Starting phenix.real_space_refine on Thu Jan 16 13:43:27 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8vq9_43435/01_2025/8vq9_43435.cif Found real_map, /net/cci-nas-00/data/ceres_data/8vq9_43435/01_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_43435/01_2025/8vq9_43435.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8vq9_43435/01_2025/8vq9_43435.map" model { file = "/net/cci-nas-00/data/ceres_data/8vq9_43435/01_2025/8vq9_43435.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8vq9_43435/01_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-5571/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: 5.86, per 1000 atoms: 0.62 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: 2.73 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: 1.01 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: 2.75 Time building geometry restraints manager: 3.12 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: 15.850 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.000 Check model and map are aligned: 0.000 Set scattering table: 0.000 Process input model: 22.750 Find NCS groups from input model: 0.410 Set up NCS constraints: 0.040 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:15.560 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 54.610 ------------------------------------------------------------------------------- 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 : 0.010 0.063 9696 Z= 0.693 Angle : 1.197 8.186 13248 Z= 0.810 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 *********************** 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 : 1.123 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: 1.3405 time to fit residues: 251.1903 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 : 1.143 ------------------------------------------------------------------------------- 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: 0.5980 chunk 114 optimal weight: 0.9980 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 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 = 0.3697 r_free = 0.3697 target = 0.151471 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3306 r_free = 0.3306 target = 0.118412 restraints weight = 9467.324| |-----------------------------------------------------------------------------| r_work (start): 0.3306 rms_B_bonded: 1.81 r_work: 0.3175 rms_B_bonded: 2.36 restraints_weight: 0.5000 r_work: 0.3041 rms_B_bonded: 3.84 restraints_weight: 0.2500 r_work (final): 0.3041 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8049 moved from start: 0.2105 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 9696 Z= 0.243 Angle : 0.595 8.654 13248 Z= 0.315 Chirality : 0.042 0.144 1650 Planarity : 0.005 0.040 1698 Dihedral : 4.109 15.120 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 : 2.50 % Allowed : 9.17 % 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: 1.67 (0.23), residues: 1248 helix: 2.55 (0.21), residues: 573 sheet: 1.19 (0.38), residues: 153 loop : -0.60 (0.25), residues: 522 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.003 TRP A 886 HIS 0.003 0.001 HIS C1101 PHE 0.022 0.002 PHE C 906 TYR 0.017 0.002 TYR C1067 ARG 0.004 0.001 ARG A 905 *********************** 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 142 residues out of total 1113 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 121 time to evaluate : 0.984 Fit side-chains REVERT: A 725 GLU cc_start: 0.8445 (tt0) cc_final: 0.8089 (tt0) REVERT: A 752 LEU cc_start: 0.8656 (mt) cc_final: 0.8332 (mt) REVERT: A 855 PHE cc_start: 0.7675 (m-80) cc_final: 0.7402 (m-80) REVERT: A 935 GLN cc_start: 0.7089 (mt0) cc_final: 0.6705 (mt0) REVERT: B 804 GLN cc_start: 0.8167 (OUTLIER) cc_final: 0.7885 (mt0) REVERT: B 904 TYR cc_start: 0.7989 (m-10) cc_final: 0.7080 (m-10) REVERT: C 725 GLU cc_start: 0.8470 (tt0) cc_final: 0.8118 (tt0) REVERT: C 752 LEU cc_start: 0.8573 (mt) cc_final: 0.8354 (mt) outliers start: 21 outliers final: 5 residues processed: 131 average time/residue: 1.2625 time to fit residues: 177.0194 Evaluate side-chains 115 residues out of total 1113 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 109 time to evaluate : 1.120 ------------------------------------------------------------------------------- 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 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: 0.2980 chunk 60 optimal weight: 0.6980 chunk 22 optimal weight: 4.9990 chunk 108 optimal weight: 1.9990 chunk 63 optimal weight: 3.9990 chunk 84 optimal weight: 0.8980 chunk 55 optimal weight: 0.1980 chunk 53 optimal weight: 0.9990 chunk 38 optimal weight: 1.9990 chunk 17 optimal weight: 1.9990 chunk 125 optimal weight: 2.9990 overall best weight: 0.6182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 = 0.3664 r_free = 0.3664 target = 0.148892 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3269 r_free = 0.3269 target = 0.115666 restraints weight = 9491.727| |-----------------------------------------------------------------------------| 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: 0.3009 rms_B_bonded: 3.68 restraints_weight: 0.2500 r_work (final): 0.3009 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8044 moved from start: 0.2677 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 9696 Z= 0.203 Angle : 0.509 4.959 13248 Z= 0.273 Chirality : 0.041 0.132 1650 Planarity : 0.004 0.045 1698 Dihedral : 3.531 15.140 1893 Min Nonbonded Distance : 2.622 Molprobity Statistics. All-atom Clashscore : 3.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.92 % Favored : 98.08 % Rotamer: Outliers : 1.90 % Allowed : 10.24 % Favored : 87.86 % 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: 1.87 (0.23), residues: 1248 helix: 2.71 (0.21), residues: 600 sheet: 1.11 (0.38), residues: 153 loop : -0.61 (0.25), residues: 495 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP A 886 HIS 0.002 0.001 HIS A1083 PHE 0.017 0.001 PHE B 906 TYR 0.019 0.002 TYR C1067 ARG 0.003 0.001 ARG B1014 *********************** 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 132 residues out of total 1113 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 116 time to evaluate : 1.171 Fit side-chains REVERT: A 725 GLU cc_start: 0.8500 (tt0) cc_final: 0.8097 (tt0) REVERT: A 731 MET cc_start: 0.8850 (ptt) cc_final: 0.8512 (ptm) REVERT: A 752 LEU cc_start: 0.8644 (mt) cc_final: 0.8355 (mt) REVERT: A 855 PHE cc_start: 0.7764 (m-80) cc_final: 0.7433 (m-80) REVERT: B 731 MET cc_start: 0.8762 (ptt) cc_final: 0.8406 (ptp) REVERT: B 904 TYR cc_start: 0.7899 (m-10) cc_final: 0.7240 (m-10) REVERT: C 725 GLU cc_start: 0.8526 (tt0) cc_final: 0.8202 (tt0) REVERT: C 904 TYR cc_start: 0.8049 (m-10) cc_final: 0.7787 (m-10) outliers start: 16 outliers final: 5 residues processed: 124 average time/residue: 1.3306 time to fit residues: 176.5225 Evaluate side-chains 112 residues out of total 1113 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 107 time to evaluate : 1.072 ------------------------------------------------------------------------------- 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: 0.0010 chunk 16 optimal weight: 0.2980 chunk 94 optimal weight: 0.6980 chunk 20 optimal weight: 1.9990 chunk 115 optimal weight: 1.9990 chunk 67 optimal weight: 2.9990 chunk 51 optimal weight: 0.3980 chunk 48 optimal weight: 2.9990 chunk 35 optimal weight: 0.0770 chunk 12 optimal weight: 0.7980 overall best weight: 0.2944 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 764 ASN B 955 ASN C 755 GLN C 764 ASN ** C 935 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3692 r_free = 0.3692 target = 0.151322 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3310 r_free = 0.3310 target = 0.118699 restraints weight = 9388.097| |-----------------------------------------------------------------------------| r_work (start): 0.3306 rms_B_bonded: 1.76 r_work: 0.3186 rms_B_bonded: 2.24 restraints_weight: 0.5000 r_work: 0.3056 rms_B_bonded: 3.64 restraints_weight: 0.2500 r_work (final): 0.3056 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7998 moved from start: 0.2942 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.024 9696 Z= 0.143 Angle : 0.465 9.532 13248 Z= 0.242 Chirality : 0.039 0.126 1650 Planarity : 0.004 0.044 1698 Dihedral : 3.274 14.006 1893 Min Nonbonded Distance : 2.618 Molprobity Statistics. All-atom Clashscore : 3.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.92 % Favored : 98.08 % Rotamer: Outliers : 1.31 % Allowed : 10.60 % Favored : 88.10 % 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: 2.04 (0.23), residues: 1248 helix: 2.95 (0.21), residues: 594 sheet: 1.09 (0.37), residues: 153 loop : -0.60 (0.25), residues: 501 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP C 886 HIS 0.001 0.001 HIS B1048 PHE 0.010 0.001 PHE C1121 TYR 0.016 0.001 TYR C1067 ARG 0.002 0.000 ARG C 995 *********************** 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 119 residues out of total 1113 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 108 time to evaluate : 1.119 Fit side-chains REVERT: A 725 GLU cc_start: 0.8456 (tt0) cc_final: 0.8058 (tt0) REVERT: A 731 MET cc_start: 0.8775 (ptt) cc_final: 0.8454 (ptm) REVERT: A 752 LEU cc_start: 0.8647 (mt) cc_final: 0.8360 (mt) REVERT: A 855 PHE cc_start: 0.7789 (m-80) cc_final: 0.7417 (m-80) REVERT: B 731 MET cc_start: 0.8714 (ptt) cc_final: 0.8409 (ptp) REVERT: B 804 GLN cc_start: 0.8123 (mm-40) cc_final: 0.7857 (mt0) REVERT: B 904 TYR cc_start: 0.7758 (m-10) cc_final: 0.7020 (m-10) REVERT: C 725 GLU cc_start: 0.8484 (tt0) cc_final: 0.8197 (tt0) REVERT: C 904 TYR cc_start: 0.7961 (m-10) cc_final: 0.7741 (m-10) outliers start: 11 outliers final: 3 residues processed: 113 average time/residue: 1.3996 time to fit residues: 168.7277 Evaluate side-chains 109 residues out of total 1113 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 106 time to evaluate : 0.993 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 999 CYS 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: 5.9990 chunk 107 optimal weight: 2.9990 chunk 31 optimal weight: 0.8980 chunk 21 optimal weight: 3.9990 chunk 111 optimal weight: 0.6980 chunk 112 optimal weight: 0.5980 chunk 65 optimal weight: 3.9990 chunk 66 optimal weight: 0.9990 chunk 30 optimal weight: 0.6980 chunk 8 optimal weight: 1.9990 overall best weight: 0.7782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 969 ASN B 955 ASN ** 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 = 0.3640 r_free = 0.3640 target = 0.146749 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3250 r_free = 0.3250 target = 0.114142 restraints weight = 9554.583| |-----------------------------------------------------------------------------| r_work (start): 0.3242 rms_B_bonded: 1.76 r_work: 0.3112 rms_B_bonded: 2.32 restraints_weight: 0.5000 r_work: 0.2977 rms_B_bonded: 3.76 restraints_weight: 0.2500 r_work (final): 0.2977 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8099 moved from start: 0.3065 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 9696 Z= 0.235 Angle : 0.523 7.062 13248 Z= 0.274 Chirality : 0.041 0.130 1650 Planarity : 0.004 0.040 1698 Dihedral : 3.624 15.815 1893 Min Nonbonded Distance : 2.618 Molprobity Statistics. All-atom Clashscore : 3.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.16 % Favored : 97.84 % Rotamer: Outliers : 1.67 % Allowed : 11.43 % Favored : 86.90 % 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 (0.23), residues: 1248 helix: 2.69 (0.21), residues: 600 sheet: 0.91 (0.37), residues: 153 loop : -0.71 (0.25), residues: 495 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP C 886 HIS 0.003 0.001 HIS C1064 PHE 0.014 0.002 PHE C 906 TYR 0.020 0.002 TYR B1067 ARG 0.003 0.000 ARG B1014 *********************** 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 126 residues out of total 1113 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 112 time to evaluate : 1.045 Fit side-chains REVERT: A 725 GLU cc_start: 0.8499 (tt0) cc_final: 0.8132 (tt0) REVERT: A 752 LEU cc_start: 0.8723 (mt) cc_final: 0.8442 (mt) REVERT: A 855 PHE cc_start: 0.7895 (m-80) cc_final: 0.7563 (m-80) REVERT: A 994 ASP cc_start: 0.6796 (m-30) cc_final: 0.6529 (p0) REVERT: B 804 GLN cc_start: 0.8245 (mm-40) cc_final: 0.7897 (mt0) REVERT: B 904 TYR cc_start: 0.7845 (m-10) cc_final: 0.7123 (m-10) REVERT: B 1119 ASN cc_start: 0.8001 (m-40) cc_final: 0.7651 (m110) REVERT: C 725 GLU cc_start: 0.8526 (tt0) cc_final: 0.8235 (tt0) REVERT: C 904 TYR cc_start: 0.8018 (m-10) cc_final: 0.7744 (m-10) REVERT: C 1119 ASN cc_start: 0.8041 (m-40) cc_final: 0.7807 (m110) outliers start: 14 outliers final: 5 residues processed: 117 average time/residue: 1.3137 time to fit residues: 164.6558 Evaluate side-chains 113 residues out of total 1113 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 108 time to evaluate : 0.964 ------------------------------------------------------------------------------- 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 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: 2.9990 chunk 26 optimal weight: 0.9980 chunk 29 optimal weight: 0.9990 chunk 80 optimal weight: 1.9990 chunk 119 optimal weight: 0.7980 chunk 56 optimal weight: 2.9990 chunk 95 optimal weight: 2.9990 chunk 74 optimal weight: 0.3980 chunk 20 optimal weight: 1.9990 chunk 44 optimal weight: 0.7980 chunk 33 optimal weight: 0.5980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 969 ASN B 955 ASN ** 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 = 0.3632 r_free = 0.3632 target = 0.146241 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3250 r_free = 0.3250 target = 0.114209 restraints weight = 9591.576| |-----------------------------------------------------------------------------| r_work (start): 0.3243 rms_B_bonded: 1.73 r_work: 0.3113 rms_B_bonded: 2.31 restraints_weight: 0.5000 r_work: 0.2977 rms_B_bonded: 3.74 restraints_weight: 0.2500 r_work (final): 0.2977 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8097 moved from start: 0.3212 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 9696 Z= 0.211 Angle : 0.500 7.315 13248 Z= 0.262 Chirality : 0.040 0.128 1650 Planarity : 0.004 0.038 1698 Dihedral : 3.622 15.443 1893 Min Nonbonded Distance : 2.617 Molprobity Statistics. All-atom Clashscore : 3.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.52 % Favored : 98.48 % 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: 1.73 (0.23), residues: 1248 helix: 2.65 (0.21), residues: 600 sheet: 0.91 (0.37), residues: 153 loop : -0.72 (0.25), residues: 495 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP C 886 HIS 0.003 0.001 HIS B1101 PHE 0.010 0.001 PHE C 906 TYR 0.018 0.002 TYR C1067 ARG 0.003 0.000 ARG B1014 *********************** 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 126 residues out of total 1113 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 113 time to evaluate : 1.076 Fit side-chains REVERT: A 725 GLU cc_start: 0.8506 (tt0) cc_final: 0.8136 (tt0) REVERT: A 752 LEU cc_start: 0.8661 (mt) cc_final: 0.8387 (mt) REVERT: A 855 PHE cc_start: 0.7916 (m-80) cc_final: 0.7594 (m-80) REVERT: A 1119 ASN cc_start: 0.7920 (m-40) cc_final: 0.7682 (m-40) REVERT: B 731 MET cc_start: 0.8848 (ptt) cc_final: 0.8473 (ptp) REVERT: B 904 TYR cc_start: 0.7807 (m-10) cc_final: 0.7086 (m-10) REVERT: B 1119 ASN cc_start: 0.8107 (m-40) cc_final: 0.7752 (m110) REVERT: C 725 GLU cc_start: 0.8543 (tt0) cc_final: 0.8246 (tt0) REVERT: C 904 TYR cc_start: 0.8051 (m-10) cc_final: 0.7768 (m-10) REVERT: C 1119 ASN cc_start: 0.8131 (m-40) cc_final: 0.7915 (m110) outliers start: 13 outliers final: 4 residues processed: 117 average time/residue: 1.3601 time to fit residues: 169.8000 Evaluate side-chains 110 residues out of total 1113 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 106 time to evaluate : 1.120 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 902 MET Chi-restraints excluded: chain A residue 999 CYS Chi-restraints excluded: chain B residue 999 CYS 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: 0.9990 chunk 0 optimal weight: 2.9990 chunk 94 optimal weight: 0.8980 chunk 98 optimal weight: 0.2980 chunk 17 optimal weight: 2.9990 chunk 75 optimal weight: 0.6980 chunk 72 optimal weight: 2.9990 chunk 15 optimal weight: 2.9990 chunk 59 optimal weight: 0.6980 chunk 117 optimal weight: 0.9980 overall best weight: 0.7180 ------------------------------------------------------------------------------- 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 = 0.145912 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3239 r_free = 0.3239 target = 0.113480 restraints weight = 9707.772| |-----------------------------------------------------------------------------| r_work (start): 0.3255 rms_B_bonded: 1.76 r_work: 0.3128 rms_B_bonded: 2.31 restraints_weight: 0.5000 r_work: 0.2993 rms_B_bonded: 3.76 restraints_weight: 0.2500 r_work (final): 0.2993 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8099 moved from start: 0.3330 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 9696 Z= 0.217 Angle : 0.512 10.235 13248 Z= 0.265 Chirality : 0.041 0.127 1650 Planarity : 0.004 0.039 1698 Dihedral : 3.684 15.742 1893 Min Nonbonded Distance : 2.627 Molprobity Statistics. All-atom Clashscore : 3.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.00 % Favored : 98.00 % 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: 1.76 (0.23), residues: 1248 helix: 2.68 (0.21), residues: 600 sheet: 0.93 (0.37), residues: 153 loop : -0.71 (0.25), residues: 495 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP C 886 HIS 0.003 0.001 HIS B1101 PHE 0.010 0.001 PHE B1121 TYR 0.018 0.002 TYR C1067 ARG 0.003 0.000 ARG B1014 *********************** 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 : 0.942 Fit side-chains REVERT: A 725 GLU cc_start: 0.8505 (tt0) cc_final: 0.8129 (tt0) REVERT: A 752 LEU cc_start: 0.8660 (mt) cc_final: 0.8379 (mt) REVERT: A 855 PHE cc_start: 0.7957 (m-80) cc_final: 0.7673 (m-80) REVERT: A 1119 ASN cc_start: 0.8001 (m-40) cc_final: 0.7732 (m-40) REVERT: B 731 MET cc_start: 0.8853 (ptt) cc_final: 0.8439 (ptp) REVERT: B 904 TYR cc_start: 0.7829 (m-10) cc_final: 0.7106 (m-10) REVERT: B 1119 ASN cc_start: 0.8127 (m-40) cc_final: 0.7791 (m110) REVERT: C 725 GLU cc_start: 0.8582 (tt0) cc_final: 0.8293 (tt0) REVERT: C 815 ARG cc_start: 0.8148 (OUTLIER) cc_final: 0.7527 (mtp180) REVERT: C 904 TYR cc_start: 0.8056 (m-10) cc_final: 0.7756 (m-10) REVERT: C 1119 ASN cc_start: 0.8126 (m-40) cc_final: 0.7894 (m110) outliers start: 17 outliers final: 5 residues processed: 112 average time/residue: 1.2994 time to fit residues: 155.4991 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 : 0.978 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 85 optimal weight: 0.6980 chunk 24 optimal weight: 2.9990 chunk 105 optimal weight: 0.5980 chunk 44 optimal weight: 0.9980 chunk 45 optimal weight: 0.7980 chunk 68 optimal weight: 0.9980 chunk 109 optimal weight: 0.0870 chunk 37 optimal weight: 2.9990 chunk 98 optimal weight: 0.0670 chunk 79 optimal weight: 0.7980 chunk 103 optimal weight: 2.9990 overall best weight: 0.4496 ------------------------------------------------------------------------------- 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 = 0.3645 r_free = 0.3645 target = 0.147443 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3261 r_free = 0.3261 target = 0.115109 restraints weight = 9778.340| |-----------------------------------------------------------------------------| r_work (start): 0.3255 rms_B_bonded: 1.77 r_work: 0.3128 rms_B_bonded: 2.34 restraints_weight: 0.5000 r_work: 0.2993 rms_B_bonded: 3.79 restraints_weight: 0.2500 r_work (final): 0.2993 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8077 moved from start: 0.3428 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 9696 Z= 0.166 Angle : 0.480 8.844 13248 Z= 0.250 Chirality : 0.040 0.125 1650 Planarity : 0.004 0.037 1698 Dihedral : 3.532 15.029 1893 Min Nonbonded Distance : 2.588 Molprobity Statistics. All-atom Clashscore : 3.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.44 % Favored : 98.56 % Rotamer: Outliers : 1.31 % Allowed : 12.74 % Favored : 85.95 % 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: 1.90 (0.24), residues: 1248 helix: 2.78 (0.21), residues: 600 sheet: 0.99 (0.37), residues: 153 loop : -0.62 (0.26), residues: 495 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP C 886 HIS 0.002 0.001 HIS B1101 PHE 0.011 0.001 PHE C 817 TYR 0.016 0.001 TYR C1067 ARG 0.001 0.000 ARG B 815 *********************** 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 117 residues out of total 1113 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 106 time to evaluate : 0.988 Fit side-chains REVERT: A 725 GLU cc_start: 0.8493 (tt0) cc_final: 0.8119 (tt0) REVERT: A 731 MET cc_start: 0.8896 (ptt) cc_final: 0.8576 (ptp) REVERT: A 855 PHE cc_start: 0.7939 (m-80) cc_final: 0.7645 (m-80) REVERT: A 1119 ASN cc_start: 0.7898 (m-40) cc_final: 0.7686 (m-40) REVERT: B 731 MET cc_start: 0.8830 (ptt) cc_final: 0.8431 (ptp) REVERT: B 904 TYR cc_start: 0.7774 (m-10) cc_final: 0.7157 (m-10) REVERT: B 1119 ASN cc_start: 0.8107 (m-40) cc_final: 0.7770 (m110) REVERT: C 765 ARG cc_start: 0.7903 (mtp-110) cc_final: 0.7507 (mtp85) REVERT: C 904 TYR cc_start: 0.8117 (m-10) cc_final: 0.7754 (m-10) REVERT: C 1119 ASN cc_start: 0.8039 (m-40) cc_final: 0.7815 (m110) outliers start: 11 outliers final: 3 residues processed: 111 average time/residue: 1.3729 time to fit residues: 162.8721 Evaluate side-chains 109 residues out of total 1113 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 106 time to evaluate : 1.066 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 999 CYS Chi-restraints excluded: chain B residue 999 CYS 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: 0.8980 chunk 10 optimal weight: 0.0470 chunk 109 optimal weight: 5.9990 chunk 80 optimal weight: 2.9990 chunk 32 optimal weight: 0.9980 chunk 110 optimal weight: 1.9990 chunk 71 optimal weight: 0.5980 chunk 98 optimal weight: 0.0980 chunk 111 optimal weight: 1.9990 chunk 58 optimal weight: 1.9990 chunk 3 optimal weight: 0.9990 overall best weight: 0.5278 ------------------------------------------------------------------------------- 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 = 0.147729 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3272 r_free = 0.3272 target = 0.115877 restraints weight = 9640.095| |-----------------------------------------------------------------------------| r_work (start): 0.3251 rms_B_bonded: 1.73 r_work: 0.3121 rms_B_bonded: 2.31 restraints_weight: 0.5000 r_work: 0.2987 rms_B_bonded: 3.76 restraints_weight: 0.2500 r_work (final): 0.2987 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8083 moved from start: 0.3484 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 9696 Z= 0.181 Angle : 0.487 9.007 13248 Z= 0.253 Chirality : 0.040 0.126 1650 Planarity : 0.004 0.038 1698 Dihedral : 3.554 15.611 1893 Min Nonbonded Distance : 2.577 Molprobity Statistics. All-atom Clashscore : 3.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.68 % Favored : 98.32 % Rotamer: Outliers : 1.31 % Allowed : 13.10 % 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: 1.90 (0.24), residues: 1248 helix: 2.79 (0.21), residues: 600 sheet: 1.01 (0.38), residues: 153 loop : -0.63 (0.25), residues: 495 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP C 886 HIS 0.002 0.001 HIS C1088 PHE 0.012 0.001 PHE C 817 TYR 0.017 0.001 TYR C1067 ARG 0.001 0.000 ARG B 815 *********************** 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 122 residues out of total 1113 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 111 time to evaluate : 0.996 Fit side-chains REVERT: A 725 GLU cc_start: 0.8484 (tt0) cc_final: 0.8118 (tt0) REVERT: A 855 PHE cc_start: 0.7962 (m-80) cc_final: 0.7657 (m-80) REVERT: A 1119 ASN cc_start: 0.7934 (m-40) cc_final: 0.7690 (m-40) REVERT: B 731 MET cc_start: 0.8845 (ptt) cc_final: 0.8432 (ptp) REVERT: B 904 TYR cc_start: 0.7791 (m-10) cc_final: 0.7078 (m-10) REVERT: B 1119 ASN cc_start: 0.8134 (m-40) cc_final: 0.7786 (m110) REVERT: C 765 ARG cc_start: 0.7910 (mtp-110) cc_final: 0.7456 (mtp85) REVERT: C 904 TYR cc_start: 0.8102 (m-10) cc_final: 0.7765 (m-10) REVERT: C 1119 ASN cc_start: 0.8097 (m-40) cc_final: 0.7872 (m110) outliers start: 11 outliers final: 5 residues processed: 116 average time/residue: 1.3473 time to fit residues: 166.6473 Evaluate side-chains 114 residues out of total 1113 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 109 time to evaluate : 1.065 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 921 LYS Chi-restraints excluded: chain A residue 999 CYS 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: 0.2980 chunk 71 optimal weight: 0.5980 chunk 59 optimal weight: 1.9990 chunk 14 optimal weight: 0.7980 chunk 40 optimal weight: 0.7980 chunk 18 optimal weight: 0.4980 chunk 75 optimal weight: 0.6980 chunk 28 optimal weight: 0.9990 chunk 81 optimal weight: 0.0970 chunk 62 optimal weight: 1.9990 chunk 1 optimal weight: 0.7980 overall best weight: 0.4378 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 935 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 = 0.3671 r_free = 0.3671 target = 0.149342 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3294 r_free = 0.3294 target = 0.117305 restraints weight = 9722.393| |-----------------------------------------------------------------------------| r_work (start): 0.3268 rms_B_bonded: 1.76 r_work: 0.3139 rms_B_bonded: 2.34 restraints_weight: 0.5000 r_work: 0.3005 rms_B_bonded: 3.80 restraints_weight: 0.2500 r_work (final): 0.3005 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8069 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 : 0.002 0.030 9696 Z= 0.164 Angle : 0.475 8.741 13248 Z= 0.248 Chirality : 0.039 0.134 1650 Planarity : 0.004 0.038 1698 Dihedral : 3.484 16.036 1893 Min Nonbonded Distance : 2.609 Molprobity Statistics. All-atom Clashscore : 3.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.52 % Favored : 98.48 % Rotamer: Outliers : 0.60 % Allowed : 14.05 % Favored : 85.36 % 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: 1.95 (0.24), residues: 1248 helix: 2.80 (0.21), residues: 603 sheet: 1.01 (0.38), residues: 153 loop : -0.57 (0.26), residues: 492 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP B 886 HIS 0.002 0.001 HIS C1088 PHE 0.014 0.001 PHE C 817 TYR 0.016 0.001 TYR C1067 ARG 0.001 0.000 ARG B1014 ********************** 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 116 residues out of total 1113 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 111 time to evaluate : 0.988 Fit side-chains REVERT: A 725 GLU cc_start: 0.8503 (tt0) cc_final: 0.8140 (tt0) REVERT: A 731 MET cc_start: 0.8902 (ptt) cc_final: 0.8602 (ptp) REVERT: A 855 PHE cc_start: 0.7948 (m-80) cc_final: 0.7636 (m-80) REVERT: A 1119 ASN cc_start: 0.7874 (m-40) cc_final: 0.7635 (m-40) REVERT: B 731 MET cc_start: 0.8837 (ptt) cc_final: 0.8414 (ptp) REVERT: B 904 TYR cc_start: 0.7768 (m-10) cc_final: 0.7065 (m-10) REVERT: B 1119 ASN cc_start: 0.8071 (m-40) cc_final: 0.7732 (m110) REVERT: C 765 ARG cc_start: 0.7895 (mtp-110) cc_final: 0.7451 (mtp85) REVERT: C 904 TYR cc_start: 0.8092 (m-10) cc_final: 0.7759 (m-10) REVERT: C 1119 ASN cc_start: 0.8037 (m-40) cc_final: 0.7823 (m110) outliers start: 5 outliers final: 4 residues processed: 114 average time/residue: 1.4820 time to fit residues: 179.1191 Evaluate side-chains 113 residues out of total 1113 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 109 time to evaluate : 1.134 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 999 CYS 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: 0.8980 chunk 74 optimal weight: 2.9990 chunk 79 optimal weight: 0.7980 chunk 37 optimal weight: 2.9990 chunk 6 optimal weight: 2.9990 chunk 61 optimal weight: 0.9990 chunk 84 optimal weight: 0.9980 chunk 14 optimal weight: 2.9990 chunk 119 optimal weight: 0.6980 chunk 4 optimal weight: 0.7980 chunk 9 optimal weight: 0.2980 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 935 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 = 0.3650 r_free = 0.3650 target = 0.147568 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3274 r_free = 0.3274 target = 0.115786 restraints weight = 9626.774| |-----------------------------------------------------------------------------| r_work (start): 0.3263 rms_B_bonded: 1.73 r_work: 0.3134 rms_B_bonded: 2.30 restraints_weight: 0.5000 r_work: 0.3001 rms_B_bonded: 3.73 restraints_weight: 0.2500 r_work (final): 0.3001 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8094 moved from start: 0.3545 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 9696 Z= 0.211 Angle : 0.507 8.715 13248 Z= 0.264 Chirality : 0.040 0.126 1650 Planarity : 0.004 0.038 1698 Dihedral : 3.641 16.472 1893 Min Nonbonded Distance : 2.603 Molprobity Statistics. All-atom Clashscore : 3.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.68 % Favored : 98.32 % Rotamer: Outliers : 1.07 % Allowed : 13.45 % 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: 1.91 (0.23), residues: 1248 helix: 2.74 (0.21), residues: 600 sheet: 1.42 (0.41), residues: 123 loop : -0.58 (0.24), 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 0.015 0.001 PHE C 817 TYR 0.018 0.002 TYR C1067 ARG 0.002 0.000 ARG B1014 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6661.89 seconds wall clock time: 119 minutes 4.66 seconds (7144.66 seconds total)