Starting phenix.real_space_refine on Wed May 14 03:17:47 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8wor_37696/05_2025/8wor_37696.cif Found real_map, /net/cci-nas-00/data/ceres_data/8wor_37696/05_2025/8wor_37696.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.66 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8wor_37696/05_2025/8wor_37696.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8wor_37696/05_2025/8wor_37696.map" model { file = "/net/cci-nas-00/data/ceres_data/8wor_37696/05_2025/8wor_37696.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8wor_37696/05_2025/8wor_37696.cif" } resolution = 2.66 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= 0.018 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 Ca 2 9.91 5 Zn 2 6.06 5 S 60 5.16 5 C 7539 2.51 5 N 1696 2.21 5 O 1919 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 14 residue(s): 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/chem_data/mon_lib" Total number of atoms: 11218 Number of models: 1 Model: "" Number of chains: 10 Chain: "A" Number of atoms: 5261 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 647, 5252 Classifications: {'peptide': 647} Link IDs: {'CIS': 1, 'PCIS': 3, 'PTRANS': 22, 'TRANS': 620} Chain breaks: 4 Conformer: "B" Number of residues, atoms: 647, 5252 Classifications: {'peptide': 647} Link IDs: {'CIS': 1, 'PCIS': 3, 'PTRANS': 22, 'TRANS': 620} Chain breaks: 4 bond proxies already assigned to first conformer: 5384 Chain: "B" Number of atoms: 5261 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 647, 5252 Classifications: {'peptide': 647} Link IDs: {'CIS': 1, 'PCIS': 3, 'PTRANS': 22, 'TRANS': 620} Chain breaks: 4 Conformer: "B" Number of residues, atoms: 647, 5252 Classifications: {'peptide': 647} Link IDs: {'CIS': 1, 'PCIS': 3, 'PTRANS': 22, 'TRANS': 620} Chain breaks: 4 bond proxies already assigned to first conformer: 5384 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: 276 Number of conformers: 1 Conformer: "" Number of residues, atoms: 13, 276 Unusual residues: {' CA': 1, ' ZN': 1, 'CLR': 7, 'NAG': 2, 'OLA': 1, 'SPL': 1} Classifications: {'undetermined': 13} Link IDs: {None: 12} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "B" Number of atoms: 304 Number of conformers: 1 Conformer: "" Number of residues, atoms: 14, 304 Unusual residues: {' CA': 1, ' ZN': 1, 'CLR': 8, 'NAG': 2, 'OLA': 1, 'SPL': 1} Classifications: {'undetermined': 14} Link IDs: {None: 13} 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: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Classifications: {'water': 2} Link IDs: {None: 1} Chain: "B" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Classifications: {'water': 2} Link IDs: {None: 1} Time building chain proxies: 11.71, per 1000 atoms: 1.04 Number of scatterers: 11218 At special positions: 0 Unit cell: (93.61, 89.355, 135.309, 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 Ca 2 19.99 S 60 16.00 O 1919 8.00 N 1696 7.00 C 7539 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=8, symmetry=0 Simple disulfide: pdb=" SG CYS A 130 " - pdb=" SG CYS A 222 " distance=2.03 Simple disulfide: pdb=" SG CYS A 212 " - pdb=" SG CYS A 271 " distance=2.03 Simple disulfide: pdb=" SG CYS A 479 " - pdb=" SG CYS A 565 " distance=2.03 Simple disulfide: pdb=" SG CYS A 485 " - pdb=" SG CYS A 787 " distance=2.03 Simple disulfide: pdb=" SG CYS B 130 " - pdb=" SG CYS B 222 " distance=2.03 Simple disulfide: pdb=" SG CYS B 212 " - pdb=" SG CYS B 271 " distance=2.03 Simple disulfide: pdb=" SG CYS B 479 " - pdb=" SG CYS B 565 " distance=2.03 Simple disulfide: pdb=" SG CYS B 485 " - pdb=" SG CYS B 787 " 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 " NAG-ASN " NAG A 903 " - " ASN A 67 " " NAG A 904 " - " ASN A 136 " " NAG B 903 " - " ASN B 67 " " NAG B 904 " - " ASN B 136 " " NAG C 1 " - " ASN A 57 " " NAG D 1 " - " ASN A 83 " " NAG E 1 " - " ASN B 57 " " NAG F 1 " - " ASN B 83 " Time building additional restraints: 3.04 Conformation dependent library (CDL) restraints added in 2.3 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN A 901 " pdb="ZN ZN A 901 " - pdb=" NE2 HIS A 563 " pdb="ZN ZN A 901 " - pdb=" NE2 HIS A 796 " pdb="ZN ZN A 901 " - pdb=" NE2 HIS A 800 " pdb=" ZN B 901 " pdb="ZN ZN B 901 " - pdb=" NE2 HIS B 563 " pdb="ZN ZN B 901 " - pdb=" NE2 HIS B 796 " pdb="ZN ZN B 901 " - pdb=" NE2 HIS B 800 " 2552 Ramachandran restraints generated. 1276 Oldfield, 0 Emsley, 1276 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2492 Finding SS restraints... Secondary structure from input PDB file: 36 helices and 10 sheets defined 49.9% alpha, 15.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.04 Creating SS restraints... Processing helix chain 'A' and resid 38 through 43 removed outlier: 4.270A pdb=" N ALA A 42 " --> pdb=" O ASP A 38 " (cutoff:3.500A) Processing helix chain 'A' and resid 251 through 253 No H-bonds generated for 'chain 'A' and resid 251 through 253' Processing helix chain 'A' and resid 302 through 335 removed outlier: 3.841A pdb=" N TYR A 306 " --> pdb=" O LYS A 302 " (cutoff:3.500A) removed outlier: 3.842A pdb=" N PHE A 317 " --> pdb=" O SER A 313 " (cutoff:3.500A) removed outlier: 4.606A pdb=" N PHE A 320 " --> pdb=" O ILE A 316 " (cutoff:3.500A) removed outlier: 4.010A pdb=" N TYR A 321 " --> pdb=" O PHE A 317 " (cutoff:3.500A) Processing helix chain 'A' and resid 441 through 474 removed outlier: 4.024A pdb=" N ILE A 448 " --> pdb=" O TYR A 444 " (cutoff:3.500A) Proline residue: A 458 - end of helix Processing helix chain 'A' and resid 482 through 486 removed outlier: 3.948A pdb=" N ALA A 486 " --> pdb=" O PHE A 483 " (cutoff:3.500A) Processing helix chain 'A' and resid 495 through 500 Processing helix chain 'A' and resid 501 through 527 removed outlier: 3.842A pdb=" N VAL A 505 " --> pdb=" O ASN A 501 " (cutoff:3.500A) Processing helix chain 'A' and resid 541 through 563 Processing helix chain 'A' and resid 570 through 594 removed outlier: 4.204A pdb=" N ASP A 574 " --> pdb=" O ASN A 570 " (cutoff:3.500A) removed outlier: 3.790A pdb=" N MET A 578 " --> pdb=" O ASP A 574 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N TYR A 579 " --> pdb=" O THR A 575 " (cutoff:3.500A) Processing helix chain 'A' and resid 602 through 621 removed outlier: 3.741A pdb=" N ALA A 606 " --> pdb=" O TYR A 602 " (cutoff:3.500A) Processing helix chain 'A' and resid 626 through 650 Processing helix chain 'A' and resid 686 through 709 Processing helix chain 'A' and resid 713 through 738 Processing helix chain 'A' and resid 745 through 767 removed outlier: 3.581A pdb=" N LEU A 749 " --> pdb=" O LEU A 745 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N PHE A 765 " --> pdb=" O ALA A 761 " (cutoff:3.500A) removed outlier: 3.843A pdb=" N PHE A 767 " --> pdb=" O LEU A 763 " (cutoff:3.500A) Processing helix chain 'A' and resid 776 through 782 Processing helix chain 'A' and resid 788 through 792 removed outlier: 3.643A pdb=" N ASP A 791 " --> pdb=" O ILE A 788 " (cutoff:3.500A) Processing helix chain 'A' and resid 794 through 816 removed outlier: 3.520A pdb=" N ILE A 798 " --> pdb=" O ASP A 794 " (cutoff:3.500A) Processing helix chain 'A' and resid 819 through 824 Processing helix chain 'B' and resid 38 through 43 removed outlier: 4.202A pdb=" N ALA B 42 " --> pdb=" O ASP B 38 " (cutoff:3.500A) Processing helix chain 'B' and resid 251 through 253 No H-bonds generated for 'chain 'B' and resid 251 through 253' Processing helix chain 'B' and resid 302 through 335 removed outlier: 3.848A pdb=" N TYR B 306 " --> pdb=" O LYS B 302 " (cutoff:3.500A) removed outlier: 3.841A pdb=" N PHE B 317 " --> pdb=" O SER B 313 " (cutoff:3.500A) removed outlier: 4.576A pdb=" N PHE B 320 " --> pdb=" O ILE B 316 " (cutoff:3.500A) removed outlier: 3.944A pdb=" N TYR B 321 " --> pdb=" O PHE B 317 " (cutoff:3.500A) Processing helix chain 'B' and resid 441 through 474 removed outlier: 4.014A pdb=" N ILE B 448 " --> pdb=" O TYR B 444 " (cutoff:3.500A) Proline residue: B 458 - end of helix Processing helix chain 'B' and resid 482 through 486 removed outlier: 3.933A pdb=" N ALA B 486 " --> pdb=" O PHE B 483 " (cutoff:3.500A) Processing helix chain 'B' and resid 495 through 500 Processing helix chain 'B' and resid 501 through 527 removed outlier: 3.860A pdb=" N VAL B 505 " --> pdb=" O ASN B 501 " (cutoff:3.500A) Processing helix chain 'B' and resid 541 through 563 Processing helix chain 'B' and resid 570 through 594 removed outlier: 4.205A pdb=" N ASP B 574 " --> pdb=" O ASN B 570 " (cutoff:3.500A) removed outlier: 3.785A pdb=" N MET B 578 " --> pdb=" O ASP B 574 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N TYR B 579 " --> pdb=" O THR B 575 " (cutoff:3.500A) Processing helix chain 'B' and resid 602 through 621 removed outlier: 3.711A pdb=" N ALA B 606 " --> pdb=" O TYR B 602 " (cutoff:3.500A) Processing helix chain 'B' and resid 624 through 650 removed outlier: 3.547A pdb=" N PHE B 628 " --> pdb=" O ASN B 624 " (cutoff:3.500A) removed outlier: 4.545A pdb=" N TRP B 629 " --> pdb=" O ASP B 625 " (cutoff:3.500A) Processing helix chain 'B' and resid 686 through 709 Processing helix chain 'B' and resid 713 through 738 Processing helix chain 'B' and resid 745 through 767 removed outlier: 3.563A pdb=" N LEU B 749 " --> pdb=" O LEU B 745 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N PHE B 765 " --> pdb=" O ALA B 761 " (cutoff:3.500A) removed outlier: 3.860A pdb=" N PHE B 767 " --> pdb=" O LEU B 763 " (cutoff:3.500A) Processing helix chain 'B' and resid 776 through 782 Processing helix chain 'B' and resid 788 through 792 removed outlier: 3.635A pdb=" N ASP B 791 " --> pdb=" O ILE B 788 " (cutoff:3.500A) Processing helix chain 'B' and resid 794 through 816 removed outlier: 3.514A pdb=" N ILE B 798 " --> pdb=" O ASP B 794 " (cutoff:3.500A) Processing helix chain 'B' and resid 819 through 824 Processing sheet with id=AA1, first strand: chain 'A' and resid 44 through 45 Processing sheet with id=AA2, first strand: chain 'A' and resid 51 through 56 removed outlier: 4.478A pdb=" N VAL A 78 " --> pdb=" O LEU A 129 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 110 through 113 Processing sheet with id=AA4, first strand: chain 'A' and resid 177 through 181 Processing sheet with id=AA5, first strand: chain 'A' and resid 187 through 192 Processing sheet with id=AA6, first strand: chain 'B' and resid 44 through 45 Processing sheet with id=AA7, first strand: chain 'B' and resid 51 through 56 removed outlier: 4.449A pdb=" N VAL B 78 " --> pdb=" O LEU B 129 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 110 through 113 Processing sheet with id=AA9, first strand: chain 'B' and resid 177 through 181 Processing sheet with id=AB1, first strand: chain 'B' and resid 187 through 192 630 hydrogen bonds defined for protein. 1795 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: 3.34 Time building geometry restraints manager: 3.44 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 3258 1.34 - 1.46: 2819 1.46 - 1.58: 5368 1.58 - 1.70: 2 1.70 - 1.82: 94 Bond restraints: 11541 Sorted by residual: bond pdb=" C10 OLA A 911 " pdb=" C9 OLA A 911 " ideal model delta sigma weight residual 1.332 1.468 -0.136 2.00e-02 2.50e+03 4.64e+01 bond pdb=" C10 OLA B 914 " pdb=" C9 OLA B 914 " ideal model delta sigma weight residual 1.332 1.468 -0.136 2.00e-02 2.50e+03 4.60e+01 bond pdb=" CB PRO B 748 " pdb=" CG PRO B 748 " ideal model delta sigma weight residual 1.492 1.589 -0.097 5.00e-02 4.00e+02 3.79e+00 bond pdb=" CB PRO A 748 " pdb=" CG PRO A 748 " ideal model delta sigma weight residual 1.492 1.585 -0.093 5.00e-02 4.00e+02 3.43e+00 bond pdb=" C1 OLA A 911 " pdb=" C2 OLA A 911 " ideal model delta sigma weight residual 1.542 1.510 0.032 2.00e-02 2.50e+03 2.60e+00 ... (remaining 11536 not shown) Histogram of bond angle deviations from ideal: 0.00 - 4.28: 15709 4.28 - 8.56: 37 8.56 - 12.85: 0 12.85 - 17.13: 0 17.13 - 21.41: 2 Bond angle restraints: 15748 Sorted by residual: angle pdb=" CA LEU B 728 " pdb=" CB LEU B 728 " pdb=" CG LEU B 728 " ideal model delta sigma weight residual 116.30 137.71 -21.41 3.50e+00 8.16e-02 3.74e+01 angle pdb=" CA PRO B 748 " pdb=" N PRO B 748 " pdb=" CD PRO B 748 " ideal model delta sigma weight residual 112.00 104.60 7.40 1.40e+00 5.10e-01 2.79e+01 angle pdb=" CA LEU A 728 " pdb=" CB LEU A 728 " pdb=" CG LEU A 728 " ideal model delta sigma weight residual 116.30 134.47 -18.17 3.50e+00 8.16e-02 2.70e+01 angle pdb=" CA PRO A 748 " pdb=" N PRO A 748 " pdb=" CD PRO A 748 " ideal model delta sigma weight residual 112.00 105.37 6.63 1.40e+00 5.10e-01 2.24e+01 angle pdb=" C ILE B 612 " pdb=" N MET B 613 " pdb=" CA MET B 613 " ideal model delta sigma weight residual 120.72 114.17 6.55 1.67e+00 3.59e-01 1.54e+01 ... (remaining 15743 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.36: 6563 17.36 - 34.73: 800 34.73 - 52.09: 223 52.09 - 69.45: 57 69.45 - 86.82: 8 Dihedral angle restraints: 7651 sinusoidal: 3791 harmonic: 3860 Sorted by residual: dihedral pdb=" CA TYR B 210 " pdb=" C TYR B 210 " pdb=" N PRO B 211 " pdb=" CA PRO B 211 " ideal model delta harmonic sigma weight residual 0.00 20.33 -20.33 0 5.00e+00 4.00e-02 1.65e+01 dihedral pdb=" CA TYR A 210 " pdb=" C TYR A 210 " pdb=" N PRO A 211 " pdb=" CA PRO A 211 " ideal model delta harmonic sigma weight residual 0.00 20.20 -20.20 0 5.00e+00 4.00e-02 1.63e+01 dihedral pdb=" CA CYS A 787 " pdb=" C CYS A 787 " pdb=" N ILE A 788 " pdb=" CA ILE A 788 " ideal model delta harmonic sigma weight residual 180.00 -161.15 -18.85 0 5.00e+00 4.00e-02 1.42e+01 ... (remaining 7648 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.057: 1583 0.057 - 0.115: 232 0.115 - 0.172: 21 0.172 - 0.229: 2 0.229 - 0.287: 2 Chirality restraints: 1840 Sorted by residual: chirality pdb=" C1 NAG E 1 " pdb=" ND2 ASN B 57 " pdb=" C2 NAG E 1 " pdb=" O5 NAG E 1 " both_signs ideal model delta sigma weight residual False -2.40 -2.11 -0.29 2.00e-01 2.50e+01 2.06e+00 chirality pdb=" C1 NAG C 1 " pdb=" ND2 ASN A 57 " pdb=" C2 NAG C 1 " pdb=" O5 NAG C 1 " both_signs ideal model delta sigma weight residual False -2.40 -2.13 -0.27 2.00e-01 2.50e+01 1.88e+00 chirality pdb=" CA MET A 613 " pdb=" N MET A 613 " pdb=" C MET A 613 " pdb=" CB MET A 613 " both_signs ideal model delta sigma weight residual False 2.51 2.32 0.19 2.00e-01 2.50e+01 8.66e-01 ... (remaining 1837 not shown) Planarity restraints: 1858 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C10 OLA A 911 " -0.185 2.00e-02 2.50e+03 1.44e-01 2.08e+02 pdb=" C11 OLA A 911 " 0.085 2.00e-02 2.50e+03 pdb=" C8 OLA A 911 " -0.085 2.00e-02 2.50e+03 pdb=" C9 OLA A 911 " 0.186 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C10 OLA B 914 " 0.185 2.00e-02 2.50e+03 1.44e-01 2.08e+02 pdb=" C11 OLA B 914 " -0.085 2.00e-02 2.50e+03 pdb=" C8 OLA B 914 " 0.085 2.00e-02 2.50e+03 pdb=" C9 OLA B 914 " -0.185 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C VAL A 747 " 0.082 5.00e-02 4.00e+02 1.21e-01 2.34e+01 pdb=" N PRO A 748 " -0.209 5.00e-02 4.00e+02 pdb=" CA PRO A 748 " 0.062 5.00e-02 4.00e+02 pdb=" CD PRO A 748 " 0.065 5.00e-02 4.00e+02 ... (remaining 1855 not shown) Histogram of nonbonded interaction distances: 1.93 - 2.52: 61 2.52 - 3.12: 8574 3.12 - 3.71: 16133 3.71 - 4.31: 22955 4.31 - 4.90: 39543 Nonbonded interactions: 87266 Sorted by model distance: nonbonded pdb="ZN ZN A 901 " pdb=" O HOH A1001 " model vdw 1.928 2.230 nonbonded pdb="ZN ZN B 901 " pdb=" O HOH B1001 " model vdw 1.928 2.230 nonbonded pdb=" OH TYR A 64 " pdb=" OH TYR A 159 " model vdw 2.080 3.040 nonbonded pdb=" OH TYR B 64 " pdb=" OH TYR B 159 " model vdw 2.085 3.040 nonbonded pdb=" O ASN B 598 " pdb=" OH TYR B 602 " model vdw 2.193 3.040 ... (remaining 87261 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: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 35 through 80 or resid 82 through 830 or resid 901 through \ 906 or resid 908 through 910 or resid 913)) selection = (chain 'B' and (resid 35 through 80 or resid 82 through 830 or resid 901 through \ 906 or resid 908 through 910 or resid 913)) } 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=0.21 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: 3.580 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.000 Extract box with map and model: 0.500 Check model and map are aligned: 0.100 Set scattering table: 0.110 Process input model: 35.220 Find NCS groups from input model: 0.500 Set up NCS constraints: 0.070 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:12.550 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 52.640 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7484 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.136 11567 Z= 0.174 Angle : 0.641 21.410 15800 Z= 0.308 Chirality : 0.041 0.287 1840 Planarity : 0.007 0.144 1850 Dihedral : 15.745 86.815 5135 Min Nonbonded Distance : 1.928 Molprobity Statistics. All-atom Clashscore : 22.33 Ramachandran Plot: Outliers : 0.16 % Allowed : 3.45 % Favored : 96.39 % Rotamer: Outliers : 5.08 % Allowed : 27.19 % Favored : 67.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 12.50 % Cis-general : 0.16 % 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: 1.60 (0.24), residues: 1276 helix: 2.90 (0.21), residues: 590 sheet: 1.34 (0.30), residues: 272 loop : -2.08 (0.27), residues: 414 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 446 HIS 0.004 0.001 HIS A 636 PHE 0.038 0.001 PHE A 732 TYR 0.011 0.001 TYR B 188 ARG 0.001 0.000 ARG B 593 Details of bonding type rmsd link_NAG-ASN : bond 0.00327 ( 8) link_NAG-ASN : angle 2.07644 ( 24) link_BETA1-4 : bond 0.00281 ( 4) link_BETA1-4 : angle 1.21617 ( 12) hydrogen bonds : bond 0.08913 ( 630) hydrogen bonds : angle 4.39253 ( 1795) metal coordination : bond 0.00167 ( 6) SS BOND : bond 0.00123 ( 8) SS BOND : angle 0.93078 ( 16) covalent geometry : bond 0.00380 (11541) covalent geometry : angle 0.63574 (15748) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2552 Ramachandran restraints generated. 1276 Oldfield, 0 Emsley, 1276 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2552 Ramachandran restraints generated. 1276 Oldfield, 0 Emsley, 1276 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 175 residues out of total 1158 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 116 time to evaluate : 1.186 Fit side-chains revert: symmetry clash REVERT: A 117 GLN cc_start: 0.8957 (mm-40) cc_final: 0.8744 (mp10) REVERT: A 158 GLN cc_start: 0.8522 (mt0) cc_final: 0.8296 (mt0) REVERT: A 554 MET cc_start: 0.7669 (tpp) cc_final: 0.7331 (mmm) REVERT: B 117 GLN cc_start: 0.9001 (mm-40) cc_final: 0.8797 (mp10) REVERT: B 554 MET cc_start: 0.7676 (tpp) cc_final: 0.7338 (mmm) REVERT: B 650 MET cc_start: 0.2997 (tpt) cc_final: 0.2770 (tpt) REVERT: B 686 MET cc_start: 0.5258 (mmt) cc_final: 0.4300 (pmm) REVERT: B 718 MET cc_start: 0.8145 (ttp) cc_final: 0.7940 (ttm) outliers start: 59 outliers final: 47 residues processed: 170 average time/residue: 0.8021 time to fit residues: 152.9703 Evaluate side-chains 160 residues out of total 1158 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 113 time to evaluate : 1.126 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 76 THR Chi-restraints excluded: chain A residue 111 LEU Chi-restraints excluded: chain A residue 161 LEU Chi-restraints excluded: chain A residue 236 VAL Chi-restraints excluded: chain A residue 260 VAL Chi-restraints excluded: chain A residue 296 THR Chi-restraints excluded: chain A residue 314 VAL Chi-restraints excluded: chain A residue 318 LEU Chi-restraints excluded: chain A residue 319 SER Chi-restraints excluded: chain A residue 327 VAL Chi-restraints excluded: chain A residue 472 VAL Chi-restraints excluded: chain A residue 521 LEU Chi-restraints excluded: chain A residue 541 HIS Chi-restraints excluded: chain A residue 559 SER Chi-restraints excluded: chain A residue 569 SER Chi-restraints excluded: chain A residue 572 GLN Chi-restraints excluded: chain A residue 589 LEU Chi-restraints excluded: chain A residue 735 ILE Chi-restraints excluded: chain A residue 755 THR Chi-restraints excluded: chain A residue 763 LEU Chi-restraints excluded: chain B residue 60 THR Chi-restraints excluded: chain B residue 76 THR Chi-restraints excluded: chain B residue 196 ASP Chi-restraints excluded: chain B residue 220 ILE Chi-restraints excluded: chain B residue 257 GLN Chi-restraints excluded: chain B residue 260 VAL Chi-restraints excluded: chain B residue 287 LEU Chi-restraints excluded: chain B residue 296 THR Chi-restraints excluded: chain B residue 309 SER Chi-restraints excluded: chain B residue 314 VAL Chi-restraints excluded: chain B residue 319 SER Chi-restraints excluded: chain B residue 324 CYS Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain B residue 470 VAL Chi-restraints excluded: chain B residue 472 VAL Chi-restraints excluded: chain B residue 520 ILE Chi-restraints excluded: chain B residue 521 LEU Chi-restraints excluded: chain B residue 541 HIS Chi-restraints excluded: chain B residue 569 SER Chi-restraints excluded: chain B residue 572 GLN Chi-restraints excluded: chain B residue 587 LEU Chi-restraints excluded: chain B residue 589 LEU Chi-restraints excluded: chain B residue 615 THR Chi-restraints excluded: chain B residue 735 ILE Chi-restraints excluded: chain B residue 755 THR Chi-restraints excluded: chain B residue 763 LEU Chi-restraints excluded: chain B residue 813 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 108 optimal weight: 7.9990 chunk 97 optimal weight: 0.6980 chunk 53 optimal weight: 0.8980 chunk 33 optimal weight: 0.8980 chunk 65 optimal weight: 2.9990 chunk 51 optimal weight: 10.0000 chunk 100 optimal weight: 3.9990 chunk 38 optimal weight: 6.9990 chunk 61 optimal weight: 4.9990 chunk 74 optimal weight: 5.9990 chunk 116 optimal weight: 3.9990 overall best weight: 1.8984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 90 ASN A 123 GLN A 142 GLN ** A 725 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 769 ASN B 71 GLN B 90 ASN B 142 GLN B 286 ASN ** B 725 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 769 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4076 r_free = 0.4076 target = 0.163634 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3338 r_free = 0.3338 target = 0.100147 restraints weight = 17138.588| |-----------------------------------------------------------------------------| r_work (start): 0.3236 rms_B_bonded: 2.81 r_work: 0.3096 rms_B_bonded: 3.37 restraints_weight: 0.5000 r_work (final): 0.3096 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3115 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3115 r_free = 0.3115 target_work(ls_wunit_k1) = 0.087 | | occupancies: max = 1.00 min = 0.21 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3114 r_free = 0.3114 target_work(ls_wunit_k1) = 0.087 | | occupancies: max = 1.00 min = 0.35 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3114 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8151 moved from start: 0.0893 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.053 11567 Z= 0.234 Angle : 0.779 18.732 15800 Z= 0.372 Chirality : 0.048 0.301 1840 Planarity : 0.005 0.075 1850 Dihedral : 9.692 59.766 2800 Min Nonbonded Distance : 1.863 Molprobity Statistics. All-atom Clashscore : 7.71 Ramachandran Plot: Outliers : 0.16 % Allowed : 4.08 % Favored : 95.76 % Rotamer: Outliers : 5.94 % Allowed : 26.08 % Favored : 67.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 12.50 % Cis-general : 0.16 % 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: 1276 helix: 2.40 (0.21), residues: 590 sheet: 1.30 (0.29), residues: 274 loop : -2.05 (0.27), residues: 412 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.002 TRP A 627 HIS 0.007 0.001 HIS B 636 PHE 0.016 0.002 PHE A 722 TYR 0.017 0.002 TYR B 188 ARG 0.004 0.001 ARG A 289 Details of bonding type rmsd link_NAG-ASN : bond 0.00373 ( 8) link_NAG-ASN : angle 2.72513 ( 24) link_BETA1-4 : bond 0.00223 ( 4) link_BETA1-4 : angle 1.68567 ( 12) hydrogen bonds : bond 0.06223 ( 630) hydrogen bonds : angle 4.10048 ( 1795) metal coordination : bond 0.00581 ( 6) SS BOND : bond 0.00116 ( 8) SS BOND : angle 1.68163 ( 16) covalent geometry : bond 0.00566 (11541) covalent geometry : angle 0.77008 (15748) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2552 Ramachandran restraints generated. 1276 Oldfield, 0 Emsley, 1276 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2552 Ramachandran restraints generated. 1276 Oldfield, 0 Emsley, 1276 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 185 residues out of total 1158 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 116 time to evaluate : 1.088 Fit side-chains REVERT: A 554 MET cc_start: 0.8400 (tpp) cc_final: 0.8096 (mmm) REVERT: A 594 HIS cc_start: 0.6521 (OUTLIER) cc_final: 0.5991 (m90) REVERT: A 605 TYR cc_start: 0.3947 (OUTLIER) cc_final: 0.3680 (p90) REVERT: A 686 MET cc_start: 0.5311 (mmt) cc_final: 0.4520 (mpt) REVERT: B 289 ARG cc_start: 0.9109 (OUTLIER) cc_final: 0.8813 (mtm180) REVERT: B 554 MET cc_start: 0.8406 (tpp) cc_final: 0.8091 (mmm) REVERT: B 605 TYR cc_start: 0.3976 (OUTLIER) cc_final: 0.3643 (p90) REVERT: B 650 MET cc_start: 0.3006 (OUTLIER) cc_final: 0.2775 (tpt) REVERT: B 686 MET cc_start: 0.5330 (mmt) cc_final: 0.4373 (pmm) REVERT: B 710 ARG cc_start: 0.8288 (mmm-85) cc_final: 0.7876 (mmt-90) REVERT: B 712 ARG cc_start: 0.5564 (mpt180) cc_final: 0.4684 (mpp80) outliers start: 69 outliers final: 32 residues processed: 173 average time/residue: 0.8734 time to fit residues: 168.0257 Evaluate side-chains 151 residues out of total 1158 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 114 time to evaluate : 1.191 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 76 THR Chi-restraints excluded: chain A residue 173 THR Chi-restraints excluded: chain A residue 220 ILE Chi-restraints excluded: chain A residue 260 VAL Chi-restraints excluded: chain A residue 296 THR Chi-restraints excluded: chain A residue 309 SER Chi-restraints excluded: chain A residue 521 LEU Chi-restraints excluded: chain A residue 544 LEU Chi-restraints excluded: chain A residue 559 SER Chi-restraints excluded: chain A residue 572 GLN Chi-restraints excluded: chain A residue 594 HIS Chi-restraints excluded: chain A residue 597 ILE Chi-restraints excluded: chain A residue 605 TYR Chi-restraints excluded: chain A residue 727 LEU Chi-restraints excluded: chain A residue 735 ILE Chi-restraints excluded: chain A residue 763 LEU Chi-restraints excluded: chain B residue 76 THR Chi-restraints excluded: chain B residue 119 SER Chi-restraints excluded: chain B residue 161 LEU Chi-restraints excluded: chain B residue 173 THR Chi-restraints excluded: chain B residue 220 ILE Chi-restraints excluded: chain B residue 236 VAL Chi-restraints excluded: chain B residue 260 VAL Chi-restraints excluded: chain B residue 286 ASN Chi-restraints excluded: chain B residue 287 LEU Chi-restraints excluded: chain B residue 289 ARG Chi-restraints excluded: chain B residue 296 THR Chi-restraints excluded: chain B residue 521 LEU Chi-restraints excluded: chain B residue 572 GLN Chi-restraints excluded: chain B residue 587 LEU Chi-restraints excluded: chain B residue 605 TYR Chi-restraints excluded: chain B residue 617 LEU Chi-restraints excluded: chain B residue 650 MET Chi-restraints excluded: chain B residue 725 ASN Chi-restraints excluded: chain B residue 727 LEU Chi-restraints excluded: chain B residue 735 ILE Chi-restraints excluded: chain B residue 763 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 85 optimal weight: 0.9990 chunk 58 optimal weight: 2.9990 chunk 107 optimal weight: 4.9990 chunk 82 optimal weight: 1.9990 chunk 30 optimal weight: 7.9990 chunk 125 optimal weight: 0.6980 chunk 93 optimal weight: 20.0000 chunk 98 optimal weight: 0.6980 chunk 47 optimal weight: 8.9990 chunk 126 optimal weight: 1.9990 chunk 123 optimal weight: 1.9990 overall best weight: 1.2786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 90 ASN ** A 725 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 769 ASN B 90 ASN B 142 GLN B 286 ASN ** B 725 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 769 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4088 r_free = 0.4088 target = 0.164833 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3336 r_free = 0.3336 target = 0.099746 restraints weight = 24410.286| |-----------------------------------------------------------------------------| r_work (start): 0.3229 rms_B_bonded: 3.20 r_work: 0.3083 rms_B_bonded: 3.69 restraints_weight: 0.5000 r_work (final): 0.3083 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3092 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3092 r_free = 0.3092 target_work(ls_wunit_k1) = 0.085 | | occupancies: max = 1.00 min = 0.35 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3092 r_free = 0.3092 target_work(ls_wunit_k1) = 0.085 | | occupancies: max = 1.00 min = 0.36 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3092 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8160 moved from start: 0.1078 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 11567 Z= 0.176 Angle : 0.722 18.717 15800 Z= 0.343 Chirality : 0.045 0.276 1840 Planarity : 0.005 0.067 1850 Dihedral : 8.812 59.785 2760 Min Nonbonded Distance : 1.920 Molprobity Statistics. All-atom Clashscore : 6.91 Ramachandran Plot: Outliers : 0.08 % Allowed : 4.24 % Favored : 95.68 % Rotamer: Outliers : 4.99 % Allowed : 26.59 % Favored : 68.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 12.50 % Cis-general : 0.16 % 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: 1.18 (0.23), residues: 1276 helix: 2.29 (0.21), residues: 590 sheet: 1.36 (0.29), residues: 274 loop : -2.04 (0.27), residues: 412 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 627 HIS 0.006 0.001 HIS B 636 PHE 0.014 0.001 PHE A 275 TYR 0.015 0.001 TYR B 188 ARG 0.003 0.000 ARG B 781 Details of bonding type rmsd link_NAG-ASN : bond 0.00426 ( 8) link_NAG-ASN : angle 2.64624 ( 24) link_BETA1-4 : bond 0.00518 ( 4) link_BETA1-4 : angle 1.42252 ( 12) hydrogen bonds : bond 0.05711 ( 630) hydrogen bonds : angle 3.99941 ( 1795) metal coordination : bond 0.00401 ( 6) SS BOND : bond 0.00112 ( 8) SS BOND : angle 1.43383 ( 16) covalent geometry : bond 0.00413 (11541) covalent geometry : angle 0.71331 (15748) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2552 Ramachandran restraints generated. 1276 Oldfield, 0 Emsley, 1276 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2552 Ramachandran restraints generated. 1276 Oldfield, 0 Emsley, 1276 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 169 residues out of total 1158 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 111 time to evaluate : 1.206 Fit side-chains REVERT: A 554 MET cc_start: 0.8360 (tpp) cc_final: 0.8058 (mmm) REVERT: A 594 HIS cc_start: 0.6643 (OUTLIER) cc_final: 0.6090 (m90) REVERT: A 605 TYR cc_start: 0.4122 (OUTLIER) cc_final: 0.3822 (p90) REVERT: A 781 ARG cc_start: 0.8969 (OUTLIER) cc_final: 0.8496 (mtm-85) REVERT: B 289 ARG cc_start: 0.9094 (OUTLIER) cc_final: 0.8781 (mtm180) REVERT: B 461 GLN cc_start: 0.8473 (OUTLIER) cc_final: 0.8247 (mt0) REVERT: B 554 MET cc_start: 0.8429 (tpp) cc_final: 0.8153 (mmm) REVERT: B 559 SER cc_start: 0.8792 (OUTLIER) cc_final: 0.8495 (p) REVERT: B 650 MET cc_start: 0.3136 (tpt) cc_final: 0.2859 (tpt) REVERT: B 686 MET cc_start: 0.5297 (mmt) cc_final: 0.4370 (pmm) REVERT: B 710 ARG cc_start: 0.8199 (mmm-85) cc_final: 0.7954 (mmt-90) REVERT: B 781 ARG cc_start: 0.8966 (OUTLIER) cc_final: 0.8394 (mtm-85) outliers start: 58 outliers final: 35 residues processed: 161 average time/residue: 0.9328 time to fit residues: 166.4103 Evaluate side-chains 153 residues out of total 1158 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 111 time to evaluate : 1.169 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 76 THR Chi-restraints excluded: chain A residue 220 ILE Chi-restraints excluded: chain A residue 260 VAL Chi-restraints excluded: chain A residue 296 THR Chi-restraints excluded: chain A residue 457 LEU Chi-restraints excluded: chain A residue 521 LEU Chi-restraints excluded: chain A residue 559 SER Chi-restraints excluded: chain A residue 572 GLN Chi-restraints excluded: chain A residue 590 TYR Chi-restraints excluded: chain A residue 594 HIS Chi-restraints excluded: chain A residue 597 ILE Chi-restraints excluded: chain A residue 605 TYR Chi-restraints excluded: chain A residue 725 ASN Chi-restraints excluded: chain A residue 727 LEU Chi-restraints excluded: chain A residue 735 ILE Chi-restraints excluded: chain A residue 763 LEU Chi-restraints excluded: chain A residue 781 ARG Chi-restraints excluded: chain B residue 76 THR Chi-restraints excluded: chain B residue 119 SER Chi-restraints excluded: chain B residue 135 THR Chi-restraints excluded: chain B residue 161 LEU Chi-restraints excluded: chain B residue 220 ILE Chi-restraints excluded: chain B residue 236 VAL Chi-restraints excluded: chain B residue 260 VAL Chi-restraints excluded: chain B residue 289 ARG Chi-restraints excluded: chain B residue 296 THR Chi-restraints excluded: chain B residue 324 CYS Chi-restraints excluded: chain B residue 457 LEU Chi-restraints excluded: chain B residue 461 GLN Chi-restraints excluded: chain B residue 521 LEU Chi-restraints excluded: chain B residue 559 SER Chi-restraints excluded: chain B residue 572 GLN Chi-restraints excluded: chain B residue 587 LEU Chi-restraints excluded: chain B residue 605 TYR Chi-restraints excluded: chain B residue 617 LEU Chi-restraints excluded: chain B residue 626 VAL Chi-restraints excluded: chain B residue 704 LEU Chi-restraints excluded: chain B residue 725 ASN Chi-restraints excluded: chain B residue 727 LEU Chi-restraints excluded: chain B residue 735 ILE Chi-restraints excluded: chain B residue 763 LEU Chi-restraints excluded: chain B residue 781 ARG Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 76 optimal weight: 1.9990 chunk 1 optimal weight: 3.9990 chunk 69 optimal weight: 0.9980 chunk 115 optimal weight: 4.9990 chunk 112 optimal weight: 20.0000 chunk 44 optimal weight: 10.0000 chunk 43 optimal weight: 1.9990 chunk 21 optimal weight: 2.9990 chunk 20 optimal weight: 0.9980 chunk 10 optimal weight: 0.8980 chunk 110 optimal weight: 1.9990 overall best weight: 1.3784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 71 GLN A 90 ASN ** A 725 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 769 ASN B 71 GLN B 90 ASN B 286 ASN B 725 ASN B 769 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4090 r_free = 0.4090 target = 0.165165 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3354 r_free = 0.3354 target = 0.101394 restraints weight = 17020.638| |-----------------------------------------------------------------------------| r_work (start): 0.3249 rms_B_bonded: 2.80 r_work: 0.3109 rms_B_bonded: 3.37 restraints_weight: 0.5000 r_work (final): 0.3109 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3119 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3119 r_free = 0.3119 target_work(ls_wunit_k1) = 0.087 | | occupancies: max = 1.00 min = 0.36 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3119 r_free = 0.3119 target_work(ls_wunit_k1) = 0.087 | | occupancies: max = 1.00 min = 0.36 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3119 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8130 moved from start: 0.1178 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 11567 Z= 0.183 Angle : 0.716 18.144 15800 Z= 0.341 Chirality : 0.045 0.284 1840 Planarity : 0.005 0.064 1850 Dihedral : 8.449 59.417 2758 Min Nonbonded Distance : 1.902 Molprobity Statistics. All-atom Clashscore : 6.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.47 % Favored : 95.53 % Rotamer: Outliers : 5.42 % Allowed : 25.56 % Favored : 69.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 12.50 % Cis-general : 0.16 % 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: 1.12 (0.23), residues: 1276 helix: 2.23 (0.21), residues: 590 sheet: 1.37 (0.29), residues: 274 loop : -2.08 (0.27), residues: 412 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 627 HIS 0.005 0.001 HIS B 636 PHE 0.013 0.001 PHE A 722 TYR 0.015 0.001 TYR B 188 ARG 0.003 0.000 ARG B 781 Details of bonding type rmsd link_NAG-ASN : bond 0.00439 ( 8) link_NAG-ASN : angle 2.63506 ( 24) link_BETA1-4 : bond 0.00542 ( 4) link_BETA1-4 : angle 1.41672 ( 12) hydrogen bonds : bond 0.05723 ( 630) hydrogen bonds : angle 3.92996 ( 1795) metal coordination : bond 0.00446 ( 6) SS BOND : bond 0.00075 ( 8) SS BOND : angle 1.39384 ( 16) covalent geometry : bond 0.00434 (11541) covalent geometry : angle 0.70728 (15748) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2552 Ramachandran restraints generated. 1276 Oldfield, 0 Emsley, 1276 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2552 Ramachandran restraints generated. 1276 Oldfield, 0 Emsley, 1276 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 175 residues out of total 1158 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 112 time to evaluate : 1.303 Fit side-chains REVERT: A 113 GLN cc_start: 0.8727 (mm-40) cc_final: 0.8491 (mm-40) REVERT: A 461 GLN cc_start: 0.8425 (OUTLIER) cc_final: 0.8221 (mt0) REVERT: A 554 MET cc_start: 0.8310 (tpp) cc_final: 0.8037 (mmm) REVERT: A 613 MET cc_start: 0.8652 (OUTLIER) cc_final: 0.8428 (pmm) REVERT: A 781 ARG cc_start: 0.8950 (OUTLIER) cc_final: 0.8245 (ttm110) REVERT: B 461 GLN cc_start: 0.8430 (OUTLIER) cc_final: 0.8200 (mt0) REVERT: B 554 MET cc_start: 0.8343 (tpp) cc_final: 0.8058 (mmm) REVERT: B 559 SER cc_start: 0.8775 (OUTLIER) cc_final: 0.8464 (p) REVERT: B 587 LEU cc_start: 0.8179 (OUTLIER) cc_final: 0.7911 (mp) REVERT: B 613 MET cc_start: 0.8709 (OUTLIER) cc_final: 0.8499 (pmm) REVERT: B 650 MET cc_start: 0.3123 (tpt) cc_final: 0.2876 (tpt) REVERT: B 686 MET cc_start: 0.5198 (mmt) cc_final: 0.4296 (pmm) REVERT: B 710 ARG cc_start: 0.8125 (mmm-85) cc_final: 0.7885 (mmt-90) REVERT: B 781 ARG cc_start: 0.8948 (OUTLIER) cc_final: 0.8350 (ttm110) outliers start: 63 outliers final: 36 residues processed: 162 average time/residue: 0.9256 time to fit residues: 165.8128 Evaluate side-chains 153 residues out of total 1158 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 109 time to evaluate : 1.117 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 76 THR Chi-restraints excluded: chain A residue 119 SER Chi-restraints excluded: chain A residue 173 THR Chi-restraints excluded: chain A residue 220 ILE Chi-restraints excluded: chain A residue 296 THR Chi-restraints excluded: chain A residue 457 LEU Chi-restraints excluded: chain A residue 461 GLN Chi-restraints excluded: chain A residue 544 LEU Chi-restraints excluded: chain A residue 559 SER Chi-restraints excluded: chain A residue 572 GLN Chi-restraints excluded: chain A residue 590 TYR Chi-restraints excluded: chain A residue 597 ILE Chi-restraints excluded: chain A residue 605 TYR Chi-restraints excluded: chain A residue 613 MET Chi-restraints excluded: chain A residue 725 ASN Chi-restraints excluded: chain A residue 727 LEU Chi-restraints excluded: chain A residue 735 ILE Chi-restraints excluded: chain A residue 763 LEU Chi-restraints excluded: chain A residue 781 ARG Chi-restraints excluded: chain B residue 76 THR Chi-restraints excluded: chain B residue 119 SER Chi-restraints excluded: chain B residue 135 THR Chi-restraints excluded: chain B residue 161 LEU Chi-restraints excluded: chain B residue 173 THR Chi-restraints excluded: chain B residue 220 ILE Chi-restraints excluded: chain B residue 236 VAL Chi-restraints excluded: chain B residue 260 VAL Chi-restraints excluded: chain B residue 296 THR Chi-restraints excluded: chain B residue 324 CYS Chi-restraints excluded: chain B residue 457 LEU Chi-restraints excluded: chain B residue 461 GLN Chi-restraints excluded: chain B residue 559 SER Chi-restraints excluded: chain B residue 572 GLN Chi-restraints excluded: chain B residue 587 LEU Chi-restraints excluded: chain B residue 605 TYR Chi-restraints excluded: chain B residue 613 MET Chi-restraints excluded: chain B residue 617 LEU Chi-restraints excluded: chain B residue 626 VAL Chi-restraints excluded: chain B residue 704 LEU Chi-restraints excluded: chain B residue 727 LEU Chi-restraints excluded: chain B residue 735 ILE Chi-restraints excluded: chain B residue 763 LEU Chi-restraints excluded: chain B residue 781 ARG Chi-restraints excluded: chain B residue 787 CYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 9 optimal weight: 1.9990 chunk 92 optimal weight: 4.9990 chunk 48 optimal weight: 10.0000 chunk 110 optimal weight: 0.9980 chunk 72 optimal weight: 1.9990 chunk 117 optimal weight: 1.9990 chunk 44 optimal weight: 0.9980 chunk 49 optimal weight: 10.0000 chunk 45 optimal weight: 0.6980 chunk 97 optimal weight: 1.9990 chunk 106 optimal weight: 0.6980 overall best weight: 1.0782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 74 GLN A 90 ASN A 142 GLN ** A 725 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 769 ASN B 74 GLN B 90 ASN B 286 ASN B 725 ASN B 769 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4095 r_free = 0.4095 target = 0.165817 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3346 r_free = 0.3346 target = 0.100646 restraints weight = 23159.429| |-----------------------------------------------------------------------------| r_work (start): 0.3239 rms_B_bonded: 3.16 r_work: 0.3097 rms_B_bonded: 3.66 restraints_weight: 0.5000 r_work (final): 0.3097 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3101 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3101 r_free = 0.3101 target_work(ls_wunit_k1) = 0.086 | | occupancies: max = 1.00 min = 0.36 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3101 r_free = 0.3101 target_work(ls_wunit_k1) = 0.086 | | occupancies: max = 1.00 min = 0.37 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3101 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8142 moved from start: 0.1281 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 11567 Z= 0.159 Angle : 0.698 18.186 15800 Z= 0.332 Chirality : 0.045 0.282 1840 Planarity : 0.005 0.060 1850 Dihedral : 8.105 59.968 2753 Min Nonbonded Distance : 1.939 Molprobity Statistics. All-atom Clashscore : 6.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.40 % Favored : 95.60 % Rotamer: Outliers : 5.08 % Allowed : 25.82 % Favored : 69.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 12.50 % Cis-general : 0.16 % 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: 1.16 (0.23), residues: 1276 helix: 2.41 (0.21), residues: 578 sheet: 1.41 (0.29), residues: 274 loop : -2.20 (0.26), residues: 424 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 627 HIS 0.005 0.001 HIS B 636 PHE 0.013 0.001 PHE A 732 TYR 0.015 0.001 TYR B 188 ARG 0.003 0.000 ARG A 781 Details of bonding type rmsd link_NAG-ASN : bond 0.00448 ( 8) link_NAG-ASN : angle 2.66220 ( 24) link_BETA1-4 : bond 0.00497 ( 4) link_BETA1-4 : angle 1.39182 ( 12) hydrogen bonds : bond 0.05368 ( 630) hydrogen bonds : angle 3.87582 ( 1795) metal coordination : bond 0.00320 ( 6) SS BOND : bond 0.00072 ( 8) SS BOND : angle 1.27806 ( 16) covalent geometry : bond 0.00369 (11541) covalent geometry : angle 0.68961 (15748) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2552 Ramachandran restraints generated. 1276 Oldfield, 0 Emsley, 1276 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2552 Ramachandran restraints generated. 1276 Oldfield, 0 Emsley, 1276 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 169 residues out of total 1158 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 110 time to evaluate : 1.139 Fit side-chains REVERT: A 461 GLN cc_start: 0.8436 (OUTLIER) cc_final: 0.8234 (mt0) REVERT: A 554 MET cc_start: 0.8311 (tpp) cc_final: 0.8051 (mmm) REVERT: A 590 TYR cc_start: 0.6445 (OUTLIER) cc_final: 0.5983 (t80) REVERT: A 613 MET cc_start: 0.8667 (OUTLIER) cc_final: 0.8444 (pmm) REVERT: A 650 MET cc_start: 0.3911 (OUTLIER) cc_final: 0.3565 (tpt) REVERT: A 781 ARG cc_start: 0.8943 (OUTLIER) cc_final: 0.8354 (ttm110) REVERT: B 461 GLN cc_start: 0.8454 (OUTLIER) cc_final: 0.8232 (mt0) REVERT: B 554 MET cc_start: 0.8371 (tpp) cc_final: 0.8102 (mmm) REVERT: B 559 SER cc_start: 0.8786 (OUTLIER) cc_final: 0.8493 (p) REVERT: B 587 LEU cc_start: 0.8262 (OUTLIER) cc_final: 0.7948 (mp) REVERT: B 590 TYR cc_start: 0.6576 (OUTLIER) cc_final: 0.6179 (t80) REVERT: B 613 MET cc_start: 0.8674 (OUTLIER) cc_final: 0.8455 (pmm) REVERT: B 686 MET cc_start: 0.5263 (mmt) cc_final: 0.4337 (pmm) REVERT: B 710 ARG cc_start: 0.8021 (mmm-85) cc_final: 0.7819 (mmt-90) REVERT: B 781 ARG cc_start: 0.8936 (OUTLIER) cc_final: 0.8242 (ttm110) outliers start: 59 outliers final: 36 residues processed: 156 average time/residue: 0.9250 time to fit residues: 159.6671 Evaluate side-chains 155 residues out of total 1158 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 108 time to evaluate : 1.103 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 76 THR Chi-restraints excluded: chain A residue 173 THR Chi-restraints excluded: chain A residue 220 ILE Chi-restraints excluded: chain A residue 260 VAL Chi-restraints excluded: chain A residue 296 THR Chi-restraints excluded: chain A residue 457 LEU Chi-restraints excluded: chain A residue 461 GLN Chi-restraints excluded: chain A residue 544 LEU Chi-restraints excluded: chain A residue 559 SER Chi-restraints excluded: chain A residue 572 GLN Chi-restraints excluded: chain A residue 590 TYR Chi-restraints excluded: chain A residue 597 ILE Chi-restraints excluded: chain A residue 605 TYR Chi-restraints excluded: chain A residue 613 MET Chi-restraints excluded: chain A residue 650 MET Chi-restraints excluded: chain A residue 725 ASN Chi-restraints excluded: chain A residue 727 LEU Chi-restraints excluded: chain A residue 735 ILE Chi-restraints excluded: chain A residue 763 LEU Chi-restraints excluded: chain A residue 781 ARG Chi-restraints excluded: chain A residue 787 CYS Chi-restraints excluded: chain B residue 76 THR Chi-restraints excluded: chain B residue 119 SER Chi-restraints excluded: chain B residue 135 THR Chi-restraints excluded: chain B residue 161 LEU Chi-restraints excluded: chain B residue 220 ILE Chi-restraints excluded: chain B residue 236 VAL Chi-restraints excluded: chain B residue 286 ASN Chi-restraints excluded: chain B residue 296 THR Chi-restraints excluded: chain B residue 324 CYS Chi-restraints excluded: chain B residue 457 LEU Chi-restraints excluded: chain B residue 461 GLN Chi-restraints excluded: chain B residue 544 LEU Chi-restraints excluded: chain B residue 559 SER Chi-restraints excluded: chain B residue 572 GLN Chi-restraints excluded: chain B residue 587 LEU Chi-restraints excluded: chain B residue 590 TYR Chi-restraints excluded: chain B residue 605 TYR Chi-restraints excluded: chain B residue 613 MET Chi-restraints excluded: chain B residue 617 LEU Chi-restraints excluded: chain B residue 626 VAL Chi-restraints excluded: chain B residue 704 LEU Chi-restraints excluded: chain B residue 727 LEU Chi-restraints excluded: chain B residue 735 ILE Chi-restraints excluded: chain B residue 763 LEU Chi-restraints excluded: chain B residue 781 ARG Chi-restraints excluded: chain B residue 787 CYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 54 optimal weight: 2.9990 chunk 79 optimal weight: 1.9990 chunk 4 optimal weight: 0.8980 chunk 84 optimal weight: 1.9990 chunk 58 optimal weight: 0.9980 chunk 80 optimal weight: 2.9990 chunk 22 optimal weight: 1.9990 chunk 113 optimal weight: 10.0000 chunk 108 optimal weight: 9.9990 chunk 23 optimal weight: 0.6980 chunk 43 optimal weight: 0.8980 overall best weight: 1.0982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 71 GLN A 74 GLN A 90 ASN A 288 GLN ** A 725 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 769 ASN B 71 GLN B 74 GLN B 90 ASN B 142 GLN B 286 ASN B 725 ASN B 769 ASN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4094 r_free = 0.4094 target = 0.165681 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3340 r_free = 0.3340 target = 0.100605 restraints weight = 27427.309| |-----------------------------------------------------------------------------| r_work (start): 0.3238 rms_B_bonded: 3.59 r_work: 0.3070 rms_B_bonded: 3.91 restraints_weight: 0.5000 r_work (final): 0.3070 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3081 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3081 r_free = 0.3081 target_work(ls_wunit_k1) = 0.084 | | occupancies: max = 1.00 min = 0.37 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3081 r_free = 0.3081 target_work(ls_wunit_k1) = 0.084 | | occupancies: max = 1.00 min = 0.37 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3081 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8144 moved from start: 0.1298 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 11567 Z= 0.160 Angle : 0.697 18.706 15800 Z= 0.331 Chirality : 0.044 0.284 1840 Planarity : 0.005 0.060 1850 Dihedral : 7.965 59.118 2752 Min Nonbonded Distance : 1.931 Molprobity Statistics. All-atom Clashscore : 5.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.40 % Favored : 95.60 % Rotamer: Outliers : 5.25 % Allowed : 25.73 % Favored : 69.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 12.50 % Cis-general : 0.16 % 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: 1.15 (0.23), residues: 1276 helix: 2.40 (0.21), residues: 578 sheet: 1.44 (0.29), residues: 274 loop : -2.23 (0.26), residues: 424 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 627 HIS 0.005 0.001 HIS B 636 PHE 0.016 0.001 PHE A 732 TYR 0.015 0.001 TYR B 188 ARG 0.003 0.000 ARG A 781 Details of bonding type rmsd link_NAG-ASN : bond 0.00455 ( 8) link_NAG-ASN : angle 2.65131 ( 24) link_BETA1-4 : bond 0.00505 ( 4) link_BETA1-4 : angle 1.41257 ( 12) hydrogen bonds : bond 0.05342 ( 630) hydrogen bonds : angle 3.85564 ( 1795) metal coordination : bond 0.00344 ( 6) SS BOND : bond 0.00070 ( 8) SS BOND : angle 1.26790 ( 16) covalent geometry : bond 0.00373 (11541) covalent geometry : angle 0.68835 (15748) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2552 Ramachandran restraints generated. 1276 Oldfield, 0 Emsley, 1276 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2552 Ramachandran restraints generated. 1276 Oldfield, 0 Emsley, 1276 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 170 residues out of total 1158 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 109 time to evaluate : 1.115 Fit side-chains REVERT: A 113 GLN cc_start: 0.8763 (mm-40) cc_final: 0.8530 (mm-40) REVERT: A 461 GLN cc_start: 0.8450 (OUTLIER) cc_final: 0.8247 (mt0) REVERT: A 554 MET cc_start: 0.8307 (tpp) cc_final: 0.8052 (mmm) REVERT: A 590 TYR cc_start: 0.6429 (OUTLIER) cc_final: 0.5989 (t80) REVERT: A 613 MET cc_start: 0.8657 (OUTLIER) cc_final: 0.8431 (pmm) REVERT: A 781 ARG cc_start: 0.8947 (OUTLIER) cc_final: 0.8356 (ttm110) REVERT: B 289 ARG cc_start: 0.9102 (OUTLIER) cc_final: 0.8801 (mtm180) REVERT: B 461 GLN cc_start: 0.8460 (OUTLIER) cc_final: 0.8253 (mt0) REVERT: B 554 MET cc_start: 0.8381 (tpp) cc_final: 0.8120 (mmm) REVERT: B 590 TYR cc_start: 0.6574 (OUTLIER) cc_final: 0.6179 (t80) REVERT: B 613 MET cc_start: 0.8684 (OUTLIER) cc_final: 0.8457 (pmm) REVERT: B 686 MET cc_start: 0.5261 (mmt) cc_final: 0.4350 (pmm) REVERT: B 781 ARG cc_start: 0.8935 (OUTLIER) cc_final: 0.8248 (ttm110) outliers start: 61 outliers final: 39 residues processed: 156 average time/residue: 0.9856 time to fit residues: 169.6301 Evaluate side-chains 153 residues out of total 1158 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 105 time to evaluate : 1.115 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 76 THR Chi-restraints excluded: chain A residue 119 SER Chi-restraints excluded: chain A residue 173 THR Chi-restraints excluded: chain A residue 220 ILE Chi-restraints excluded: chain A residue 260 VAL Chi-restraints excluded: chain A residue 296 THR Chi-restraints excluded: chain A residue 457 LEU Chi-restraints excluded: chain A residue 461 GLN Chi-restraints excluded: chain A residue 521 LEU Chi-restraints excluded: chain A residue 544 LEU Chi-restraints excluded: chain A residue 559 SER Chi-restraints excluded: chain A residue 572 GLN Chi-restraints excluded: chain A residue 590 TYR Chi-restraints excluded: chain A residue 597 ILE Chi-restraints excluded: chain A residue 605 TYR Chi-restraints excluded: chain A residue 613 MET Chi-restraints excluded: chain A residue 725 ASN Chi-restraints excluded: chain A residue 727 LEU Chi-restraints excluded: chain A residue 735 ILE Chi-restraints excluded: chain A residue 763 LEU Chi-restraints excluded: chain A residue 781 ARG Chi-restraints excluded: chain A residue 787 CYS Chi-restraints excluded: chain B residue 76 THR Chi-restraints excluded: chain B residue 119 SER Chi-restraints excluded: chain B residue 161 LEU Chi-restraints excluded: chain B residue 173 THR Chi-restraints excluded: chain B residue 220 ILE Chi-restraints excluded: chain B residue 236 VAL Chi-restraints excluded: chain B residue 289 ARG Chi-restraints excluded: chain B residue 309 SER Chi-restraints excluded: chain B residue 324 CYS Chi-restraints excluded: chain B residue 457 LEU Chi-restraints excluded: chain B residue 461 GLN Chi-restraints excluded: chain B residue 521 LEU Chi-restraints excluded: chain B residue 544 LEU Chi-restraints excluded: chain B residue 572 GLN Chi-restraints excluded: chain B residue 590 TYR Chi-restraints excluded: chain B residue 597 ILE Chi-restraints excluded: chain B residue 605 TYR Chi-restraints excluded: chain B residue 613 MET Chi-restraints excluded: chain B residue 617 LEU Chi-restraints excluded: chain B residue 626 VAL Chi-restraints excluded: chain B residue 704 LEU Chi-restraints excluded: chain B residue 727 LEU Chi-restraints excluded: chain B residue 735 ILE Chi-restraints excluded: chain B residue 763 LEU Chi-restraints excluded: chain B residue 781 ARG Chi-restraints excluded: chain B residue 787 CYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 60 optimal weight: 2.9990 chunk 58 optimal weight: 2.9990 chunk 29 optimal weight: 0.9990 chunk 17 optimal weight: 2.9990 chunk 24 optimal weight: 10.0000 chunk 74 optimal weight: 3.9990 chunk 1 optimal weight: 3.9990 chunk 96 optimal weight: 0.8980 chunk 42 optimal weight: 0.9990 chunk 18 optimal weight: 0.9980 chunk 70 optimal weight: 1.9990 overall best weight: 1.1786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 74 GLN A 90 ASN A 142 GLN ** A 725 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 769 ASN B 74 GLN B 90 ASN B 142 GLN B 286 ASN B 725 ASN B 769 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4094 r_free = 0.4094 target = 0.165722 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3367 r_free = 0.3367 target = 0.102433 restraints weight = 15062.313| |-----------------------------------------------------------------------------| r_work (start): 0.3271 rms_B_bonded: 2.68 r_work: 0.3134 rms_B_bonded: 3.26 restraints_weight: 0.5000 r_work: 0.2992 rms_B_bonded: 4.91 restraints_weight: 0.2500 r_work (final): 0.2992 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2971 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2971 r_free = 0.2971 target_work(ls_wunit_k1) = 0.078 | | occupancies: max = 1.00 min = 0.37 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2971 r_free = 0.2971 target_work(ls_wunit_k1) = 0.078 | | occupancies: max = 1.00 min = 0.38 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2971 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8219 moved from start: 0.1366 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 11567 Z= 0.165 Angle : 0.704 17.683 15800 Z= 0.333 Chirality : 0.045 0.282 1840 Planarity : 0.004 0.061 1850 Dihedral : 7.781 58.933 2749 Min Nonbonded Distance : 1.923 Molprobity Statistics. All-atom Clashscore : 6.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.32 % Favored : 95.68 % Rotamer: Outliers : 5.85 % Allowed : 25.39 % Favored : 68.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 12.50 % Cis-general : 0.16 % 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: 1.13 (0.23), residues: 1276 helix: 2.39 (0.21), residues: 578 sheet: 1.43 (0.29), residues: 274 loop : -2.24 (0.26), residues: 424 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP B 629 HIS 0.004 0.001 HIS B 636 PHE 0.026 0.001 PHE B 628 TYR 0.015 0.001 TYR B 188 ARG 0.004 0.000 ARG B 710 Details of bonding type rmsd link_NAG-ASN : bond 0.00456 ( 8) link_NAG-ASN : angle 2.62098 ( 24) link_BETA1-4 : bond 0.00518 ( 4) link_BETA1-4 : angle 1.41326 ( 12) hydrogen bonds : bond 0.05382 ( 630) hydrogen bonds : angle 3.85409 ( 1795) metal coordination : bond 0.00371 ( 6) SS BOND : bond 0.00074 ( 8) SS BOND : angle 1.32475 ( 16) covalent geometry : bond 0.00387 (11541) covalent geometry : angle 0.69538 (15748) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2552 Ramachandran restraints generated. 1276 Oldfield, 0 Emsley, 1276 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2552 Ramachandran restraints generated. 1276 Oldfield, 0 Emsley, 1276 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 176 residues out of total 1158 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 108 time to evaluate : 1.273 Fit side-chains REVERT: A 554 MET cc_start: 0.8396 (tpp) cc_final: 0.8159 (mmm) REVERT: A 590 TYR cc_start: 0.6486 (OUTLIER) cc_final: 0.6036 (t80) REVERT: A 613 MET cc_start: 0.8666 (OUTLIER) cc_final: 0.8442 (pmm) REVERT: A 781 ARG cc_start: 0.8976 (OUTLIER) cc_final: 0.8396 (ttm110) REVERT: B 554 MET cc_start: 0.8474 (tpp) cc_final: 0.8219 (mmm) REVERT: B 559 SER cc_start: 0.8831 (OUTLIER) cc_final: 0.8546 (p) REVERT: B 590 TYR cc_start: 0.6609 (OUTLIER) cc_final: 0.6214 (t80) REVERT: B 613 MET cc_start: 0.8688 (OUTLIER) cc_final: 0.8468 (pmm) REVERT: B 686 MET cc_start: 0.5278 (mmt) cc_final: 0.4397 (pmm) REVERT: B 710 ARG cc_start: 0.7867 (OUTLIER) cc_final: 0.7583 (mmt-90) REVERT: B 781 ARG cc_start: 0.8966 (OUTLIER) cc_final: 0.8381 (ttm110) outliers start: 68 outliers final: 49 residues processed: 159 average time/residue: 0.9583 time to fit residues: 169.1186 Evaluate side-chains 163 residues out of total 1158 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 106 time to evaluate : 1.257 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 76 THR Chi-restraints excluded: chain A residue 119 SER Chi-restraints excluded: chain A residue 141 LEU Chi-restraints excluded: chain A residue 173 THR Chi-restraints excluded: chain A residue 220 ILE Chi-restraints excluded: chain A residue 260 VAL Chi-restraints excluded: chain A residue 296 THR Chi-restraints excluded: chain A residue 309 SER Chi-restraints excluded: chain A residue 457 LEU Chi-restraints excluded: chain A residue 521 LEU Chi-restraints excluded: chain A residue 544 LEU Chi-restraints excluded: chain A residue 559 SER Chi-restraints excluded: chain A residue 572 GLN Chi-restraints excluded: chain A residue 590 TYR Chi-restraints excluded: chain A residue 597 ILE Chi-restraints excluded: chain A residue 605 TYR Chi-restraints excluded: chain A residue 613 MET Chi-restraints excluded: chain A residue 650 MET Chi-restraints excluded: chain A residue 725 ASN Chi-restraints excluded: chain A residue 727 LEU Chi-restraints excluded: chain A residue 735 ILE Chi-restraints excluded: chain A residue 763 LEU Chi-restraints excluded: chain A residue 781 ARG Chi-restraints excluded: chain A residue 787 CYS Chi-restraints excluded: chain B residue 76 THR Chi-restraints excluded: chain B residue 119 SER Chi-restraints excluded: chain B residue 135 THR Chi-restraints excluded: chain B residue 161 LEU Chi-restraints excluded: chain B residue 173 THR Chi-restraints excluded: chain B residue 220 ILE Chi-restraints excluded: chain B residue 236 VAL Chi-restraints excluded: chain B residue 277 ILE Chi-restraints excluded: chain B residue 286 ASN Chi-restraints excluded: chain B residue 296 THR Chi-restraints excluded: chain B residue 309 SER Chi-restraints excluded: chain B residue 324 CYS Chi-restraints excluded: chain B residue 457 LEU Chi-restraints excluded: chain B residue 510 LEU Chi-restraints excluded: chain B residue 521 LEU Chi-restraints excluded: chain B residue 544 LEU Chi-restraints excluded: chain B residue 559 SER Chi-restraints excluded: chain B residue 572 GLN Chi-restraints excluded: chain B residue 590 TYR Chi-restraints excluded: chain B residue 597 ILE Chi-restraints excluded: chain B residue 605 TYR Chi-restraints excluded: chain B residue 613 MET Chi-restraints excluded: chain B residue 617 LEU Chi-restraints excluded: chain B residue 626 VAL Chi-restraints excluded: chain B residue 650 MET Chi-restraints excluded: chain B residue 704 LEU Chi-restraints excluded: chain B residue 710 ARG Chi-restraints excluded: chain B residue 727 LEU Chi-restraints excluded: chain B residue 735 ILE Chi-restraints excluded: chain B residue 763 LEU Chi-restraints excluded: chain B residue 771 SER Chi-restraints excluded: chain B residue 781 ARG Chi-restraints excluded: chain B residue 787 CYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 51 optimal weight: 5.9990 chunk 14 optimal weight: 0.8980 chunk 42 optimal weight: 1.9990 chunk 49 optimal weight: 9.9990 chunk 98 optimal weight: 1.9990 chunk 3 optimal weight: 1.9990 chunk 40 optimal weight: 3.9990 chunk 22 optimal weight: 0.7980 chunk 93 optimal weight: 0.5980 chunk 15 optimal weight: 0.9980 chunk 41 optimal weight: 0.7980 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 71 GLN A 74 GLN A 90 ASN ** A 725 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 769 ASN B 71 GLN B 74 GLN B 90 ASN B 286 ASN B 725 ASN B 769 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4102 r_free = 0.4102 target = 0.166573 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3369 r_free = 0.3369 target = 0.102313 restraints weight = 18514.114| |-----------------------------------------------------------------------------| r_work (start): 0.3271 rms_B_bonded: 2.91 r_work: 0.3131 rms_B_bonded: 3.46 restraints_weight: 0.5000 r_work (final): 0.3131 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3146 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3146 r_free = 0.3146 target_work(ls_wunit_k1) = 0.089 | | occupancies: max = 1.00 min = 0.38 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3146 r_free = 0.3146 target_work(ls_wunit_k1) = 0.089 | | occupancies: max = 1.00 min = 0.36 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3146 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8111 moved from start: 0.1402 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 11567 Z= 0.142 Angle : 0.692 17.473 15800 Z= 0.328 Chirality : 0.044 0.284 1840 Planarity : 0.004 0.058 1850 Dihedral : 7.585 56.911 2749 Min Nonbonded Distance : 1.969 Molprobity Statistics. All-atom Clashscore : 6.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.24 % Favored : 95.76 % Rotamer: Outliers : 4.82 % Allowed : 26.08 % Favored : 69.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 12.50 % Cis-general : 0.16 % 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: 1.18 (0.23), residues: 1276 helix: 2.42 (0.21), residues: 578 sheet: 1.48 (0.29), residues: 274 loop : -2.22 (0.26), residues: 424 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP B 629 HIS 0.004 0.001 HIS B 636 PHE 0.020 0.001 PHE B 628 TYR 0.014 0.001 TYR A 188 ARG 0.003 0.000 ARG B 289 Details of bonding type rmsd link_NAG-ASN : bond 0.00463 ( 8) link_NAG-ASN : angle 2.65451 ( 24) link_BETA1-4 : bond 0.00472 ( 4) link_BETA1-4 : angle 1.39166 ( 12) hydrogen bonds : bond 0.05040 ( 630) hydrogen bonds : angle 3.81483 ( 1795) metal coordination : bond 0.00252 ( 6) SS BOND : bond 0.00074 ( 8) SS BOND : angle 1.16458 ( 16) covalent geometry : bond 0.00323 (11541) covalent geometry : angle 0.68313 (15748) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2552 Ramachandran restraints generated. 1276 Oldfield, 0 Emsley, 1276 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2552 Ramachandran restraints generated. 1276 Oldfield, 0 Emsley, 1276 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 165 residues out of total 1158 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 109 time to evaluate : 1.139 Fit side-chains REVERT: A 554 MET cc_start: 0.8303 (tpp) cc_final: 0.8061 (mmm) REVERT: A 590 TYR cc_start: 0.6536 (OUTLIER) cc_final: 0.6052 (t80) REVERT: A 613 MET cc_start: 0.8641 (OUTLIER) cc_final: 0.8412 (pmm) REVERT: A 781 ARG cc_start: 0.8920 (OUTLIER) cc_final: 0.8333 (ttm110) REVERT: B 554 MET cc_start: 0.8352 (tpp) cc_final: 0.8097 (mmm) REVERT: B 559 SER cc_start: 0.8774 (OUTLIER) cc_final: 0.8481 (p) REVERT: B 590 TYR cc_start: 0.6603 (OUTLIER) cc_final: 0.6215 (t80) REVERT: B 613 MET cc_start: 0.8655 (OUTLIER) cc_final: 0.8436 (pmm) REVERT: B 686 MET cc_start: 0.5213 (mmt) cc_final: 0.4371 (pmm) REVERT: B 710 ARG cc_start: 0.7814 (OUTLIER) cc_final: 0.6679 (mmm160) REVERT: B 781 ARG cc_start: 0.8918 (OUTLIER) cc_final: 0.8330 (ttm110) outliers start: 56 outliers final: 39 residues processed: 152 average time/residue: 0.9408 time to fit residues: 157.9751 Evaluate side-chains 153 residues out of total 1158 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 106 time to evaluate : 1.100 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 76 THR Chi-restraints excluded: chain A residue 119 SER Chi-restraints excluded: chain A residue 220 ILE Chi-restraints excluded: chain A residue 260 VAL Chi-restraints excluded: chain A residue 309 SER Chi-restraints excluded: chain A residue 457 LEU Chi-restraints excluded: chain A residue 472 VAL Chi-restraints excluded: chain A residue 521 LEU Chi-restraints excluded: chain A residue 559 SER Chi-restraints excluded: chain A residue 572 GLN Chi-restraints excluded: chain A residue 590 TYR Chi-restraints excluded: chain A residue 597 ILE Chi-restraints excluded: chain A residue 605 TYR Chi-restraints excluded: chain A residue 613 MET Chi-restraints excluded: chain A residue 650 MET Chi-restraints excluded: chain A residue 725 ASN Chi-restraints excluded: chain A residue 727 LEU Chi-restraints excluded: chain A residue 735 ILE Chi-restraints excluded: chain A residue 763 LEU Chi-restraints excluded: chain A residue 781 ARG Chi-restraints excluded: chain A residue 787 CYS Chi-restraints excluded: chain B residue 76 THR Chi-restraints excluded: chain B residue 173 THR Chi-restraints excluded: chain B residue 220 ILE Chi-restraints excluded: chain B residue 236 VAL Chi-restraints excluded: chain B residue 277 ILE Chi-restraints excluded: chain B residue 296 THR Chi-restraints excluded: chain B residue 324 CYS Chi-restraints excluded: chain B residue 457 LEU Chi-restraints excluded: chain B residue 510 LEU Chi-restraints excluded: chain B residue 521 LEU Chi-restraints excluded: chain B residue 544 LEU Chi-restraints excluded: chain B residue 559 SER Chi-restraints excluded: chain B residue 572 GLN Chi-restraints excluded: chain B residue 590 TYR Chi-restraints excluded: chain B residue 597 ILE Chi-restraints excluded: chain B residue 605 TYR Chi-restraints excluded: chain B residue 613 MET Chi-restraints excluded: chain B residue 617 LEU Chi-restraints excluded: chain B residue 704 LEU Chi-restraints excluded: chain B residue 710 ARG Chi-restraints excluded: chain B residue 727 LEU Chi-restraints excluded: chain B residue 735 ILE Chi-restraints excluded: chain B residue 763 LEU Chi-restraints excluded: chain B residue 771 SER Chi-restraints excluded: chain B residue 781 ARG Chi-restraints excluded: chain B residue 787 CYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 89 optimal weight: 1.9990 chunk 93 optimal weight: 9.9990 chunk 104 optimal weight: 4.9990 chunk 90 optimal weight: 0.9980 chunk 43 optimal weight: 5.9990 chunk 127 optimal weight: 0.7980 chunk 74 optimal weight: 1.9990 chunk 87 optimal weight: 2.9990 chunk 26 optimal weight: 0.8980 chunk 23 optimal weight: 2.9990 chunk 115 optimal weight: 6.9990 overall best weight: 1.3384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 74 GLN A 90 ASN A 142 GLN ** A 725 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 769 ASN B 71 GLN B 74 GLN B 90 ASN B 286 ASN B 725 ASN B 769 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4091 r_free = 0.4091 target = 0.165543 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3338 r_free = 0.3338 target = 0.100132 restraints weight = 24325.135| |-----------------------------------------------------------------------------| r_work (start): 0.3234 rms_B_bonded: 3.21 r_work: 0.3091 rms_B_bonded: 3.69 restraints_weight: 0.5000 r_work (final): 0.3091 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3078 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3078 r_free = 0.3078 target_work(ls_wunit_k1) = 0.084 | | occupancies: max = 1.00 min = 0.36 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3078 r_free = 0.3078 target_work(ls_wunit_k1) = 0.084 | | occupancies: max = 1.00 min = 0.36 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3078 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8168 moved from start: 0.1464 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 11567 Z= 0.178 Angle : 0.715 17.117 15800 Z= 0.342 Chirality : 0.045 0.280 1840 Planarity : 0.004 0.059 1850 Dihedral : 7.568 56.847 2748 Min Nonbonded Distance : 1.899 Molprobity Statistics. All-atom Clashscore : 5.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.55 % Favored : 95.45 % Rotamer: Outliers : 4.82 % Allowed : 26.16 % Favored : 69.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 12.50 % Cis-general : 0.16 % 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: 1.12 (0.23), residues: 1276 helix: 2.36 (0.21), residues: 578 sheet: 1.45 (0.29), residues: 274 loop : -2.24 (0.26), residues: 424 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP B 629 HIS 0.004 0.001 HIS B 636 PHE 0.018 0.001 PHE B 732 TYR 0.016 0.001 TYR A 188 ARG 0.003 0.000 ARG B 710 Details of bonding type rmsd link_NAG-ASN : bond 0.00457 ( 8) link_NAG-ASN : angle 2.61889 ( 24) link_BETA1-4 : bond 0.00507 ( 4) link_BETA1-4 : angle 1.42027 ( 12) hydrogen bonds : bond 0.05503 ( 630) hydrogen bonds : angle 3.85639 ( 1795) metal coordination : bond 0.00440 ( 6) SS BOND : bond 0.00073 ( 8) SS BOND : angle 1.37545 ( 16) covalent geometry : bond 0.00424 (11541) covalent geometry : angle 0.70604 (15748) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2552 Ramachandran restraints generated. 1276 Oldfield, 0 Emsley, 1276 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2552 Ramachandran restraints generated. 1276 Oldfield, 0 Emsley, 1276 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 163 residues out of total 1158 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 107 time to evaluate : 1.239 Fit side-chains REVERT: A 554 MET cc_start: 0.8349 (tpp) cc_final: 0.8119 (mmm) REVERT: A 590 TYR cc_start: 0.6432 (OUTLIER) cc_final: 0.5971 (t80) REVERT: A 613 MET cc_start: 0.8631 (OUTLIER) cc_final: 0.8387 (pmm) REVERT: A 781 ARG cc_start: 0.8977 (OUTLIER) cc_final: 0.8383 (ttm110) REVERT: B 554 MET cc_start: 0.8399 (tpp) cc_final: 0.8162 (mmm) REVERT: B 559 SER cc_start: 0.8799 (OUTLIER) cc_final: 0.8505 (p) REVERT: B 590 TYR cc_start: 0.6637 (OUTLIER) cc_final: 0.6219 (t80) REVERT: B 613 MET cc_start: 0.8667 (OUTLIER) cc_final: 0.8449 (pmm) REVERT: B 686 MET cc_start: 0.5197 (mmt) cc_final: 0.4387 (pmm) REVERT: B 710 ARG cc_start: 0.7712 (OUTLIER) cc_final: 0.6648 (mmm160) REVERT: B 736 MET cc_start: 0.7988 (tpp) cc_final: 0.7183 (mpp) REVERT: B 781 ARG cc_start: 0.8965 (OUTLIER) cc_final: 0.8369 (ttm110) outliers start: 56 outliers final: 40 residues processed: 150 average time/residue: 0.9759 time to fit residues: 161.5632 Evaluate side-chains 150 residues out of total 1158 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 102 time to evaluate : 1.163 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 76 THR Chi-restraints excluded: chain A residue 119 SER Chi-restraints excluded: chain A residue 220 ILE Chi-restraints excluded: chain A residue 260 VAL Chi-restraints excluded: chain A residue 309 SER Chi-restraints excluded: chain A residue 457 LEU Chi-restraints excluded: chain A residue 472 VAL Chi-restraints excluded: chain A residue 559 SER Chi-restraints excluded: chain A residue 572 GLN Chi-restraints excluded: chain A residue 590 TYR Chi-restraints excluded: chain A residue 597 ILE Chi-restraints excluded: chain A residue 605 TYR Chi-restraints excluded: chain A residue 613 MET Chi-restraints excluded: chain A residue 650 MET Chi-restraints excluded: chain A residue 725 ASN Chi-restraints excluded: chain A residue 727 LEU Chi-restraints excluded: chain A residue 735 ILE Chi-restraints excluded: chain A residue 763 LEU Chi-restraints excluded: chain A residue 771 SER Chi-restraints excluded: chain A residue 781 ARG Chi-restraints excluded: chain A residue 787 CYS Chi-restraints excluded: chain B residue 76 THR Chi-restraints excluded: chain B residue 141 LEU Chi-restraints excluded: chain B residue 173 THR Chi-restraints excluded: chain B residue 220 ILE Chi-restraints excluded: chain B residue 236 VAL Chi-restraints excluded: chain B residue 277 ILE Chi-restraints excluded: chain B residue 296 THR Chi-restraints excluded: chain B residue 309 SER Chi-restraints excluded: chain B residue 324 CYS Chi-restraints excluded: chain B residue 510 LEU Chi-restraints excluded: chain B residue 521 LEU Chi-restraints excluded: chain B residue 544 LEU Chi-restraints excluded: chain B residue 559 SER Chi-restraints excluded: chain B residue 572 GLN Chi-restraints excluded: chain B residue 590 TYR Chi-restraints excluded: chain B residue 597 ILE Chi-restraints excluded: chain B residue 605 TYR Chi-restraints excluded: chain B residue 613 MET Chi-restraints excluded: chain B residue 617 LEU Chi-restraints excluded: chain B residue 650 MET Chi-restraints excluded: chain B residue 704 LEU Chi-restraints excluded: chain B residue 710 ARG Chi-restraints excluded: chain B residue 727 LEU Chi-restraints excluded: chain B residue 763 LEU Chi-restraints excluded: chain B residue 771 SER Chi-restraints excluded: chain B residue 781 ARG Chi-restraints excluded: chain B residue 787 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 21 optimal weight: 0.7980 chunk 73 optimal weight: 1.9990 chunk 56 optimal weight: 0.0030 chunk 35 optimal weight: 0.0870 chunk 48 optimal weight: 6.9990 chunk 41 optimal weight: 0.5980 chunk 103 optimal weight: 4.9990 chunk 54 optimal weight: 2.9990 chunk 97 optimal weight: 1.9990 chunk 31 optimal weight: 0.5980 chunk 14 optimal weight: 0.6980 overall best weight: 0.3968 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 71 GLN A 74 GLN A 90 ASN ** A 725 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 769 ASN B 74 GLN B 90 ASN B 142 GLN B 286 ASN B 725 ASN B 769 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4121 r_free = 0.4121 target = 0.168429 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3407 r_free = 0.3407 target = 0.104954 restraints weight = 16987.437| |-----------------------------------------------------------------------------| r_work (start): 0.3308 rms_B_bonded: 2.83 r_work: 0.3172 rms_B_bonded: 3.39 restraints_weight: 0.5000 r_work (final): 0.3172 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3183 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3183 r_free = 0.3183 target_work(ls_wunit_k1) = 0.091 | | occupancies: max = 1.00 min = 0.36 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3183 r_free = 0.3183 target_work(ls_wunit_k1) = 0.091 | | occupancies: max = 1.00 min = 0.36 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3183 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8063 moved from start: 0.1538 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 11567 Z= 0.122 Angle : 0.668 16.317 15800 Z= 0.317 Chirality : 0.043 0.290 1840 Planarity : 0.004 0.056 1850 Dihedral : 7.245 59.351 2746 Min Nonbonded Distance : 2.058 Molprobity Statistics. All-atom Clashscore : 5.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.63 % Favored : 95.37 % Rotamer: Outliers : 3.53 % Allowed : 27.45 % Favored : 69.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 12.50 % Cis-general : 0.16 % 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: 1276 helix: 2.43 (0.21), residues: 578 sheet: 1.55 (0.28), residues: 274 loop : -2.17 (0.26), residues: 424 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP B 629 HIS 0.004 0.001 HIS B 636 PHE 0.017 0.001 PHE B 732 TYR 0.015 0.001 TYR B 210 ARG 0.003 0.000 ARG B 710 Details of bonding type rmsd link_NAG-ASN : bond 0.00484 ( 8) link_NAG-ASN : angle 2.70068 ( 24) link_BETA1-4 : bond 0.00417 ( 4) link_BETA1-4 : angle 1.36968 ( 12) hydrogen bonds : bond 0.04506 ( 630) hydrogen bonds : angle 3.74243 ( 1795) metal coordination : bond 0.00091 ( 6) SS BOND : bond 0.00085 ( 8) SS BOND : angle 0.96781 ( 16) covalent geometry : bond 0.00266 (11541) covalent geometry : angle 0.65940 (15748) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2552 Ramachandran restraints generated. 1276 Oldfield, 0 Emsley, 1276 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2552 Ramachandran restraints generated. 1276 Oldfield, 0 Emsley, 1276 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 145 residues out of total 1158 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 104 time to evaluate : 1.292 Fit side-chains REVERT: A 117 GLN cc_start: 0.8879 (mm-40) cc_final: 0.8661 (mp10) REVERT: A 554 MET cc_start: 0.8305 (tpp) cc_final: 0.8048 (mmm) REVERT: A 590 TYR cc_start: 0.6498 (OUTLIER) cc_final: 0.6029 (t80) REVERT: A 613 MET cc_start: 0.8672 (OUTLIER) cc_final: 0.8435 (pmm) REVERT: A 781 ARG cc_start: 0.8840 (OUTLIER) cc_final: 0.8296 (mtm-85) REVERT: B 554 MET cc_start: 0.8332 (tpp) cc_final: 0.8068 (mmm) REVERT: B 559 SER cc_start: 0.8791 (OUTLIER) cc_final: 0.8514 (p) REVERT: B 590 TYR cc_start: 0.6526 (OUTLIER) cc_final: 0.6188 (t80) REVERT: B 613 MET cc_start: 0.8622 (OUTLIER) cc_final: 0.8401 (pmm) REVERT: B 686 MET cc_start: 0.5104 (mmt) cc_final: 0.4235 (pmm) REVERT: B 710 ARG cc_start: 0.7654 (OUTLIER) cc_final: 0.6625 (mmm160) REVERT: B 736 MET cc_start: 0.7919 (tpp) cc_final: 0.7108 (mpp) REVERT: B 781 ARG cc_start: 0.8832 (OUTLIER) cc_final: 0.8213 (ttm110) outliers start: 41 outliers final: 24 residues processed: 136 average time/residue: 1.1412 time to fit residues: 169.9694 Evaluate side-chains 137 residues out of total 1158 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 105 time to evaluate : 1.259 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 119 SER Chi-restraints excluded: chain A residue 220 ILE Chi-restraints excluded: chain A residue 260 VAL Chi-restraints excluded: chain A residue 572 GLN Chi-restraints excluded: chain A residue 590 TYR Chi-restraints excluded: chain A residue 597 ILE Chi-restraints excluded: chain A residue 613 MET Chi-restraints excluded: chain A residue 727 LEU Chi-restraints excluded: chain A residue 735 ILE Chi-restraints excluded: chain A residue 763 LEU Chi-restraints excluded: chain A residue 771 SER Chi-restraints excluded: chain A residue 781 ARG Chi-restraints excluded: chain A residue 787 CYS Chi-restraints excluded: chain B residue 76 THR Chi-restraints excluded: chain B residue 141 LEU Chi-restraints excluded: chain B residue 173 THR Chi-restraints excluded: chain B residue 236 VAL Chi-restraints excluded: chain B residue 277 ILE Chi-restraints excluded: chain B residue 296 THR Chi-restraints excluded: chain B residue 510 LEU Chi-restraints excluded: chain B residue 559 SER Chi-restraints excluded: chain B residue 572 GLN Chi-restraints excluded: chain B residue 590 TYR Chi-restraints excluded: chain B residue 597 ILE Chi-restraints excluded: chain B residue 605 TYR Chi-restraints excluded: chain B residue 613 MET Chi-restraints excluded: chain B residue 617 LEU Chi-restraints excluded: chain B residue 650 MET Chi-restraints excluded: chain B residue 710 ARG Chi-restraints excluded: chain B residue 727 LEU Chi-restraints excluded: chain B residue 771 SER Chi-restraints excluded: chain B residue 781 ARG Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 122 optimal weight: 2.9990 chunk 72 optimal weight: 0.8980 chunk 103 optimal weight: 4.9990 chunk 91 optimal weight: 0.7980 chunk 34 optimal weight: 0.6980 chunk 125 optimal weight: 0.4980 chunk 32 optimal weight: 0.8980 chunk 98 optimal weight: 0.7980 chunk 33 optimal weight: 0.9990 chunk 127 optimal weight: 0.3980 chunk 22 optimal weight: 0.1980 overall best weight: 0.5180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 74 GLN A 90 ASN A 142 GLN ** A 725 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 769 ASN B 71 GLN B 90 ASN B 142 GLN B 286 ASN B 725 ASN B 769 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4127 r_free = 0.4127 target = 0.168840 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3403 r_free = 0.3403 target = 0.104718 restraints weight = 19074.470| |-----------------------------------------------------------------------------| r_work (start): 0.3301 rms_B_bonded: 2.97 r_work: 0.3162 rms_B_bonded: 3.51 restraints_weight: 0.5000 r_work (final): 0.3162 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3176 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3176 r_free = 0.3176 target_work(ls_wunit_k1) = 0.091 | | occupancies: max = 1.00 min = 0.36 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3176 r_free = 0.3176 target_work(ls_wunit_k1) = 0.091 | | occupancies: max = 1.00 min = 0.35 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3176 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8056 moved from start: 0.1633 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 11567 Z= 0.123 Angle : 0.659 16.405 15800 Z= 0.311 Chirality : 0.043 0.284 1840 Planarity : 0.004 0.056 1850 Dihedral : 6.941 57.478 2740 Min Nonbonded Distance : 1.973 Molprobity Statistics. All-atom Clashscore : 5.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.08 % Favored : 95.92 % Rotamer: Outliers : 3.01 % Allowed : 27.88 % Favored : 69.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 12.50 % Cis-general : 0.16 % 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: 1.28 (0.23), residues: 1276 helix: 2.44 (0.21), residues: 578 sheet: 1.61 (0.28), residues: 276 loop : -2.17 (0.26), residues: 422 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP B 629 HIS 0.004 0.001 HIS B 636 PHE 0.017 0.001 PHE B 732 TYR 0.013 0.001 TYR A 188 ARG 0.003 0.000 ARG A 593 Details of bonding type rmsd link_NAG-ASN : bond 0.00459 ( 8) link_NAG-ASN : angle 2.57685 ( 24) link_BETA1-4 : bond 0.00558 ( 4) link_BETA1-4 : angle 1.42155 ( 12) hydrogen bonds : bond 0.04516 ( 630) hydrogen bonds : angle 3.69929 ( 1795) metal coordination : bond 0.00226 ( 6) SS BOND : bond 0.00082 ( 8) SS BOND : angle 0.93017 ( 16) covalent geometry : bond 0.00270 (11541) covalent geometry : angle 0.65030 (15748) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 9573.01 seconds wall clock time: 165 minutes 13.78 seconds (9913.78 seconds total)