.93 1.00e+00 1.00e+00 7.97e+01 angle pdb=" O5' UDP A1001 " pdb=" PA UDP A1001 " pdb=" O1A UDP A1001 " ideal model delta sigma weight residual 106.70 111.06 -4.36 1.00e+00 1.00e+00 1.90e+01 ... (remaining 18127 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.72: 7329 16.72 - 33.43: 315 33.43 - 50.15: 62 50.15 - 66.86: 12 66.86 - 83.58: 4 Dihedral angle restraints: 7722 sinusoidal: 3030 harmonic: 4692 Sorted by residual: dihedral pdb=" CA GLN B 602 " pdb=" C GLN B 602 " pdb=" N GLY B 603 " pdb=" CA GLY B 603 " ideal model delta harmonic sigma weight residual 180.00 158.45 21.55 0 5.00e+00 4.00e-02 1.86e+01 dihedral pdb=" CA GLN A 602 " pdb=" C GLN A 602 " pdb=" N GLY A 603 " pdb=" CA GLY A 603 " ideal model delta harmonic sigma weight residual 180.00 158.48 21.52 0 5.00e+00 4.00e-02 1.85e+01 dihedral pdb=" N ARG B 780 " pdb=" CA ARG B 780 " pdb=" CB ARG B 780 " pdb=" CG ARG B 780 " ideal model delta sinusoidal sigma weight residual -180.00 -124.30 -55.70 3 1.50e+01 4.44e-03 9.36e+00 ... (remaining 7719 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.026: 1175 0.026 - 0.051: 525 0.051 - 0.077: 187 0.077 - 0.103: 73 0.103 - 0.129: 46 Chirality restraints: 2006 Sorted by residual: chirality pdb=" C2 NAG D 1 " pdb=" C1 NAG D 1 " pdb=" C3 NAG D 1 " pdb=" N2 NAG D 1 " both_signs ideal model delta sigma weight residual False -2.49 -2.62 0.13 2.00e-01 2.50e+01 4.13e-01 chirality pdb=" C2 NAG C 1 " pdb=" C1 NAG C 1 " pdb=" C3 NAG C 1 " pdb=" N2 NAG C 1 " both_signs ideal model delta sigma weight residual False -2.49 -2.62 0.13 2.00e-01 2.50e+01 4.11e-01 chirality pdb=" C5 NAG D 3 " pdb=" C4 NAG D 3 " pdb=" C6 NAG D 3 " pdb=" O5 NAG D 3 " both_signs ideal model delta sigma weight residual False -2.41 -2.54 0.13 2.00e-01 2.50e+01 3.93e-01 ... (remaining 2003 not shown) Planarity restraints: 2278 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA PHE B 598 " 0.011 2.00e-02 2.50e+03 2.17e-02 4.70e+00 pdb=" C PHE B 598 " -0.037 2.00e-02 2.50e+03 pdb=" O PHE B 598 " 0.014 2.00e-02 2.50e+03 pdb=" N ILE B 599 " 0.013 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA PHE A 598 " -0.011 2.00e-02 2.50e+03 2.17e-02 4.69e+00 pdb=" C PHE A 598 " 0.037 2.00e-02 2.50e+03 pdb=" O PHE A 598 " -0.014 2.00e-02 2.50e+03 pdb=" N ILE A 599 " -0.013 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ILE B 599 " 0.010 2.00e-02 2.50e+03 2.04e-02 4.17e+00 pdb=" C ILE B 599 " -0.035 2.00e-02 2.50e+03 pdb=" O ILE B 599 " 0.013 2.00e-02 2.50e+03 pdb=" N VAL B 600 " 0.012 2.00e-02 2.50e+03 ... (remaining 2275 not shown) Histogram of nonbonded interaction distances: 2.20 - 2.74: 1212 2.74 - 3.28: 12473 3.28 - 3.82: 20996 3.82 - 4.36: 22205 4.36 - 4.90: 41749 Nonbonded interactions: 98635 Sorted by model distance: nonbonded pdb=" PB UDP B1001 " pdb="MN MN B1002 " model vdw 2.204 2.680 nonbonded pdb=" PB UDP A1001 " pdb="MN MN A1002 " model vdw 2.204 2.680 nonbonded pdb=" OH TYR B 593 " pdb=" OD1 ASN B 630 " model vdw 2.289 3.040 nonbonded pdb=" OH TYR A 593 " pdb=" OD1 ASN A 630 " model vdw 2.289 3.040 nonbonded pdb=" O SER A 390 " pdb=" ND1 HIS A 394 " model vdw 2.291 3.120 ... (remaining 98630 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' } ncs_group { reference = 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: 2.240 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.020 Extract box with map and model: 0.250 Check model and map are aligned: 0.050 Set scattering table: 0.030 Process input model: 17.230 Find NCS groups from input model: 0.140 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.240 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 21.250 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8266 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 : 0.004 0.105 13352 Z= 0.193 Angle : 0.524 9.177 18144 Z= 0.298 Chirality : 0.038 0.129 2006 Planarity : 0.003 0.026 2278 Dihedral : 10.086 83.577 4710 Min Nonbonded Distance : 2.204 Molprobity Statistics. All-atom Clashscore : 4.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.39 % Favored : 95.61 % Rotamer: Outliers : 0.00 % Allowed : 6.82 % Favored : 93.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.05 (0.22), residues: 1594 helix: 2.87 (0.17), residues: 958 sheet: 0.08 (0.43), residues: 156 loop : -1.51 (0.27), residues: 480 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 103 TYR 0.009 0.001 TYR B 365 PHE 0.012 0.001 PHE B 601 TRP 0.009 0.001 TRP A 804 HIS 0.002 0.001 HIS A 403 Details of bonding type rmsd/Z covalent geometry : bond 0.00371 / 0.19 (13348) covalent geometry : angle 0.52259 / 0.30 (18132) hydrogen bonds : bond 0.12442 / 8.20 ( 816) hydrogen bonds : angle 5.13974 / 3.70 ( 2412) link_BETA1-4 : bond 0.00607 / 0.37 ( 4) link_BETA1-4 : angle 1.68412 / 0.89 ( 12) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3188 Ramachandran restraints generated. 1594 Oldfield, 0 Emsley, 1594 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3188 Ramachandran restraints generated. 1594 Oldfield, 0 Emsley, 1594 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 297 residues out of total 1378 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 297 time to evaluate : 0.486 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 169 HIS cc_start: 0.7672 (m90) cc_final: 0.7035 (m90) REVERT: A 179 ILE cc_start: 0.8950 (pt) cc_final: 0.8718 (mp) REVERT: A 201 MET cc_start: 0.7951 (ptm) cc_final: 0.7652 (ppp) REVERT: A 207 TYR cc_start: 0.8082 (t80) cc_final: 0.7578 (t80) REVERT: A 233 MET cc_start: 0.8580 (mtp) cc_final: 0.8264 (mtp) REVERT: A 523 THR cc_start: 0.9554 (p) cc_final: 0.9229 (t) REVERT: A 607 ASN cc_start: 0.7617 (t0) cc_final: 0.7397 (p0) REVERT: B 95 GLU cc_start: 0.7738 (tm-30) cc_final: 0.7352 (tm-30) REVERT: B 152 ASN cc_start: 0.8165 (m-40) cc_final: 0.7960 (m110) REVERT: B 336 SER cc_start: 0.8419 (t) cc_final: 0.8201 (p) REVERT: B 390 SER cc_start: 0.7996 (m) cc_final: 0.7346 (p) REVERT: B 457 PHE cc_start: 0.7602 (t80) cc_final: 0.7253 (t80) REVERT: B 492 TYR cc_start: 0.8498 (t80) cc_final: 0.7709 (t80) REVERT: B 493 LEU cc_start: 0.8923 (mt) cc_final: 0.8643 (mt) REVERT: B 607 ASN cc_start: 0.7430 (t0) cc_final: 0.7142 (t0) REVERT: B 850 ILE cc_start: 0.8639 (tt) cc_final: 0.8437 (tt) outliers start: 0 outliers final: 0 residues processed: 297 average time/residue: 0.1141 time to fit residues: 50.0989 Evaluate side-chains 181 residues out of total 1378 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 181 time to evaluate : 0.494 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 98 optimal weight: 0.8980 chunk 107 optimal weight: 2.9990 chunk 10 optimal weight: 0.5980 chunk 66 optimal weight: 4.9990 chunk 130 optimal weight: 0.9990 chunk 124 optimal weight: 3.9990 chunk 103 optimal weight: 1.9990 chunk 77 optimal weight: 3.9990 chunk 122 optimal weight: 3.9990 chunk 91 optimal weight: 3.9990 chunk 149 optimal weight: 2.9990 overall best weight: 1.4986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 175 HIS A 605 GLN B 141 ASN B 256 ASN B 605 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3531 r_free = 0.3531 target = 0.137838 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3229 r_free = 0.3229 target = 0.112696 restraints weight = 17477.416| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3241 r_free = 0.3241 target = 0.114019 restraints weight = 15415.648| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3250 r_free = 0.3250 target = 0.114749 restraints weight = 13199.229| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3255 r_free = 0.3255 target = 0.115173 restraints weight = 10901.206| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3276 r_free = 0.3276 target = 0.116979 restraints weight = 9892.747| |-----------------------------------------------------------------------------| r_work (final): 0.3183 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8361 moved from start: 0.1866 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 13352 Z= 0.197 Angle : 0.590 7.317 18144 Z= 0.308 Chirality : 0.041 0.133 2006 Planarity : 0.004 0.053 2278 Dihedral : 3.944 19.356 1758 Min Nonbonded Distance : 2.083 Molprobity Statistics. All-atom Clashscore : 5.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.02 % Favored : 93.98 % Rotamer: Outliers : 3.27 % Allowed : 11.68 % Favored : 85.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.71 (0.22), residues: 1594 helix: 2.49 (0.17), residues: 974 sheet: -0.02 (0.44), residues: 150 loop : -1.49 (0.28), residues: 470 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A 856 TYR 0.021 0.001 TYR B 575 PHE 0.014 0.001 PHE A 597 TRP 0.008 0.001 TRP B 424 HIS 0.004 0.001 HIS B 327 Details of bonding type rmsd/Z covalent geometry : bond 0.00448 / 0.20 (13348) covalent geometry : angle 0.58790 / 0.31 (18132) hydrogen bonds : bond 0.06008 / 4.07 ( 816) hydrogen bonds : angle 4.60890 / 3.32 ( 2412) link_BETA1-4 : bond 0.00404 / 0.24 ( 4) link_BETA1-4 : angle 2.00815 / 1.03 ( 12) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3188 Ramachandran restraints generated. 1594 Oldfield, 0 Emsley, 1594 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3188 Ramachandran restraints generated. 1594 Oldfield, 0 Emsley, 1594 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 222 residues out of total 1378 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 177 time to evaluate : 0.473 Fit side-chains REVERT: A 134 GLN cc_start: 0.8524 (tp40) cc_final: 0.8256 (mm110) REVERT: A 179 ILE cc_start: 0.8970 (pt) cc_final: 0.8694 (mp) REVERT: A 201 MET cc_start: 0.8006 (ptm) cc_final: 0.7610 (ppp) REVERT: A 207 TYR cc_start: 0.8222 (t80) cc_final: 0.7819 (t80) REVERT: A 233 MET cc_start: 0.8771 (mtp) cc_final: 0.8365 (mtp) REVERT: A 397 PHE cc_start: 0.8464 (t80) cc_final: 0.7693 (t80) REVERT: A 492 TYR cc_start: 0.8643 (t80) cc_final: 0.8301 (t80) REVERT: A 607 ASN cc_start: 0.7494 (t0) cc_final: 0.7030 (t0) REVERT: A 665 LEU cc_start: 0.7851 (OUTLIER) cc_final: 0.7639 (tp) REVERT: A 694 THR cc_start: 0.8539 (t) cc_final: 0.8138 (p) REVERT: B 95 GLU cc_start: 0.7815 (tm-30) cc_final: 0.7459 (tm-30) REVERT: B 152 ASN cc_start: 0.8275 (m-40) cc_final: 0.8020 (m110) REVERT: B 318 ASN cc_start: 0.8880 (OUTLIER) cc_final: 0.8332 (t0) REVERT: B 390 SER cc_start: 0.8225 (m) cc_final: 0.7488 (p) REVERT: B 492 TYR cc_start: 0.8537 (t80) cc_final: 0.7762 (t80) REVERT: B 493 LEU cc_start: 0.9064 (mt) cc_final: 0.8605 (mt) REVERT: B 607 ASN cc_start: 0.7749 (t0) cc_final: 0.7392 (t0) REVERT: B 850 ILE cc_start: 0.8666 (tt) cc_final: 0.8404 (tt) outliers start: 45 outliers final: 26 residues processed: 209 average time/residue: 0.0952 time to fit residues: 30.8373 Evaluate side-chains 182 residues out of total 1378 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 154 time to evaluate : 0.516 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 85 VAL Chi-restraints excluded: chain A residue 94 VAL Chi-restraints excluded: chain A residue 386 MET Chi-restraints excluded: chain A residue 396 LEU Chi-restraints excluded: chain A residue 435 ILE Chi-restraints excluded: chain A residue 512 THR Chi-restraints excluded: chain A residue 552 TRP Chi-restraints excluded: chain A residue 634 LEU Chi-restraints excluded: chain A residue 665 LEU Chi-restraints excluded: chain A residue 690 VAL Chi-restraints excluded: chain A residue 692 ILE Chi-restraints excluded: chain A residue 719 THR Chi-restraints excluded: chain A residue 797 ARG Chi-restraints excluded: chain A residue 852 THR Chi-restraints excluded: chain B residue 150 THR Chi-restraints excluded: chain B residue 223 CYS Chi-restraints excluded: chain B residue 318 ASN Chi-restraints excluded: chain B residue 333 LEU Chi-restraints excluded: chain B residue 512 THR Chi-restraints excluded: chain B residue 564 THR Chi-restraints excluded: chain B residue 654 LEU Chi-restraints excluded: chain B residue 665 LEU Chi-restraints excluded: chain B residue 690 VAL Chi-restraints excluded: chain B residue 719 THR Chi-restraints excluded: chain B residue 781 GLU Chi-restraints excluded: chain B residue 800 VAL Chi-restraints excluded: chain B residue 815 VAL Chi-restraints excluded: chain B residue 844 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 21 optimal weight: 0.8980 chunk 35 optimal weight: 0.9990 chunk 72 optimal weight: 2.9990 chunk 17 optimal weight: 2.9990 chunk 29 optimal weight: 4.9990 chunk 115 optimal weight: 0.9980 chunk 112 optimal weight: 0.7980 chunk 117 optimal weight: 0.5980 chunk 151 optimal weight: 0.9980 chunk 83 optimal weight: 7.9990 chunk 141 optimal weight: 2.9990 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 175 HIS ** A 372 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 851 HIS B 851 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3662 r_free = 0.3662 target = 0.145605 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3330 r_free = 0.3330 target = 0.118183 restraints weight = 18195.633| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3352 r_free = 0.3352 target = 0.120746 restraints weight = 13367.528| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3364 r_free = 0.3364 target = 0.122061 restraints weight = 10942.712| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3376 r_free = 0.3376 target = 0.123045 restraints weight = 8341.102| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3391 r_free = 0.3391 target = 0.124675 restraints weight = 7935.662| |-----------------------------------------------------------------------------| r_work (final): 0.3400 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8371 moved from start: 0.2195 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.060 13352 Z= 0.139 Angle : 0.536 10.781 18144 Z= 0.275 Chirality : 0.039 0.130 2006 Planarity : 0.004 0.041 2278 Dihedral : 3.919 19.588 1758 Min Nonbonded Distance : 2.099 Molprobity Statistics. All-atom Clashscore : 5.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.08 % Favored : 94.92 % Rotamer: Outliers : 2.90 % Allowed : 13.79 % Favored : 83.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.79 (0.22), residues: 1594 helix: 2.55 (0.17), residues: 974 sheet: -0.25 (0.43), residues: 156 loop : -1.38 (0.29), residues: 464 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 856 TYR 0.024 0.001 TYR B 88 PHE 0.014 0.001 PHE B 601 TRP 0.007 0.001 TRP B 804 HIS 0.005 0.001 HIS B 514 Details of bonding type rmsd/Z covalent geometry : bond 0.00304 / 0.14 (13348) covalent geometry : angle 0.53366 / 0.27 (18132) hydrogen bonds : bond 0.05420 / 3.68 ( 816) hydrogen bonds : angle 4.48726 / 3.23 ( 2412) link_BETA1-4 : bond 0.00374 / 0.22 ( 4) link_BETA1-4 : angle 1.87431 / 0.96 ( 12) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3188 Ramachandran restraints generated. 1594 Oldfield, 0 Emsley, 1594 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3188 Ramachandran restraints generated. 1594 Oldfield, 0 Emsley, 1594 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 202 residues out of total 1378 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 162 time to evaluate : 0.428 Fit side-chains REVERT: A 179 ILE cc_start: 0.8913 (pt) cc_final: 0.8682 (mp) REVERT: A 201 MET cc_start: 0.7944 (ptm) cc_final: 0.7671 (ppp) REVERT: A 207 TYR cc_start: 0.8227 (t80) cc_final: 0.7827 (t80) REVERT: A 233 MET cc_start: 0.8669 (mtp) cc_final: 0.8324 (mtp) REVERT: A 397 PHE cc_start: 0.8369 (t80) cc_final: 0.7704 (t80) REVERT: A 607 ASN cc_start: 0.7360 (t0) cc_final: 0.6895 (t0) REVERT: A 665 LEU cc_start: 0.7917 (OUTLIER) cc_final: 0.7716 (tp) REVERT: A 694 THR cc_start: 0.8590 (t) cc_final: 0.8211 (p) REVERT: B 95 GLU cc_start: 0.7776 (tm-30) cc_final: 0.7479 (tm-30) REVERT: B 152 ASN cc_start: 0.8240 (m-40) cc_final: 0.8029 (m110) REVERT: B 390 SER cc_start: 0.7929 (m) cc_final: 0.7248 (p) REVERT: B 607 ASN cc_start: 0.7718 (t0) cc_final: 0.7368 (t0) REVERT: B 850 ILE cc_start: 0.8598 (tt) cc_final: 0.8393 (tt) outliers start: 40 outliers final: 27 residues processed: 188 average time/residue: 0.0869 time to fit residues: 26.3967 Evaluate side-chains 179 residues out of total 1378 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 151 time to evaluate : 0.499 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 85 VAL Chi-restraints excluded: chain A residue 253 LEU Chi-restraints excluded: chain A residue 318 ASN Chi-restraints excluded: chain A residue 396 LEU Chi-restraints excluded: chain A residue 435 ILE Chi-restraints excluded: chain A residue 500 SER Chi-restraints excluded: chain A residue 552 TRP Chi-restraints excluded: chain A residue 564 THR Chi-restraints excluded: chain A residue 634 LEU Chi-restraints excluded: chain A residue 640 LEU Chi-restraints excluded: chain A residue 665 LEU Chi-restraints excluded: chain A residue 690 VAL Chi-restraints excluded: chain A residue 797 ARG Chi-restraints excluded: chain A residue 851 HIS Chi-restraints excluded: chain B residue 223 CYS Chi-restraints excluded: chain B residue 291 ASP Chi-restraints excluded: chain B residue 333 LEU Chi-restraints excluded: chain B residue 435 ILE Chi-restraints excluded: chain B residue 491 MET Chi-restraints excluded: chain B residue 500 SER Chi-restraints excluded: chain B residue 564 THR Chi-restraints excluded: chain B residue 634 LEU Chi-restraints excluded: chain B residue 640 LEU Chi-restraints excluded: chain B residue 665 LEU Chi-restraints excluded: chain B residue 690 VAL Chi-restraints excluded: chain B residue 722 ILE Chi-restraints excluded: chain B residue 800 VAL Chi-restraints excluded: chain B residue 851 HIS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 156 optimal weight: 1.9990 chunk 94 optimal weight: 2.9990 chunk 73 optimal weight: 2.9990 chunk 74 optimal weight: 0.6980 chunk 138 optimal weight: 0.9990 chunk 135 optimal weight: 1.9990 chunk 31 optimal weight: 1.9990 chunk 85 optimal weight: 0.8980 chunk 150 optimal weight: 7.9990 chunk 12 optimal weight: 6.9990 chunk 159 optimal weight: 0.0980 overall best weight: 0.9384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 169 HIS A 175 HIS A 647 ASN A 851 HIS B 318 ASN B 851 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3687 r_free = 0.3687 target = 0.147583 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3359 r_free = 0.3359 target = 0.120052 restraints weight = 17893.747| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3368 r_free = 0.3368 target = 0.122235 restraints weight = 15166.727| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3385 r_free = 0.3385 target = 0.123702 restraints weight = 10453.122| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3413 r_free = 0.3413 target = 0.126433 restraints weight = 8229.195| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3414 r_free = 0.3414 target = 0.126550 restraints weight = 6803.120| |-----------------------------------------------------------------------------| r_work (final): 0.3402 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8387 moved from start: 0.2404 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 13352 Z= 0.141 Angle : 0.531 13.346 18144 Z= 0.270 Chirality : 0.039 0.129 2006 Planarity : 0.004 0.041 2278 Dihedral : 3.884 19.727 1758 Min Nonbonded Distance : 2.073 Molprobity Statistics. All-atom Clashscore : 5.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.96 % Favored : 94.04 % Rotamer: Outliers : 3.05 % Allowed : 14.59 % Favored : 82.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.85 (0.22), residues: 1594 helix: 2.60 (0.17), residues: 972 sheet: -0.28 (0.43), residues: 158 loop : -1.32 (0.29), residues: 464 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 856 TYR 0.033 0.001 TYR B 88 PHE 0.013 0.001 PHE B 601 TRP 0.006 0.001 TRP B 804 HIS 0.011 0.001 HIS A 851 Details of bonding type rmsd/Z covalent geometry : bond 0.00311 / 0.14 (13348) covalent geometry : angle 0.52950 / 0.27 (18132) hydrogen bonds : bond 0.05343 / 3.63 ( 816) hydrogen bonds : angle 4.46085 / 3.21 ( 2412) link_BETA1-4 : bond 0.00411 / 0.25 ( 4) link_BETA1-4 : angle 1.82816 / 0.93 ( 12) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3188 Ramachandran restraints generated. 1594 Oldfield, 0 Emsley, 1594 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3188 Ramachandran restraints generated. 1594 Oldfield, 0 Emsley, 1594 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 200 residues out of total 1378 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 158 time to evaluate : 0.491 Fit side-chains REVERT: A 134 GLN cc_start: 0.8415 (tp40) cc_final: 0.8188 (mm110) REVERT: A 179 ILE cc_start: 0.8918 (pt) cc_final: 0.8693 (mp) REVERT: A 201 MET cc_start: 0.7957 (ptm) cc_final: 0.7748 (ppp) REVERT: A 233 MET cc_start: 0.8613 (mtp) cc_final: 0.8283 (mtp) REVERT: A 607 ASN cc_start: 0.7320 (t0) cc_final: 0.6825 (t0) REVERT: A 694 THR cc_start: 0.8429 (t) cc_final: 0.8044 (p) REVERT: A 831 PHE cc_start: 0.8308 (OUTLIER) cc_final: 0.7929 (t80) REVERT: B 95 GLU cc_start: 0.7809 (tm-30) cc_final: 0.7511 (tm-30) REVERT: B 260 LEU cc_start: 0.9039 (OUTLIER) cc_final: 0.8799 (tt) REVERT: B 390 SER cc_start: 0.7857 (m) cc_final: 0.7224 (p) REVERT: B 492 TYR cc_start: 0.8426 (t80) cc_final: 0.7935 (t80) REVERT: B 607 ASN cc_start: 0.7698 (t0) cc_final: 0.7357 (t0) outliers start: 42 outliers final: 32 residues processed: 188 average time/residue: 0.0881 time to fit residues: 26.7659 Evaluate side-chains 186 residues out of total 1378 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 152 time to evaluate : 0.525 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 85 VAL Chi-restraints excluded: chain A residue 253 LEU Chi-restraints excluded: chain A residue 318 ASN Chi-restraints excluded: chain A residue 396 LEU Chi-restraints excluded: chain A residue 435 ILE Chi-restraints excluded: chain A residue 500 SER Chi-restraints excluded: chain A residue 552 TRP Chi-restraints excluded: chain A residue 634 LEU Chi-restraints excluded: chain A residue 640 LEU Chi-restraints excluded: chain A residue 654 LEU Chi-restraints excluded: chain A residue 690 VAL Chi-restraints excluded: chain A residue 713 MET Chi-restraints excluded: chain A residue 719 THR Chi-restraints excluded: chain A residue 797 ARG Chi-restraints excluded: chain A residue 831 PHE Chi-restraints excluded: chain A residue 850 ILE Chi-restraints excluded: chain B residue 223 CYS Chi-restraints excluded: chain B residue 260 LEU Chi-restraints excluded: chain B residue 291 ASP Chi-restraints excluded: chain B residue 318 ASN Chi-restraints excluded: chain B residue 333 LEU Chi-restraints excluded: chain B residue 336 SER Chi-restraints excluded: chain B residue 435 ILE Chi-restraints excluded: chain B residue 500 SER Chi-restraints excluded: chain B residue 564 THR Chi-restraints excluded: chain B residue 634 LEU Chi-restraints excluded: chain B residue 639 MET Chi-restraints excluded: chain B residue 640 LEU Chi-restraints excluded: chain B residue 654 LEU Chi-restraints excluded: chain B residue 665 LEU Chi-restraints excluded: chain B residue 690 VAL Chi-restraints excluded: chain B residue 722 ILE Chi-restraints excluded: chain B residue 800 VAL Chi-restraints excluded: chain B residue 851 HIS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 71 optimal weight: 5.9990 chunk 76 optimal weight: 1.9990 chunk 158 optimal weight: 4.9990 chunk 144 optimal weight: 0.9980 chunk 48 optimal weight: 3.9990 chunk 132 optimal weight: 4.9990 chunk 28 optimal weight: 6.9990 chunk 67 optimal weight: 2.9990 chunk 34 optimal weight: 0.9980 chunk 37 optimal weight: 1.9990 chunk 98 optimal weight: 4.9990 overall best weight: 1.7986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 175 HIS B 152 ASN B 318 ASN B 851 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3592 r_free = 0.3592 target = 0.139585 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3256 r_free = 0.3256 target = 0.113178 restraints weight = 18299.708| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3252 r_free = 0.3252 target = 0.113208 restraints weight = 13834.907| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3273 r_free = 0.3273 target = 0.115576 restraints weight = 12842.426| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3282 r_free = 0.3282 target = 0.116113 restraints weight = 9193.343| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3298 r_free = 0.3298 target = 0.117805 restraints weight = 8874.217| |-----------------------------------------------------------------------------| r_work (final): 0.3321 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8463 moved from start: 0.2762 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.040 13352 Z= 0.226 Angle : 0.609 13.430 18144 Z= 0.315 Chirality : 0.042 0.139 2006 Planarity : 0.004 0.043 2278 Dihedral : 4.059 19.961 1758 Min Nonbonded Distance : 2.017 Molprobity Statistics. All-atom Clashscore : 5.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.46 % Favored : 93.54 % Rotamer: Outliers : 3.12 % Allowed : 16.55 % Favored : 80.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.54 (0.22), residues: 1594 helix: 2.32 (0.17), residues: 986 sheet: -0.43 (0.40), residues: 168 loop : -1.50 (0.30), residues: 440 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 856 TYR 0.021 0.002 TYR B 88 PHE 0.019 0.001 PHE A 597 TRP 0.008 0.001 TRP B 804 HIS 0.022 0.001 HIS B 851 Details of bonding type rmsd/Z covalent geometry : bond 0.00528 / 0.23 (13348) covalent geometry : angle 0.60743 / 0.31 (18132) hydrogen bonds : bond 0.06101 / 4.14 ( 816) hydrogen bonds : angle 4.60353 / 3.32 ( 2412) link_BETA1-4 : bond 0.00153 / 0.09 ( 4) link_BETA1-4 : angle 1.91822 / 0.94 ( 12) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3188 Ramachandran restraints generated. 1594 Oldfield, 0 Emsley, 1594 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3188 Ramachandran restraints generated. 1594 Oldfield, 0 Emsley, 1594 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 197 residues out of total 1378 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 154 time to evaluate : 0.496 Fit side-chains REVERT: A 54 THR cc_start: 0.7898 (m) cc_final: 0.7692 (p) REVERT: A 201 MET cc_start: 0.8097 (ptm) cc_final: 0.7803 (ppp) REVERT: A 207 TYR cc_start: 0.8511 (t80) cc_final: 0.8275 (t80) REVERT: A 233 MET cc_start: 0.8728 (mtp) cc_final: 0.8348 (mtp) REVERT: A 492 TYR cc_start: 0.8619 (t80) cc_final: 0.8341 (t80) REVERT: A 607 ASN cc_start: 0.7443 (t0) cc_final: 0.6979 (t0) REVERT: B 95 GLU cc_start: 0.7960 (tm-30) cc_final: 0.7647 (tm-30) REVERT: B 102 ASP cc_start: 0.8865 (t70) cc_final: 0.8394 (t0) REVERT: B 492 TYR cc_start: 0.8550 (t80) cc_final: 0.8099 (t80) REVERT: B 607 ASN cc_start: 0.7807 (t0) cc_final: 0.7526 (t0) outliers start: 43 outliers final: 35 residues processed: 187 average time/residue: 0.0936 time to fit residues: 28.0002 Evaluate side-chains 185 residues out of total 1378 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 150 time to evaluate : 0.453 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 253 LEU Chi-restraints excluded: chain A residue 318 ASN Chi-restraints excluded: chain A residue 386 MET Chi-restraints excluded: chain A residue 396 LEU Chi-restraints excluded: chain A residue 435 ILE Chi-restraints excluded: chain A residue 500 SER Chi-restraints excluded: chain A residue 512 THR Chi-restraints excluded: chain A residue 564 THR Chi-restraints excluded: chain A residue 634 LEU Chi-restraints excluded: chain A residue 654 LEU Chi-restraints excluded: chain A residue 690 VAL Chi-restraints excluded: chain A residue 713 MET Chi-restraints excluded: chain A residue 719 THR Chi-restraints excluded: chain A residue 797 ARG Chi-restraints excluded: chain B residue 145 SER Chi-restraints excluded: chain B residue 223 CYS Chi-restraints excluded: chain B residue 291 ASP Chi-restraints excluded: chain B residue 333 LEU Chi-restraints excluded: chain B residue 336 SER Chi-restraints excluded: chain B residue 435 ILE Chi-restraints excluded: chain B residue 444 GLU Chi-restraints excluded: chain B residue 500 SER Chi-restraints excluded: chain B residue 512 THR Chi-restraints excluded: chain B residue 564 THR Chi-restraints excluded: chain B residue 634 LEU Chi-restraints excluded: chain B residue 639 MET Chi-restraints excluded: chain B residue 640 LEU Chi-restraints excluded: chain B residue 654 LEU Chi-restraints excluded: chain B residue 665 LEU Chi-restraints excluded: chain B residue 690 VAL Chi-restraints excluded: chain B residue 719 THR Chi-restraints excluded: chain B residue 722 ILE Chi-restraints excluded: chain B residue 781 GLU Chi-restraints excluded: chain B residue 800 VAL Chi-restraints excluded: chain B residue 851 HIS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 142 optimal weight: 0.7980 chunk 81 optimal weight: 0.6980 chunk 144 optimal weight: 0.2980 chunk 75 optimal weight: 0.9980 chunk 18 optimal weight: 3.9990 chunk 41 optimal weight: 1.9990 chunk 61 optimal weight: 0.5980 chunk 124 optimal weight: 0.0000 chunk 87 optimal weight: 5.9990 chunk 17 optimal weight: 0.5980 chunk 53 optimal weight: 1.9990 overall best weight: 0.4384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 851 HIS B 318 ASN B 851 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3694 r_free = 0.3694 target = 0.148171 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3335 r_free = 0.3335 target = 0.119434 restraints weight = 17757.764| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3352 r_free = 0.3352 target = 0.121334 restraints weight = 11470.442| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3369 r_free = 0.3369 target = 0.122983 restraints weight = 9555.312| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3376 r_free = 0.3376 target = 0.123578 restraints weight = 7875.678| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3380 r_free = 0.3380 target = 0.123950 restraints weight = 7322.537| |-----------------------------------------------------------------------------| r_work (final): 0.3371 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8427 moved from start: 0.2804 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 13352 Z= 0.115 Angle : 0.521 12.116 18144 Z= 0.266 Chirality : 0.038 0.127 2006 Planarity : 0.004 0.037 2278 Dihedral : 3.881 19.563 1758 Min Nonbonded Distance : 2.130 Molprobity Statistics. All-atom Clashscore : 5.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.21 % Favored : 94.79 % Rotamer: Outliers : 3.12 % Allowed : 17.27 % Favored : 79.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.78 (0.22), residues: 1594 helix: 2.57 (0.17), residues: 970 sheet: -0.44 (0.42), residues: 158 loop : -1.31 (0.29), residues: 466 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 522 TYR 0.037 0.001 TYR B 88 PHE 0.016 0.001 PHE B 601 TRP 0.007 0.001 TRP B 804 HIS 0.009 0.001 HIS B 851 Details of bonding type rmsd/Z covalent geometry : bond 0.00228 / 0.11 (13348) covalent geometry : angle 0.51936 / 0.27 (18132) hydrogen bonds : bond 0.05155 / 3.51 ( 816) hydrogen bonds : angle 4.43829 / 3.19 ( 2412) link_BETA1-4 : bond 0.00448 / 0.27 ( 4) link_BETA1-4 : angle 1.83365 / 0.94 ( 12) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3188 Ramachandran restraints generated. 1594 Oldfield, 0 Emsley, 1594 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3188 Ramachandran restraints generated. 1594 Oldfield, 0 Emsley, 1594 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 208 residues out of total 1378 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 165 time to evaluate : 0.482 Fit side-chains REVERT: A 71 MET cc_start: 0.4447 (OUTLIER) cc_final: 0.4200 (mmm) REVERT: A 134 GLN cc_start: 0.8594 (tp40) cc_final: 0.8329 (mm110) REVERT: A 207 TYR cc_start: 0.8386 (t80) cc_final: 0.7939 (t80) REVERT: A 443 LEU cc_start: 0.9429 (tp) cc_final: 0.9165 (tp) REVERT: A 607 ASN cc_start: 0.7254 (t0) cc_final: 0.6776 (t0) REVERT: A 694 THR cc_start: 0.8402 (t) cc_final: 0.8194 (p) REVERT: B 95 GLU cc_start: 0.7863 (tm-30) cc_final: 0.7510 (tm-30) REVERT: B 102 ASP cc_start: 0.8804 (t70) cc_final: 0.8241 (t0) REVERT: B 313 ASP cc_start: 0.8139 (m-30) cc_final: 0.7861 (m-30) REVERT: B 492 TYR cc_start: 0.8439 (t80) cc_final: 0.8050 (t80) REVERT: B 607 ASN cc_start: 0.7738 (t0) cc_final: 0.7422 (t0) REVERT: B 856 ARG cc_start: 0.6056 (ttp80) cc_final: 0.5505 (tpt90) outliers start: 43 outliers final: 31 residues processed: 193 average time/residue: 0.0907 time to fit residues: 28.1330 Evaluate side-chains 186 residues out of total 1378 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 154 time to evaluate : 0.488 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 71 MET Chi-restraints excluded: chain A residue 120 TYR Chi-restraints excluded: chain A residue 253 LEU Chi-restraints excluded: chain A residue 318 ASN Chi-restraints excluded: chain A residue 396 LEU Chi-restraints excluded: chain A residue 435 ILE Chi-restraints excluded: chain A residue 500 SER Chi-restraints excluded: chain A residue 552 TRP Chi-restraints excluded: chain A residue 564 THR Chi-restraints excluded: chain A residue 634 LEU Chi-restraints excluded: chain A residue 640 LEU Chi-restraints excluded: chain A residue 651 HIS Chi-restraints excluded: chain A residue 654 LEU Chi-restraints excluded: chain A residue 690 VAL Chi-restraints excluded: chain A residue 713 MET Chi-restraints excluded: chain A residue 719 THR Chi-restraints excluded: chain A residue 797 ARG Chi-restraints excluded: chain A residue 851 HIS Chi-restraints excluded: chain B residue 145 SER Chi-restraints excluded: chain B residue 291 ASP Chi-restraints excluded: chain B residue 318 ASN Chi-restraints excluded: chain B residue 333 LEU Chi-restraints excluded: chain B residue 435 ILE Chi-restraints excluded: chain B residue 500 SER Chi-restraints excluded: chain B residue 564 THR Chi-restraints excluded: chain B residue 634 LEU Chi-restraints excluded: chain B residue 640 LEU Chi-restraints excluded: chain B residue 654 LEU Chi-restraints excluded: chain B residue 665 LEU Chi-restraints excluded: chain B residue 690 VAL Chi-restraints excluded: chain B residue 722 ILE Chi-restraints excluded: chain B residue 851 HIS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 127 optimal weight: 0.9990 chunk 60 optimal weight: 1.9990 chunk 15 optimal weight: 4.9990 chunk 103 optimal weight: 4.9990 chunk 131 optimal weight: 2.9990 chunk 134 optimal weight: 0.8980 chunk 52 optimal weight: 4.9990 chunk 21 optimal weight: 2.9990 chunk 39 optimal weight: 2.9990 chunk 33 optimal weight: 2.9990 chunk 145 optimal weight: 0.7980 overall best weight: 1.5386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 175 HIS A 851 HIS B 318 ASN B 851 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3627 r_free = 0.3627 target = 0.142430 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3303 r_free = 0.3303 target = 0.116735 restraints weight = 18087.897| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3300 r_free = 0.3300 target = 0.117013 restraints weight = 14519.524| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3314 r_free = 0.3314 target = 0.118577 restraints weight = 14550.902| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3324 r_free = 0.3324 target = 0.119261 restraints weight = 10390.692| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3325 r_free = 0.3325 target = 0.119468 restraints weight = 10357.207| |-----------------------------------------------------------------------------| r_work (final): 0.3324 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8453 moved from start: 0.3000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.033 13352 Z= 0.197 Angle : 0.587 12.014 18144 Z= 0.301 Chirality : 0.041 0.132 2006 Planarity : 0.004 0.037 2278 Dihedral : 3.946 20.130 1758 Min Nonbonded Distance : 2.022 Molprobity Statistics. All-atom Clashscore : 5.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.27 % Favored : 93.73 % Rotamer: Outliers : 3.34 % Allowed : 18.00 % Favored : 78.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.58 (0.22), residues: 1594 helix: 2.31 (0.17), residues: 996 sheet: -0.50 (0.40), residues: 168 loop : -1.41 (0.30), residues: 430 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 522 TYR 0.029 0.002 TYR B 88 PHE 0.029 0.001 PHE A 611 TRP 0.011 0.001 TRP A 554 HIS 0.018 0.001 HIS A 851 Details of bonding type rmsd/Z covalent geometry : bond 0.00456 / 0.20 (13348) covalent geometry : angle 0.58487 / 0.30 (18132) hydrogen bonds : bond 0.05762 / 3.91 ( 816) hydrogen bonds : angle 4.53335 / 3.28 ( 2412) link_BETA1-4 : bond 0.00256 / 0.17 ( 4) link_BETA1-4 : angle 1.85446 / 0.91 ( 12) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3188 Ramachandran restraints generated. 1594 Oldfield, 0 Emsley, 1594 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3188 Ramachandran restraints generated. 1594 Oldfield, 0 Emsley, 1594 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 197 residues out of total 1378 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 151 time to evaluate : 0.506 Fit side-chains REVERT: A 134 GLN cc_start: 0.8638 (tp40) cc_final: 0.8416 (mm110) REVERT: A 207 TYR cc_start: 0.8507 (t80) cc_final: 0.8133 (t80) REVERT: A 233 MET cc_start: 0.8765 (mtp) cc_final: 0.8559 (mtp) REVERT: A 443 LEU cc_start: 0.9472 (tp) cc_final: 0.9173 (tp) REVERT: A 607 ASN cc_start: 0.7365 (t0) cc_final: 0.6922 (t0) REVERT: A 694 THR cc_start: 0.8449 (t) cc_final: 0.8167 (p) REVERT: B 95 GLU cc_start: 0.7989 (tm-30) cc_final: 0.7631 (tm-30) REVERT: B 102 ASP cc_start: 0.8904 (t70) cc_final: 0.8325 (t0) REVERT: B 313 ASP cc_start: 0.8198 (m-30) cc_final: 0.7929 (m-30) REVERT: B 492 TYR cc_start: 0.8581 (t80) cc_final: 0.8151 (t80) REVERT: B 607 ASN cc_start: 0.7823 (t0) cc_final: 0.7582 (t0) outliers start: 46 outliers final: 41 residues processed: 183 average time/residue: 0.0920 time to fit residues: 26.9048 Evaluate side-chains 188 residues out of total 1378 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 147 time to evaluate : 0.509 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 120 TYR Chi-restraints excluded: chain A residue 179 ILE Chi-restraints excluded: chain A residue 253 LEU Chi-restraints excluded: chain A residue 318 ASN Chi-restraints excluded: chain A residue 386 MET Chi-restraints excluded: chain A residue 396 LEU Chi-restraints excluded: chain A residue 435 ILE Chi-restraints excluded: chain A residue 500 SER Chi-restraints excluded: chain A residue 512 THR Chi-restraints excluded: chain A residue 564 THR Chi-restraints excluded: chain A residue 634 LEU Chi-restraints excluded: chain A residue 640 LEU Chi-restraints excluded: chain A residue 651 HIS Chi-restraints excluded: chain A residue 654 LEU Chi-restraints excluded: chain A residue 690 VAL Chi-restraints excluded: chain A residue 713 MET Chi-restraints excluded: chain A residue 719 THR Chi-restraints excluded: chain A residue 797 ARG Chi-restraints excluded: chain A residue 850 ILE Chi-restraints excluded: chain A residue 851 HIS Chi-restraints excluded: chain B residue 127 MET Chi-restraints excluded: chain B residue 145 SER Chi-restraints excluded: chain B residue 204 THR Chi-restraints excluded: chain B residue 223 CYS Chi-restraints excluded: chain B residue 291 ASP Chi-restraints excluded: chain B residue 333 LEU Chi-restraints excluded: chain B residue 435 ILE Chi-restraints excluded: chain B residue 500 SER Chi-restraints excluded: chain B residue 512 THR Chi-restraints excluded: chain B residue 564 THR Chi-restraints excluded: chain B residue 634 LEU Chi-restraints excluded: chain B residue 639 MET Chi-restraints excluded: chain B residue 640 LEU Chi-restraints excluded: chain B residue 654 LEU Chi-restraints excluded: chain B residue 665 LEU Chi-restraints excluded: chain B residue 690 VAL Chi-restraints excluded: chain B residue 692 ILE Chi-restraints excluded: chain B residue 722 ILE Chi-restraints excluded: chain B residue 781 GLU Chi-restraints excluded: chain B residue 800 VAL Chi-restraints excluded: chain B residue 851 HIS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 156 optimal weight: 0.9990 chunk 1 optimal weight: 0.9990 chunk 139 optimal weight: 0.9980 chunk 61 optimal weight: 0.4980 chunk 31 optimal weight: 2.9990 chunk 150 optimal weight: 0.0770 chunk 13 optimal weight: 0.6980 chunk 25 optimal weight: 2.9990 chunk 109 optimal weight: 2.9990 chunk 60 optimal weight: 3.9990 chunk 8 optimal weight: 5.9990 overall best weight: 0.6540 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 175 HIS A 851 HIS B 318 ASN B 851 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3662 r_free = 0.3662 target = 0.145409 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3350 r_free = 0.3350 target = 0.119745 restraints weight = 17732.212| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 24)----------------| | r_work = 0.3356 r_free = 0.3356 target = 0.120572 restraints weight = 14482.212| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3371 r_free = 0.3371 target = 0.122278 restraints weight = 13830.925| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3377 r_free = 0.3377 target = 0.122637 restraints weight = 9842.885| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3380 r_free = 0.3380 target = 0.123061 restraints weight = 9874.790| |-----------------------------------------------------------------------------| r_work (final): 0.3376 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8400 moved from start: 0.3040 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 13352 Z= 0.125 Angle : 0.545 10.999 18144 Z= 0.275 Chirality : 0.039 0.291 2006 Planarity : 0.004 0.044 2278 Dihedral : 3.864 19.767 1758 Min Nonbonded Distance : 2.095 Molprobity Statistics. All-atom Clashscore : 5.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.40 % Favored : 94.60 % Rotamer: Outliers : 3.12 % Allowed : 18.43 % Favored : 78.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.74 (0.22), residues: 1594 helix: 2.50 (0.17), residues: 982 sheet: -0.52 (0.42), residues: 158 loop : -1.31 (0.30), residues: 454 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG B 856 TYR 0.026 0.001 TYR B 88 PHE 0.026 0.001 PHE A 611 TRP 0.007 0.001 TRP B 804 HIS 0.015 0.001 HIS A 851 Details of bonding type rmsd/Z covalent geometry : bond 0.00259 / 0.12 (13348) covalent geometry : angle 0.54285 / 0.27 (18132) hydrogen bonds : bond 0.05251 / 3.57 ( 816) hydrogen bonds : angle 4.44256 / 3.20 ( 2412) link_BETA1-4 : bond 0.00454 / 0.27 ( 4) link_BETA1-4 : angle 1.79850 / 0.92 ( 12) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3188 Ramachandran restraints generated. 1594 Oldfield, 0 Emsley, 1594 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3188 Ramachandran restraints generated. 1594 Oldfield, 0 Emsley, 1594 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 200 residues out of total 1378 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 157 time to evaluate : 0.493 Fit side-chains REVERT: A 207 TYR cc_start: 0.8471 (t80) cc_final: 0.8034 (t80) REVERT: A 233 MET cc_start: 0.8622 (mtp) cc_final: 0.8419 (mtp) REVERT: A 397 PHE cc_start: 0.8490 (t80) cc_final: 0.8105 (t80) REVERT: A 443 LEU cc_start: 0.9415 (tp) cc_final: 0.9134 (tp) REVERT: A 607 ASN cc_start: 0.7308 (t0) cc_final: 0.6827 (t0) REVERT: B 95 GLU cc_start: 0.7905 (tm-30) cc_final: 0.7568 (tm-30) REVERT: B 102 ASP cc_start: 0.8865 (t70) cc_final: 0.8296 (t0) REVERT: B 313 ASP cc_start: 0.8063 (m-30) cc_final: 0.7732 (m-30) REVERT: B 492 TYR cc_start: 0.8484 (t80) cc_final: 0.8141 (t80) REVERT: B 495 GLU cc_start: 0.8273 (mp0) cc_final: 0.8047 (mp0) REVERT: B 607 ASN cc_start: 0.7779 (t0) cc_final: 0.7487 (t0) REVERT: B 856 ARG cc_start: 0.5924 (ttp80) cc_final: 0.5146 (tpt90) outliers start: 43 outliers final: 38 residues processed: 186 average time/residue: 0.0900 time to fit residues: 27.0423 Evaluate side-chains 190 residues out of total 1378 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 152 time to evaluate : 0.479 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 120 TYR Chi-restraints excluded: chain A residue 179 ILE Chi-restraints excluded: chain A residue 204 THR Chi-restraints excluded: chain A residue 253 LEU Chi-restraints excluded: chain A residue 318 ASN Chi-restraints excluded: chain A residue 327 HIS Chi-restraints excluded: chain A residue 386 MET Chi-restraints excluded: chain A residue 396 LEU Chi-restraints excluded: chain A residue 435 ILE Chi-restraints excluded: chain A residue 500 SER Chi-restraints excluded: chain A residue 564 THR Chi-restraints excluded: chain A residue 634 LEU Chi-restraints excluded: chain A residue 640 LEU Chi-restraints excluded: chain A residue 651 HIS Chi-restraints excluded: chain A residue 654 LEU Chi-restraints excluded: chain A residue 665 LEU Chi-restraints excluded: chain A residue 690 VAL Chi-restraints excluded: chain A residue 713 MET Chi-restraints excluded: chain A residue 719 THR Chi-restraints excluded: chain A residue 797 ARG Chi-restraints excluded: chain A residue 851 HIS Chi-restraints excluded: chain B residue 127 MET Chi-restraints excluded: chain B residue 145 SER Chi-restraints excluded: chain B residue 151 LEU Chi-restraints excluded: chain B residue 223 CYS Chi-restraints excluded: chain B residue 291 ASP Chi-restraints excluded: chain B residue 318 ASN Chi-restraints excluded: chain B residue 333 LEU Chi-restraints excluded: chain B residue 435 ILE Chi-restraints excluded: chain B residue 500 SER Chi-restraints excluded: chain B residue 564 THR Chi-restraints excluded: chain B residue 634 LEU Chi-restraints excluded: chain B residue 640 LEU Chi-restraints excluded: chain B residue 654 LEU Chi-restraints excluded: chain B residue 665 LEU Chi-restraints excluded: chain B residue 690 VAL Chi-restraints excluded: chain B residue 722 ILE Chi-restraints excluded: chain B residue 781 GLU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 42 optimal weight: 2.9990 chunk 127 optimal weight: 0.9990 chunk 52 optimal weight: 4.9990 chunk 131 optimal weight: 2.9990 chunk 138 optimal weight: 0.5980 chunk 92 optimal weight: 2.9990 chunk 121 optimal weight: 1.9990 chunk 137 optimal weight: 0.0980 chunk 145 optimal weight: 0.8980 chunk 43 optimal weight: 0.5980 chunk 86 optimal weight: 5.9990 overall best weight: 0.6382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 175 HIS A 851 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3669 r_free = 0.3669 target = 0.146138 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3351 r_free = 0.3351 target = 0.120381 restraints weight = 18005.808| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3351 r_free = 0.3351 target = 0.120949 restraints weight = 14745.978| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3366 r_free = 0.3366 target = 0.122469 restraints weight = 13924.502| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3371 r_free = 0.3371 target = 0.122906 restraints weight = 10590.715| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3376 r_free = 0.3376 target = 0.123350 restraints weight = 10237.944| |-----------------------------------------------------------------------------| r_work (final): 0.3380 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8403 moved from start: 0.3097 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 13352 Z= 0.122 Angle : 0.534 10.505 18144 Z= 0.270 Chirality : 0.039 0.289 2006 Planarity : 0.004 0.035 2278 Dihedral : 3.821 19.622 1758 Min Nonbonded Distance : 2.091 Molprobity Statistics. All-atom Clashscore : 5.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.77 % Favored : 94.23 % Rotamer: Outliers : 2.98 % Allowed : 18.65 % Favored : 78.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.78 (0.23), residues: 1594 helix: 2.55 (0.17), residues: 980 sheet: -0.53 (0.43), residues: 154 loop : -1.33 (0.29), residues: 460 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG B 856 TYR 0.024 0.001 TYR B 88 PHE 0.031 0.001 PHE A 715 TRP 0.007 0.001 TRP A 554 HIS 0.019 0.001 HIS A 851 Details of bonding type rmsd/Z covalent geometry : bond 0.00256 / 0.12 (13348) covalent geometry : angle 0.53261 / 0.27 (18132) hydrogen bonds : bond 0.05102 / 3.47 ( 816) hydrogen bonds : angle 4.42329 / 3.18 ( 2412) link_BETA1-4 : bond 0.00386 / 0.22 ( 4) link_BETA1-4 : angle 1.78836 / 0.92 ( 12) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3188 Ramachandran restraints generated. 1594 Oldfield, 0 Emsley, 1594 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3188 Ramachandran restraints generated. 1594 Oldfield, 0 Emsley, 1594 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 201 residues out of total 1378 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 160 time to evaluate : 0.524 Fit side-chains REVERT: A 207 TYR cc_start: 0.8477 (t80) cc_final: 0.8009 (t80) REVERT: A 397 PHE cc_start: 0.8513 (t80) cc_final: 0.8139 (t80) REVERT: A 443 LEU cc_start: 0.9398 (tp) cc_final: 0.9129 (tp) REVERT: A 607 ASN cc_start: 0.7299 (t0) cc_final: 0.6823 (t0) REVERT: A 694 THR cc_start: 0.8399 (t) cc_final: 0.8185 (p) REVERT: B 95 GLU cc_start: 0.7901 (tm-30) cc_final: 0.7450 (tm-30) REVERT: B 102 ASP cc_start: 0.8896 (t70) cc_final: 0.8323 (t0) REVERT: B 318 ASN cc_start: 0.8811 (OUTLIER) cc_final: 0.8475 (t0) REVERT: B 492 TYR cc_start: 0.8512 (t80) cc_final: 0.8143 (t80) REVERT: B 607 ASN cc_start: 0.7769 (t0) cc_final: 0.7507 (t0) outliers start: 41 outliers final: 36 residues processed: 190 average time/residue: 0.0778 time to fit residues: 23.9783 Evaluate side-chains 189 residues out of total 1378 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 152 time to evaluate : 0.466 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 120 TYR Chi-restraints excluded: chain A residue 179 ILE Chi-restraints excluded: chain A residue 204 THR Chi-restraints excluded: chain A residue 253 LEU Chi-restraints excluded: chain A residue 318 ASN Chi-restraints excluded: chain A residue 327 HIS Chi-restraints excluded: chain A residue 386 MET Chi-restraints excluded: chain A residue 396 LEU Chi-restraints excluded: chain A residue 435 ILE Chi-restraints excluded: chain A residue 500 SER Chi-restraints excluded: chain A residue 552 TRP Chi-restraints excluded: chain A residue 564 THR Chi-restraints excluded: chain A residue 651 HIS Chi-restraints excluded: chain A residue 654 LEU Chi-restraints excluded: chain A residue 665 LEU Chi-restraints excluded: chain A residue 690 VAL Chi-restraints excluded: chain A residue 713 MET Chi-restraints excluded: chain A residue 851 HIS Chi-restraints excluded: chain B residue 127 MET Chi-restraints excluded: chain B residue 145 SER Chi-restraints excluded: chain B residue 151 LEU Chi-restraints excluded: chain B residue 204 THR Chi-restraints excluded: chain B residue 223 CYS Chi-restraints excluded: chain B residue 291 ASP Chi-restraints excluded: chain B residue 318 ASN Chi-restraints excluded: chain B residue 333 LEU Chi-restraints excluded: chain B residue 435 ILE Chi-restraints excluded: chain B residue 500 SER Chi-restraints excluded: chain B residue 512 THR Chi-restraints excluded: chain B residue 564 THR Chi-restraints excluded: chain B residue 634 LEU Chi-restraints excluded: chain B residue 640 LEU Chi-restraints excluded: chain B residue 651 HIS Chi-restraints excluded: chain B residue 654 LEU Chi-restraints excluded: chain B residue 665 LEU Chi-restraints excluded: chain B residue 690 VAL Chi-restraints excluded: chain B residue 722 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 74 optimal weight: 2.9990 chunk 91 optimal weight: 0.7980 chunk 136 optimal weight: 0.9990 chunk 100 optimal weight: 0.0020 chunk 146 optimal weight: 3.9990 chunk 137 optimal weight: 0.0570 chunk 109 optimal weight: 4.9990 chunk 90 optimal weight: 0.6980 chunk 110 optimal weight: 0.7980 chunk 129 optimal weight: 2.9990 chunk 93 optimal weight: 0.8980 overall best weight: 0.4706 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 175 HIS A 851 HIS B 318 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3687 r_free = 0.3687 target = 0.147570 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3373 r_free = 0.3373 target = 0.121422 restraints weight = 18034.717| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.3399 r_free = 0.3399 target = 0.124288 restraints weight = 15231.362| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3410 r_free = 0.3410 target = 0.125502 restraints weight = 11670.400| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3411 r_free = 0.3411 target = 0.125521 restraints weight = 8671.812| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3414 r_free = 0.3414 target = 0.125843 restraints weight = 9072.531| |-----------------------------------------------------------------------------| r_work (final): 0.3409 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8363 moved from start: 0.3153 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 13352 Z= 0.114 Angle : 0.534 10.700 18144 Z= 0.268 Chirality : 0.038 0.282 2006 Planarity : 0.004 0.043 2278 Dihedral : 3.761 19.351 1758 Min Nonbonded Distance : 2.115 Molprobity Statistics. All-atom Clashscore : 5.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.40 % Favored : 94.60 % Rotamer: Outliers : 2.61 % Allowed : 19.16 % Favored : 78.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.83 (0.23), residues: 1594 helix: 2.59 (0.17), residues: 980 sheet: -0.44 (0.44), residues: 152 loop : -1.34 (0.29), residues: 462 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG B 856 TYR 0.023 0.001 TYR B 88 PHE 0.027 0.001 PHE A 715 TRP 0.006 0.001 TRP B 804 HIS 0.024 0.001 HIS A 851 Details of bonding type rmsd/Z covalent geometry : bond 0.00234 / 0.11 (13348) covalent geometry : angle 0.53276 / 0.27 (18132) hydrogen bonds : bond 0.04838 / 3.30 ( 816) hydrogen bonds : angle 4.38311 / 3.15 ( 2412) link_BETA1-4 : bond 0.00409 / 0.24 ( 4) link_BETA1-4 : angle 1.75514 / 0.90 ( 12) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3188 Ramachandran restraints generated. 1594 Oldfield, 0 Emsley, 1594 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3188 Ramachandran restraints generated. 1594 Oldfield, 0 Emsley, 1594 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 195 residues out of total 1378 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 159 time to evaluate : 0.337 Fit side-chains revert: symmetry clash REVERT: A 207 TYR cc_start: 0.8412 (t80) cc_final: 0.8143 (t80) REVERT: A 443 LEU cc_start: 0.9406 (tp) cc_final: 0.9133 (tp) REVERT: A 607 ASN cc_start: 0.7288 (t0) cc_final: 0.6778 (t0) REVERT: A 694 THR cc_start: 0.8422 (t) cc_final: 0.8199 (p) REVERT: B 95 GLU cc_start: 0.7802 (tm-30) cc_final: 0.7401 (tm-30) REVERT: B 443 LEU cc_start: 0.9334 (tp) cc_final: 0.9071 (tp) REVERT: B 492 TYR cc_start: 0.8478 (t80) cc_final: 0.8127 (t80) REVERT: B 607 ASN cc_start: 0.7761 (t0) cc_final: 0.7457 (t0) outliers start: 36 outliers final: 33 residues processed: 185 average time/residue: 0.0827 time to fit residues: 24.6085 Evaluate side-chains 187 residues out of total 1378 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 154 time to evaluate : 0.314 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 204 THR Chi-restraints excluded: chain A residue 253 LEU Chi-restraints excluded: chain A residue 318 ASN Chi-restraints excluded: chain A residue 327 HIS Chi-restraints excluded: chain A residue 386 MET Chi-restraints excluded: chain A residue 396 LEU Chi-restraints excluded: chain A residue 435 ILE Chi-restraints excluded: chain A residue 500 SER Chi-restraints excluded: chain A residue 552 TRP Chi-restraints excluded: chain A residue 564 THR Chi-restraints excluded: chain A residue 651 HIS Chi-restraints excluded: chain A residue 654 LEU Chi-restraints excluded: chain A residue 665 LEU Chi-restraints excluded: chain A residue 690 VAL Chi-restraints excluded: chain A residue 713 MET Chi-restraints excluded: chain A residue 851 HIS Chi-restraints excluded: chain B residue 127 MET Chi-restraints excluded: chain B residue 145 SER Chi-restraints excluded: chain B residue 151 LEU Chi-restraints excluded: chain B residue 204 THR Chi-restraints excluded: chain B residue 291 ASP Chi-restraints excluded: chain B residue 318 ASN Chi-restraints excluded: chain B residue 435 ILE Chi-restraints excluded: chain B residue 500 SER Chi-restraints excluded: chain B residue 512 THR Chi-restraints excluded: chain B residue 564 THR Chi-restraints excluded: chain B residue 634 LEU Chi-restraints excluded: chain B residue 640 LEU Chi-restraints excluded: chain B residue 651 HIS Chi-restraints excluded: chain B residue 654 LEU Chi-restraints excluded: chain B residue 665 LEU Chi-restraints excluded: chain B residue 690 VAL Chi-restraints excluded: chain B residue 722 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 105 optimal weight: 4.9990 chunk 141 optimal weight: 0.5980 chunk 20 optimal weight: 0.5980 chunk 154 optimal weight: 2.9990 chunk 142 optimal weight: 0.9990 chunk 117 optimal weight: 1.9990 chunk 27 optimal weight: 0.8980 chunk 21 optimal weight: 0.9990 chunk 109 optimal weight: 3.9990 chunk 94 optimal weight: 0.0870 chunk 24 optimal weight: 1.9990 overall best weight: 0.6360 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 175 HIS A 851 HIS B 318 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3683 r_free = 0.3683 target = 0.147313 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3368 r_free = 0.3368 target = 0.121503 restraints weight = 17939.601| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 24)----------------| | r_work = 0.3367 r_free = 0.3367 target = 0.121899 restraints weight = 14571.206| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3382 r_free = 0.3382 target = 0.123572 restraints weight = 14691.902| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3391 r_free = 0.3391 target = 0.124235 restraints weight = 10234.520| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3395 r_free = 0.3395 target = 0.124769 restraints weight = 9862.301| |-----------------------------------------------------------------------------| r_work (final): 0.3391 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8383 moved from start: 0.3197 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 13352 Z= 0.121 Angle : 0.541 10.454 18144 Z= 0.271 Chirality : 0.039 0.282 2006 Planarity : 0.004 0.041 2278 Dihedral : 3.742 19.370 1758 Min Nonbonded Distance : 2.091 Molprobity Statistics. All-atom Clashscore : 5.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.58 % Favored : 94.42 % Rotamer: Outliers : 2.76 % Allowed : 19.23 % Favored : 78.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.77 (0.23), residues: 1594 helix: 2.50 (0.17), residues: 992 sheet: -0.39 (0.44), residues: 152 loop : -1.40 (0.30), residues: 450 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG B 856 TYR 0.044 0.001 TYR A 365 PHE 0.027 0.001 PHE A 611 TRP 0.007 0.001 TRP A 847 HIS 0.017 0.001 HIS A 851 Details of bonding type rmsd/Z covalent geometry : bond 0.00259 / 0.12 (13348) covalent geometry : angle 0.53907 / 0.27 (18132) hydrogen bonds : bond 0.04849 / 3.31 ( 816) hydrogen bonds : angle 4.37239 / 3.15 ( 2412) link_BETA1-4 : bond 0.00397 / 0.24 ( 4) link_BETA1-4 : angle 1.74651 / 0.88 ( 12) =============================================================================== Job complete usr+sys time: 1807.34 seconds wall clock time: 32 minutes 13.93 seconds (1933.93 seconds total)