Starting phenix.real_space_refine on Tue May 13 01:22:21 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8vq9_43435/05_2025/8vq9_43435.cif Found real_map, /net/cci-nas-00/data/ceres_data/8vq9_43435/05_2025/8vq9_43435.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.7 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8vq9_43435/05_2025/8vq9_43435.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8vq9_43435/05_2025/8vq9_43435.map" model { file = "/net/cci-nas-00/data/ceres_data/8vq9_43435/05_2025/8vq9_43435.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8vq9_43435/05_2025/8vq9_43435.cif" } resolution = 2.7 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= 0.001 sd= 0.105 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: 4 Type Number sf(0) Gaussians S 63 5.16 5 C 6090 2.51 5 N 1614 2.21 5 O 1746 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 51 residue(s): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/chem_data/mon_lib" Total number of atoms: 9513 Number of models: 1 Model: "" Number of chains: 15 Chain: "A" Number of atoms: 3045 Number of conformers: 1 Conformer: "" Number of residues, atoms: 426, 3045 Classifications: {'peptide': 426} Incomplete info: {'truncation_to_alanine': 91} Link IDs: {'PTRANS': 20, 'TRANS': 405} Chain breaks: 4 Unresolved non-hydrogen bonds: 243 Unresolved non-hydrogen angles: 303 Unresolved non-hydrogen dihedrals: 183 Unresolved non-hydrogen chiralities: 28 Planarities with less than four sites: {'GLN:plan1': 3, 'GLU:plan': 11, 'ASN:plan1': 2, 'ARG:plan': 2, 'ASP:plan': 14} Unresolved non-hydrogen planarities: 114 Chain: "B" Number of atoms: 3045 Number of conformers: 1 Conformer: "" Number of residues, atoms: 426, 3045 Classifications: {'peptide': 426} Incomplete info: {'truncation_to_alanine': 91} Link IDs: {'PTRANS': 20, 'TRANS': 405} Chain breaks: 4 Unresolved non-hydrogen bonds: 243 Unresolved non-hydrogen angles: 303 Unresolved non-hydrogen dihedrals: 183 Unresolved non-hydrogen chiralities: 28 Planarities with less than four sites: {'GLN:plan1': 3, 'GLU:plan': 11, 'ASN:plan1': 2, 'ARG:plan': 2, 'ASP:plan': 14} Unresolved non-hydrogen planarities: 114 Chain: "C" Number of atoms: 3045 Number of conformers: 1 Conformer: "" Number of residues, atoms: 426, 3045 Classifications: {'peptide': 426} Incomplete info: {'truncation_to_alanine': 91} Link IDs: {'PTRANS': 20, 'TRANS': 405} Chain breaks: 4 Unresolved non-hydrogen bonds: 243 Unresolved non-hydrogen angles: 303 Unresolved non-hydrogen dihedrals: 183 Unresolved non-hydrogen chiralities: 28 Planarities with less than four sites: {'GLN:plan1': 3, 'GLU:plan': 11, 'ASN:plan1': 2, 'ARG:plan': 2, 'ASP:plan': 14} Unresolved non-hydrogen planarities: 114 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: "G" 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: "H" 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: "I" 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: "J" 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: "K" 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: "L" 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: 42 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 42 Unusual residues: {'NAG': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "B" Number of atoms: 42 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 42 Unusual residues: {'NAG': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "C" Number of atoms: 42 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 42 Unusual residues: {'NAG': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Time building chain proxies: 6.06, per 1000 atoms: 0.64 Number of scatterers: 9513 At special positions: 0 Unit cell: (88, 91, 136, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 63 16.00 O 1746 8.00 N 1614 7.00 C 6090 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=21, symmetry=0 Simple disulfide: pdb=" SG CYS A 707 " - pdb=" SG CYS C 883 " distance=2.20 Simple disulfide: pdb=" SG CYS A 738 " - pdb=" SG CYS A 760 " distance=2.10 Simple disulfide: pdb=" SG CYS A 743 " - pdb=" SG CYS A 749 " distance=2.03 Simple disulfide: pdb=" SG CYS A 840 " - pdb=" SG CYS A 851 " distance=2.03 Simple disulfide: pdb=" SG CYS A 883 " - pdb=" SG CYS B 707 " distance=2.20 Simple disulfide: pdb=" SG CYS A 970 " - pdb=" SG CYS A 999 " distance=2.02 Simple disulfide: pdb=" SG CYS A1032 " - pdb=" SG CYS A1043 " distance=2.03 Simple disulfide: pdb=" SG CYS A1082 " - pdb=" SG CYS A1126 " distance=2.02 Simple disulfide: pdb=" SG CYS B 738 " - pdb=" SG CYS B 760 " distance=2.10 Simple disulfide: pdb=" SG CYS B 743 " - pdb=" SG CYS B 749 " distance=2.03 Simple disulfide: pdb=" SG CYS B 840 " - pdb=" SG CYS B 851 " distance=2.03 Simple disulfide: pdb=" SG CYS B 883 " - pdb=" SG CYS C 707 " distance=2.20 Simple disulfide: pdb=" SG CYS B 970 " - pdb=" SG CYS B 999 " distance=2.02 Simple disulfide: pdb=" SG CYS B1032 " - pdb=" SG CYS B1043 " distance=2.03 Simple disulfide: pdb=" SG CYS B1082 " - pdb=" SG CYS B1126 " distance=2.02 Simple disulfide: pdb=" SG CYS C 738 " - pdb=" SG CYS C 760 " distance=2.10 Simple disulfide: pdb=" SG CYS C 743 " - pdb=" SG CYS C 749 " distance=2.03 Simple disulfide: pdb=" SG CYS C 840 " - pdb=" SG CYS C 851 " distance=2.03 Simple disulfide: pdb=" SG CYS C 970 " - pdb=" SG CYS C 999 " distance=2.02 Simple disulfide: pdb=" SG CYS C1032 " - pdb=" SG CYS C1043 " distance=2.03 Simple disulfide: pdb=" SG CYS C1082 " - pdb=" SG CYS C1126 " distance=2.02 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 D 1 " - " NAG D 2 " " NAG E 1 " - " NAG E 2 " " NAG F 1 " - " NAG F 2 " " NAG G 1 " - " NAG G 2 " " NAG H 1 " - " NAG H 2 " " NAG I 1 " - " NAG I 2 " " NAG J 1 " - " NAG J 2 " " NAG K 1 " - " NAG K 2 " " NAG L 1 " - " NAG L 2 " NAG-ASN " NAG A1301 " - " ASN A 709 " " NAG A1302 " - " ASN A1074 " " NAG A1303 " - " ASN A1134 " " NAG B1301 " - " ASN B 709 " " NAG B1302 " - " ASN B1074 " " NAG B1303 " - " ASN B1134 " " NAG C1301 " - " ASN C 709 " " NAG C1302 " - " ASN C1074 " " NAG C1303 " - " ASN C1134 " " NAG D 1 " - " ASN A 717 " " NAG E 1 " - " ASN A 801 " " NAG F 1 " - " ASN A1098 " " NAG G 1 " - " ASN B 717 " " NAG H 1 " - " ASN B 801 " " NAG I 1 " - " ASN B1098 " " NAG J 1 " - " ASN C 717 " " NAG K 1 " - " ASN C 801 " " NAG L 1 " - " ASN C1098 " Time building additional restraints: 2.79 Conformation dependent library (CDL) restraints added in 1.1 seconds 2496 Ramachandran restraints generated. 1248 Oldfield, 0 Emsley, 1248 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2406 Finding SS restraints... Secondary structure from input PDB file: 45 helices and 12 sheets defined 50.7% alpha, 13.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.01 Creating SS restraints... Processing helix chain 'A' and resid 737 through 743 Processing helix chain 'A' and resid 746 through 755 removed outlier: 4.115A pdb=" N GLN A 755 " --> pdb=" O ASN A 751 " (cutoff:3.500A) Processing helix chain 'A' and resid 758 through 783 removed outlier: 3.949A pdb=" N ASP A 775 " --> pdb=" O ALA A 771 " (cutoff:3.500A) Processing helix chain 'A' and resid 816 through 823 Processing helix chain 'A' and resid 834 through 841 Processing helix chain 'A' and resid 849 through 855 Processing helix chain 'A' and resid 866 through 885 Processing helix chain 'A' and resid 886 through 891 removed outlier: 4.216A pdb=" N GLY A 891 " --> pdb=" O PHE A 888 " (cutoff:3.500A) Processing helix chain 'A' and resid 897 through 908 Processing helix chain 'A' and resid 912 through 919 removed outlier: 4.396A pdb=" N LEU A 916 " --> pdb=" O THR A 912 " (cutoff:3.500A) Processing helix chain 'A' and resid 919 through 940 Processing helix chain 'A' and resid 945 through 966 removed outlier: 3.841A pdb=" N VAL A 951 " --> pdb=" O LYS A 947 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N LEU A 966 " --> pdb=" O LEU A 962 " (cutoff:3.500A) Processing helix chain 'A' and resid 977 through 982 Processing helix chain 'A' and resid 985 through 1033 Processing helix chain 'A' and resid 1141 through 1145 Processing helix chain 'B' and resid 737 through 743 Processing helix chain 'B' and resid 746 through 755 removed outlier: 4.114A pdb=" N GLN B 755 " --> pdb=" O ASN B 751 " (cutoff:3.500A) Processing helix chain 'B' and resid 758 through 783 removed outlier: 3.949A pdb=" N ASP B 775 " --> pdb=" O ALA B 771 " (cutoff:3.500A) Processing helix chain 'B' and resid 816 through 823 Processing helix chain 'B' and resid 834 through 841 Processing helix chain 'B' and resid 849 through 855 Processing helix chain 'B' and resid 866 through 885 Processing helix chain 'B' and resid 886 through 891 removed outlier: 4.216A pdb=" N GLY B 891 " --> pdb=" O PHE B 888 " (cutoff:3.500A) Processing helix chain 'B' and resid 897 through 908 Processing helix chain 'B' and resid 912 through 919 removed outlier: 4.396A pdb=" N LEU B 916 " --> pdb=" O THR B 912 " (cutoff:3.500A) Processing helix chain 'B' and resid 919 through 940 Processing helix chain 'B' and resid 945 through 966 removed outlier: 3.841A pdb=" N VAL B 951 " --> pdb=" O LYS B 947 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N LEU B 966 " --> pdb=" O LEU B 962 " (cutoff:3.500A) Processing helix chain 'B' and resid 977 through 982 Processing helix chain 'B' and resid 985 through 1033 Processing helix chain 'B' and resid 1141 through 1145 Processing helix chain 'C' and resid 737 through 743 Processing helix chain 'C' and resid 746 through 755 removed outlier: 4.114A pdb=" N GLN C 755 " --> pdb=" O ASN C 751 " (cutoff:3.500A) Processing helix chain 'C' and resid 758 through 783 removed outlier: 3.949A pdb=" N ASP C 775 " --> pdb=" O ALA C 771 " (cutoff:3.500A) Processing helix chain 'C' and resid 816 through 823 Processing helix chain 'C' and resid 834 through 841 Processing helix chain 'C' and resid 849 through 855 Processing helix chain 'C' and resid 866 through 885 Processing helix chain 'C' and resid 886 through 891 removed outlier: 4.216A pdb=" N GLY C 891 " --> pdb=" O PHE C 888 " (cutoff:3.500A) Processing helix chain 'C' and resid 897 through 908 Processing helix chain 'C' and resid 912 through 919 removed outlier: 4.395A pdb=" N LEU C 916 " --> pdb=" O THR C 912 " (cutoff:3.500A) Processing helix chain 'C' and resid 919 through 940 Processing helix chain 'C' and resid 945 through 966 removed outlier: 3.841A pdb=" N VAL C 951 " --> pdb=" O LYS C 947 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N LEU C 966 " --> pdb=" O LEU C 962 " (cutoff:3.500A) Processing helix chain 'C' and resid 977 through 982 Processing helix chain 'C' and resid 985 through 1033 Processing helix chain 'C' and resid 1141 through 1145 Processing sheet with id=AA1, first strand: chain 'A' and resid 711 through 715 Processing sheet with id=AA2, first strand: chain 'A' and resid 718 through 728 removed outlier: 6.134A pdb=" N TYR A1067 " --> pdb=" O HIS A1048 " (cutoff:3.500A) removed outlier: 5.731A pdb=" N HIS A1048 " --> pdb=" O TYR A1067 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 733 through 736 removed outlier: 4.227A pdb=" N LYS A 733 " --> pdb=" O LEU A 861 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 1120 through 1122 Processing sheet with id=AA5, first strand: chain 'B' and resid 711 through 715 Processing sheet with id=AA6, first strand: chain 'B' and resid 718 through 728 removed outlier: 6.134A pdb=" N TYR B1067 " --> pdb=" O HIS B1048 " (cutoff:3.500A) removed outlier: 5.731A pdb=" N HIS B1048 " --> pdb=" O TYR B1067 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 733 through 736 removed outlier: 4.227A pdb=" N LYS B 733 " --> pdb=" O LEU B 861 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 1120 through 1122 Processing sheet with id=AA9, first strand: chain 'C' and resid 711 through 715 Processing sheet with id=AB1, first strand: chain 'C' and resid 718 through 728 removed outlier: 6.134A pdb=" N TYR C1067 " --> pdb=" O HIS C1048 " (cutoff:3.500A) removed outlier: 5.730A pdb=" N HIS C1048 " --> pdb=" O TYR C1067 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'C' and resid 733 through 736 removed outlier: 4.227A pdb=" N LYS C 733 " --> pdb=" O LEU C 861 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'C' and resid 1120 through 1122 567 hydrogen bonds defined for protein. 1647 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 2.49 Time building geometry restraints manager: 3.19 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.33: 2535 1.33 - 1.45: 1860 1.45 - 1.58: 5217 1.58 - 1.70: 0 1.70 - 1.83: 84 Bond restraints: 9696 Sorted by residual: bond pdb=" C5 NAG L 1 " pdb=" O5 NAG L 1 " ideal model delta sigma weight residual 1.413 1.476 -0.063 2.00e-02 2.50e+03 1.00e+01 bond pdb=" C5 NAG F 1 " pdb=" O5 NAG F 1 " ideal model delta sigma weight residual 1.413 1.476 -0.063 2.00e-02 2.50e+03 1.00e+01 bond pdb=" C5 NAG I 1 " pdb=" O5 NAG I 1 " ideal model delta sigma weight residual 1.413 1.476 -0.063 2.00e-02 2.50e+03 1.00e+01 bond pdb=" C5 NAG G 1 " pdb=" O5 NAG G 1 " ideal model delta sigma weight residual 1.413 1.471 -0.058 2.00e-02 2.50e+03 8.27e+00 bond pdb=" C5 NAG D 1 " pdb=" O5 NAG D 1 " ideal model delta sigma weight residual 1.413 1.470 -0.057 2.00e-02 2.50e+03 8.19e+00 ... (remaining 9691 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.64: 11722 1.64 - 3.27: 1275 3.27 - 4.91: 128 4.91 - 6.55: 90 6.55 - 8.19: 33 Bond angle restraints: 13248 Sorted by residual: angle pdb=" C ALA C1078 " pdb=" N PRO C1079 " pdb=" CA PRO C1079 " ideal model delta sigma weight residual 119.24 127.43 -8.19 1.04e+00 9.25e-01 6.20e+01 angle pdb=" C ALA B1078 " pdb=" N PRO B1079 " pdb=" CA PRO B1079 " ideal model delta sigma weight residual 119.24 127.38 -8.14 1.04e+00 9.25e-01 6.12e+01 angle pdb=" C ALA A1078 " pdb=" N PRO A1079 " pdb=" CA PRO A1079 " ideal model delta sigma weight residual 119.24 127.38 -8.14 1.04e+00 9.25e-01 6.12e+01 angle pdb=" C PRO C 862 " pdb=" N PRO C 863 " pdb=" CA PRO C 863 " ideal model delta sigma weight residual 120.03 127.68 -7.65 9.90e-01 1.02e+00 5.97e+01 angle pdb=" C PRO A 862 " pdb=" N PRO A 863 " pdb=" CA PRO A 863 " ideal model delta sigma weight residual 120.03 127.66 -7.63 9.90e-01 1.02e+00 5.95e+01 ... (remaining 13243 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.95: 5868 17.95 - 35.91: 201 35.91 - 53.86: 39 53.86 - 71.82: 6 71.82 - 89.77: 9 Dihedral angle restraints: 6123 sinusoidal: 2418 harmonic: 3705 Sorted by residual: dihedral pdb=" CB CYS B 883 " pdb=" SG CYS B 883 " pdb=" SG CYS C 707 " pdb=" CB CYS C 707 " ideal model delta sinusoidal sigma weight residual -86.00 -37.56 -48.44 1 1.00e+01 1.00e-02 3.23e+01 dihedral pdb=" CB CYS A 883 " pdb=" SG CYS A 883 " pdb=" SG CYS B 707 " pdb=" CB CYS B 707 " ideal model delta sinusoidal sigma weight residual -86.00 -37.57 -48.43 1 1.00e+01 1.00e-02 3.23e+01 dihedral pdb=" CB CYS A 707 " pdb=" SG CYS A 707 " pdb=" SG CYS C 883 " pdb=" CB CYS C 883 " ideal model delta sinusoidal sigma weight residual -86.00 -37.59 -48.41 1 1.00e+01 1.00e-02 3.23e+01 ... (remaining 6120 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.078: 1230 0.078 - 0.156: 318 0.156 - 0.234: 63 0.234 - 0.312: 27 0.312 - 0.390: 12 Chirality restraints: 1650 Sorted by residual: chirality pdb=" C1 NAG E 2 " pdb=" O4 NAG E 1 " pdb=" C2 NAG E 2 " pdb=" O5 NAG E 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.55 0.15 2.00e-02 2.50e+03 5.27e+01 chirality pdb=" C1 NAG H 2 " pdb=" O4 NAG H 1 " pdb=" C2 NAG H 2 " pdb=" O5 NAG H 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.55 0.15 2.00e-02 2.50e+03 5.26e+01 chirality pdb=" C1 NAG K 2 " pdb=" O4 NAG K 1 " pdb=" C2 NAG K 2 " pdb=" O5 NAG K 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.54 0.14 2.00e-02 2.50e+03 5.24e+01 ... (remaining 1647 not shown) Planarity restraints: 1716 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TYR B 904 " 0.052 2.00e-02 2.50e+03 2.75e-02 1.51e+01 pdb=" CG TYR B 904 " -0.021 2.00e-02 2.50e+03 pdb=" CD1 TYR B 904 " -0.021 2.00e-02 2.50e+03 pdb=" CD2 TYR B 904 " -0.021 2.00e-02 2.50e+03 pdb=" CE1 TYR B 904 " -0.014 2.00e-02 2.50e+03 pdb=" CE2 TYR B 904 " -0.014 2.00e-02 2.50e+03 pdb=" CZ TYR B 904 " -0.000 2.00e-02 2.50e+03 pdb=" OH TYR B 904 " 0.040 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR C 904 " -0.051 2.00e-02 2.50e+03 2.73e-02 1.49e+01 pdb=" CG TYR C 904 " 0.021 2.00e-02 2.50e+03 pdb=" CD1 TYR C 904 " 0.020 2.00e-02 2.50e+03 pdb=" CD2 TYR C 904 " 0.021 2.00e-02 2.50e+03 pdb=" CE1 TYR C 904 " 0.014 2.00e-02 2.50e+03 pdb=" CE2 TYR C 904 " 0.014 2.00e-02 2.50e+03 pdb=" CZ TYR C 904 " 0.001 2.00e-02 2.50e+03 pdb=" OH TYR C 904 " -0.040 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR A 904 " -0.051 2.00e-02 2.50e+03 2.73e-02 1.49e+01 pdb=" CG TYR A 904 " 0.021 2.00e-02 2.50e+03 pdb=" CD1 TYR A 904 " 0.020 2.00e-02 2.50e+03 pdb=" CD2 TYR A 904 " 0.021 2.00e-02 2.50e+03 pdb=" CE1 TYR A 904 " 0.014 2.00e-02 2.50e+03 pdb=" CE2 TYR A 904 " 0.014 2.00e-02 2.50e+03 pdb=" CZ TYR A 904 " 0.000 2.00e-02 2.50e+03 pdb=" OH TYR A 904 " -0.040 2.00e-02 2.50e+03 ... (remaining 1713 not shown) Histogram of nonbonded interaction distances: 2.51 - 2.99: 4997 2.99 - 3.47: 9255 3.47 - 3.94: 15145 3.94 - 4.42: 17532 4.42 - 4.90: 27446 Nonbonded interactions: 74375 Sorted by model distance: nonbonded pdb=" NZ LYS A1028 " pdb=" O PHE A1042 " model vdw 2.511 3.120 nonbonded pdb=" NZ LYS C1028 " pdb=" O PHE C1042 " model vdw 2.511 3.120 nonbonded pdb=" NZ LYS B1028 " pdb=" O PHE B1042 " model vdw 2.511 3.120 nonbonded pdb=" OE1 GLN B1011 " pdb=" NH1 ARG B1014 " model vdw 2.582 3.120 nonbonded pdb=" OE1 GLN A1011 " pdb=" NH1 ARG A1014 " model vdw 2.582 3.120 ... (remaining 74370 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' selection = chain 'B' selection = chain 'C' } ncs_group { reference = chain 'D' selection = chain 'E' selection = chain 'F' selection = chain 'G' selection = chain 'H' selection = chain 'I' selection = chain 'J' selection = chain 'K' selection = chain 'L' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.700 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.360 Check model and map are aligned: 0.060 Set scattering table: 0.090 Process input model: 23.790 Find NCS groups from input model: 0.380 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:11.070 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 38.510 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7248 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 : 0.011 0.171 9744 Z= 0.626 Angle : 1.223 8.186 13371 Z= 0.814 Chirality : 0.082 0.390 1650 Planarity : 0.004 0.028 1698 Dihedral : 9.901 89.774 3654 Min Nonbonded Distance : 2.511 Molprobity Statistics. All-atom Clashscore : 0.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.88 % Favored : 97.12 % Rotamer: Outliers : 0.00 % Allowed : 0.71 % Favored : 99.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.54 (0.21), residues: 1248 helix: 1.19 (0.20), residues: 570 sheet: 1.57 (0.43), residues: 120 loop : -0.78 (0.22), residues: 558 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.006 TRP C 886 HIS 0.002 0.001 HIS B1048 PHE 0.017 0.003 PHE C 833 TYR 0.052 0.005 TYR B 904 ARG 0.003 0.000 ARG A1019 Details of bonding type rmsd link_NAG-ASN : bond 0.05500 ( 18) link_NAG-ASN : angle 2.38757 ( 54) link_BETA1-4 : bond 0.05208 ( 9) link_BETA1-4 : angle 3.08948 ( 27) hydrogen bonds : bond 0.20761 ( 567) hydrogen bonds : angle 7.24409 ( 1647) SS BOND : bond 0.07067 ( 21) SS BOND : angle 3.35327 ( 42) covalent geometry : bond 0.01044 ( 9696) covalent geometry : angle 1.19681 (13248) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2496 Ramachandran restraints generated. 1248 Oldfield, 0 Emsley, 1248 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2496 Ramachandran restraints generated. 1248 Oldfield, 0 Emsley, 1248 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 176 residues out of total 1113 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 176 time to evaluate : 1.014 Fit side-chains REVERT: A 725 GLU cc_start: 0.7970 (tt0) cc_final: 0.7712 (tt0) REVERT: A 855 PHE cc_start: 0.7618 (m-80) cc_final: 0.7404 (m-80) REVERT: A 935 GLN cc_start: 0.7494 (mt0) cc_final: 0.7268 (mt0) REVERT: B 1029 MET cc_start: 0.8402 (tpp) cc_final: 0.8088 (tpp) REVERT: C 725 GLU cc_start: 0.8028 (tt0) cc_final: 0.7764 (tt0) REVERT: C 752 LEU cc_start: 0.8316 (mt) cc_final: 0.8089 (mt) REVERT: C 803 SER cc_start: 0.8512 (p) cc_final: 0.8217 (p) REVERT: C 1138 TYR cc_start: 0.7781 (t80) cc_final: 0.7420 (t80) outliers start: 0 outliers final: 0 residues processed: 176 average time/residue: 1.2751 time to fit residues: 238.9399 Evaluate side-chains 117 residues out of total 1113 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 117 time to evaluate : 1.123 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 106 optimal weight: 0.9980 chunk 95 optimal weight: 1.9990 chunk 52 optimal weight: 1.9990 chunk 32 optimal weight: 0.9980 chunk 64 optimal weight: 2.9990 chunk 51 optimal weight: 0.5980 chunk 98 optimal weight: 0.9980 chunk 38 optimal weight: 0.6980 chunk 60 optimal weight: 0.5980 chunk 73 optimal weight: 0.4980 chunk 114 optimal weight: 0.9980 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 755 GLN A 907 ASN A 913 GLN ** A 935 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 954 GLN A1005 GLN B 755 GLN B 907 ASN B 913 GLN ** B 935 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 954 GLN C 907 ASN C 913 GLN ** C 935 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 955 ASN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3699 r_free = 0.3699 target = 0.151677 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3308 r_free = 0.3308 target = 0.118635 restraints weight = 9466.215| |-----------------------------------------------------------------------------| r_work (start): 0.3315 rms_B_bonded: 1.81 r_work: 0.3185 rms_B_bonded: 2.36 restraints_weight: 0.5000 r_work: 0.3051 rms_B_bonded: 3.82 restraints_weight: 0.2500 r_work (final): 0.3051 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8043 moved from start: 0.2093 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 9744 Z= 0.169 Angle : 0.619 8.801 13371 Z= 0.321 Chirality : 0.042 0.141 1650 Planarity : 0.005 0.040 1698 Dihedral : 4.103 15.245 1893 Min Nonbonded Distance : 2.613 Molprobity Statistics. All-atom Clashscore : 3.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.16 % Favored : 97.84 % Rotamer: Outliers : 2.62 % Allowed : 9.05 % Favored : 88.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 1.69 (0.23), residues: 1248 helix: 2.57 (0.21), residues: 573 sheet: 1.20 (0.38), residues: 153 loop : -0.60 (0.25), residues: 522 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP A 886 HIS 0.003 0.001 HIS C1101 PHE 0.021 0.002 PHE C 906 TYR 0.016 0.002 TYR C1067 ARG 0.004 0.001 ARG A 905 Details of bonding type rmsd link_NAG-ASN : bond 0.00663 ( 18) link_NAG-ASN : angle 1.93234 ( 54) link_BETA1-4 : bond 0.00738 ( 9) link_BETA1-4 : angle 2.15483 ( 27) hydrogen bonds : bond 0.06835 ( 567) hydrogen bonds : angle 5.05678 ( 1647) SS BOND : bond 0.00593 ( 21) SS BOND : angle 1.59521 ( 42) covalent geometry : bond 0.00366 ( 9696) covalent geometry : angle 0.59492 (13248) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2496 Ramachandran restraints generated. 1248 Oldfield, 0 Emsley, 1248 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2496 Ramachandran restraints generated. 1248 Oldfield, 0 Emsley, 1248 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 143 residues out of total 1113 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 121 time to evaluate : 1.047 Fit side-chains REVERT: A 725 GLU cc_start: 0.8440 (tt0) cc_final: 0.8084 (tt0) REVERT: A 752 LEU cc_start: 0.8654 (mt) cc_final: 0.8330 (mt) REVERT: A 855 PHE cc_start: 0.7670 (m-80) cc_final: 0.7400 (m-80) REVERT: A 935 GLN cc_start: 0.7091 (mt0) cc_final: 0.6711 (mt0) REVERT: B 804 GLN cc_start: 0.8160 (OUTLIER) cc_final: 0.7892 (mt0) REVERT: B 904 TYR cc_start: 0.7991 (m-10) cc_final: 0.7080 (m-10) REVERT: C 725 GLU cc_start: 0.8467 (tt0) cc_final: 0.8115 (tt0) REVERT: C 752 LEU cc_start: 0.8572 (mt) cc_final: 0.8354 (mt) outliers start: 22 outliers final: 6 residues processed: 131 average time/residue: 1.1993 time to fit residues: 168.3624 Evaluate side-chains 116 residues out of total 1113 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 109 time to evaluate : 0.965 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 998 THR Chi-restraints excluded: chain A residue 999 CYS Chi-restraints excluded: chain A residue 1105 THR Chi-restraints excluded: chain B residue 804 GLN Chi-restraints excluded: chain B residue 999 CYS Chi-restraints excluded: chain B residue 1028 LYS Chi-restraints excluded: chain C residue 999 CYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 67 optimal weight: 0.4980 chunk 60 optimal weight: 0.7980 chunk 22 optimal weight: 4.9990 chunk 108 optimal weight: 0.1980 chunk 63 optimal weight: 2.9990 chunk 84 optimal weight: 0.7980 chunk 55 optimal weight: 0.7980 chunk 53 optimal weight: 1.9990 chunk 38 optimal weight: 1.9990 chunk 17 optimal weight: 1.9990 chunk 125 optimal weight: 2.9990 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 935 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 935 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 955 ASN B1054 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3665 r_free = 0.3665 target = 0.148981 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3269 r_free = 0.3269 target = 0.115637 restraints weight = 9490.874| |-----------------------------------------------------------------------------| r_work (start): 0.3265 rms_B_bonded: 1.78 r_work: 0.3142 rms_B_bonded: 2.27 restraints_weight: 0.5000 r_work: 0.3010 rms_B_bonded: 3.67 restraints_weight: 0.2500 r_work (final): 0.3010 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8043 moved from start: 0.2583 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 9744 Z= 0.141 Angle : 0.530 4.870 13371 Z= 0.278 Chirality : 0.040 0.129 1650 Planarity : 0.004 0.045 1698 Dihedral : 3.553 15.036 1893 Min Nonbonded Distance : 2.621 Molprobity Statistics. All-atom Clashscore : 3.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.92 % Favored : 98.08 % Rotamer: Outliers : 2.14 % Allowed : 10.24 % Favored : 87.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.82 (0.23), residues: 1248 helix: 2.68 (0.21), residues: 588 sheet: 1.10 (0.38), residues: 153 loop : -0.58 (0.25), residues: 507 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP A 886 HIS 0.002 0.001 HIS B1101 PHE 0.016 0.001 PHE B 906 TYR 0.019 0.002 TYR C1067 ARG 0.003 0.000 ARG B1014 Details of bonding type rmsd link_NAG-ASN : bond 0.00476 ( 18) link_NAG-ASN : angle 1.71513 ( 54) link_BETA1-4 : bond 0.00684 ( 9) link_BETA1-4 : angle 1.60504 ( 27) hydrogen bonds : bond 0.05978 ( 567) hydrogen bonds : angle 4.76988 ( 1647) SS BOND : bond 0.00389 ( 21) SS BOND : angle 1.43803 ( 42) covalent geometry : bond 0.00308 ( 9696) covalent geometry : angle 0.50973 (13248) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2496 Ramachandran restraints generated. 1248 Oldfield, 0 Emsley, 1248 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2496 Ramachandran restraints generated. 1248 Oldfield, 0 Emsley, 1248 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 130 residues out of total 1113 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 112 time to evaluate : 1.228 Fit side-chains REVERT: A 725 GLU cc_start: 0.8504 (tt0) cc_final: 0.8101 (tt0) REVERT: A 752 LEU cc_start: 0.8656 (mt) cc_final: 0.8377 (mt) REVERT: A 855 PHE cc_start: 0.7767 (m-80) cc_final: 0.7430 (m-80) REVERT: A 886 TRP cc_start: 0.7787 (p90) cc_final: 0.7583 (p90) REVERT: B 731 MET cc_start: 0.8780 (ptt) cc_final: 0.8452 (ptp) REVERT: B 804 GLN cc_start: 0.8102 (OUTLIER) cc_final: 0.7902 (mm-40) REVERT: B 904 TYR cc_start: 0.7873 (m-10) cc_final: 0.7123 (m-10) REVERT: C 725 GLU cc_start: 0.8514 (tt0) cc_final: 0.8193 (tt0) REVERT: C 752 LEU cc_start: 0.8585 (mt) cc_final: 0.8377 (mt) REVERT: C 935 GLN cc_start: 0.7231 (mt0) cc_final: 0.6983 (mt0) outliers start: 18 outliers final: 6 residues processed: 121 average time/residue: 1.2997 time to fit residues: 168.0872 Evaluate side-chains 114 residues out of total 1113 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 107 time to evaluate : 1.082 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 999 CYS Chi-restraints excluded: chain A residue 1105 THR Chi-restraints excluded: chain B residue 804 GLN Chi-restraints excluded: chain B residue 900 MET Chi-restraints excluded: chain B residue 999 CYS Chi-restraints excluded: chain C residue 779 GLN Chi-restraints excluded: chain C residue 999 CYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 98 optimal weight: 3.9990 chunk 97 optimal weight: 0.7980 chunk 16 optimal weight: 0.9990 chunk 94 optimal weight: 0.1980 chunk 20 optimal weight: 1.9990 chunk 115 optimal weight: 1.9990 chunk 67 optimal weight: 4.9990 chunk 51 optimal weight: 0.2980 chunk 48 optimal weight: 2.9990 chunk 35 optimal weight: 1.9990 chunk 12 optimal weight: 0.8980 overall best weight: 0.6382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 764 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3655 r_free = 0.3655 target = 0.148109 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3263 r_free = 0.3263 target = 0.115150 restraints weight = 9350.432| |-----------------------------------------------------------------------------| r_work (start): 0.3231 rms_B_bonded: 1.76 r_work: 0.3108 rms_B_bonded: 2.23 restraints_weight: 0.5000 r_work: 0.2974 rms_B_bonded: 3.62 restraints_weight: 0.2500 r_work (final): 0.2974 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8057 moved from start: 0.2978 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 9744 Z= 0.135 Angle : 0.522 5.026 13371 Z= 0.270 Chirality : 0.040 0.127 1650 Planarity : 0.004 0.041 1698 Dihedral : 3.530 14.955 1893 Min Nonbonded Distance : 2.628 Molprobity Statistics. All-atom Clashscore : 3.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.08 % Favored : 97.92 % Rotamer: Outliers : 1.19 % Allowed : 11.19 % Favored : 87.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.81 (0.23), residues: 1248 helix: 2.72 (0.21), residues: 597 sheet: 0.98 (0.37), residues: 153 loop : -0.68 (0.25), residues: 498 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.003 TRP C 886 HIS 0.003 0.001 HIS B1101 PHE 0.015 0.002 PHE C 906 TYR 0.018 0.001 TYR C1067 ARG 0.003 0.001 ARG B1014 Details of bonding type rmsd link_NAG-ASN : bond 0.00336 ( 18) link_NAG-ASN : angle 1.64380 ( 54) link_BETA1-4 : bond 0.00535 ( 9) link_BETA1-4 : angle 1.36434 ( 27) hydrogen bonds : bond 0.05468 ( 567) hydrogen bonds : angle 4.65007 ( 1647) SS BOND : bond 0.00356 ( 21) SS BOND : angle 1.35968 ( 42) covalent geometry : bond 0.00305 ( 9696) covalent geometry : angle 0.50464 (13248) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2496 Ramachandran restraints generated. 1248 Oldfield, 0 Emsley, 1248 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2496 Ramachandran restraints generated. 1248 Oldfield, 0 Emsley, 1248 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 121 residues out of total 1113 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 111 time to evaluate : 1.253 Fit side-chains REVERT: A 725 GLU cc_start: 0.8454 (tt0) cc_final: 0.8071 (tt0) REVERT: A 731 MET cc_start: 0.8914 (ptt) cc_final: 0.8665 (ptt) REVERT: A 752 LEU cc_start: 0.8663 (mt) cc_final: 0.8359 (mt) REVERT: A 855 PHE cc_start: 0.7835 (m-80) cc_final: 0.7462 (m-80) REVERT: B 731 MET cc_start: 0.8823 (ptt) cc_final: 0.8494 (ptp) REVERT: B 904 TYR cc_start: 0.7778 (m-10) cc_final: 0.7042 (m-10) REVERT: C 725 GLU cc_start: 0.8526 (tt0) cc_final: 0.8202 (tt0) REVERT: C 752 LEU cc_start: 0.8644 (mt) cc_final: 0.8410 (mt) outliers start: 10 outliers final: 5 residues processed: 116 average time/residue: 1.2820 time to fit residues: 158.9131 Evaluate side-chains 108 residues out of total 1113 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 103 time to evaluate : 0.971 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 900 MET Chi-restraints excluded: chain A residue 999 CYS Chi-restraints excluded: chain B residue 900 MET Chi-restraints excluded: chain B residue 999 CYS Chi-restraints excluded: chain C residue 999 CYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 47 optimal weight: 1.9990 chunk 110 optimal weight: 0.7980 chunk 107 optimal weight: 1.9990 chunk 31 optimal weight: 0.9980 chunk 21 optimal weight: 2.9990 chunk 111 optimal weight: 0.9980 chunk 112 optimal weight: 0.9990 chunk 65 optimal weight: 2.9990 chunk 66 optimal weight: 1.9990 chunk 30 optimal weight: 0.6980 chunk 8 optimal weight: 0.0970 overall best weight: 0.7178 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 935 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3637 r_free = 0.3637 target = 0.146625 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3250 r_free = 0.3250 target = 0.114224 restraints weight = 9565.386| |-----------------------------------------------------------------------------| r_work (start): 0.3276 rms_B_bonded: 1.75 r_work: 0.3149 rms_B_bonded: 2.30 restraints_weight: 0.5000 r_work: 0.3016 rms_B_bonded: 3.73 restraints_weight: 0.2500 r_work (final): 0.3016 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8093 moved from start: 0.3145 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 9744 Z= 0.142 Angle : 0.530 10.388 13371 Z= 0.272 Chirality : 0.041 0.130 1650 Planarity : 0.004 0.039 1698 Dihedral : 3.628 15.675 1893 Min Nonbonded Distance : 2.620 Molprobity Statistics. All-atom Clashscore : 3.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.76 % Favored : 98.24 % Rotamer: Outliers : 1.79 % Allowed : 12.14 % Favored : 86.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.74 (0.23), residues: 1248 helix: 2.71 (0.21), residues: 597 sheet: 0.89 (0.37), residues: 153 loop : -0.76 (0.25), residues: 498 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP C 886 HIS 0.003 0.001 HIS C1088 PHE 0.012 0.002 PHE C 906 TYR 0.018 0.002 TYR C1067 ARG 0.003 0.000 ARG B1014 Details of bonding type rmsd link_NAG-ASN : bond 0.00314 ( 18) link_NAG-ASN : angle 1.60542 ( 54) link_BETA1-4 : bond 0.00531 ( 9) link_BETA1-4 : angle 1.23698 ( 27) hydrogen bonds : bond 0.05526 ( 567) hydrogen bonds : angle 4.63845 ( 1647) SS BOND : bond 0.00348 ( 21) SS BOND : angle 1.29346 ( 42) covalent geometry : bond 0.00325 ( 9696) covalent geometry : angle 0.51408 (13248) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2496 Ramachandran restraints generated. 1248 Oldfield, 0 Emsley, 1248 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2496 Ramachandran restraints generated. 1248 Oldfield, 0 Emsley, 1248 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 125 residues out of total 1113 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 110 time to evaluate : 1.119 Fit side-chains REVERT: A 725 GLU cc_start: 0.8497 (tt0) cc_final: 0.8116 (tt0) REVERT: A 752 LEU cc_start: 0.8700 (mt) cc_final: 0.8415 (mt) REVERT: A 855 PHE cc_start: 0.7896 (m-80) cc_final: 0.7607 (m-80) REVERT: B 731 MET cc_start: 0.8790 (ptt) cc_final: 0.8463 (ptp) REVERT: B 904 TYR cc_start: 0.7798 (m-10) cc_final: 0.7094 (m-10) REVERT: C 725 GLU cc_start: 0.8545 (tt0) cc_final: 0.8284 (tt0) REVERT: C 752 LEU cc_start: 0.8635 (mt) cc_final: 0.8399 (mt) REVERT: C 1050 MET cc_start: 0.8862 (ptm) cc_final: 0.8637 (ptp) outliers start: 15 outliers final: 6 residues processed: 115 average time/residue: 1.2551 time to fit residues: 154.4733 Evaluate side-chains 109 residues out of total 1113 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 103 time to evaluate : 0.990 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 900 MET Chi-restraints excluded: chain A residue 999 CYS Chi-restraints excluded: chain A residue 1105 THR Chi-restraints excluded: chain B residue 900 MET Chi-restraints excluded: chain B residue 999 CYS Chi-restraints excluded: chain C residue 999 CYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 32 optimal weight: 0.0030 chunk 26 optimal weight: 0.9990 chunk 29 optimal weight: 1.9990 chunk 80 optimal weight: 1.9990 chunk 119 optimal weight: 0.9980 chunk 56 optimal weight: 0.0770 chunk 95 optimal weight: 3.9990 chunk 74 optimal weight: 2.9990 chunk 20 optimal weight: 1.9990 chunk 44 optimal weight: 0.6980 chunk 33 optimal weight: 0.9980 overall best weight: 0.5548 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 935 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3655 r_free = 0.3655 target = 0.148045 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3274 r_free = 0.3274 target = 0.116008 restraints weight = 9574.642| |-----------------------------------------------------------------------------| r_work (start): 0.3286 rms_B_bonded: 1.74 r_work: 0.3159 rms_B_bonded: 2.30 restraints_weight: 0.5000 r_work: 0.3027 rms_B_bonded: 3.74 restraints_weight: 0.2500 r_work (final): 0.3027 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8079 moved from start: 0.3256 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 9744 Z= 0.124 Angle : 0.510 10.270 13371 Z= 0.259 Chirality : 0.040 0.126 1650 Planarity : 0.004 0.038 1698 Dihedral : 3.550 15.482 1893 Min Nonbonded Distance : 2.609 Molprobity Statistics. All-atom Clashscore : 3.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.60 % Favored : 98.40 % Rotamer: Outliers : 2.26 % Allowed : 11.31 % Favored : 86.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.84 (0.23), residues: 1248 helix: 2.76 (0.21), residues: 600 sheet: 0.94 (0.37), residues: 153 loop : -0.69 (0.25), residues: 495 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP C 886 HIS 0.002 0.001 HIS C1088 PHE 0.010 0.001 PHE B1121 TYR 0.017 0.001 TYR C1067 ARG 0.002 0.000 ARG B1014 Details of bonding type rmsd link_NAG-ASN : bond 0.00298 ( 18) link_NAG-ASN : angle 1.52606 ( 54) link_BETA1-4 : bond 0.00498 ( 9) link_BETA1-4 : angle 1.16519 ( 27) hydrogen bonds : bond 0.05169 ( 567) hydrogen bonds : angle 4.54664 ( 1647) SS BOND : bond 0.00344 ( 21) SS BOND : angle 1.29411 ( 42) covalent geometry : bond 0.00276 ( 9696) covalent geometry : angle 0.49445 (13248) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2496 Ramachandran restraints generated. 1248 Oldfield, 0 Emsley, 1248 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2496 Ramachandran restraints generated. 1248 Oldfield, 0 Emsley, 1248 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 123 residues out of total 1113 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 104 time to evaluate : 1.111 Fit side-chains REVERT: A 725 GLU cc_start: 0.8488 (tt0) cc_final: 0.8105 (tt0) REVERT: A 752 LEU cc_start: 0.8708 (mt) cc_final: 0.8425 (mt) REVERT: A 855 PHE cc_start: 0.7909 (m-80) cc_final: 0.7538 (m-80) REVERT: A 873 TYR cc_start: 0.8716 (m-80) cc_final: 0.8514 (m-80) REVERT: B 731 MET cc_start: 0.8798 (ptt) cc_final: 0.8427 (ptp) REVERT: B 904 TYR cc_start: 0.7756 (m-10) cc_final: 0.7059 (m-10) REVERT: C 725 GLU cc_start: 0.8584 (tt0) cc_final: 0.8338 (tt0) REVERT: C 752 LEU cc_start: 0.8649 (mt) cc_final: 0.8444 (mt) REVERT: C 815 ARG cc_start: 0.8124 (OUTLIER) cc_final: 0.7498 (mtp180) REVERT: C 1050 MET cc_start: 0.8858 (ptm) cc_final: 0.8631 (ptp) outliers start: 19 outliers final: 7 residues processed: 112 average time/residue: 1.2893 time to fit residues: 154.6014 Evaluate side-chains 109 residues out of total 1113 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 101 time to evaluate : 0.999 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 900 MET Chi-restraints excluded: chain A residue 964 LYS Chi-restraints excluded: chain A residue 999 CYS Chi-restraints excluded: chain A residue 1105 THR Chi-restraints excluded: chain B residue 999 CYS Chi-restraints excluded: chain C residue 779 GLN Chi-restraints excluded: chain C residue 815 ARG Chi-restraints excluded: chain C residue 999 CYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 58 optimal weight: 3.9990 chunk 47 optimal weight: 0.4980 chunk 0 optimal weight: 2.9990 chunk 94 optimal weight: 0.6980 chunk 98 optimal weight: 0.6980 chunk 17 optimal weight: 2.9990 chunk 75 optimal weight: 0.6980 chunk 72 optimal weight: 1.9990 chunk 15 optimal weight: 2.9990 chunk 59 optimal weight: 0.6980 chunk 117 optimal weight: 0.6980 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 935 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3650 r_free = 0.3650 target = 0.147561 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3268 r_free = 0.3268 target = 0.115462 restraints weight = 9653.015| |-----------------------------------------------------------------------------| r_work (start): 0.3245 rms_B_bonded: 1.74 r_work: 0.3114 rms_B_bonded: 2.32 restraints_weight: 0.5000 r_work: 0.2979 rms_B_bonded: 3.75 restraints_weight: 0.2500 r_work (final): 0.2979 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8097 moved from start: 0.3353 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 9744 Z= 0.134 Angle : 0.522 8.471 13371 Z= 0.267 Chirality : 0.040 0.134 1650 Planarity : 0.004 0.038 1698 Dihedral : 3.628 15.842 1893 Min Nonbonded Distance : 2.554 Molprobity Statistics. All-atom Clashscore : 3.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.00 % Favored : 98.00 % Rotamer: Outliers : 1.90 % Allowed : 12.02 % Favored : 86.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.80 (0.23), residues: 1248 helix: 2.72 (0.21), residues: 600 sheet: 0.95 (0.37), residues: 153 loop : -0.70 (0.25), residues: 495 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.002 TRP C 886 HIS 0.003 0.001 HIS C1088 PHE 0.011 0.001 PHE B1121 TYR 0.018 0.001 TYR C1067 ARG 0.002 0.000 ARG B1014 Details of bonding type rmsd link_NAG-ASN : bond 0.00260 ( 18) link_NAG-ASN : angle 1.54715 ( 54) link_BETA1-4 : bond 0.00496 ( 9) link_BETA1-4 : angle 1.13008 ( 27) hydrogen bonds : bond 0.05292 ( 567) hydrogen bonds : angle 4.55727 ( 1647) SS BOND : bond 0.00323 ( 21) SS BOND : angle 1.28557 ( 42) covalent geometry : bond 0.00306 ( 9696) covalent geometry : angle 0.50718 (13248) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2496 Ramachandran restraints generated. 1248 Oldfield, 0 Emsley, 1248 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2496 Ramachandran restraints generated. 1248 Oldfield, 0 Emsley, 1248 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 121 residues out of total 1113 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 105 time to evaluate : 1.054 Fit side-chains REVERT: A 725 GLU cc_start: 0.8511 (tt0) cc_final: 0.8131 (tt0) REVERT: A 752 LEU cc_start: 0.8730 (mt) cc_final: 0.8450 (mt) REVERT: A 855 PHE cc_start: 0.7951 (m-80) cc_final: 0.7617 (m-80) REVERT: B 731 MET cc_start: 0.8812 (ptt) cc_final: 0.8456 (ptp) REVERT: B 904 TYR cc_start: 0.7800 (m-10) cc_final: 0.7098 (m-10) REVERT: C 725 GLU cc_start: 0.8558 (tt0) cc_final: 0.8287 (tt0) REVERT: C 815 ARG cc_start: 0.8166 (OUTLIER) cc_final: 0.7484 (mtp180) outliers start: 16 outliers final: 8 residues processed: 111 average time/residue: 1.2946 time to fit residues: 153.8382 Evaluate side-chains 111 residues out of total 1113 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 102 time to evaluate : 0.992 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 900 MET Chi-restraints excluded: chain A residue 921 LYS Chi-restraints excluded: chain A residue 964 LYS Chi-restraints excluded: chain A residue 999 CYS Chi-restraints excluded: chain A residue 1105 THR Chi-restraints excluded: chain B residue 999 CYS Chi-restraints excluded: chain C residue 815 ARG Chi-restraints excluded: chain C residue 902 MET Chi-restraints excluded: chain C residue 999 CYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 85 optimal weight: 0.2980 chunk 24 optimal weight: 0.9990 chunk 105 optimal weight: 0.8980 chunk 44 optimal weight: 0.7980 chunk 45 optimal weight: 0.9980 chunk 68 optimal weight: 2.9990 chunk 109 optimal weight: 4.9990 chunk 37 optimal weight: 2.9990 chunk 98 optimal weight: 0.9980 chunk 79 optimal weight: 0.7980 chunk 103 optimal weight: 0.9990 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 804 GLN ** C 935 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3632 r_free = 0.3632 target = 0.146202 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3245 r_free = 0.3245 target = 0.113823 restraints weight = 9735.952| |-----------------------------------------------------------------------------| r_work (start): 0.3240 rms_B_bonded: 1.76 r_work: 0.3109 rms_B_bonded: 2.33 restraints_weight: 0.5000 r_work: 0.2974 rms_B_bonded: 3.78 restraints_weight: 0.2500 r_work (final): 0.2974 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8108 moved from start: 0.3423 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 9744 Z= 0.144 Angle : 0.536 8.651 13371 Z= 0.275 Chirality : 0.041 0.133 1650 Planarity : 0.004 0.039 1698 Dihedral : 3.702 15.982 1893 Min Nonbonded Distance : 2.585 Molprobity Statistics. All-atom Clashscore : 3.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.68 % Favored : 98.32 % Rotamer: Outliers : 1.79 % Allowed : 12.14 % Favored : 86.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.73 (0.23), residues: 1248 helix: 2.64 (0.21), residues: 600 sheet: 0.94 (0.37), residues: 153 loop : -0.72 (0.25), residues: 495 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.002 TRP B 886 HIS 0.003 0.001 HIS C1088 PHE 0.011 0.001 PHE B1121 TYR 0.018 0.002 TYR C1067 ARG 0.002 0.000 ARG B1014 Details of bonding type rmsd link_NAG-ASN : bond 0.00248 ( 18) link_NAG-ASN : angle 1.57127 ( 54) link_BETA1-4 : bond 0.00479 ( 9) link_BETA1-4 : angle 1.11415 ( 27) hydrogen bonds : bond 0.05433 ( 567) hydrogen bonds : angle 4.59377 ( 1647) SS BOND : bond 0.00331 ( 21) SS BOND : angle 1.28265 ( 42) covalent geometry : bond 0.00334 ( 9696) covalent geometry : angle 0.52129 (13248) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2496 Ramachandran restraints generated. 1248 Oldfield, 0 Emsley, 1248 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2496 Ramachandran restraints generated. 1248 Oldfield, 0 Emsley, 1248 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 119 residues out of total 1113 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 104 time to evaluate : 0.998 Fit side-chains REVERT: A 725 GLU cc_start: 0.8528 (tt0) cc_final: 0.8150 (tt0) REVERT: A 855 PHE cc_start: 0.7978 (m-80) cc_final: 0.7672 (m-80) REVERT: B 731 MET cc_start: 0.8796 (ptt) cc_final: 0.8442 (ptp) REVERT: B 904 TYR cc_start: 0.7860 (m-10) cc_final: 0.7129 (m-10) REVERT: C 725 GLU cc_start: 0.8565 (tt0) cc_final: 0.8303 (tt0) REVERT: C 765 ARG cc_start: 0.7981 (mtp-110) cc_final: 0.7725 (mtp85) REVERT: C 815 ARG cc_start: 0.8184 (OUTLIER) cc_final: 0.7481 (mtp180) outliers start: 15 outliers final: 8 residues processed: 110 average time/residue: 1.3023 time to fit residues: 153.0599 Evaluate side-chains 112 residues out of total 1113 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 103 time to evaluate : 1.074 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 900 MET Chi-restraints excluded: chain A residue 921 LYS Chi-restraints excluded: chain A residue 964 LYS Chi-restraints excluded: chain A residue 999 CYS Chi-restraints excluded: chain A residue 1105 THR Chi-restraints excluded: chain B residue 999 CYS Chi-restraints excluded: chain C residue 815 ARG Chi-restraints excluded: chain C residue 902 MET Chi-restraints excluded: chain C residue 999 CYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 119 optimal weight: 0.4980 chunk 10 optimal weight: 0.7980 chunk 109 optimal weight: 0.6980 chunk 80 optimal weight: 1.9990 chunk 32 optimal weight: 0.2980 chunk 110 optimal weight: 0.7980 chunk 71 optimal weight: 0.9990 chunk 98 optimal weight: 0.9990 chunk 111 optimal weight: 0.9980 chunk 58 optimal weight: 2.9990 chunk 3 optimal weight: 1.9990 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 969 ASN ** C 935 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3636 r_free = 0.3636 target = 0.146669 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3249 r_free = 0.3249 target = 0.114149 restraints weight = 9651.588| |-----------------------------------------------------------------------------| r_work (start): 0.3238 rms_B_bonded: 1.76 r_work: 0.3107 rms_B_bonded: 2.33 restraints_weight: 0.5000 r_work: 0.2972 rms_B_bonded: 3.77 restraints_weight: 0.2500 r_work (final): 0.2972 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8099 moved from start: 0.3485 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 9744 Z= 0.130 Angle : 0.517 8.217 13371 Z= 0.266 Chirality : 0.040 0.125 1650 Planarity : 0.004 0.038 1698 Dihedral : 3.656 16.213 1893 Min Nonbonded Distance : 2.574 Molprobity Statistics. All-atom Clashscore : 3.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.60 % Favored : 98.40 % Rotamer: Outliers : 1.31 % Allowed : 13.21 % Favored : 85.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.77 (0.24), residues: 1248 helix: 2.69 (0.21), residues: 600 sheet: 0.99 (0.38), residues: 153 loop : -0.72 (0.25), residues: 495 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 886 HIS 0.003 0.001 HIS C1088 PHE 0.012 0.001 PHE C 817 TYR 0.017 0.001 TYR C1067 ARG 0.002 0.000 ARG B 815 Details of bonding type rmsd link_NAG-ASN : bond 0.00244 ( 18) link_NAG-ASN : angle 1.49688 ( 54) link_BETA1-4 : bond 0.00478 ( 9) link_BETA1-4 : angle 1.07172 ( 27) hydrogen bonds : bond 0.05160 ( 567) hydrogen bonds : angle 4.55654 ( 1647) SS BOND : bond 0.00307 ( 21) SS BOND : angle 1.23699 ( 42) covalent geometry : bond 0.00293 ( 9696) covalent geometry : angle 0.50348 (13248) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2496 Ramachandran restraints generated. 1248 Oldfield, 0 Emsley, 1248 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2496 Ramachandran restraints generated. 1248 Oldfield, 0 Emsley, 1248 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 116 residues out of total 1113 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 105 time to evaluate : 0.984 Fit side-chains REVERT: A 725 GLU cc_start: 0.8518 (tt0) cc_final: 0.8145 (tt0) REVERT: A 855 PHE cc_start: 0.7990 (m-80) cc_final: 0.7675 (m-80) REVERT: B 731 MET cc_start: 0.8821 (ptt) cc_final: 0.8465 (ptp) REVERT: B 855 PHE cc_start: 0.7803 (m-80) cc_final: 0.7599 (m-80) REVERT: B 904 TYR cc_start: 0.7837 (m-10) cc_final: 0.7120 (m-10) REVERT: C 765 ARG cc_start: 0.7936 (mtp-110) cc_final: 0.7667 (mtp85) REVERT: C 815 ARG cc_start: 0.8182 (OUTLIER) cc_final: 0.7473 (mtp180) REVERT: C 904 TYR cc_start: 0.8038 (m-10) cc_final: 0.7647 (m-10) REVERT: C 1050 MET cc_start: 0.8856 (ptm) cc_final: 0.8633 (ptp) outliers start: 11 outliers final: 6 residues processed: 110 average time/residue: 1.3353 time to fit residues: 156.2786 Evaluate side-chains 109 residues out of total 1113 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 102 time to evaluate : 1.016 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 900 MET Chi-restraints excluded: chain A residue 999 CYS Chi-restraints excluded: chain A residue 1105 THR Chi-restraints excluded: chain B residue 999 CYS Chi-restraints excluded: chain C residue 815 ARG Chi-restraints excluded: chain C residue 902 MET Chi-restraints excluded: chain C residue 999 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 24 optimal weight: 0.3980 chunk 71 optimal weight: 0.6980 chunk 59 optimal weight: 1.9990 chunk 14 optimal weight: 1.9990 chunk 40 optimal weight: 0.5980 chunk 18 optimal weight: 0.7980 chunk 75 optimal weight: 0.8980 chunk 28 optimal weight: 0.7980 chunk 81 optimal weight: 0.3980 chunk 62 optimal weight: 1.9990 chunk 1 optimal weight: 0.5980 overall best weight: 0.5380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 969 ASN ** C 935 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3658 r_free = 0.3658 target = 0.148289 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3281 r_free = 0.3281 target = 0.116343 restraints weight = 9714.745| |-----------------------------------------------------------------------------| r_work (start): 0.3256 rms_B_bonded: 1.75 r_work: 0.3126 rms_B_bonded: 2.32 restraints_weight: 0.5000 r_work: 0.2991 rms_B_bonded: 3.78 restraints_weight: 0.2500 r_work (final): 0.2991 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8087 moved from start: 0.3538 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 9744 Z= 0.123 Angle : 0.509 8.371 13371 Z= 0.261 Chirality : 0.040 0.125 1650 Planarity : 0.004 0.038 1698 Dihedral : 3.611 16.819 1893 Min Nonbonded Distance : 2.593 Molprobity Statistics. All-atom Clashscore : 3.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.52 % Favored : 98.48 % Rotamer: Outliers : 1.31 % Allowed : 13.57 % Favored : 85.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.88 (0.24), residues: 1248 helix: 2.71 (0.21), residues: 600 sheet: 1.46 (0.41), residues: 123 loop : -0.60 (0.25), residues: 525 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 886 HIS 0.002 0.001 HIS C1088 PHE 0.014 0.001 PHE C 817 TYR 0.017 0.001 TYR C1067 ARG 0.001 0.000 ARG A1039 Details of bonding type rmsd link_NAG-ASN : bond 0.00238 ( 18) link_NAG-ASN : angle 1.45498 ( 54) link_BETA1-4 : bond 0.00469 ( 9) link_BETA1-4 : angle 1.03612 ( 27) hydrogen bonds : bond 0.04981 ( 567) hydrogen bonds : angle 4.53038 ( 1647) SS BOND : bond 0.00294 ( 21) SS BOND : angle 1.20168 ( 42) covalent geometry : bond 0.00274 ( 9696) covalent geometry : angle 0.49573 (13248) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2496 Ramachandran restraints generated. 1248 Oldfield, 0 Emsley, 1248 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2496 Ramachandran restraints generated. 1248 Oldfield, 0 Emsley, 1248 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 117 residues out of total 1113 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 106 time to evaluate : 1.095 Fit side-chains REVERT: A 725 GLU cc_start: 0.8508 (tt0) cc_final: 0.8138 (tt0) REVERT: B 731 MET cc_start: 0.8790 (ptt) cc_final: 0.8448 (ptp) REVERT: B 855 PHE cc_start: 0.7823 (m-80) cc_final: 0.7620 (m-80) REVERT: B 904 TYR cc_start: 0.7801 (m-10) cc_final: 0.7087 (m-10) REVERT: C 765 ARG cc_start: 0.7910 (mtp-110) cc_final: 0.7640 (mtp85) REVERT: C 815 ARG cc_start: 0.8170 (OUTLIER) cc_final: 0.7468 (mtp180) REVERT: C 904 TYR cc_start: 0.8039 (m-10) cc_final: 0.7639 (m-10) outliers start: 11 outliers final: 8 residues processed: 110 average time/residue: 1.3799 time to fit residues: 161.5388 Evaluate side-chains 112 residues out of total 1113 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 103 time to evaluate : 1.140 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 900 MET Chi-restraints excluded: chain A residue 902 MET Chi-restraints excluded: chain A residue 921 LYS Chi-restraints excluded: chain A residue 999 CYS Chi-restraints excluded: chain A residue 1105 THR Chi-restraints excluded: chain B residue 999 CYS Chi-restraints excluded: chain C residue 815 ARG Chi-restraints excluded: chain C residue 902 MET Chi-restraints excluded: chain C residue 999 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 101 optimal weight: 0.5980 chunk 74 optimal weight: 0.9990 chunk 79 optimal weight: 0.7980 chunk 37 optimal weight: 2.9990 chunk 6 optimal weight: 3.9990 chunk 61 optimal weight: 0.9980 chunk 84 optimal weight: 0.9980 chunk 14 optimal weight: 0.5980 chunk 119 optimal weight: 0.9980 chunk 4 optimal weight: 0.8980 chunk 9 optimal weight: 0.4980 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 913 GLN C 935 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3621 r_free = 0.3621 target = 0.145651 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3232 r_free = 0.3232 target = 0.113050 restraints weight = 9683.748| |-----------------------------------------------------------------------------| r_work (start): 0.3255 rms_B_bonded: 1.77 r_work: 0.3126 rms_B_bonded: 2.33 restraints_weight: 0.5000 r_work: 0.2990 rms_B_bonded: 3.78 restraints_weight: 0.2500 r_work (final): 0.2990 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8098 moved from start: 0.3560 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 9744 Z= 0.135 Angle : 0.526 7.938 13371 Z= 0.270 Chirality : 0.040 0.127 1650 Planarity : 0.004 0.039 1698 Dihedral : 3.693 17.205 1893 Min Nonbonded Distance : 2.606 Molprobity Statistics. All-atom Clashscore : 3.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.68 % Favored : 98.32 % Rotamer: Outliers : 1.31 % Allowed : 13.81 % Favored : 84.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.82 (0.23), residues: 1248 helix: 2.66 (0.21), residues: 600 sheet: 1.43 (0.41), residues: 123 loop : -0.63 (0.25), residues: 525 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.002 TRP B 886 HIS 0.003 0.001 HIS C1088 PHE 0.018 0.001 PHE C 817 TYR 0.018 0.002 TYR C1067 ARG 0.001 0.000 ARG A1039 Details of bonding type rmsd link_NAG-ASN : bond 0.00221 ( 18) link_NAG-ASN : angle 1.52429 ( 54) link_BETA1-4 : bond 0.00461 ( 9) link_BETA1-4 : angle 1.03520 ( 27) hydrogen bonds : bond 0.05211 ( 567) hydrogen bonds : angle 4.57321 ( 1647) SS BOND : bond 0.00309 ( 21) SS BOND : angle 1.25308 ( 42) covalent geometry : bond 0.00309 ( 9696) covalent geometry : angle 0.51260 (13248) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6572.46 seconds wall clock time: 113 minutes 35.88 seconds (6815.88 seconds total)