Starting phenix.real_space_refine on Mon Jul 28 20:39:26 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8xbs_38227/07_2025/8xbs_38227.cif Found real_map, /net/cci-nas-00/data/ceres_data/8xbs_38227/07_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_38227/07_2025/8xbs_38227.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8xbs_38227/07_2025/8xbs_38227.map" model { file = "/net/cci-nas-00/data/ceres_data/8xbs_38227/07_2025/8xbs_38227.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8xbs_38227/07_2025/8xbs_38227.cif" } resolution = 2.21 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 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): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/modules/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: {'GLU:plan': 1, 'ASN:plan1': 1, 'ASP:plan': 1, 'HIS: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: {'GLU:plan': 1, 'ASN:plan1': 1, 'ASP:plan': 1, 'HIS: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: 6.83, per 1000 atoms: 0.64 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: 2.72 Conformation dependent library (CDL) restraints added in 1.4 seconds 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: 1.09 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: 3.23 Time building geometry restraints manager: 3.20 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: 0.05 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: 0.740 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.390 Check model and map are aligned: 0.070 Set scattering table: 0.090 Process input model: 27.960 Find NCS groups from input model: 0.340 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:11.610 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 41.270 ------------------------------------------------------------------------------- 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.61 (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 TRP 0.007 0.001 TRP B 567 HIS 0.004 0.001 HIS A 571 PHE 0.014 0.002 PHE A 528 TYR 0.031 0.002 TYR B 238 ARG 0.012 0.001 ARG B 240 Details of bonding type rmsd link_BETA1-4 : bond 0.01914 ( 4) link_BETA1-4 : angle 6.54517 ( 12) hydrogen bonds : bond 0.15726 ( 578) hydrogen bonds : angle 5.26152 ( 1626) metal coordination : bond 0.00661 ( 6) SS BOND : bond 0.00109 ( 6) SS BOND : angle 0.69658 ( 12) covalent geometry : bond 0.00634 (10908) covalent geometry : angle 1.17399 (14808) *********************** 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 : 1.091 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: 1.1137 time to fit residues: 179.6488 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 : 1.238 ------------------------------------------------------------------------------- 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 108 optimal weight: 0.0870 chunk 97 optimal weight: 1.9990 chunk 53 optimal weight: 6.9990 chunk 33 optimal weight: 9.9990 chunk 65 optimal weight: 9.9990 chunk 51 optimal weight: 3.9990 chunk 100 optimal weight: 7.9990 chunk 38 optimal weight: 5.9990 chunk 61 optimal weight: 4.9990 chunk 74 optimal weight: 7.9990 chunk 116 optimal weight: 0.2980 overall best weight: 2.2764 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 54 ASN A 571 HIS 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 = 0.3636 r_free = 0.3636 target = 0.132324 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3196 r_free = 0.3196 target = 0.098939 restraints weight = 10796.628| |-----------------------------------------------------------------------------| r_work (start): 0.3195 rms_B_bonded: 1.62 r_work: 0.3063 rms_B_bonded: 2.27 restraints_weight: 0.5000 r_work: 0.2951 rms_B_bonded: 3.56 restraints_weight: 0.2500 r_work (final): 0.2951 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8546 moved from start: 0.0774 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.041 10924 Z= 0.205 Angle : 0.792 10.851 14832 Z= 0.378 Chirality : 0.051 0.333 1770 Planarity : 0.006 0.073 1760 Dihedral : 18.855 105.828 2218 Min Nonbonded Distance : 2.352 Molprobity Statistics. All-atom Clashscore : 5.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.88 % Favored : 96.12 % Rotamer: Outliers : 3.87 % Allowed : 18.49 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.71 (0.24), residues: 1262 helix: 2.01 (0.22), residues: 542 sheet: 2.64 (0.32), residues: 250 loop : -0.85 (0.28), residues: 470 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.002 TRP B 567 HIS 0.006 0.001 HIS A 740 PHE 0.018 0.002 PHE A 528 TYR 0.024 0.002 TYR A 650 ARG 0.008 0.001 ARG B 258 Details of bonding type rmsd link_BETA1-4 : bond 0.01475 ( 4) link_BETA1-4 : angle 6.55964 ( 12) hydrogen bonds : bond 0.06603 ( 578) hydrogen bonds : angle 4.50682 ( 1626) metal coordination : bond 0.00860 ( 6) SS BOND : bond 0.00165 ( 6) SS BOND : angle 0.87290 ( 12) covalent geometry : bond 0.00463 (10908) covalent geometry : angle 0.77003 (14808) *********************** 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 173 residues out of total 1150 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 129 time to evaluate : 1.288 Fit side-chains REVERT: A 129 GLN cc_start: 0.8432 (OUTLIER) cc_final: 0.8118 (mp10) REVERT: A 622 GLU cc_start: 0.7902 (tp30) cc_final: 0.7646 (tp30) REVERT: A 628 GLU cc_start: 0.4878 (OUTLIER) cc_final: 0.4539 (mm-30) REVERT: B 129 GLN cc_start: 0.8421 (OUTLIER) cc_final: 0.8108 (mp10) REVERT: B 145 PHE cc_start: 0.8533 (m-80) cc_final: 0.8276 (m-80) REVERT: B 622 GLU cc_start: 0.7924 (tp30) cc_final: 0.7664 (tp30) REVERT: B 628 GLU cc_start: 0.4897 (OUTLIER) cc_final: 0.4649 (mm-30) outliers start: 44 outliers final: 27 residues processed: 159 average time/residue: 1.0439 time to fit residues: 181.4960 Evaluate side-chains 155 residues out of total 1150 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 124 time to evaluate : 1.241 ------------------------------------------------------------------------------- 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 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 Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 126 optimal weight: 2.9990 chunk 14 optimal weight: 6.9990 chunk 70 optimal weight: 6.9990 chunk 48 optimal weight: 10.0000 chunk 100 optimal weight: 6.9990 chunk 4 optimal weight: 6.9990 chunk 28 optimal weight: 6.9990 chunk 7 optimal weight: 3.9990 chunk 32 optimal weight: 3.9990 chunk 62 optimal weight: 3.9990 chunk 2 optimal weight: 9.9990 overall best weight: 4.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 205 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 556 GLN A 571 HIS B 54 ASN ** B 205 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 556 GLN B 571 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3593 r_free = 0.3593 target = 0.129190 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3142 r_free = 0.3142 target = 0.095640 restraints weight = 10923.361| |-----------------------------------------------------------------------------| r_work (start): 0.3143 rms_B_bonded: 1.63 r_work: 0.3010 rms_B_bonded: 2.28 restraints_weight: 0.5000 r_work: 0.2898 rms_B_bonded: 3.55 restraints_weight: 0.2500 r_work (final): 0.2898 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8575 moved from start: 0.1103 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.057 10924 Z= 0.334 Angle : 0.889 11.286 14832 Z= 0.434 Chirality : 0.057 0.261 1770 Planarity : 0.007 0.081 1760 Dihedral : 17.152 115.302 2202 Min Nonbonded Distance : 2.285 Molprobity Statistics. All-atom Clashscore : 5.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.04 % Favored : 95.96 % Rotamer: Outliers : 4.31 % Allowed : 17.34 % Favored : 78.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.88 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.23 (0.23), residues: 1262 helix: 1.44 (0.21), residues: 544 sheet: 2.49 (0.32), residues: 250 loop : -0.92 (0.28), residues: 468 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.003 TRP B 567 HIS 0.010 0.002 HIS A 740 PHE 0.022 0.003 PHE A 528 TYR 0.024 0.003 TYR B 673 ARG 0.011 0.001 ARG B 258 Details of bonding type rmsd link_BETA1-4 : bond 0.01184 ( 4) link_BETA1-4 : angle 7.46511 ( 12) hydrogen bonds : bond 0.08042 ( 578) hydrogen bonds : angle 4.71384 ( 1626) metal coordination : bond 0.01567 ( 6) SS BOND : bond 0.00250 ( 6) SS BOND : angle 1.25875 ( 12) covalent geometry : bond 0.00785 (10908) covalent geometry : angle 0.86368 (14808) *********************** 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 175 residues out of total 1150 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 126 time to evaluate : 1.733 Fit side-chains REVERT: A 129 GLN cc_start: 0.8438 (OUTLIER) cc_final: 0.8109 (mp10) REVERT: A 521 LEU cc_start: 0.8907 (OUTLIER) cc_final: 0.8593 (tt) REVERT: A 622 GLU cc_start: 0.7933 (tp30) cc_final: 0.7580 (tp30) REVERT: A 691 LYS cc_start: 0.8069 (ttpp) cc_final: 0.7815 (ttpp) REVERT: A 764 ASP cc_start: 0.8306 (OUTLIER) cc_final: 0.7876 (p0) REVERT: B 129 GLN cc_start: 0.8427 (OUTLIER) cc_final: 0.8097 (mp10) REVERT: B 521 LEU cc_start: 0.8900 (OUTLIER) cc_final: 0.8587 (tt) REVERT: B 622 GLU cc_start: 0.7944 (tp30) cc_final: 0.7593 (tp30) REVERT: B 691 LYS cc_start: 0.8060 (ttpp) cc_final: 0.7813 (ttpp) outliers start: 49 outliers final: 33 residues processed: 158 average time/residue: 1.3781 time to fit residues: 238.3116 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 : 1.243 ------------------------------------------------------------------------------- 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 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 435 VAL 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 628 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 69 LEU 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 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 775 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 16 optimal weight: 0.7980 chunk 17 optimal weight: 1.9990 chunk 4 optimal weight: 4.9990 chunk 56 optimal weight: 0.7980 chunk 76 optimal weight: 2.9990 chunk 7 optimal weight: 1.9990 chunk 115 optimal weight: 3.9990 chunk 58 optimal weight: 4.9990 chunk 57 optimal weight: 3.9990 chunk 19 optimal weight: 2.9990 chunk 38 optimal weight: 1.9990 overall best weight: 1.5186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 450 HIS A 571 HIS A 684 HIS B 450 HIS B 571 HIS B 684 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3631 r_free = 0.3631 target = 0.132369 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3191 r_free = 0.3191 target = 0.098997 restraints weight = 10875.642| |-----------------------------------------------------------------------------| r_work (start): 0.3190 rms_B_bonded: 1.63 r_work: 0.3059 rms_B_bonded: 2.28 restraints_weight: 0.5000 r_work: 0.2949 rms_B_bonded: 3.57 restraints_weight: 0.2500 r_work (final): 0.2949 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8525 moved from start: 0.1102 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 10924 Z= 0.156 Angle : 0.694 10.095 14832 Z= 0.334 Chirality : 0.046 0.284 1770 Planarity : 0.005 0.070 1760 Dihedral : 15.514 105.092 2200 Min Nonbonded Distance : 2.432 Molprobity Statistics. All-atom Clashscore : 4.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.09 % Favored : 96.91 % Rotamer: Outliers : 3.43 % Allowed : 18.40 % Favored : 78.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.88 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.78 (0.24), residues: 1262 helix: 2.10 (0.22), residues: 540 sheet: 2.71 (0.32), residues: 250 loop : -0.87 (0.28), residues: 472 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 567 HIS 0.005 0.001 HIS A 740 PHE 0.014 0.002 PHE A 528 TYR 0.024 0.002 TYR A 650 ARG 0.004 0.001 ARG A 258 Details of bonding type rmsd link_BETA1-4 : bond 0.01649 ( 4) link_BETA1-4 : angle 6.68897 ( 12) hydrogen bonds : bond 0.05596 ( 578) hydrogen bonds : angle 4.40925 ( 1626) metal coordination : bond 0.00714 ( 6) SS BOND : bond 0.00080 ( 6) SS BOND : angle 0.62183 ( 12) covalent geometry : bond 0.00345 (10908) covalent geometry : angle 0.66754 (14808) *********************** 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 161 residues out of total 1150 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 122 time to evaluate : 1.605 Fit side-chains REVERT: A 129 GLN cc_start: 0.8436 (OUTLIER) cc_final: 0.8111 (mp10) REVERT: A 622 GLU cc_start: 0.7923 (OUTLIER) cc_final: 0.7583 (tp30) REVERT: A 628 GLU cc_start: 0.4754 (OUTLIER) cc_final: 0.4107 (mm-30) REVERT: A 764 ASP cc_start: 0.8316 (OUTLIER) cc_final: 0.7908 (p0) REVERT: B 129 GLN cc_start: 0.8430 (OUTLIER) cc_final: 0.8105 (mp10) REVERT: B 622 GLU cc_start: 0.7931 (OUTLIER) cc_final: 0.7595 (tp30) outliers start: 39 outliers final: 22 residues processed: 149 average time/residue: 1.2450 time to fit residues: 202.3512 Evaluate side-chains 145 residues out of total 1150 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 117 time to evaluate : 1.195 ------------------------------------------------------------------------------- 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 221 GLU Chi-restraints excluded: chain A residue 229 ILE Chi-restraints excluded: chain A residue 278 VAL Chi-restraints excluded: chain A residue 435 VAL 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 764 ASP 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 221 GLU Chi-restraints excluded: chain B residue 229 ILE Chi-restraints excluded: chain B residue 278 VAL Chi-restraints excluded: chain B residue 435 VAL Chi-restraints excluded: chain B residue 490 THR Chi-restraints excluded: chain B residue 622 GLU Chi-restraints excluded: chain B residue 674 LEU 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 68 optimal weight: 3.9990 chunk 104 optimal weight: 2.9990 chunk 65 optimal weight: 9.9990 chunk 111 optimal weight: 5.9990 chunk 77 optimal weight: 5.9990 chunk 17 optimal weight: 7.9990 chunk 73 optimal weight: 2.9990 chunk 25 optimal weight: 4.9990 chunk 82 optimal weight: 4.9990 chunk 87 optimal weight: 1.9990 chunk 116 optimal weight: 7.9990 overall best weight: 3.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 54 ASN A 205 ASN A 571 HIS ** A 580 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 54 ASN B 205 ASN B 571 HIS ** B 580 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3601 r_free = 0.3601 target = 0.129868 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3151 r_free = 0.3151 target = 0.096280 restraints weight = 10813.356| |-----------------------------------------------------------------------------| r_work (start): 0.3153 rms_B_bonded: 1.63 r_work: 0.3020 rms_B_bonded: 2.26 restraints_weight: 0.5000 r_work: 0.2909 rms_B_bonded: 3.54 restraints_weight: 0.2500 r_work (final): 0.2909 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8562 moved from start: 0.1215 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.064 10924 Z= 0.267 Angle : 0.806 10.218 14832 Z= 0.392 Chirality : 0.052 0.303 1770 Planarity : 0.006 0.071 1760 Dihedral : 15.510 104.876 2196 Min Nonbonded Distance : 2.430 Molprobity Statistics. All-atom Clashscore : 4.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.12 % Favored : 95.88 % Rotamer: Outliers : 3.87 % Allowed : 18.05 % Favored : 78.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.88 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.47 (0.24), residues: 1262 helix: 1.68 (0.22), residues: 546 sheet: 2.62 (0.32), residues: 250 loop : -0.87 (0.28), residues: 466 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP A 567 HIS 0.009 0.002 HIS B 740 PHE 0.020 0.003 PHE B 528 TYR 0.022 0.002 TYR B 673 ARG 0.007 0.001 ARG B 258 Details of bonding type rmsd link_BETA1-4 : bond 0.01451 ( 4) link_BETA1-4 : angle 7.28359 ( 12) hydrogen bonds : bond 0.07246 ( 578) hydrogen bonds : angle 4.61488 ( 1626) metal coordination : bond 0.01240 ( 6) SS BOND : bond 0.00181 ( 6) SS BOND : angle 1.01001 ( 12) covalent geometry : bond 0.00625 (10908) covalent geometry : angle 0.77941 (14808) *********************** 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 169 residues out of total 1150 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 125 time to evaluate : 1.816 Fit side-chains REVERT: A 129 GLN cc_start: 0.8439 (OUTLIER) cc_final: 0.8114 (mp10) REVERT: A 521 LEU cc_start: 0.8842 (OUTLIER) cc_final: 0.8421 (tp) REVERT: A 622 GLU cc_start: 0.7917 (OUTLIER) cc_final: 0.7574 (tp30) REVERT: A 764 ASP cc_start: 0.8308 (OUTLIER) cc_final: 0.7902 (p0) REVERT: B 129 GLN cc_start: 0.8430 (OUTLIER) cc_final: 0.8104 (mp10) REVERT: B 521 LEU cc_start: 0.8839 (OUTLIER) cc_final: 0.8416 (tp) REVERT: B 622 GLU cc_start: 0.7919 (OUTLIER) cc_final: 0.7575 (tp30) REVERT: B 628 GLU cc_start: 0.4908 (OUTLIER) cc_final: 0.4704 (tp30) REVERT: B 764 ASP cc_start: 0.8348 (OUTLIER) cc_final: 0.7929 (p0) outliers start: 44 outliers final: 31 residues processed: 153 average time/residue: 1.1156 time to fit residues: 186.5743 Evaluate side-chains 161 residues out of total 1150 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 121 time to evaluate : 1.223 ------------------------------------------------------------------------------- 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 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 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 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 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 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 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 29 optimal weight: 20.0000 chunk 94 optimal weight: 0.9980 chunk 121 optimal weight: 5.9990 chunk 119 optimal weight: 3.9990 chunk 113 optimal weight: 0.5980 chunk 96 optimal weight: 2.9990 chunk 13 optimal weight: 0.9990 chunk 52 optimal weight: 6.9990 chunk 0 optimal weight: 8.9990 chunk 33 optimal weight: 6.9990 chunk 34 optimal weight: 1.9990 overall best weight: 1.5186 ------------------------------------------------------------------------------- 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 = 0.3632 r_free = 0.3632 target = 0.132391 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3188 r_free = 0.3188 target = 0.098826 restraints weight = 10933.148| |-----------------------------------------------------------------------------| r_work (start): 0.3189 rms_B_bonded: 1.64 r_work: 0.3056 rms_B_bonded: 2.30 restraints_weight: 0.5000 r_work: 0.2946 rms_B_bonded: 3.59 restraints_weight: 0.2500 r_work (final): 0.2946 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8527 moved from start: 0.1232 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 10924 Z= 0.155 Angle : 0.656 10.057 14832 Z= 0.322 Chirality : 0.045 0.289 1770 Planarity : 0.005 0.070 1760 Dihedral : 14.149 103.136 2196 Min Nonbonded Distance : 2.504 Molprobity Statistics. All-atom Clashscore : 4.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.69 % Favored : 97.31 % Rotamer: Outliers : 3.43 % Allowed : 18.22 % Favored : 78.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.88 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.80 (0.24), residues: 1262 helix: 2.18 (0.22), residues: 542 sheet: 2.54 (0.32), residues: 254 loop : -0.86 (0.29), residues: 466 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 567 HIS 0.005 0.001 HIS B 740 PHE 0.014 0.002 PHE A 528 TYR 0.022 0.002 TYR A 650 ARG 0.004 0.001 ARG B 258 Details of bonding type rmsd link_BETA1-4 : bond 0.01530 ( 4) link_BETA1-4 : angle 6.19966 ( 12) hydrogen bonds : bond 0.05556 ( 578) hydrogen bonds : angle 4.38474 ( 1626) metal coordination : bond 0.00650 ( 6) SS BOND : bond 0.00113 ( 6) SS BOND : angle 0.60488 ( 12) covalent geometry : bond 0.00345 (10908) covalent geometry : angle 0.63236 (14808) *********************** 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 166 residues out of total 1150 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 127 time to evaluate : 1.133 Fit side-chains REVERT: A 129 GLN cc_start: 0.8460 (OUTLIER) cc_final: 0.8133 (mp10) REVERT: A 222 ASP cc_start: 0.8708 (OUTLIER) cc_final: 0.8261 (p0) REVERT: A 622 GLU cc_start: 0.7908 (OUTLIER) cc_final: 0.7575 (tp30) REVERT: A 764 ASP cc_start: 0.8313 (OUTLIER) cc_final: 0.7893 (p0) REVERT: B 129 GLN cc_start: 0.8453 (OUTLIER) cc_final: 0.8130 (mp10) REVERT: B 622 GLU cc_start: 0.7910 (OUTLIER) cc_final: 0.7553 (tp30) REVERT: B 628 GLU cc_start: 0.4904 (OUTLIER) cc_final: 0.4633 (tp30) REVERT: B 764 ASP cc_start: 0.8296 (OUTLIER) cc_final: 0.7890 (p0) outliers start: 39 outliers final: 27 residues processed: 152 average time/residue: 1.0823 time to fit residues: 179.6588 Evaluate side-chains 154 residues out of total 1150 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 119 time to evaluate : 1.550 ------------------------------------------------------------------------------- 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 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 611 VAL Chi-restraints excluded: chain A residue 622 GLU Chi-restraints excluded: chain A residue 625 LEU 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 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 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 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 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 125 optimal weight: 3.9990 chunk 63 optimal weight: 8.9990 chunk 96 optimal weight: 4.9990 chunk 2 optimal weight: 6.9990 chunk 60 optimal weight: 0.1980 chunk 26 optimal weight: 0.0570 chunk 64 optimal weight: 5.9990 chunk 101 optimal weight: 9.9990 chunk 12 optimal weight: 8.9990 chunk 105 optimal weight: 7.9990 chunk 30 optimal weight: 1.9990 overall best weight: 2.2504 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 54 ASN 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: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3618 r_free = 0.3618 target = 0.131201 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3168 r_free = 0.3168 target = 0.097401 restraints weight = 11049.415| |-----------------------------------------------------------------------------| r_work (start): 0.3169 rms_B_bonded: 1.65 r_work: 0.3036 rms_B_bonded: 2.30 restraints_weight: 0.5000 r_work: 0.2923 rms_B_bonded: 3.60 restraints_weight: 0.2500 r_work (final): 0.2923 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8546 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 : 0.005 0.069 10924 Z= 0.196 Angle : 0.704 10.096 14832 Z= 0.347 Chirality : 0.047 0.291 1770 Planarity : 0.005 0.063 1760 Dihedral : 14.036 102.625 2196 Min Nonbonded Distance : 2.459 Molprobity Statistics. All-atom Clashscore : 5.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.49 % Favored : 96.51 % Rotamer: Outliers : 3.87 % Allowed : 18.40 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.75 (0.24), residues: 1262 helix: 2.04 (0.22), residues: 542 sheet: 2.63 (0.32), residues: 250 loop : -0.80 (0.29), residues: 470 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP B 567 HIS 0.007 0.001 HIS B 740 PHE 0.017 0.002 PHE B 528 TYR 0.022 0.002 TYR A 650 ARG 0.005 0.001 ARG B 258 Details of bonding type rmsd link_BETA1-4 : bond 0.01498 ( 4) link_BETA1-4 : angle 6.29292 ( 12) hydrogen bonds : bond 0.06282 ( 578) hydrogen bonds : angle 4.47102 ( 1626) metal coordination : bond 0.00858 ( 6) SS BOND : bond 0.00102 ( 6) SS BOND : angle 0.76259 ( 12) covalent geometry : bond 0.00453 (10908) covalent geometry : angle 0.68132 (14808) *********************** 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 174 residues out of total 1150 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 130 time to evaluate : 1.373 Fit side-chains REVERT: A 129 GLN cc_start: 0.8452 (OUTLIER) cc_final: 0.8126 (mp10) REVERT: A 521 LEU cc_start: 0.8776 (OUTLIER) cc_final: 0.8317 (tp) REVERT: A 622 GLU cc_start: 0.7901 (OUTLIER) cc_final: 0.7588 (tp30) REVERT: A 764 ASP cc_start: 0.8314 (OUTLIER) cc_final: 0.7900 (p0) REVERT: B 129 GLN cc_start: 0.8445 (OUTLIER) cc_final: 0.8125 (mp10) REVERT: B 521 LEU cc_start: 0.8776 (OUTLIER) cc_final: 0.8346 (tp) REVERT: B 622 GLU cc_start: 0.7884 (OUTLIER) cc_final: 0.7533 (tp30) REVERT: B 764 ASP cc_start: 0.8315 (OUTLIER) cc_final: 0.7916 (p0) outliers start: 44 outliers final: 30 residues processed: 159 average time/residue: 1.0677 time to fit residues: 185.9778 Evaluate side-chains 164 residues out of total 1150 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 126 time to evaluate : 1.192 ------------------------------------------------------------------------------- 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 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 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 611 VAL Chi-restraints excluded: chain A residue 622 GLU Chi-restraints excluded: chain A residue 625 LEU 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 69 LEU 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 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 455 SER 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 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 96 optimal weight: 3.9990 chunk 48 optimal weight: 9.9990 chunk 12 optimal weight: 9.9990 chunk 99 optimal weight: 5.9990 chunk 123 optimal weight: 1.9990 chunk 112 optimal weight: 5.9990 chunk 51 optimal weight: 4.9990 chunk 119 optimal weight: 5.9990 chunk 7 optimal weight: 2.9990 chunk 115 optimal weight: 4.9990 chunk 90 optimal weight: 0.7980 overall best weight: 2.9588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 54 ASN ** A 205 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 571 HIS ** A 580 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 54 ASN ** B 205 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 571 HIS ** B 580 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3607 r_free = 0.3607 target = 0.130291 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3158 r_free = 0.3158 target = 0.096675 restraints weight = 10854.917| |-----------------------------------------------------------------------------| r_work (start): 0.3157 rms_B_bonded: 1.64 r_work: 0.3022 rms_B_bonded: 2.29 restraints_weight: 0.5000 r_work: 0.2911 rms_B_bonded: 3.56 restraints_weight: 0.2500 r_work (final): 0.2911 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8559 moved from start: 0.1301 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.070 10924 Z= 0.240 Angle : 0.759 10.402 14832 Z= 0.374 Chirality : 0.050 0.294 1770 Planarity : 0.005 0.073 1760 Dihedral : 14.124 103.390 2196 Min Nonbonded Distance : 2.430 Molprobity Statistics. All-atom Clashscore : 4.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.49 % Favored : 96.51 % Rotamer: Outliers : 4.49 % Allowed : 17.69 % Favored : 77.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.88 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.47 (0.24), residues: 1262 helix: 1.68 (0.22), residues: 552 sheet: 2.58 (0.33), residues: 250 loop : -0.87 (0.29), residues: 460 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP B 567 HIS 0.008 0.002 HIS B 740 PHE 0.019 0.002 PHE B 528 TYR 0.021 0.002 TYR B 673 ARG 0.007 0.001 ARG A 258 Details of bonding type rmsd link_BETA1-4 : bond 0.01546 ( 4) link_BETA1-4 : angle 6.50668 ( 12) hydrogen bonds : bond 0.06914 ( 578) hydrogen bonds : angle 4.57028 ( 1626) metal coordination : bond 0.01160 ( 6) SS BOND : bond 0.00150 ( 6) SS BOND : angle 0.94566 ( 12) covalent geometry : bond 0.00559 (10908) covalent geometry : angle 0.73591 (14808) *********************** 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 177 residues out of total 1150 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 126 time to evaluate : 1.104 Fit side-chains REVERT: A 129 GLN cc_start: 0.8426 (OUTLIER) cc_final: 0.8102 (mp10) REVERT: A 222 ASP cc_start: 0.8745 (OUTLIER) cc_final: 0.8330 (p0) REVERT: A 521 LEU cc_start: 0.8808 (OUTLIER) cc_final: 0.8387 (tp) REVERT: A 622 GLU cc_start: 0.7896 (OUTLIER) cc_final: 0.7546 (tp30) REVERT: A 764 ASP cc_start: 0.8278 (OUTLIER) cc_final: 0.7844 (p0) REVERT: B 129 GLN cc_start: 0.8428 (OUTLIER) cc_final: 0.8102 (mp10) REVERT: B 521 LEU cc_start: 0.8806 (OUTLIER) cc_final: 0.8385 (tp) REVERT: B 622 GLU cc_start: 0.7897 (OUTLIER) cc_final: 0.7542 (tp30) REVERT: B 764 ASP cc_start: 0.8280 (OUTLIER) cc_final: 0.7863 (p0) outliers start: 51 outliers final: 30 residues processed: 158 average time/residue: 1.0192 time to fit residues: 176.4273 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 : 1.233 ------------------------------------------------------------------------------- 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 69 LEU 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 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 611 VAL Chi-restraints excluded: chain A residue 622 GLU 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 69 LEU 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 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 455 SER 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 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 71 optimal weight: 1.9990 chunk 54 optimal weight: 3.9990 chunk 113 optimal weight: 0.7980 chunk 44 optimal weight: 0.7980 chunk 38 optimal weight: 1.9990 chunk 82 optimal weight: 0.6980 chunk 65 optimal weight: 10.0000 chunk 5 optimal weight: 0.9980 chunk 93 optimal weight: 3.9990 chunk 102 optimal weight: 6.9990 chunk 110 optimal weight: 0.2980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 54 ASN A 571 HIS B 54 ASN ** B 205 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 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 = 0.134156 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3219 r_free = 0.3219 target = 0.100805 restraints weight = 11061.457| |-----------------------------------------------------------------------------| r_work (start): 0.3218 rms_B_bonded: 1.65 r_work: 0.3085 rms_B_bonded: 2.32 restraints_weight: 0.5000 r_work: 0.2975 rms_B_bonded: 3.63 restraints_weight: 0.2500 r_work (final): 0.2975 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8501 moved from start: 0.1403 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.055 10924 Z= 0.122 Angle : 0.605 9.904 14832 Z= 0.298 Chirality : 0.043 0.272 1770 Planarity : 0.004 0.064 1760 Dihedral : 13.341 100.748 2196 Min Nonbonded Distance : 2.547 Molprobity Statistics. All-atom Clashscore : 4.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.77 % Favored : 97.23 % Rotamer: Outliers : 2.90 % Allowed : 19.28 % Favored : 77.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.88 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.99 (0.24), residues: 1262 helix: 2.41 (0.22), residues: 542 sheet: 2.47 (0.32), residues: 254 loop : -0.76 (0.29), residues: 466 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 567 HIS 0.004 0.001 HIS B 571 PHE 0.011 0.001 PHE A 202 TYR 0.023 0.001 TYR B 650 ARG 0.002 0.000 ARG A 258 Details of bonding type rmsd link_BETA1-4 : bond 0.01529 ( 4) link_BETA1-4 : angle 5.47403 ( 12) hydrogen bonds : bond 0.04686 ( 578) hydrogen bonds : angle 4.23636 ( 1626) metal coordination : bond 0.00340 ( 6) SS BOND : bond 0.00037 ( 6) SS BOND : angle 0.35630 ( 12) covalent geometry : bond 0.00261 (10908) covalent geometry : angle 0.58495 (14808) *********************** 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 163 residues out of total 1150 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 130 time to evaluate : 1.210 Fit side-chains REVERT: A 129 GLN cc_start: 0.8446 (OUTLIER) cc_final: 0.8112 (mp10) REVERT: A 222 ASP cc_start: 0.8692 (OUTLIER) cc_final: 0.8229 (p0) REVERT: A 622 GLU cc_start: 0.7975 (tp30) cc_final: 0.7705 (tp30) REVERT: A 628 GLU cc_start: 0.4882 (OUTLIER) cc_final: 0.4353 (mm-30) REVERT: A 764 ASP cc_start: 0.8298 (OUTLIER) cc_final: 0.7890 (p0) REVERT: B 129 GLN cc_start: 0.8447 (OUTLIER) cc_final: 0.8114 (mp10) REVERT: B 622 GLU cc_start: 0.7915 (OUTLIER) cc_final: 0.7647 (tp30) outliers start: 33 outliers final: 17 residues processed: 150 average time/residue: 1.2435 time to fit residues: 205.0159 Evaluate side-chains 144 residues out of total 1150 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 121 time to evaluate : 1.203 ------------------------------------------------------------------------------- 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 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 278 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 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 278 VAL Chi-restraints excluded: chain B residue 455 SER Chi-restraints excluded: chain B residue 490 THR Chi-restraints excluded: chain B residue 611 VAL Chi-restraints excluded: chain B residue 622 GLU Chi-restraints excluded: chain B residue 674 LEU 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 40 optimal weight: 0.8980 chunk 14 optimal weight: 7.9990 chunk 91 optimal weight: 0.5980 chunk 102 optimal weight: 5.9990 chunk 25 optimal weight: 0.9980 chunk 44 optimal weight: 0.4980 chunk 37 optimal weight: 8.9990 chunk 66 optimal weight: 8.9990 chunk 63 optimal weight: 0.9990 chunk 34 optimal weight: 0.4980 chunk 28 optimal weight: 4.9990 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 54 ASN A 571 HIS 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 = 0.3663 r_free = 0.3663 target = 0.134841 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3227 r_free = 0.3227 target = 0.101444 restraints weight = 10999.052| |-----------------------------------------------------------------------------| r_work (start): 0.3227 rms_B_bonded: 1.65 r_work: 0.3094 rms_B_bonded: 2.32 restraints_weight: 0.5000 r_work: 0.2984 rms_B_bonded: 3.63 restraints_weight: 0.2500 r_work (final): 0.2984 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8490 moved from start: 0.1533 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.055 10924 Z= 0.116 Angle : 0.588 9.850 14832 Z= 0.289 Chirality : 0.042 0.267 1770 Planarity : 0.004 0.057 1760 Dihedral : 12.832 97.463 2190 Min Nonbonded Distance : 2.550 Molprobity Statistics. All-atom Clashscore : 4.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.09 % Favored : 96.91 % Rotamer: Outliers : 2.38 % Allowed : 19.98 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.20 (0.25), residues: 1262 helix: 2.53 (0.22), residues: 556 sheet: 2.49 (0.32), residues: 254 loop : -0.61 (0.30), residues: 452 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 567 HIS 0.004 0.001 HIS A 571 PHE 0.012 0.001 PHE A 202 TYR 0.022 0.001 TYR A 650 ARG 0.003 0.000 ARG B 240 Details of bonding type rmsd link_BETA1-4 : bond 0.01397 ( 4) link_BETA1-4 : angle 5.33785 ( 12) hydrogen bonds : bond 0.04545 ( 578) hydrogen bonds : angle 4.16995 ( 1626) metal coordination : bond 0.00324 ( 6) SS BOND : bond 0.00024 ( 6) SS BOND : angle 0.37135 ( 12) covalent geometry : bond 0.00251 (10908) covalent geometry : angle 0.56832 (14808) ********************** 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 159 residues out of total 1150 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 132 time to evaluate : 1.306 Fit side-chains REVERT: A 129 GLN cc_start: 0.8453 (mp-120) cc_final: 0.8107 (mp10) REVERT: A 222 ASP cc_start: 0.8684 (OUTLIER) cc_final: 0.8206 (p0) REVERT: A 622 GLU cc_start: 0.7932 (OUTLIER) cc_final: 0.7660 (tp30) REVERT: A 764 ASP cc_start: 0.8317 (OUTLIER) cc_final: 0.7901 (p0) REVERT: B 129 GLN cc_start: 0.8454 (mp-120) cc_final: 0.8111 (mp10) REVERT: B 622 GLU cc_start: 0.7931 (OUTLIER) cc_final: 0.7656 (tp30) outliers start: 27 outliers final: 17 residues processed: 151 average time/residue: 1.1468 time to fit residues: 188.2171 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 : 1.089 ------------------------------------------------------------------------------- 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 222 ASP Chi-restraints excluded: chain A residue 229 ILE Chi-restraints excluded: chain A residue 278 VAL 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 674 LEU 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 221 GLU 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 611 VAL Chi-restraints excluded: chain B residue 622 GLU Chi-restraints excluded: chain B residue 625 LEU Chi-restraints excluded: chain B residue 674 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 15 optimal weight: 3.9990 chunk 49 optimal weight: 0.9980 chunk 88 optimal weight: 9.9990 chunk 120 optimal weight: 4.9990 chunk 86 optimal weight: 2.9990 chunk 60 optimal weight: 3.9990 chunk 70 optimal weight: 4.9990 chunk 56 optimal weight: 4.9990 chunk 38 optimal weight: 5.9990 chunk 106 optimal weight: 0.8980 chunk 77 optimal weight: 1.9990 overall best weight: 2.1786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 54 ASN 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: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3626 r_free = 0.3626 target = 0.131764 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3177 r_free = 0.3177 target = 0.098005 restraints weight = 10921.715| |-----------------------------------------------------------------------------| r_work (start): 0.3176 rms_B_bonded: 1.65 r_work: 0.3041 rms_B_bonded: 2.31 restraints_weight: 0.5000 r_work: 0.2930 rms_B_bonded: 3.60 restraints_weight: 0.2500 r_work (final): 0.2930 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8540 moved from start: 0.1401 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.063 10924 Z= 0.192 Angle : 0.682 9.931 14832 Z= 0.337 Chirality : 0.046 0.273 1770 Planarity : 0.005 0.063 1760 Dihedral : 13.008 97.209 2187 Min Nonbonded Distance : 2.496 Molprobity Statistics. All-atom Clashscore : 4.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.33 % Favored : 96.67 % Rotamer: Outliers : 2.29 % Allowed : 20.07 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.99 (0.24), residues: 1262 helix: 2.25 (0.22), residues: 542 sheet: 2.62 (0.32), residues: 250 loop : -0.60 (0.29), residues: 470 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP B 567 HIS 0.007 0.001 HIS A 740 PHE 0.017 0.002 PHE A 528 TYR 0.021 0.002 TYR B 650 ARG 0.005 0.001 ARG B 258 Details of bonding type rmsd link_BETA1-4 : bond 0.01334 ( 4) link_BETA1-4 : angle 5.68656 ( 12) hydrogen bonds : bond 0.06065 ( 578) hydrogen bonds : angle 4.41558 ( 1626) metal coordination : bond 0.00824 ( 6) SS BOND : bond 0.00075 ( 6) SS BOND : angle 0.76126 ( 12) covalent geometry : bond 0.00444 (10908) covalent geometry : angle 0.66253 (14808) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 9766.54 seconds wall clock time: 173 minutes 44.70 seconds (10424.70 seconds total)