Starting phenix.real_space_refine on Wed Sep 17 19:15:14 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8xbs_38227/09_2025/8xbs_38227.cif Found real_map, /net/cci-nas-00/data/ceres_data/8xbs_38227/09_2025/8xbs_38227.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.21 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8xbs_38227/09_2025/8xbs_38227.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8xbs_38227/09_2025/8xbs_38227.map" model { file = "/net/cci-nas-00/data/ceres_data/8xbs_38227/09_2025/8xbs_38227.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8xbs_38227/09_2025/8xbs_38227.cif" } resolution = 2.21 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.125 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 Zn 2 6.06 5 P 2 5.49 5 S 68 5.16 5 C 7018 2.51 5 N 1682 2.21 5 O 1886 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 41 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 10658 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" Number of atoms: 5094 Number of conformers: 1 Conformer: "" Number of residues, atoms: 641, 5094 Classifications: {'peptide': 641} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 7} Link IDs: {'PCIS': 1, 'PTRANS': 16, 'TRANS': 623} Chain breaks: 4 Unresolved non-hydrogen bonds: 27 Unresolved non-hydrogen angles: 33 Unresolved non-hydrogen dihedrals: 23 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'HIS:plan': 1, 'ASN:plan1': 1, 'GLU:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 15 Chain: "B" Number of atoms: 5094 Number of conformers: 1 Conformer: "" Number of residues, atoms: 641, 5094 Classifications: {'peptide': 641} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 7} Link IDs: {'PCIS': 1, 'PTRANS': 16, 'TRANS': 623} Chain breaks: 4 Unresolved non-hydrogen bonds: 27 Unresolved non-hydrogen angles: 33 Unresolved non-hydrogen dihedrals: 23 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'HIS:plan': 1, 'ASN:plan1': 1, 'GLU:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 15 Chain: "C" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "D" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "E" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "F" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "A" Number of atoms: 179 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 179 Unusual residues: {' ZN': 1, 'CLR': 4, 'NAG': 1, 'POV': 1} Classifications: {'undetermined': 7} Link IDs: {None: 6} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "B" Number of atoms: 179 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 179 Unusual residues: {' ZN': 1, 'CLR': 4, 'NAG': 1, 'POV': 1} Classifications: {'undetermined': 7} Link IDs: {None: 6} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Time building chain proxies: 2.83, per 1000 atoms: 0.27 Number of scatterers: 10658 At special positions: 0 Unit cell: (92.0125, 87.6825, 128.817, 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) Zn 2 29.99 S 68 16.00 P 2 15.00 O 1886 8.00 N 1682 7.00 C 7018 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=6, symmetry=0 Simple disulfide: pdb=" SG CYS A 225 " - pdb=" SG CYS A 287 " distance=2.03 Simple disulfide: pdb=" SG CYS A 464 " - pdb=" SG CYS A 542 " distance=2.03 Simple disulfide: pdb=" SG CYS A 470 " - pdb=" SG CYS A 731 " distance=2.03 Simple disulfide: pdb=" SG CYS B 225 " - pdb=" SG CYS B 287 " distance=2.03 Simple disulfide: pdb=" SG CYS B 464 " - pdb=" SG CYS B 542 " distance=2.03 Simple disulfide: pdb=" SG CYS B 470 " - pdb=" SG CYS B 731 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied BETA1-4 " NAG C 1 " - " NAG C 2 " " NAG D 1 " - " NAG D 2 " " NAG E 1 " - " NAG E 2 " " NAG F 1 " - " NAG F 2 " Time building additional restraints: 1.25 Conformation dependent library (CDL) restraints added in 648.7 milliseconds Enol-peptide restraints added in 953.7 nanoseconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN A 801 " pdb="ZN ZN A 801 " - pdb=" NE2 HIS A 740 " pdb="ZN ZN A 801 " - pdb=" NE2 HIS A 744 " pdb="ZN ZN A 801 " - pdb=" NE2 HIS A 540 " pdb=" ZN B 801 " pdb="ZN ZN B 801 " - pdb=" NE2 HIS B 740 " pdb="ZN ZN B 801 " - pdb=" NE2 HIS B 744 " pdb="ZN ZN B 801 " - pdb=" NE2 HIS B 540 " 2524 Ramachandran restraints generated. 1262 Oldfield, 0 Emsley, 1262 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2464 Finding SS restraints... Secondary structure from input PDB file: 52 helices and 10 sheets defined 50.4% alpha, 15.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.53 Creating SS restraints... Processing helix chain 'A' and resid 64 through 68 removed outlier: 3.628A pdb=" N ILE A 68 " --> pdb=" O GLN A 65 " (cutoff:3.500A) Processing helix chain 'A' and resid 80 through 85 Processing helix chain 'A' and resid 127 through 131 Processing helix chain 'A' and resid 206 through 210 Processing helix chain 'A' and resid 264 through 272 Processing helix chain 'A' and resid 314 through 327 Processing helix chain 'A' and resid 328 through 332 Processing helix chain 'A' and resid 335 through 343 Processing helix chain 'A' and resid 426 through 431 removed outlier: 3.500A pdb=" N LEU A 431 " --> pdb=" O HIS A 427 " (cutoff:3.500A) Processing helix chain 'A' and resid 435 through 437 No H-bonds generated for 'chain 'A' and resid 435 through 437' Processing helix chain 'A' and resid 438 through 454 Processing helix chain 'A' and resid 456 through 464 removed outlier: 3.869A pdb=" N ASP A 461 " --> pdb=" O MET A 457 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N GLU A 462 " --> pdb=" O ALA A 458 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N CYS A 464 " --> pdb=" O ARG A 460 " (cutoff:3.500A) Processing helix chain 'A' and resid 467 through 471 removed outlier: 3.762A pdb=" N ALA A 471 " --> pdb=" O HIS A 468 " (cutoff:3.500A) Processing helix chain 'A' and resid 479 through 485 removed outlier: 3.607A pdb=" N ILE A 483 " --> pdb=" O ALA A 479 " (cutoff:3.500A) Processing helix chain 'A' and resid 486 through 504 removed outlier: 3.704A pdb=" N THR A 490 " --> pdb=" O ASN A 486 " (cutoff:3.500A) Processing helix chain 'A' and resid 518 through 540 Processing helix chain 'A' and resid 552 through 569 removed outlier: 3.987A pdb=" N GLN A 556 " --> pdb=" O THR A 552 " (cutoff:3.500A) Processing helix chain 'A' and resid 577 through 596 Processing helix chain 'A' and resid 601 through 626 Processing helix chain 'A' and resid 628 through 652 removed outlier: 3.947A pdb=" N PHE A 634 " --> pdb=" O LEU A 630 " (cutoff:3.500A) Processing helix chain 'A' and resid 657 through 659 No H-bonds generated for 'chain 'A' and resid 657 through 659' Processing helix chain 'A' and resid 660 through 684 Processing helix chain 'A' and resid 689 through 711 Processing helix chain 'A' and resid 720 through 726 Processing helix chain 'A' and resid 738 through 761 Processing helix chain 'A' and resid 762 through 766 removed outlier: 3.889A pdb=" N ILE A 766 " --> pdb=" O ASP A 763 " (cutoff:3.500A) Processing helix chain 'B' and resid 64 through 68 removed outlier: 3.628A pdb=" N ILE B 68 " --> pdb=" O GLN B 65 " (cutoff:3.500A) Processing helix chain 'B' and resid 80 through 85 Processing helix chain 'B' and resid 127 through 131 Processing helix chain 'B' and resid 206 through 210 Processing helix chain 'B' and resid 264 through 272 Processing helix chain 'B' and resid 314 through 327 Processing helix chain 'B' and resid 328 through 332 Processing helix chain 'B' and resid 335 through 343 Processing helix chain 'B' and resid 426 through 431 removed outlier: 3.500A pdb=" N LEU B 431 " --> pdb=" O HIS B 427 " (cutoff:3.500A) Processing helix chain 'B' and resid 435 through 437 No H-bonds generated for 'chain 'B' and resid 435 through 437' Processing helix chain 'B' and resid 438 through 454 Processing helix chain 'B' and resid 456 through 464 removed outlier: 3.868A pdb=" N ASP B 461 " --> pdb=" O MET B 457 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N GLU B 462 " --> pdb=" O ALA B 458 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N CYS B 464 " --> pdb=" O ARG B 460 " (cutoff:3.500A) Processing helix chain 'B' and resid 467 through 471 removed outlier: 3.763A pdb=" N ALA B 471 " --> pdb=" O HIS B 468 " (cutoff:3.500A) Processing helix chain 'B' and resid 479 through 485 removed outlier: 3.607A pdb=" N ILE B 483 " --> pdb=" O ALA B 479 " (cutoff:3.500A) Processing helix chain 'B' and resid 486 through 504 removed outlier: 3.704A pdb=" N THR B 490 " --> pdb=" O ASN B 486 " (cutoff:3.500A) Processing helix chain 'B' and resid 518 through 540 Processing helix chain 'B' and resid 552 through 569 removed outlier: 3.987A pdb=" N GLN B 556 " --> pdb=" O THR B 552 " (cutoff:3.500A) Processing helix chain 'B' and resid 577 through 596 Processing helix chain 'B' and resid 601 through 626 Processing helix chain 'B' and resid 628 through 652 removed outlier: 3.947A pdb=" N PHE B 634 " --> pdb=" O LEU B 630 " (cutoff:3.500A) Processing helix chain 'B' and resid 657 through 659 No H-bonds generated for 'chain 'B' and resid 657 through 659' Processing helix chain 'B' and resid 660 through 684 Processing helix chain 'B' and resid 689 through 711 Processing helix chain 'B' and resid 720 through 726 Processing helix chain 'B' and resid 738 through 761 Processing helix chain 'B' and resid 762 through 766 removed outlier: 3.888A pdb=" N ILE B 766 " --> pdb=" O ASP B 763 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 35 through 39 removed outlier: 6.180A pdb=" N LEU A 36 " --> pdb=" O VAL A 58 " (cutoff:3.500A) removed outlier: 7.601A pdb=" N ARG A 60 " --> pdb=" O LEU A 36 " (cutoff:3.500A) removed outlier: 6.604A pdb=" N PHE A 38 " --> pdb=" O ARG A 60 " (cutoff:3.500A) removed outlier: 8.088A pdb=" N GLU A 62 " --> pdb=" O PHE A 38 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 46 through 51 removed outlier: 3.758A pdb=" N THR A 72 " --> pdb=" O LEU A 123 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 109 through 110 Processing sheet with id=AA4, first strand: chain 'A' and resid 186 through 194 removed outlier: 3.619A pdb=" N ASN A 191 " --> pdb=" O ILE A 302 " (cutoff:3.500A) removed outlier: 5.881A pdb=" N ILE A 302 " --> pdb=" O ASN A 191 " (cutoff:3.500A) removed outlier: 4.479A pdb=" N LYS A 193 " --> pdb=" O LYS A 300 " (cutoff:3.500A) removed outlier: 6.434A pdb=" N LYS A 300 " --> pdb=" O LYS A 193 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 200 through 205 Processing sheet with id=AA6, first strand: chain 'B' and resid 35 through 39 removed outlier: 6.180A pdb=" N LEU B 36 " --> pdb=" O VAL B 58 " (cutoff:3.500A) removed outlier: 7.601A pdb=" N ARG B 60 " --> pdb=" O LEU B 36 " (cutoff:3.500A) removed outlier: 6.604A pdb=" N PHE B 38 " --> pdb=" O ARG B 60 " (cutoff:3.500A) removed outlier: 8.088A pdb=" N GLU B 62 " --> pdb=" O PHE B 38 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 46 through 51 removed outlier: 3.757A pdb=" N THR B 72 " --> pdb=" O LEU B 123 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 109 through 110 Processing sheet with id=AA9, first strand: chain 'B' and resid 186 through 194 removed outlier: 3.619A pdb=" N ASN B 191 " --> pdb=" O ILE B 302 " (cutoff:3.500A) removed outlier: 5.880A pdb=" N ILE B 302 " --> pdb=" O ASN B 191 " (cutoff:3.500A) removed outlier: 4.479A pdb=" N LYS B 193 " --> pdb=" O LYS B 300 " (cutoff:3.500A) removed outlier: 6.434A pdb=" N LYS B 300 " --> pdb=" O LYS B 193 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 200 through 205 578 hydrogen bonds defined for protein. 1626 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 2.33 Time building geometry restraints manager: 1.51 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.09 - 1.24: 1320 1.24 - 1.38: 2808 1.38 - 1.53: 5523 1.53 - 1.67: 1155 1.67 - 1.82: 102 Bond restraints: 10908 Sorted by residual: bond pdb=" CA ASP A 239 " pdb=" C ASP A 239 " ideal model delta sigma weight residual 1.524 1.398 0.126 1.23e-02 6.61e+03 1.04e+02 bond pdb=" CA ASP B 239 " pdb=" C ASP B 239 " ideal model delta sigma weight residual 1.524 1.399 0.124 1.23e-02 6.61e+03 1.02e+02 bond pdb=" C TYR A 238 " pdb=" O TYR A 238 " ideal model delta sigma weight residual 1.232 1.094 0.138 1.38e-02 5.25e+03 1.00e+02 bond pdb=" C TYR B 238 " pdb=" O TYR B 238 " ideal model delta sigma weight residual 1.232 1.095 0.137 1.38e-02 5.25e+03 9.92e+01 bond pdb=" C ASP A 239 " pdb=" O ASP A 239 " ideal model delta sigma weight residual 1.234 1.118 0.116 1.34e-02 5.57e+03 7.51e+01 ... (remaining 10903 not shown) Histogram of bond angle deviations from ideal: 0.00 - 5.97: 14734 5.97 - 11.95: 56 11.95 - 17.92: 6 17.92 - 23.90: 8 23.90 - 29.87: 4 Bond angle restraints: 14808 Sorted by residual: angle pdb=" C SER B 244 " pdb=" CA SER B 244 " pdb=" CB SER B 244 " ideal model delta sigma weight residual 110.78 87.26 23.52 1.60e+00 3.91e-01 2.16e+02 angle pdb=" C SER A 244 " pdb=" CA SER A 244 " pdb=" CB SER A 244 " ideal model delta sigma weight residual 110.78 87.27 23.51 1.60e+00 3.91e-01 2.16e+02 angle pdb=" C ASP A 171 " pdb=" CA ASP A 171 " pdb=" CB ASP A 171 " ideal model delta sigma weight residual 110.29 86.97 23.32 1.64e+00 3.72e-01 2.02e+02 angle pdb=" C ASP B 171 " pdb=" CA ASP B 171 " pdb=" CB ASP B 171 " ideal model delta sigma weight residual 110.29 86.99 23.30 1.64e+00 3.72e-01 2.02e+02 angle pdb=" C SER B 33 " pdb=" CA SER B 33 " pdb=" CB SER B 33 " ideal model delta sigma weight residual 110.10 86.16 23.94 1.90e+00 2.77e-01 1.59e+02 ... (remaining 14803 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 25.28: 6250 25.28 - 50.55: 554 50.55 - 75.83: 108 75.83 - 101.10: 34 101.10 - 126.38: 42 Dihedral angle restraints: 6988 sinusoidal: 3212 harmonic: 3776 Sorted by residual: dihedral pdb=" C ASP A 171 " pdb=" N ASP A 171 " pdb=" CA ASP A 171 " pdb=" CB ASP A 171 " ideal model delta harmonic sigma weight residual -122.60 -89.92 -32.68 0 2.50e+00 1.60e-01 1.71e+02 dihedral pdb=" C ASP B 171 " pdb=" N ASP B 171 " pdb=" CA ASP B 171 " pdb=" CB ASP B 171 " ideal model delta harmonic sigma weight residual -122.60 -89.92 -32.68 0 2.50e+00 1.60e-01 1.71e+02 dihedral pdb=" C SER B 244 " pdb=" N SER B 244 " pdb=" CA SER B 244 " pdb=" CB SER B 244 " ideal model delta harmonic sigma weight residual -122.60 -92.61 -29.99 0 2.50e+00 1.60e-01 1.44e+02 ... (remaining 6985 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.226: 1740 0.226 - 0.451: 20 0.451 - 0.677: 4 0.677 - 0.903: 2 0.903 - 1.128: 4 Chirality restraints: 1770 Sorted by residual: chirality pdb=" CA PHE A 296 " pdb=" N PHE A 296 " pdb=" C PHE A 296 " pdb=" CB PHE A 296 " both_signs ideal model delta sigma weight residual False 2.51 1.38 1.13 2.00e-01 2.50e+01 3.18e+01 chirality pdb=" CA PHE B 296 " pdb=" N PHE B 296 " pdb=" C PHE B 296 " pdb=" CB PHE B 296 " both_signs ideal model delta sigma weight residual False 2.51 1.38 1.13 2.00e-01 2.50e+01 3.18e+01 chirality pdb=" CA ILE A 243 " pdb=" N ILE A 243 " pdb=" C ILE A 243 " pdb=" CB ILE A 243 " both_signs ideal model delta sigma weight residual False 2.43 1.43 1.01 2.00e-01 2.50e+01 2.53e+01 ... (remaining 1767 not shown) Planarity restraints: 1760 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C2 NAG A 807 " 0.291 2.00e-02 2.50e+03 2.55e-01 8.10e+02 pdb=" C7 NAG A 807 " -0.044 2.00e-02 2.50e+03 pdb=" C8 NAG A 807 " 0.060 2.00e-02 2.50e+03 pdb=" N2 NAG A 807 " -0.459 2.00e-02 2.50e+03 pdb=" O7 NAG A 807 " 0.152 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG B 807 " -0.291 2.00e-02 2.50e+03 2.54e-01 8.09e+02 pdb=" C7 NAG B 807 " 0.045 2.00e-02 2.50e+03 pdb=" C8 NAG B 807 " -0.060 2.00e-02 2.50e+03 pdb=" N2 NAG B 807 " 0.458 2.00e-02 2.50e+03 pdb=" O7 NAG B 807 " -0.152 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C THR B 327 " 0.065 5.00e-02 4.00e+02 9.78e-02 1.53e+01 pdb=" N PRO B 328 " -0.169 5.00e-02 4.00e+02 pdb=" CA PRO B 328 " 0.050 5.00e-02 4.00e+02 pdb=" CD PRO B 328 " 0.054 5.00e-02 4.00e+02 ... (remaining 1757 not shown) Histogram of nonbonded interaction distances: 2.19 - 2.73: 656 2.73 - 3.27: 9933 3.27 - 3.82: 17651 3.82 - 4.36: 22060 4.36 - 4.90: 36937 Nonbonded interactions: 87237 Sorted by model distance: nonbonded pdb=" O SER A 244 " pdb=" CB SER A 244 " model vdw 2.189 2.752 nonbonded pdb=" O SER B 244 " pdb=" CB SER B 244 " model vdw 2.189 2.752 nonbonded pdb=" OH TYR B 677 " pdb=" OD2 ASP B 762 " model vdw 2.277 3.040 nonbonded pdb=" OH TYR A 677 " pdb=" OD2 ASP A 762 " model vdw 2.277 3.040 nonbonded pdb=" O ILE B 612 " pdb=" OG SER B 616 " model vdw 2.284 3.040 ... (remaining 87232 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: 0.02 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' } ncs_group { reference = chain 'C' selection = chain 'D' selection = chain 'E' selection = chain 'F' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.110 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.160 Check model and map are aligned: 0.030 Set scattering table: 0.030 Process input model: 14.060 Find NCS groups from input model: 0.190 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:7.810 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 23.420 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8481 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 : 0.006 0.138 10924 Z= 0.387 Angle : 1.188 29.874 14832 Z= 0.671 Chirality : 0.083 1.128 1770 Planarity : 0.010 0.255 1760 Dihedral : 22.127 126.381 4506 Min Nonbonded Distance : 2.189 Molprobity Statistics. All-atom Clashscore : 8.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.65 % Favored : 96.35 % Rotamer: Outliers : 3.17 % Allowed : 20.77 % Favored : 76.06 % Cbeta Deviations : 1.95 % Peptide Plane: Cis-proline : 5.88 % 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 aren not related in a simple way. whole: 1.61 (0.24), residues: 1262 helix: 1.87 (0.22), residues: 552 sheet: 2.64 (0.31), residues: 252 loop : -0.93 (0.29), residues: 458 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG B 240 TYR 0.031 0.002 TYR B 238 PHE 0.014 0.002 PHE A 528 TRP 0.007 0.001 TRP B 567 HIS 0.004 0.001 HIS A 571 Details of bonding type rmsd covalent geometry : bond 0.00634 (10908) covalent geometry : angle 1.17399 (14808) SS BOND : bond 0.00109 ( 6) SS BOND : angle 0.69658 ( 12) hydrogen bonds : bond 0.15726 ( 578) hydrogen bonds : angle 5.26152 ( 1626) metal coordination : bond 0.00661 ( 6) link_BETA1-4 : bond 0.01914 ( 4) link_BETA1-4 : angle 6.54517 ( 12) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2524 Ramachandran restraints generated. 1262 Oldfield, 0 Emsley, 1262 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2524 Ramachandran restraints generated. 1262 Oldfield, 0 Emsley, 1262 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 155 residues out of total 1150 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 119 time to evaluate : 0.448 Fit side-chains REVERT: A 129 GLN cc_start: 0.8271 (mp-120) cc_final: 0.7957 (mp10) REVERT: B 129 GLN cc_start: 0.8269 (mp-120) cc_final: 0.7949 (mp10) outliers start: 36 outliers final: 30 residues processed: 148 average time/residue: 0.5657 time to fit residues: 90.9233 Evaluate side-chains 146 residues out of total 1150 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 116 time to evaluate : 0.426 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 34 SER Chi-restraints excluded: chain A residue 55 THR Chi-restraints excluded: chain A residue 66 SER Chi-restraints excluded: chain A residue 69 LEU Chi-restraints excluded: chain A residue 110 VAL Chi-restraints excluded: chain A residue 185 THR Chi-restraints excluded: chain A residue 197 VAL Chi-restraints excluded: chain A residue 221 GLU Chi-restraints excluded: chain A residue 229 ILE Chi-restraints excluded: chain A residue 244 SER Chi-restraints excluded: chain A residue 278 VAL Chi-restraints excluded: chain A residue 594 SER Chi-restraints excluded: chain A residue 616 SER Chi-restraints excluded: chain A residue 685 SER Chi-restraints excluded: chain A residue 775 ILE Chi-restraints excluded: chain B residue 34 SER Chi-restraints excluded: chain B residue 55 THR Chi-restraints excluded: chain B residue 66 SER Chi-restraints excluded: chain B residue 69 LEU Chi-restraints excluded: chain B residue 110 VAL Chi-restraints excluded: chain B residue 185 THR Chi-restraints excluded: chain B residue 197 VAL Chi-restraints excluded: chain B residue 221 GLU Chi-restraints excluded: chain B residue 229 ILE Chi-restraints excluded: chain B residue 244 SER Chi-restraints excluded: chain B residue 278 VAL Chi-restraints excluded: chain B residue 594 SER Chi-restraints excluded: chain B residue 616 SER Chi-restraints excluded: chain B residue 659 ASN Chi-restraints excluded: chain B residue 685 SER Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 98 optimal weight: 3.9990 chunk 107 optimal weight: 4.9990 chunk 10 optimal weight: 5.9990 chunk 66 optimal weight: 7.9990 chunk 124 optimal weight: 4.9990 chunk 103 optimal weight: 4.9990 chunk 77 optimal weight: 0.7980 chunk 122 optimal weight: 0.8980 chunk 91 optimal weight: 2.9990 chunk 55 optimal weight: 8.9990 chunk 35 optimal weight: 4.9990 overall best weight: 2.7386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 54 ASN A 556 GLN A 571 HIS B 54 ASN B 556 GLN B 571 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3629 r_free = 0.3629 target = 0.131719 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3186 r_free = 0.3186 target = 0.098250 restraints weight = 10876.261| |-----------------------------------------------------------------------------| r_work (start): 0.3185 rms_B_bonded: 1.63 r_work: 0.3053 rms_B_bonded: 2.27 restraints_weight: 0.5000 r_work: 0.2941 rms_B_bonded: 3.57 restraints_weight: 0.2500 r_work (final): 0.2941 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8556 moved from start: 0.0787 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.044 10924 Z= 0.233 Angle : 0.814 10.985 14832 Z= 0.392 Chirality : 0.052 0.333 1770 Planarity : 0.006 0.073 1760 Dihedral : 19.248 107.902 2218 Min Nonbonded Distance : 2.329 Molprobity Statistics. All-atom Clashscore : 5.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.80 % Favored : 96.20 % Rotamer: Outliers : 3.79 % Allowed : 17.96 % Favored : 78.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.88 % 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 aren not related in a simple way. whole: 1.60 (0.24), residues: 1262 helix: 1.93 (0.22), residues: 540 sheet: 2.60 (0.32), residues: 250 loop : -0.90 (0.28), residues: 472 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 258 TYR 0.024 0.002 TYR A 650 PHE 0.019 0.002 PHE A 528 TRP 0.010 0.002 TRP B 567 HIS 0.007 0.002 HIS A 740 Details of bonding type rmsd covalent geometry : bond 0.00534 (10908) covalent geometry : angle 0.79158 (14808) SS BOND : bond 0.00189 ( 6) SS BOND : angle 0.97708 ( 12) hydrogen bonds : bond 0.06954 ( 578) hydrogen bonds : angle 4.55726 ( 1626) metal coordination : bond 0.01034 ( 6) link_BETA1-4 : bond 0.01410 ( 4) link_BETA1-4 : angle 6.65542 ( 12) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2524 Ramachandran restraints generated. 1262 Oldfield, 0 Emsley, 1262 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2524 Ramachandran restraints generated. 1262 Oldfield, 0 Emsley, 1262 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 168 residues out of total 1150 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 125 time to evaluate : 0.439 Fit side-chains REVERT: A 129 GLN cc_start: 0.8448 (OUTLIER) cc_final: 0.8134 (mp10) REVERT: A 622 GLU cc_start: 0.7904 (tp30) cc_final: 0.7649 (tp30) REVERT: A 625 LEU cc_start: 0.7776 (mp) cc_final: 0.7529 (mp) REVERT: A 628 GLU cc_start: 0.4880 (OUTLIER) cc_final: 0.4539 (mm-30) REVERT: A 764 ASP cc_start: 0.8359 (OUTLIER) cc_final: 0.7980 (p0) REVERT: B 129 GLN cc_start: 0.8425 (OUTLIER) cc_final: 0.8115 (mp10) REVERT: B 145 PHE cc_start: 0.8519 (m-80) cc_final: 0.8259 (m-80) REVERT: B 622 GLU cc_start: 0.7926 (tp30) cc_final: 0.7663 (tp30) REVERT: B 628 GLU cc_start: 0.4954 (OUTLIER) cc_final: 0.4468 (mm-30) REVERT: B 764 ASP cc_start: 0.8356 (OUTLIER) cc_final: 0.7969 (p0) outliers start: 43 outliers final: 28 residues processed: 155 average time/residue: 0.5127 time to fit residues: 86.7008 Evaluate side-chains 154 residues out of total 1150 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 120 time to evaluate : 0.423 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 55 THR Chi-restraints excluded: chain A residue 69 LEU Chi-restraints excluded: chain A residue 91 ILE Chi-restraints excluded: chain A residue 110 VAL Chi-restraints excluded: chain A residue 114 LEU Chi-restraints excluded: chain A residue 129 GLN Chi-restraints excluded: chain A residue 185 THR Chi-restraints excluded: chain A residue 197 VAL Chi-restraints excluded: chain A residue 221 GLU Chi-restraints excluded: chain A residue 229 ILE Chi-restraints excluded: chain A residue 295 SER Chi-restraints excluded: chain A residue 435 VAL Chi-restraints excluded: chain A residue 490 THR Chi-restraints excluded: chain A residue 600 SER Chi-restraints excluded: chain A residue 628 GLU Chi-restraints excluded: chain A residue 764 ASP Chi-restraints excluded: chain A residue 775 ILE Chi-restraints excluded: chain B residue 55 THR Chi-restraints excluded: chain B residue 69 LEU Chi-restraints excluded: chain B residue 91 ILE Chi-restraints excluded: chain B residue 110 VAL Chi-restraints excluded: chain B residue 114 LEU Chi-restraints excluded: chain B residue 129 GLN Chi-restraints excluded: chain B residue 185 THR Chi-restraints excluded: chain B residue 197 VAL Chi-restraints excluded: chain B residue 221 GLU Chi-restraints excluded: chain B residue 229 ILE Chi-restraints excluded: chain B residue 295 SER Chi-restraints excluded: chain B residue 435 VAL Chi-restraints excluded: chain B residue 490 THR Chi-restraints excluded: chain B residue 600 SER Chi-restraints excluded: chain B residue 628 GLU Chi-restraints excluded: chain B residue 764 ASP Chi-restraints excluded: chain B residue 775 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 101 optimal weight: 0.9980 chunk 62 optimal weight: 0.7980 chunk 27 optimal weight: 0.8980 chunk 35 optimal weight: 3.9990 chunk 51 optimal weight: 3.9990 chunk 77 optimal weight: 0.9980 chunk 70 optimal weight: 6.9990 chunk 119 optimal weight: 6.9990 chunk 66 optimal weight: 6.9990 chunk 57 optimal weight: 0.0030 chunk 15 optimal weight: 2.9990 overall best weight: 0.7390 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 205 ASN A 450 HIS A 571 HIS B 54 ASN B 205 ASN B 450 HIS B 571 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3665 r_free = 0.3665 target = 0.135187 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3234 r_free = 0.3234 target = 0.101835 restraints weight = 11077.200| |-----------------------------------------------------------------------------| r_work (start): 0.3232 rms_B_bonded: 1.65 r_work: 0.3104 rms_B_bonded: 2.31 restraints_weight: 0.5000 r_work: 0.2995 rms_B_bonded: 3.62 restraints_weight: 0.2500 r_work (final): 0.2995 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8482 moved from start: 0.1062 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 10924 Z= 0.119 Angle : 0.638 9.640 14832 Z= 0.303 Chirality : 0.044 0.247 1770 Planarity : 0.004 0.059 1760 Dihedral : 14.873 103.264 2202 Min Nonbonded Distance : 2.537 Molprobity Statistics. All-atom Clashscore : 5.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.54 % Favored : 97.46 % Rotamer: Outliers : 3.08 % Allowed : 18.93 % Favored : 77.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.88 % 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 aren not related in a simple way. whole: 2.01 (0.24), residues: 1262 helix: 2.38 (0.22), residues: 542 sheet: 2.65 (0.31), residues: 254 loop : -0.81 (0.29), residues: 466 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 172 TYR 0.023 0.001 TYR A 650 PHE 0.012 0.001 PHE B 279 TRP 0.007 0.001 TRP B 567 HIS 0.004 0.001 HIS A 571 Details of bonding type rmsd covalent geometry : bond 0.00247 (10908) covalent geometry : angle 0.61543 (14808) SS BOND : bond 0.00016 ( 6) SS BOND : angle 0.32770 ( 12) hydrogen bonds : bond 0.04724 ( 578) hydrogen bonds : angle 4.23710 ( 1626) metal coordination : bond 0.00426 ( 6) link_BETA1-4 : bond 0.01661 ( 4) link_BETA1-4 : angle 5.95854 ( 12) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2524 Ramachandran restraints generated. 1262 Oldfield, 0 Emsley, 1262 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2524 Ramachandran restraints generated. 1262 Oldfield, 0 Emsley, 1262 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 171 residues out of total 1150 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 136 time to evaluate : 0.560 Fit side-chains REVERT: A 129 GLN cc_start: 0.8420 (OUTLIER) cc_final: 0.8088 (mp10) REVERT: A 145 PHE cc_start: 0.8481 (m-80) cc_final: 0.8261 (m-80) REVERT: A 622 GLU cc_start: 0.7949 (tp30) cc_final: 0.7678 (tp30) REVERT: A 628 GLU cc_start: 0.4731 (OUTLIER) cc_final: 0.4287 (mm-30) REVERT: B 129 GLN cc_start: 0.8407 (OUTLIER) cc_final: 0.8072 (mp10) REVERT: B 145 PHE cc_start: 0.8525 (m-80) cc_final: 0.8295 (m-80) REVERT: B 622 GLU cc_start: 0.7909 (tp30) cc_final: 0.7645 (tp30) REVERT: B 628 GLU cc_start: 0.4688 (OUTLIER) cc_final: 0.4222 (mm-30) REVERT: B 764 ASP cc_start: 0.8326 (OUTLIER) cc_final: 0.8122 (p0) outliers start: 35 outliers final: 16 residues processed: 160 average time/residue: 0.5564 time to fit residues: 96.5470 Evaluate side-chains 145 residues out of total 1150 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 124 time to evaluate : 0.391 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 55 THR Chi-restraints excluded: chain A residue 91 ILE Chi-restraints excluded: chain A residue 110 VAL Chi-restraints excluded: chain A residue 129 GLN Chi-restraints excluded: chain A residue 221 GLU Chi-restraints excluded: chain A residue 229 ILE Chi-restraints excluded: chain A residue 435 VAL Chi-restraints excluded: chain A residue 490 THR Chi-restraints excluded: chain A residue 628 GLU Chi-restraints excluded: chain A residue 674 LEU Chi-restraints excluded: chain B residue 55 THR Chi-restraints excluded: chain B residue 91 ILE Chi-restraints excluded: chain B residue 110 VAL Chi-restraints excluded: chain B residue 129 GLN Chi-restraints excluded: chain B residue 221 GLU Chi-restraints excluded: chain B residue 229 ILE Chi-restraints excluded: chain B residue 435 VAL Chi-restraints excluded: chain B residue 490 THR Chi-restraints excluded: chain B residue 628 GLU Chi-restraints excluded: chain B residue 674 LEU Chi-restraints excluded: chain B residue 764 ASP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 29 optimal weight: 9.9990 chunk 77 optimal weight: 5.9990 chunk 75 optimal weight: 6.9990 chunk 118 optimal weight: 6.9990 chunk 85 optimal weight: 6.9990 chunk 79 optimal weight: 2.9990 chunk 67 optimal weight: 9.9990 chunk 88 optimal weight: 8.9990 chunk 54 optimal weight: 6.9990 chunk 80 optimal weight: 0.8980 chunk 6 optimal weight: 0.8980 overall best weight: 3.5586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 571 HIS ** A 580 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 54 ASN B 571 HIS ** B 580 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3606 r_free = 0.3606 target = 0.130337 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3154 r_free = 0.3154 target = 0.096465 restraints weight = 11056.498| |-----------------------------------------------------------------------------| r_work (start): 0.3153 rms_B_bonded: 1.66 r_work: 0.3021 rms_B_bonded: 2.29 restraints_weight: 0.5000 r_work: 0.2910 rms_B_bonded: 3.58 restraints_weight: 0.2500 r_work (final): 0.2910 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8561 moved from start: 0.1106 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.054 10924 Z= 0.279 Angle : 0.794 10.285 14832 Z= 0.392 Chirality : 0.052 0.295 1770 Planarity : 0.006 0.079 1760 Dihedral : 14.487 103.999 2192 Min Nonbonded Distance : 2.401 Molprobity Statistics. All-atom Clashscore : 4.91 Ramachandran Plot: Outliers : 0.16 % Allowed : 3.65 % Favored : 96.20 % Rotamer: Outliers : 4.23 % Allowed : 16.64 % Favored : 79.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.88 % 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 aren not related in a simple way. whole: 1.60 (0.24), residues: 1262 helix: 1.78 (0.22), residues: 548 sheet: 2.65 (0.32), residues: 250 loop : -0.77 (0.29), residues: 464 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 258 TYR 0.021 0.003 TYR A 673 PHE 0.021 0.003 PHE B 528 TRP 0.010 0.003 TRP B 567 HIS 0.009 0.002 HIS B 740 Details of bonding type rmsd covalent geometry : bond 0.00652 (10908) covalent geometry : angle 0.76937 (14808) SS BOND : bond 0.00178 ( 6) SS BOND : angle 1.11396 ( 12) hydrogen bonds : bond 0.07317 ( 578) hydrogen bonds : angle 4.57798 ( 1626) metal coordination : bond 0.01216 ( 6) link_BETA1-4 : bond 0.01482 ( 4) link_BETA1-4 : angle 6.90566 ( 12) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2524 Ramachandran restraints generated. 1262 Oldfield, 0 Emsley, 1262 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2524 Ramachandran restraints generated. 1262 Oldfield, 0 Emsley, 1262 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 175 residues out of total 1150 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 127 time to evaluate : 0.415 Fit side-chains REVERT: A 129 GLN cc_start: 0.8432 (OUTLIER) cc_final: 0.8110 (mp10) REVERT: A 521 LEU cc_start: 0.8850 (OUTLIER) cc_final: 0.8412 (tp) REVERT: A 622 GLU cc_start: 0.7990 (OUTLIER) cc_final: 0.7674 (tp30) REVERT: A 628 GLU cc_start: 0.4735 (OUTLIER) cc_final: 0.4153 (mm-30) REVERT: B 129 GLN cc_start: 0.8427 (OUTLIER) cc_final: 0.8109 (mp10) REVERT: B 521 LEU cc_start: 0.8884 (OUTLIER) cc_final: 0.8447 (tp) REVERT: B 622 GLU cc_start: 0.7944 (OUTLIER) cc_final: 0.7590 (tp30) REVERT: B 764 ASP cc_start: 0.8355 (OUTLIER) cc_final: 0.7942 (p0) outliers start: 48 outliers final: 30 residues processed: 158 average time/residue: 0.5118 time to fit residues: 88.2264 Evaluate side-chains 159 residues out of total 1150 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 121 time to evaluate : 0.369 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 55 THR Chi-restraints excluded: chain A residue 91 ILE Chi-restraints excluded: chain A residue 109 THR Chi-restraints excluded: chain A residue 110 VAL Chi-restraints excluded: chain A residue 114 LEU Chi-restraints excluded: chain A residue 129 GLN Chi-restraints excluded: chain A residue 197 VAL Chi-restraints excluded: chain A residue 221 GLU Chi-restraints excluded: chain A residue 229 ILE Chi-restraints excluded: chain A residue 247 THR Chi-restraints excluded: chain A residue 322 MET Chi-restraints excluded: chain A residue 435 VAL Chi-restraints excluded: chain A residue 490 THR Chi-restraints excluded: chain A residue 521 LEU Chi-restraints excluded: chain A residue 622 GLU Chi-restraints excluded: chain A residue 625 LEU Chi-restraints excluded: chain A residue 628 GLU Chi-restraints excluded: chain A residue 674 LEU Chi-restraints excluded: chain A residue 775 ILE Chi-restraints excluded: chain B residue 55 THR Chi-restraints excluded: chain B residue 91 ILE Chi-restraints excluded: chain B residue 109 THR Chi-restraints excluded: chain B residue 110 VAL Chi-restraints excluded: chain B residue 114 LEU Chi-restraints excluded: chain B residue 129 GLN Chi-restraints excluded: chain B residue 197 VAL Chi-restraints excluded: chain B residue 221 GLU Chi-restraints excluded: chain B residue 229 ILE Chi-restraints excluded: chain B residue 247 THR Chi-restraints excluded: chain B residue 435 VAL Chi-restraints excluded: chain B residue 490 THR Chi-restraints excluded: chain B residue 521 LEU Chi-restraints excluded: chain B residue 622 GLU Chi-restraints excluded: chain B residue 625 LEU Chi-restraints excluded: chain B residue 628 GLU Chi-restraints excluded: chain B residue 674 LEU Chi-restraints excluded: chain B residue 764 ASP Chi-restraints excluded: chain B residue 775 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 39 optimal weight: 3.9990 chunk 56 optimal weight: 2.9990 chunk 76 optimal weight: 6.9990 chunk 29 optimal weight: 20.0000 chunk 119 optimal weight: 4.9990 chunk 80 optimal weight: 1.9990 chunk 55 optimal weight: 0.8980 chunk 15 optimal weight: 0.9990 chunk 63 optimal weight: 6.9990 chunk 92 optimal weight: 5.9990 chunk 116 optimal weight: 6.9990 overall best weight: 2.1788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 571 HIS B 54 ASN B 571 HIS B 580 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3622 r_free = 0.3622 target = 0.131664 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3177 r_free = 0.3177 target = 0.098045 restraints weight = 10918.689| |-----------------------------------------------------------------------------| r_work (start): 0.3176 rms_B_bonded: 1.64 r_work: 0.3043 rms_B_bonded: 2.29 restraints_weight: 0.5000 r_work: 0.2933 rms_B_bonded: 3.57 restraints_weight: 0.2500 r_work (final): 0.2933 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8539 moved from start: 0.1138 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 10924 Z= 0.191 Angle : 0.699 10.051 14832 Z= 0.343 Chirality : 0.047 0.283 1770 Planarity : 0.005 0.081 1760 Dihedral : 14.171 103.540 2192 Min Nonbonded Distance : 2.471 Molprobity Statistics. All-atom Clashscore : 4.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.49 % Favored : 96.51 % Rotamer: Outliers : 3.43 % Allowed : 17.43 % Favored : 79.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.88 % 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 aren not related in a simple way. whole: 1.77 (0.24), residues: 1262 helix: 2.06 (0.22), residues: 540 sheet: 2.66 (0.32), residues: 250 loop : -0.78 (0.28), residues: 472 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG B 258 TYR 0.022 0.002 TYR B 650 PHE 0.017 0.002 PHE A 528 TRP 0.010 0.002 TRP B 567 HIS 0.006 0.001 HIS B 740 Details of bonding type rmsd covalent geometry : bond 0.00436 (10908) covalent geometry : angle 0.67327 (14808) SS BOND : bond 0.00124 ( 6) SS BOND : angle 0.82263 ( 12) hydrogen bonds : bond 0.06165 ( 578) hydrogen bonds : angle 4.44792 ( 1626) metal coordination : bond 0.00922 ( 6) link_BETA1-4 : bond 0.01617 ( 4) link_BETA1-4 : angle 6.62063 ( 12) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2524 Ramachandran restraints generated. 1262 Oldfield, 0 Emsley, 1262 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2524 Ramachandran restraints generated. 1262 Oldfield, 0 Emsley, 1262 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 165 residues out of total 1150 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 126 time to evaluate : 0.339 Fit side-chains REVERT: A 129 GLN cc_start: 0.8449 (OUTLIER) cc_final: 0.8123 (mp10) REVERT: A 222 ASP cc_start: 0.8714 (OUTLIER) cc_final: 0.8258 (p0) REVERT: A 521 LEU cc_start: 0.8761 (OUTLIER) cc_final: 0.8325 (tp) REVERT: A 622 GLU cc_start: 0.7904 (tp30) cc_final: 0.7542 (tp30) REVERT: B 129 GLN cc_start: 0.8444 (OUTLIER) cc_final: 0.8121 (mp10) REVERT: B 521 LEU cc_start: 0.8775 (OUTLIER) cc_final: 0.8334 (tp) REVERT: B 622 GLU cc_start: 0.7912 (tp30) cc_final: 0.7552 (tp30) REVERT: B 764 ASP cc_start: 0.8312 (OUTLIER) cc_final: 0.7906 (p0) outliers start: 39 outliers final: 25 residues processed: 154 average time/residue: 0.4901 time to fit residues: 82.1360 Evaluate side-chains 151 residues out of total 1150 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 120 time to evaluate : 0.394 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 55 THR Chi-restraints excluded: chain A residue 91 ILE Chi-restraints excluded: chain A residue 110 VAL Chi-restraints excluded: chain A residue 114 LEU Chi-restraints excluded: chain A residue 129 GLN Chi-restraints excluded: chain A residue 197 VAL Chi-restraints excluded: chain A residue 221 GLU Chi-restraints excluded: chain A residue 222 ASP Chi-restraints excluded: chain A residue 229 ILE Chi-restraints excluded: chain A residue 278 VAL Chi-restraints excluded: chain A residue 322 MET Chi-restraints excluded: chain A residue 490 THR Chi-restraints excluded: chain A residue 521 LEU Chi-restraints excluded: chain A residue 625 LEU Chi-restraints excluded: chain A residue 674 LEU Chi-restraints excluded: chain A residue 775 ILE Chi-restraints excluded: chain B residue 55 THR Chi-restraints excluded: chain B residue 91 ILE Chi-restraints excluded: chain B residue 110 VAL Chi-restraints excluded: chain B residue 114 LEU Chi-restraints excluded: chain B residue 129 GLN Chi-restraints excluded: chain B residue 221 GLU Chi-restraints excluded: chain B residue 229 ILE Chi-restraints excluded: chain B residue 278 VAL Chi-restraints excluded: chain B residue 322 MET Chi-restraints excluded: chain B residue 490 THR Chi-restraints excluded: chain B residue 521 LEU Chi-restraints excluded: chain B residue 625 LEU Chi-restraints excluded: chain B residue 674 LEU Chi-restraints excluded: chain B residue 764 ASP Chi-restraints excluded: chain B residue 775 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 68 optimal weight: 4.9990 chunk 38 optimal weight: 5.9990 chunk 4 optimal weight: 3.9990 chunk 40 optimal weight: 0.0670 chunk 19 optimal weight: 6.9990 chunk 99 optimal weight: 4.9990 chunk 123 optimal weight: 3.9990 chunk 58 optimal weight: 6.9990 chunk 43 optimal weight: 4.9990 chunk 71 optimal weight: 0.9990 chunk 88 optimal weight: 10.0000 overall best weight: 2.8126 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 571 HIS ** A 580 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 54 ASN B 571 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3608 r_free = 0.3608 target = 0.130477 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3158 r_free = 0.3158 target = 0.096693 restraints weight = 10990.374| |-----------------------------------------------------------------------------| r_work (start): 0.3159 rms_B_bonded: 1.65 r_work: 0.3026 rms_B_bonded: 2.29 restraints_weight: 0.5000 r_work: 0.2914 rms_B_bonded: 3.58 restraints_weight: 0.2500 r_work (final): 0.2914 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8556 moved from start: 0.1234 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.060 10924 Z= 0.232 Angle : 0.749 10.112 14832 Z= 0.370 Chirality : 0.049 0.293 1770 Planarity : 0.006 0.080 1760 Dihedral : 14.144 103.741 2192 Min Nonbonded Distance : 2.446 Molprobity Statistics. All-atom Clashscore : 4.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.49 % Favored : 96.51 % Rotamer: Outliers : 3.96 % Allowed : 17.78 % Favored : 78.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.88 % 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 aren not related in a simple way. whole: 1.59 (0.24), residues: 1262 helix: 1.78 (0.22), residues: 548 sheet: 2.61 (0.32), residues: 250 loop : -0.78 (0.29), residues: 464 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 258 TYR 0.021 0.002 TYR B 673 PHE 0.019 0.002 PHE A 528 TRP 0.010 0.002 TRP B 567 HIS 0.008 0.002 HIS B 740 Details of bonding type rmsd covalent geometry : bond 0.00538 (10908) covalent geometry : angle 0.72604 (14808) SS BOND : bond 0.00153 ( 6) SS BOND : angle 0.93530 ( 12) hydrogen bonds : bond 0.06907 ( 578) hydrogen bonds : angle 4.54086 ( 1626) metal coordination : bond 0.01036 ( 6) link_BETA1-4 : bond 0.01520 ( 4) link_BETA1-4 : angle 6.53062 ( 12) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2524 Ramachandran restraints generated. 1262 Oldfield, 0 Emsley, 1262 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2524 Ramachandran restraints generated. 1262 Oldfield, 0 Emsley, 1262 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 171 residues out of total 1150 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 126 time to evaluate : 0.406 Fit side-chains REVERT: A 129 GLN cc_start: 0.8435 (OUTLIER) cc_final: 0.8108 (mp10) REVERT: A 521 LEU cc_start: 0.8828 (OUTLIER) cc_final: 0.8387 (tp) REVERT: A 622 GLU cc_start: 0.7960 (OUTLIER) cc_final: 0.7617 (tp30) REVERT: A 628 GLU cc_start: 0.4914 (OUTLIER) cc_final: 0.4704 (tp30) REVERT: A 764 ASP cc_start: 0.8300 (OUTLIER) cc_final: 0.7881 (p0) REVERT: B 129 GLN cc_start: 0.8431 (OUTLIER) cc_final: 0.8108 (mp10) REVERT: B 521 LEU cc_start: 0.8823 (OUTLIER) cc_final: 0.8383 (tp) REVERT: B 622 GLU cc_start: 0.7918 (OUTLIER) cc_final: 0.7561 (tp30) REVERT: B 628 GLU cc_start: 0.4920 (OUTLIER) cc_final: 0.4699 (tp30) REVERT: B 764 ASP cc_start: 0.8309 (OUTLIER) cc_final: 0.7885 (p0) outliers start: 45 outliers final: 29 residues processed: 153 average time/residue: 0.5118 time to fit residues: 85.1105 Evaluate side-chains 162 residues out of total 1150 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 123 time to evaluate : 0.329 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 55 THR Chi-restraints excluded: chain A residue 66 SER Chi-restraints excluded: chain A residue 91 ILE Chi-restraints excluded: chain A residue 110 VAL Chi-restraints excluded: chain A residue 114 LEU Chi-restraints excluded: chain A residue 129 GLN Chi-restraints excluded: chain A residue 221 GLU Chi-restraints excluded: chain A residue 229 ILE Chi-restraints excluded: chain A residue 247 THR Chi-restraints excluded: chain A residue 278 VAL Chi-restraints excluded: chain A residue 322 MET Chi-restraints excluded: chain A residue 490 THR Chi-restraints excluded: chain A residue 521 LEU Chi-restraints excluded: chain A residue 622 GLU Chi-restraints excluded: chain A residue 625 LEU Chi-restraints excluded: chain A residue 628 GLU Chi-restraints excluded: chain A residue 641 MET Chi-restraints excluded: chain A residue 674 LEU Chi-restraints excluded: chain A residue 764 ASP Chi-restraints excluded: chain A residue 775 ILE Chi-restraints excluded: chain B residue 55 THR Chi-restraints excluded: chain B residue 91 ILE Chi-restraints excluded: chain B residue 110 VAL Chi-restraints excluded: chain B residue 114 LEU Chi-restraints excluded: chain B residue 129 GLN Chi-restraints excluded: chain B residue 221 GLU Chi-restraints excluded: chain B residue 229 ILE Chi-restraints excluded: chain B residue 247 THR Chi-restraints excluded: chain B residue 278 VAL Chi-restraints excluded: chain B residue 322 MET Chi-restraints excluded: chain B residue 490 THR Chi-restraints excluded: chain B residue 521 LEU Chi-restraints excluded: chain B residue 622 GLU Chi-restraints excluded: chain B residue 625 LEU Chi-restraints excluded: chain B residue 628 GLU Chi-restraints excluded: chain B residue 641 MET Chi-restraints excluded: chain B residue 674 LEU Chi-restraints excluded: chain B residue 764 ASP Chi-restraints excluded: chain B residue 775 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 72 optimal weight: 4.9990 chunk 94 optimal weight: 0.8980 chunk 24 optimal weight: 8.9990 chunk 48 optimal weight: 10.0000 chunk 26 optimal weight: 0.0470 chunk 119 optimal weight: 4.9990 chunk 117 optimal weight: 3.9990 chunk 38 optimal weight: 3.9990 chunk 43 optimal weight: 3.9990 chunk 92 optimal weight: 1.9990 chunk 55 optimal weight: 3.9990 overall best weight: 2.1884 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 571 HIS A 580 ASN B 54 ASN B 571 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3655 r_free = 0.3655 target = 0.133537 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3220 r_free = 0.3220 target = 0.100118 restraints weight = 10916.852| |-----------------------------------------------------------------------------| r_work (start): 0.3215 rms_B_bonded: 1.64 r_work: 0.3087 rms_B_bonded: 2.28 restraints_weight: 0.5000 r_work: 0.2979 rms_B_bonded: 3.56 restraints_weight: 0.2500 r_work (final): 0.2979 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8559 moved from start: 0.1258 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.057 10924 Z= 0.191 Angle : 0.690 10.026 14832 Z= 0.340 Chirality : 0.047 0.284 1770 Planarity : 0.005 0.078 1760 Dihedral : 13.861 103.260 2192 Min Nonbonded Distance : 2.473 Molprobity Statistics. All-atom Clashscore : 5.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.85 % Favored : 97.15 % Rotamer: Outliers : 3.61 % Allowed : 18.49 % Favored : 77.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.88 % 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 aren not related in a simple way. whole: 1.77 (0.24), residues: 1262 helix: 2.06 (0.22), residues: 542 sheet: 2.65 (0.33), residues: 250 loop : -0.79 (0.29), residues: 470 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG B 258 TYR 0.022 0.002 TYR B 650 PHE 0.016 0.002 PHE A 528 TRP 0.010 0.002 TRP B 567 HIS 0.006 0.001 HIS A 740 Details of bonding type rmsd covalent geometry : bond 0.00436 (10908) covalent geometry : angle 0.66694 (14808) SS BOND : bond 0.00109 ( 6) SS BOND : angle 0.79264 ( 12) hydrogen bonds : bond 0.06131 ( 578) hydrogen bonds : angle 4.43658 ( 1626) metal coordination : bond 0.00886 ( 6) link_BETA1-4 : bond 0.01559 ( 4) link_BETA1-4 : angle 6.22570 ( 12) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2524 Ramachandran restraints generated. 1262 Oldfield, 0 Emsley, 1262 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2524 Ramachandran restraints generated. 1262 Oldfield, 0 Emsley, 1262 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 169 residues out of total 1150 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 128 time to evaluate : 0.437 Fit side-chains REVERT: A 129 GLN cc_start: 0.8445 (OUTLIER) cc_final: 0.8122 (mp10) REVERT: A 521 LEU cc_start: 0.8761 (OUTLIER) cc_final: 0.8309 (tp) REVERT: A 622 GLU cc_start: 0.7928 (OUTLIER) cc_final: 0.7582 (tp30) REVERT: A 764 ASP cc_start: 0.8272 (OUTLIER) cc_final: 0.7852 (p0) REVERT: B 129 GLN cc_start: 0.8450 (OUTLIER) cc_final: 0.8131 (mp10) REVERT: B 521 LEU cc_start: 0.8747 (OUTLIER) cc_final: 0.8288 (tp) REVERT: B 622 GLU cc_start: 0.7942 (OUTLIER) cc_final: 0.7600 (tp30) REVERT: B 628 GLU cc_start: 0.4913 (OUTLIER) cc_final: 0.4706 (tp30) REVERT: B 764 ASP cc_start: 0.8276 (OUTLIER) cc_final: 0.7853 (p0) outliers start: 41 outliers final: 26 residues processed: 150 average time/residue: 0.5617 time to fit residues: 91.4031 Evaluate side-chains 159 residues out of total 1150 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 124 time to evaluate : 0.456 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 55 THR Chi-restraints excluded: chain A residue 66 SER Chi-restraints excluded: chain A residue 91 ILE Chi-restraints excluded: chain A residue 110 VAL Chi-restraints excluded: chain A residue 114 LEU Chi-restraints excluded: chain A residue 129 GLN Chi-restraints excluded: chain A residue 221 GLU Chi-restraints excluded: chain A residue 229 ILE Chi-restraints excluded: chain A residue 278 VAL Chi-restraints excluded: chain A residue 322 MET Chi-restraints excluded: chain A residue 490 THR Chi-restraints excluded: chain A residue 521 LEU Chi-restraints excluded: chain A residue 622 GLU Chi-restraints excluded: chain A residue 625 LEU Chi-restraints excluded: chain A residue 641 MET Chi-restraints excluded: chain A residue 674 LEU Chi-restraints excluded: chain A residue 764 ASP Chi-restraints excluded: chain A residue 775 ILE Chi-restraints excluded: chain B residue 55 THR Chi-restraints excluded: chain B residue 91 ILE Chi-restraints excluded: chain B residue 110 VAL Chi-restraints excluded: chain B residue 114 LEU Chi-restraints excluded: chain B residue 129 GLN Chi-restraints excluded: chain B residue 221 GLU Chi-restraints excluded: chain B residue 229 ILE Chi-restraints excluded: chain B residue 278 VAL Chi-restraints excluded: chain B residue 322 MET Chi-restraints excluded: chain B residue 490 THR Chi-restraints excluded: chain B residue 521 LEU Chi-restraints excluded: chain B residue 622 GLU Chi-restraints excluded: chain B residue 625 LEU Chi-restraints excluded: chain B residue 628 GLU Chi-restraints excluded: chain B residue 641 MET Chi-restraints excluded: chain B residue 674 LEU Chi-restraints excluded: chain B residue 764 ASP Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 68 optimal weight: 10.0000 chunk 54 optimal weight: 5.9990 chunk 28 optimal weight: 2.9990 chunk 49 optimal weight: 0.1980 chunk 40 optimal weight: 0.3980 chunk 116 optimal weight: 7.9990 chunk 42 optimal weight: 5.9990 chunk 48 optimal weight: 8.9990 chunk 13 optimal weight: 0.0020 chunk 61 optimal weight: 0.8980 chunk 119 optimal weight: 6.9990 overall best weight: 0.8990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 571 HIS B 54 ASN B 486 ASN B 571 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3686 r_free = 0.3686 target = 0.136012 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3260 r_free = 0.3260 target = 0.102863 restraints weight = 11015.757| |-----------------------------------------------------------------------------| r_work (start): 0.3264 rms_B_bonded: 1.62 r_work: 0.3134 rms_B_bonded: 2.28 restraints_weight: 0.5000 r_work: 0.3028 rms_B_bonded: 3.57 restraints_weight: 0.2500 r_work (final): 0.3028 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8527 moved from start: 0.1385 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.072 10924 Z= 0.125 Angle : 0.606 9.905 14832 Z= 0.298 Chirality : 0.043 0.271 1770 Planarity : 0.004 0.068 1760 Dihedral : 13.255 100.547 2192 Min Nonbonded Distance : 2.543 Molprobity Statistics. All-atom Clashscore : 5.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.93 % Favored : 97.07 % Rotamer: Outliers : 3.43 % Allowed : 18.84 % Favored : 77.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.88 % 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 aren not related in a simple way. whole: 2.04 (0.24), residues: 1262 helix: 2.43 (0.22), residues: 542 sheet: 2.57 (0.32), residues: 254 loop : -0.74 (0.29), residues: 466 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 570 TYR 0.022 0.001 TYR A 650 PHE 0.012 0.001 PHE A 202 TRP 0.009 0.001 TRP A 567 HIS 0.004 0.001 HIS B 571 Details of bonding type rmsd covalent geometry : bond 0.00277 (10908) covalent geometry : angle 0.58536 (14808) SS BOND : bond 0.00041 ( 6) SS BOND : angle 0.38907 ( 12) hydrogen bonds : bond 0.04777 ( 578) hydrogen bonds : angle 4.21983 ( 1626) metal coordination : bond 0.00511 ( 6) link_BETA1-4 : bond 0.01482 ( 4) link_BETA1-4 : angle 5.54236 ( 12) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2524 Ramachandran restraints generated. 1262 Oldfield, 0 Emsley, 1262 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2524 Ramachandran restraints generated. 1262 Oldfield, 0 Emsley, 1262 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 169 residues out of total 1150 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 130 time to evaluate : 0.420 Fit side-chains REVERT: A 129 GLN cc_start: 0.8465 (OUTLIER) cc_final: 0.8142 (mp10) REVERT: A 222 ASP cc_start: 0.8684 (OUTLIER) cc_final: 0.8223 (p0) REVERT: A 622 GLU cc_start: 0.7984 (OUTLIER) cc_final: 0.7707 (tp30) REVERT: A 628 GLU cc_start: 0.4609 (OUTLIER) cc_final: 0.4280 (mm-30) REVERT: A 764 ASP cc_start: 0.8293 (OUTLIER) cc_final: 0.7876 (p0) REVERT: B 129 GLN cc_start: 0.8469 (OUTLIER) cc_final: 0.8150 (mp10) REVERT: B 222 ASP cc_start: 0.8719 (OUTLIER) cc_final: 0.8283 (p0) REVERT: B 622 GLU cc_start: 0.7992 (OUTLIER) cc_final: 0.7695 (tp30) REVERT: B 628 GLU cc_start: 0.4903 (OUTLIER) cc_final: 0.4670 (tp30) REVERT: B 764 ASP cc_start: 0.8301 (OUTLIER) cc_final: 0.7889 (p0) outliers start: 39 outliers final: 22 residues processed: 152 average time/residue: 0.5513 time to fit residues: 90.8826 Evaluate side-chains 154 residues out of total 1150 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 122 time to evaluate : 0.367 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 55 THR Chi-restraints excluded: chain A residue 66 SER Chi-restraints excluded: chain A residue 91 ILE Chi-restraints excluded: chain A residue 114 LEU Chi-restraints excluded: chain A residue 129 GLN Chi-restraints excluded: chain A residue 221 GLU Chi-restraints excluded: chain A residue 222 ASP Chi-restraints excluded: chain A residue 229 ILE Chi-restraints excluded: chain A residue 247 THR Chi-restraints excluded: chain A residue 278 VAL Chi-restraints excluded: chain A residue 322 MET Chi-restraints excluded: chain A residue 490 THR Chi-restraints excluded: chain A residue 622 GLU Chi-restraints excluded: chain A residue 628 GLU Chi-restraints excluded: chain A residue 674 LEU Chi-restraints excluded: chain A residue 764 ASP Chi-restraints excluded: chain B residue 55 THR Chi-restraints excluded: chain B residue 66 SER Chi-restraints excluded: chain B residue 91 ILE Chi-restraints excluded: chain B residue 114 LEU Chi-restraints excluded: chain B residue 129 GLN Chi-restraints excluded: chain B residue 221 GLU Chi-restraints excluded: chain B residue 222 ASP Chi-restraints excluded: chain B residue 229 ILE Chi-restraints excluded: chain B residue 278 VAL Chi-restraints excluded: chain B residue 490 THR Chi-restraints excluded: chain B residue 622 GLU Chi-restraints excluded: chain B residue 625 LEU Chi-restraints excluded: chain B residue 628 GLU Chi-restraints excluded: chain B residue 674 LEU Chi-restraints excluded: chain B residue 764 ASP Chi-restraints excluded: chain B residue 775 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 126 optimal weight: 2.9990 chunk 106 optimal weight: 5.9990 chunk 78 optimal weight: 3.9990 chunk 37 optimal weight: 8.9990 chunk 122 optimal weight: 5.9990 chunk 41 optimal weight: 7.9990 chunk 121 optimal weight: 4.9990 chunk 46 optimal weight: 2.9990 chunk 102 optimal weight: 4.9990 chunk 33 optimal weight: 5.9990 chunk 111 optimal weight: 5.9990 overall best weight: 3.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 191 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 571 HIS B 54 ASN B 571 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3598 r_free = 0.3598 target = 0.129652 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3149 r_free = 0.3149 target = 0.096059 restraints weight = 10865.736| |-----------------------------------------------------------------------------| r_work (start): 0.3149 rms_B_bonded: 1.63 r_work: 0.3014 rms_B_bonded: 2.27 restraints_weight: 0.5000 r_work: 0.2903 rms_B_bonded: 3.54 restraints_weight: 0.2500 r_work (final): 0.2903 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8567 moved from start: 0.1371 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.076 10924 Z= 0.303 Angle : 0.804 10.121 14832 Z= 0.398 Chirality : 0.053 0.292 1770 Planarity : 0.006 0.069 1760 Dihedral : 13.888 103.142 2190 Min Nonbonded Distance : 2.397 Molprobity Statistics. All-atom Clashscore : 5.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.04 % Favored : 95.96 % Rotamer: Outliers : 3.17 % Allowed : 19.28 % Favored : 77.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.88 % 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 aren not related in a simple way. whole: 1.52 (0.24), residues: 1262 helix: 1.67 (0.22), residues: 550 sheet: 2.60 (0.32), residues: 250 loop : -0.76 (0.29), residues: 462 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 258 TYR 0.023 0.003 TYR B 673 PHE 0.021 0.003 PHE A 528 TRP 0.010 0.003 TRP A 703 HIS 0.010 0.002 HIS A 740 Details of bonding type rmsd covalent geometry : bond 0.00716 (10908) covalent geometry : angle 0.78324 (14808) SS BOND : bond 0.00196 ( 6) SS BOND : angle 1.10222 ( 12) hydrogen bonds : bond 0.07471 ( 578) hydrogen bonds : angle 4.60814 ( 1626) metal coordination : bond 0.01391 ( 6) link_BETA1-4 : bond 0.01312 ( 4) link_BETA1-4 : angle 6.39756 ( 12) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2524 Ramachandran restraints generated. 1262 Oldfield, 0 Emsley, 1262 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2524 Ramachandran restraints generated. 1262 Oldfield, 0 Emsley, 1262 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 164 residues out of total 1150 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 128 time to evaluate : 0.484 Fit side-chains REVERT: A 129 GLN cc_start: 0.8429 (OUTLIER) cc_final: 0.8104 (mp10) REVERT: A 521 LEU cc_start: 0.8850 (OUTLIER) cc_final: 0.8443 (tp) REVERT: A 622 GLU cc_start: 0.7966 (OUTLIER) cc_final: 0.7620 (tp30) REVERT: A 641 MET cc_start: 0.8014 (OUTLIER) cc_final: 0.7758 (mmp) REVERT: A 764 ASP cc_start: 0.8301 (OUTLIER) cc_final: 0.7900 (p0) REVERT: B 129 GLN cc_start: 0.8429 (OUTLIER) cc_final: 0.8109 (mp10) REVERT: B 622 GLU cc_start: 0.7929 (OUTLIER) cc_final: 0.7572 (tp30) REVERT: B 628 GLU cc_start: 0.4968 (OUTLIER) cc_final: 0.4764 (tp30) REVERT: B 764 ASP cc_start: 0.8309 (OUTLIER) cc_final: 0.7901 (p0) outliers start: 36 outliers final: 24 residues processed: 146 average time/residue: 0.5590 time to fit residues: 88.4325 Evaluate side-chains 155 residues out of total 1150 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 122 time to evaluate : 0.408 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 55 THR Chi-restraints excluded: chain A residue 66 SER Chi-restraints excluded: chain A residue 91 ILE Chi-restraints excluded: chain A residue 114 LEU Chi-restraints excluded: chain A residue 129 GLN Chi-restraints excluded: chain A residue 221 GLU Chi-restraints excluded: chain A residue 229 ILE Chi-restraints excluded: chain A residue 247 THR Chi-restraints excluded: chain A residue 278 VAL Chi-restraints excluded: chain A residue 322 MET Chi-restraints excluded: chain A residue 490 THR Chi-restraints excluded: chain A residue 521 LEU Chi-restraints excluded: chain A residue 622 GLU Chi-restraints excluded: chain A residue 641 MET Chi-restraints excluded: chain A residue 764 ASP Chi-restraints excluded: chain A residue 775 ILE Chi-restraints excluded: chain B residue 55 THR Chi-restraints excluded: chain B residue 66 SER Chi-restraints excluded: chain B residue 91 ILE Chi-restraints excluded: chain B residue 114 LEU Chi-restraints excluded: chain B residue 129 GLN Chi-restraints excluded: chain B residue 221 GLU Chi-restraints excluded: chain B residue 229 ILE Chi-restraints excluded: chain B residue 247 THR Chi-restraints excluded: chain B residue 278 VAL Chi-restraints excluded: chain B residue 322 MET Chi-restraints excluded: chain B residue 490 THR Chi-restraints excluded: chain B residue 622 GLU Chi-restraints excluded: chain B residue 625 LEU Chi-restraints excluded: chain B residue 628 GLU Chi-restraints excluded: chain B residue 674 LEU Chi-restraints excluded: chain B residue 764 ASP Chi-restraints excluded: chain B residue 775 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 6 optimal weight: 0.9980 chunk 32 optimal weight: 2.9990 chunk 11 optimal weight: 3.9990 chunk 97 optimal weight: 1.9990 chunk 18 optimal weight: 0.8980 chunk 44 optimal weight: 0.9990 chunk 49 optimal weight: 0.7980 chunk 81 optimal weight: 4.9990 chunk 16 optimal weight: 0.6980 chunk 35 optimal weight: 3.9990 chunk 15 optimal weight: 0.8980 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 571 HIS B 54 ASN B 205 ASN B 571 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3643 r_free = 0.3643 target = 0.133254 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3206 r_free = 0.3206 target = 0.099930 restraints weight = 10870.365| |-----------------------------------------------------------------------------| r_work (start): 0.3204 rms_B_bonded: 1.64 r_work: 0.3071 rms_B_bonded: 2.30 restraints_weight: 0.5000 r_work: 0.2961 rms_B_bonded: 3.60 restraints_weight: 0.2500 r_work (final): 0.2961 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8511 moved from start: 0.1377 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.057 10924 Z= 0.129 Angle : 0.616 9.954 14832 Z= 0.304 Chirality : 0.043 0.276 1770 Planarity : 0.005 0.073 1760 Dihedral : 13.373 100.851 2190 Min Nonbonded Distance : 2.497 Molprobity Statistics. All-atom Clashscore : 4.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.69 % Favored : 97.31 % Rotamer: Outliers : 2.90 % Allowed : 19.45 % Favored : 77.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.88 % 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 aren not related in a simple way. whole: 1.97 (0.24), residues: 1262 helix: 2.32 (0.22), residues: 542 sheet: 2.51 (0.32), residues: 254 loop : -0.70 (0.29), residues: 466 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 570 TYR 0.022 0.001 TYR B 650 PHE 0.011 0.001 PHE B 202 TRP 0.009 0.001 TRP B 567 HIS 0.004 0.001 HIS B 571 Details of bonding type rmsd covalent geometry : bond 0.00281 (10908) covalent geometry : angle 0.59643 (14808) SS BOND : bond 0.00059 ( 6) SS BOND : angle 0.47744 ( 12) hydrogen bonds : bond 0.05030 ( 578) hydrogen bonds : angle 4.27189 ( 1626) metal coordination : bond 0.00460 ( 6) link_BETA1-4 : bond 0.01533 ( 4) link_BETA1-4 : angle 5.52829 ( 12) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2524 Ramachandran restraints generated. 1262 Oldfield, 0 Emsley, 1262 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2524 Ramachandran restraints generated. 1262 Oldfield, 0 Emsley, 1262 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 160 residues out of total 1150 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 127 time to evaluate : 0.391 Fit side-chains REVERT: A 129 GLN cc_start: 0.8440 (OUTLIER) cc_final: 0.8105 (mp10) REVERT: A 222 ASP cc_start: 0.8695 (OUTLIER) cc_final: 0.8228 (p0) REVERT: A 622 GLU cc_start: 0.7900 (OUTLIER) cc_final: 0.7612 (tp30) REVERT: A 764 ASP cc_start: 0.8294 (OUTLIER) cc_final: 0.7884 (p0) REVERT: B 129 GLN cc_start: 0.8438 (OUTLIER) cc_final: 0.8104 (mp10) REVERT: B 521 LEU cc_start: 0.8712 (OUTLIER) cc_final: 0.8287 (tp) REVERT: B 622 GLU cc_start: 0.7904 (OUTLIER) cc_final: 0.7559 (tp30) REVERT: B 628 GLU cc_start: 0.4911 (OUTLIER) cc_final: 0.4647 (tp30) REVERT: B 764 ASP cc_start: 0.8301 (OUTLIER) cc_final: 0.7891 (p0) outliers start: 33 outliers final: 19 residues processed: 146 average time/residue: 0.5820 time to fit residues: 91.9859 Evaluate side-chains 149 residues out of total 1150 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 121 time to evaluate : 0.409 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 55 THR Chi-restraints excluded: chain A residue 66 SER Chi-restraints excluded: chain A residue 91 ILE Chi-restraints excluded: chain A residue 114 LEU Chi-restraints excluded: chain A residue 129 GLN Chi-restraints excluded: chain A residue 221 GLU Chi-restraints excluded: chain A residue 222 ASP Chi-restraints excluded: chain A residue 229 ILE Chi-restraints excluded: chain A residue 247 THR Chi-restraints excluded: chain A residue 490 THR Chi-restraints excluded: chain A residue 611 VAL Chi-restraints excluded: chain A residue 622 GLU Chi-restraints excluded: chain A residue 764 ASP Chi-restraints excluded: chain B residue 55 THR Chi-restraints excluded: chain B residue 91 ILE Chi-restraints excluded: chain B residue 129 GLN Chi-restraints excluded: chain B residue 221 GLU Chi-restraints excluded: chain B residue 229 ILE Chi-restraints excluded: chain B residue 247 THR Chi-restraints excluded: chain B residue 278 VAL Chi-restraints excluded: chain B residue 490 THR Chi-restraints excluded: chain B residue 521 LEU Chi-restraints excluded: chain B residue 611 VAL Chi-restraints excluded: chain B residue 622 GLU Chi-restraints excluded: chain B residue 625 LEU Chi-restraints excluded: chain B residue 628 GLU Chi-restraints excluded: chain B residue 674 LEU Chi-restraints excluded: chain B residue 764 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 105 optimal weight: 0.7980 chunk 84 optimal weight: 4.9990 chunk 20 optimal weight: 0.8980 chunk 36 optimal weight: 3.9990 chunk 61 optimal weight: 1.9990 chunk 119 optimal weight: 5.9990 chunk 83 optimal weight: 5.9990 chunk 115 optimal weight: 4.9990 chunk 101 optimal weight: 9.9990 chunk 85 optimal weight: 3.9990 chunk 73 optimal weight: 3.9990 overall best weight: 2.3386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 571 HIS B 54 ASN B 571 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3619 r_free = 0.3619 target = 0.131196 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3170 r_free = 0.3170 target = 0.097491 restraints weight = 10960.595| |-----------------------------------------------------------------------------| r_work (start): 0.3168 rms_B_bonded: 1.65 r_work: 0.3034 rms_B_bonded: 2.30 restraints_weight: 0.5000 r_work: 0.2923 rms_B_bonded: 3.59 restraints_weight: 0.2500 r_work (final): 0.2923 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8545 moved from start: 0.1347 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.066 10924 Z= 0.200 Angle : 0.698 9.997 14832 Z= 0.345 Chirality : 0.047 0.282 1770 Planarity : 0.005 0.064 1760 Dihedral : 13.583 101.967 2190 Min Nonbonded Distance : 2.482 Molprobity Statistics. All-atom Clashscore : 4.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.65 % Favored : 96.35 % Rotamer: Outliers : 2.82 % Allowed : 19.63 % Favored : 77.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.88 % 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 aren not related in a simple way. whole: 1.82 (0.24), residues: 1262 helix: 2.06 (0.22), residues: 546 sheet: 2.61 (0.32), residues: 250 loop : -0.69 (0.30), residues: 466 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG B 258 TYR 0.021 0.002 TYR A 650 PHE 0.017 0.002 PHE A 528 TRP 0.010 0.002 TRP B 567 HIS 0.007 0.001 HIS A 740 Details of bonding type rmsd covalent geometry : bond 0.00463 (10908) covalent geometry : angle 0.67769 (14808) SS BOND : bond 0.00104 ( 6) SS BOND : angle 0.81408 ( 12) hydrogen bonds : bond 0.06256 ( 578) hydrogen bonds : angle 4.43933 ( 1626) metal coordination : bond 0.00870 ( 6) link_BETA1-4 : bond 0.01342 ( 4) link_BETA1-4 : angle 5.87410 ( 12) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4595.40 seconds wall clock time: 79 minutes 1.90 seconds (4741.90 seconds total)