Starting phenix.real_space_refine on Sun Sep 13 05:32:59 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/5aco_3121/09_2026/5aco_3121.cif Found real_map, /net/cci-nas-00/data/ceres_data/5aco_3121/09_2026/5aco_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 { restraint_files = "/net/cci-nas-00/data/ceres_data/5aco_3121/09_2026/5aco_3121.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/5aco_3121/09_2026/5aco_3121.cif" model { file = "/net/cci-nas-00/data/ceres_data/5aco_3121/09_2026/5aco_3121.cif" } default_model = "/net/cci-nas-00/data/ceres_data/5aco_3121/09_2026/5aco_3121.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/5aco_3121/09_2026/5aco_3121.map" default_real_map = "/net/cci-nas-00/data/ceres_data/5aco_3121/09_2026/5aco_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-2.2.1-6174/lib/python3.11/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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 chiralities: 2 Time building chain proxies: 5.06, 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: 2.86 Conformation dependent library (CDL) restraints added in 838.1 milliseconds 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: 0.74 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: 4.31 Time building geometry restraints manager: 3.51 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 - 17.21: 11046 17.21 - 34.41: 360 34.41 - 51.62: 60 51.62 - 68.82: 54 68.82 - 86.03: 12 Dihedral angle restraints: 11532 sinusoidal: 4599 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 11529 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: 0.06 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: 1.100 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: 0.020 Extract box with map and model: 0.360 Check model and map are aligned: 0.060 Set scattering table: 0.060 Process input model: 21.970 Find NCS groups from input model: 0.660 Set up NCS constraints: 0.110 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: 0.010 Load rotamer database and sin/cos tables:1.390 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 25.740 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6780 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 : 10.102 86.027 6930 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 are 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/Z covalent geometry : bond 0.01232 / 0.81 (21711) covalent geometry : angle 1.98087 / 1.17 (29532) SS BOND : bond 0.13212 / 8.39 ( 42) SS BOND : angle 7.57399 / 5.76 ( 84) hydrogen bonds : bond 0.20828 / 14.09 ( 704) hydrogen bonds : angle 8.97476 / 6.20 ( 2118) link_ALPHA1-2 : bond 0.01962 / 1.10 ( 12) link_ALPHA1-2 : angle 4.77549 / 3.05 ( 36) link_ALPHA1-3 : bond 0.04462 / 2.90 ( 21) link_ALPHA1-3 : angle 7.38689 / 4.81 ( 63) link_ALPHA1-6 : bond 0.03748 / 2.28 ( 18) link_ALPHA1-6 : angle 5.29164 / 3.73 ( 54) link_BETA1-4 : bond 0.04228 / 2.68 ( 81) link_BETA1-4 : angle 6.03626 / 4.21 ( 243) link_NAG-ASN : bond 0.14324 / 9.39 ( 60) link_NAG-ASN : angle 11.49146 / 8.30 ( 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 : 0.656 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: 0.8070 (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: 0.8600 (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: 0.5312 (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: 0.1663 time to fit residues: 133.7771 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 : 0.719 ------------------------------------------------------------------------------- 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... ** 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 = 0.3246 r_free = 0.3246 target = 0.058597 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2863 r_free = 0.2863 target = 0.045360 restraints weight = 104352.432| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.2908 r_free = 0.2908 target = 0.046880 restraints weight = 57625.152| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.2938 r_free = 0.2938 target = 0.047891 restraints weight = 39569.222| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.2958 r_free = 0.2958 target = 0.048567 restraints weight = 31148.988| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 37)----------------| | r_work = 0.2971 r_free = 0.2971 target = 0.048996 restraints weight = 26719.283| |-----------------------------------------------------------------------------| r_work (final): 0.2954 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8122 moved from start: 0.2971 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= 0.182 Angle : 0.992 14.406 30192 Z= 0.454 Chirality : 0.048 0.502 3924 Planarity : 0.004 0.047 3450 Dihedral : 5.337 22.919 2562 Min Nonbonded Distance : 2.391 Molprobity Statistics. All-atom Clashscore : 8.41 Ramachandran Plot: Outliers : 0.51 % Allowed : 6.18 % Favored : 93.31 % 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 are not related in a simple way. whole: -1.51 (0.16), residues: 2361 helix: -0.96 (0.25), residues: 393 sheet: -0.44 (0.20), residues: 678 loop : -1.30 (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 0.015 0.002 TRP J 95 HIS 0.005 0.001 HIS L 39 Details of bonding type rmsd/Z covalent geometry : bond 0.00382 / 0.18 (21711) covalent geometry : angle 0.90074 / 0.43 (29532) SS BOND : bond 0.00252 / 0.16 ( 42) SS BOND : angle 1.19154 / 0.87 ( 84) hydrogen bonds : bond 0.05415 / 3.65 ( 704) hydrogen bonds : angle 6.57775 / 4.53 ( 2118) link_ALPHA1-2 : bond 0.00379 / 0.25 ( 12) link_ALPHA1-2 : angle 1.75062 / 1.21 ( 36) link_ALPHA1-3 : bond 0.00824 / 0.52 ( 21) link_ALPHA1-3 : angle 1.64425 / 1.18 ( 63) link_ALPHA1-6 : bond 0.00356 / 0.21 ( 18) link_ALPHA1-6 : angle 1.60664 / 1.16 ( 54) link_BETA1-4 : bond 0.00539 / 0.34 ( 81) link_BETA1-4 : angle 2.63807 / 1.79 ( 243) link_NAG-ASN : bond 0.00714 / 0.45 ( 60) link_NAG-ASN : angle 4.41564 / 3.10 ( 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 : 0.793 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: 0.9064 (tpp) cc_final: 0.8621 (tpp) REVERT: A 434 MET cc_start: 0.9112 (tmm) cc_final: 0.8649 (tmm) REVERT: B 543 ASN cc_start: 0.8680 (t0) cc_final: 0.8188 (t0) REVERT: B 544 LEU cc_start: 0.8034 (mt) cc_final: 0.7787 (mt) REVERT: B 571 TRP cc_start: 0.8022 (m-10) cc_final: 0.7820 (m-10) REVERT: B 584 GLU cc_start: 0.8466 (tm-30) cc_final: 0.8239 (tm-30) REVERT: B 631 TRP cc_start: 0.9489 (t-100) cc_final: 0.8591 (t-100) REVERT: B 634 GLU cc_start: 0.8551 (pm20) cc_final: 0.8311 (pm20) REVERT: C 180 ASP cc_start: 0.8693 (m-30) cc_final: 0.8457 (m-30) REVERT: C 271 MET cc_start: 0.8084 (mmp) cc_final: 0.7841 (mmm) REVERT: C 434 MET cc_start: 0.8913 (tmm) cc_final: 0.8017 (tmm) REVERT: D 434 MET cc_start: 0.9037 (tmm) cc_final: 0.8222 (tmm) REVERT: D 475 MET cc_start: 0.8642 (mmm) cc_final: 0.8389 (mmm) REVERT: E 530 MET cc_start: 0.8446 (mtt) cc_final: 0.8212 (mtt) REVERT: E 543 ASN cc_start: 0.8593 (t0) cc_final: 0.8088 (t0) REVERT: E 544 LEU cc_start: 0.8185 (mt) cc_final: 0.7890 (mt) REVERT: E 631 TRP cc_start: 0.9487 (t-100) cc_final: 0.9201 (t-100) REVERT: E 642 ILE cc_start: 0.9711 (mt) cc_final: 0.9475 (tp) REVERT: E 650 GLN cc_start: 0.8304 (tt0) cc_final: 0.7308 (tt0) REVERT: F 530 MET cc_start: 0.8332 (mtt) cc_final: 0.7870 (mtt) REVERT: F 543 ASN cc_start: 0.8758 (t0) cc_final: 0.8216 (t0) REVERT: F 544 LEU cc_start: 0.8183 (mt) cc_final: 0.7921 (mt) REVERT: F 571 TRP cc_start: 0.8218 (m-10) cc_final: 0.7973 (m-90) REVERT: F 631 TRP cc_start: 0.9541 (t-100) cc_final: 0.9200 (t-100) REVERT: G 22 CYS cc_start: 0.1473 (t) cc_final: 0.0458 (t) REVERT: G 58 TYR cc_start: 0.9087 (m-80) cc_final: 0.8678 (m-80) REVERT: G 72 ASP cc_start: 0.8193 (t0) cc_final: 0.6091 (t0) REVERT: G 75 LYS cc_start: 0.9315 (mttt) cc_final: 0.9047 (mttp) REVERT: H 13 GLU cc_start: 0.7678 (pp20) cc_final: 0.6981 (pp20) REVERT: H 72 ASP cc_start: 0.8173 (t0) cc_final: 0.6261 (t0) REVERT: I 16 GLU cc_start: 0.8549 (pt0) cc_final: 0.8028 (pt0) REVERT: I 72 ASP cc_start: 0.8263 (t0) cc_final: 0.5917 (t0) REVERT: I 95 PHE cc_start: 0.8310 (m-80) cc_final: 0.7875 (m-80) REVERT: I 98 GLU cc_start: 0.8527 (tp30) cc_final: 0.7950 (tm-30) REVERT: J 24 THR cc_start: 0.8832 (m) cc_final: 0.8210 (m) REVERT: J 87 TYR cc_start: 0.8409 (m-80) cc_final: 0.8191 (m-80) REVERT: J 104 LEU cc_start: 0.9413 (tp) cc_final: 0.9151 (tp) REVERT: K 24 THR cc_start: 0.9124 (m) cc_final: 0.8784 (m) REVERT: K 104 LEU cc_start: 0.9400 (tp) cc_final: 0.9174 (tp) REVERT: L 24 THR cc_start: 0.8858 (m) cc_final: 0.8655 (m) REVERT: L 45 LYS cc_start: 0.9346 (mtmm) cc_final: 0.8930 (mtmm) REVERT: L 53 LYS cc_start: 0.8263 (mppt) cc_final: 0.7884 (mmtt) outliers start: 3 outliers final: 0 residues processed: 351 average time/residue: 0.1634 time to fit residues: 87.3213 Evaluate side-chains 250 residues out of total 2103 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 250 time to evaluate : 0.792 ------------------------------------------------------------------------------- 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: 4.9990 chunk 128 optimal weight: 10.0000 chunk 172 optimal weight: 0.9980 chunk 122 optimal weight: 9.9990 chunk 0 optimal weight: 8.9990 chunk 91 optimal weight: 3.9990 chunk 193 optimal weight: 4.9990 chunk 72 optimal weight: 1.9990 chunk 52 optimal weight: 7.9990 chunk 41 optimal weight: 4.9990 overall best weight: 3.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 195 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 607 ASN ** B 630 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 293 GLN ** D 195 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 422 GLN G 5 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3168 r_free = 0.3168 target = 0.055622 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2772 r_free = 0.2772 target = 0.042396 restraints weight = 106742.290| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.2814 r_free = 0.2814 target = 0.043751 restraints weight = 60834.452| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.2842 r_free = 0.2842 target = 0.044657 restraints weight = 42801.258| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.2860 r_free = 0.2860 target = 0.045245 restraints weight = 34397.553| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 35)----------------| | r_work = 0.2871 r_free = 0.2871 target = 0.045617 restraints weight = 29975.522| |-----------------------------------------------------------------------------| r_work (final): 0.2852 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8274 moved from start: 0.3924 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.067 21945 Z= 0.235 Angle : 0.897 13.744 30192 Z= 0.415 Chirality : 0.045 0.324 3924 Planarity : 0.004 0.038 3450 Dihedral : 5.476 24.537 2562 Min Nonbonded Distance : 2.374 Molprobity Statistics. All-atom Clashscore : 10.18 Ramachandran Plot: Outliers : 0.51 % Allowed : 6.95 % Favored : 92.55 % Rotamer: Outliers : 0.05 % Allowed : 2.62 % Favored : 97.34 % 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 are not related in a simple way. whole: -1.17 (0.17), residues: 2361 helix: -0.51 (0.26), residues: 393 sheet: 0.04 (0.19), residues: 723 loop : -1.36 (0.17), residues: 1245 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG B 588 TYR 0.026 0.002 TYR H 58 PHE 0.042 0.002 PHE C 53 TRP 0.024 0.002 TRP A 427 HIS 0.008 0.001 HIS L 39 Details of bonding type rmsd/Z covalent geometry : bond 0.00498 / 0.23 (21711) covalent geometry : angle 0.84810 / 0.41 (29532) SS BOND : bond 0.00568 / 0.40 ( 42) SS BOND : angle 0.94849 / 0.64 ( 84) hydrogen bonds : bond 0.04925 / 3.34 ( 704) hydrogen bonds : angle 6.07201 / 4.16 ( 2118) link_ALPHA1-2 : bond 0.00314 / 0.21 ( 12) link_ALPHA1-2 : angle 1.65664 / 1.10 ( 36) link_ALPHA1-3 : bond 0.00395 / 0.28 ( 21) link_ALPHA1-3 : angle 1.73186 / 1.26 ( 63) link_ALPHA1-6 : bond 0.00276 / 0.16 ( 18) link_ALPHA1-6 : angle 1.63040 / 1.16 ( 54) link_BETA1-4 : bond 0.00437 / 0.28 ( 81) link_BETA1-4 : angle 2.08085 / 1.41 ( 243) link_NAG-ASN : bond 0.00749 / 0.48 ( 60) link_NAG-ASN : angle 2.86163 / 2.00 ( 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 297 residues out of total 2103 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 296 time to evaluate : 0.856 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: A 161 MET cc_start: 0.9121 (tpp) cc_final: 0.8876 (tpp) REVERT: A 271 MET cc_start: 0.8001 (mmm) cc_final: 0.7578 (mmm) REVERT: A 434 MET cc_start: 0.9115 (tmm) cc_final: 0.8607 (tmm) REVERT: B 543 ASN cc_start: 0.8972 (t0) cc_final: 0.8482 (t0) REVERT: B 584 GLU cc_start: 0.8672 (tm-30) cc_final: 0.8352 (tm-30) REVERT: B 647 GLU cc_start: 0.8724 (tp30) cc_final: 0.8310 (tp30) REVERT: C 180 ASP cc_start: 0.8551 (m-30) cc_final: 0.8179 (m-30) REVERT: C 424 ILE cc_start: 0.9259 (pt) cc_final: 0.8976 (pt) REVERT: C 434 MET cc_start: 0.8827 (tmm) cc_final: 0.7982 (tmm) REVERT: D 102 GLU cc_start: 0.9352 (mp0) cc_final: 0.9088 (mp0) REVERT: D 109 ILE cc_start: 0.9449 (mt) cc_final: 0.9244 (tt) REVERT: D 180 ASP cc_start: 0.8735 (m-30) cc_final: 0.8518 (m-30) REVERT: D 270 VAL cc_start: 0.8917 (t) cc_final: 0.8682 (t) REVERT: D 271 MET cc_start: 0.8249 (mmm) cc_final: 0.8008 (mmm) REVERT: D 434 MET cc_start: 0.8983 (tmm) cc_final: 0.8709 (tmm) REVERT: E 543 ASN cc_start: 0.8887 (t0) cc_final: 0.8359 (t0) REVERT: F 543 ASN cc_start: 0.9035 (t0) cc_final: 0.8593 (t0) REVERT: F 584 GLU cc_start: 0.8751 (tm-30) cc_final: 0.8464 (tm-30) REVERT: F 631 TRP cc_start: 0.9598 (t-100) cc_final: 0.8833 (t-100) REVERT: F 634 GLU cc_start: 0.8558 (pm20) cc_final: 0.8145 (pm20) REVERT: F 635 ILE cc_start: 0.9536 (tp) cc_final: 0.9294 (tt) REVERT: F 648 GLU cc_start: 0.8135 (tp30) cc_final: 0.7691 (tp30) REVERT: F 651 ASN cc_start: 0.8452 (t0) cc_final: 0.8169 (t0) REVERT: G 22 CYS cc_start: 0.0163 (t) cc_final: -0.0259 (t) REVERT: G 33 ASN cc_start: 0.9427 (m-40) cc_final: 0.9213 (m-40) REVERT: G 72 ASP cc_start: 0.8218 (t0) cc_final: 0.6412 (t0) REVERT: G 75 LYS cc_start: 0.9370 (mttt) cc_final: 0.9070 (mttp) REVERT: G 98 GLU cc_start: 0.8600 (tp30) cc_final: 0.8380 (tp30) REVERT: H 13 GLU cc_start: 0.7738 (pp20) cc_final: 0.7149 (pp20) REVERT: H 72 ASP cc_start: 0.8303 (t0) cc_final: 0.7108 (t0) REVERT: H 75 LYS cc_start: 0.9002 (mtmm) cc_final: 0.8690 (mttp) REVERT: I 33 ASN cc_start: 0.9444 (m-40) cc_final: 0.8913 (p0) REVERT: I 58 TYR cc_start: 0.8818 (m-10) cc_final: 0.8442 (m-10) REVERT: I 100 ASP cc_start: 0.9282 (m-30) cc_final: 0.8983 (m-30) REVERT: J 33 VAL cc_start: 0.9088 (t) cc_final: 0.8616 (p) REVERT: J 87 TYR cc_start: 0.8374 (m-80) cc_final: 0.8141 (m-80) REVERT: K 24 THR cc_start: 0.8981 (m) cc_final: 0.8318 (m) REVERT: K 91 LEU cc_start: 0.9307 (tp) cc_final: 0.8955 (mt) REVERT: K 104 LEU cc_start: 0.9386 (tp) cc_final: 0.9157 (tp) REVERT: L 45 LYS cc_start: 0.9290 (mtmm) cc_final: 0.8668 (mmmt) REVERT: L 87 TYR cc_start: 0.8476 (m-80) cc_final: 0.8092 (m-80) outliers start: 1 outliers final: 0 residues processed: 296 average time/residue: 0.1539 time to fit residues: 69.9543 Evaluate side-chains 214 residues out of total 2103 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 214 time to evaluate : 0.684 ------------------------------------------------------------------------------- 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: 9.9990 chunk 33 optimal weight: 0.9990 chunk 158 optimal weight: 8.9990 chunk 178 optimal weight: 1.9990 chunk 70 optimal weight: 0.9980 chunk 142 optimal weight: 10.0000 chunk 67 optimal weight: 0.9990 chunk 140 optimal weight: 8.9990 chunk 150 optimal weight: 9.9990 chunk 153 optimal weight: 0.9980 chunk 160 optimal weight: 0.9990 overall best weight: 0.9986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 85 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 188 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 374 HIS B 630 GLN D 188 ASN E 656 ASN ** F 540 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 5 GLN ** L 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 94 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3200 r_free = 0.3200 target = 0.056956 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2803 r_free = 0.2803 target = 0.043465 restraints weight = 106601.598| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.2846 r_free = 0.2846 target = 0.044874 restraints weight = 60864.185| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.2874 r_free = 0.2874 target = 0.045799 restraints weight = 42929.483| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.2891 r_free = 0.2891 target = 0.046395 restraints weight = 34541.486| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.2903 r_free = 0.2903 target = 0.046780 restraints weight = 30160.732| |-----------------------------------------------------------------------------| r_work (final): 0.2889 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8232 moved from start: 0.4197 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 21945 Z= 0.129 Angle : 0.773 13.507 30192 Z= 0.360 Chirality : 0.043 0.349 3924 Planarity : 0.003 0.031 3450 Dihedral : 5.160 22.630 2562 Min Nonbonded Distance : 2.433 Molprobity Statistics. All-atom Clashscore : 8.19 Ramachandran Plot: Outliers : 0.51 % Allowed : 6.06 % Favored : 93.43 % Rotamer: Outliers : 0.05 % Allowed : 1.62 % Favored : 98.34 % 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 are not related in a simple way. whole: -1.03 (0.17), residues: 2361 helix: -0.06 (0.26), residues: 378 sheet: 0.14 (0.19), residues: 702 loop : -1.37 (0.16), residues: 1281 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG E 617 TYR 0.021 0.001 TYR H 58 PHE 0.013 0.001 PHE C 317 TRP 0.037 0.002 TRP E 571 HIS 0.007 0.001 HIS A 374 Details of bonding type rmsd/Z covalent geometry : bond 0.00270 / 0.13 (21711) covalent geometry : angle 0.72545 / 0.35 (29532) SS BOND : bond 0.00162 / 0.11 ( 42) SS BOND : angle 0.70527 / 0.49 ( 84) hydrogen bonds : bond 0.04109 / 2.78 ( 704) hydrogen bonds : angle 5.72779 / 3.91 ( 2118) link_ALPHA1-2 : bond 0.00442 / 0.28 ( 12) link_ALPHA1-2 : angle 1.40813 / 0.95 ( 36) link_ALPHA1-3 : bond 0.00504 / 0.32 ( 21) link_ALPHA1-3 : angle 1.46780 / 1.04 ( 63) link_ALPHA1-6 : bond 0.00376 / 0.23 ( 18) link_ALPHA1-6 : angle 1.51748 / 1.09 ( 54) link_BETA1-4 : bond 0.00336 / 0.22 ( 81) link_BETA1-4 : angle 1.97684 / 1.34 ( 243) link_NAG-ASN : bond 0.00343 / 0.23 ( 60) link_NAG-ASN : angle 2.54840 / 1.81 ( 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 296 residues out of total 2103 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 295 time to evaluate : 0.717 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: 0.9049 (tpp) cc_final: 0.8635 (tpp) REVERT: A 180 ASP cc_start: 0.8666 (m-30) cc_final: 0.8461 (m-30) REVERT: A 434 MET cc_start: 0.9044 (tmm) cc_final: 0.8600 (tmm) REVERT: B 543 ASN cc_start: 0.9031 (t0) cc_final: 0.8463 (t0) REVERT: B 584 GLU cc_start: 0.8681 (tm-30) cc_final: 0.8376 (tm-30) REVERT: B 647 GLU cc_start: 0.8565 (tp30) cc_final: 0.8223 (tp30) REVERT: B 650 GLN cc_start: 0.8372 (tt0) cc_final: 0.7848 (tt0) REVERT: C 180 ASP cc_start: 0.8562 (m-30) cc_final: 0.8289 (m-30) REVERT: C 271 MET cc_start: 0.8174 (mmp) cc_final: 0.7945 (mmm) REVERT: C 424 ILE cc_start: 0.9080 (pt) cc_final: 0.8871 (pt) REVERT: C 434 MET cc_start: 0.8763 (tmm) cc_final: 0.7995 (tmm) REVERT: D 109 ILE cc_start: 0.9457 (mt) cc_final: 0.9252 (tt) REVERT: D 270 VAL cc_start: 0.8747 (t) cc_final: 0.8507 (t) REVERT: D 271 MET cc_start: 0.8160 (mmm) cc_final: 0.7884 (mmm) REVERT: D 434 MET cc_start: 0.8989 (tmm) cc_final: 0.8397 (tmm) REVERT: E 543 ASN cc_start: 0.8883 (t0) cc_final: 0.8320 (t0) REVERT: E 584 GLU cc_start: 0.8702 (tm-30) cc_final: 0.8398 (tm-30) REVERT: F 543 ASN cc_start: 0.8970 (t0) cc_final: 0.8504 (t0) REVERT: F 602 LEU cc_start: 0.9015 (mm) cc_final: 0.8791 (tp) REVERT: F 631 TRP cc_start: 0.9498 (t-100) cc_final: 0.8679 (t-100) REVERT: F 634 GLU cc_start: 0.8286 (pm20) cc_final: 0.7948 (pm20) REVERT: F 635 ILE cc_start: 0.9489 (tp) cc_final: 0.9258 (tp) REVERT: F 655 LYS cc_start: 0.9342 (mmpt) cc_final: 0.8970 (mmmt) REVERT: G 22 CYS cc_start: 0.0542 (t) cc_final: 0.0322 (t) REVERT: G 72 ASP cc_start: 0.8218 (t0) cc_final: 0.6399 (t0) REVERT: G 75 LYS cc_start: 0.9379 (mttt) cc_final: 0.9055 (mttp) REVERT: G 98 GLU cc_start: 0.8564 (tp30) cc_final: 0.8200 (tp30) REVERT: G 101 ASP cc_start: 0.8641 (t0) cc_final: 0.8432 (t0) REVERT: H 58 TYR cc_start: 0.9017 (m-10) cc_final: 0.8455 (m-10) REVERT: H 72 ASP cc_start: 0.8383 (t0) cc_final: 0.7175 (t0) REVERT: H 75 LYS cc_start: 0.9186 (mtmm) cc_final: 0.8807 (mttp) REVERT: H 100 ASP cc_start: 0.9135 (m-30) cc_final: 0.8903 (m-30) REVERT: I 13 GLU cc_start: 0.7619 (pp20) cc_final: 0.7286 (pp20) REVERT: I 33 ASN cc_start: 0.9425 (m-40) cc_final: 0.8919 (p0) REVERT: I 75 LYS cc_start: 0.9254 (ptpp) cc_final: 0.8980 (ptpp) REVERT: I 100 ASP cc_start: 0.9224 (m-30) cc_final: 0.8974 (m-30) REVERT: J 33 VAL cc_start: 0.9114 (t) cc_final: 0.8698 (p) REVERT: J 91 LEU cc_start: 0.9108 (tp) cc_final: 0.8892 (mt) REVERT: K 24 THR cc_start: 0.8970 (m) cc_final: 0.8387 (m) REVERT: K 33 VAL cc_start: 0.9142 (t) cc_final: 0.8771 (p) REVERT: K 91 LEU cc_start: 0.9285 (tp) cc_final: 0.8989 (mt) REVERT: L 45 LYS cc_start: 0.9311 (mtmm) cc_final: 0.8574 (mmmt) REVERT: L 87 TYR cc_start: 0.8424 (m-80) cc_final: 0.8176 (m-80) outliers start: 1 outliers final: 0 residues processed: 295 average time/residue: 0.1626 time to fit residues: 73.5122 Evaluate side-chains 217 residues out of total 2103 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 217 time to evaluate : 0.787 ------------------------------------------------------------------------------- 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: 10.0000 chunk 92 optimal weight: 0.0980 chunk 16 optimal weight: 0.4980 chunk 152 optimal weight: 5.9990 chunk 181 optimal weight: 8.9990 chunk 124 optimal weight: 0.6980 chunk 225 optimal weight: 5.9990 chunk 160 optimal weight: 0.8980 chunk 59 optimal weight: 0.1980 chunk 97 optimal weight: 7.9990 chunk 141 optimal weight: 3.9990 overall best weight: 0.4780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 85 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 188 ASN B 607 ASN B 630 GLN D 99 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3218 r_free = 0.3218 target = 0.057500 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2833 r_free = 0.2833 target = 0.044318 restraints weight = 104721.144| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.2876 r_free = 0.2876 target = 0.045752 restraints weight = 59335.415| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.2905 r_free = 0.2905 target = 0.046717 restraints weight = 41440.025| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.2924 r_free = 0.2924 target = 0.047347 restraints weight = 32903.589| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 36)----------------| | r_work = 0.2936 r_free = 0.2936 target = 0.047752 restraints weight = 28401.776| |-----------------------------------------------------------------------------| r_work (final): 0.2925 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8195 moved from start: 0.4457 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.043 21945 Z= 0.118 Angle : 0.738 13.264 30192 Z= 0.346 Chirality : 0.043 0.299 3924 Planarity : 0.004 0.069 3450 Dihedral : 4.948 22.960 2562 Min Nonbonded Distance : 2.431 Molprobity Statistics. All-atom Clashscore : 7.64 Ramachandran Plot: Outliers : 0.51 % Allowed : 6.61 % Favored : 92.88 % Rotamer: Outliers : 0.05 % Allowed : 1.28 % Favored : 98.67 % 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 are not related in a simple way. whole: -0.92 (0.17), residues: 2361 helix: -0.01 (0.27), residues: 390 sheet: 0.22 (0.20), residues: 672 loop : -1.28 (0.17), residues: 1299 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG E 588 TYR 0.015 0.001 TYR H 58 PHE 0.011 0.001 PHE A 376 TRP 0.035 0.001 TRP E 571 HIS 0.004 0.001 HIS L 39 Details of bonding type rmsd/Z covalent geometry : bond 0.00239 / 0.12 (21711) covalent geometry : angle 0.69622 / 0.34 (29532) SS BOND : bond 0.00202 / 0.15 ( 42) SS BOND : angle 0.70194 / 0.50 ( 84) hydrogen bonds : bond 0.03831 / 2.61 ( 704) hydrogen bonds : angle 5.49131 / 3.75 ( 2118) link_ALPHA1-2 : bond 0.00559 / 0.36 ( 12) link_ALPHA1-2 : angle 1.43392 / 0.98 ( 36) link_ALPHA1-3 : bond 0.00521 / 0.34 ( 21) link_ALPHA1-3 : angle 1.43366 / 1.01 ( 63) link_ALPHA1-6 : bond 0.00406 / 0.24 ( 18) link_ALPHA1-6 : angle 1.47901 / 1.05 ( 54) link_BETA1-4 : bond 0.00372 / 0.23 ( 81) link_BETA1-4 : angle 1.86444 / 1.26 ( 243) link_NAG-ASN : bond 0.00316 / 0.20 ( 60) link_NAG-ASN : angle 2.27686 / 1.62 ( 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 294 residues out of total 2103 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 293 time to evaluate : 1.011 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: 0.9009 (tpp) cc_final: 0.8555 (tpp) REVERT: A 180 ASP cc_start: 0.8602 (m-30) cc_final: 0.8400 (m-30) REVERT: A 271 MET cc_start: 0.8003 (mmm) cc_final: 0.7612 (mmm) REVERT: A 434 MET cc_start: 0.9050 (tmm) cc_final: 0.8485 (tmm) REVERT: B 543 ASN cc_start: 0.8927 (t0) cc_final: 0.8344 (t0) REVERT: B 584 GLU cc_start: 0.8726 (tm-30) cc_final: 0.8351 (tm-30) REVERT: B 650 GLN cc_start: 0.8227 (tt0) cc_final: 0.7834 (tt0) REVERT: C 104 MET cc_start: 0.9368 (mmm) cc_final: 0.9022 (tpp) REVERT: C 180 ASP cc_start: 0.8566 (m-30) cc_final: 0.8318 (m-30) REVERT: C 271 MET cc_start: 0.8134 (mmp) cc_final: 0.7891 (mmm) REVERT: C 424 ILE cc_start: 0.8967 (pt) cc_final: 0.8715 (pt) REVERT: C 434 MET cc_start: 0.8749 (tmm) cc_final: 0.7986 (tmm) REVERT: D 104 MET cc_start: 0.9236 (mmm) cc_final: 0.9019 (tpp) REVERT: D 109 ILE cc_start: 0.9419 (mt) cc_final: 0.9206 (tt) REVERT: D 270 VAL cc_start: 0.8652 (t) cc_final: 0.8418 (t) REVERT: D 271 MET cc_start: 0.8093 (mmm) cc_final: 0.7789 (mmm) REVERT: D 434 MET cc_start: 0.8946 (tmm) cc_final: 0.8262 (tmm) REVERT: D 475 MET cc_start: 0.8642 (mmm) cc_final: 0.8354 (mmm) REVERT: E 543 ASN cc_start: 0.8908 (t0) cc_final: 0.8300 (t0) REVERT: E 642 ILE cc_start: 0.9735 (mt) cc_final: 0.9472 (tp) REVERT: F 537 LEU cc_start: 0.9357 (mt) cc_final: 0.9130 (mp) REVERT: F 543 ASN cc_start: 0.9053 (t0) cc_final: 0.8511 (t0) REVERT: G 33 ASN cc_start: 0.9431 (m-40) cc_final: 0.9017 (p0) REVERT: G 72 ASP cc_start: 0.8216 (t0) cc_final: 0.6459 (t0) REVERT: G 75 LYS cc_start: 0.9394 (mttt) cc_final: 0.9061 (mttp) REVERT: H 33 ASN cc_start: 0.9280 (m-40) cc_final: 0.8719 (p0) REVERT: H 72 ASP cc_start: 0.8376 (t0) cc_final: 0.7103 (t0) REVERT: H 75 LYS cc_start: 0.9157 (mtmm) cc_final: 0.8747 (mttp) REVERT: H 100 ASP cc_start: 0.9156 (m-30) cc_final: 0.8844 (m-30) REVERT: I 33 ASN cc_start: 0.9430 (m-40) cc_final: 0.8947 (p0) REVERT: I 98 GLU cc_start: 0.8564 (tp30) cc_final: 0.8339 (tp30) REVERT: I 100 ASP cc_start: 0.9273 (m-30) cc_final: 0.9056 (m-30) REVERT: J 33 VAL cc_start: 0.9099 (t) cc_final: 0.8640 (p) REVERT: J 91 LEU cc_start: 0.9010 (tp) cc_final: 0.8797 (mt) REVERT: K 24 THR cc_start: 0.8988 (m) cc_final: 0.8785 (p) REVERT: K 33 VAL cc_start: 0.9148 (t) cc_final: 0.8779 (p) REVERT: K 104 LEU cc_start: 0.9304 (tp) cc_final: 0.9012 (tp) REVERT: L 33 VAL cc_start: 0.9128 (t) cc_final: 0.8807 (p) REVERT: L 45 LYS cc_start: 0.9280 (mtmm) cc_final: 0.8571 (mmmt) REVERT: L 87 TYR cc_start: 0.8402 (m-80) cc_final: 0.8162 (m-80) outliers start: 1 outliers final: 0 residues processed: 293 average time/residue: 0.1603 time to fit residues: 72.5413 Evaluate side-chains 207 residues out of total 2103 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 207 time to evaluate : 0.760 ------------------------------------------------------------------------------- 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: 0.9980 chunk 113 optimal weight: 6.9990 chunk 27 optimal weight: 2.9990 chunk 108 optimal weight: 8.9990 chunk 139 optimal weight: 0.9990 chunk 49 optimal weight: 0.9990 chunk 52 optimal weight: 8.9990 chunk 121 optimal weight: 0.9980 chunk 17 optimal weight: 5.9990 chunk 145 optimal weight: 7.9990 chunk 111 optimal weight: 6.9990 overall best weight: 1.3986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 85 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 630 GLN ** D 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 656 ASN L 38 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3206 r_free = 0.3206 target = 0.057030 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.2811 r_free = 0.2811 target = 0.043650 restraints weight = 106510.189| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.2855 r_free = 0.2855 target = 0.045067 restraints weight = 61062.928| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.2883 r_free = 0.2883 target = 0.045994 restraints weight = 43084.685| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 41)----------------| | r_work = 0.2901 r_free = 0.2901 target = 0.046596 restraints weight = 34659.379| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 38)----------------| | r_work = 0.2912 r_free = 0.2912 target = 0.046972 restraints weight = 30239.998| |-----------------------------------------------------------------------------| r_work (final): 0.2897 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8235 moved from start: 0.4695 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 21945 Z= 0.131 Angle : 0.722 12.930 30192 Z= 0.338 Chirality : 0.042 0.290 3924 Planarity : 0.003 0.030 3450 Dihedral : 4.874 23.324 2562 Min Nonbonded Distance : 2.388 Molprobity Statistics. All-atom Clashscore : 8.10 Ramachandran Plot: Outliers : 0.51 % Allowed : 5.93 % Favored : 93.56 % Rotamer: Outliers : 0.00 % Allowed : 0.71 % 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 are not related in a simple way. whole: -0.86 (0.17), residues: 2361 helix: 0.31 (0.28), residues: 375 sheet: 0.18 (0.20), residues: 675 loop : -1.26 (0.16), residues: 1311 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG F 588 TYR 0.012 0.001 TYR B 586 PHE 0.012 0.001 PHE A 382 TRP 0.032 0.001 TRP B 571 HIS 0.004 0.001 HIS I 59 Details of bonding type rmsd/Z covalent geometry : bond 0.00276 / 0.13 (21711) covalent geometry : angle 0.68304 / 0.33 (29532) SS BOND : bond 0.00251 / 0.16 ( 42) SS BOND : angle 0.76682 / 0.53 ( 84) hydrogen bonds : bond 0.03829 / 2.60 ( 704) hydrogen bonds : angle 5.42801 / 3.69 ( 2118) link_ALPHA1-2 : bond 0.00384 / 0.26 ( 12) link_ALPHA1-2 : angle 1.56588 / 1.06 ( 36) link_ALPHA1-3 : bond 0.00405 / 0.26 ( 21) link_ALPHA1-3 : angle 1.50567 / 1.07 ( 63) link_ALPHA1-6 : bond 0.00348 / 0.21 ( 18) link_ALPHA1-6 : angle 1.50700 / 1.07 ( 54) link_BETA1-4 : bond 0.00342 / 0.21 ( 81) link_BETA1-4 : angle 1.77990 / 1.20 ( 243) link_NAG-ASN : bond 0.00295 / 0.19 ( 60) link_NAG-ASN : angle 2.09372 / 1.48 ( 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 279 residues out of total 2103 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 279 time to evaluate : 0.851 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: A 104 MET cc_start: 0.9367 (mmm) cc_final: 0.9156 (mmm) REVERT: A 161 MET cc_start: 0.9046 (tpp) cc_final: 0.8546 (tpp) REVERT: A 180 ASP cc_start: 0.8665 (m-30) cc_final: 0.8460 (m-30) REVERT: A 271 MET cc_start: 0.8075 (mmm) cc_final: 0.7651 (mmm) REVERT: A 434 MET cc_start: 0.9032 (tmm) cc_final: 0.8528 (tmm) REVERT: B 543 ASN cc_start: 0.8997 (t0) cc_final: 0.8447 (t0) REVERT: B 650 GLN cc_start: 0.8221 (tt0) cc_final: 0.7864 (tt0) REVERT: C 180 ASP cc_start: 0.8523 (m-30) cc_final: 0.8216 (m-30) REVERT: C 424 ILE cc_start: 0.9055 (pt) cc_final: 0.8840 (pt) REVERT: C 426 MET cc_start: 0.8372 (tpp) cc_final: 0.7855 (tpp) REVERT: C 434 MET cc_start: 0.8775 (tmm) cc_final: 0.7980 (tmm) REVERT: D 109 ILE cc_start: 0.9409 (mt) cc_final: 0.9153 (tt) REVERT: D 180 ASP cc_start: 0.8811 (m-30) cc_final: 0.8604 (m-30) REVERT: D 270 VAL cc_start: 0.8660 (t) cc_final: 0.8437 (t) REVERT: D 271 MET cc_start: 0.8042 (mmm) cc_final: 0.7736 (mmm) REVERT: D 434 MET cc_start: 0.8973 (tmm) cc_final: 0.8317 (tmm) REVERT: D 475 MET cc_start: 0.8527 (mmm) cc_final: 0.8276 (mmm) REVERT: E 543 ASN cc_start: 0.8847 (t0) cc_final: 0.8286 (t0) REVERT: F 543 ASN cc_start: 0.9070 (t0) cc_final: 0.8559 (t0) REVERT: G 33 ASN cc_start: 0.9435 (m-40) cc_final: 0.9032 (p0) REVERT: G 72 ASP cc_start: 0.8239 (t0) cc_final: 0.6471 (t0) REVERT: G 75 LYS cc_start: 0.9397 (mttt) cc_final: 0.9061 (mttp) REVERT: H 33 ASN cc_start: 0.9321 (m-40) cc_final: 0.8727 (p0) REVERT: H 72 ASP cc_start: 0.8479 (t0) cc_final: 0.7215 (t0) REVERT: H 75 LYS cc_start: 0.9001 (mtmm) cc_final: 0.8626 (mttp) REVERT: H 98 GLU cc_start: 0.8793 (tp30) cc_final: 0.8585 (tp30) REVERT: I 33 ASN cc_start: 0.9454 (m-40) cc_final: 0.8956 (p0) REVERT: J 33 VAL cc_start: 0.9086 (t) cc_final: 0.8630 (p) REVERT: J 91 LEU cc_start: 0.9033 (tp) cc_final: 0.8830 (mt) REVERT: L 33 VAL cc_start: 0.9087 (t) cc_final: 0.8758 (p) REVERT: L 45 LYS cc_start: 0.9292 (mtmm) cc_final: 0.8880 (mtmm) REVERT: L 87 TYR cc_start: 0.8379 (m-80) cc_final: 0.8176 (m-80) outliers start: 0 outliers final: 0 residues processed: 279 average time/residue: 0.1489 time to fit residues: 65.3730 Evaluate side-chains 207 residues out of total 2103 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 207 time to evaluate : 0.826 ------------------------------------------------------------------------------- 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: 10.0000 chunk 22 optimal weight: 0.5980 chunk 163 optimal weight: 5.9990 chunk 201 optimal weight: 9.9990 chunk 68 optimal weight: 4.9990 chunk 195 optimal weight: 0.0870 chunk 224 optimal weight: 10.0000 chunk 211 optimal weight: 0.6980 chunk 34 optimal weight: 7.9990 chunk 182 optimal weight: 6.9990 chunk 142 optimal weight: 2.9990 overall best weight: 1.8762 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 630 GLN ** C 188 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3182 r_free = 0.3182 target = 0.056124 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2779 r_free = 0.2779 target = 0.042602 restraints weight = 108098.958| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.2824 r_free = 0.2824 target = 0.044044 restraints weight = 60853.791| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.2853 r_free = 0.2853 target = 0.044994 restraints weight = 42463.686| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.2871 r_free = 0.2871 target = 0.045590 restraints weight = 33876.456| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.2883 r_free = 0.2883 target = 0.045979 restraints weight = 29527.413| |-----------------------------------------------------------------------------| r_work (final): 0.2874 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8266 moved from start: 0.4878 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 21945 Z= 0.145 Angle : 0.712 12.701 30192 Z= 0.334 Chirality : 0.041 0.290 3924 Planarity : 0.003 0.050 3450 Dihedral : 4.861 23.745 2562 Min Nonbonded Distance : 2.339 Molprobity Statistics. All-atom Clashscore : 8.36 Ramachandran Plot: Outliers : 0.51 % Allowed : 6.14 % Favored : 93.35 % Rotamer: Outliers : 0.00 % Allowed : 0.52 % Favored : 99.48 % 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 are not related in a simple way. whole: -0.90 (0.17), residues: 2361 helix: 0.30 (0.28), residues: 384 sheet: 0.17 (0.20), residues: 675 loop : -1.31 (0.17), residues: 1302 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG E 542 TYR 0.021 0.001 TYR D 217 PHE 0.012 0.001 PHE D 382 TRP 0.031 0.001 TRP B 571 HIS 0.003 0.001 HIS G 52A Details of bonding type rmsd/Z covalent geometry : bond 0.00313 / 0.14 (21711) covalent geometry : angle 0.67502 / 0.33 (29532) SS BOND : bond 0.00204 / 0.16 ( 42) SS BOND : angle 0.78321 / 0.56 ( 84) hydrogen bonds : bond 0.03787 / 2.57 ( 704) hydrogen bonds : angle 5.35515 / 3.63 ( 2118) link_ALPHA1-2 : bond 0.00356 / 0.24 ( 12) link_ALPHA1-2 : angle 1.55846 / 1.04 ( 36) link_ALPHA1-3 : bond 0.00363 / 0.24 ( 21) link_ALPHA1-3 : angle 1.53420 / 1.09 ( 63) link_ALPHA1-6 : bond 0.00318 / 0.19 ( 18) link_ALPHA1-6 : angle 1.52027 / 1.08 ( 54) link_BETA1-4 : bond 0.00336 / 0.21 ( 81) link_BETA1-4 : angle 1.74006 / 1.17 ( 243) link_NAG-ASN : bond 0.00320 / 0.20 ( 60) link_NAG-ASN : angle 1.97295 / 1.38 ( 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 270 residues out of total 2103 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 270 time to evaluate : 0.641 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 104 MET cc_start: 0.9362 (mmm) cc_final: 0.9121 (mmm) REVERT: A 161 MET cc_start: 0.9108 (tpp) cc_final: 0.8583 (tpp) REVERT: A 271 MET cc_start: 0.8072 (mmm) cc_final: 0.7613 (mmm) REVERT: A 434 MET cc_start: 0.9038 (tmm) cc_final: 0.8480 (tmm) REVERT: B 543 ASN cc_start: 0.9027 (t0) cc_final: 0.8478 (t0) REVERT: B 546 SER cc_start: 0.8368 (p) cc_final: 0.7998 (p) REVERT: B 638 TYR cc_start: 0.8156 (m-80) cc_final: 0.7660 (m-80) REVERT: C 180 ASP cc_start: 0.8531 (m-30) cc_final: 0.8202 (m-30) REVERT: C 434 MET cc_start: 0.8704 (tmm) cc_final: 0.8321 (ttm) REVERT: D 109 ILE cc_start: 0.9389 (mt) cc_final: 0.9144 (tt) REVERT: D 161 MET cc_start: 0.9100 (tpp) cc_final: 0.8866 (tpp) REVERT: D 180 ASP cc_start: 0.8745 (m-30) cc_final: 0.8519 (m-30) REVERT: D 434 MET cc_start: 0.8948 (tmm) cc_final: 0.8359 (tmm) REVERT: D 475 MET cc_start: 0.8537 (mmm) cc_final: 0.8318 (mmm) REVERT: E 543 ASN cc_start: 0.8920 (t0) cc_final: 0.8333 (t0) REVERT: F 539 VAL cc_start: 0.9435 (m) cc_final: 0.9200 (p) REVERT: F 543 ASN cc_start: 0.9115 (t0) cc_final: 0.8602 (t0) REVERT: G 33 ASN cc_start: 0.9436 (m-40) cc_final: 0.9028 (p0) REVERT: G 72 ASP cc_start: 0.8273 (t0) cc_final: 0.6023 (t0) REVERT: G 75 LYS cc_start: 0.9389 (mttt) cc_final: 0.9034 (mttp) REVERT: G 98 GLU cc_start: 0.8848 (mm-30) cc_final: 0.8284 (tp30) REVERT: G 100 LYS cc_start: 0.9009 (mttp) cc_final: 0.8764 (mttm) REVERT: H 33 ASN cc_start: 0.9324 (m-40) cc_final: 0.8709 (p0) REVERT: H 72 ASP cc_start: 0.8424 (t0) cc_final: 0.7151 (t0) REVERT: H 75 LYS cc_start: 0.9132 (mtmm) cc_final: 0.8706 (mttp) REVERT: I 33 ASN cc_start: 0.9448 (m-40) cc_final: 0.8947 (p0) REVERT: I 98 GLU cc_start: 0.8593 (tp30) cc_final: 0.8261 (tp30) REVERT: J 33 VAL cc_start: 0.9080 (t) cc_final: 0.8626 (p) REVERT: J 91 LEU cc_start: 0.9017 (tp) cc_final: 0.8796 (mt) REVERT: K 104 LEU cc_start: 0.9298 (tp) cc_final: 0.9005 (tp) REVERT: L 45 LYS cc_start: 0.9287 (mtmm) cc_final: 0.8873 (mtmm) REVERT: L 87 TYR cc_start: 0.8357 (m-80) cc_final: 0.8141 (m-80) outliers start: 0 outliers final: 0 residues processed: 270 average time/residue: 0.1550 time to fit residues: 65.6679 Evaluate side-chains 199 residues out of total 2103 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 199 time to evaluate : 0.799 ------------------------------------------------------------------------------- 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: 0.5980 chunk 157 optimal weight: 0.7980 chunk 63 optimal weight: 1.9990 chunk 124 optimal weight: 3.9990 chunk 40 optimal weight: 0.9980 chunk 72 optimal weight: 0.2980 chunk 103 optimal weight: 9.9990 chunk 178 optimal weight: 10.0000 chunk 82 optimal weight: 7.9990 chunk 217 optimal weight: 20.0000 chunk 45 optimal weight: 0.9980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 85 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 630 GLN C 374 HIS D 374 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3206 r_free = 0.3206 target = 0.057021 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2816 r_free = 0.2816 target = 0.043737 restraints weight = 106031.820| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.2859 r_free = 0.2859 target = 0.045156 restraints weight = 60170.949| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.2887 r_free = 0.2887 target = 0.046098 restraints weight = 42093.034| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.2905 r_free = 0.2905 target = 0.046703 restraints weight = 33612.396| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 37)----------------| | r_work = 0.2917 r_free = 0.2917 target = 0.047087 restraints weight = 29189.257| |-----------------------------------------------------------------------------| r_work (final): 0.2903 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8219 moved from start: 0.5034 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.045 21945 Z= 0.114 Angle : 0.693 12.472 30192 Z= 0.326 Chirality : 0.041 0.267 3924 Planarity : 0.003 0.047 3450 Dihedral : 4.762 23.583 2562 Min Nonbonded Distance : 2.422 Molprobity Statistics. All-atom Clashscore : 7.81 Ramachandran Plot: Outliers : 0.51 % Allowed : 5.72 % Favored : 93.77 % Rotamer: Outliers : 0.05 % Allowed : 0.71 % Favored : 99.24 % 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 are not related in a simple way. whole: -0.86 (0.17), residues: 2361 helix: 0.15 (0.28), residues: 390 sheet: 0.27 (0.20), residues: 684 loop : -1.29 (0.17), residues: 1287 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG E 542 TYR 0.025 0.001 TYR D 40 PHE 0.010 0.001 PHE A 376 TRP 0.035 0.001 TRP B 571 HIS 0.003 0.001 HIS D 374 Details of bonding type rmsd/Z covalent geometry : bond 0.00240 / 0.11 (21711) covalent geometry : angle 0.66038 / 0.32 (29532) SS BOND : bond 0.00175 / 0.13 ( 42) SS BOND : angle 0.69303 / 0.45 ( 84) hydrogen bonds : bond 0.03530 / 2.39 ( 704) hydrogen bonds : angle 5.26381 / 3.56 ( 2118) link_ALPHA1-2 : bond 0.00580 / 0.35 ( 12) link_ALPHA1-2 : angle 1.43786 / 0.96 ( 36) link_ALPHA1-3 : bond 0.00470 / 0.30 ( 21) link_ALPHA1-3 : angle 1.44271 / 1.01 ( 63) link_ALPHA1-6 : bond 0.00380 / 0.23 ( 18) link_ALPHA1-6 : angle 1.46165 / 1.04 ( 54) link_BETA1-4 : bond 0.00370 / 0.23 ( 81) link_BETA1-4 : angle 1.71459 / 1.15 ( 243) link_NAG-ASN : bond 0.00200 / 0.13 ( 60) link_NAG-ASN : angle 1.74269 / 1.22 ( 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 279 residues out of total 2103 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 278 time to evaluate : 0.814 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: A 104 MET cc_start: 0.9410 (mmm) cc_final: 0.9136 (mmm) REVERT: A 161 MET cc_start: 0.9186 (tpp) cc_final: 0.8677 (tpp) REVERT: A 180 ASP cc_start: 0.8697 (m-30) cc_final: 0.8440 (m-30) REVERT: A 271 MET cc_start: 0.8074 (mmm) cc_final: 0.7582 (mmm) REVERT: A 434 MET cc_start: 0.9020 (tmm) cc_final: 0.8398 (tmm) REVERT: B 543 ASN cc_start: 0.9031 (t0) cc_final: 0.8455 (t0) REVERT: B 638 TYR cc_start: 0.8172 (m-80) cc_final: 0.7655 (m-80) REVERT: B 650 GLN cc_start: 0.8347 (tt0) cc_final: 0.7941 (tt0) REVERT: C 104 MET cc_start: 0.9366 (tpt) cc_final: 0.9133 (tpp) REVERT: C 180 ASP cc_start: 0.8723 (m-30) cc_final: 0.8388 (m-30) REVERT: C 271 MET cc_start: 0.7938 (mmt) cc_final: 0.7697 (mmt) REVERT: D 109 ILE cc_start: 0.9360 (mt) cc_final: 0.9142 (tt) REVERT: D 161 MET cc_start: 0.9072 (tpp) cc_final: 0.8781 (tpp) REVERT: D 180 ASP cc_start: 0.8845 (m-30) cc_final: 0.8583 (m-30) REVERT: D 271 MET cc_start: 0.8229 (mmm) cc_final: 0.7979 (mmm) REVERT: E 543 ASN cc_start: 0.8901 (t0) cc_final: 0.8322 (t0) REVERT: F 543 ASN cc_start: 0.9124 (t0) cc_final: 0.8606 (t0) REVERT: F 655 LYS cc_start: 0.9449 (mmmt) cc_final: 0.9055 (mmtm) REVERT: G 33 ASN cc_start: 0.9455 (m-40) cc_final: 0.9071 (p0) REVERT: G 72 ASP cc_start: 0.8421 (t0) cc_final: 0.6345 (t0) REVERT: G 75 LYS cc_start: 0.9373 (mttt) cc_final: 0.9017 (mttp) REVERT: G 98 GLU cc_start: 0.8896 (mm-30) cc_final: 0.8206 (tp30) REVERT: H 22 CYS cc_start: 0.2904 (t) cc_final: 0.2625 (t) REVERT: H 33 ASN cc_start: 0.9315 (m-40) cc_final: 0.8709 (p0) REVERT: H 72 ASP cc_start: 0.8438 (t0) cc_final: 0.7160 (t0) REVERT: H 75 LYS cc_start: 0.9197 (mtmm) cc_final: 0.8801 (mttp) REVERT: H 98 GLU cc_start: 0.8722 (tp30) cc_final: 0.8376 (tp30) REVERT: I 33 ASN cc_start: 0.9447 (m-40) cc_final: 0.8955 (p0) REVERT: I 98 GLU cc_start: 0.8571 (tp30) cc_final: 0.8142 (tp30) REVERT: K 24 THR cc_start: 0.8892 (p) cc_final: 0.8221 (t) REVERT: K 69 ASN cc_start: 0.8676 (t0) cc_final: 0.8395 (t0) REVERT: K 104 LEU cc_start: 0.9344 (tp) cc_final: 0.9143 (tp) REVERT: L 45 LYS cc_start: 0.9323 (mtmm) cc_final: 0.8907 (mtmm) REVERT: L 87 TYR cc_start: 0.8470 (m-80) cc_final: 0.8234 (m-80) outliers start: 1 outliers final: 0 residues processed: 279 average time/residue: 0.1422 time to fit residues: 62.9615 Evaluate side-chains 203 residues out of total 2103 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 203 time to evaluate : 0.806 ------------------------------------------------------------------------------- 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: 6.9990 chunk 71 optimal weight: 3.9990 chunk 45 optimal weight: 2.9990 chunk 222 optimal weight: 9.9990 chunk 180 optimal weight: 8.9990 chunk 230 optimal weight: 8.9990 chunk 62 optimal weight: 1.9990 chunk 64 optimal weight: 0.9990 chunk 235 optimal weight: 9.9990 chunk 178 optimal weight: 5.9990 chunk 63 optimal weight: 0.2980 overall best weight: 2.0588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 630 GLN C 99 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3182 r_free = 0.3182 target = 0.056041 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2787 r_free = 0.2787 target = 0.042803 restraints weight = 106020.753| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.2831 r_free = 0.2831 target = 0.044199 restraints weight = 60344.879| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.2858 r_free = 0.2858 target = 0.045117 restraints weight = 42280.550| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.2876 r_free = 0.2876 target = 0.045704 restraints weight = 33815.610| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.2887 r_free = 0.2887 target = 0.046063 restraints weight = 29425.340| |-----------------------------------------------------------------------------| r_work (final): 0.2870 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8267 moved from start: 0.5211 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 21945 Z= 0.154 Angle : 0.710 12.170 30192 Z= 0.333 Chirality : 0.041 0.265 3924 Planarity : 0.003 0.040 3450 Dihedral : 4.800 24.742 2562 Min Nonbonded Distance : 2.353 Molprobity Statistics. All-atom Clashscore : 8.48 Ramachandran Plot: Outliers : 0.51 % Allowed : 6.23 % Favored : 93.27 % 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 are not related in a simple way. whole: -0.88 (0.17), residues: 2361 helix: 0.41 (0.28), residues: 384 sheet: 0.24 (0.20), residues: 654 loop : -1.35 (0.17), residues: 1323 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG E 542 TYR 0.022 0.002 TYR G 58 PHE 0.012 0.001 PHE D 382 TRP 0.036 0.002 TRP B 571 HIS 0.009 0.001 HIS G 59 Details of bonding type rmsd/Z covalent geometry : bond 0.00334 / 0.15 (21711) covalent geometry : angle 0.67588 / 0.33 (29532) SS BOND : bond 0.00208 / 0.15 ( 42) SS BOND : angle 0.86003 / 0.56 ( 84) hydrogen bonds : bond 0.03743 / 2.51 ( 704) hydrogen bonds : angle 5.31315 / 3.60 ( 2118) link_ALPHA1-2 : bond 0.00348 / 0.24 ( 12) link_ALPHA1-2 : angle 1.65729 / 1.09 ( 36) link_ALPHA1-3 : bond 0.00325 / 0.21 ( 21) link_ALPHA1-3 : angle 1.56310 / 1.11 ( 63) link_ALPHA1-6 : bond 0.00306 / 0.18 ( 18) link_ALPHA1-6 : angle 1.51942 / 1.08 ( 54) link_BETA1-4 : bond 0.00336 / 0.20 ( 81) link_BETA1-4 : angle 1.68497 / 1.13 ( 243) link_NAG-ASN : bond 0.00351 / 0.22 ( 60) link_NAG-ASN : angle 1.83744 / 1.28 ( 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 256 residues out of total 2103 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 256 time to evaluate : 0.647 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: A 104 MET cc_start: 0.9380 (mmm) cc_final: 0.9106 (mmm) REVERT: A 161 MET cc_start: 0.9213 (tpp) cc_final: 0.8692 (tpp) REVERT: A 180 ASP cc_start: 0.8753 (m-30) cc_final: 0.8536 (m-30) REVERT: A 271 MET cc_start: 0.8093 (mmm) cc_final: 0.7643 (mmm) REVERT: A 434 MET cc_start: 0.9025 (tmm) cc_final: 0.8396 (tmm) REVERT: B 539 VAL cc_start: 0.9556 (m) cc_final: 0.9289 (p) REVERT: B 543 ASN cc_start: 0.8998 (t0) cc_final: 0.8413 (t0) REVERT: B 638 TYR cc_start: 0.8178 (m-80) cc_final: 0.7613 (m-80) REVERT: B 650 GLN cc_start: 0.8396 (tt0) cc_final: 0.8056 (tt0) REVERT: C 180 ASP cc_start: 0.8659 (m-30) cc_final: 0.8279 (m-30) REVERT: C 271 MET cc_start: 0.8029 (mmt) cc_final: 0.7795 (mmt) REVERT: D 109 ILE cc_start: 0.9369 (mt) cc_final: 0.9138 (tt) REVERT: D 180 ASP cc_start: 0.8782 (m-30) cc_final: 0.8536 (m-30) REVERT: E 539 VAL cc_start: 0.9450 (m) cc_final: 0.9201 (p) REVERT: E 543 ASN cc_start: 0.8970 (t0) cc_final: 0.8396 (t0) REVERT: F 543 ASN cc_start: 0.9163 (t0) cc_final: 0.8711 (t0) REVERT: F 655 LYS cc_start: 0.9443 (mmmt) cc_final: 0.9078 (mmtm) REVERT: G 22 CYS cc_start: 0.0611 (t) cc_final: -0.0147 (t) REVERT: G 33 ASN cc_start: 0.9438 (m-40) cc_final: 0.9062 (p0) REVERT: G 72 ASP cc_start: 0.8307 (t0) cc_final: 0.6009 (t0) REVERT: G 75 LYS cc_start: 0.9374 (mttt) cc_final: 0.9019 (mttp) REVERT: G 98 GLU cc_start: 0.8903 (mm-30) cc_final: 0.8394 (tp30) REVERT: G 100 LYS cc_start: 0.8902 (mttp) cc_final: 0.8701 (mttp) REVERT: H 22 CYS cc_start: 0.2636 (t) cc_final: 0.2372 (t) REVERT: H 33 ASN cc_start: 0.9345 (m-40) cc_final: 0.8711 (p0) REVERT: H 72 ASP cc_start: 0.8418 (t0) cc_final: 0.7148 (t0) REVERT: H 75 LYS cc_start: 0.9160 (mtmm) cc_final: 0.8752 (mttp) REVERT: H 98 GLU cc_start: 0.8783 (tp30) cc_final: 0.8496 (tp30) REVERT: I 22 CYS cc_start: 0.2965 (t) cc_final: 0.2743 (t) REVERT: I 33 ASN cc_start: 0.9457 (m-40) cc_final: 0.8992 (p0) REVERT: I 98 GLU cc_start: 0.8661 (tp30) cc_final: 0.8209 (tp30) REVERT: K 104 LEU cc_start: 0.9346 (tp) cc_final: 0.9044 (tp) REVERT: L 31 ASN cc_start: 0.8188 (p0) cc_final: 0.7469 (t0) REVERT: L 45 LYS cc_start: 0.9356 (mtmm) cc_final: 0.8970 (mtmm) REVERT: L 87 TYR cc_start: 0.8436 (m-80) cc_final: 0.8191 (m-80) outliers start: 0 outliers final: 0 residues processed: 256 average time/residue: 0.1449 time to fit residues: 59.6936 Evaluate side-chains 198 residues out of total 2103 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 198 time to evaluate : 0.733 ------------------------------------------------------------------------------- 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: 10.0000 chunk 181 optimal weight: 5.9990 chunk 44 optimal weight: 9.9990 chunk 112 optimal weight: 0.9990 chunk 123 optimal weight: 6.9990 chunk 139 optimal weight: 2.9990 chunk 102 optimal weight: 0.4980 chunk 121 optimal weight: 4.9990 chunk 87 optimal weight: 0.7980 chunk 21 optimal weight: 5.9990 chunk 47 optimal weight: 6.9990 overall best weight: 2.0586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 630 GLN ** D 293 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3170 r_free = 0.3170 target = 0.055667 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.2771 r_free = 0.2771 target = 0.042380 restraints weight = 107371.832| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.2814 r_free = 0.2814 target = 0.043755 restraints weight = 61133.037| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.2842 r_free = 0.2842 target = 0.044680 restraints weight = 42965.794| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 41)----------------| | r_work = 0.2861 r_free = 0.2861 target = 0.045274 restraints weight = 34407.306| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 42)----------------| | r_work = 0.2872 r_free = 0.2872 target = 0.045652 restraints weight = 29926.269| |-----------------------------------------------------------------------------| r_work (final): 0.2858 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8280 moved from start: 0.5403 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 21945 Z= 0.148 Angle : 0.708 11.902 30192 Z= 0.333 Chirality : 0.041 0.261 3924 Planarity : 0.003 0.040 3450 Dihedral : 4.828 24.517 2562 Min Nonbonded Distance : 2.403 Molprobity Statistics. All-atom Clashscore : 8.55 Ramachandran Plot: Outliers : 0.47 % Allowed : 5.93 % Favored : 93.60 % Rotamer: Outliers : 0.00 % Allowed : 0.14 % Favored : 99.86 % 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 are not related in a simple way. whole: -0.89 (0.17), residues: 2361 helix: 0.42 (0.28), residues: 384 sheet: 0.23 (0.20), residues: 654 loop : -1.37 (0.17), residues: 1323 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG E 542 TYR 0.015 0.001 TYR I 52E PHE 0.012 0.001 PHE A 382 TRP 0.038 0.002 TRP B 571 HIS 0.004 0.001 HIS D 374 Details of bonding type rmsd/Z covalent geometry : bond 0.00321 / 0.15 (21711) covalent geometry : angle 0.67569 / 0.33 (29532) SS BOND : bond 0.00301 / 0.24 ( 42) SS BOND : angle 0.92717 / 0.60 ( 84) hydrogen bonds : bond 0.03771 / 2.54 ( 704) hydrogen bonds : angle 5.30917 / 3.59 ( 2118) link_ALPHA1-2 : bond 0.00374 / 0.25 ( 12) link_ALPHA1-2 : angle 1.58323 / 1.03 ( 36) link_ALPHA1-3 : bond 0.00329 / 0.22 ( 21) link_ALPHA1-3 : angle 1.53667 / 1.09 ( 63) link_ALPHA1-6 : bond 0.00292 / 0.17 ( 18) link_ALPHA1-6 : angle 1.50860 / 1.08 ( 54) link_BETA1-4 : bond 0.00339 / 0.21 ( 81) link_BETA1-4 : angle 1.65422 / 1.11 ( 243) link_NAG-ASN : bond 0.00306 / 0.19 ( 60) link_NAG-ASN : angle 1.75271 / 1.22 ( 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 255 residues out of total 2103 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 255 time to evaluate : 0.829 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: A 104 MET cc_start: 0.9410 (mmm) cc_final: 0.9104 (mmm) REVERT: A 161 MET cc_start: 0.9264 (tpp) cc_final: 0.8767 (tpp) REVERT: A 180 ASP cc_start: 0.8765 (m-30) cc_final: 0.8532 (m-30) REVERT: A 271 MET cc_start: 0.8102 (mmm) cc_final: 0.7653 (mmm) REVERT: A 424 ILE cc_start: 0.9120 (pt) cc_final: 0.8918 (pt) REVERT: A 434 MET cc_start: 0.8986 (tmm) cc_final: 0.8373 (tmm) REVERT: B 539 VAL cc_start: 0.9545 (m) cc_final: 0.9268 (p) REVERT: B 543 ASN cc_start: 0.9006 (t0) cc_final: 0.8425 (t0) REVERT: B 638 TYR cc_start: 0.8449 (m-80) cc_final: 0.7868 (m-80) REVERT: B 650 GLN cc_start: 0.8440 (tt0) cc_final: 0.8078 (tt0) REVERT: C 180 ASP cc_start: 0.8681 (m-30) cc_final: 0.8315 (m-30) REVERT: C 271 MET cc_start: 0.8044 (mmt) cc_final: 0.7844 (mmt) REVERT: D 109 ILE cc_start: 0.9361 (mt) cc_final: 0.9119 (tt) REVERT: D 180 ASP cc_start: 0.8816 (m-30) cc_final: 0.8579 (m-30) REVERT: E 539 VAL cc_start: 0.9471 (m) cc_final: 0.9244 (p) REVERT: E 543 ASN cc_start: 0.8968 (t0) cc_final: 0.8429 (t0) REVERT: F 543 ASN cc_start: 0.9173 (t0) cc_final: 0.8698 (t0) REVERT: F 655 LYS cc_start: 0.9366 (mmmt) cc_final: 0.9158 (mmtm) REVERT: G 33 ASN cc_start: 0.9399 (m-40) cc_final: 0.9044 (p0) REVERT: G 72 ASP cc_start: 0.8250 (t0) cc_final: 0.5841 (t0) REVERT: G 75 LYS cc_start: 0.9372 (mttt) cc_final: 0.9034 (mttp) REVERT: G 98 GLU cc_start: 0.8934 (mm-30) cc_final: 0.8282 (tp30) REVERT: G 100 LYS cc_start: 0.8936 (mttp) cc_final: 0.8735 (mttm) REVERT: H 22 CYS cc_start: 0.2617 (t) cc_final: 0.2326 (t) REVERT: H 33 ASN cc_start: 0.9405 (m-40) cc_final: 0.8766 (p0) REVERT: H 72 ASP cc_start: 0.8439 (t0) cc_final: 0.7212 (t0) REVERT: H 75 LYS cc_start: 0.9165 (mtmm) cc_final: 0.8806 (mttp) REVERT: H 98 GLU cc_start: 0.8831 (tp30) cc_final: 0.8523 (tp30) REVERT: I 22 CYS cc_start: 0.3347 (t) cc_final: 0.3015 (t) REVERT: I 33 ASN cc_start: 0.9463 (m-40) cc_final: 0.8999 (p0) REVERT: I 98 GLU cc_start: 0.8626 (tp30) cc_final: 0.8148 (tp30) REVERT: J 53 LYS cc_start: 0.8989 (mmtt) cc_final: 0.8762 (mmtm) REVERT: K 31 ASN cc_start: 0.8116 (p0) cc_final: 0.7373 (t0) REVERT: K 104 LEU cc_start: 0.9319 (tp) cc_final: 0.9010 (tp) REVERT: L 31 ASN cc_start: 0.8234 (p0) cc_final: 0.7486 (t0) REVERT: L 45 LYS cc_start: 0.9387 (mtmm) cc_final: 0.8769 (mmmt) REVERT: L 87 TYR cc_start: 0.8439 (m-80) cc_final: 0.8191 (m-80) outliers start: 0 outliers final: 0 residues processed: 255 average time/residue: 0.1480 time to fit residues: 60.0132 Evaluate side-chains 196 residues out of total 2103 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 196 time to evaluate : 0.806 ------------------------------------------------------------------------------- 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: 2.9990 chunk 38 optimal weight: 7.9990 chunk 216 optimal weight: 0.9980 chunk 235 optimal weight: 4.9990 chunk 57 optimal weight: 9.9990 chunk 48 optimal weight: 1.9990 chunk 201 optimal weight: 10.0000 chunk 91 optimal weight: 2.9990 chunk 84 optimal weight: 4.9990 chunk 12 optimal weight: 0.1980 chunk 198 optimal weight: 0.8980 overall best weight: 1.4184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 293 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 630 GLN ** D 293 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3179 r_free = 0.3179 target = 0.055971 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2784 r_free = 0.2784 target = 0.042774 restraints weight = 106461.090| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.2828 r_free = 0.2828 target = 0.044166 restraints weight = 60250.266| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.2856 r_free = 0.2856 target = 0.045079 restraints weight = 42154.241| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.2874 r_free = 0.2874 target = 0.045680 restraints weight = 33729.210| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.2885 r_free = 0.2885 target = 0.046056 restraints weight = 29272.311| |-----------------------------------------------------------------------------| r_work (final): 0.2869 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8271 moved from start: 0.5524 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= 0.127 Angle : 0.687 11.759 30192 Z= 0.323 Chirality : 0.041 0.250 3924 Planarity : 0.003 0.035 3450 Dihedral : 4.721 24.241 2562 Min Nonbonded Distance : 2.405 Molprobity Statistics. All-atom Clashscore : 8.31 Ramachandran Plot: Outliers : 0.47 % Allowed : 6.06 % Favored : 93.48 % 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 are not related in a simple way. whole: -0.83 (0.17), residues: 2361 helix: 0.48 (0.29), residues: 384 sheet: 0.30 (0.20), residues: 663 loop : -1.36 (0.17), residues: 1314 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG E 542 TYR 0.013 0.001 TYR B 586 PHE 0.011 0.001 PHE C 376 TRP 0.034 0.001 TRP B 571 HIS 0.006 0.001 HIS G 59 Details of bonding type rmsd/Z covalent geometry : bond 0.00275 / 0.13 (21711) covalent geometry : angle 0.65628 / 0.32 (29532) SS BOND : bond 0.00178 / 0.13 ( 42) SS BOND : angle 0.80783 / 0.52 ( 84) hydrogen bonds : bond 0.03601 / 2.42 ( 704) hydrogen bonds : angle 5.22168 / 3.53 ( 2118) link_ALPHA1-2 : bond 0.00433 / 0.29 ( 12) link_ALPHA1-2 : angle 1.50178 / 0.99 ( 36) link_ALPHA1-3 : bond 0.00378 / 0.25 ( 21) link_ALPHA1-3 : angle 1.50046 / 1.06 ( 63) link_ALPHA1-6 : bond 0.00340 / 0.20 ( 18) link_ALPHA1-6 : angle 1.47407 / 1.05 ( 54) link_BETA1-4 : bond 0.00342 / 0.21 ( 81) link_BETA1-4 : angle 1.63479 / 1.09 ( 243) link_NAG-ASN : bond 0.00230 / 0.15 ( 60) link_NAG-ASN : angle 1.62577 / 1.14 ( 180) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3223.02 seconds wall clock time: 57 minutes 29.47 seconds (3449.47 seconds total)