Starting phenix.real_space_refine on Mon Mar 18 15:37:17 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5aco_3121/03_2024/5aco_3121.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5aco_3121/03_2024/5aco_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 { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5aco_3121/03_2024/5aco_3121.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5aco_3121/03_2024/5aco_3121.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5aco_3121/03_2024/5aco_3121.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5aco_3121/03_2024/5aco_3121.pdb" } resolution = 4.36 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 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 Residue "A PHE 376": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 21297 Number of models: 1 Model: "" Number of chains: 69 Chain: "A" Number of atoms: 3453 Number of conformers: 1 Conformer: "" Number of residues, atoms: 438, 3453 Classifications: {'peptide': 438} Link IDs: {'CIS': 2, 'PCIS': 1, 'PTRANS': 21, 'TRANS': 413} Chain breaks: 4 Chain: "B" Number of atoms: 1051 Number of conformers: 1 Conformer: "" Number of residues, atoms: 132, 1051 Classifications: {'peptide': 132} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 130} Chain breaks: 1 Chain: "C" Number of atoms: 3453 Number of conformers: 1 Conformer: "" Number of residues, atoms: 438, 3453 Classifications: {'peptide': 438} Link IDs: {'CIS': 2, 'PCIS': 1, 'PTRANS': 21, 'TRANS': 413} Chain breaks: 4 Chain: "D" Number of atoms: 3453 Number of conformers: 1 Conformer: "" Number of residues, atoms: 438, 3453 Classifications: {'peptide': 438} Link IDs: {'CIS': 2, 'PCIS': 1, 'PTRANS': 21, 'TRANS': 413} Chain breaks: 4 Chain: "E" Number of atoms: 1051 Number of conformers: 1 Conformer: "" Number of residues, atoms: 132, 1051 Classifications: {'peptide': 132} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 130} Chain breaks: 1 Chain: "F" Number of atoms: 1051 Number of conformers: 1 Conformer: "" Number of residues, atoms: 132, 1051 Classifications: {'peptide': 132} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 130} Chain breaks: 1 Chain: "G" Number of atoms: 1028 Number of conformers: 1 Conformer: "" Number of residues, atoms: 132, 1028 Classifications: {'peptide': 132} Link IDs: {'PTRANS': 7, 'TRANS': 124} Chain: "H" Number of atoms: 1028 Number of conformers: 1 Conformer: "" Number of residues, atoms: 132, 1028 Classifications: {'peptide': 132} Link IDs: {'PTRANS': 7, 'TRANS': 124} Chain: "I" Number of atoms: 1028 Number of conformers: 1 Conformer: "" Number of residues, atoms: 132, 1028 Classifications: {'peptide': 132} Link IDs: {'PTRANS': 7, 'TRANS': 124} Chain: "J" Number of atoms: 752 Number of conformers: 1 Conformer: "" Number of residues, atoms: 103, 752 Classifications: {'peptide': 103} Link IDs: {'CIS': 1, 'PTRANS': 6, 'TRANS': 95} Chain: "K" Number of atoms: 752 Number of conformers: 1 Conformer: "" Number of residues, atoms: 103, 752 Classifications: {'peptide': 103} Link IDs: {'CIS': 1, 'PTRANS': 6, 'TRANS': 95} Chain: "L" Number of atoms: 752 Number of conformers: 1 Conformer: "" Number of residues, atoms: 103, 752 Classifications: {'peptide': 103} Link IDs: {'CIS': 1, 'PTRANS': 6, 'TRANS': 95} Chain: "M" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "N" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "O" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "P" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "Q" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "R" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "S" Number of atoms: 83 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 83 Unusual residues: {'BMA': 1, 'MAN': 4, 'NAG': 2} Classifications: {'undetermined': 7} Link IDs: {None: 6} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 21 Unresolved non-hydrogen chiralities: 7 Chain: "T" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "U" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Chain: "V" Number of atoms: 83 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 83 Unusual residues: {'BMA': 1, 'MAN': 4, 'NAG': 2} Classifications: {'undetermined': 7} Link IDs: {None: 6} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 21 Unresolved non-hydrogen chiralities: 7 Chain: "W" Number of atoms: 116 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 116 Unusual residues: {'BMA': 1, 'MAN': 7, 'NAG': 2} Classifications: {'undetermined': 10} Link IDs: {None: 9} Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 20 Unresolved non-hydrogen dihedrals: 30 Unresolved non-hydrogen chiralities: 10 Chain: "X" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "Y" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "Z" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "a" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "b" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "c" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "d" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "e" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "f" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "g" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "h" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "i" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "j" Number of atoms: 83 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 83 Unusual residues: {'BMA': 1, 'MAN': 4, 'NAG': 2} Classifications: {'undetermined': 7} Link IDs: {None: 6} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 21 Unresolved non-hydrogen chiralities: 7 Chain: "k" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "l" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Chain: "m" Number of atoms: 83 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 83 Unusual residues: {'BMA': 1, 'MAN': 4, 'NAG': 2} Classifications: {'undetermined': 7} Link IDs: {None: 6} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 21 Unresolved non-hydrogen chiralities: 7 Chain: "n" Number of atoms: 116 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 116 Unusual residues: {'BMA': 1, 'MAN': 7, 'NAG': 2} Classifications: {'undetermined': 10} Link IDs: {None: 9} Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 20 Unresolved non-hydrogen dihedrals: 30 Unresolved non-hydrogen chiralities: 10 Chain: "o" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "p" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "q" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "r" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "s" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "t" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "u" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "v" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "w" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "x" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "y" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "z" Number of atoms: 83 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 83 Unusual residues: {'BMA': 1, 'MAN': 4, 'NAG': 2} Classifications: {'undetermined': 7} Link IDs: {None: 6} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 21 Unresolved non-hydrogen chiralities: 7 Chain: "0" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "1" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Chain: "2" Number of atoms: 83 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 83 Unusual residues: {'BMA': 1, 'MAN': 4, 'NAG': 2} Classifications: {'undetermined': 7} Link IDs: {None: 6} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 21 Unresolved non-hydrogen chiralities: 7 Chain: "3" Number of atoms: 116 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 116 Unusual residues: {'BMA': 1, 'MAN': 7, 'NAG': 2} Classifications: {'undetermined': 10} Link IDs: {None: 9} Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 20 Unresolved non-hydrogen dihedrals: 30 Unresolved non-hydrogen chiralities: 10 Chain: "4" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "5" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "6" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "7" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "8" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "9" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "AA" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "A" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "B" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "C" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "D" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "E" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "F" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Time building chain proxies: 11.17, per 1000 atoms: 0.52 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 - 3.50 Amino acid : False - 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: 11.17 Conformation dependent library (CDL) restraints added in 3.3 seconds 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: 2.66 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: 7.65 Time building geometry restraints manager: 11.75 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: 93.55 - 104.69: 624 104.69 - 115.82: 15132 115.82 - 126.96: 13355 126.96 - 138.09: 402 138.09 - 149.23: 19 Bond angle restraints: 29532 Sorted by residual: angle pdb=" N GLU E 648 " pdb=" CA GLU E 648 " pdb=" C GLU E 648 " ideal model delta sigma weight residual 110.80 149.23 -38.43 2.13e+00 2.20e-01 3.26e+02 angle pdb=" N GLU B 648 " pdb=" CA GLU B 648 " pdb=" C GLU B 648 " ideal model delta sigma weight residual 110.80 149.22 -38.42 2.13e+00 2.20e-01 3.25e+02 angle pdb=" N GLU F 648 " pdb=" CA GLU F 648 " pdb=" C GLU F 648 " ideal model delta sigma weight residual 110.80 149.17 -38.37 2.13e+00 2.20e-01 3.25e+02 angle pdb=" O LEU D 86 " pdb=" C LEU D 86 " pdb=" N GLU D 87 " ideal model delta sigma weight residual 122.87 102.49 20.38 1.23e+00 6.61e-01 2.74e+02 angle pdb=" O LEU A 86 " pdb=" C LEU A 86 " pdb=" N GLU A 87 " ideal model delta sigma weight residual 122.87 102.49 20.38 1.23e+00 6.61e-01 2.74e+02 ... (remaining 29527 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 21.93: 14559 21.93 - 43.86: 438 43.86 - 65.79: 102 65.79 - 87.72: 177 87.72 - 109.65: 126 Dihedral angle restraints: 15402 sinusoidal: 8469 harmonic: 6933 Sorted by residual: dihedral pdb=" CB CYS C 378 " pdb=" SG CYS C 378 " pdb=" SG CYS C 445 " pdb=" CB CYS C 445 " ideal model delta sinusoidal sigma weight residual -86.00 -162.25 76.25 1 1.00e+01 1.00e-02 7.32e+01 dihedral pdb=" CB CYS D 378 " pdb=" SG CYS D 378 " pdb=" SG CYS D 445 " pdb=" CB CYS D 445 " ideal model delta sinusoidal sigma weight residual -86.00 -162.24 76.24 1 1.00e+01 1.00e-02 7.32e+01 dihedral pdb=" CB CYS A 378 " pdb=" SG CYS A 378 " pdb=" SG CYS A 445 " pdb=" CB CYS A 445 " ideal model delta sinusoidal sigma weight residual -86.00 -162.24 76.24 1 1.00e+01 1.00e-02 7.32e+01 ... (remaining 15399 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.227: 3774 0.227 - 0.455: 129 0.455 - 0.682: 15 0.682 - 0.909: 3 0.909 - 1.137: 3 Chirality restraints: 3924 Sorted by residual: chirality pdb=" C1 MAN S 7 " pdb=" O3 MAN S 6 " pdb=" C2 MAN S 7 " pdb=" O5 MAN S 7 " both_signs ideal model delta sigma weight residual False 2.40 1.62 0.78 2.00e-02 2.50e+03 1.53e+03 chirality pdb=" C1 MAN j 7 " pdb=" O3 MAN j 6 " pdb=" C2 MAN j 7 " pdb=" O5 MAN j 7 " both_signs ideal model delta sigma weight residual False 2.40 1.62 0.78 2.00e-02 2.50e+03 1.52e+03 chirality pdb=" C1 MAN z 7 " pdb=" O3 MAN z 6 " pdb=" C2 MAN z 7 " pdb=" O5 MAN z 7 " both_signs ideal model delta sigma weight residual False 2.40 1.62 0.78 2.00e-02 2.50e+03 1.51e+03 ... (remaining 3921 not shown) Planarity restraints: 3510 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB ASN E 637 " -0.193 2.00e-02 2.50e+03 2.16e-01 5.85e+02 pdb=" CG ASN E 637 " 0.074 2.00e-02 2.50e+03 pdb=" OD1 ASN E 637 " 0.028 2.00e-02 2.50e+03 pdb=" ND2 ASN E 637 " 0.351 2.00e-02 2.50e+03 pdb=" C1 NAG E1637 " -0.259 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN B 637 " 0.193 2.00e-02 2.50e+03 2.16e-01 5.84e+02 pdb=" CG ASN B 637 " -0.074 2.00e-02 2.50e+03 pdb=" OD1 ASN B 637 " -0.028 2.00e-02 2.50e+03 pdb=" ND2 ASN B 637 " -0.351 2.00e-02 2.50e+03 pdb=" C1 NAG B1637 " 0.259 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN F 637 " -0.193 2.00e-02 2.50e+03 2.16e-01 5.84e+02 pdb=" CG ASN F 637 " 0.074 2.00e-02 2.50e+03 pdb=" OD1 ASN F 637 " 0.028 2.00e-02 2.50e+03 pdb=" ND2 ASN F 637 " 0.351 2.00e-02 2.50e+03 pdb=" C1 NAG F1637 " -0.259 2.00e-02 2.50e+03 ... (remaining 3507 not shown) Histogram of nonbonded interaction distances: 1.99 - 2.57: 209 2.57 - 3.15: 17972 3.15 - 3.73: 29769 3.73 - 4.32: 45133 4.32 - 4.90: 69912 Nonbonded interactions: 162995 Sorted by model distance: nonbonded pdb=" ND2 ASN D 279 " pdb=" O6 NAG 0 1 " model vdw 1.986 2.520 nonbonded pdb=" ND2 ASN A 279 " pdb=" O6 NAG T 1 " model vdw 1.987 2.520 nonbonded pdb=" ND2 ASN C 279 " pdb=" O6 NAG k 1 " model vdw 1.987 2.520 nonbonded pdb=" O ALA I 52C" pdb=" N2 NAG 2 1 " model vdw 2.062 2.520 nonbonded pdb=" O ALA H 52C" pdb=" N2 NAG V 1 " model vdw 2.063 2.520 ... (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 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: 0.980 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.010 Extract box with map and model: 4.760 Check model and map are aligned: 0.310 Set scattering table: 0.200 Process input model: 57.950 Find NCS groups from input model: 1.440 Set up NCS constraints: 0.560 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:2.710 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 68.940 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6813 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.012 0.278 21711 Z= 0.781 Angle : 1.981 38.429 29532 Z= 1.168 Chirality : 0.109 1.137 3924 Planarity : 0.015 0.198 3450 Dihedral : 17.674 109.654 10800 Min Nonbonded Distance : 1.986 Molprobity Statistics. All-atom Clashscore : 10.73 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.40 (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 TRP 0.040 0.001 TRP G 100J HIS 0.001 0.000 HIS H 59 PHE 0.003 0.000 PHE D 382 TYR 0.020 0.001 TYR J 87 ARG 0.002 0.000 ARG C 360 *********************** 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 fitting. rotamer outliers: 6 poor density : 533 time to evaluate : 2.123 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 95 MET cc_start: 0.8071 (ptm) cc_final: 0.7855 (ptp) REVERT: A 195 ASN cc_start: 0.8943 (p0) cc_final: 0.8520 (t0) REVERT: A 377 ASN cc_start: 0.9037 (t0) cc_final: 0.8638 (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: 0.6463 (t) REVERT: B 571 TRP cc_start: 0.7966 (m-10) cc_final: 0.7323 (m-10) REVERT: B 576 LEU cc_start: 0.7974 (tp) cc_final: 0.7682 (tp) REVERT: B 642 ILE cc_start: 0.8771 (mt) cc_final: 0.8530 (tp) REVERT: C 95 MET cc_start: 0.7875 (ptm) cc_final: 0.7564 (ptp) REVERT: C 100 MET cc_start: 0.7004 (mtp) cc_final: 0.6569 (ttt) REVERT: C 201 ILE cc_start: 0.9223 (tt) cc_final: 0.8834 (tt) REVERT: C 377 ASN cc_start: 0.8989 (t0) cc_final: 0.8646 (t0) REVERT: D 95 MET cc_start: 0.8040 (ptm) cc_final: 0.7644 (ptp) REVERT: D 201 ILE cc_start: 0.9262 (tt) cc_final: 0.9040 (tt) REVERT: D 377 ASN cc_start: 0.8977 (t0) cc_final: 0.8598 (t0) REVERT: D 423 ILE cc_start: 0.9430 (mt) cc_final: 0.9224 (mt) REVERT: E 571 TRP cc_start: 0.7542 (m-10) cc_final: 0.7186 (m-10) REVERT: E 576 LEU cc_start: 0.8151 (tp) cc_final: 0.7763 (tt) REVERT: E 642 ILE cc_start: 0.8835 (mt) cc_final: 0.8575 (tp) REVERT: F 571 TRP cc_start: 0.7883 (m-10) cc_final: 0.7285 (m-10) REVERT: F 576 LEU cc_start: 0.8357 (tp) cc_final: 0.8076 (tt) REVERT: G 24 VAL cc_start: 0.7870 (t) cc_final: 0.7585 (t) REVERT: J 46 LEU cc_start: 0.8387 (tp) cc_final: 0.8160 (tt) REVERT: J 86 TYR cc_start: 0.5311 (m-80) cc_final: 0.5002 (m-10) REVERT: K 46 LEU cc_start: 0.8407 (tp) cc_final: 0.8074 (tt) REVERT: K 91 LEU cc_start: 0.7821 (tp) cc_final: 0.7581 (tp) outliers start: 6 outliers final: 3 residues processed: 539 average time/residue: 0.3654 time to fit residues: 288.4834 Evaluate side-chains 269 residues out of total 2103 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 266 time to evaluate : 2.263 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 237 random chunks: chunk 200 optimal weight: 1.9990 chunk 179 optimal weight: 2.9990 chunk 99 optimal weight: 7.9990 chunk 61 optimal weight: 1.9990 chunk 121 optimal weight: 2.9990 chunk 95 optimal weight: 10.0000 chunk 185 optimal weight: 5.9990 chunk 71 optimal weight: 0.8980 chunk 112 optimal weight: 5.9990 chunk 138 optimal weight: 10.0000 chunk 215 optimal weight: 8.9990 overall best weight: 2.1788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 85 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 293 GLN A 300 ASN A 348 GLN ** B 540 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 607 ASN B 630 GLN C 136 ASN 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 ** L 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 39 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7008 moved from start: 0.3017 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 21711 Z= 0.267 Angle : 0.911 14.485 29532 Z= 0.433 Chirality : 0.051 0.564 3924 Planarity : 0.004 0.049 3450 Dihedral : 15.808 88.789 6432 Min Nonbonded Distance : 2.012 Molprobity Statistics. All-atom Clashscore : 8.91 Ramachandran Plot: Outliers : 0.51 % Allowed : 6.44 % Favored : 93.05 % Rotamer: Outliers : 0.14 % Allowed : 1.76 % Favored : 98.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.78 % Cis-general : 0.39 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.53 (0.16), residues: 2361 helix: -0.98 (0.24), residues: 411 sheet: -0.44 (0.20), residues: 669 loop : -1.32 (0.16), residues: 1281 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP B 623 HIS 0.006 0.001 HIS L 39 PHE 0.016 0.002 PHE A 382 TYR 0.031 0.002 TYR I 58 ARG 0.006 0.001 ARG C 166 *********************** 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 339 residues out of total 2103 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 336 time to evaluate : 2.546 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: A 161 MET cc_start: 0.8346 (tpp) cc_final: 0.8079 (tpp) REVERT: A 377 ASN cc_start: 0.8994 (t0) cc_final: 0.8667 (t0) REVERT: B 536 THR cc_start: 0.6169 (m) cc_final: 0.5856 (m) REVERT: B 543 ASN cc_start: 0.7737 (t0) cc_final: 0.7385 (t0) REVERT: B 642 ILE cc_start: 0.8698 (mt) cc_final: 0.8450 (tp) REVERT: C 100 MET cc_start: 0.6993 (mtp) cc_final: 0.6336 (mtp) REVERT: C 377 ASN cc_start: 0.9073 (t0) cc_final: 0.8858 (t0) REVERT: D 377 ASN cc_start: 0.9113 (t0) cc_final: 0.8709 (t0) REVERT: E 543 ASN cc_start: 0.7523 (t0) cc_final: 0.7240 (t0) REVERT: E 642 ILE cc_start: 0.8973 (mt) cc_final: 0.8539 (tp) REVERT: F 543 ASN cc_start: 0.7743 (t0) cc_final: 0.7423 (t0) REVERT: G 22 CYS cc_start: -0.0896 (t) cc_final: -0.1210 (t) REVERT: G 33 ASN cc_start: 0.8135 (p0) cc_final: 0.7646 (p0) REVERT: G 72 ASP cc_start: 0.4343 (t0) cc_final: 0.1061 (t0) REVERT: H 33 ASN cc_start: 0.7909 (p0) cc_final: 0.7491 (p0) REVERT: I 100 ASP cc_start: 0.7694 (m-30) cc_final: 0.7423 (m-30) REVERT: J 24 THR cc_start: 0.6111 (m) cc_final: 0.5472 (m) REVERT: K 24 THR cc_start: 0.6252 (m) cc_final: 0.5934 (m) REVERT: L 47 VAL cc_start: 0.7305 (m) cc_final: 0.7068 (p) outliers start: 3 outliers final: 0 residues processed: 337 average time/residue: 0.3447 time to fit residues: 174.9114 Evaluate side-chains 233 residues out of total 2103 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 233 time to evaluate : 2.246 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 237 random chunks: chunk 119 optimal weight: 5.9990 chunk 66 optimal weight: 8.9990 chunk 179 optimal weight: 5.9990 chunk 146 optimal weight: 2.9990 chunk 59 optimal weight: 20.0000 chunk 215 optimal weight: 9.9990 chunk 232 optimal weight: 4.9990 chunk 192 optimal weight: 0.6980 chunk 213 optimal weight: 20.0000 chunk 73 optimal weight: 3.9990 chunk 172 optimal weight: 6.9990 overall best weight: 3.7388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 195 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 630 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 195 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 293 GLN ** D 195 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 422 GLN K 17 GLN K 94 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7172 moved from start: 0.4048 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.061 21711 Z= 0.331 Angle : 0.871 13.734 29532 Z= 0.416 Chirality : 0.048 0.396 3924 Planarity : 0.004 0.040 3450 Dihedral : 12.758 85.218 6432 Min Nonbonded Distance : 2.076 Molprobity Statistics. All-atom Clashscore : 11.97 Ramachandran Plot: Outliers : 0.51 % Allowed : 7.67 % Favored : 91.83 % Rotamer: Outliers : 0.05 % Allowed : 1.76 % Favored : 98.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.78 % Cis-general : 0.39 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.27 (0.17), residues: 2361 helix: -0.55 (0.25), residues: 411 sheet: -0.08 (0.19), residues: 747 loop : -1.44 (0.17), residues: 1203 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.002 TRP B 571 HIS 0.011 0.002 HIS L 39 PHE 0.018 0.002 PHE C 382 TYR 0.028 0.002 TYR H 58 ARG 0.008 0.001 ARG G 66 *********************** 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 287 residues out of total 2103 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 286 time to evaluate : 2.177 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 109 ILE cc_start: 0.9167 (mt) cc_final: 0.8835 (tt) REVERT: A 161 MET cc_start: 0.8366 (tpp) cc_final: 0.7977 (tpp) REVERT: A 309 ILE cc_start: 0.8161 (mp) cc_final: 0.7802 (mp) REVERT: B 543 ASN cc_start: 0.8019 (t0) cc_final: 0.7685 (t0) REVERT: B 642 ILE cc_start: 0.8778 (mt) cc_final: 0.8467 (tp) REVERT: B 647 GLU cc_start: 0.5723 (tp30) cc_final: 0.5514 (tp30) REVERT: C 100 MET cc_start: 0.7029 (mtp) cc_final: 0.6588 (mtp) REVERT: C 434 MET cc_start: 0.8720 (tmm) cc_final: 0.8349 (ttm) REVERT: D 109 ILE cc_start: 0.8931 (mt) cc_final: 0.8484 (tt) REVERT: E 543 ASN cc_start: 0.7964 (t0) cc_final: 0.7625 (t0) REVERT: E 642 ILE cc_start: 0.8992 (mt) cc_final: 0.8630 (tp) REVERT: G 33 ASN cc_start: 0.8077 (p0) cc_final: 0.7670 (p0) REVERT: H 33 ASN cc_start: 0.8047 (p0) cc_final: 0.7657 (p0) REVERT: I 100 ASP cc_start: 0.8466 (m-30) cc_final: 0.7965 (m-30) REVERT: J 24 THR cc_start: 0.6454 (m) cc_final: 0.5953 (m) outliers start: 1 outliers final: 0 residues processed: 286 average time/residue: 0.3439 time to fit residues: 147.7637 Evaluate side-chains 190 residues out of total 2103 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 190 time to evaluate : 2.247 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 237 random chunks: chunk 213 optimal weight: 10.0000 chunk 162 optimal weight: 9.9990 chunk 111 optimal weight: 1.9990 chunk 23 optimal weight: 9.9990 chunk 102 optimal weight: 10.0000 chunk 144 optimal weight: 5.9990 chunk 216 optimal weight: 9.9990 chunk 229 optimal weight: 3.9990 chunk 113 optimal weight: 5.9990 chunk 205 optimal weight: 4.9990 chunk 61 optimal weight: 1.9990 overall best weight: 3.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 607 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 630 GLN ** B 650 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 653 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 656 ASN C 422 GLN ** E 650 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 59 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7241 moved from start: 0.4710 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.054 21711 Z= 0.331 Angle : 0.816 13.246 29532 Z= 0.393 Chirality : 0.047 0.400 3924 Planarity : 0.004 0.047 3450 Dihedral : 10.878 80.592 6432 Min Nonbonded Distance : 2.030 Molprobity Statistics. All-atom Clashscore : 13.04 Ramachandran Plot: Outliers : 0.51 % Allowed : 7.29 % Favored : 92.21 % Rotamer: Outliers : 0.05 % Allowed : 2.28 % Favored : 97.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.78 % Cis-general : 0.39 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.18 (0.17), residues: 2361 helix: -0.22 (0.27), residues: 390 sheet: 0.06 (0.19), residues: 699 loop : -1.48 (0.16), residues: 1272 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.045 0.002 TRP F 571 HIS 0.004 0.001 HIS H 52A PHE 0.020 0.002 PHE D 53 TYR 0.027 0.002 TYR H 58 ARG 0.006 0.001 ARG G 94 *********************** 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 249 residues out of total 2103 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 248 time to evaluate : 2.154 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 109 ILE cc_start: 0.9078 (mt) cc_final: 0.8795 (tt) REVERT: A 161 MET cc_start: 0.8502 (tpp) cc_final: 0.8141 (tpp) REVERT: A 188 ASN cc_start: 0.8078 (p0) cc_final: 0.7794 (p0) REVERT: A 309 ILE cc_start: 0.8260 (mp) cc_final: 0.7808 (mp) REVERT: B 543 ASN cc_start: 0.7988 (t0) cc_final: 0.7696 (t0) REVERT: B 642 ILE cc_start: 0.8907 (mt) cc_final: 0.8544 (tp) REVERT: C 434 MET cc_start: 0.8322 (tmm) cc_final: 0.7970 (ttm) REVERT: D 434 MET cc_start: 0.8617 (tmm) cc_final: 0.8270 (tmm) REVERT: E 642 ILE cc_start: 0.8998 (mt) cc_final: 0.8605 (tp) REVERT: G 33 ASN cc_start: 0.8024 (p0) cc_final: 0.7814 (p0) REVERT: H 33 ASN cc_start: 0.8091 (p0) cc_final: 0.7740 (p0) REVERT: I 33 ASN cc_start: 0.8127 (p0) cc_final: 0.7880 (p0) outliers start: 1 outliers final: 1 residues processed: 249 average time/residue: 0.3315 time to fit residues: 128.5605 Evaluate side-chains 182 residues out of total 2103 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 181 time to evaluate : 2.284 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 237 random chunks: chunk 190 optimal weight: 20.0000 chunk 130 optimal weight: 2.9990 chunk 3 optimal weight: 7.9990 chunk 170 optimal weight: 8.9990 chunk 94 optimal weight: 3.9990 chunk 195 optimal weight: 20.0000 chunk 158 optimal weight: 0.9980 chunk 0 optimal weight: 8.9990 chunk 116 optimal weight: 8.9990 chunk 205 optimal weight: 0.6980 chunk 57 optimal weight: 0.2980 overall best weight: 1.7984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 293 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 607 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 650 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 653 GLN ** D 99 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 293 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 17 GLN ** L 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7180 moved from start: 0.4918 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 21711 Z= 0.205 Angle : 0.724 12.939 29532 Z= 0.350 Chirality : 0.047 0.423 3924 Planarity : 0.004 0.037 3450 Dihedral : 9.880 76.136 6432 Min Nonbonded Distance : 2.131 Molprobity Statistics. All-atom Clashscore : 10.20 Ramachandran Plot: Outliers : 0.51 % Allowed : 7.20 % Favored : 92.29 % Rotamer: Outliers : 0.05 % Allowed : 1.05 % Favored : 98.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.78 % Cis-general : 0.39 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.01 (0.17), residues: 2361 helix: 0.21 (0.28), residues: 390 sheet: 0.12 (0.20), residues: 654 loop : -1.39 (0.17), residues: 1317 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.038 0.002 TRP F 571 HIS 0.005 0.001 HIS D 374 PHE 0.014 0.001 PHE D 317 TYR 0.020 0.002 TYR H 58 ARG 0.004 0.000 ARG B 588 *********************** 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 249 residues out of total 2103 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 248 time to evaluate : 2.150 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 109 ILE cc_start: 0.9041 (mt) cc_final: 0.8777 (tt) REVERT: A 161 MET cc_start: 0.8481 (tpp) cc_final: 0.8060 (tpp) REVERT: A 309 ILE cc_start: 0.8281 (mp) cc_final: 0.7790 (mp) REVERT: B 543 ASN cc_start: 0.7976 (t0) cc_final: 0.7759 (t0) REVERT: B 642 ILE cc_start: 0.8892 (mt) cc_final: 0.8516 (tp) REVERT: C 434 MET cc_start: 0.8281 (tmm) cc_final: 0.7778 (ttm) REVERT: D 109 ILE cc_start: 0.9053 (mt) cc_final: 0.8573 (tt) REVERT: E 642 ILE cc_start: 0.8879 (mt) cc_final: 0.8626 (tp) REVERT: G 33 ASN cc_start: 0.8278 (p0) cc_final: 0.8004 (p0) REVERT: H 33 ASN cc_start: 0.7926 (p0) cc_final: 0.7533 (p0) REVERT: I 33 ASN cc_start: 0.8120 (p0) cc_final: 0.7860 (p0) outliers start: 1 outliers final: 1 residues processed: 249 average time/residue: 0.3206 time to fit residues: 124.7119 Evaluate side-chains 178 residues out of total 2103 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 177 time to evaluate : 2.152 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 237 random chunks: chunk 77 optimal weight: 9.9990 chunk 206 optimal weight: 10.0000 chunk 45 optimal weight: 0.9990 chunk 134 optimal weight: 0.0470 chunk 56 optimal weight: 10.0000 chunk 229 optimal weight: 9.9990 chunk 190 optimal weight: 20.0000 chunk 106 optimal weight: 0.9990 chunk 19 optimal weight: 9.9990 chunk 75 optimal weight: 2.9990 chunk 120 optimal weight: 6.9990 overall best weight: 2.4086 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 293 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 99 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 293 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 5 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7212 moved from start: 0.5204 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.060 21711 Z= 0.237 Angle : 0.721 12.682 29532 Z= 0.347 Chirality : 0.046 0.394 3924 Planarity : 0.004 0.037 3450 Dihedral : 9.336 72.546 6432 Min Nonbonded Distance : 2.035 Molprobity Statistics. All-atom Clashscore : 11.08 Ramachandran Plot: Outliers : 0.51 % Allowed : 7.45 % Favored : 92.04 % Rotamer: Outliers : 0.00 % Allowed : 1.14 % Favored : 98.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.78 % Cis-general : 0.39 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.00 (0.17), residues: 2361 helix: 0.41 (0.28), residues: 387 sheet: 0.13 (0.20), residues: 651 loop : -1.45 (0.17), residues: 1323 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.002 TRP F 571 HIS 0.004 0.001 HIS A 374 PHE 0.014 0.002 PHE D 53 TYR 0.017 0.002 TYR H 58 ARG 0.002 0.000 ARG G 94 *********************** 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 238 residues out of total 2103 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 238 time to evaluate : 2.742 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 109 ILE cc_start: 0.9057 (mt) cc_final: 0.8765 (tt) REVERT: A 161 MET cc_start: 0.8382 (tpp) cc_final: 0.7942 (tpp) REVERT: A 309 ILE cc_start: 0.8239 (mp) cc_final: 0.7733 (mp) REVERT: B 543 ASN cc_start: 0.7984 (t0) cc_final: 0.7756 (t0) REVERT: B 642 ILE cc_start: 0.8883 (mt) cc_final: 0.8537 (tp) REVERT: C 100 MET cc_start: 0.6984 (mtp) cc_final: 0.6780 (mtp) REVERT: C 434 MET cc_start: 0.8282 (tmm) cc_final: 0.7485 (ttm) REVERT: D 109 ILE cc_start: 0.9011 (mt) cc_final: 0.8524 (tt) REVERT: G 33 ASN cc_start: 0.8311 (p0) cc_final: 0.8007 (p0) REVERT: H 24 VAL cc_start: 0.7900 (t) cc_final: 0.7688 (t) REVERT: H 33 ASN cc_start: 0.8099 (p0) cc_final: 0.7718 (p0) REVERT: I 33 ASN cc_start: 0.8097 (p0) cc_final: 0.7877 (p0) outliers start: 0 outliers final: 0 residues processed: 238 average time/residue: 0.3049 time to fit residues: 116.7005 Evaluate side-chains 181 residues out of total 2103 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 181 time to evaluate : 2.158 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 237 random chunks: chunk 221 optimal weight: 0.9980 chunk 25 optimal weight: 0.5980 chunk 130 optimal weight: 4.9990 chunk 167 optimal weight: 2.9990 chunk 129 optimal weight: 5.9990 chunk 193 optimal weight: 8.9990 chunk 128 optimal weight: 4.9990 chunk 228 optimal weight: 30.0000 chunk 142 optimal weight: 0.8980 chunk 139 optimal weight: 2.9990 chunk 105 optimal weight: 0.8980 overall best weight: 1.2782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 85 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 293 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 374 HIS ** B 607 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 650 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 99 ASN C 374 HIS ** D 99 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 293 GLN ** D 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7168 moved from start: 0.5346 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 21711 Z= 0.170 Angle : 0.685 12.410 29532 Z= 0.330 Chirality : 0.046 0.382 3924 Planarity : 0.003 0.034 3450 Dihedral : 8.728 66.641 6432 Min Nonbonded Distance : 2.090 Molprobity Statistics. All-atom Clashscore : 9.96 Ramachandran Plot: Outliers : 0.51 % Allowed : 6.78 % Favored : 92.71 % Rotamer: Outliers : 0.05 % Allowed : 0.76 % Favored : 99.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.78 % Cis-general : 0.39 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.98 (0.17), residues: 2361 helix: 0.45 (0.28), residues: 390 sheet: 0.17 (0.20), residues: 654 loop : -1.47 (0.17), residues: 1317 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.001 TRP F 571 HIS 0.003 0.001 HIS A 374 PHE 0.018 0.001 PHE B 519 TYR 0.016 0.001 TYR H 58 ARG 0.006 0.000 ARG A 500 *********************** 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 239 residues out of total 2103 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 238 time to evaluate : 2.487 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: A 109 ILE cc_start: 0.9014 (mt) cc_final: 0.8774 (tt) REVERT: A 161 MET cc_start: 0.8305 (tpp) cc_final: 0.7862 (tpp) REVERT: A 309 ILE cc_start: 0.8235 (mp) cc_final: 0.7681 (mp) REVERT: B 543 ASN cc_start: 0.7944 (t0) cc_final: 0.7699 (t0) REVERT: B 642 ILE cc_start: 0.8853 (mt) cc_final: 0.8529 (tp) REVERT: C 434 MET cc_start: 0.8139 (tmm) cc_final: 0.7451 (ttm) REVERT: D 109 ILE cc_start: 0.9002 (mt) cc_final: 0.8503 (tt) REVERT: D 434 MET cc_start: 0.8510 (tmm) cc_final: 0.8276 (tmm) REVERT: G 33 ASN cc_start: 0.8335 (p0) cc_final: 0.7968 (p0) REVERT: H 33 ASN cc_start: 0.8004 (p0) cc_final: 0.7687 (p0) REVERT: I 33 ASN cc_start: 0.8007 (p0) cc_final: 0.7802 (p0) REVERT: I 48 VAL cc_start: 0.6512 (t) cc_final: 0.6302 (t) outliers start: 1 outliers final: 0 residues processed: 239 average time/residue: 0.2973 time to fit residues: 113.6783 Evaluate side-chains 178 residues out of total 2103 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 178 time to evaluate : 2.215 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 237 random chunks: chunk 141 optimal weight: 7.9990 chunk 91 optimal weight: 0.8980 chunk 136 optimal weight: 6.9990 chunk 68 optimal weight: 0.4980 chunk 44 optimal weight: 9.9990 chunk 145 optimal weight: 0.2980 chunk 155 optimal weight: 0.4980 chunk 112 optimal weight: 5.9990 chunk 21 optimal weight: 5.9990 chunk 179 optimal weight: 1.9990 chunk 207 optimal weight: 20.0000 overall best weight: 0.8382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 85 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 293 GLN ** B 607 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 650 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 99 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 651 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7145 moved from start: 0.5461 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 21711 Z= 0.156 Angle : 0.671 12.244 29532 Z= 0.323 Chirality : 0.045 0.367 3924 Planarity : 0.003 0.034 3450 Dihedral : 8.247 59.890 6432 Min Nonbonded Distance : 2.109 Molprobity Statistics. All-atom Clashscore : 9.46 Ramachandran Plot: Outliers : 0.51 % Allowed : 6.44 % Favored : 93.05 % Rotamer: Outliers : 0.00 % Allowed : 0.43 % Favored : 99.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.78 % Cis-general : 0.39 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.91 (0.17), residues: 2361 helix: 0.48 (0.28), residues: 390 sheet: 0.28 (0.20), residues: 660 loop : -1.46 (0.17), residues: 1311 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.001 TRP B 571 HIS 0.005 0.001 HIS A 374 PHE 0.018 0.001 PHE B 519 TYR 0.027 0.001 TYR D 40 ARG 0.002 0.000 ARG G 94 *********************** 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 241 residues out of total 2103 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 241 time to evaluate : 2.276 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 109 ILE cc_start: 0.9001 (mt) cc_final: 0.8732 (tt) REVERT: A 161 MET cc_start: 0.8257 (tpp) cc_final: 0.7788 (tpp) REVERT: A 309 ILE cc_start: 0.8205 (mp) cc_final: 0.7655 (mp) REVERT: A 434 MET cc_start: 0.8512 (tmm) cc_final: 0.8305 (tmm) REVERT: B 543 ASN cc_start: 0.7889 (t0) cc_final: 0.7662 (t0) REVERT: B 642 ILE cc_start: 0.8868 (mt) cc_final: 0.8538 (tp) REVERT: C 434 MET cc_start: 0.8182 (tmm) cc_final: 0.7495 (ttm) REVERT: D 109 ILE cc_start: 0.8948 (mt) cc_final: 0.8487 (tt) REVERT: E 642 ILE cc_start: 0.8912 (mt) cc_final: 0.8650 (tp) REVERT: G 24 VAL cc_start: 0.8172 (t) cc_final: 0.7944 (t) REVERT: G 33 ASN cc_start: 0.8303 (p0) cc_final: 0.7925 (p0) REVERT: H 33 ASN cc_start: 0.8041 (p0) cc_final: 0.7685 (p0) REVERT: I 33 ASN cc_start: 0.7928 (p0) cc_final: 0.7615 (p0) REVERT: I 48 VAL cc_start: 0.6479 (t) cc_final: 0.6199 (t) REVERT: K 47 VAL cc_start: 0.7068 (m) cc_final: 0.6788 (p) outliers start: 0 outliers final: 0 residues processed: 241 average time/residue: 0.3055 time to fit residues: 117.6861 Evaluate side-chains 176 residues out of total 2103 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 176 time to evaluate : 2.276 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 237 random chunks: chunk 218 optimal weight: 40.0000 chunk 199 optimal weight: 9.9990 chunk 212 optimal weight: 6.9990 chunk 128 optimal weight: 2.9990 chunk 92 optimal weight: 0.9980 chunk 167 optimal weight: 0.0870 chunk 65 optimal weight: 6.9990 chunk 192 optimal weight: 0.9990 chunk 201 optimal weight: 9.9990 chunk 139 optimal weight: 10.0000 chunk 225 optimal weight: 5.9990 overall best weight: 2.2164 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 607 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 650 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 99 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 59 HIS ** K 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7197 moved from start: 0.5645 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 21711 Z= 0.226 Angle : 0.695 11.930 29532 Z= 0.333 Chirality : 0.045 0.373 3924 Planarity : 0.003 0.036 3450 Dihedral : 8.133 59.751 6432 Min Nonbonded Distance : 2.073 Molprobity Statistics. All-atom Clashscore : 11.42 Ramachandran Plot: Outliers : 0.51 % Allowed : 7.12 % Favored : 92.38 % Rotamer: Outliers : 0.00 % Allowed : 0.24 % Favored : 99.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.78 % Cis-general : 0.39 % Twisted Proline : 0.00 % Twisted General : 0.09 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.95 (0.17), residues: 2361 helix: 0.53 (0.29), residues: 390 sheet: 0.18 (0.20), residues: 654 loop : -1.46 (0.17), residues: 1317 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.032 0.002 TRP B 571 HIS 0.003 0.001 HIS A 216 PHE 0.018 0.002 PHE B 519 TYR 0.014 0.002 TYR K 87 ARG 0.002 0.000 ARG A 273 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4722 Ramachandran restraints generated. 2361 Oldfield, 0 Emsley, 2361 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4722 Ramachandran restraints generated. 2361 Oldfield, 0 Emsley, 2361 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 232 residues out of total 2103 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 232 time to evaluate : 2.698 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 109 ILE cc_start: 0.9019 (mt) cc_final: 0.8747 (tt) REVERT: A 161 MET cc_start: 0.8335 (tpp) cc_final: 0.7842 (tpp) REVERT: A 309 ILE cc_start: 0.8175 (mp) cc_final: 0.7653 (mp) REVERT: B 642 ILE cc_start: 0.8872 (mt) cc_final: 0.8576 (tp) REVERT: C 434 MET cc_start: 0.8133 (tmm) cc_final: 0.7506 (ttm) REVERT: E 642 ILE cc_start: 0.8977 (mt) cc_final: 0.8687 (tp) REVERT: G 24 VAL cc_start: 0.8295 (t) cc_final: 0.8068 (t) REVERT: G 33 ASN cc_start: 0.8335 (p0) cc_final: 0.7890 (p0) REVERT: H 33 ASN cc_start: 0.8108 (p0) cc_final: 0.7827 (p0) REVERT: I 33 ASN cc_start: 0.8130 (p0) cc_final: 0.7819 (p0) outliers start: 0 outliers final: 0 residues processed: 232 average time/residue: 0.3155 time to fit residues: 115.7686 Evaluate side-chains 172 residues out of total 2103 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 172 time to evaluate : 2.292 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 237 random chunks: chunk 137 optimal weight: 9.9990 chunk 106 optimal weight: 1.9990 chunk 156 optimal weight: 10.0000 chunk 236 optimal weight: 6.9990 chunk 217 optimal weight: 20.0000 chunk 188 optimal weight: 9.9990 chunk 19 optimal weight: 7.9990 chunk 145 optimal weight: 0.2980 chunk 115 optimal weight: 0.2980 chunk 149 optimal weight: 0.7980 chunk 200 optimal weight: 5.9990 overall best weight: 1.8784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 85 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 607 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 650 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 99 ASN D 374 HIS ** E 650 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 651 ASN E 656 ASN ** K 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7185 moved from start: 0.5818 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 21711 Z= 0.199 Angle : 0.677 11.680 29532 Z= 0.327 Chirality : 0.045 0.360 3924 Planarity : 0.003 0.035 3450 Dihedral : 7.892 59.850 6432 Min Nonbonded Distance : 2.021 Molprobity Statistics. All-atom Clashscore : 11.47 Ramachandran Plot: Outliers : 0.51 % Allowed : 6.44 % Favored : 93.05 % 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 : 0.09 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.89 (0.17), residues: 2361 helix: 0.60 (0.29), residues: 384 sheet: 0.24 (0.20), residues: 651 loop : -1.43 (0.17), residues: 1326 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.032 0.001 TRP B 571 HIS 0.005 0.001 HIS D 374 PHE 0.019 0.001 PHE B 519 TYR 0.037 0.002 TYR A 217 ARG 0.002 0.000 ARG I 105 ********************** 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 236 residues out of total 2103 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 236 time to evaluate : 2.499 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 109 ILE cc_start: 0.8969 (mt) cc_final: 0.8669 (tt) REVERT: A 484 TYR cc_start: 0.7511 (p90) cc_final: 0.7261 (p90) REVERT: B 642 ILE cc_start: 0.8850 (mt) cc_final: 0.8324 (tp) REVERT: C 434 MET cc_start: 0.8151 (tmm) cc_final: 0.7567 (ttm) REVERT: D 434 MET cc_start: 0.8595 (tmm) cc_final: 0.8242 (tmm) REVERT: E 543 ASN cc_start: 0.7635 (t0) cc_final: 0.7162 (t0) REVERT: G 33 ASN cc_start: 0.8320 (p0) cc_final: 0.7982 (p0) REVERT: H 33 ASN cc_start: 0.8145 (p0) cc_final: 0.7927 (p0) REVERT: I 33 ASN cc_start: 0.8043 (p0) cc_final: 0.7828 (p0) outliers start: 0 outliers final: 0 residues processed: 236 average time/residue: 0.3019 time to fit residues: 112.7949 Evaluate side-chains 169 residues out of total 2103 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 169 time to evaluate : 2.305 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 237 random chunks: chunk 57 optimal weight: 8.9990 chunk 173 optimal weight: 9.9990 chunk 27 optimal weight: 6.9990 chunk 52 optimal weight: 9.9990 chunk 188 optimal weight: 7.9990 chunk 78 optimal weight: 0.5980 chunk 193 optimal weight: 9.9990 chunk 23 optimal weight: 8.9990 chunk 34 optimal weight: 7.9990 chunk 165 optimal weight: 3.9990 chunk 10 optimal weight: 10.0000 overall best weight: 5.5188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 136 ASN A 170 GLN B 550 GLN ** B 607 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 630 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 650 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 630 GLN ** K 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3088 r_free = 0.3088 target = 0.053018 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2679 r_free = 0.2679 target = 0.039726 restraints weight = 111226.279| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.2720 r_free = 0.2720 target = 0.041034 restraints weight = 64734.704| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.2747 r_free = 0.2747 target = 0.041880 restraints weight = 46186.286| |-----------------------------------------------------------------------------| r_work (final): 0.2727 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8442 moved from start: 0.6177 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.091 21711 Z= 0.457 Angle : 0.883 11.208 29532 Z= 0.423 Chirality : 0.048 0.402 3924 Planarity : 0.005 0.042 3450 Dihedral : 8.741 56.005 6432 Min Nonbonded Distance : 2.046 Molprobity Statistics. All-atom Clashscore : 17.42 Ramachandran Plot: Outliers : 0.51 % Allowed : 8.47 % Favored : 91.02 % Rotamer: Outliers : 0.00 % Allowed : 0.48 % Favored : 99.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.78 % Cis-general : 0.39 % Twisted Proline : 0.00 % Twisted General : 0.09 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.31 (0.17), residues: 2361 helix: -0.01 (0.27), residues: 396 sheet: -0.15 (0.20), residues: 666 loop : -1.56 (0.17), residues: 1299 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.003 TRP D 427 HIS 0.009 0.002 HIS K 39 PHE 0.019 0.003 PHE J 62 TYR 0.031 0.003 TYR D 217 ARG 0.005 0.001 ARG I 105 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3733.14 seconds wall clock time: 69 minutes 48.33 seconds (4188.33 seconds total)