Starting phenix.real_space_refine on Thu Sep 18 23:35:27 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/5aco_3121/09_2025/5aco_3121.cif Found real_map, /net/cci-nas-00/data/ceres_data/5aco_3121/09_2025/5aco_3121.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.36 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/5aco_3121/09_2025/5aco_3121.cif" } default_model = "/net/cci-nas-00/data/ceres_data/5aco_3121/09_2025/5aco_3121.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/5aco_3121/09_2025/5aco_3121.map" default_real_map = "/net/cci-nas-00/data/ceres_data/5aco_3121/09_2025/5aco_3121.map" } resolution = 4.36 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.005 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 120 5.16 5 C 13269 2.51 5 N 3390 2.21 5 O 4518 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 1 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 21297 Number of models: 1 Model: "" Number of chains: 69 Chain: "A" Number of atoms: 3453 Number of conformers: 1 Conformer: "" Number of residues, atoms: 438, 3453 Classifications: {'peptide': 438} Link IDs: {'CIS': 2, 'PCIS': 1, 'PTRANS': 21, 'TRANS': 413} Chain breaks: 4 Chain: "B" Number of atoms: 1051 Number of conformers: 1 Conformer: "" Number of residues, atoms: 132, 1051 Classifications: {'peptide': 132} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 130} Chain breaks: 1 Chain: "C" Number of atoms: 3453 Number of conformers: 1 Conformer: "" Number of residues, atoms: 438, 3453 Classifications: {'peptide': 438} Link IDs: {'CIS': 2, 'PCIS': 1, 'PTRANS': 21, 'TRANS': 413} Chain breaks: 4 Chain: "D" Number of atoms: 3453 Number of conformers: 1 Conformer: "" Number of residues, atoms: 438, 3453 Classifications: {'peptide': 438} Link IDs: {'CIS': 2, 'PCIS': 1, 'PTRANS': 21, 'TRANS': 413} Chain breaks: 4 Chain: "E" Number of atoms: 1051 Number of conformers: 1 Conformer: "" Number of residues, atoms: 132, 1051 Classifications: {'peptide': 132} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 130} Chain breaks: 1 Chain: "F" Number of atoms: 1051 Number of conformers: 1 Conformer: "" Number of residues, atoms: 132, 1051 Classifications: {'peptide': 132} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 130} Chain breaks: 1 Chain: "G" Number of atoms: 1028 Number of conformers: 1 Conformer: "" Number of residues, atoms: 132, 1028 Classifications: {'peptide': 132} Link IDs: {'PTRANS': 7, 'TRANS': 124} Chain: "H" Number of atoms: 1028 Number of conformers: 1 Conformer: "" Number of residues, atoms: 132, 1028 Classifications: {'peptide': 132} Link IDs: {'PTRANS': 7, 'TRANS': 124} Chain: "I" Number of atoms: 1028 Number of conformers: 1 Conformer: "" Number of residues, atoms: 132, 1028 Classifications: {'peptide': 132} Link IDs: {'PTRANS': 7, 'TRANS': 124} Chain: "J" Number of atoms: 752 Number of conformers: 1 Conformer: "" Number of residues, atoms: 103, 752 Classifications: {'peptide': 103} Link IDs: {'CIS': 1, 'PTRANS': 6, 'TRANS': 95} Chain: "K" Number of atoms: 752 Number of conformers: 1 Conformer: "" Number of residues, atoms: 103, 752 Classifications: {'peptide': 103} Link IDs: {'CIS': 1, 'PTRANS': 6, 'TRANS': 95} Chain: "L" Number of atoms: 752 Number of conformers: 1 Conformer: "" Number of residues, atoms: 103, 752 Classifications: {'peptide': 103} Link IDs: {'CIS': 1, 'PTRANS': 6, 'TRANS': 95} Chain: "M" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} 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: "N" 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: "O" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} 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: "P" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} 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: "Q" 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: "R" 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: "S" Number of atoms: 83 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 83 Unusual residues: {'BMA': 1, 'MAN': 4, 'NAG': 2} Classifications: {'undetermined': 7} Link IDs: {None: 6} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 21 Unresolved non-hydrogen chiralities: 7 Chain: "T" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} 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: "U" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Chain: "V" Number of atoms: 83 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 83 Unusual residues: {'BMA': 1, 'MAN': 4, 'NAG': 2} Classifications: {'undetermined': 7} Link IDs: {None: 6} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 21 Unresolved non-hydrogen chiralities: 7 Chain: "W" Number of atoms: 116 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 116 Unusual residues: {'BMA': 1, 'MAN': 7, 'NAG': 2} Classifications: {'undetermined': 10} Link IDs: {None: 9} Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 20 Unresolved non-hydrogen dihedrals: 30 Unresolved non-hydrogen chiralities: 10 Chain: "X" 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: "Y" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} 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: "Z" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} 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: "a" 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: "b" 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: "c" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "d" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} 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: "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: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} 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: "g" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} 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: "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: 83 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 83 Unusual residues: {'BMA': 1, 'MAN': 4, 'NAG': 2} Classifications: {'undetermined': 7} Link IDs: {None: 6} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 21 Unresolved non-hydrogen chiralities: 7 Chain: "k" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} 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: "l" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Chain: "m" Number of atoms: 83 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 83 Unusual residues: {'BMA': 1, 'MAN': 4, 'NAG': 2} Classifications: {'undetermined': 7} Link IDs: {None: 6} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 21 Unresolved non-hydrogen chiralities: 7 Chain: "n" Number of atoms: 116 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 116 Unusual residues: {'BMA': 1, 'MAN': 7, 'NAG': 2} Classifications: {'undetermined': 10} Link IDs: {None: 9} Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 20 Unresolved non-hydrogen dihedrals: 30 Unresolved non-hydrogen chiralities: 10 Chain: "o" 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: "p" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} 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: "q" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} 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: "r" 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: "s" 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: "t" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} 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: "u" 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: "v" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} 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: "w" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} 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: "x" 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: "y" 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: "z" Number of atoms: 83 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 83 Unusual residues: {'BMA': 1, 'MAN': 4, 'NAG': 2} Classifications: {'undetermined': 7} Link IDs: {None: 6} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 21 Unresolved non-hydrogen chiralities: 7 Chain: "0" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} 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: "1" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Chain: "2" Number of atoms: 83 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 83 Unusual residues: {'BMA': 1, 'MAN': 4, 'NAG': 2} Classifications: {'undetermined': 7} Link IDs: {None: 6} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 21 Unresolved non-hydrogen chiralities: 7 Chain: "3" Number of atoms: 116 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 116 Unusual residues: {'BMA': 1, 'MAN': 7, 'NAG': 2} Classifications: {'undetermined': 10} Link IDs: {None: 9} Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 20 Unresolved non-hydrogen dihedrals: 30 Unresolved non-hydrogen chiralities: 10 Chain: "4" 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: "5" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} 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: "6" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} 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: "7" 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: "8" 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: "9" 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: "AA" 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: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "B" Number of atoms: 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: "C" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "D" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 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 Time building chain proxies: 5.12, per 1000 atoms: 0.24 Number of scatterers: 21297 At special positions: 0 Unit cell: (151.96, 154.58, 148.03, 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 120 16.00 O 4518 8.00 N 3390 7.00 C 13269 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=42, symmetry=0 Simple disulfide: pdb=" SG CYS A 54 " - pdb=" SG CYS A 74 " distance=2.10 Simple disulfide: pdb=" SG CYS A 119 " - pdb=" SG CYS A 205 " distance=2.11 Simple disulfide: pdb=" SG CYS A 126 " - pdb=" SG CYS A 196 " distance=2.11 Simple disulfide: pdb=" SG CYS A 131 " - pdb=" SG CYS A 157 " distance=2.03 Simple disulfide: pdb=" SG CYS A 218 " - pdb=" SG CYS A 247 " distance=2.04 Simple disulfide: pdb=" SG CYS A 228 " - pdb=" SG CYS A 239 " distance=1.62 Simple disulfide: pdb=" SG CYS A 296 " - pdb=" SG CYS A 331 " distance=2.03 Simple disulfide: pdb=" SG CYS A 378 " - pdb=" SG CYS A 445 " distance=2.11 Simple disulfide: pdb=" SG CYS A 385 " - pdb=" SG CYS A 418 " distance=2.09 Simple disulfide: pdb=" SG CYS A 501 " - pdb=" SG CYS B 605 " distance=2.22 Simple disulfide: pdb=" SG CYS B 598 " - pdb=" SG CYS B 604 " distance=2.03 Simple disulfide: pdb=" SG CYS C 54 " - pdb=" SG CYS C 74 " distance=2.10 Simple disulfide: pdb=" SG CYS C 119 " - pdb=" SG CYS C 205 " distance=2.11 Simple disulfide: pdb=" SG CYS C 126 " - pdb=" SG CYS C 196 " distance=2.11 Simple disulfide: pdb=" SG CYS C 131 " - pdb=" SG CYS C 157 " distance=2.03 Simple disulfide: pdb=" SG CYS C 218 " - pdb=" SG CYS C 247 " distance=2.04 Simple disulfide: pdb=" SG CYS C 228 " - pdb=" SG CYS C 239 " distance=1.62 Simple disulfide: pdb=" SG CYS C 296 " - pdb=" SG CYS C 331 " distance=2.03 Simple disulfide: pdb=" SG CYS C 378 " - pdb=" SG CYS C 445 " distance=2.11 Simple disulfide: pdb=" SG CYS C 385 " - pdb=" SG CYS C 418 " distance=2.09 Simple disulfide: pdb=" SG CYS C 501 " - pdb=" SG CYS E 605 " distance=2.22 Simple disulfide: pdb=" SG CYS D 54 " - pdb=" SG CYS D 74 " distance=2.10 Simple disulfide: pdb=" SG CYS D 119 " - pdb=" SG CYS D 205 " distance=2.11 Simple disulfide: pdb=" SG CYS D 126 " - pdb=" SG CYS D 196 " distance=2.11 Simple disulfide: pdb=" SG CYS D 131 " - pdb=" SG CYS D 157 " distance=2.03 Simple disulfide: pdb=" SG CYS D 218 " - pdb=" SG CYS D 247 " distance=2.04 Simple disulfide: pdb=" SG CYS D 228 " - pdb=" SG CYS D 239 " distance=1.62 Simple disulfide: pdb=" SG CYS D 296 " - pdb=" SG CYS D 331 " distance=2.03 Simple disulfide: pdb=" SG CYS D 378 " - pdb=" SG CYS D 445 " distance=2.11 Simple disulfide: pdb=" SG CYS D 385 " - pdb=" SG CYS D 418 " distance=2.09 Simple disulfide: pdb=" SG CYS D 501 " - pdb=" SG CYS F 605 " distance=2.22 Simple disulfide: pdb=" SG CYS E 598 " - pdb=" SG CYS E 604 " distance=2.03 Simple disulfide: pdb=" SG CYS F 598 " - pdb=" SG CYS F 604 " distance=2.03 Simple disulfide: pdb=" SG CYS G 22 " - pdb=" SG CYS G 92 " distance=2.03 Simple disulfide: pdb=" SG CYS G 32 " - pdb=" SG CYS G 52B" distance=2.14 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 92 " distance=2.03 Simple disulfide: pdb=" SG CYS H 32 " - pdb=" SG CYS H 52B" distance=2.14 Simple disulfide: pdb=" SG CYS I 22 " - pdb=" SG CYS I 92 " distance=2.03 Simple disulfide: pdb=" SG CYS I 32 " - pdb=" SG CYS I 52B" distance=2.14 Simple disulfide: pdb=" SG CYS J 23 " - pdb=" SG CYS J 88 " distance=2.05 Simple disulfide: pdb=" SG CYS K 23 " - pdb=" SG CYS K 88 " distance=2.05 Simple disulfide: pdb=" SG CYS L 23 " - pdb=" SG CYS L 88 " distance=2.05 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 Atom "HETATM19960 O5 NAG l 1 .*. O " rejected from bonding due to valence issues. Atom "HETATM19187 O5 NAG U 1 .*. O " rejected from bonding due to valence issues. Atom "HETATM20705 O5 NAG 1 1 .*. O " rejected from bonding due to valence issues. Atom "HETATM20527 O5 NAG x 1 .*. O " rejected from bonding due to valence issues. Atom "HETATM19009 O5 NAG Q 1 .*. O " rejected from bonding due to valence issues. Atom "HETATM19782 O5 NAG h 1 .*. O " rejected from bonding due to valence issues. Atom "HETATM19810 O5 NAG i 1 .*. O " rejected from bonding due to valence issues. Atom "HETATM19037 O5 NAG R 1 .*. O " rejected from bonding due to valence issues. Atom "HETATM20555 O5 NAG y 1 .*. O " rejected from bonding due to valence issues. Number of custom bonds: simple=0, symmetry=0 Links applied ALPHA1-2 " MAN 3 4 " - " MAN 3 5 " " MAN 3 5 " - " MAN 3 6 " " MAN 3 8 " - " MAN 3 9 " " MAN S 4 " - " MAN S 5 " " MAN W 4 " - " MAN W 5 " " MAN W 5 " - " MAN W 6 " " MAN W 8 " - " MAN W 9 " " MAN j 4 " - " MAN j 5 " " MAN n 4 " - " MAN n 5 " " MAN n 5 " - " MAN n 6 " " MAN n 8 " - " MAN n 9 " " MAN z 4 " - " MAN z 5 " ALPHA1-3 " BMA 1 3 " - " MAN 1 4 " " BMA 2 3 " - " MAN 2 7 " " MAN 2 4 " - " MAN 2 5 " " BMA 3 3 " - " MAN 3 4 " " MAN 3 7 " - " MAN 3 10 " " BMA S 3 " - " MAN S 4 " " MAN S 6 " - " MAN S 7 " " BMA U 3 " - " MAN U 4 " " BMA V 3 " - " MAN V 7 " " MAN V 4 " - " MAN V 5 " " BMA W 3 " - " MAN W 4 " " MAN W 7 " - " MAN W 10 " " BMA j 3 " - " MAN j 4 " " MAN j 6 " - " MAN j 7 " " BMA l 3 " - " MAN l 4 " " BMA m 3 " - " MAN m 7 " " MAN m 4 " - " MAN m 5 " " BMA n 3 " - " MAN n 4 " " MAN n 7 " - " MAN n 10 " " BMA z 3 " - " MAN z 4 " " MAN z 6 " - " MAN z 7 " ALPHA1-6 " BMA 1 3 " - " MAN 1 5 " " BMA 2 3 " - " MAN 2 4 " " MAN 2 4 " - " MAN 2 6 " " BMA 3 3 " - " MAN 3 7 " " MAN 3 7 " - " MAN 3 8 " " BMA S 3 " - " MAN S 6 " " BMA U 3 " - " MAN U 5 " " BMA V 3 " - " MAN V 4 " " MAN V 4 " - " MAN V 6 " " BMA W 3 " - " MAN W 7 " " MAN W 7 " - " MAN W 8 " " BMA j 3 " - " MAN j 6 " " BMA l 3 " - " MAN l 5 " " BMA m 3 " - " MAN m 4 " " MAN m 4 " - " MAN m 6 " " BMA n 3 " - " MAN n 7 " " MAN n 7 " - " MAN n 8 " " BMA z 3 " - " MAN z 6 " BETA1-4 " NAG 0 1 " - " NAG 0 2 " " NAG 0 2 " - " BMA 0 3 " " NAG 1 1 " - " NAG 1 2 " " NAG 1 2 " - " BMA 1 3 " " NAG 2 1 " - " NAG 2 2 " " NAG 2 2 " - " BMA 2 3 " " NAG 3 1 " - " NAG 3 2 " " NAG 3 2 " - " BMA 3 3 " " NAG 4 1 " - " NAG 4 2 " " NAG 5 1 " - " NAG 5 2 " " NAG 5 2 " - " BMA 5 3 " " NAG 6 1 " - " NAG 6 2 " " NAG 6 2 " - " BMA 6 3 " " NAG 7 1 " - " NAG 7 2 " " NAG 8 1 " - " NAG 8 2 " " NAG 9 1 " - " NAG 9 2 " " NAG M 1 " - " NAG M 2 " " NAG M 2 " - " BMA M 3 " " NAG N 1 " - " NAG N 2 " " NAG O 1 " - " NAG O 2 " " NAG O 2 " - " BMA O 3 " " NAG P 1 " - " NAG P 2 " " NAG P 2 " - " BMA P 3 " " NAG Q 1 " - " NAG Q 2 " " NAG R 1 " - " NAG R 2 " " NAG S 1 " - " NAG S 2 " " NAG S 2 " - " BMA S 3 " " NAG T 1 " - " NAG T 2 " " NAG T 2 " - " BMA T 3 " " NAG U 1 " - " NAG U 2 " " NAG U 2 " - " BMA U 3 " " NAG V 1 " - " NAG V 2 " " NAG V 2 " - " BMA V 3 " " NAG W 1 " - " NAG W 2 " " NAG W 2 " - " BMA W 3 " " NAG X 1 " - " NAG X 2 " " NAG Y 1 " - " NAG Y 2 " " NAG Y 2 " - " BMA Y 3 " " NAG Z 1 " - " NAG Z 2 " " NAG Z 2 " - " BMA Z 3 " " NAG a 1 " - " NAG a 2 " " NAG b 1 " - " NAG b 2 " " NAG c 1 " - " NAG c 2 " " NAG d 1 " - " NAG d 2 " " NAG d 2 " - " BMA d 3 " " NAG e 1 " - " NAG e 2 " " NAG f 1 " - " NAG f 2 " " NAG f 2 " - " BMA f 3 " " NAG g 1 " - " NAG g 2 " " NAG g 2 " - " BMA g 3 " " NAG h 1 " - " NAG h 2 " " NAG i 1 " - " NAG i 2 " " NAG j 1 " - " NAG j 2 " " NAG j 2 " - " BMA j 3 " " NAG k 1 " - " NAG k 2 " " NAG k 2 " - " BMA k 3 " " NAG l 1 " - " NAG l 2 " " NAG l 2 " - " BMA l 3 " " NAG m 1 " - " NAG m 2 " " NAG m 2 " - " BMA m 3 " " NAG n 1 " - " NAG n 2 " " NAG n 2 " - " BMA n 3 " " NAG o 1 " - " NAG o 2 " " NAG p 1 " - " NAG p 2 " " NAG p 2 " - " BMA p 3 " " NAG q 1 " - " NAG q 2 " " NAG q 2 " - " BMA q 3 " " NAG r 1 " - " NAG r 2 " " NAG s 1 " - " NAG s 2 " " NAG t 1 " - " NAG t 2 " " NAG t 2 " - " BMA t 3 " " NAG u 1 " - " NAG u 2 " " NAG v 1 " - " NAG v 2 " " NAG v 2 " - " BMA v 3 " " NAG w 1 " - " NAG w 2 " " NAG w 2 " - " BMA w 3 " " NAG x 1 " - " NAG x 2 " " NAG y 1 " - " NAG y 2 " " NAG z 1 " - " NAG z 2 " " NAG z 2 " - " BMA z 3 " " NAGAA 1 " - " NAGAA 2 " NAG-ASN " NAG 0 1 " - " ASN D 276 " " NAG 1 1 " - " ASN D 295 " " NAG 2 1 " - " ASN D 301 " " NAG 3 1 " - " ASN D 332 " " NAG 4 1 " - " ASN D 355 " " NAG 5 1 " - " ASN D 363 " " NAG 6 1 " - " ASN D 386 " " NAG 7 1 " - " ASN D 392 " " NAG 8 1 " - " ASN D 448 " " NAG 9 1 " - " ASN E 611 " " NAG A1343 " - " ASN A 339 " " NAG B1618 " - " ASN B 618 " " NAG B1637 " - " ASN B 637 " " NAG C1343 " - " ASN C 339 " " NAG D1343 " - " ASN D 339 " " NAG E1618 " - " ASN E 618 " " NAG E1637 " - " ASN E 637 " " NAG F1618 " - " ASN F 618 " " NAG F1637 " - " ASN F 637 " " NAG M 1 " - " ASN A 88 " " NAG N 1 " - " ASN A 133 " " NAG O 1 " - " ASN A 156 " " NAG P 1 " - " ASN A 160 " " NAG Q 1 " - " ASN A 197 " " NAG R 1 " - " ASN A 234 " " NAG S 1 " - " ASN A 262 " " NAG T 1 " - " ASN A 276 " " NAG U 1 " - " ASN A 295 " " NAG V 1 " - " ASN A 301 " " NAG W 1 " - " ASN A 332 " " NAG X 1 " - " ASN A 355 " " NAG Y 1 " - " ASN A 363 " " NAG Z 1 " - " ASN A 386 " " NAG a 1 " - " ASN A 392 " " NAG b 1 " - " ASN A 448 " " NAG c 1 " - " ASN B 611 " " NAG d 1 " - " ASN C 88 " " NAG e 1 " - " ASN C 133 " " NAG f 1 " - " ASN C 156 " " NAG g 1 " - " ASN C 160 " " NAG h 1 " - " ASN C 197 " " NAG i 1 " - " ASN C 234 " " NAG j 1 " - " ASN C 262 " " NAG k 1 " - " ASN C 276 " " NAG l 1 " - " ASN C 295 " " NAG m 1 " - " ASN C 301 " " NAG n 1 " - " ASN C 332 " " NAG o 1 " - " ASN C 355 " " NAG p 1 " - " ASN C 363 " " NAG q 1 " - " ASN C 386 " " NAG r 1 " - " ASN C 392 " " NAG s 1 " - " ASN C 448 " " NAG t 1 " - " ASN D 88 " " NAG u 1 " - " ASN D 133 " " NAG v 1 " - " ASN D 156 " " NAG w 1 " - " ASN D 160 " " NAG x 1 " - " ASN D 197 " " NAG y 1 " - " ASN D 234 " " NAG z 1 " - " ASN D 262 " " NAGAA 1 " - " ASN F 611 " Time building additional restraints: 2.93 Conformation dependent library (CDL) restraints added in 638.1 milliseconds Enol-peptide restraints added in 476.8 nanoseconds 4722 Ramachandran restraints generated. 2361 Oldfield, 0 Emsley, 2361 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4476 Finding SS restraints... Secondary structure from input PDB file: 57 helices and 63 sheets defined 20.2% alpha, 41.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.68 Creating SS restraints... Processing helix chain 'A' and resid 99 through 115 Processing helix chain 'A' and resid 122 through 126 Processing helix chain 'A' and resid 195 through 198 Processing helix chain 'A' and resid 335 through 351 removed outlier: 3.679A pdb=" N GLN A 348 " --> pdb=" O LYS A 344 " (cutoff:3.500A) Processing helix chain 'A' and resid 368 through 373 Processing helix chain 'A' and resid 387 through 390 Processing helix chain 'A' and resid 425 through 429 removed outlier: 4.272A pdb=" N GLN A 428 " --> pdb=" O ASN A 425 " (cutoff:3.500A) Processing helix chain 'A' and resid 475 through 484 removed outlier: 3.904A pdb=" N GLU A 482 " --> pdb=" O ASN A 478 " (cutoff:3.500A) Processing helix chain 'B' and resid 529 through 534 Processing helix chain 'B' and resid 536 through 546 removed outlier: 4.059A pdb=" N GLN B 540 " --> pdb=" O THR B 536 " (cutoff:3.500A) removed outlier: 4.620A pdb=" N ASN B 543 " --> pdb=" O VAL B 539 " (cutoff:3.500A) removed outlier: 4.215A pdb=" N LEU B 545 " --> pdb=" O ALA B 541 " (cutoff:3.500A) Processing helix chain 'B' and resid 573 through 596 removed outlier: 4.140A pdb=" N ASP B 589 " --> pdb=" O ARG B 585 " (cutoff:3.500A) removed outlier: 4.084A pdb=" N LEU B 592 " --> pdb=" O ARG B 588 " (cutoff:3.500A) Processing helix chain 'B' and resid 618 through 623 Processing helix chain 'B' and resid 627 through 636 removed outlier: 3.726A pdb=" N GLU B 634 " --> pdb=" O GLN B 630 " (cutoff:3.500A) Processing helix chain 'B' and resid 638 through 648 removed outlier: 3.978A pdb=" N LEU B 645 " --> pdb=" O ILE B 641 " (cutoff:3.500A) Processing helix chain 'B' and resid 648 through 654 Processing helix chain 'B' and resid 656 through 662 Processing helix chain 'C' and resid 99 through 115 Processing helix chain 'C' and resid 122 through 126 Processing helix chain 'C' and resid 195 through 198 Processing helix chain 'C' and resid 335 through 351 removed outlier: 3.679A pdb=" N GLN C 348 " --> pdb=" O LYS C 344 " (cutoff:3.500A) Processing helix chain 'C' and resid 368 through 373 Processing helix chain 'C' and resid 387 through 390 Processing helix chain 'C' and resid 425 through 429 removed outlier: 4.272A pdb=" N GLN C 428 " --> pdb=" O ASN C 425 " (cutoff:3.500A) Processing helix chain 'C' and resid 475 through 484 removed outlier: 3.905A pdb=" N GLU C 482 " --> pdb=" O ASN C 478 " (cutoff:3.500A) Processing helix chain 'D' and resid 99 through 115 Processing helix chain 'D' and resid 122 through 126 Processing helix chain 'D' and resid 195 through 198 Processing helix chain 'D' and resid 335 through 351 removed outlier: 3.678A pdb=" N GLN D 348 " --> pdb=" O LYS D 344 " (cutoff:3.500A) Processing helix chain 'D' and resid 368 through 373 Processing helix chain 'D' and resid 387 through 390 Processing helix chain 'D' and resid 425 through 429 removed outlier: 4.272A pdb=" N GLN D 428 " --> pdb=" O ASN D 425 " (cutoff:3.500A) Processing helix chain 'D' and resid 475 through 484 removed outlier: 3.905A pdb=" N GLU D 482 " --> pdb=" O ASN D 478 " (cutoff:3.500A) Processing helix chain 'E' and resid 529 through 534 Processing helix chain 'E' and resid 536 through 546 removed outlier: 4.059A pdb=" N GLN E 540 " --> pdb=" O THR E 536 " (cutoff:3.500A) removed outlier: 4.619A pdb=" N ASN E 543 " --> pdb=" O VAL E 539 " (cutoff:3.500A) removed outlier: 4.215A pdb=" N LEU E 545 " --> pdb=" O ALA E 541 " (cutoff:3.500A) Processing helix chain 'E' and resid 573 through 596 removed outlier: 4.141A pdb=" N ASP E 589 " --> pdb=" O ARG E 585 " (cutoff:3.500A) removed outlier: 4.084A pdb=" N LEU E 592 " --> pdb=" O ARG E 588 " (cutoff:3.500A) Processing helix chain 'E' and resid 618 through 623 Processing helix chain 'E' and resid 627 through 636 removed outlier: 3.727A pdb=" N GLU E 634 " --> pdb=" O GLN E 630 " (cutoff:3.500A) Processing helix chain 'E' and resid 638 through 648 removed outlier: 3.978A pdb=" N LEU E 645 " --> pdb=" O ILE E 641 " (cutoff:3.500A) Processing helix chain 'E' and resid 648 through 654 Processing helix chain 'E' and resid 656 through 662 Processing helix chain 'F' and resid 529 through 534 Processing helix chain 'F' and resid 536 through 546 removed outlier: 4.059A pdb=" N GLN F 540 " --> pdb=" O THR F 536 " (cutoff:3.500A) removed outlier: 4.620A pdb=" N ASN F 543 " --> pdb=" O VAL F 539 " (cutoff:3.500A) removed outlier: 4.215A pdb=" N LEU F 545 " --> pdb=" O ALA F 541 " (cutoff:3.500A) Processing helix chain 'F' and resid 573 through 596 removed outlier: 4.140A pdb=" N ASP F 589 " --> pdb=" O ARG F 585 " (cutoff:3.500A) removed outlier: 4.084A pdb=" N LEU F 592 " --> pdb=" O ARG F 588 " (cutoff:3.500A) Processing helix chain 'F' and resid 618 through 623 Processing helix chain 'F' and resid 627 through 636 removed outlier: 3.727A pdb=" N GLU F 634 " --> pdb=" O GLN F 630 " (cutoff:3.500A) Processing helix chain 'F' and resid 638 through 648 removed outlier: 3.979A pdb=" N LEU F 645 " --> pdb=" O ILE F 641 " (cutoff:3.500A) Processing helix chain 'F' and resid 648 through 654 Processing helix chain 'F' and resid 656 through 662 Processing helix chain 'G' and resid 63 through 65 No H-bonds generated for 'chain 'G' and resid 63 through 65' Processing helix chain 'G' and resid 83 through 87 Processing helix chain 'H' and resid 63 through 65 No H-bonds generated for 'chain 'H' and resid 63 through 65' Processing helix chain 'H' and resid 83 through 87 Processing helix chain 'I' and resid 63 through 65 No H-bonds generated for 'chain 'I' and resid 63 through 65' Processing helix chain 'I' and resid 83 through 87 Processing helix chain 'J' and resid 79 through 83 Processing helix chain 'K' and resid 79 through 83 Processing helix chain 'L' and resid 79 through 83 Processing sheet with id=AA, first strand: chain 'A' and resid 494 through 499 Processing sheet with id=AB, first strand: chain 'A' and resid 45 through 47 removed outlier: 4.044A pdb=" N ILE A 225 " --> pdb=" O VAL A 245 " (cutoff:3.500A) Processing sheet with id=AC, first strand: chain 'A' and resid 53 through 55 Processing sheet with id=AD, first strand: chain 'A' and resid 92 through 94 Processing sheet with id=AE, first strand: chain 'A' and resid 129 through 131 Processing sheet with id=AF, first strand: chain 'A' and resid 154 through 161 Processing sheet with id=AG, first strand: chain 'A' and resid 201 through 203 Processing sheet with id=AH, first strand: chain 'A' and resid 259 through 261 removed outlier: 6.503A pdb=" N LEU A 260 " --> pdb=" O THR A 450 " (cutoff:3.500A) Processing sheet with id=AI, first strand: chain 'A' and resid 271 through 273 Processing sheet with id=AJ, first strand: chain 'A' and resid 374 through 378 removed outlier: 4.413A pdb=" N PHE A 382 " --> pdb=" O LYS A 421 " (cutoff:3.500A) removed outlier: 4.402A pdb=" N SER A 334 " --> pdb=" O GLN A 293 " (cutoff:3.500A) removed outlier: 7.079A pdb=" N GLN A 293 " --> pdb=" O SER A 334 " (cutoff:3.500A) removed outlier: 10.596A pdb=" N VAL A 286 " --> pdb=" O THR A 455 " (cutoff:3.500A) removed outlier: 10.747A pdb=" N THR A 455 " --> pdb=" O VAL A 286 " (cutoff:3.500A) removed outlier: 12.279A pdb=" N PHE A 288 " --> pdb=" O ILE A 453 " (cutoff:3.500A) removed outlier: 12.163A pdb=" N ILE A 453 " --> pdb=" O PHE A 288 " (cutoff:3.500A) removed outlier: 10.770A pdb=" N THR A 290 " --> pdb=" O GLY A 451 " (cutoff:3.500A) removed outlier: 7.193A pdb=" N GLY A 451 " --> pdb=" O THR A 290 " (cutoff:3.500A) Processing sheet with id=AK, first strand: chain 'A' and resid 374 through 378 removed outlier: 4.413A pdb=" N PHE A 382 " --> pdb=" O LYS A 421 " (cutoff:3.500A) removed outlier: 4.402A pdb=" N SER A 334 " --> pdb=" O GLN A 293 " (cutoff:3.500A) removed outlier: 7.079A pdb=" N GLN A 293 " --> pdb=" O SER A 334 " (cutoff:3.500A) Processing sheet with id=AL, first strand: chain 'A' and resid 306 through 307 Processing sheet with id=AM, first strand: chain 'A' and resid 324 through 325 Processing sheet with id=CA, first strand: chain 'C' and resid 494 through 499 Processing sheet with id=CB, first strand: chain 'C' and resid 45 through 47 removed outlier: 4.045A pdb=" N ILE C 225 " --> pdb=" O VAL C 245 " (cutoff:3.500A) Processing sheet with id=CC, first strand: chain 'C' and resid 53 through 55 Processing sheet with id=CD, first strand: chain 'C' and resid 92 through 94 Processing sheet with id=CE, first strand: chain 'C' and resid 129 through 131 Processing sheet with id=CF, first strand: chain 'C' and resid 154 through 161 Processing sheet with id=CG, first strand: chain 'C' and resid 201 through 203 Processing sheet with id=CH, first strand: chain 'C' and resid 259 through 261 removed outlier: 6.503A pdb=" N LEU C 260 " --> pdb=" O THR C 450 " (cutoff:3.500A) Processing sheet with id=CI, first strand: chain 'C' and resid 271 through 273 removed outlier: 12.783A pdb=" N MET C 271 " --> pdb=" O ASN C 283 " (cutoff:3.500A) removed outlier: 6.155A pdb=" N LEU C 285 " --> pdb=" O MET C 271 " (cutoff:3.500A) removed outlier: 7.670A pdb=" N GLN C 287 " --> pdb=" O ARG C 273 " (cutoff:3.500A) Processing sheet with id=CJ, first strand: chain 'C' and resid 374 through 378 removed outlier: 4.414A pdb=" N PHE C 382 " --> pdb=" O LYS C 421 " (cutoff:3.500A) removed outlier: 4.402A pdb=" N SER C 334 " --> pdb=" O GLN C 293 " (cutoff:3.500A) removed outlier: 7.079A pdb=" N GLN C 293 " --> pdb=" O SER C 334 " (cutoff:3.500A) removed outlier: 10.596A pdb=" N VAL C 286 " --> pdb=" O THR C 455 " (cutoff:3.500A) removed outlier: 10.747A pdb=" N THR C 455 " --> pdb=" O VAL C 286 " (cutoff:3.500A) removed outlier: 12.279A pdb=" N PHE C 288 " --> pdb=" O ILE C 453 " (cutoff:3.500A) removed outlier: 12.163A pdb=" N ILE C 453 " --> pdb=" O PHE C 288 " (cutoff:3.500A) removed outlier: 10.769A pdb=" N THR C 290 " --> pdb=" O GLY C 451 " (cutoff:3.500A) removed outlier: 7.193A pdb=" N GLY C 451 " --> pdb=" O THR C 290 " (cutoff:3.500A) Processing sheet with id=CK, first strand: chain 'C' and resid 374 through 378 removed outlier: 4.414A pdb=" N PHE C 382 " --> pdb=" O LYS C 421 " (cutoff:3.500A) removed outlier: 4.402A pdb=" N SER C 334 " --> pdb=" O GLN C 293 " (cutoff:3.500A) removed outlier: 7.079A pdb=" N GLN C 293 " --> pdb=" O SER C 334 " (cutoff:3.500A) removed outlier: 6.202A pdb=" N MET C 271 " --> pdb=" O LEU C 285 " (cutoff:3.500A) removed outlier: 8.115A pdb=" N ARG C 273 " --> pdb=" O GLN C 287 " (cutoff:3.500A) removed outlier: 14.170A pdb=" N ASN C 289 " --> pdb=" O ARG C 273 " (cutoff:3.500A) Processing sheet with id=CL, first strand: chain 'C' and resid 306 through 307 Processing sheet with id=CM, first strand: chain 'C' and resid 324 through 325 Processing sheet with id=DA, first strand: chain 'D' and resid 494 through 499 Processing sheet with id=DB, first strand: chain 'D' and resid 45 through 47 removed outlier: 4.044A pdb=" N ILE D 225 " --> pdb=" O VAL D 245 " (cutoff:3.500A) Processing sheet with id=DC, first strand: chain 'D' and resid 53 through 55 Processing sheet with id=DD, first strand: chain 'D' and resid 92 through 94 Processing sheet with id=DE, first strand: chain 'D' and resid 129 through 131 Processing sheet with id=DF, first strand: chain 'D' and resid 154 through 161 Processing sheet with id=DG, first strand: chain 'D' and resid 201 through 203 Processing sheet with id=DH, first strand: chain 'D' and resid 259 through 261 removed outlier: 6.503A pdb=" N LEU D 260 " --> pdb=" O THR D 450 " (cutoff:3.500A) Processing sheet with id=DI, first strand: chain 'D' and resid 271 through 273 removed outlier: 12.784A pdb=" N MET D 271 " --> pdb=" O ASN D 283 " (cutoff:3.500A) removed outlier: 6.156A pdb=" N LEU D 285 " --> pdb=" O MET D 271 " (cutoff:3.500A) removed outlier: 7.670A pdb=" N GLN D 287 " --> pdb=" O ARG D 273 " (cutoff:3.500A) Processing sheet with id=DJ, first strand: chain 'D' and resid 374 through 378 removed outlier: 4.414A pdb=" N PHE D 382 " --> pdb=" O LYS D 421 " (cutoff:3.500A) removed outlier: 4.402A pdb=" N SER D 334 " --> pdb=" O GLN D 293 " (cutoff:3.500A) removed outlier: 7.079A pdb=" N GLN D 293 " --> pdb=" O SER D 334 " (cutoff:3.500A) removed outlier: 10.596A pdb=" N VAL D 286 " --> pdb=" O THR D 455 " (cutoff:3.500A) removed outlier: 10.747A pdb=" N THR D 455 " --> pdb=" O VAL D 286 " (cutoff:3.500A) removed outlier: 12.280A pdb=" N PHE D 288 " --> pdb=" O ILE D 453 " (cutoff:3.500A) removed outlier: 12.163A pdb=" N ILE D 453 " --> pdb=" O PHE D 288 " (cutoff:3.500A) removed outlier: 10.770A pdb=" N THR D 290 " --> pdb=" O GLY D 451 " (cutoff:3.500A) removed outlier: 7.193A pdb=" N GLY D 451 " --> pdb=" O THR D 290 " (cutoff:3.500A) Processing sheet with id=DK, first strand: chain 'D' and resid 374 through 378 removed outlier: 4.414A pdb=" N PHE D 382 " --> pdb=" O LYS D 421 " (cutoff:3.500A) removed outlier: 4.402A pdb=" N SER D 334 " --> pdb=" O GLN D 293 " (cutoff:3.500A) removed outlier: 7.079A pdb=" N GLN D 293 " --> pdb=" O SER D 334 " (cutoff:3.500A) removed outlier: 6.202A pdb=" N MET D 271 " --> pdb=" O LEU D 285 " (cutoff:3.500A) removed outlier: 8.115A pdb=" N ARG D 273 " --> pdb=" O GLN D 287 " (cutoff:3.500A) removed outlier: 14.170A pdb=" N ASN D 289 " --> pdb=" O ARG D 273 " (cutoff:3.500A) Processing sheet with id=DL, first strand: chain 'D' and resid 306 through 307 Processing sheet with id=DM, first strand: chain 'D' and resid 324 through 325 Processing sheet with id=GA, first strand: chain 'G' and resid 18 through 23 Processing sheet with id=GB, first strand: chain 'G' and resid 56 through 59 removed outlier: 6.081A pdb=" N TRP G 47 " --> pdb=" O ARG G 38 " (cutoff:3.500A) removed outlier: 6.121A pdb=" N ARG G 38 " --> pdb=" O TRP G 47 " (cutoff:3.500A) removed outlier: 6.672A pdb=" N CYS G 92 " --> pdb=" O LEU G 102 " (cutoff:3.500A) removed outlier: 6.732A pdb=" N LEU G 102 " --> pdb=" O CYS G 92 " (cutoff:3.500A) removed outlier: 6.014A pdb=" N ARG G 94 " --> pdb=" O VAL G 100K" (cutoff:3.500A) removed outlier: 4.326A pdb=" N VAL G 100K" --> pdb=" O ARG G 94 " (cutoff:3.500A) removed outlier: 6.653A pdb=" N GLY G 96 " --> pdb=" O ALA G 100I" (cutoff:3.500A) Processing sheet with id=GC, first strand: chain 'G' and resid 56 through 59 removed outlier: 6.081A pdb=" N TRP G 47 " --> pdb=" O ARG G 38 " (cutoff:3.500A) removed outlier: 6.121A pdb=" N ARG G 38 " --> pdb=" O TRP G 47 " (cutoff:3.500A) Processing sheet with id=GD, first strand: chain 'G' and resid 100G through 103 removed outlier: 5.833A pdb=" N GLU G 98 " --> pdb=" O PRO G 100H" (cutoff:3.500A) removed outlier: 6.545A pdb=" N ARG G 94 " --> pdb=" O ASP G 101 " (cutoff:3.500A) removed outlier: 4.816A pdb=" N TRP G 103 " --> pdb=" O CYS G 92 " (cutoff:3.500A) removed outlier: 6.915A pdb=" N CYS G 92 " --> pdb=" O TRP G 103 " (cutoff:3.500A) Processing sheet with id=HA, first strand: chain 'H' and resid 18 through 23 Processing sheet with id=HB, first strand: chain 'H' and resid 56 through 59 removed outlier: 6.081A pdb=" N TRP H 47 " --> pdb=" O ARG H 38 " (cutoff:3.500A) removed outlier: 6.121A pdb=" N ARG H 38 " --> pdb=" O TRP H 47 " (cutoff:3.500A) removed outlier: 6.671A pdb=" N CYS H 92 " --> pdb=" O LEU H 102 " (cutoff:3.500A) removed outlier: 6.731A pdb=" N LEU H 102 " --> pdb=" O CYS H 92 " (cutoff:3.500A) removed outlier: 6.014A pdb=" N ARG H 94 " --> pdb=" O VAL H 100K" (cutoff:3.500A) removed outlier: 4.326A pdb=" N VAL H 100K" --> pdb=" O ARG H 94 " (cutoff:3.500A) removed outlier: 6.653A pdb=" N GLY H 96 " --> pdb=" O ALA H 100I" (cutoff:3.500A) Processing sheet with id=HC, first strand: chain 'H' and resid 56 through 59 removed outlier: 6.081A pdb=" N TRP H 47 " --> pdb=" O ARG H 38 " (cutoff:3.500A) removed outlier: 6.121A pdb=" N ARG H 38 " --> pdb=" O TRP H 47 " (cutoff:3.500A) Processing sheet with id=HD, first strand: chain 'H' and resid 100G through 103 removed outlier: 5.832A pdb=" N GLU H 98 " --> pdb=" O PRO H 100H" (cutoff:3.500A) removed outlier: 6.546A pdb=" N ARG H 94 " --> pdb=" O ASP H 101 " (cutoff:3.500A) removed outlier: 4.815A pdb=" N TRP H 103 " --> pdb=" O CYS H 92 " (cutoff:3.500A) removed outlier: 6.915A pdb=" N CYS H 92 " --> pdb=" O TRP H 103 " (cutoff:3.500A) Processing sheet with id=IA, first strand: chain 'I' and resid 18 through 23 Processing sheet with id=IB, first strand: chain 'I' and resid 56 through 59 removed outlier: 6.080A pdb=" N TRP I 47 " --> pdb=" O ARG I 38 " (cutoff:3.500A) removed outlier: 6.121A pdb=" N ARG I 38 " --> pdb=" O TRP I 47 " (cutoff:3.500A) removed outlier: 6.671A pdb=" N CYS I 92 " --> pdb=" O LEU I 102 " (cutoff:3.500A) removed outlier: 6.732A pdb=" N LEU I 102 " --> pdb=" O CYS I 92 " (cutoff:3.500A) removed outlier: 6.015A pdb=" N ARG I 94 " --> pdb=" O VAL I 100K" (cutoff:3.500A) removed outlier: 4.325A pdb=" N VAL I 100K" --> pdb=" O ARG I 94 " (cutoff:3.500A) removed outlier: 6.652A pdb=" N GLY I 96 " --> pdb=" O ALA I 100I" (cutoff:3.500A) Processing sheet with id=IC, first strand: chain 'I' and resid 56 through 59 removed outlier: 6.080A pdb=" N TRP I 47 " --> pdb=" O ARG I 38 " (cutoff:3.500A) removed outlier: 6.121A pdb=" N ARG I 38 " --> pdb=" O TRP I 47 " (cutoff:3.500A) Processing sheet with id=ID, first strand: chain 'I' and resid 100G through 103 removed outlier: 5.833A pdb=" N GLU I 98 " --> pdb=" O PRO I 100H" (cutoff:3.500A) removed outlier: 6.547A pdb=" N ARG I 94 " --> pdb=" O ASP I 101 " (cutoff:3.500A) removed outlier: 4.815A pdb=" N TRP I 103 " --> pdb=" O CYS I 92 " (cutoff:3.500A) removed outlier: 6.915A pdb=" N CYS I 92 " --> pdb=" O TRP I 103 " (cutoff:3.500A) Processing sheet with id=JA, first strand: chain 'J' and resid 9 through 12 removed outlier: 6.169A pdb=" N ASP J 95A" --> pdb=" O SER J 90 " (cutoff:3.500A) removed outlier: 7.148A pdb=" N ILE J 97 " --> pdb=" O VAL J 92 " (cutoff:3.500A) Processing sheet with id=JB, first strand: chain 'J' and resid 9 through 12 removed outlier: 6.592A pdb=" N TRP J 35 " --> pdb=" O VAL J 47 " (cutoff:3.500A) Processing sheet with id=JC, first strand: chain 'J' and resid 95A through 98 removed outlier: 12.853A pdb=" N ASP J 95A" --> pdb=" O CYS J 88 " (cutoff:3.500A) removed outlier: 6.127A pdb=" N SER J 90 " --> pdb=" O ASP J 95A" (cutoff:3.500A) removed outlier: 7.263A pdb=" N VAL J 92 " --> pdb=" O ILE J 97 " (cutoff:3.500A) Processing sheet with id=JD, first strand: chain 'J' and resid 18 through 24 Processing sheet with id=KA, first strand: chain 'K' and resid 9 through 12 removed outlier: 6.169A pdb=" N ASP K 95A" --> pdb=" O SER K 90 " (cutoff:3.500A) removed outlier: 7.148A pdb=" N ILE K 97 " --> pdb=" O VAL K 92 " (cutoff:3.500A) Processing sheet with id=KB, first strand: chain 'K' and resid 9 through 12 removed outlier: 6.592A pdb=" N TRP K 35 " --> pdb=" O VAL K 47 " (cutoff:3.500A) Processing sheet with id=KC, first strand: chain 'K' and resid 95A through 98 removed outlier: 12.852A pdb=" N ASP K 95A" --> pdb=" O CYS K 88 " (cutoff:3.500A) removed outlier: 6.127A pdb=" N SER K 90 " --> pdb=" O ASP K 95A" (cutoff:3.500A) removed outlier: 7.263A pdb=" N VAL K 92 " --> pdb=" O ILE K 97 " (cutoff:3.500A) Processing sheet with id=KD, first strand: chain 'K' and resid 18 through 24 Processing sheet with id=LA, first strand: chain 'L' and resid 9 through 12 removed outlier: 6.169A pdb=" N ASP L 95A" --> pdb=" O SER L 90 " (cutoff:3.500A) removed outlier: 7.148A pdb=" N ILE L 97 " --> pdb=" O VAL L 92 " (cutoff:3.500A) Processing sheet with id=LB, first strand: chain 'L' and resid 9 through 12 removed outlier: 6.592A pdb=" N TRP L 35 " --> pdb=" O VAL L 47 " (cutoff:3.500A) Processing sheet with id=LC, first strand: chain 'L' and resid 95A through 98 removed outlier: 12.853A pdb=" N ASP L 95A" --> pdb=" O CYS L 88 " (cutoff:3.500A) removed outlier: 6.127A pdb=" N SER L 90 " --> pdb=" O ASP L 95A" (cutoff:3.500A) removed outlier: 7.264A pdb=" N VAL L 92 " --> pdb=" O ILE L 97 " (cutoff:3.500A) Processing sheet with id=LD, first strand: chain 'L' and resid 18 through 24 825 hydrogen bonds defined for protein. 2118 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 3.67 Time building geometry restraints manager: 3.55 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.31: 3384 1.31 - 1.44: 6086 1.44 - 1.56: 12064 1.56 - 1.69: 21 1.69 - 1.81: 156 Bond restraints: 21711 Sorted by residual: bond pdb=" C PRO L 8 " pdb=" N SER L 9 " ideal model delta sigma weight residual 1.331 1.584 -0.253 1.23e-02 6.61e+03 4.25e+02 bond pdb=" C PRO J 8 " pdb=" N SER J 9 " ideal model delta sigma weight residual 1.331 1.584 -0.253 1.23e-02 6.61e+03 4.24e+02 bond pdb=" C PRO K 8 " pdb=" N SER K 9 " ideal model delta sigma weight residual 1.331 1.584 -0.253 1.23e-02 6.61e+03 4.23e+02 bond pdb=" C GLN F 658 " pdb=" N ASP F 659 " ideal model delta sigma weight residual 1.335 1.613 -0.278 1.36e-02 5.41e+03 4.18e+02 bond pdb=" C GLN B 658 " pdb=" N ASP B 659 " ideal model delta sigma weight residual 1.335 1.613 -0.278 1.36e-02 5.41e+03 4.18e+02 ... (remaining 21706 not shown) Histogram of bond angle deviations from ideal: 0.00 - 7.69: 29287 7.69 - 15.37: 194 15.37 - 23.06: 48 23.06 - 30.74: 0 30.74 - 38.43: 3 Bond angle restraints: 29532 Sorted by residual: angle pdb=" N GLU E 648 " pdb=" CA GLU E 648 " pdb=" C GLU E 648 " ideal model delta sigma weight residual 110.80 149.23 -38.43 2.13e+00 2.20e-01 3.26e+02 angle pdb=" N GLU B 648 " pdb=" CA GLU B 648 " pdb=" C GLU B 648 " ideal model delta sigma weight residual 110.80 149.22 -38.42 2.13e+00 2.20e-01 3.25e+02 angle pdb=" N GLU F 648 " pdb=" CA GLU F 648 " pdb=" C GLU F 648 " ideal model delta sigma weight residual 110.80 149.17 -38.37 2.13e+00 2.20e-01 3.25e+02 angle pdb=" O LEU D 86 " pdb=" C LEU D 86 " pdb=" N GLU D 87 " ideal model delta sigma weight residual 122.87 102.49 20.38 1.23e+00 6.61e-01 2.74e+02 angle pdb=" O LEU A 86 " pdb=" C LEU A 86 " pdb=" N GLU A 87 " ideal model delta sigma weight residual 122.87 102.49 20.38 1.23e+00 6.61e-01 2.74e+02 ... (remaining 29527 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 21.93: 14559 21.93 - 43.86: 438 43.86 - 65.79: 102 65.79 - 87.72: 177 87.72 - 109.65: 126 Dihedral angle restraints: 15402 sinusoidal: 8469 harmonic: 6933 Sorted by residual: dihedral pdb=" CB CYS C 378 " pdb=" SG CYS C 378 " pdb=" SG CYS C 445 " pdb=" CB CYS C 445 " ideal model delta sinusoidal sigma weight residual -86.00 -162.25 76.25 1 1.00e+01 1.00e-02 7.32e+01 dihedral pdb=" CB CYS D 378 " pdb=" SG CYS D 378 " pdb=" SG CYS D 445 " pdb=" CB CYS D 445 " ideal model delta sinusoidal sigma weight residual -86.00 -162.24 76.24 1 1.00e+01 1.00e-02 7.32e+01 dihedral pdb=" CB CYS A 378 " pdb=" SG CYS A 378 " pdb=" SG CYS A 445 " pdb=" CB CYS A 445 " ideal model delta sinusoidal sigma weight residual -86.00 -162.24 76.24 1 1.00e+01 1.00e-02 7.32e+01 ... (remaining 15399 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.227: 3774 0.227 - 0.455: 129 0.455 - 0.682: 15 0.682 - 0.909: 3 0.909 - 1.137: 3 Chirality restraints: 3924 Sorted by residual: chirality pdb=" C1 MAN S 7 " pdb=" O3 MAN S 6 " pdb=" C2 MAN S 7 " pdb=" O5 MAN S 7 " both_signs ideal model delta sigma weight residual False 2.40 1.62 0.78 2.00e-02 2.50e+03 1.53e+03 chirality pdb=" C1 MAN j 7 " pdb=" O3 MAN j 6 " pdb=" C2 MAN j 7 " pdb=" O5 MAN j 7 " both_signs ideal model delta sigma weight residual False 2.40 1.62 0.78 2.00e-02 2.50e+03 1.52e+03 chirality pdb=" C1 MAN z 7 " pdb=" O3 MAN z 6 " pdb=" C2 MAN z 7 " pdb=" O5 MAN z 7 " both_signs ideal model delta sigma weight residual False 2.40 1.62 0.78 2.00e-02 2.50e+03 1.51e+03 ... (remaining 3921 not shown) Planarity restraints: 3510 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB ASN E 637 " -0.193 2.00e-02 2.50e+03 2.16e-01 5.85e+02 pdb=" CG ASN E 637 " 0.074 2.00e-02 2.50e+03 pdb=" OD1 ASN E 637 " 0.028 2.00e-02 2.50e+03 pdb=" ND2 ASN E 637 " 0.351 2.00e-02 2.50e+03 pdb=" C1 NAG E1637 " -0.259 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN B 637 " 0.193 2.00e-02 2.50e+03 2.16e-01 5.84e+02 pdb=" CG ASN B 637 " -0.074 2.00e-02 2.50e+03 pdb=" OD1 ASN B 637 " -0.028 2.00e-02 2.50e+03 pdb=" ND2 ASN B 637 " -0.351 2.00e-02 2.50e+03 pdb=" C1 NAG B1637 " 0.259 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN F 637 " -0.193 2.00e-02 2.50e+03 2.16e-01 5.84e+02 pdb=" CG ASN F 637 " 0.074 2.00e-02 2.50e+03 pdb=" OD1 ASN F 637 " 0.028 2.00e-02 2.50e+03 pdb=" ND2 ASN F 637 " 0.351 2.00e-02 2.50e+03 pdb=" C1 NAG F1637 " -0.259 2.00e-02 2.50e+03 ... (remaining 3507 not shown) Histogram of nonbonded interaction distances: 1.99 - 2.57: 209 2.57 - 3.15: 17972 3.15 - 3.73: 29769 3.73 - 4.32: 45133 4.32 - 4.90: 69912 Nonbonded interactions: 162995 Sorted by model distance: nonbonded pdb=" ND2 ASN D 279 " pdb=" O6 NAG 0 1 " model vdw 1.986 3.120 nonbonded pdb=" ND2 ASN A 279 " pdb=" O6 NAG T 1 " model vdw 1.987 3.120 nonbonded pdb=" ND2 ASN C 279 " pdb=" O6 NAG k 1 " model vdw 1.987 3.120 nonbonded pdb=" O ALA I 52C" pdb=" N2 NAG 2 1 " model vdw 2.062 3.120 nonbonded pdb=" O ALA H 52C" pdb=" N2 NAG V 1 " model vdw 2.063 3.120 ... (remaining 162990 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.05 Found NCS groups: ncs_group { reference = chain '0' selection = chain '5' selection = chain '6' selection = chain 'M' selection = chain 'O' selection = chain 'P' selection = chain 'T' selection = chain 'Y' selection = chain 'Z' selection = chain 'd' selection = chain 'f' selection = chain 'g' selection = chain 'k' selection = chain 'p' selection = chain 'q' selection = chain 't' selection = chain 'v' selection = chain 'w' } ncs_group { reference = chain '1' selection = chain 'U' selection = chain 'l' } ncs_group { reference = chain '2' selection = chain 'S' selection = chain 'V' selection = chain 'j' selection = chain 'm' selection = chain 'z' } ncs_group { reference = chain '3' selection = chain 'W' selection = chain 'n' } ncs_group { reference = chain '4' selection = chain '7' selection = chain '8' selection = chain '9' selection = chain 'AA' selection = chain 'N' selection = chain 'Q' selection = chain 'R' selection = chain 'X' selection = chain 'a' selection = chain 'b' selection = chain 'c' selection = chain 'e' selection = chain 'h' selection = chain 'i' selection = chain 'o' selection = chain 'r' selection = chain 's' selection = chain 'u' selection = chain 'x' selection = chain 'y' } ncs_group { reference = chain 'A' selection = chain 'C' selection = chain 'D' } ncs_group { reference = chain 'B' selection = chain 'E' selection = chain 'F' } ncs_group { reference = chain 'G' selection = chain 'H' selection = chain 'I' } ncs_group { reference = 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 group one per residue 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: 1.010 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: 0.260 Check model and map are aligned: 0.040 Set scattering table: 0.050 Process input model: 19.700 Find NCS groups from input model: 0.680 Set up NCS constraints: 0.100 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:1.280 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 23.130 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6813 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 : 0.016 0.413 21945 Z= 0.945 Angle : 2.296 38.429 30192 Z= 1.230 Chirality : 0.109 1.137 3924 Planarity : 0.015 0.198 3450 Dihedral : 17.674 109.654 10800 Min Nonbonded Distance : 1.986 Molprobity Statistics. All-atom Clashscore : 10.59 Ramachandran Plot: Outliers : 1.91 % Allowed : 9.15 % Favored : 88.95 % Rotamer: Outliers : 0.29 % Allowed : 0.71 % Favored : 99.00 % Cbeta Deviations : 0.13 % Peptide Plane: Cis-proline : 2.78 % Cis-general : 0.39 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -2.40 (0.15), residues: 2361 helix: -2.40 (0.20), residues: 417 sheet: -0.63 (0.20), residues: 639 loop : -1.83 (0.15), residues: 1305 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 360 TYR 0.020 0.001 TYR J 87 PHE 0.003 0.000 PHE D 382 TRP 0.040 0.001 TRP G 100J HIS 0.001 0.000 HIS H 59 Details of bonding type rmsd covalent geometry : bond 0.01232 (21711) covalent geometry : angle 1.98087 (29532) SS BOND : bond 0.13212 ( 42) SS BOND : angle 7.57399 ( 84) hydrogen bonds : bond 0.20828 ( 704) hydrogen bonds : angle 8.97476 ( 2118) link_ALPHA1-2 : bond 0.01962 ( 12) link_ALPHA1-2 : angle 4.77549 ( 36) link_ALPHA1-3 : bond 0.04462 ( 21) link_ALPHA1-3 : angle 7.38689 ( 63) link_ALPHA1-6 : bond 0.03748 ( 18) link_ALPHA1-6 : angle 5.29164 ( 54) link_BETA1-4 : bond 0.04228 ( 81) link_BETA1-4 : angle 6.03626 ( 243) link_NAG-ASN : bond 0.14324 ( 60) link_NAG-ASN : angle 11.49146 ( 180) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4722 Ramachandran restraints generated. 2361 Oldfield, 0 Emsley, 2361 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4722 Ramachandran restraints generated. 2361 Oldfield, 0 Emsley, 2361 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 539 residues out of total 2103 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 533 time to evaluate : 0.730 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 95 MET cc_start: 0.8071 (ptm) cc_final: 0.7847 (ptp) REVERT: A 195 ASN cc_start: 0.8943 (p0) cc_final: 0.8517 (t0) REVERT: A 377 ASN cc_start: 0.9037 (t0) cc_final: 0.8640 (t0) REVERT: A 423 ILE cc_start: 0.9434 (mt) cc_final: 0.9179 (mt) REVERT: B 546 SER cc_start: 0.6668 (t) cc_final: 0.6459 (t) REVERT: B 571 TRP cc_start: 0.7966 (m-10) cc_final: 0.7321 (m-10) REVERT: B 576 LEU cc_start: 0.7974 (tp) cc_final: 0.7685 (tp) REVERT: B 642 ILE cc_start: 0.8771 (mt) cc_final: 0.8521 (tp) REVERT: C 95 MET cc_start: 0.7875 (ptm) cc_final: 0.7557 (ptp) REVERT: C 100 MET cc_start: 0.7004 (mtp) cc_final: 0.6574 (ttt) REVERT: C 201 ILE cc_start: 0.9223 (tt) cc_final: 0.8846 (tt) REVERT: C 377 ASN cc_start: 0.8989 (t0) cc_final: 0.8660 (t0) REVERT: D 95 MET cc_start: 0.8040 (ptm) cc_final: 0.7635 (ptp) REVERT: D 201 ILE cc_start: 0.9262 (tt) cc_final: 0.9045 (tt) REVERT: D 377 ASN cc_start: 0.8977 (t0) cc_final: 0.8601 (t0) REVERT: D 423 ILE cc_start: 0.9430 (mt) cc_final: 0.9223 (mt) REVERT: E 571 TRP cc_start: 0.7542 (m-10) cc_final: 0.7183 (m-10) REVERT: E 576 LEU cc_start: 0.8151 (tp) cc_final: 0.7766 (tt) REVERT: E 642 ILE cc_start: 0.8835 (mt) cc_final: 0.8546 (tp) REVERT: F 571 TRP cc_start: 0.7883 (m-10) cc_final: 0.7280 (m-10) REVERT: F 576 LEU cc_start: 0.8357 (tp) cc_final: 0.8075 (tt) REVERT: G 24 VAL cc_start: 0.7870 (t) cc_final: 0.7576 (t) REVERT: J 46 LEU cc_start: 0.8387 (tp) cc_final: 0.8157 (tt) REVERT: J 86 TYR cc_start: 0.5311 (m-80) cc_final: 0.5001 (m-10) REVERT: K 46 LEU cc_start: 0.8407 (tp) cc_final: 0.8075 (tt) REVERT: K 91 LEU cc_start: 0.7821 (tp) cc_final: 0.7588 (tp) outliers start: 6 outliers final: 3 residues processed: 539 average time/residue: 0.1659 time to fit residues: 132.2005 Evaluate side-chains 267 residues out of total 2103 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 264 time to evaluate : 0.742 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 237 random chunks: chunk 216 optimal weight: 5.9990 chunk 98 optimal weight: 0.9990 chunk 194 optimal weight: 0.3980 chunk 227 optimal weight: 6.9990 chunk 107 optimal weight: 2.9990 chunk 10 optimal weight: 0.7980 chunk 66 optimal weight: 1.9990 chunk 130 optimal weight: 8.9990 chunk 124 optimal weight: 3.9990 chunk 103 optimal weight: 6.9990 chunk 235 optimal weight: 2.9990 overall best weight: 1.4386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 85 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 293 GLN A 300 ASN A 348 GLN ** B 540 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 607 ASN B 630 GLN C 293 GLN C 300 ASN C 348 GLN D 293 GLN D 300 ASN ** E 540 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 607 ASN ** F 540 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 591 GLN F 607 ASN G 3 GLN H 3 GLN I 3 GLN K 94 ASN Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3247 r_free = 0.3247 target = 0.058623 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2865 r_free = 0.2865 target = 0.045404 restraints weight = 104822.334| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.2909 r_free = 0.2909 target = 0.046879 restraints weight = 59217.904| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.2939 r_free = 0.2939 target = 0.047871 restraints weight = 41231.925| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.2958 r_free = 0.2958 target = 0.048524 restraints weight = 32758.254| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.2970 r_free = 0.2970 target = 0.048941 restraints weight = 28266.872| |-----------------------------------------------------------------------------| r_work (final): 0.2955 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8143 moved from start: 0.3002 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 21945 Z= 0.181 Angle : 1.020 14.453 30192 Z= 0.461 Chirality : 0.051 0.558 3924 Planarity : 0.005 0.049 3450 Dihedral : 15.905 92.218 6432 Min Nonbonded Distance : 2.426 Molprobity Statistics. All-atom Clashscore : 8.00 Ramachandran Plot: Outliers : 0.51 % Allowed : 6.23 % Favored : 93.27 % Rotamer: Outliers : 0.14 % Allowed : 1.62 % Favored : 98.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.78 % Cis-general : 0.39 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.52 (0.16), residues: 2361 helix: -0.97 (0.25), residues: 393 sheet: -0.44 (0.20), residues: 678 loop : -1.31 (0.16), residues: 1290 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG G 66 TYR 0.030 0.002 TYR I 58 PHE 0.015 0.001 PHE A 382 TRP 0.014 0.002 TRP E 571 HIS 0.005 0.001 HIS L 39 Details of bonding type rmsd covalent geometry : bond 0.00379 (21711) covalent geometry : angle 0.91526 (29532) SS BOND : bond 0.00309 ( 42) SS BOND : angle 1.26261 ( 84) hydrogen bonds : bond 0.05514 ( 704) hydrogen bonds : angle 6.58883 ( 2118) link_ALPHA1-2 : bond 0.00452 ( 12) link_ALPHA1-2 : angle 1.81240 ( 36) link_ALPHA1-3 : bond 0.01008 ( 21) link_ALPHA1-3 : angle 1.91483 ( 63) link_ALPHA1-6 : bond 0.00529 ( 18) link_ALPHA1-6 : angle 1.90324 ( 54) link_BETA1-4 : bond 0.00568 ( 81) link_BETA1-4 : angle 3.15966 ( 243) link_NAG-ASN : bond 0.00573 ( 60) link_NAG-ASN : angle 4.44719 ( 180) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4722 Ramachandran restraints generated. 2361 Oldfield, 0 Emsley, 2361 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4722 Ramachandran restraints generated. 2361 Oldfield, 0 Emsley, 2361 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 354 residues out of total 2103 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 351 time to evaluate : 0.782 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 161 MET cc_start: 0.9096 (tpp) cc_final: 0.8679 (tpp) REVERT: A 434 MET cc_start: 0.9111 (tmm) cc_final: 0.8651 (tmm) REVERT: B 543 ASN cc_start: 0.8678 (t0) cc_final: 0.8187 (t0) REVERT: B 544 LEU cc_start: 0.8040 (mt) cc_final: 0.7796 (mt) REVERT: B 584 GLU cc_start: 0.8462 (tm-30) cc_final: 0.8235 (tm-30) REVERT: B 631 TRP cc_start: 0.9487 (t-100) cc_final: 0.8601 (t-100) REVERT: C 180 ASP cc_start: 0.8665 (m-30) cc_final: 0.8426 (m-30) REVERT: C 271 MET cc_start: 0.8062 (mmp) cc_final: 0.7832 (mmm) REVERT: C 434 MET cc_start: 0.8954 (tmm) cc_final: 0.8097 (tmm) REVERT: D 434 MET cc_start: 0.9034 (tmm) cc_final: 0.8239 (tmm) REVERT: D 475 MET cc_start: 0.8630 (mmm) cc_final: 0.8381 (mmm) REVERT: E 530 MET cc_start: 0.8481 (mtt) cc_final: 0.8222 (mtt) REVERT: E 535 MET cc_start: 0.8493 (mmm) cc_final: 0.8274 (mpp) REVERT: E 543 ASN cc_start: 0.8588 (t0) cc_final: 0.8077 (t0) REVERT: E 544 LEU cc_start: 0.8191 (mt) cc_final: 0.7904 (mt) REVERT: E 631 TRP cc_start: 0.9483 (t-100) cc_final: 0.9131 (t-100) REVERT: E 642 ILE cc_start: 0.9711 (mt) cc_final: 0.9472 (tp) REVERT: F 530 MET cc_start: 0.8307 (mtt) cc_final: 0.7871 (mtt) REVERT: F 543 ASN cc_start: 0.8756 (t0) cc_final: 0.8206 (t0) REVERT: F 544 LEU cc_start: 0.8166 (mt) cc_final: 0.7905 (mt) REVERT: F 571 TRP cc_start: 0.8220 (m-10) cc_final: 0.7971 (m-90) REVERT: F 631 TRP cc_start: 0.9519 (t-100) cc_final: 0.9180 (t-100) REVERT: G 22 CYS cc_start: 0.1096 (t) cc_final: 0.0111 (t) REVERT: G 58 TYR cc_start: 0.9077 (m-80) cc_final: 0.8776 (m-80) REVERT: G 72 ASP cc_start: 0.8155 (t0) cc_final: 0.6002 (t0) REVERT: G 75 LYS cc_start: 0.9335 (mttt) cc_final: 0.9065 (mttp) REVERT: H 13 GLU cc_start: 0.7669 (pp20) cc_final: 0.6977 (pp20) REVERT: H 72 ASP cc_start: 0.8173 (t0) cc_final: 0.6255 (t0) REVERT: I 16 GLU cc_start: 0.8558 (pt0) cc_final: 0.7799 (pt0) REVERT: I 72 ASP cc_start: 0.8262 (t0) cc_final: 0.5902 (t0) REVERT: I 95 PHE cc_start: 0.8300 (m-80) cc_final: 0.7881 (m-80) REVERT: I 98 GLU cc_start: 0.8532 (tp30) cc_final: 0.7964 (tm-30) REVERT: J 24 THR cc_start: 0.8826 (m) cc_final: 0.8198 (m) REVERT: J 87 TYR cc_start: 0.8311 (m-80) cc_final: 0.8100 (m-80) REVERT: J 104 LEU cc_start: 0.9405 (tp) cc_final: 0.9154 (tp) REVERT: K 24 THR cc_start: 0.9120 (m) cc_final: 0.8779 (m) REVERT: K 104 LEU cc_start: 0.9393 (tp) cc_final: 0.9167 (tp) REVERT: L 24 THR cc_start: 0.8848 (m) cc_final: 0.8645 (m) REVERT: L 45 LYS cc_start: 0.9372 (mtmm) cc_final: 0.8963 (mtmm) REVERT: L 53 LYS cc_start: 0.8312 (mppt) cc_final: 0.7913 (mmtt) outliers start: 3 outliers final: 0 residues processed: 351 average time/residue: 0.1533 time to fit residues: 81.5449 Evaluate side-chains 246 residues out of total 2103 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 246 time to evaluate : 0.817 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 237 random chunks: chunk 191 optimal weight: 10.0000 chunk 7 optimal weight: 0.9990 chunk 128 optimal weight: 10.0000 chunk 172 optimal weight: 5.9990 chunk 122 optimal weight: 10.0000 chunk 0 optimal weight: 8.9990 chunk 91 optimal weight: 4.9990 chunk 193 optimal weight: 5.9990 chunk 72 optimal weight: 3.9990 chunk 52 optimal weight: 5.9990 chunk 41 optimal weight: 7.9990 overall best weight: 4.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 195 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 630 GLN C 136 ASN C 293 GLN C 422 GLN D 136 ASN ** D 195 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 422 GLN G 5 GLN ** L 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3143 r_free = 0.3143 target = 0.054814 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2736 r_free = 0.2736 target = 0.041366 restraints weight = 109374.006| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.2777 r_free = 0.2777 target = 0.042660 restraints weight = 64840.768| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.2804 r_free = 0.2804 target = 0.043514 restraints weight = 46894.519| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.2820 r_free = 0.2820 target = 0.044053 restraints weight = 38317.607| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 35)----------------| | r_work = 0.2831 r_free = 0.2831 target = 0.044396 restraints weight = 33881.731| |-----------------------------------------------------------------------------| r_work (final): 0.2811 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8340 moved from start: 0.4165 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.070 21945 Z= 0.288 Angle : 1.005 13.970 30192 Z= 0.459 Chirality : 0.051 0.400 3924 Planarity : 0.005 0.069 3450 Dihedral : 12.830 91.167 6432 Min Nonbonded Distance : 2.320 Molprobity Statistics. All-atom Clashscore : 11.49 Ramachandran Plot: Outliers : 0.51 % Allowed : 7.62 % Favored : 91.87 % Rotamer: Outliers : 0.10 % Allowed : 2.81 % Favored : 97.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.78 % Cis-general : 0.39 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.24 (0.17), residues: 2361 helix: -0.58 (0.25), residues: 402 sheet: 0.02 (0.20), residues: 693 loop : -1.40 (0.16), residues: 1266 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG B 588 TYR 0.027 0.003 TYR L 87 PHE 0.034 0.002 PHE C 53 TRP 0.027 0.003 TRP E 571 HIS 0.004 0.002 HIS A 330 Details of bonding type rmsd covalent geometry : bond 0.00620 (21711) covalent geometry : angle 0.93983 (29532) SS BOND : bond 0.00396 ( 42) SS BOND : angle 0.94577 ( 84) hydrogen bonds : bond 0.05294 ( 704) hydrogen bonds : angle 6.26427 ( 2118) link_ALPHA1-2 : bond 0.00426 ( 12) link_ALPHA1-2 : angle 1.89759 ( 36) link_ALPHA1-3 : bond 0.00517 ( 21) link_ALPHA1-3 : angle 2.08190 ( 63) link_ALPHA1-6 : bond 0.00480 ( 18) link_ALPHA1-6 : angle 2.08363 ( 54) link_BETA1-4 : bond 0.00508 ( 81) link_BETA1-4 : angle 2.74330 ( 243) link_NAG-ASN : bond 0.00940 ( 60) link_NAG-ASN : angle 3.20013 ( 180) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4722 Ramachandran restraints generated. 2361 Oldfield, 0 Emsley, 2361 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4722 Ramachandran restraints generated. 2361 Oldfield, 0 Emsley, 2361 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 280 residues out of total 2103 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 278 time to evaluate : 0.784 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 161 MET cc_start: 0.9154 (tpp) cc_final: 0.8910 (tpp) REVERT: A 434 MET cc_start: 0.9052 (tmm) cc_final: 0.8554 (tmm) REVERT: B 543 ASN cc_start: 0.8983 (t0) cc_final: 0.8504 (t0) REVERT: B 571 TRP cc_start: 0.7928 (m-10) cc_final: 0.7695 (m-10) REVERT: B 584 GLU cc_start: 0.8710 (tm-30) cc_final: 0.8387 (tm-30) REVERT: B 647 GLU cc_start: 0.8858 (tp30) cc_final: 0.8558 (tp30) REVERT: C 180 ASP cc_start: 0.8601 (m-30) cc_final: 0.8211 (m-30) REVERT: C 434 MET cc_start: 0.8835 (tmm) cc_final: 0.8096 (tmm) REVERT: D 109 ILE cc_start: 0.9457 (mt) cc_final: 0.9255 (tt) REVERT: E 543 ASN cc_start: 0.8845 (t0) cc_final: 0.8376 (t0) REVERT: E 650 GLN cc_start: 0.8163 (tt0) cc_final: 0.7471 (tt0) REVERT: E 651 ASN cc_start: 0.8392 (t0) cc_final: 0.7963 (t0) REVERT: F 543 ASN cc_start: 0.9094 (t0) cc_final: 0.8656 (t0) REVERT: F 584 GLU cc_start: 0.8706 (tm-30) cc_final: 0.8437 (tm-30) REVERT: F 602 LEU cc_start: 0.9197 (mm) cc_final: 0.8944 (tp) REVERT: F 631 TRP cc_start: 0.9624 (t-100) cc_final: 0.9326 (t-100) REVERT: F 651 ASN cc_start: 0.8539 (t0) cc_final: 0.8238 (t0) REVERT: G 22 CYS cc_start: 0.0298 (t) cc_final: -0.0189 (t) REVERT: G 33 ASN cc_start: 0.9422 (m-40) cc_final: 0.9208 (m-40) REVERT: G 72 ASP cc_start: 0.8108 (t0) cc_final: 0.6164 (t0) REVERT: G 75 LYS cc_start: 0.9366 (mttt) cc_final: 0.9064 (mttp) REVERT: G 98 GLU cc_start: 0.8739 (tp30) cc_final: 0.8527 (tp30) REVERT: H 13 GLU cc_start: 0.7857 (pp20) cc_final: 0.7267 (pp20) REVERT: H 58 TYR cc_start: 0.8737 (m-10) cc_final: 0.8517 (m-10) REVERT: H 72 ASP cc_start: 0.8362 (t0) cc_final: 0.7085 (t0) REVERT: H 75 LYS cc_start: 0.8986 (mtmm) cc_final: 0.8698 (mttp) REVERT: H 98 GLU cc_start: 0.8711 (tp30) cc_final: 0.8395 (tp30) REVERT: H 100 ASP cc_start: 0.9301 (m-30) cc_final: 0.9100 (m-30) REVERT: I 33 ASN cc_start: 0.9465 (m-40) cc_final: 0.8984 (p0) REVERT: I 98 GLU cc_start: 0.8706 (tp30) cc_final: 0.8349 (tp30) REVERT: J 33 VAL cc_start: 0.9122 (t) cc_final: 0.8669 (p) REVERT: J 87 TYR cc_start: 0.8422 (m-80) cc_final: 0.8196 (m-80) REVERT: K 24 THR cc_start: 0.9024 (m) cc_final: 0.8406 (m) REVERT: K 33 VAL cc_start: 0.9228 (t) cc_final: 0.8864 (p) REVERT: K 91 LEU cc_start: 0.9331 (tp) cc_final: 0.9033 (mt) REVERT: K 104 LEU cc_start: 0.9442 (tp) cc_final: 0.9236 (tp) REVERT: L 45 LYS cc_start: 0.9350 (mtmm) cc_final: 0.8728 (mmmt) REVERT: L 87 TYR cc_start: 0.8484 (m-80) cc_final: 0.8081 (m-80) outliers start: 2 outliers final: 1 residues processed: 278 average time/residue: 0.1616 time to fit residues: 68.0916 Evaluate side-chains 196 residues out of total 2103 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 195 time to evaluate : 0.532 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 237 random chunks: chunk 22 optimal weight: 7.9990 chunk 33 optimal weight: 0.9990 chunk 158 optimal weight: 0.0270 chunk 178 optimal weight: 5.9990 chunk 70 optimal weight: 3.9990 chunk 142 optimal weight: 0.9980 chunk 67 optimal weight: 3.9990 chunk 140 optimal weight: 4.9990 chunk 150 optimal weight: 10.0000 chunk 153 optimal weight: 0.8980 chunk 160 optimal weight: 0.7980 overall best weight: 0.7440 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 85 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 188 ASN B 630 GLN ** C 188 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 374 HIS ** F 540 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 5 GLN J 94 ASN L 94 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3196 r_free = 0.3196 target = 0.056837 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2798 r_free = 0.2798 target = 0.043321 restraints weight = 105795.884| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.2842 r_free = 0.2842 target = 0.044750 restraints weight = 60093.851| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.2870 r_free = 0.2870 target = 0.045687 restraints weight = 42209.249| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.2889 r_free = 0.2889 target = 0.046291 restraints weight = 33841.814| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.2900 r_free = 0.2900 target = 0.046660 restraints weight = 29503.519| |-----------------------------------------------------------------------------| r_work (final): 0.2885 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8243 moved from start: 0.4414 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 21945 Z= 0.131 Angle : 0.812 13.524 30192 Z= 0.374 Chirality : 0.048 0.360 3924 Planarity : 0.004 0.049 3450 Dihedral : 11.029 84.528 6432 Min Nonbonded Distance : 2.394 Molprobity Statistics. All-atom Clashscore : 7.50 Ramachandran Plot: Outliers : 0.51 % Allowed : 6.01 % Favored : 93.48 % Rotamer: Outliers : 0.05 % Allowed : 1.66 % Favored : 98.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.78 % Cis-general : 0.39 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.09 (0.17), residues: 2361 helix: -0.12 (0.26), residues: 396 sheet: 0.02 (0.19), residues: 729 loop : -1.40 (0.17), residues: 1236 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG E 617 TYR 0.014 0.001 TYR J 86 PHE 0.020 0.001 PHE D 53 TRP 0.044 0.002 TRP F 571 HIS 0.007 0.001 HIS D 374 Details of bonding type rmsd covalent geometry : bond 0.00270 (21711) covalent geometry : angle 0.75655 (29532) SS BOND : bond 0.00188 ( 42) SS BOND : angle 0.81840 ( 84) hydrogen bonds : bond 0.04092 ( 704) hydrogen bonds : angle 5.66144 ( 2118) link_ALPHA1-2 : bond 0.00675 ( 12) link_ALPHA1-2 : angle 1.41565 ( 36) link_ALPHA1-3 : bond 0.00894 ( 21) link_ALPHA1-3 : angle 1.60021 ( 63) link_ALPHA1-6 : bond 0.00670 ( 18) link_ALPHA1-6 : angle 1.88868 ( 54) link_BETA1-4 : bond 0.00423 ( 81) link_BETA1-4 : angle 2.43676 ( 243) link_NAG-ASN : bond 0.00259 ( 60) link_NAG-ASN : angle 2.45852 ( 180) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4722 Ramachandran restraints generated. 2361 Oldfield, 0 Emsley, 2361 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4722 Ramachandran restraints generated. 2361 Oldfield, 0 Emsley, 2361 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 288 residues out of total 2103 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 287 time to evaluate : 0.744 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 161 MET cc_start: 0.9045 (tpp) cc_final: 0.8663 (tpp) REVERT: A 180 ASP cc_start: 0.8685 (m-30) cc_final: 0.8475 (m-30) REVERT: A 271 MET cc_start: 0.8151 (mmm) cc_final: 0.7774 (mmm) REVERT: A 434 MET cc_start: 0.8988 (tmm) cc_final: 0.8459 (tmm) REVERT: B 543 ASN cc_start: 0.8933 (t0) cc_final: 0.8305 (t0) REVERT: B 584 GLU cc_start: 0.8715 (tm-30) cc_final: 0.8387 (tm-30) REVERT: B 622 ILE cc_start: 0.9046 (mt) cc_final: 0.8786 (mt) REVERT: C 180 ASP cc_start: 0.8633 (m-30) cc_final: 0.8342 (m-30) REVERT: C 271 MET cc_start: 0.8210 (mmp) cc_final: 0.7945 (mmm) REVERT: C 424 ILE cc_start: 0.9032 (pt) cc_final: 0.8829 (pt) REVERT: C 434 MET cc_start: 0.8707 (tmm) cc_final: 0.7930 (tmm) REVERT: D 180 ASP cc_start: 0.8889 (m-30) cc_final: 0.8681 (m-30) REVERT: E 543 ASN cc_start: 0.8915 (t0) cc_final: 0.8368 (t0) REVERT: E 584 GLU cc_start: 0.8721 (tm-30) cc_final: 0.8405 (tm-30) REVERT: E 588 ARG cc_start: 0.7898 (tpp-160) cc_final: 0.7663 (tpp-160) REVERT: E 622 ILE cc_start: 0.9142 (mt) cc_final: 0.8882 (mt) REVERT: E 650 GLN cc_start: 0.8142 (tt0) cc_final: 0.7558 (tt0) REVERT: E 651 ASN cc_start: 0.8161 (t0) cc_final: 0.7912 (t0) REVERT: F 543 ASN cc_start: 0.8960 (t0) cc_final: 0.8552 (t0) REVERT: F 584 GLU cc_start: 0.8711 (tm-30) cc_final: 0.8497 (tm-30) REVERT: F 602 LEU cc_start: 0.9113 (mm) cc_final: 0.8877 (tp) REVERT: F 631 TRP cc_start: 0.9443 (t-100) cc_final: 0.9178 (t-100) REVERT: G 22 CYS cc_start: 0.0645 (t) cc_final: 0.0380 (t) REVERT: G 72 ASP cc_start: 0.8206 (t0) cc_final: 0.6335 (t0) REVERT: G 75 LYS cc_start: 0.9388 (mttt) cc_final: 0.9052 (mttp) REVERT: G 98 GLU cc_start: 0.8650 (tp30) cc_final: 0.8239 (tp30) REVERT: H 58 TYR cc_start: 0.8969 (m-10) cc_final: 0.8499 (m-80) REVERT: H 72 ASP cc_start: 0.8420 (t0) cc_final: 0.7110 (t0) REVERT: H 75 LYS cc_start: 0.9185 (mtmm) cc_final: 0.8812 (mttp) REVERT: H 98 GLU cc_start: 0.8645 (tp30) cc_final: 0.8368 (tp30) REVERT: H 100 ASP cc_start: 0.9155 (m-30) cc_final: 0.8923 (m-30) REVERT: I 33 ASN cc_start: 0.9410 (m-40) cc_final: 0.8908 (p0) REVERT: I 58 TYR cc_start: 0.8797 (m-10) cc_final: 0.8558 (m-80) REVERT: I 95 PHE cc_start: 0.8367 (m-80) cc_final: 0.8106 (m-80) REVERT: I 98 GLU cc_start: 0.8607 (tp30) cc_final: 0.8402 (tp30) REVERT: J 33 VAL cc_start: 0.9144 (t) cc_final: 0.8717 (p) REVERT: J 87 TYR cc_start: 0.8457 (m-80) cc_final: 0.8181 (m-80) REVERT: J 91 LEU cc_start: 0.9113 (tp) cc_final: 0.8891 (mt) REVERT: K 24 THR cc_start: 0.9049 (m) cc_final: 0.8832 (p) REVERT: K 91 LEU cc_start: 0.9240 (tp) cc_final: 0.8932 (mt) REVERT: L 45 LYS cc_start: 0.9398 (mtmm) cc_final: 0.9100 (mtmm) outliers start: 1 outliers final: 0 residues processed: 287 average time/residue: 0.1558 time to fit residues: 68.1128 Evaluate side-chains 219 residues out of total 2103 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 219 time to evaluate : 0.822 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 237 random chunks: chunk 200 optimal weight: 9.9990 chunk 92 optimal weight: 0.8980 chunk 16 optimal weight: 10.0000 chunk 152 optimal weight: 5.9990 chunk 181 optimal weight: 8.9990 chunk 124 optimal weight: 0.0370 chunk 225 optimal weight: 8.9990 chunk 160 optimal weight: 0.9990 chunk 59 optimal weight: 0.0970 chunk 97 optimal weight: 4.9990 chunk 141 optimal weight: 7.9990 overall best weight: 1.4060 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 85 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 374 HIS B 630 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3184 r_free = 0.3184 target = 0.056357 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.2787 r_free = 0.2787 target = 0.042899 restraints weight = 105986.180| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 23)----------------| | r_work = 0.2829 r_free = 0.2829 target = 0.044275 restraints weight = 61010.963| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.2857 r_free = 0.2857 target = 0.045194 restraints weight = 43236.566| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.2875 r_free = 0.2875 target = 0.045785 restraints weight = 34819.136| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.2885 r_free = 0.2885 target = 0.046123 restraints weight = 30415.283| |-----------------------------------------------------------------------------| r_work (final): 0.2870 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8260 moved from start: 0.4721 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 21945 Z= 0.138 Angle : 0.767 13.218 30192 Z= 0.353 Chirality : 0.046 0.390 3924 Planarity : 0.004 0.034 3450 Dihedral : 10.044 81.874 6432 Min Nonbonded Distance : 2.391 Molprobity Statistics. All-atom Clashscore : 8.03 Ramachandran Plot: Outliers : 0.51 % Allowed : 6.78 % Favored : 92.71 % Rotamer: Outliers : 0.00 % Allowed : 1.52 % Favored : 98.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.78 % Cis-general : 0.39 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.96 (0.17), residues: 2361 helix: -0.00 (0.27), residues: 396 sheet: 0.11 (0.20), residues: 675 loop : -1.26 (0.17), residues: 1290 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 617 TYR 0.014 0.001 TYR D 217 PHE 0.014 0.001 PHE A 53 TRP 0.034 0.002 TRP F 571 HIS 0.003 0.001 HIS H 52A Details of bonding type rmsd covalent geometry : bond 0.00292 (21711) covalent geometry : angle 0.70906 (29532) SS BOND : bond 0.00301 ( 42) SS BOND : angle 0.73436 ( 84) hydrogen bonds : bond 0.03959 ( 704) hydrogen bonds : angle 5.48671 ( 2118) link_ALPHA1-2 : bond 0.00347 ( 12) link_ALPHA1-2 : angle 1.69814 ( 36) link_ALPHA1-3 : bond 0.00741 ( 21) link_ALPHA1-3 : angle 1.71888 ( 63) link_ALPHA1-6 : bond 0.00674 ( 18) link_ALPHA1-6 : angle 1.90725 ( 54) link_BETA1-4 : bond 0.00367 ( 81) link_BETA1-4 : angle 2.26909 ( 243) link_NAG-ASN : bond 0.00443 ( 60) link_NAG-ASN : angle 2.49659 ( 180) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4722 Ramachandran restraints generated. 2361 Oldfield, 0 Emsley, 2361 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4722 Ramachandran restraints generated. 2361 Oldfield, 0 Emsley, 2361 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 277 residues out of total 2103 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 277 time to evaluate : 0.811 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 161 MET cc_start: 0.9064 (tpp) cc_final: 0.8586 (tpp) REVERT: A 434 MET cc_start: 0.8964 (tmm) cc_final: 0.8443 (tmm) REVERT: B 543 ASN cc_start: 0.8939 (t0) cc_final: 0.8407 (t0) REVERT: B 638 TYR cc_start: 0.8224 (m-80) cc_final: 0.7749 (m-80) REVERT: B 648 GLU cc_start: 0.8296 (tp30) cc_final: 0.8069 (tp30) REVERT: C 180 ASP cc_start: 0.8624 (m-30) cc_final: 0.8311 (m-30) REVERT: C 424 ILE cc_start: 0.9064 (pt) cc_final: 0.8780 (pt) REVERT: C 434 MET cc_start: 0.8717 (tmm) cc_final: 0.7913 (tmm) REVERT: D 180 ASP cc_start: 0.8878 (m-30) cc_final: 0.8634 (m-30) REVERT: D 271 MET cc_start: 0.8214 (mmm) cc_final: 0.7998 (mmm) REVERT: D 475 MET cc_start: 0.8620 (mmm) cc_final: 0.8413 (mmm) REVERT: E 543 ASN cc_start: 0.8957 (t0) cc_final: 0.8390 (t0) REVERT: E 650 GLN cc_start: 0.8243 (tt0) cc_final: 0.7493 (tt0) REVERT: E 651 ASN cc_start: 0.8321 (t0) cc_final: 0.8057 (t0) REVERT: F 543 ASN cc_start: 0.9071 (t0) cc_final: 0.8578 (t0) REVERT: F 584 GLU cc_start: 0.8737 (tm-30) cc_final: 0.8454 (tm-30) REVERT: G 33 ASN cc_start: 0.9413 (m-40) cc_final: 0.8999 (p0) REVERT: G 72 ASP cc_start: 0.8234 (t0) cc_final: 0.5886 (t0) REVERT: G 75 LYS cc_start: 0.9392 (mttt) cc_final: 0.9035 (mttp) REVERT: G 98 GLU cc_start: 0.8746 (tp30) cc_final: 0.8495 (tp30) REVERT: H 58 TYR cc_start: 0.8966 (m-10) cc_final: 0.8653 (m-80) REVERT: H 72 ASP cc_start: 0.8402 (t0) cc_final: 0.7065 (t0) REVERT: H 75 LYS cc_start: 0.9054 (mtmm) cc_final: 0.8702 (mttp) REVERT: H 98 GLU cc_start: 0.8777 (tp30) cc_final: 0.8419 (tp30) REVERT: I 33 ASN cc_start: 0.9434 (m-40) cc_final: 0.8913 (p0) REVERT: I 58 TYR cc_start: 0.8875 (m-10) cc_final: 0.8675 (m-80) REVERT: I 98 GLU cc_start: 0.8739 (tp30) cc_final: 0.8472 (tp30) REVERT: J 33 VAL cc_start: 0.9159 (t) cc_final: 0.8696 (p) REVERT: J 87 TYR cc_start: 0.8472 (m-80) cc_final: 0.8201 (m-80) REVERT: J 91 LEU cc_start: 0.9079 (tp) cc_final: 0.8862 (mt) REVERT: K 33 VAL cc_start: 0.9189 (t) cc_final: 0.8812 (p) REVERT: K 104 LEU cc_start: 0.9357 (tp) cc_final: 0.9039 (tp) REVERT: L 45 LYS cc_start: 0.9396 (mtmm) cc_final: 0.9091 (mtmm) REVERT: L 104 LEU cc_start: 0.9091 (tp) cc_final: 0.8882 (tp) outliers start: 0 outliers final: 0 residues processed: 277 average time/residue: 0.1464 time to fit residues: 62.3097 Evaluate side-chains 201 residues out of total 2103 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 201 time to evaluate : 0.783 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 237 random chunks: chunk 102 optimal weight: 2.9990 chunk 113 optimal weight: 2.9990 chunk 27 optimal weight: 0.8980 chunk 108 optimal weight: 10.0000 chunk 139 optimal weight: 5.9990 chunk 49 optimal weight: 6.9990 chunk 52 optimal weight: 0.4980 chunk 121 optimal weight: 0.9980 chunk 17 optimal weight: 7.9990 chunk 145 optimal weight: 5.9990 chunk 111 optimal weight: 5.9990 overall best weight: 1.6784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 85 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 630 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3181 r_free = 0.3181 target = 0.056272 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2782 r_free = 0.2782 target = 0.042742 restraints weight = 106240.238| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.2825 r_free = 0.2825 target = 0.044149 restraints weight = 60820.858| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.2853 r_free = 0.2853 target = 0.045066 restraints weight = 43036.439| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.2871 r_free = 0.2871 target = 0.045657 restraints weight = 34725.700| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.2881 r_free = 0.2881 target = 0.045997 restraints weight = 30362.678| |-----------------------------------------------------------------------------| r_work (final): 0.2864 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8274 moved from start: 0.4948 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 21945 Z= 0.141 Angle : 0.754 12.901 30192 Z= 0.349 Chirality : 0.046 0.374 3924 Planarity : 0.003 0.032 3450 Dihedral : 9.567 78.913 6432 Min Nonbonded Distance : 2.393 Molprobity Statistics. All-atom Clashscore : 8.19 Ramachandran Plot: Outliers : 0.51 % Allowed : 5.84 % Favored : 93.65 % Rotamer: Outliers : 0.05 % Allowed : 0.67 % Favored : 99.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.78 % Cis-general : 0.39 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.89 (0.17), residues: 2361 helix: 0.52 (0.28), residues: 369 sheet: 0.13 (0.20), residues: 675 loop : -1.34 (0.17), residues: 1317 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG E 588 TYR 0.014 0.001 TYR L 87 PHE 0.011 0.001 PHE A 376 TRP 0.032 0.001 TRP B 571 HIS 0.003 0.001 HIS H 52A Details of bonding type rmsd covalent geometry : bond 0.00302 (21711) covalent geometry : angle 0.70471 (29532) SS BOND : bond 0.00181 ( 42) SS BOND : angle 0.69667 ( 84) hydrogen bonds : bond 0.03890 ( 704) hydrogen bonds : angle 5.41475 ( 2118) link_ALPHA1-2 : bond 0.00486 ( 12) link_ALPHA1-2 : angle 1.61644 ( 36) link_ALPHA1-3 : bond 0.00783 ( 21) link_ALPHA1-3 : angle 1.68154 ( 63) link_ALPHA1-6 : bond 0.00679 ( 18) link_ALPHA1-6 : angle 1.87733 ( 54) link_BETA1-4 : bond 0.00342 ( 81) link_BETA1-4 : angle 2.09890 ( 243) link_NAG-ASN : bond 0.00339 ( 60) link_NAG-ASN : angle 2.25584 ( 180) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4722 Ramachandran restraints generated. 2361 Oldfield, 0 Emsley, 2361 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4722 Ramachandran restraints generated. 2361 Oldfield, 0 Emsley, 2361 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 268 residues out of total 2103 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 267 time to evaluate : 0.832 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 161 MET cc_start: 0.9094 (tpp) cc_final: 0.8557 (tpp) REVERT: A 180 ASP cc_start: 0.8684 (m-30) cc_final: 0.8462 (m-30) REVERT: A 271 MET cc_start: 0.8199 (mmm) cc_final: 0.7753 (mmm) REVERT: A 434 MET cc_start: 0.8999 (tmm) cc_final: 0.8426 (tmm) REVERT: B 543 ASN cc_start: 0.8936 (t0) cc_final: 0.8449 (t0) REVERT: B 633 LYS cc_start: 0.9629 (ptpt) cc_final: 0.9390 (ptpp) REVERT: B 638 TYR cc_start: 0.8165 (m-80) cc_final: 0.7709 (m-80) REVERT: C 180 ASP cc_start: 0.8635 (m-30) cc_final: 0.8341 (m-30) REVERT: C 424 ILE cc_start: 0.9051 (pt) cc_final: 0.8792 (pt) REVERT: C 434 MET cc_start: 0.8729 (tmm) cc_final: 0.7909 (tmm) REVERT: D 180 ASP cc_start: 0.8853 (m-30) cc_final: 0.8604 (m-30) REVERT: D 270 VAL cc_start: 0.8778 (t) cc_final: 0.8523 (t) REVERT: D 271 MET cc_start: 0.8206 (mmm) cc_final: 0.7870 (mmm) REVERT: D 475 MET cc_start: 0.8562 (mmm) cc_final: 0.8322 (mmm) REVERT: E 539 VAL cc_start: 0.9422 (m) cc_final: 0.9190 (p) REVERT: E 543 ASN cc_start: 0.9002 (t0) cc_final: 0.8443 (t0) REVERT: E 632 ASP cc_start: 0.8940 (p0) cc_final: 0.8713 (p0) REVERT: F 543 ASN cc_start: 0.9088 (t0) cc_final: 0.8606 (t0) REVERT: F 601 LYS cc_start: 0.8552 (pttt) cc_final: 0.8288 (ptmt) REVERT: F 632 ASP cc_start: 0.8856 (p0) cc_final: 0.8624 (p0) REVERT: G 33 ASN cc_start: 0.9402 (m-40) cc_final: 0.8993 (p0) REVERT: G 72 ASP cc_start: 0.8251 (t0) cc_final: 0.5863 (t0) REVERT: G 75 LYS cc_start: 0.9398 (mttt) cc_final: 0.9038 (mttp) REVERT: H 22 CYS cc_start: 0.2797 (t) cc_final: 0.2448 (t) REVERT: H 33 ASN cc_start: 0.9361 (m-40) cc_final: 0.8755 (p0) REVERT: H 58 TYR cc_start: 0.8843 (m-10) cc_final: 0.8562 (m-80) REVERT: H 72 ASP cc_start: 0.8423 (t0) cc_final: 0.7036 (t0) REVERT: H 75 LYS cc_start: 0.9061 (mtmm) cc_final: 0.8709 (mttp) REVERT: H 98 GLU cc_start: 0.8771 (tp30) cc_final: 0.8546 (tp30) REVERT: I 33 ASN cc_start: 0.9462 (m-40) cc_final: 0.8958 (p0) REVERT: I 58 TYR cc_start: 0.8853 (m-10) cc_final: 0.8592 (m-80) REVERT: I 98 GLU cc_start: 0.8668 (tp30) cc_final: 0.8378 (tp30) REVERT: J 33 VAL cc_start: 0.9131 (t) cc_final: 0.8665 (p) REVERT: J 87 TYR cc_start: 0.8444 (m-80) cc_final: 0.8187 (m-80) outliers start: 1 outliers final: 1 residues processed: 268 average time/residue: 0.1609 time to fit residues: 67.2061 Evaluate side-chains 202 residues out of total 2103 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 201 time to evaluate : 0.833 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 237 random chunks: chunk 75 optimal weight: 0.9990 chunk 22 optimal weight: 10.0000 chunk 163 optimal weight: 6.9990 chunk 201 optimal weight: 10.0000 chunk 68 optimal weight: 5.9990 chunk 195 optimal weight: 0.7980 chunk 224 optimal weight: 7.9990 chunk 211 optimal weight: 10.0000 chunk 34 optimal weight: 8.9990 chunk 182 optimal weight: 6.9990 chunk 142 optimal weight: 0.4980 overall best weight: 3.0586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 293 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 630 GLN ** C 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 293 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 5 GLN G 59 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3141 r_free = 0.3141 target = 0.054769 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2733 r_free = 0.2733 target = 0.041276 restraints weight = 108254.855| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.2775 r_free = 0.2775 target = 0.042613 restraints weight = 62567.001| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.2803 r_free = 0.2803 target = 0.043491 restraints weight = 44543.911| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.2820 r_free = 0.2820 target = 0.044055 restraints weight = 36093.133| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 39)----------------| | r_work = 0.2831 r_free = 0.2831 target = 0.044406 restraints weight = 31667.758| |-----------------------------------------------------------------------------| r_work (final): 0.2815 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8336 moved from start: 0.5310 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 21945 Z= 0.202 Angle : 0.793 12.457 30192 Z= 0.367 Chirality : 0.046 0.396 3924 Planarity : 0.004 0.036 3450 Dihedral : 9.286 77.964 6432 Min Nonbonded Distance : 2.331 Molprobity Statistics. All-atom Clashscore : 10.25 Ramachandran Plot: Outliers : 0.51 % Allowed : 6.69 % Favored : 92.80 % Rotamer: Outliers : 0.00 % Allowed : 1.09 % Favored : 98.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.78 % Cis-general : 0.39 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.02 (0.17), residues: 2361 helix: 0.37 (0.28), residues: 375 sheet: 0.04 (0.20), residues: 651 loop : -1.39 (0.16), residues: 1335 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG B 588 TYR 0.018 0.002 TYR D 217 PHE 0.018 0.002 PHE A 53 TRP 0.033 0.002 TRP B 571 HIS 0.004 0.001 HIS C 374 Details of bonding type rmsd covalent geometry : bond 0.00437 (21711) covalent geometry : angle 0.74553 (29532) SS BOND : bond 0.00240 ( 42) SS BOND : angle 0.91198 ( 84) hydrogen bonds : bond 0.04152 ( 704) hydrogen bonds : angle 5.56087 ( 2118) link_ALPHA1-2 : bond 0.00328 ( 12) link_ALPHA1-2 : angle 1.86568 ( 36) link_ALPHA1-3 : bond 0.00611 ( 21) link_ALPHA1-3 : angle 1.88562 ( 63) link_ALPHA1-6 : bond 0.00629 ( 18) link_ALPHA1-6 : angle 1.89479 ( 54) link_BETA1-4 : bond 0.00364 ( 81) link_BETA1-4 : angle 2.04093 ( 243) link_NAG-ASN : bond 0.00540 ( 60) link_NAG-ASN : angle 2.30513 ( 180) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4722 Ramachandran restraints generated. 2361 Oldfield, 0 Emsley, 2361 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4722 Ramachandran restraints generated. 2361 Oldfield, 0 Emsley, 2361 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 245 residues out of total 2103 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 245 time to evaluate : 0.888 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 161 MET cc_start: 0.9178 (tpp) cc_final: 0.8653 (tpp) REVERT: A 424 ILE cc_start: 0.9267 (pt) cc_final: 0.9061 (pt) REVERT: A 434 MET cc_start: 0.8951 (tmm) cc_final: 0.8411 (tmm) REVERT: B 571 TRP cc_start: 0.8144 (m-10) cc_final: 0.7933 (m-10) REVERT: B 638 TYR cc_start: 0.8278 (m-80) cc_final: 0.7757 (m-80) REVERT: C 180 ASP cc_start: 0.8657 (m-30) cc_final: 0.8202 (m-30) REVERT: C 434 MET cc_start: 0.8685 (tmm) cc_final: 0.8214 (tmm) REVERT: E 539 VAL cc_start: 0.9473 (m) cc_final: 0.9188 (p) REVERT: E 543 ASN cc_start: 0.9019 (t0) cc_final: 0.8463 (t0) REVERT: F 539 VAL cc_start: 0.9495 (m) cc_final: 0.9247 (p) REVERT: G 33 ASN cc_start: 0.9380 (m-40) cc_final: 0.9029 (p0) REVERT: G 72 ASP cc_start: 0.8173 (t0) cc_final: 0.5540 (t0) REVERT: G 75 LYS cc_start: 0.9384 (mttt) cc_final: 0.9035 (mttp) REVERT: G 98 GLU cc_start: 0.8863 (tp30) cc_final: 0.8565 (tp30) REVERT: H 22 CYS cc_start: 0.2414 (t) cc_final: 0.2171 (t) REVERT: H 33 ASN cc_start: 0.9368 (m-40) cc_final: 0.8747 (p0) REVERT: H 58 TYR cc_start: 0.8993 (m-10) cc_final: 0.8391 (m-80) REVERT: H 72 ASP cc_start: 0.8346 (t0) cc_final: 0.6791 (t0) REVERT: H 75 LYS cc_start: 0.9037 (mtmm) cc_final: 0.8751 (mttp) REVERT: H 98 GLU cc_start: 0.8842 (tp30) cc_final: 0.8615 (tp30) REVERT: I 22 CYS cc_start: 0.3327 (t) cc_final: 0.3116 (t) REVERT: I 33 ASN cc_start: 0.9429 (m-40) cc_final: 0.9036 (p0) REVERT: I 58 TYR cc_start: 0.9027 (m-10) cc_final: 0.8452 (m-10) REVERT: I 98 GLU cc_start: 0.8683 (tp30) cc_final: 0.8361 (tp30) REVERT: J 87 TYR cc_start: 0.8461 (m-80) cc_final: 0.8183 (m-80) REVERT: J 104 LEU cc_start: 0.9301 (tp) cc_final: 0.9100 (tp) REVERT: K 87 TYR cc_start: 0.8240 (m-80) cc_final: 0.8037 (m-80) REVERT: K 104 LEU cc_start: 0.9331 (tp) cc_final: 0.9022 (tp) REVERT: L 45 LYS cc_start: 0.9413 (mtmm) cc_final: 0.9121 (mtmm) outliers start: 0 outliers final: 0 residues processed: 245 average time/residue: 0.1516 time to fit residues: 58.3887 Evaluate side-chains 185 residues out of total 2103 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 185 time to evaluate : 0.798 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 237 random chunks: chunk 21 optimal weight: 9.9990 chunk 157 optimal weight: 0.8980 chunk 63 optimal weight: 0.9990 chunk 124 optimal weight: 0.9990 chunk 40 optimal weight: 4.9990 chunk 72 optimal weight: 9.9990 chunk 103 optimal weight: 8.9990 chunk 178 optimal weight: 9.9990 chunk 82 optimal weight: 7.9990 chunk 217 optimal weight: 20.0000 chunk 45 optimal weight: 7.9990 overall best weight: 3.1788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 293 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 630 GLN C 99 ASN ** C 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 99 ASN ** D 293 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 652 GLN ** L 37 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 = 0.3132 r_free = 0.3132 target = 0.054456 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2724 r_free = 0.2724 target = 0.041015 restraints weight = 108386.989| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.2766 r_free = 0.2766 target = 0.042345 restraints weight = 62569.001| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.2794 r_free = 0.2794 target = 0.043220 restraints weight = 44496.540| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.2811 r_free = 0.2811 target = 0.043781 restraints weight = 36071.886| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.2822 r_free = 0.2822 target = 0.044127 restraints weight = 31688.463| |-----------------------------------------------------------------------------| r_work (final): 0.2804 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8352 moved from start: 0.5525 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.067 21945 Z= 0.204 Angle : 0.786 12.074 30192 Z= 0.366 Chirality : 0.046 0.388 3924 Planarity : 0.004 0.034 3450 Dihedral : 9.048 76.341 6432 Min Nonbonded Distance : 2.368 Molprobity Statistics. All-atom Clashscore : 10.06 Ramachandran Plot: Outliers : 0.51 % Allowed : 6.35 % Favored : 93.14 % Rotamer: Outliers : 0.00 % Allowed : 0.90 % Favored : 99.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.78 % Cis-general : 0.39 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.13 (0.17), residues: 2361 helix: 0.33 (0.28), residues: 375 sheet: -0.08 (0.20), residues: 654 loop : -1.45 (0.16), residues: 1332 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 588 TYR 0.021 0.002 TYR G 52E PHE 0.016 0.002 PHE B 519 TRP 0.027 0.002 TRP C 427 HIS 0.004 0.001 HIS H 52A Details of bonding type rmsd covalent geometry : bond 0.00444 (21711) covalent geometry : angle 0.74124 (29532) SS BOND : bond 0.00211 ( 42) SS BOND : angle 0.92865 ( 84) hydrogen bonds : bond 0.04169 ( 704) hydrogen bonds : angle 5.56524 ( 2118) link_ALPHA1-2 : bond 0.00325 ( 12) link_ALPHA1-2 : angle 1.73624 ( 36) link_ALPHA1-3 : bond 0.00648 ( 21) link_ALPHA1-3 : angle 1.81121 ( 63) link_ALPHA1-6 : bond 0.00626 ( 18) link_ALPHA1-6 : angle 1.81928 ( 54) link_BETA1-4 : bond 0.00362 ( 81) link_BETA1-4 : angle 1.99587 ( 243) link_NAG-ASN : bond 0.00490 ( 60) link_NAG-ASN : angle 2.21525 ( 180) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4722 Ramachandran restraints generated. 2361 Oldfield, 0 Emsley, 2361 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4722 Ramachandran restraints generated. 2361 Oldfield, 0 Emsley, 2361 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 242 residues out of total 2103 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 242 time to evaluate : 0.764 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 161 MET cc_start: 0.9283 (tpp) cc_final: 0.8797 (tpp) REVERT: A 434 MET cc_start: 0.8919 (tmm) cc_final: 0.8426 (tmm) REVERT: B 571 TRP cc_start: 0.8229 (m-10) cc_final: 0.7964 (m-10) REVERT: B 638 TYR cc_start: 0.8254 (m-80) cc_final: 0.7676 (m-80) REVERT: C 180 ASP cc_start: 0.8669 (m-30) cc_final: 0.8216 (m-30) REVERT: D 102 GLU cc_start: 0.9177 (mp0) cc_final: 0.8877 (mp0) REVERT: D 180 ASP cc_start: 0.8815 (m-30) cc_final: 0.8596 (m-30) REVERT: D 271 MET cc_start: 0.8093 (mmm) cc_final: 0.7853 (mmm) REVERT: E 539 VAL cc_start: 0.9471 (m) cc_final: 0.9186 (p) REVERT: E 543 ASN cc_start: 0.8993 (t0) cc_final: 0.8380 (t0) REVERT: E 632 ASP cc_start: 0.9006 (p0) cc_final: 0.8786 (p0) REVERT: F 539 VAL cc_start: 0.9463 (m) cc_final: 0.9213 (p) REVERT: G 33 ASN cc_start: 0.9377 (m-40) cc_final: 0.9013 (p0) REVERT: G 72 ASP cc_start: 0.8150 (t0) cc_final: 0.5875 (t0) REVERT: G 75 LYS cc_start: 0.9384 (mttt) cc_final: 0.8988 (mttp) REVERT: G 98 GLU cc_start: 0.8914 (tp30) cc_final: 0.8704 (tp30) REVERT: H 33 ASN cc_start: 0.9361 (m-40) cc_final: 0.8825 (p0) REVERT: H 58 TYR cc_start: 0.9050 (m-10) cc_final: 0.8488 (m-80) REVERT: H 72 ASP cc_start: 0.8372 (t0) cc_final: 0.6795 (t0) REVERT: H 75 LYS cc_start: 0.9076 (mtmm) cc_final: 0.8807 (mttp) REVERT: H 98 GLU cc_start: 0.8835 (tp30) cc_final: 0.8610 (tp30) REVERT: I 22 CYS cc_start: 0.3919 (t) cc_final: 0.3686 (t) REVERT: I 33 ASN cc_start: 0.9389 (m-40) cc_final: 0.8972 (p0) REVERT: I 58 TYR cc_start: 0.9148 (m-10) cc_final: 0.8497 (m-10) REVERT: I 98 GLU cc_start: 0.8703 (tp30) cc_final: 0.8391 (tp30) REVERT: J 87 TYR cc_start: 0.8428 (m-80) cc_final: 0.8116 (m-80) REVERT: K 87 TYR cc_start: 0.8254 (m-80) cc_final: 0.8030 (m-80) REVERT: L 31 ASN cc_start: 0.8163 (p0) cc_final: 0.7421 (t0) REVERT: L 45 LYS cc_start: 0.9418 (mtmm) cc_final: 0.8770 (mmmt) REVERT: L 104 LEU cc_start: 0.9146 (tp) cc_final: 0.8883 (tp) outliers start: 0 outliers final: 0 residues processed: 242 average time/residue: 0.1439 time to fit residues: 55.2769 Evaluate side-chains 186 residues out of total 2103 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 186 time to evaluate : 0.660 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 237 random chunks: chunk 94 optimal weight: 8.9990 chunk 71 optimal weight: 6.9990 chunk 45 optimal weight: 1.9990 chunk 222 optimal weight: 7.9990 chunk 180 optimal weight: 9.9990 chunk 230 optimal weight: 9.9990 chunk 62 optimal weight: 3.9990 chunk 64 optimal weight: 2.9990 chunk 235 optimal weight: 5.9990 chunk 178 optimal weight: 2.9990 chunk 63 optimal weight: 0.7980 overall best weight: 2.5588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 293 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 630 GLN C 99 ASN C 374 HIS ** D 293 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 52AHIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3138 r_free = 0.3138 target = 0.054631 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2732 r_free = 0.2732 target = 0.041189 restraints weight = 107466.585| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.2774 r_free = 0.2774 target = 0.042540 restraints weight = 61367.200| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.2801 r_free = 0.2801 target = 0.043415 restraints weight = 43467.228| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.2819 r_free = 0.2819 target = 0.043978 restraints weight = 35170.420| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 38)----------------| | r_work = 0.2830 r_free = 0.2830 target = 0.044342 restraints weight = 30828.169| |-----------------------------------------------------------------------------| r_work (final): 0.2814 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8349 moved from start: 0.5686 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 21945 Z= 0.178 Angle : 0.768 12.009 30192 Z= 0.359 Chirality : 0.046 0.374 3924 Planarity : 0.004 0.035 3450 Dihedral : 8.799 74.762 6432 Min Nonbonded Distance : 2.324 Molprobity Statistics. All-atom Clashscore : 9.75 Ramachandran Plot: Outliers : 0.51 % Allowed : 6.52 % Favored : 92.97 % Rotamer: Outliers : 0.00 % Allowed : 0.29 % Favored : 99.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.78 % Cis-general : 0.39 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.11 (0.17), residues: 2361 helix: 0.37 (0.28), residues: 372 sheet: -0.08 (0.19), residues: 657 loop : -1.44 (0.17), residues: 1332 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 588 TYR 0.018 0.002 TYR D 217 PHE 0.012 0.002 PHE A 376 TRP 0.030 0.002 TRP E 571 HIS 0.007 0.001 HIS C 374 Details of bonding type rmsd covalent geometry : bond 0.00387 (21711) covalent geometry : angle 0.72498 (29532) SS BOND : bond 0.00182 ( 42) SS BOND : angle 0.98276 ( 84) hydrogen bonds : bond 0.04083 ( 704) hydrogen bonds : angle 5.59177 ( 2118) link_ALPHA1-2 : bond 0.00370 ( 12) link_ALPHA1-2 : angle 1.66400 ( 36) link_ALPHA1-3 : bond 0.00700 ( 21) link_ALPHA1-3 : angle 1.77786 ( 63) link_ALPHA1-6 : bond 0.00695 ( 18) link_ALPHA1-6 : angle 1.73522 ( 54) link_BETA1-4 : bond 0.00356 ( 81) link_BETA1-4 : angle 1.95882 ( 243) link_NAG-ASN : bond 0.00408 ( 60) link_NAG-ASN : angle 2.09545 ( 180) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4722 Ramachandran restraints generated. 2361 Oldfield, 0 Emsley, 2361 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4722 Ramachandran restraints generated. 2361 Oldfield, 0 Emsley, 2361 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 232 residues out of total 2103 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 232 time to evaluate : 0.628 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 161 MET cc_start: 0.9269 (tpp) cc_final: 0.8769 (tpp) REVERT: A 180 ASP cc_start: 0.8830 (m-30) cc_final: 0.8598 (m-30) REVERT: A 195 ASN cc_start: 0.9515 (p0) cc_final: 0.9256 (p0) REVERT: A 271 MET cc_start: 0.7977 (mmt) cc_final: 0.7659 (mmt) REVERT: A 434 MET cc_start: 0.8896 (tmm) cc_final: 0.8518 (tmm) REVERT: B 571 TRP cc_start: 0.8205 (m-10) cc_final: 0.7890 (m-10) REVERT: B 638 TYR cc_start: 0.8235 (m-80) cc_final: 0.7706 (m-80) REVERT: B 650 GLN cc_start: 0.8446 (tt0) cc_final: 0.8147 (tt0) REVERT: C 180 ASP cc_start: 0.8683 (m-30) cc_final: 0.8179 (m-30) REVERT: D 180 ASP cc_start: 0.8811 (m-30) cc_final: 0.8592 (m-30) REVERT: D 195 ASN cc_start: 0.9435 (p0) cc_final: 0.9197 (p0) REVERT: E 539 VAL cc_start: 0.9434 (m) cc_final: 0.9158 (p) REVERT: E 543 ASN cc_start: 0.9020 (t0) cc_final: 0.8390 (t0) REVERT: E 632 ASP cc_start: 0.9003 (p0) cc_final: 0.8758 (p0) REVERT: F 539 VAL cc_start: 0.9430 (m) cc_final: 0.9154 (p) REVERT: G 33 ASN cc_start: 0.9338 (m-40) cc_final: 0.9022 (p0) REVERT: G 72 ASP cc_start: 0.8094 (t0) cc_final: 0.5702 (t0) REVERT: G 75 LYS cc_start: 0.9401 (mttt) cc_final: 0.9024 (mttp) REVERT: G 98 GLU cc_start: 0.8897 (tp30) cc_final: 0.8656 (tp30) REVERT: H 33 ASN cc_start: 0.9404 (m-40) cc_final: 0.8903 (p0) REVERT: H 58 TYR cc_start: 0.9031 (m-10) cc_final: 0.8416 (m-80) REVERT: H 72 ASP cc_start: 0.8372 (t0) cc_final: 0.6802 (t0) REVERT: H 75 LYS cc_start: 0.9103 (mtmm) cc_final: 0.8843 (mttp) REVERT: I 22 CYS cc_start: 0.3887 (t) cc_final: 0.3677 (t) REVERT: I 33 ASN cc_start: 0.9374 (m-40) cc_final: 0.8972 (p0) REVERT: I 58 TYR cc_start: 0.9092 (m-10) cc_final: 0.8335 (m-10) REVERT: I 98 GLU cc_start: 0.8700 (tp30) cc_final: 0.8430 (tp30) REVERT: J 53 LYS cc_start: 0.9010 (mmtt) cc_final: 0.8777 (mmtm) REVERT: J 87 TYR cc_start: 0.8433 (m-80) cc_final: 0.8127 (m-80) REVERT: K 31 ASN cc_start: 0.8083 (p0) cc_final: 0.7370 (t0) REVERT: K 87 TYR cc_start: 0.8337 (m-80) cc_final: 0.8131 (m-80) REVERT: K 104 LEU cc_start: 0.9311 (tp) cc_final: 0.9089 (tp) REVERT: L 31 ASN cc_start: 0.8189 (p0) cc_final: 0.7453 (t0) REVERT: L 45 LYS cc_start: 0.9408 (mtmm) cc_final: 0.8772 (mmmt) REVERT: L 104 LEU cc_start: 0.9118 (tp) cc_final: 0.8857 (tp) outliers start: 0 outliers final: 0 residues processed: 232 average time/residue: 0.1456 time to fit residues: 53.3126 Evaluate side-chains 186 residues out of total 2103 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 186 time to evaluate : 0.785 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 237 random chunks: chunk 103 optimal weight: 8.9990 chunk 181 optimal weight: 8.9990 chunk 44 optimal weight: 10.0000 chunk 112 optimal weight: 8.9990 chunk 123 optimal weight: 2.9990 chunk 139 optimal weight: 3.9990 chunk 102 optimal weight: 0.5980 chunk 121 optimal weight: 0.9990 chunk 87 optimal weight: 9.9990 chunk 21 optimal weight: 8.9990 chunk 47 optimal weight: 3.9990 overall best weight: 2.5188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 293 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 630 GLN C 99 ASN ** D 293 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 651 ASN F 652 GLN ** I 52AHIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 37 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 = 0.3135 r_free = 0.3135 target = 0.054555 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2729 r_free = 0.2729 target = 0.041106 restraints weight = 107912.975| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.2771 r_free = 0.2771 target = 0.042462 restraints weight = 61377.214| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.2798 r_free = 0.2798 target = 0.043342 restraints weight = 43395.674| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 40)----------------| | r_work = 0.2816 r_free = 0.2816 target = 0.043906 restraints weight = 35084.385| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.2827 r_free = 0.2827 target = 0.044263 restraints weight = 30736.139| |-----------------------------------------------------------------------------| r_work (final): 0.2810 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8344 moved from start: 0.5856 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 21945 Z= 0.176 Angle : 0.760 11.699 30192 Z= 0.356 Chirality : 0.045 0.370 3924 Planarity : 0.004 0.036 3450 Dihedral : 8.586 72.566 6432 Min Nonbonded Distance : 2.346 Molprobity Statistics. All-atom Clashscore : 9.68 Ramachandran Plot: Outliers : 0.51 % Allowed : 6.44 % Favored : 93.05 % Rotamer: Outliers : 0.00 % Allowed : 0.19 % Favored : 99.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.78 % Cis-general : 0.39 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.08 (0.17), residues: 2361 helix: 0.45 (0.28), residues: 372 sheet: -0.06 (0.20), residues: 657 loop : -1.44 (0.17), residues: 1332 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 588 TYR 0.022 0.002 TYR C 217 PHE 0.013 0.002 PHE C 382 TRP 0.027 0.002 TRP E 571 HIS 0.005 0.001 HIS C 374 Details of bonding type rmsd covalent geometry : bond 0.00380 (21711) covalent geometry : angle 0.71823 (29532) SS BOND : bond 0.00284 ( 42) SS BOND : angle 0.96543 ( 84) hydrogen bonds : bond 0.04096 ( 704) hydrogen bonds : angle 5.50082 ( 2118) link_ALPHA1-2 : bond 0.00373 ( 12) link_ALPHA1-2 : angle 1.63218 ( 36) link_ALPHA1-3 : bond 0.00682 ( 21) link_ALPHA1-3 : angle 1.77629 ( 63) link_ALPHA1-6 : bond 0.00706 ( 18) link_ALPHA1-6 : angle 1.69665 ( 54) link_BETA1-4 : bond 0.00369 ( 81) link_BETA1-4 : angle 1.93202 ( 243) link_NAG-ASN : bond 0.00413 ( 60) link_NAG-ASN : angle 2.06140 ( 180) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4722 Ramachandran restraints generated. 2361 Oldfield, 0 Emsley, 2361 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4722 Ramachandran restraints generated. 2361 Oldfield, 0 Emsley, 2361 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 232 residues out of total 2103 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 232 time to evaluate : 0.746 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 161 MET cc_start: 0.9285 (tpp) cc_final: 0.8710 (tpp) REVERT: A 180 ASP cc_start: 0.8912 (m-30) cc_final: 0.8663 (m-30) REVERT: A 195 ASN cc_start: 0.9513 (p0) cc_final: 0.9225 (p0) REVERT: A 271 MET cc_start: 0.7973 (mmt) cc_final: 0.7618 (mmt) REVERT: A 424 ILE cc_start: 0.9212 (pt) cc_final: 0.9002 (pt) REVERT: A 434 MET cc_start: 0.8971 (tmm) cc_final: 0.8410 (tmm) REVERT: B 571 TRP cc_start: 0.8161 (m-10) cc_final: 0.7761 (m-10) REVERT: B 638 TYR cc_start: 0.8468 (m-80) cc_final: 0.7960 (m-80) REVERT: B 650 GLN cc_start: 0.8529 (tt0) cc_final: 0.8203 (tt0) REVERT: C 180 ASP cc_start: 0.8762 (m-30) cc_final: 0.8234 (m-30) REVERT: C 195 ASN cc_start: 0.9446 (p0) cc_final: 0.9232 (p0) REVERT: D 180 ASP cc_start: 0.8869 (m-30) cc_final: 0.8623 (m-30) REVERT: D 195 ASN cc_start: 0.9352 (p0) cc_final: 0.9134 (p0) REVERT: D 271 MET cc_start: 0.8382 (mmm) cc_final: 0.8080 (mmm) REVERT: D 475 MET cc_start: 0.8665 (mmm) cc_final: 0.8426 (mmm) REVERT: E 539 VAL cc_start: 0.9465 (m) cc_final: 0.9181 (p) REVERT: E 543 ASN cc_start: 0.9024 (t0) cc_final: 0.8386 (t0) REVERT: E 632 ASP cc_start: 0.9043 (p0) cc_final: 0.8801 (p0) REVERT: F 539 VAL cc_start: 0.9415 (m) cc_final: 0.9150 (p) REVERT: G 33 ASN cc_start: 0.9360 (m-40) cc_final: 0.9031 (p0) REVERT: G 98 GLU cc_start: 0.8935 (tp30) cc_final: 0.8648 (tp30) REVERT: H 33 ASN cc_start: 0.9429 (m-40) cc_final: 0.8932 (p0) REVERT: H 58 TYR cc_start: 0.8982 (m-10) cc_final: 0.8368 (m-10) REVERT: H 72 ASP cc_start: 0.8386 (t0) cc_final: 0.6875 (t0) REVERT: H 75 LYS cc_start: 0.9119 (mtmm) cc_final: 0.8863 (mttp) REVERT: I 33 ASN cc_start: 0.9398 (m-40) cc_final: 0.8992 (p0) REVERT: I 58 TYR cc_start: 0.9074 (m-10) cc_final: 0.8204 (m-10) REVERT: I 98 GLU cc_start: 0.8737 (tp30) cc_final: 0.8442 (tp30) REVERT: J 31 ASN cc_start: 0.7650 (p0) cc_final: 0.7280 (t0) REVERT: J 53 LYS cc_start: 0.8888 (mmtt) cc_final: 0.8637 (mmtm) REVERT: J 87 TYR cc_start: 0.8479 (m-80) cc_final: 0.8176 (m-80) REVERT: K 31 ASN cc_start: 0.8084 (p0) cc_final: 0.7396 (t0) REVERT: K 87 TYR cc_start: 0.8463 (m-80) cc_final: 0.8246 (m-80) REVERT: K 104 LEU cc_start: 0.9331 (tp) cc_final: 0.9114 (tp) REVERT: L 45 LYS cc_start: 0.9392 (mtmm) cc_final: 0.8779 (mmmt) REVERT: L 104 LEU cc_start: 0.9168 (tp) cc_final: 0.8859 (tp) outliers start: 0 outliers final: 0 residues processed: 232 average time/residue: 0.1483 time to fit residues: 54.0848 Evaluate side-chains 186 residues out of total 2103 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 186 time to evaluate : 0.782 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 237 random chunks: chunk 223 optimal weight: 0.0050 chunk 38 optimal weight: 8.9990 chunk 216 optimal weight: 10.0000 chunk 235 optimal weight: 5.9990 chunk 57 optimal weight: 0.5980 chunk 48 optimal weight: 5.9990 chunk 201 optimal weight: 1.9990 chunk 91 optimal weight: 0.9990 chunk 84 optimal weight: 3.9990 chunk 12 optimal weight: 4.9990 chunk 198 optimal weight: 3.9990 overall best weight: 1.5200 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 293 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 630 GLN ** D 293 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 651 ASN ** I 52AHIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 37 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 = 0.3150 r_free = 0.3150 target = 0.055103 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.2746 r_free = 0.2746 target = 0.041659 restraints weight = 107065.702| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.2789 r_free = 0.2789 target = 0.043039 restraints weight = 60808.175| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.2817 r_free = 0.2817 target = 0.043937 restraints weight = 42806.961| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.2835 r_free = 0.2835 target = 0.044511 restraints weight = 34572.681| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.2846 r_free = 0.2846 target = 0.044870 restraints weight = 30279.198| |-----------------------------------------------------------------------------| r_work (final): 0.2830 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8324 moved from start: 0.5928 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 21945 Z= 0.136 Angle : 0.731 11.706 30192 Z= 0.344 Chirality : 0.045 0.360 3924 Planarity : 0.003 0.037 3450 Dihedral : 8.285 69.757 6432 Min Nonbonded Distance : 2.368 Molprobity Statistics. All-atom Clashscore : 8.53 Ramachandran Plot: Outliers : 0.51 % Allowed : 6.23 % Favored : 93.27 % Rotamer: Outliers : 0.00 % Allowed : 0.19 % Favored : 99.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.78 % Cis-general : 0.39 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.98 (0.17), residues: 2361 helix: 0.49 (0.29), residues: 372 sheet: 0.09 (0.20), residues: 657 loop : -1.41 (0.17), residues: 1332 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 588 TYR 0.017 0.001 TYR C 217 PHE 0.013 0.001 PHE C 376 TRP 0.030 0.001 TRP C 427 HIS 0.003 0.001 HIS H 52A Details of bonding type rmsd covalent geometry : bond 0.00291 (21711) covalent geometry : angle 0.69229 (29532) SS BOND : bond 0.00226 ( 42) SS BOND : angle 0.88507 ( 84) hydrogen bonds : bond 0.03867 ( 704) hydrogen bonds : angle 5.40960 ( 2118) link_ALPHA1-2 : bond 0.00428 ( 12) link_ALPHA1-2 : angle 1.53704 ( 36) link_ALPHA1-3 : bond 0.00762 ( 21) link_ALPHA1-3 : angle 1.67375 ( 63) link_ALPHA1-6 : bond 0.00764 ( 18) link_ALPHA1-6 : angle 1.62516 ( 54) link_BETA1-4 : bond 0.00362 ( 81) link_BETA1-4 : angle 1.90229 ( 243) link_NAG-ASN : bond 0.00271 ( 60) link_NAG-ASN : angle 1.89240 ( 180) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3008.18 seconds wall clock time: 53 minutes 20.23 seconds (3200.23 seconds total)