Starting phenix.real_space_refine on Sun Jul 27 17:23:29 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8vq9_43435/07_2025/8vq9_43435.cif Found real_map, /net/cci-nas-00/data/ceres_data/8vq9_43435/07_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_43435/07_2025/8vq9_43435.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8vq9_43435/07_2025/8vq9_43435.map" model { file = "/net/cci-nas-00/data/ceres_data/8vq9_43435/07_2025/8vq9_43435.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8vq9_43435/07_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-5711/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: 6.73, per 1000 atoms: 0.71 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: 2.76 Conformation dependent library (CDL) restraints added in 1.2 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: 1.12 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: 2.77 Time building geometry restraints manager: 3.22 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: 3.220 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: 0.370 Check model and map are aligned: 0.070 Set scattering table: 0.100 Process input model: 25.730 Find NCS groups from input model: 0.350 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:13.960 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 43.860 ------------------------------------------------------------------------------- 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 : 0.952 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: 1.2565 time to fit residues: 235.4585 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 : 0.985 ------------------------------------------------------------------------------- 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 = 50)----------------| | r_work = 0.3308 r_free = 0.3308 target = 0.118600 restraints weight = 9466.211| |-----------------------------------------------------------------------------| 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: 0.3050 rms_B_bonded: 3.83 restraints_weight: 0.2500 r_work (final): 0.3050 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8044 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 : 1.189 Fit side-chains REVERT: A 725 GLU cc_start: 0.8442 (tt0) cc_final: 0.8086 (tt0) REVERT: A 752 LEU cc_start: 0.8657 (mt) cc_final: 0.8334 (mt) REVERT: A 855 PHE cc_start: 0.7674 (m-80) cc_final: 0.7404 (m-80) REVERT: A 935 GLN cc_start: 0.7086 (mt0) cc_final: 0.6704 (mt0) REVERT: B 804 GLN cc_start: 0.8155 (OUTLIER) cc_final: 0.7886 (mt0) REVERT: B 904 TYR cc_start: 0.7995 (m-10) cc_final: 0.7087 (m-10) REVERT: C 725 GLU cc_start: 0.8468 (tt0) cc_final: 0.8116 (tt0) REVERT: C 752 LEU cc_start: 0.8574 (mt) cc_final: 0.8356 (mt) outliers start: 22 outliers final: 6 residues processed: 131 average time/residue: 1.5852 time to fit residues: 223.2017 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 : 0.985 ------------------------------------------------------------------------------- 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: 0.4980 chunk 22 optimal weight: 4.9990 chunk 108 optimal weight: 0.1980 chunk 63 optimal weight: 2.9990 chunk 84 optimal weight: 0.9980 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: 0.5980 ------------------------------------------------------------------------------- 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 = 0.3679 r_free = 0.3679 target = 0.149945 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3286 r_free = 0.3286 target = 0.116792 restraints weight = 9451.959| |-----------------------------------------------------------------------------| r_work (start): 0.3264 rms_B_bonded: 1.78 r_work: 0.3141 rms_B_bonded: 2.26 restraints_weight: 0.5000 r_work: 0.3009 rms_B_bonded: 3.67 restraints_weight: 0.2500 r_work (final): 0.3009 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8040 moved from start: 0.2592 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= 0.138 Angle : 0.530 4.895 13371 Z= 0.276 Chirality : 0.040 0.132 1650 Planarity : 0.004 0.045 1698 Dihedral : 3.543 14.882 1893 Min Nonbonded Distance : 2.622 Molprobity Statistics. All-atom Clashscore : 3.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.92 % Favored : 98.08 % Rotamer: Outliers : 2.02 % Allowed : 10.24 % Favored : 87.74 % 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: 1.83 (0.23), residues: 1248 helix: 2.69 (0.21), residues: 588 sheet: 1.11 (0.38), residues: 153 loop : -0.58 (0.25), residues: 507 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP A 886 HIS 0.002 0.001 HIS A1083 PHE 0.016 0.001 PHE C 906 TYR 0.019 0.002 TYR C1067 ARG 0.002 0.000 ARG B 995 Details of bonding type rmsd link_NAG-ASN : bond 0.00484 ( 18) link_NAG-ASN : angle 1.71169 ( 54) link_BETA1-4 : bond 0.00686 ( 9) link_BETA1-4 : angle 1.57185 ( 27) hydrogen bonds : bond 0.05903 ( 567) hydrogen bonds : angle 4.76020 ( 1647) SS BOND : bond 0.00368 ( 21) SS BOND : angle 1.43631 ( 42) covalent geometry : bond 0.00301 ( 9696) covalent geometry : angle 0.50959 (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: 17 poor density : 113 time to evaluate : 0.962 Fit side-chains REVERT: A 725 GLU cc_start: 0.8502 (tt0) cc_final: 0.8102 (tt0) REVERT: A 731 MET cc_start: 0.8879 (ptt) cc_final: 0.8580 (ptt) REVERT: A 752 LEU cc_start: 0.8654 (mt) cc_final: 0.8353 (mt) REVERT: A 855 PHE cc_start: 0.7762 (m-80) cc_final: 0.7423 (m-80) REVERT: A 886 TRP cc_start: 0.7789 (p90) cc_final: 0.7587 (p90) REVERT: B 731 MET cc_start: 0.8768 (ptt) cc_final: 0.8446 (ptp) REVERT: B 904 TYR cc_start: 0.7866 (m-10) cc_final: 0.7116 (m-10) REVERT: C 725 GLU cc_start: 0.8511 (tt0) cc_final: 0.8190 (tt0) REVERT: C 752 LEU cc_start: 0.8584 (mt) cc_final: 0.8376 (mt) outliers start: 17 outliers final: 5 residues processed: 122 average time/residue: 1.3713 time to fit residues: 178.7628 Evaluate side-chains 111 residues out of total 1113 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 106 time to evaluate : 1.010 ------------------------------------------------------------------------------- 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 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: 0.8980 chunk 16 optimal weight: 0.9990 chunk 94 optimal weight: 1.9990 chunk 20 optimal weight: 1.9990 chunk 115 optimal weight: 1.9990 chunk 67 optimal weight: 0.9990 chunk 51 optimal weight: 0.1980 chunk 48 optimal weight: 2.9990 chunk 35 optimal weight: 1.9990 chunk 12 optimal weight: 0.9980 overall best weight: 0.8184 ------------------------------------------------------------------------------- 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 = 0.3626 r_free = 0.3626 target = 0.145920 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3222 r_free = 0.3222 target = 0.112321 restraints weight = 9414.082| |-----------------------------------------------------------------------------| r_work (start): 0.3231 rms_B_bonded: 1.79 r_work: 0.3109 rms_B_bonded: 2.25 restraints_weight: 0.5000 r_work: 0.2976 rms_B_bonded: 3.65 restraints_weight: 0.2500 r_work (final): 0.2976 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8080 moved from start: 0.2970 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 9744 Z= 0.156 Angle : 0.556 4.991 13371 Z= 0.288 Chirality : 0.041 0.132 1650 Planarity : 0.004 0.041 1698 Dihedral : 3.679 15.954 1893 Min Nonbonded Distance : 2.626 Molprobity Statistics. All-atom Clashscore : 2.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.08 % Favored : 97.92 % Rotamer: Outliers : 1.19 % Allowed : 11.07 % Favored : 87.74 % 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: 1.66 (0.23), residues: 1248 helix: 2.58 (0.21), residues: 597 sheet: 0.96 (0.37), residues: 153 loop : -0.74 (0.25), residues: 498 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.003 TRP C 886 HIS 0.003 0.001 HIS A1083 PHE 0.017 0.002 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 0.00357 ( 18) link_NAG-ASN : angle 1.78343 ( 54) link_BETA1-4 : bond 0.00540 ( 9) link_BETA1-4 : angle 1.45488 ( 27) hydrogen bonds : bond 0.05899 ( 567) hydrogen bonds : angle 4.75859 ( 1647) SS BOND : bond 0.00394 ( 21) SS BOND : angle 1.47788 ( 42) covalent geometry : bond 0.00364 ( 9696) covalent geometry : angle 0.53663 (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 : 1.013 Fit side-chains REVERT: A 725 GLU cc_start: 0.8465 (tt0) cc_final: 0.8079 (tt0) REVERT: A 752 LEU cc_start: 0.8684 (mt) cc_final: 0.8386 (mt) REVERT: A 855 PHE cc_start: 0.7869 (m-80) cc_final: 0.7489 (m-80) REVERT: B 804 GLN cc_start: 0.8227 (mm-40) cc_final: 0.7324 (mp10) REVERT: B 904 TYR cc_start: 0.7835 (m-10) cc_final: 0.7095 (m-10) REVERT: B 1119 ASN cc_start: 0.7764 (m-40) cc_final: 0.7448 (m110) REVERT: C 725 GLU cc_start: 0.8536 (tt0) cc_final: 0.8210 (tt0) REVERT: C 752 LEU cc_start: 0.8630 (mt) cc_final: 0.8408 (mt) outliers start: 10 outliers final: 7 residues processed: 116 average time/residue: 1.7298 time to fit residues: 214.5677 Evaluate side-chains 111 residues out of total 1113 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 104 time to evaluate : 1.146 ------------------------------------------------------------------------------- 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 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=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 47 optimal weight: 1.9990 chunk 110 optimal weight: 0.1980 chunk 107 optimal weight: 1.9990 chunk 31 optimal weight: 0.6980 chunk 21 optimal weight: 2.9990 chunk 111 optimal weight: 1.9990 chunk 112 optimal weight: 0.6980 chunk 65 optimal weight: 3.9990 chunk 66 optimal weight: 0.6980 chunk 30 optimal weight: 0.7980 chunk 8 optimal weight: 0.6980 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 955 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 = 0.3640 r_free = 0.3640 target = 0.147068 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3254 r_free = 0.3254 target = 0.114651 restraints weight = 9579.375| |-----------------------------------------------------------------------------| r_work (start): 0.3234 rms_B_bonded: 1.75 r_work: 0.3104 rms_B_bonded: 2.32 restraints_weight: 0.5000 r_work: 0.2968 rms_B_bonded: 3.78 restraints_weight: 0.2500 r_work (final): 0.2968 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8091 moved from start: 0.3132 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= 0.129 Angle : 0.511 9.395 13371 Z= 0.263 Chirality : 0.040 0.127 1650 Planarity : 0.004 0.038 1698 Dihedral : 3.558 15.287 1893 Min Nonbonded Distance : 2.621 Molprobity Statistics. All-atom Clashscore : 3.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.60 % Favored : 98.40 % Rotamer: Outliers : 1.55 % Allowed : 12.26 % Favored : 86.19 % 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: 1.79 (0.23), residues: 1248 helix: 2.76 (0.21), residues: 597 sheet: 0.91 (0.37), residues: 153 loop : -0.74 (0.25), residues: 498 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.002 TRP C 886 HIS 0.002 0.001 HIS B1101 PHE 0.011 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 0.00319 ( 18) link_NAG-ASN : angle 1.54508 ( 54) link_BETA1-4 : bond 0.00570 ( 9) link_BETA1-4 : angle 1.23209 ( 27) hydrogen bonds : bond 0.05296 ( 567) hydrogen bonds : angle 4.61152 ( 1647) SS BOND : bond 0.00346 ( 21) SS BOND : angle 1.31048 ( 42) covalent geometry : bond 0.00288 ( 9696) covalent geometry : angle 0.49552 (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 121 residues out of total 1113 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 108 time to evaluate : 0.946 Fit side-chains REVERT: A 725 GLU cc_start: 0.8502 (tt0) cc_final: 0.8124 (tt0) REVERT: A 752 LEU cc_start: 0.8696 (mt) cc_final: 0.8418 (mt) REVERT: A 855 PHE cc_start: 0.7874 (m-80) cc_final: 0.7597 (m-80) REVERT: B 731 MET cc_start: 0.8860 (ptt) cc_final: 0.8451 (ptp) REVERT: B 904 TYR cc_start: 0.7810 (m-10) cc_final: 0.7113 (m-10) REVERT: C 725 GLU cc_start: 0.8543 (tt0) cc_final: 0.8280 (tt0) REVERT: C 752 LEU cc_start: 0.8657 (mt) cc_final: 0.8415 (mt) REVERT: C 815 ARG cc_start: 0.8138 (OUTLIER) cc_final: 0.7541 (mtp180) REVERT: C 1050 MET cc_start: 0.8873 (ptm) cc_final: 0.8641 (ptp) outliers start: 13 outliers final: 6 residues processed: 113 average time/residue: 1.3550 time to fit residues: 164.0633 Evaluate side-chains 111 residues out of total 1113 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 104 time to evaluate : 1.047 ------------------------------------------------------------------------------- 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 815 ARG 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: 0.0770 chunk 26 optimal weight: 1.9990 chunk 29 optimal weight: 0.9980 chunk 80 optimal weight: 2.9990 chunk 119 optimal weight: 1.9990 chunk 56 optimal weight: 2.9990 chunk 95 optimal weight: 3.9990 chunk 74 optimal weight: 2.9990 chunk 20 optimal weight: 1.9990 chunk 44 optimal weight: 0.7980 chunk 33 optimal weight: 0.5980 overall best weight: 0.8940 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 913 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 = 0.3642 r_free = 0.3642 target = 0.146797 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3261 r_free = 0.3261 target = 0.114727 restraints weight = 9562.723| |-----------------------------------------------------------------------------| r_work (start): 0.3249 rms_B_bonded: 1.74 r_work: 0.3119 rms_B_bonded: 2.30 restraints_weight: 0.5000 r_work: 0.2985 rms_B_bonded: 3.73 restraints_weight: 0.2500 r_work (final): 0.2985 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8113 moved from start: 0.3248 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 9744 Z= 0.162 Angle : 0.559 10.655 13371 Z= 0.284 Chirality : 0.041 0.137 1650 Planarity : 0.004 0.039 1698 Dihedral : 3.769 16.069 1893 Min Nonbonded Distance : 2.604 Molprobity Statistics. All-atom Clashscore : 3.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.68 % Favored : 98.32 % Rotamer: Outliers : 1.79 % Allowed : 11.67 % Favored : 86.55 % 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: 1.67 (0.23), residues: 1248 helix: 2.59 (0.21), residues: 600 sheet: 0.93 (0.37), residues: 153 loop : -0.76 (0.25), residues: 495 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 0.019 0.002 TYR C1067 ARG 0.003 0.000 ARG B1014 Details of bonding type rmsd link_NAG-ASN : bond 0.00283 ( 18) link_NAG-ASN : angle 1.68554 ( 54) link_BETA1-4 : bond 0.00518 ( 9) link_BETA1-4 : angle 1.23408 ( 27) hydrogen bonds : bond 0.05790 ( 567) hydrogen bonds : angle 4.68366 ( 1647) SS BOND : bond 0.00355 ( 21) SS BOND : angle 1.40675 ( 42) covalent geometry : bond 0.00382 ( 9696) covalent geometry : angle 0.54287 (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 122 residues out of total 1113 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 107 time to evaluate : 1.189 Fit side-chains REVERT: A 725 GLU cc_start: 0.8510 (tt0) cc_final: 0.8130 (tt0) REVERT: A 752 LEU cc_start: 0.8641 (mt) cc_final: 0.8349 (mt) REVERT: A 855 PHE cc_start: 0.7943 (m-80) cc_final: 0.7625 (m-80) REVERT: B 731 MET cc_start: 0.8859 (ptt) cc_final: 0.8441 (ptp) REVERT: B 804 GLN cc_start: 0.8290 (mm-40) cc_final: 0.7368 (mp10) REVERT: B 904 TYR cc_start: 0.7836 (m-10) cc_final: 0.7117 (m-10) REVERT: B 1119 ASN cc_start: 0.7838 (m-40) cc_final: 0.7581 (m110) REVERT: C 725 GLU cc_start: 0.8595 (tt0) cc_final: 0.8297 (tt0) REVERT: C 752 LEU cc_start: 0.8643 (mt) cc_final: 0.8412 (mt) REVERT: C 815 ARG cc_start: 0.8142 (OUTLIER) cc_final: 0.7465 (mtp180) REVERT: C 1050 MET cc_start: 0.8869 (ptm) cc_final: 0.8647 (ptp) outliers start: 15 outliers final: 10 residues processed: 112 average time/residue: 1.3986 time to fit residues: 167.5283 Evaluate side-chains 114 residues out of total 1113 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 103 time to evaluate : 1.001 ------------------------------------------------------------------------------- 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 964 LYS 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 815 ARG Chi-restraints excluded: chain C residue 902 MET 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: 2.9990 chunk 47 optimal weight: 0.9990 chunk 0 optimal weight: 1.9990 chunk 94 optimal weight: 0.9980 chunk 98 optimal weight: 0.6980 chunk 17 optimal weight: 2.9990 chunk 75 optimal weight: 1.9990 chunk 72 optimal weight: 1.9990 chunk 15 optimal weight: 2.9990 chunk 59 optimal weight: 0.8980 chunk 117 optimal weight: 0.5980 overall best weight: 0.8382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 913 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 = 0.3606 r_free = 0.3606 target = 0.144466 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3211 r_free = 0.3211 target = 0.111653 restraints weight = 9703.376| |-----------------------------------------------------------------------------| r_work (start): 0.3232 rms_B_bonded: 1.77 r_work: 0.3102 rms_B_bonded: 2.33 restraints_weight: 0.5000 r_work: 0.2967 rms_B_bonded: 3.77 restraints_weight: 0.2500 r_work (final): 0.2967 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8115 moved from start: 0.3340 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 9744 Z= 0.152 Angle : 0.544 8.351 13371 Z= 0.279 Chirality : 0.041 0.147 1650 Planarity : 0.004 0.039 1698 Dihedral : 3.786 16.128 1893 Min Nonbonded Distance : 2.577 Molprobity Statistics. All-atom Clashscore : 3.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.68 % Favored : 98.32 % Rotamer: Outliers : 2.02 % Allowed : 11.90 % 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: 1.65 (0.23), residues: 1248 helix: 2.59 (0.21), residues: 600 sheet: 0.93 (0.37), residues: 153 loop : -0.78 (0.25), residues: 495 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.002 TRP B 886 HIS 0.003 0.001 HIS C1088 PHE 0.011 0.002 PHE B1121 TYR 0.018 0.002 TYR C1067 ARG 0.003 0.000 ARG B1014 Details of bonding type rmsd link_NAG-ASN : bond 0.00266 ( 18) link_NAG-ASN : angle 1.61216 ( 54) link_BETA1-4 : bond 0.00505 ( 9) link_BETA1-4 : angle 1.18181 ( 27) hydrogen bonds : bond 0.05620 ( 567) hydrogen bonds : angle 4.66607 ( 1647) SS BOND : bond 0.00346 ( 21) SS BOND : angle 1.35293 ( 42) covalent geometry : bond 0.00357 ( 9696) covalent geometry : angle 0.52862 (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 122 residues out of total 1113 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 105 time to evaluate : 1.118 Fit side-chains REVERT: A 725 GLU cc_start: 0.8534 (tt0) cc_final: 0.8158 (tt0) REVERT: A 855 PHE cc_start: 0.7970 (m-80) cc_final: 0.7684 (m-80) REVERT: A 873 TYR cc_start: 0.8785 (m-80) cc_final: 0.8581 (m-80) REVERT: A 994 ASP cc_start: 0.6703 (m-30) cc_final: 0.6451 (p0) REVERT: B 731 MET cc_start: 0.8868 (ptt) cc_final: 0.8462 (ptp) REVERT: B 804 GLN cc_start: 0.8312 (mm-40) cc_final: 0.7378 (mp10) REVERT: B 904 TYR cc_start: 0.7814 (m-10) cc_final: 0.7103 (m-10) REVERT: B 1119 ASN cc_start: 0.7859 (m-40) cc_final: 0.7615 (m110) REVERT: C 725 GLU cc_start: 0.8564 (tt0) cc_final: 0.8327 (tt0) REVERT: C 815 ARG cc_start: 0.8173 (OUTLIER) cc_final: 0.7497 (mtp180) outliers start: 17 outliers final: 10 residues processed: 113 average time/residue: 1.5752 time to fit residues: 190.3185 Evaluate side-chains 115 residues out of total 1113 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 104 time to evaluate : 0.998 ------------------------------------------------------------------------------- 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 964 LYS 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 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: 0.3980 chunk 24 optimal weight: 2.9990 chunk 105 optimal weight: 0.8980 chunk 44 optimal weight: 0.9990 chunk 45 optimal weight: 0.8980 chunk 68 optimal weight: 0.6980 chunk 109 optimal weight: 4.9990 chunk 37 optimal weight: 1.9990 chunk 98 optimal weight: 0.6980 chunk 79 optimal weight: 0.9980 chunk 103 optimal weight: 0.6980 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 804 GLN B 969 ASN ** C 913 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 935 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3638 r_free = 0.3638 target = 0.146669 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3255 r_free = 0.3255 target = 0.114446 restraints weight = 9743.029| |-----------------------------------------------------------------------------| r_work (start): 0.3244 rms_B_bonded: 1.75 r_work: 0.3114 rms_B_bonded: 2.33 restraints_weight: 0.5000 r_work: 0.2979 rms_B_bonded: 3.76 restraints_weight: 0.2500 r_work (final): 0.2979 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8104 moved from start: 0.3427 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 9744 Z= 0.136 Angle : 0.525 8.591 13371 Z= 0.269 Chirality : 0.040 0.130 1650 Planarity : 0.004 0.039 1698 Dihedral : 3.721 16.770 1893 Min Nonbonded Distance : 2.567 Molprobity Statistics. All-atom Clashscore : 3.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.60 % Favored : 98.40 % Rotamer: Outliers : 1.79 % Allowed : 11.90 % Favored : 86.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 2.68 (0.21), residues: 597 sheet: 0.97 (0.38), residues: 153 loop : -0.77 (0.25), residues: 498 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.002 TRP B 886 HIS 0.003 0.001 HIS C1088 PHE 0.011 0.001 PHE B1121 TYR 0.017 0.001 TYR C1067 ARG 0.002 0.000 ARG C 995 Details of bonding type rmsd link_NAG-ASN : bond 0.00257 ( 18) link_NAG-ASN : angle 1.54032 ( 54) link_BETA1-4 : bond 0.00490 ( 9) link_BETA1-4 : angle 1.11626 ( 27) hydrogen bonds : bond 0.05319 ( 567) hydrogen bonds : angle 4.59894 ( 1647) SS BOND : bond 0.00312 ( 21) SS BOND : angle 1.25643 ( 42) covalent geometry : bond 0.00313 ( 9696) covalent geometry : angle 0.51136 (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 120 residues out of total 1113 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 105 time to evaluate : 2.767 Fit side-chains REVERT: A 725 GLU cc_start: 0.8521 (tt0) cc_final: 0.8152 (tt0) REVERT: A 855 PHE cc_start: 0.7975 (m-80) cc_final: 0.7668 (m-80) REVERT: B 731 MET cc_start: 0.8865 (ptt) cc_final: 0.8485 (ptp) REVERT: B 804 GLN cc_start: 0.8285 (mm-40) cc_final: 0.7395 (mp10) REVERT: B 904 TYR cc_start: 0.7780 (m-10) cc_final: 0.7087 (m-10) REVERT: B 1119 ASN cc_start: 0.7825 (m-40) cc_final: 0.7585 (m110) REVERT: C 765 ARG cc_start: 0.7975 (mtp-110) cc_final: 0.7713 (mtp85) REVERT: C 815 ARG cc_start: 0.8196 (OUTLIER) cc_final: 0.7492 (mtp180) outliers start: 15 outliers final: 8 residues processed: 111 average time/residue: 1.7187 time to fit residues: 205.5854 Evaluate side-chains 113 residues out of total 1113 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 104 time to evaluate : 0.840 ------------------------------------------------------------------------------- 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 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 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: 1.9990 chunk 10 optimal weight: 0.0970 chunk 109 optimal weight: 0.2980 chunk 80 optimal weight: 1.9990 chunk 32 optimal weight: 0.8980 chunk 110 optimal weight: 2.9990 chunk 71 optimal weight: 0.5980 chunk 98 optimal weight: 0.9980 chunk 111 optimal weight: 0.5980 chunk 58 optimal weight: 2.9990 chunk 3 optimal weight: 0.6980 overall best weight: 0.4578 ------------------------------------------------------------------------------- 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 ** 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 = 0.3627 r_free = 0.3627 target = 0.146363 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3245 r_free = 0.3245 target = 0.114134 restraints weight = 9688.072| |-----------------------------------------------------------------------------| r_work (start): 0.3254 rms_B_bonded: 1.75 r_work: 0.3123 rms_B_bonded: 2.33 restraints_weight: 0.5000 r_work: 0.2989 rms_B_bonded: 3.78 restraints_weight: 0.2500 r_work (final): 0.2989 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8082 moved from start: 0.3513 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 9744 Z= 0.115 Angle : 0.496 8.199 13371 Z= 0.254 Chirality : 0.040 0.128 1650 Planarity : 0.004 0.038 1698 Dihedral : 3.589 17.444 1893 Min Nonbonded Distance : 2.593 Molprobity Statistics. All-atom Clashscore : 3.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.60 % Favored : 98.40 % Rotamer: Outliers : 1.43 % Allowed : 12.50 % 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: 1.88 (0.24), residues: 1248 helix: 2.77 (0.21), residues: 600 sheet: 1.01 (0.38), residues: 153 loop : -0.65 (0.25), residues: 495 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 886 HIS 0.002 0.001 HIS C1088 PHE 0.010 0.001 PHE C 817 TYR 0.017 0.001 TYR C1067 ARG 0.001 0.000 ARG C 995 Details of bonding type rmsd link_NAG-ASN : bond 0.00253 ( 18) link_NAG-ASN : angle 1.41145 ( 54) link_BETA1-4 : bond 0.00472 ( 9) link_BETA1-4 : angle 1.04455 ( 27) hydrogen bonds : bond 0.04871 ( 567) hydrogen bonds : angle 4.50441 ( 1647) SS BOND : bond 0.00288 ( 21) SS BOND : angle 1.19614 ( 42) covalent geometry : bond 0.00252 ( 9696) covalent geometry : angle 0.48334 (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 124 residues out of total 1113 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 112 time to evaluate : 0.930 Fit side-chains REVERT: A 725 GLU cc_start: 0.8512 (tt0) cc_final: 0.8140 (tt0) REVERT: A 731 MET cc_start: 0.8903 (ptt) cc_final: 0.8578 (ptp) REVERT: A 855 PHE cc_start: 0.7952 (m-80) cc_final: 0.7641 (m-80) REVERT: B 731 MET cc_start: 0.8814 (ptt) cc_final: 0.8438 (ptp) REVERT: B 804 GLN cc_start: 0.8274 (mm110) cc_final: 0.7310 (mp10) REVERT: B 904 TYR cc_start: 0.7725 (m-10) cc_final: 0.7113 (m-10) REVERT: C 765 ARG cc_start: 0.7907 (mtp-110) cc_final: 0.7636 (mtp85) outliers start: 12 outliers final: 6 residues processed: 118 average time/residue: 1.3583 time to fit residues: 170.5821 Evaluate side-chains 112 residues out of total 1113 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 106 time to evaluate : 0.915 ------------------------------------------------------------------------------- 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 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: 2.9990 chunk 71 optimal weight: 0.6980 chunk 59 optimal weight: 1.9990 chunk 14 optimal weight: 1.9990 chunk 40 optimal weight: 0.3980 chunk 18 optimal weight: 0.7980 chunk 75 optimal weight: 0.7980 chunk 28 optimal weight: 1.9990 chunk 81 optimal weight: 0.8980 chunk 62 optimal weight: 0.9990 chunk 1 optimal weight: 0.6980 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 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 = 0.3624 r_free = 0.3624 target = 0.145825 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3238 r_free = 0.3238 target = 0.113327 restraints weight = 9787.909| |-----------------------------------------------------------------------------| r_work (start): 0.3245 rms_B_bonded: 1.78 r_work: 0.3115 rms_B_bonded: 2.34 restraints_weight: 0.5000 r_work: 0.2980 rms_B_bonded: 3.80 restraints_weight: 0.2500 r_work (final): 0.2980 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8102 moved from start: 0.3544 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= 0.136 Angle : 0.523 8.240 13371 Z= 0.268 Chirality : 0.040 0.127 1650 Planarity : 0.004 0.039 1698 Dihedral : 3.685 17.474 1893 Min Nonbonded Distance : 2.555 Molprobity Statistics. All-atom Clashscore : 3.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.52 % Favored : 98.48 % Rotamer: Outliers : 0.95 % Allowed : 13.33 % Favored : 85.71 % 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: 1.86 (0.23), residues: 1248 helix: 2.70 (0.21), residues: 597 sheet: 1.47 (0.41), residues: 123 loop : -0.61 (0.24), residues: 528 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.002 TRP B 886 HIS 0.003 0.001 HIS C1088 PHE 0.014 0.001 PHE C 817 TYR 0.018 0.002 TYR C1067 ARG 0.002 0.000 ARG C 995 Details of bonding type rmsd link_NAG-ASN : bond 0.00225 ( 18) link_NAG-ASN : angle 1.51356 ( 54) link_BETA1-4 : bond 0.00471 ( 9) link_BETA1-4 : angle 1.04691 ( 27) hydrogen bonds : bond 0.05232 ( 567) hydrogen bonds : angle 4.56734 ( 1647) SS BOND : bond 0.00302 ( 21) SS BOND : angle 1.23600 ( 42) covalent geometry : bond 0.00312 ( 9696) covalent geometry : angle 0.50949 (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 114 residues out of total 1113 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 106 time to evaluate : 1.067 Fit side-chains REVERT: A 725 GLU cc_start: 0.8509 (tt0) cc_final: 0.8142 (tt0) REVERT: A 1119 ASN cc_start: 0.8085 (m-40) cc_final: 0.7846 (m110) REVERT: B 731 MET cc_start: 0.8865 (ptt) cc_final: 0.8476 (ptp) REVERT: B 804 GLN cc_start: 0.8290 (mm110) cc_final: 0.7325 (mp10) REVERT: B 904 TYR cc_start: 0.7799 (m-10) cc_final: 0.7096 (m-10) REVERT: C 765 ARG cc_start: 0.7951 (mtp-110) cc_final: 0.7677 (mtp85) outliers start: 8 outliers final: 6 residues processed: 110 average time/residue: 1.4768 time to fit residues: 172.8349 Evaluate side-chains 110 residues out of total 1113 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 104 time to evaluate : 1.056 ------------------------------------------------------------------------------- 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 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: 2.9990 chunk 74 optimal weight: 2.9990 chunk 79 optimal weight: 0.6980 chunk 37 optimal weight: 2.9990 chunk 6 optimal weight: 2.9990 chunk 61 optimal weight: 0.0970 chunk 84 optimal weight: 0.9980 chunk 14 optimal weight: 0.5980 chunk 119 optimal weight: 0.9990 chunk 4 optimal weight: 2.9990 chunk 9 optimal weight: 0.0270 overall best weight: 0.4836 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 935 GLN 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 = 0.148127 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3282 r_free = 0.3282 target = 0.116459 restraints weight = 9642.062| |-----------------------------------------------------------------------------| r_work (start): 0.3260 rms_B_bonded: 1.73 r_work: 0.3131 rms_B_bonded: 2.31 restraints_weight: 0.5000 r_work: 0.2996 rms_B_bonded: 3.76 restraints_weight: 0.2500 r_work (final): 0.2996 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8082 moved from start: 0.3592 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 9744 Z= 0.117 Angle : 0.497 8.040 13371 Z= 0.255 Chirality : 0.040 0.125 1650 Planarity : 0.004 0.038 1698 Dihedral : 3.590 17.619 1893 Min Nonbonded Distance : 2.559 Molprobity Statistics. All-atom Clashscore : 3.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.60 % Favored : 98.40 % Rotamer: Outliers : 0.95 % Allowed : 13.45 % Favored : 85.60 % 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: 1.94 (0.23), residues: 1248 helix: 2.78 (0.21), residues: 597 sheet: 1.46 (0.41), residues: 123 loop : -0.57 (0.24), residues: 528 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 886 HIS 0.002 0.001 HIS C1088 PHE 0.016 0.001 PHE C 817 TYR 0.016 0.001 TYR C1067 ARG 0.001 0.000 ARG A 765 Details of bonding type rmsd link_NAG-ASN : bond 0.00244 ( 18) link_NAG-ASN : angle 1.41566 ( 54) link_BETA1-4 : bond 0.00450 ( 9) link_BETA1-4 : angle 1.01812 ( 27) hydrogen bonds : bond 0.04848 ( 567) hydrogen bonds : angle 4.50006 ( 1647) SS BOND : bond 0.00283 ( 21) SS BOND : angle 1.18874 ( 42) covalent geometry : bond 0.00258 ( 9696) covalent geometry : angle 0.48399 (13248) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7275.62 seconds wall clock time: 131 minutes 14.23 seconds (7874.23 seconds total)