Starting phenix.real_space_refine on Wed Nov 20 01:58:45 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7rso_24676/11_2024/7rso_24676.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7rso_24676/11_2024/7rso_24676.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7rso_24676/11_2024/7rso_24676.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7rso_24676/11_2024/7rso_24676.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7rso_24676/11_2024/7rso_24676.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7rso_24676/11_2024/7rso_24676.cif" } resolution = 4.1 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.066 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 12888 2.51 5 N 3348 2.21 5 O 4212 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 78 residue(s): 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5513/modules/chem_data/mon_lib" Total number of atoms: 20568 Number of models: 1 Model: "" Number of chains: 54 Chain: "A" Number of atoms: 3453 Number of conformers: 1 Conformer: "" Number of residues, atoms: 437, 3453 Classifications: {'peptide': 437} Link IDs: {'PTRANS': 22, 'TRANS': 414} Chain breaks: 3 Chain: "B" Number of atoms: 989 Number of conformers: 1 Conformer: "" Number of residues, atoms: 124, 989 Classifications: {'peptide': 124} Link IDs: {'PTRANS': 1, 'TRANS': 122} Chain breaks: 1 Chain: "H" Number of atoms: 985 Number of conformers: 1 Conformer: "" Number of residues, atoms: 124, 985 Classifications: {'peptide': 124} Link IDs: {'PTRANS': 3, 'TRANS': 120} Chain: "L" Number of atoms: 784 Number of conformers: 1 Conformer: "" Number of residues, atoms: 100, 784 Classifications: {'peptide': 100} Link IDs: {'PCIS': 1, 'PTRANS': 6, 'TRANS': 92} Chain: "C" Number of atoms: 3453 Number of conformers: 1 Conformer: "" Number of residues, atoms: 437, 3453 Classifications: {'peptide': 437} Link IDs: {'PTRANS': 22, 'TRANS': 414} Chain breaks: 3 Chain: "E" Number of atoms: 989 Number of conformers: 1 Conformer: "" Number of residues, atoms: 124, 989 Classifications: {'peptide': 124} Link IDs: {'PTRANS': 1, 'TRANS': 122} Chain breaks: 1 Chain: "D" Number of atoms: 3453 Number of conformers: 1 Conformer: "" Number of residues, atoms: 437, 3453 Classifications: {'peptide': 437} Link IDs: {'PTRANS': 22, 'TRANS': 414} Chain breaks: 3 Chain: "F" Number of atoms: 989 Number of conformers: 1 Conformer: "" Number of residues, atoms: 124, 989 Classifications: {'peptide': 124} Link IDs: {'PTRANS': 1, 'TRANS': 122} Chain breaks: 1 Chain: "G" Number of atoms: 985 Number of conformers: 1 Conformer: "" Number of residues, atoms: 124, 985 Classifications: {'peptide': 124} Link IDs: {'PTRANS': 3, 'TRANS': 120} Chain: "J" Number of atoms: 784 Number of conformers: 1 Conformer: "" Number of residues, atoms: 100, 784 Classifications: {'peptide': 100} Link IDs: {'PCIS': 1, 'PTRANS': 6, 'TRANS': 92} Chain: "I" Number of atoms: 985 Number of conformers: 1 Conformer: "" Number of residues, atoms: 124, 985 Classifications: {'peptide': 124} Link IDs: {'PTRANS': 3, 'TRANS': 120} Chain: "K" Number of atoms: 784 Number of conformers: 1 Conformer: "" Number of residues, atoms: 100, 784 Classifications: {'peptide': 100} Link IDs: {'PCIS': 1, 'PTRANS': 6, 'TRANS': 92} Chain: "M" 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: "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: 72 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 72 Unusual residues: {'BMA': 1, 'MAN': 3, 'NAG': 2} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 18 Unresolved non-hydrogen chiralities: 6 Chain: "Q" 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: "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: 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: "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: 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: "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: 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: 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: "b" Number of atoms: 72 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 72 Unusual residues: {'BMA': 1, 'MAN': 3, 'NAG': 2} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 18 Unresolved non-hydrogen chiralities: 6 Chain: "c" 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: "d" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "e" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "f" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "g" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "h" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "i" Number of atoms: 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: "j" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "k" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "l" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "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: 72 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 72 Unusual residues: {'BMA': 1, 'MAN': 3, 'NAG': 2} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 18 Unresolved non-hydrogen chiralities: 6 Chain: "o" 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: "p" 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: "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: 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: 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: "u" 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: "v" 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: 168 Number of conformers: 1 Conformer: "" Number of residues, atoms: 12, 168 Unusual residues: {'NAG': 12} Classifications: {'undetermined': 12} Link IDs: {None: 11} Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 24 Unresolved non-hydrogen dihedrals: 36 Unresolved non-hydrogen chiralities: 12 Chain: "B" Number of atoms: 42 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 42 Unusual residues: {'NAG': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "C" Number of atoms: 168 Number of conformers: 1 Conformer: "" Number of residues, atoms: 12, 168 Unusual residues: {'NAG': 12} Classifications: {'undetermined': 12} Link IDs: {None: 11} Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 24 Unresolved non-hydrogen dihedrals: 36 Unresolved non-hydrogen chiralities: 12 Chain: "E" Number of atoms: 42 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 42 Unusual residues: {'NAG': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "D" Number of atoms: 168 Number of conformers: 1 Conformer: "" Number of residues, atoms: 12, 168 Unusual residues: {'NAG': 12} Classifications: {'undetermined': 12} Link IDs: {None: 11} Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 24 Unresolved non-hydrogen dihedrals: 36 Unresolved non-hydrogen chiralities: 12 Chain: "F" Number of atoms: 42 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 42 Unusual residues: {'NAG': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Time building chain proxies: 12.35, per 1000 atoms: 0.60 Number of scatterers: 20568 At special positions: 0 Unit cell: (146.72, 150.65, 121.83, 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 4212 8.00 N 3348 7.00 C 12888 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=33, symmetry=0 Simple disulfide: pdb=" SG CYS A 54 " - pdb=" SG CYS A 74 " distance=2.03 Simple disulfide: pdb=" SG CYS A 126 " - pdb=" SG CYS A 196 " distance=2.03 Simple disulfide: pdb=" SG CYS A 131 " - pdb=" SG CYS A 157 " distance=2.06 Simple disulfide: pdb=" SG CYS A 218 " - pdb=" SG CYS A 247 " distance=2.03 Simple disulfide: pdb=" SG CYS A 228 " - pdb=" SG CYS A 239 " distance=2.04 Simple disulfide: pdb=" SG CYS A 296 " - pdb=" SG CYS A 331 " distance=2.04 Simple disulfide: pdb=" SG CYS A 378 " - pdb=" SG CYS A 445 " distance=2.03 Simple disulfide: pdb=" SG CYS A 385 " - pdb=" SG CYS A 418 " distance=2.03 Simple disulfide: pdb=" SG CYS B 598 " - pdb=" SG CYS B 604 " distance=2.02 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 92 " distance=2.03 Simple disulfide: pdb=" SG CYS L 23 " - pdb=" SG CYS L 88 " distance=2.03 Simple disulfide: pdb=" SG CYS C 54 " - pdb=" SG CYS C 74 " distance=2.03 Simple disulfide: pdb=" SG CYS C 126 " - pdb=" SG CYS C 196 " distance=2.03 Simple disulfide: pdb=" SG CYS C 131 " - pdb=" SG CYS C 157 " distance=2.06 Simple disulfide: pdb=" SG CYS C 218 " - pdb=" SG CYS C 247 " distance=2.03 Simple disulfide: pdb=" SG CYS C 228 " - pdb=" SG CYS C 239 " distance=2.04 Simple disulfide: pdb=" SG CYS C 296 " - pdb=" SG CYS C 331 " distance=2.04 Simple disulfide: pdb=" SG CYS C 378 " - pdb=" SG CYS C 445 " distance=2.03 Simple disulfide: pdb=" SG CYS C 385 " - pdb=" SG CYS C 418 " distance=2.03 Simple disulfide: pdb=" SG CYS E 598 " - pdb=" SG CYS E 604 " distance=2.02 Simple disulfide: pdb=" SG CYS D 54 " - pdb=" SG CYS D 74 " distance=2.03 Simple disulfide: pdb=" SG CYS D 126 " - pdb=" SG CYS D 196 " distance=2.03 Simple disulfide: pdb=" SG CYS D 131 " - pdb=" SG CYS D 157 " distance=2.06 Simple disulfide: pdb=" SG CYS D 218 " - pdb=" SG CYS D 247 " distance=2.03 Simple disulfide: pdb=" SG CYS D 228 " - pdb=" SG CYS D 239 " distance=2.04 Simple disulfide: pdb=" SG CYS D 296 " - pdb=" SG CYS D 331 " distance=2.04 Simple disulfide: pdb=" SG CYS D 378 " - pdb=" SG CYS D 445 " distance=2.03 Simple disulfide: pdb=" SG CYS D 385 " - pdb=" SG CYS D 418 " distance=2.03 Simple disulfide: pdb=" SG CYS F 598 " - pdb=" SG CYS F 604 " distance=2.02 Simple disulfide: pdb=" SG CYS G 22 " - pdb=" SG CYS G 92 " distance=2.03 Simple disulfide: pdb=" SG CYS J 23 " - pdb=" SG CYS J 88 " distance=2.03 Simple disulfide: pdb=" SG CYS I 22 " - pdb=" SG CYS I 92 " distance=2.03 Simple disulfide: pdb=" SG CYS K 23 " - pdb=" SG CYS K 88 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied ALPHA1-2 " MAN P 4 " - " MAN P 5 " " MAN b 4 " - " MAN b 5 " " MAN n 4 " - " MAN n 5 " ALPHA1-3 " BMA P 3 " - " MAN P 4 " " BMA Q 3 " - " MAN Q 4 " " BMA b 3 " - " MAN b 4 " " BMA c 3 " - " MAN c 4 " " BMA n 3 " - " MAN n 4 " " BMA o 3 " - " MAN o 4 " ALPHA1-6 " BMA P 3 " - " MAN P 6 " " BMA Q 3 " - " MAN Q 5 " " BMA b 3 " - " MAN b 6 " " BMA c 3 " - " MAN c 5 " " BMA n 3 " - " MAN n 6 " " BMA o 3 " - " MAN o 5 " BETA1-4 " NAG M 1 " - " NAG M 2 " " 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 Q 2 " - " BMA Q 3 " " NAG R 1 " - " NAG R 2 " " NAG S 1 " - " NAG S 2 " " NAG T 1 " - " NAG T 2 " " NAG U 1 " - " NAG U 2 " " NAG V 1 " - " NAG V 2 " " 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 a 1 " - " NAG a 2 " " NAG a 2 " - " BMA a 3 " " NAG b 1 " - " NAG b 2 " " NAG b 2 " - " BMA b 3 " " NAG c 1 " - " NAG c 2 " " NAG c 2 " - " BMA c 3 " " NAG d 1 " - " NAG d 2 " " NAG e 1 " - " NAG e 2 " " NAG f 1 " - " NAG f 2 " " NAG g 1 " - " NAG g 2 " " NAG h 1 " - " NAG h 2 " " NAG i 1 " - " NAG i 2 " " NAG i 2 " - " BMA i 3 " " NAG j 1 " - " NAG j 2 " " NAG k 1 " - " NAG k 2 " " NAG l 1 " - " NAG l 2 " " 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 o 2 " - " BMA o 3 " " NAG p 1 " - " NAG p 2 " " NAG q 1 " - " NAG q 2 " " NAG r 1 " - " NAG r 2 " " NAG s 1 " - " NAG s 2 " " NAG t 1 " - " NAG t 2 " " NAG u 1 " - " NAG u 2 " " NAG u 2 " - " BMA u 3 " " NAG v 1 " - " NAG v 2 " NAG-ASN " NAG A 601 " - " ASN A 197 " " NAG A 602 " - " ASN A 88 " " NAG A 603 " - " ASN A 230 " " NAG A 604 " - " ASN A 325 " " NAG A 605 " - " ASN A 355 " " NAG A 606 " - " ASN A 392 " " NAG A 607 " - " ASN A 301 " " NAG A 608 " - " ASN A 405 " " NAG A 609 " - " ASN A 289 " " NAG A 610 " - " ASN A 188 " " NAG A 611 " - " ASN A 160 " " NAG A 612 " - " ASN A 462 " " NAG B 701 " - " ASN B 611 " " NAG B 702 " - " ASN B 637 " " NAG B 703 " - " ASN B 625 " " NAG C 601 " - " ASN C 197 " " NAG C 602 " - " ASN C 88 " " NAG C 603 " - " ASN C 230 " " NAG C 604 " - " ASN C 325 " " NAG C 605 " - " ASN C 355 " " NAG C 606 " - " ASN C 392 " " NAG C 607 " - " ASN C 301 " " NAG C 608 " - " ASN C 405 " " NAG C 609 " - " ASN C 289 " " NAG C 610 " - " ASN C 188 " " NAG C 611 " - " ASN C 160 " " NAG C 612 " - " ASN C 462 " " NAG D 601 " - " ASN D 197 " " NAG D 602 " - " ASN D 88 " " NAG D 603 " - " ASN D 230 " " NAG D 604 " - " ASN D 325 " " NAG D 605 " - " ASN D 355 " " NAG D 606 " - " ASN D 392 " " NAG D 607 " - " ASN D 301 " " NAG D 608 " - " ASN D 405 " " NAG D 609 " - " ASN D 289 " " NAG D 610 " - " ASN D 188 " " NAG D 611 " - " ASN D 160 " " NAG D 612 " - " ASN D 462 " " NAG E 701 " - " ASN E 611 " " NAG E 702 " - " ASN E 637 " " NAG E 703 " - " ASN E 625 " " NAG F 701 " - " ASN F 611 " " NAG F 702 " - " ASN F 637 " " NAG F 703 " - " ASN F 625 " " NAG M 1 " - " ASN A 156 " " NAG N 1 " - " ASN A 234 " " NAG O 1 " - " ASN A 241 " " NAG P 1 " - " ASN A 262 " " NAG Q 1 " - " ASN A 276 " " NAG R 1 " - " ASN A 448 " " NAG S 1 " - " ASN A 339 " " NAG T 1 " - " ASN A 386 " " NAG U 1 " - " ASN A 130 " " NAG V 1 " - " ASN A 295 " " NAG W 1 " - " ASN A 413 " " NAG X 1 " - " ASN A 332 " " NAG Y 1 " - " ASN C 156 " " NAG Z 1 " - " ASN C 234 " " NAG a 1 " - " ASN C 241 " " NAG b 1 " - " ASN C 262 " " NAG c 1 " - " ASN C 276 " " NAG d 1 " - " ASN C 448 " " NAG e 1 " - " ASN C 339 " " NAG f 1 " - " ASN C 386 " " NAG g 1 " - " ASN C 130 " " NAG h 1 " - " ASN C 295 " " NAG i 1 " - " ASN C 413 " " NAG j 1 " - " ASN C 332 " " NAG k 1 " - " ASN D 156 " " NAG l 1 " - " ASN D 234 " " NAG m 1 " - " ASN D 241 " " NAG n 1 " - " ASN D 262 " " NAG o 1 " - " ASN D 276 " " NAG p 1 " - " ASN D 448 " " NAG q 1 " - " ASN D 339 " " NAG r 1 " - " ASN D 386 " " NAG s 1 " - " ASN D 130 " " NAG t 1 " - " ASN D 295 " " NAG u 1 " - " ASN D 413 " " NAG v 1 " - " ASN D 332 " Time building additional restraints: 6.52 Conformation dependent library (CDL) restraints added in 2.4 seconds 4614 Ramachandran restraints generated. 2307 Oldfield, 0 Emsley, 2307 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4356 Finding SS restraints... Secondary structure from input PDB file: 57 helices and 51 sheets defined 23.3% alpha, 34.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 3.17 Creating SS restraints... Processing helix chain 'A' and resid 98 through 117 removed outlier: 3.658A pdb=" N GLU A 102 " --> pdb=" O ASN A 98 " (cutoff:3.500A) Processing helix chain 'A' and resid 123 through 126 Processing helix chain 'A' and resid 335 through 351 Processing helix chain 'A' and resid 368 through 373 Processing helix chain 'A' and resid 387 through 391 Processing helix chain 'A' and resid 425 through 429 removed outlier: 4.052A pdb=" N GLU A 429 " --> pdb=" O LEU A 426 " (cutoff:3.500A) Processing helix chain 'A' and resid 475 through 483 removed outlier: 3.937A pdb=" N SER A 481 " --> pdb=" O ASP A 477 " (cutoff:3.500A) Processing helix chain 'B' and resid 523 through 528 removed outlier: 4.343A pdb=" N GLY B 527 " --> pdb=" O GLY B 524 " (cutoff:3.500A) Processing helix chain 'B' and resid 531 through 535 Processing helix chain 'B' and resid 536 through 543 removed outlier: 3.787A pdb=" N GLN B 543 " --> pdb=" O VAL B 539 " (cutoff:3.500A) Processing helix chain 'B' and resid 569 through 596 removed outlier: 3.521A pdb=" N LYS B 574 " --> pdb=" O VAL B 570 " (cutoff:3.500A) Processing helix chain 'B' and resid 618 through 622 Processing helix chain 'B' and resid 627 through 635 Processing helix chain 'B' and resid 638 through 663 Processing helix chain 'H' and resid 25 through 30 Processing helix chain 'H' and resid 60 through 66 Processing helix chain 'H' and resid 83 through 87 Processing helix chain 'H' and resid 99 through 100C Processing helix chain 'L' and resid 77 through 83 Proline residue: L 80 - end of helix Processing helix chain 'C' and resid 98 through 117 removed outlier: 3.658A pdb=" N GLU C 102 " --> pdb=" O ASN C 98 " (cutoff:3.500A) Processing helix chain 'C' and resid 123 through 126 Processing helix chain 'C' and resid 335 through 351 Processing helix chain 'C' and resid 368 through 373 Processing helix chain 'C' and resid 387 through 391 Processing helix chain 'C' and resid 425 through 429 removed outlier: 4.052A pdb=" N GLU C 429 " --> pdb=" O LEU C 426 " (cutoff:3.500A) Processing helix chain 'C' and resid 475 through 483 removed outlier: 3.937A pdb=" N SER C 481 " --> pdb=" O ASP C 477 " (cutoff:3.500A) Processing helix chain 'E' and resid 523 through 528 removed outlier: 4.342A pdb=" N GLY E 527 " --> pdb=" O GLY E 524 " (cutoff:3.500A) Processing helix chain 'E' and resid 531 through 535 Processing helix chain 'E' and resid 536 through 543 removed outlier: 3.788A pdb=" N GLN E 543 " --> pdb=" O VAL E 539 " (cutoff:3.500A) Processing helix chain 'E' and resid 569 through 596 removed outlier: 3.521A pdb=" N LYS E 574 " --> pdb=" O VAL E 570 " (cutoff:3.500A) Processing helix chain 'E' and resid 618 through 622 Processing helix chain 'E' and resid 627 through 635 Processing helix chain 'E' and resid 638 through 663 Processing helix chain 'D' and resid 98 through 117 removed outlier: 3.659A pdb=" N GLU D 102 " --> pdb=" O ASN D 98 " (cutoff:3.500A) Processing helix chain 'D' and resid 123 through 126 Processing helix chain 'D' and resid 335 through 351 Processing helix chain 'D' and resid 368 through 373 Processing helix chain 'D' and resid 387 through 391 Processing helix chain 'D' and resid 425 through 429 removed outlier: 4.052A pdb=" N GLU D 429 " --> pdb=" O LEU D 426 " (cutoff:3.500A) Processing helix chain 'D' and resid 475 through 483 removed outlier: 3.937A pdb=" N SER D 481 " --> pdb=" O ASP D 477 " (cutoff:3.500A) Processing helix chain 'F' and resid 523 through 528 removed outlier: 4.343A pdb=" N GLY F 527 " --> pdb=" O GLY F 524 " (cutoff:3.500A) Processing helix chain 'F' and resid 531 through 535 Processing helix chain 'F' and resid 536 through 543 removed outlier: 3.788A pdb=" N GLN F 543 " --> pdb=" O VAL F 539 " (cutoff:3.500A) Processing helix chain 'F' and resid 569 through 596 removed outlier: 3.521A pdb=" N LYS F 574 " --> pdb=" O VAL F 570 " (cutoff:3.500A) Processing helix chain 'F' and resid 618 through 622 Processing helix chain 'F' and resid 627 through 635 Processing helix chain 'F' and resid 638 through 663 Processing helix chain 'G' and resid 25 through 30 Processing helix chain 'G' and resid 60 through 66 Processing helix chain 'G' and resid 83 through 87 Processing helix chain 'G' and resid 99 through 100C Processing helix chain 'J' and resid 77 through 83 Proline residue: J 80 - end of helix Processing helix chain 'I' and resid 25 through 30 Processing helix chain 'I' and resid 60 through 66 Processing helix chain 'I' and resid 83 through 87 Processing helix chain 'I' and resid 99 through 100C Processing helix chain 'K' and resid 77 through 83 Proline residue: K 80 - end of helix Processing sheet with id=AA1, first strand: chain 'A' and resid 494 through 499 removed outlier: 5.399A pdb=" N VAL B 608 " --> pdb=" O VAL A 36 " (cutoff:3.500A) removed outlier: 7.729A pdb=" N VAL A 38 " --> pdb=" O THR B 606 " (cutoff:3.500A) removed outlier: 7.936A pdb=" N THR B 606 " --> pdb=" O VAL A 38 " (cutoff:3.500A) removed outlier: 7.751A pdb=" N TYR A 40 " --> pdb=" O CYS B 604 " (cutoff:3.500A) removed outlier: 8.157A pdb=" N CYS B 604 " --> pdb=" O TYR A 40 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 45 through 47 Processing sheet with id=AA3, first strand: chain 'A' and resid 53 through 55 Processing sheet with id=AA4, first strand: chain 'A' and resid 67 through 68 removed outlier: 6.209A pdb=" N ASN A 67 " --> pdb=" O SER A 209 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA4 Processing sheet with id=AA5, first strand: chain 'A' and resid 91 through 94 Processing sheet with id=AA6, first strand: chain 'A' and resid 120 through 121 removed outlier: 6.261A pdb=" N VAL A 200 " --> pdb=" O ALA A 433 " (cutoff:3.500A) removed outlier: 7.345A pdb=" N TYR A 435 " --> pdb=" O VAL A 200 " (cutoff:3.500A) removed outlier: 6.572A pdb=" N THR A 202 " --> pdb=" O TYR A 435 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 129 through 130 Processing sheet with id=AA8, first strand: chain 'A' and resid 154 through 162 Processing sheet with id=AA9, first strand: chain 'A' and resid 259 through 261 removed outlier: 6.481A pdb=" N LEU A 260 " --> pdb=" O THR A 450 " (cutoff:3.500A) removed outlier: 10.367A pdb=" N GLN A 442 " --> pdb=" O CYS A 296 " (cutoff:3.500A) removed outlier: 11.231A pdb=" N CYS A 296 " --> pdb=" O GLN A 442 " (cutoff:3.500A) removed outlier: 10.303A pdb=" N ARG A 444 " --> pdb=" O ILE A 294 " (cutoff:3.500A) removed outlier: 12.191A pdb=" N ILE A 294 " --> pdb=" O ARG A 444 " (cutoff:3.500A) removed outlier: 10.006A pdb=" N SER A 446 " --> pdb=" O VAL A 292 " (cutoff:3.500A) removed outlier: 11.002A pdb=" N VAL A 292 " --> pdb=" O SER A 446 " (cutoff:3.500A) removed outlier: 9.710A pdb=" N ASN A 448 " --> pdb=" O GLU A 290 " (cutoff:3.500A) removed outlier: 10.327A pdb=" N GLU A 290 " --> pdb=" O ASN A 448 " (cutoff:3.500A) removed outlier: 6.808A pdb=" N THR A 450 " --> pdb=" O LEU A 288 " (cutoff:3.500A) removed outlier: 6.343A pdb=" N GLU A 293 " --> pdb=" O SER A 334 " (cutoff:3.500A) removed outlier: 3.828A pdb=" N ALA A 329 " --> pdb=" O CYS A 418 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 271 through 273 removed outlier: 6.808A pdb=" N THR A 450 " --> pdb=" O LEU A 288 " (cutoff:3.500A) removed outlier: 10.327A pdb=" N GLU A 290 " --> pdb=" O ASN A 448 " (cutoff:3.500A) removed outlier: 9.710A pdb=" N ASN A 448 " --> pdb=" O GLU A 290 " (cutoff:3.500A) removed outlier: 11.002A pdb=" N VAL A 292 " --> pdb=" O SER A 446 " (cutoff:3.500A) removed outlier: 10.006A pdb=" N SER A 446 " --> pdb=" O VAL A 292 " (cutoff:3.500A) removed outlier: 12.191A pdb=" N ILE A 294 " --> pdb=" O ARG A 444 " (cutoff:3.500A) removed outlier: 10.303A pdb=" N ARG A 444 " --> pdb=" O ILE A 294 " (cutoff:3.500A) removed outlier: 11.231A pdb=" N CYS A 296 " --> pdb=" O GLN A 442 " (cutoff:3.500A) removed outlier: 10.367A pdb=" N GLN A 442 " --> pdb=" O CYS A 296 " (cutoff:3.500A) removed outlier: 6.312A pdb=" N THR A 358 " --> pdb=" O GLU A 466 " (cutoff:3.500A) removed outlier: 7.643A pdb=" N PHE A 468 " --> pdb=" O THR A 358 " (cutoff:3.500A) removed outlier: 6.421A pdb=" N VAL A 360 " --> pdb=" O PHE A 468 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 304 through 308 Processing sheet with id=AB3, first strand: chain 'H' and resid 5 through 6 removed outlier: 3.638A pdb=" N THR H 77 " --> pdb=" O ASP H 72 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'H' and resid 11 through 12 removed outlier: 6.740A pdb=" N ILE H 35 " --> pdb=" O TRP H 50 " (cutoff:3.500A) removed outlier: 4.577A pdb=" N TRP H 50 " --> pdb=" O ILE H 35 " (cutoff:3.500A) removed outlier: 6.735A pdb=" N TRP H 36 " --> pdb=" O ILE H 48 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'H' and resid 11 through 12 removed outlier: 3.632A pdb=" N LEU H 102 " --> pdb=" O ARG H 94 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'L' and resid 4 through 7 Processing sheet with id=AB7, first strand: chain 'L' and resid 10 through 12 removed outlier: 6.565A pdb=" N LEU L 11 " --> pdb=" O GLU L 105 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB7 Processing sheet with id=AB8, first strand: chain 'L' and resid 45 through 48 removed outlier: 6.986A pdb=" N TRP L 35 " --> pdb=" O LEU L 47 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'C' and resid 494 through 499 removed outlier: 5.399A pdb=" N VAL E 608 " --> pdb=" O VAL C 36 " (cutoff:3.500A) removed outlier: 7.729A pdb=" N VAL C 38 " --> pdb=" O THR E 606 " (cutoff:3.500A) removed outlier: 7.937A pdb=" N THR E 606 " --> pdb=" O VAL C 38 " (cutoff:3.500A) removed outlier: 7.751A pdb=" N TYR C 40 " --> pdb=" O CYS E 604 " (cutoff:3.500A) removed outlier: 8.157A pdb=" N CYS E 604 " --> pdb=" O TYR C 40 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'C' and resid 45 through 47 Processing sheet with id=AC2, first strand: chain 'C' and resid 53 through 55 Processing sheet with id=AC3, first strand: chain 'C' and resid 67 through 68 removed outlier: 6.210A pdb=" N ASN C 67 " --> pdb=" O SER C 209 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC3 Processing sheet with id=AC4, first strand: chain 'C' and resid 91 through 94 Processing sheet with id=AC5, first strand: chain 'C' and resid 120 through 121 removed outlier: 6.261A pdb=" N VAL C 200 " --> pdb=" O ALA C 433 " (cutoff:3.500A) removed outlier: 7.345A pdb=" N TYR C 435 " --> pdb=" O VAL C 200 " (cutoff:3.500A) removed outlier: 6.572A pdb=" N THR C 202 " --> pdb=" O TYR C 435 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'C' and resid 129 through 130 Processing sheet with id=AC7, first strand: chain 'C' and resid 154 through 162 Processing sheet with id=AC8, first strand: chain 'C' and resid 259 through 261 removed outlier: 6.481A pdb=" N LEU C 260 " --> pdb=" O THR C 450 " (cutoff:3.500A) removed outlier: 10.367A pdb=" N GLN C 442 " --> pdb=" O CYS C 296 " (cutoff:3.500A) removed outlier: 11.231A pdb=" N CYS C 296 " --> pdb=" O GLN C 442 " (cutoff:3.500A) removed outlier: 10.303A pdb=" N ARG C 444 " --> pdb=" O ILE C 294 " (cutoff:3.500A) removed outlier: 12.191A pdb=" N ILE C 294 " --> pdb=" O ARG C 444 " (cutoff:3.500A) removed outlier: 10.006A pdb=" N SER C 446 " --> pdb=" O VAL C 292 " (cutoff:3.500A) removed outlier: 11.002A pdb=" N VAL C 292 " --> pdb=" O SER C 446 " (cutoff:3.500A) removed outlier: 9.710A pdb=" N ASN C 448 " --> pdb=" O GLU C 290 " (cutoff:3.500A) removed outlier: 10.327A pdb=" N GLU C 290 " --> pdb=" O ASN C 448 " (cutoff:3.500A) removed outlier: 6.808A pdb=" N THR C 450 " --> pdb=" O LEU C 288 " (cutoff:3.500A) removed outlier: 6.343A pdb=" N GLU C 293 " --> pdb=" O SER C 334 " (cutoff:3.500A) removed outlier: 3.828A pdb=" N ALA C 329 " --> pdb=" O CYS C 418 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'C' and resid 271 through 273 removed outlier: 6.808A pdb=" N THR C 450 " --> pdb=" O LEU C 288 " (cutoff:3.500A) removed outlier: 10.327A pdb=" N GLU C 290 " --> pdb=" O ASN C 448 " (cutoff:3.500A) removed outlier: 9.710A pdb=" N ASN C 448 " --> pdb=" O GLU C 290 " (cutoff:3.500A) removed outlier: 11.002A pdb=" N VAL C 292 " --> pdb=" O SER C 446 " (cutoff:3.500A) removed outlier: 10.006A pdb=" N SER C 446 " --> pdb=" O VAL C 292 " (cutoff:3.500A) removed outlier: 12.191A pdb=" N ILE C 294 " --> pdb=" O ARG C 444 " (cutoff:3.500A) removed outlier: 10.303A pdb=" N ARG C 444 " --> pdb=" O ILE C 294 " (cutoff:3.500A) removed outlier: 11.231A pdb=" N CYS C 296 " --> pdb=" O GLN C 442 " (cutoff:3.500A) removed outlier: 10.367A pdb=" N GLN C 442 " --> pdb=" O CYS C 296 " (cutoff:3.500A) removed outlier: 6.312A pdb=" N THR C 358 " --> pdb=" O GLU C 466 " (cutoff:3.500A) removed outlier: 7.643A pdb=" N PHE C 468 " --> pdb=" O THR C 358 " (cutoff:3.500A) removed outlier: 6.421A pdb=" N VAL C 360 " --> pdb=" O PHE C 468 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'C' and resid 304 through 308 Processing sheet with id=AD2, first strand: chain 'D' and resid 494 through 499 removed outlier: 5.399A pdb=" N VAL F 608 " --> pdb=" O VAL D 36 " (cutoff:3.500A) removed outlier: 7.729A pdb=" N VAL D 38 " --> pdb=" O THR F 606 " (cutoff:3.500A) removed outlier: 7.937A pdb=" N THR F 606 " --> pdb=" O VAL D 38 " (cutoff:3.500A) removed outlier: 7.751A pdb=" N TYR D 40 " --> pdb=" O CYS F 604 " (cutoff:3.500A) removed outlier: 8.157A pdb=" N CYS F 604 " --> pdb=" O TYR D 40 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'D' and resid 45 through 47 Processing sheet with id=AD4, first strand: chain 'D' and resid 53 through 55 Processing sheet with id=AD5, first strand: chain 'D' and resid 67 through 68 removed outlier: 6.209A pdb=" N ASN D 67 " --> pdb=" O SER D 209 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD5 Processing sheet with id=AD6, first strand: chain 'D' and resid 91 through 94 Processing sheet with id=AD7, first strand: chain 'D' and resid 120 through 121 removed outlier: 6.261A pdb=" N VAL D 200 " --> pdb=" O ALA D 433 " (cutoff:3.500A) removed outlier: 7.346A pdb=" N TYR D 435 " --> pdb=" O VAL D 200 " (cutoff:3.500A) removed outlier: 6.571A pdb=" N THR D 202 " --> pdb=" O TYR D 435 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'D' and resid 129 through 130 Processing sheet with id=AD9, first strand: chain 'D' and resid 154 through 162 Processing sheet with id=AE1, first strand: chain 'D' and resid 259 through 261 removed outlier: 6.481A pdb=" N LEU D 260 " --> pdb=" O THR D 450 " (cutoff:3.500A) removed outlier: 10.367A pdb=" N GLN D 442 " --> pdb=" O CYS D 296 " (cutoff:3.500A) removed outlier: 11.231A pdb=" N CYS D 296 " --> pdb=" O GLN D 442 " (cutoff:3.500A) removed outlier: 10.303A pdb=" N ARG D 444 " --> pdb=" O ILE D 294 " (cutoff:3.500A) removed outlier: 12.191A pdb=" N ILE D 294 " --> pdb=" O ARG D 444 " (cutoff:3.500A) removed outlier: 10.006A pdb=" N SER D 446 " --> pdb=" O VAL D 292 " (cutoff:3.500A) removed outlier: 11.002A pdb=" N VAL D 292 " --> pdb=" O SER D 446 " (cutoff:3.500A) removed outlier: 9.710A pdb=" N ASN D 448 " --> pdb=" O GLU D 290 " (cutoff:3.500A) removed outlier: 10.327A pdb=" N GLU D 290 " --> pdb=" O ASN D 448 " (cutoff:3.500A) removed outlier: 6.808A pdb=" N THR D 450 " --> pdb=" O LEU D 288 " (cutoff:3.500A) removed outlier: 6.343A pdb=" N GLU D 293 " --> pdb=" O SER D 334 " (cutoff:3.500A) removed outlier: 3.828A pdb=" N ALA D 329 " --> pdb=" O CYS D 418 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'D' and resid 271 through 273 removed outlier: 6.808A pdb=" N THR D 450 " --> pdb=" O LEU D 288 " (cutoff:3.500A) removed outlier: 10.327A pdb=" N GLU D 290 " --> pdb=" O ASN D 448 " (cutoff:3.500A) removed outlier: 9.710A pdb=" N ASN D 448 " --> pdb=" O GLU D 290 " (cutoff:3.500A) removed outlier: 11.002A pdb=" N VAL D 292 " --> pdb=" O SER D 446 " (cutoff:3.500A) removed outlier: 10.006A pdb=" N SER D 446 " --> pdb=" O VAL D 292 " (cutoff:3.500A) removed outlier: 12.191A pdb=" N ILE D 294 " --> pdb=" O ARG D 444 " (cutoff:3.500A) removed outlier: 10.303A pdb=" N ARG D 444 " --> pdb=" O ILE D 294 " (cutoff:3.500A) removed outlier: 11.231A pdb=" N CYS D 296 " --> pdb=" O GLN D 442 " (cutoff:3.500A) removed outlier: 10.367A pdb=" N GLN D 442 " --> pdb=" O CYS D 296 " (cutoff:3.500A) removed outlier: 6.312A pdb=" N THR D 358 " --> pdb=" O GLU D 466 " (cutoff:3.500A) removed outlier: 7.643A pdb=" N PHE D 468 " --> pdb=" O THR D 358 " (cutoff:3.500A) removed outlier: 6.422A pdb=" N VAL D 360 " --> pdb=" O PHE D 468 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'D' and resid 304 through 308 Processing sheet with id=AE4, first strand: chain 'G' and resid 5 through 6 removed outlier: 3.638A pdb=" N THR G 77 " --> pdb=" O ASP G 72 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'G' and resid 11 through 12 removed outlier: 6.740A pdb=" N ILE G 35 " --> pdb=" O TRP G 50 " (cutoff:3.500A) removed outlier: 4.578A pdb=" N TRP G 50 " --> pdb=" O ILE G 35 " (cutoff:3.500A) removed outlier: 6.735A pdb=" N TRP G 36 " --> pdb=" O ILE G 48 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'G' and resid 11 through 12 removed outlier: 3.632A pdb=" N LEU G 102 " --> pdb=" O ARG G 94 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'J' and resid 4 through 7 Processing sheet with id=AE8, first strand: chain 'J' and resid 10 through 12 removed outlier: 6.565A pdb=" N LEU J 11 " --> pdb=" O GLU J 105 " (cutoff:3.500A) No H-bonds generated for sheet with id=AE8 Processing sheet with id=AE9, first strand: chain 'J' and resid 45 through 48 removed outlier: 6.986A pdb=" N TRP J 35 " --> pdb=" O LEU J 47 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'I' and resid 5 through 6 removed outlier: 3.638A pdb=" N THR I 77 " --> pdb=" O ASP I 72 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'I' and resid 11 through 12 removed outlier: 6.740A pdb=" N ILE I 35 " --> pdb=" O TRP I 50 " (cutoff:3.500A) removed outlier: 4.578A pdb=" N TRP I 50 " --> pdb=" O ILE I 35 " (cutoff:3.500A) removed outlier: 6.735A pdb=" N TRP I 36 " --> pdb=" O ILE I 48 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'I' and resid 11 through 12 removed outlier: 3.632A pdb=" N LEU I 102 " --> pdb=" O ARG I 94 " (cutoff:3.500A) Processing sheet with id=AF4, first strand: chain 'K' and resid 4 through 7 Processing sheet with id=AF5, first strand: chain 'K' and resid 10 through 12 removed outlier: 6.564A pdb=" N LEU K 11 " --> pdb=" O GLU K 105 " (cutoff:3.500A) No H-bonds generated for sheet with id=AF5 Processing sheet with id=AF6, first strand: chain 'K' and resid 45 through 48 removed outlier: 6.986A pdb=" N TRP K 35 " --> pdb=" O LEU K 47 " (cutoff:3.500A) 765 hydrogen bonds defined for protein. 1926 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: 7.41 Time building geometry restraints manager: 7.23 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.35: 6118 1.35 - 1.50: 7224 1.50 - 1.66: 7475 1.66 - 1.81: 108 1.81 - 1.97: 54 Bond restraints: 20979 Sorted by residual: bond pdb=" CB TYR G 100E" pdb=" CG TYR G 100E" ideal model delta sigma weight residual 1.512 1.348 0.164 2.20e-02 2.07e+03 5.56e+01 bond pdb=" CB TYR I 100E" pdb=" CG TYR I 100E" ideal model delta sigma weight residual 1.512 1.348 0.164 2.20e-02 2.07e+03 5.55e+01 bond pdb=" CB TYR H 100E" pdb=" CG TYR H 100E" ideal model delta sigma weight residual 1.512 1.348 0.164 2.20e-02 2.07e+03 5.54e+01 bond pdb=" CB LEU B 663 " pdb=" CG LEU B 663 " ideal model delta sigma weight residual 1.530 1.654 -0.124 2.00e-02 2.50e+03 3.85e+01 bond pdb=" CB LEU E 663 " pdb=" CG LEU E 663 " ideal model delta sigma weight residual 1.530 1.654 -0.124 2.00e-02 2.50e+03 3.84e+01 ... (remaining 20974 not shown) Histogram of bond angle deviations from ideal: 0.00 - 7.28: 28391 7.28 - 14.56: 61 14.56 - 21.85: 0 21.85 - 29.13: 0 29.13 - 36.41: 6 Bond angle restraints: 28458 Sorted by residual: angle pdb=" C2 NAG C 609 " pdb=" N2 NAG C 609 " pdb=" C7 NAG C 609 " ideal model delta sigma weight residual 124.56 160.97 -36.41 3.00e+00 1.11e-01 1.47e+02 angle pdb=" C2 NAG D 609 " pdb=" N2 NAG D 609 " pdb=" C7 NAG D 609 " ideal model delta sigma weight residual 124.56 160.96 -36.40 3.00e+00 1.11e-01 1.47e+02 angle pdb=" C2 NAG A 609 " pdb=" N2 NAG A 609 " pdb=" C7 NAG A 609 " ideal model delta sigma weight residual 124.56 160.95 -36.39 3.00e+00 1.11e-01 1.47e+02 angle pdb=" C2 NAG v 2 " pdb=" N2 NAG v 2 " pdb=" C7 NAG v 2 " ideal model delta sigma weight residual 124.56 160.37 -35.81 3.00e+00 1.11e-01 1.42e+02 angle pdb=" C2 NAG j 2 " pdb=" N2 NAG j 2 " pdb=" C7 NAG j 2 " ideal model delta sigma weight residual 124.56 160.37 -35.81 3.00e+00 1.11e-01 1.42e+02 ... (remaining 28453 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 21.14: 13737 21.14 - 42.27: 360 42.27 - 63.40: 114 63.40 - 84.54: 90 84.54 - 105.67: 60 Dihedral angle restraints: 14361 sinusoidal: 7605 harmonic: 6756 Sorted by residual: dihedral pdb=" CB CYS C 54 " pdb=" SG CYS C 54 " pdb=" SG CYS C 74 " pdb=" CB CYS C 74 " ideal model delta sinusoidal sigma weight residual 93.00 143.60 -50.60 1 1.00e+01 1.00e-02 3.51e+01 dihedral pdb=" CB CYS A 54 " pdb=" SG CYS A 54 " pdb=" SG CYS A 74 " pdb=" CB CYS A 74 " ideal model delta sinusoidal sigma weight residual 93.00 143.59 -50.59 1 1.00e+01 1.00e-02 3.51e+01 dihedral pdb=" CB CYS D 54 " pdb=" SG CYS D 54 " pdb=" SG CYS D 74 " pdb=" CB CYS D 74 " ideal model delta sinusoidal sigma weight residual 93.00 143.59 -50.59 1 1.00e+01 1.00e-02 3.51e+01 ... (remaining 14358 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.100: 2096 0.100 - 0.200: 813 0.200 - 0.300: 358 0.300 - 0.399: 195 0.399 - 0.499: 120 Chirality restraints: 3582 Sorted by residual: chirality pdb=" C1 NAG Z 2 " pdb=" O4 NAG Z 1 " pdb=" C2 NAG Z 2 " pdb=" O5 NAG Z 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.69 0.29 2.00e-02 2.50e+03 2.16e+02 chirality pdb=" C1 NAG l 2 " pdb=" O4 NAG l 1 " pdb=" C2 NAG l 2 " pdb=" O5 NAG l 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.69 0.29 2.00e-02 2.50e+03 2.13e+02 chirality pdb=" C1 NAG N 2 " pdb=" O4 NAG N 1 " pdb=" C2 NAG N 2 " pdb=" O5 NAG N 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.69 0.29 2.00e-02 2.50e+03 2.12e+02 ... (remaining 3579 not shown) Planarity restraints: 3498 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C2 NAG p 1 " 0.163 2.00e-02 2.50e+03 1.33e-01 2.22e+02 pdb=" C7 NAG p 1 " -0.046 2.00e-02 2.50e+03 pdb=" C8 NAG p 1 " 0.121 2.00e-02 2.50e+03 pdb=" N2 NAG p 1 " -0.211 2.00e-02 2.50e+03 pdb=" O7 NAG p 1 " -0.027 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG R 1 " -0.163 2.00e-02 2.50e+03 1.33e-01 2.22e+02 pdb=" C7 NAG R 1 " 0.047 2.00e-02 2.50e+03 pdb=" C8 NAG R 1 " -0.121 2.00e-02 2.50e+03 pdb=" N2 NAG R 1 " 0.211 2.00e-02 2.50e+03 pdb=" O7 NAG R 1 " 0.027 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG d 1 " 0.163 2.00e-02 2.50e+03 1.33e-01 2.22e+02 pdb=" C7 NAG d 1 " -0.046 2.00e-02 2.50e+03 pdb=" C8 NAG d 1 " 0.121 2.00e-02 2.50e+03 pdb=" N2 NAG d 1 " -0.211 2.00e-02 2.50e+03 pdb=" O7 NAG d 1 " -0.027 2.00e-02 2.50e+03 ... (remaining 3495 not shown) Histogram of nonbonded interaction distances: 2.41 - 2.91: 7714 2.91 - 3.40: 18478 3.40 - 3.90: 34610 3.90 - 4.40: 39772 4.40 - 4.90: 61451 Nonbonded interactions: 162025 Sorted by model distance: nonbonded pdb=" OD1 ASP C 113 " pdb=" NZ LYS C 432 " model vdw 2.407 3.120 nonbonded pdb=" OD1 ASP A 113 " pdb=" NZ LYS A 432 " model vdw 2.407 3.120 nonbonded pdb=" OD1 ASP D 113 " pdb=" NZ LYS D 432 " model vdw 2.407 3.120 nonbonded pdb=" OE2 GLU A 290 " pdb=" NZ LYS A 337 " model vdw 2.429 3.120 nonbonded pdb=" OE2 GLU C 290 " pdb=" NZ LYS C 337 " model vdw 2.429 3.120 ... (remaining 162020 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'A' selection = chain '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' } ncs_group { reference = chain 'M' selection = chain 'N' selection = chain 'R' selection = chain 'S' selection = chain 'T' selection = chain 'U' selection = chain 'V' selection = chain 'X' selection = chain 'Y' selection = chain 'Z' selection = chain 'd' selection = chain 'e' selection = chain 'f' selection = chain 'g' selection = chain 'h' selection = chain 'j' selection = chain 'k' selection = chain 'l' selection = chain 'p' selection = chain 'q' selection = chain 'r' selection = chain 's' selection = chain 't' selection = chain 'v' } ncs_group { reference = chain 'O' selection = chain 'W' selection = chain 'a' selection = chain 'i' selection = chain 'm' selection = chain 'u' } ncs_group { reference = chain 'P' selection = chain 'b' selection = chain 'n' } ncs_group { reference = chain 'Q' selection = chain 'c' selection = chain 'o' } 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: 0.740 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.740 Check model and map are aligned: 0.140 Set scattering table: 0.180 Process input model: 47.000 Find NCS groups from input model: 1.030 Set up NCS constraints: 0.160 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:3.170 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 53.170 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7721 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 : 0.023 0.164 20979 Z= 1.432 Angle : 1.853 36.410 28458 Z= 1.149 Chirality : 0.161 0.499 3582 Planarity : 0.009 0.133 3417 Dihedral : 14.246 105.674 9906 Min Nonbonded Distance : 2.407 Molprobity Statistics. All-atom Clashscore : 0.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.43 % Favored : 98.57 % Rotamer: Outliers : 0.15 % Allowed : 0.87 % Favored : 98.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.79 (0.16), residues: 2307 helix: 0.03 (0.22), residues: 444 sheet: 0.89 (0.18), residues: 738 loop : 0.67 (0.18), residues: 1125 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.050 0.010 TRP K 35 HIS 0.008 0.003 HIS G 35A PHE 0.036 0.005 PHE G 76 TYR 0.047 0.009 TYR I 100E ARG 0.006 0.001 ARG A 273 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4614 Ramachandran restraints generated. 2307 Oldfield, 0 Emsley, 2307 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4614 Ramachandran restraints generated. 2307 Oldfield, 0 Emsley, 2307 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 902 residues out of total 2064 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 899 time to evaluate : 2.392 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 95 MET cc_start: 0.7636 (ptm) cc_final: 0.7160 (ptm) REVERT: A 98 ASN cc_start: 0.8542 (t0) cc_final: 0.7521 (m-40) REVERT: A 100 MET cc_start: 0.7323 (mtp) cc_final: 0.6819 (ttm) REVERT: A 110 SER cc_start: 0.9470 (m) cc_final: 0.9135 (t) REVERT: A 129 LEU cc_start: 0.9263 (mt) cc_final: 0.8768 (mp) REVERT: A 131 CYS cc_start: 0.5903 (p) cc_final: 0.5647 (p) REVERT: A 338 TRP cc_start: 0.9110 (t-100) cc_final: 0.8738 (t-100) REVERT: A 377 ASN cc_start: 0.8320 (t0) cc_final: 0.8065 (t0) REVERT: B 584 GLU cc_start: 0.8891 (tt0) cc_final: 0.8657 (tt0) REVERT: B 601 LYS cc_start: 0.8816 (mttt) cc_final: 0.8603 (mtmm) REVERT: B 634 GLU cc_start: 0.8132 (tt0) cc_final: 0.7638 (tp30) REVERT: H 9 SER cc_start: 0.8153 (m) cc_final: 0.7819 (p) REVERT: H 33 GLU cc_start: 0.8325 (mm-30) cc_final: 0.7348 (mp0) REVERT: H 100 GLN cc_start: 0.8392 (tt0) cc_final: 0.7901 (tt0) REVERT: H 100 TRP cc_start: 0.8294 (m-10) cc_final: 0.7919 (m-10) REVERT: H 108 LEU cc_start: 0.9201 (tp) cc_final: 0.8994 (tp) REVERT: L 78 MET cc_start: 0.8379 (mmm) cc_final: 0.8109 (mmm) REVERT: L 96 GLU cc_start: 0.8311 (pt0) cc_final: 0.7630 (pt0) REVERT: C 95 MET cc_start: 0.8138 (ptm) cc_final: 0.7368 (ptm) REVERT: C 98 ASN cc_start: 0.8340 (t0) cc_final: 0.7285 (m110) REVERT: C 100 MET cc_start: 0.7952 (mtp) cc_final: 0.7317 (ttm) REVERT: C 110 SER cc_start: 0.9462 (m) cc_final: 0.9186 (t) REVERT: C 297 THR cc_start: 0.9273 (m) cc_final: 0.9016 (p) REVERT: C 377 ASN cc_start: 0.8348 (t0) cc_final: 0.8062 (t0) REVERT: C 427 TRP cc_start: 0.8415 (m-90) cc_final: 0.8079 (m-90) REVERT: C 474 ASP cc_start: 0.7449 (t0) cc_final: 0.7204 (t0) REVERT: E 540 GLN cc_start: 0.8320 (mm110) cc_final: 0.7870 (mm-40) REVERT: E 590 GLN cc_start: 0.9366 (mm-40) cc_final: 0.9043 (tp40) REVERT: E 592 LEU cc_start: 0.9399 (tp) cc_final: 0.9150 (mt) REVERT: E 593 LEU cc_start: 0.8957 (mt) cc_final: 0.8697 (mm) REVERT: E 601 LYS cc_start: 0.8919 (mttt) cc_final: 0.8660 (mtmm) REVERT: E 616 ASN cc_start: 0.8100 (p0) cc_final: 0.7802 (p0) REVERT: E 634 GLU cc_start: 0.7871 (tt0) cc_final: 0.7510 (tp30) REVERT: E 639 THR cc_start: 0.8550 (m) cc_final: 0.8266 (p) REVERT: D 95 MET cc_start: 0.7950 (ptm) cc_final: 0.7691 (ptm) REVERT: D 98 ASN cc_start: 0.8295 (t0) cc_final: 0.7315 (m110) REVERT: D 104 MET cc_start: 0.8444 (ttm) cc_final: 0.7828 (tpp) REVERT: D 110 SER cc_start: 0.9344 (m) cc_final: 0.9015 (t) REVERT: D 165 VAL cc_start: 0.7750 (t) cc_final: 0.7530 (t) REVERT: D 217 TYR cc_start: 0.8133 (m-80) cc_final: 0.7186 (m-80) REVERT: D 352 GLN cc_start: 0.8902 (mm-40) cc_final: 0.8415 (mm-40) REVERT: D 371 ILE cc_start: 0.8501 (mm) cc_final: 0.8200 (mm) REVERT: D 377 ASN cc_start: 0.8574 (t0) cc_final: 0.8155 (t0) REVERT: F 540 GLN cc_start: 0.8257 (mm110) cc_final: 0.7705 (mm-40) REVERT: F 601 LYS cc_start: 0.8918 (mttt) cc_final: 0.8516 (mttm) REVERT: F 634 GLU cc_start: 0.8339 (tt0) cc_final: 0.7928 (tp30) REVERT: G 36 TRP cc_start: 0.9295 (m100) cc_final: 0.8620 (m100) REVERT: G 89 THR cc_start: 0.9350 (m) cc_final: 0.8927 (p) REVERT: G 99 THR cc_start: 0.6348 (p) cc_final: 0.6080 (p) REVERT: G 100 GLN cc_start: 0.8285 (tt0) cc_final: 0.7556 (tt0) REVERT: J 33 MET cc_start: 0.8009 (ttm) cc_final: 0.7443 (mpp) REVERT: I 33 GLU cc_start: 0.8535 (mm-30) cc_final: 0.7308 (mp0) REVERT: I 57 ASN cc_start: 0.9064 (t0) cc_final: 0.8811 (t0) REVERT: I 89 THR cc_start: 0.9405 (m) cc_final: 0.8979 (p) REVERT: I 100 GLN cc_start: 0.8392 (tt0) cc_final: 0.8111 (tt0) REVERT: K 96 GLU cc_start: 0.8508 (pt0) cc_final: 0.8291 (pt0) outliers start: 3 outliers final: 0 residues processed: 902 average time/residue: 0.3743 time to fit residues: 493.2858 Evaluate side-chains 461 residues out of total 2064 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 461 time to evaluate : 2.502 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 231 random chunks: chunk 195 optimal weight: 1.9990 chunk 175 optimal weight: 0.9980 chunk 97 optimal weight: 1.9990 chunk 59 optimal weight: 0.7980 chunk 118 optimal weight: 1.9990 chunk 93 optimal weight: 0.7980 chunk 181 optimal weight: 2.9990 chunk 70 optimal weight: 0.9980 chunk 110 optimal weight: 0.9990 chunk 134 optimal weight: 2.9990 chunk 209 optimal weight: 3.9990 overall best weight: 0.9182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 203 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 302 ASN ** A 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 460 ASN ** B 540 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 653 GLN H 57 ASN L 32 HIS ** L 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 90 GLN C 99 ASN C 103 GLN ** C 203 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 302 ASN C 460 ASN E 653 GLN D 99 ASN D 103 GLN ** D 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 32 HIS J 42 GLN I 39 GLN I 95 GLN K 32 HIS Total number of N/Q/H flips: 18 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7849 moved from start: 0.3965 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.060 20979 Z= 0.260 Angle : 0.789 10.351 28458 Z= 0.402 Chirality : 0.057 0.807 3582 Planarity : 0.006 0.060 3417 Dihedral : 11.591 80.353 5478 Min Nonbonded Distance : 2.494 Molprobity Statistics. All-atom Clashscore : 9.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.60 % Favored : 98.40 % Rotamer: Outliers : 0.19 % Allowed : 3.00 % Favored : 96.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.74 (0.17), residues: 2307 helix: 1.17 (0.23), residues: 432 sheet: 0.69 (0.18), residues: 756 loop : 0.20 (0.18), residues: 1119 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP B 610 HIS 0.007 0.001 HIS D 374 PHE 0.035 0.003 PHE I 58 TYR 0.033 0.002 TYR E 643 ARG 0.009 0.001 ARG I 31 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4614 Ramachandran restraints generated. 2307 Oldfield, 0 Emsley, 2307 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4614 Ramachandran restraints generated. 2307 Oldfield, 0 Emsley, 2307 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 638 residues out of total 2064 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 634 time to evaluate : 2.414 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: A 69 TRP cc_start: 0.6764 (p-90) cc_final: 0.6543 (p-90) REVERT: A 217 TYR cc_start: 0.7831 (m-80) cc_final: 0.7264 (m-80) REVERT: A 460 ASN cc_start: 0.8612 (m110) cc_final: 0.7956 (m-40) REVERT: B 634 GLU cc_start: 0.8126 (tt0) cc_final: 0.7694 (tp30) REVERT: B 651 ASN cc_start: 0.7789 (t0) cc_final: 0.7578 (t0) REVERT: H 9 SER cc_start: 0.8855 (m) cc_final: 0.8619 (p) REVERT: H 33 GLU cc_start: 0.8106 (mm-30) cc_final: 0.7087 (mp0) REVERT: H 39 GLN cc_start: 0.8986 (tp40) cc_final: 0.8739 (tp40) REVERT: H 89 THR cc_start: 0.9070 (m) cc_final: 0.8725 (p) REVERT: H 100 TRP cc_start: 0.8128 (m-10) cc_final: 0.7896 (m-10) REVERT: H 108 LEU cc_start: 0.9350 (tp) cc_final: 0.9147 (tp) REVERT: L 5 THR cc_start: 0.7922 (m) cc_final: 0.7255 (p) REVERT: L 96 GLU cc_start: 0.8110 (pt0) cc_final: 0.7586 (pt0) REVERT: C 430 VAL cc_start: 0.8857 (t) cc_final: 0.8636 (m) REVERT: E 601 LYS cc_start: 0.8881 (mttt) cc_final: 0.8555 (mtmm) REVERT: E 616 ASN cc_start: 0.7995 (p0) cc_final: 0.7622 (p0) REVERT: E 634 GLU cc_start: 0.8341 (tt0) cc_final: 0.7788 (tp30) REVERT: E 639 THR cc_start: 0.8926 (m) cc_final: 0.8160 (p) REVERT: D 69 TRP cc_start: 0.6566 (p-90) cc_final: 0.5541 (p-90) REVERT: D 111 LEU cc_start: 0.9041 (tp) cc_final: 0.8548 (tp) REVERT: D 217 TYR cc_start: 0.8108 (m-80) cc_final: 0.7381 (m-80) REVERT: D 460 ASN cc_start: 0.8378 (m-40) cc_final: 0.7119 (m110) REVERT: F 584 GLU cc_start: 0.8936 (tt0) cc_final: 0.8701 (tt0) REVERT: F 601 LYS cc_start: 0.8801 (mttt) cc_final: 0.8406 (mttm) REVERT: F 634 GLU cc_start: 0.8524 (tt0) cc_final: 0.8147 (tp30) REVERT: F 644 ASN cc_start: 0.7995 (m110) cc_final: 0.7457 (m110) REVERT: F 648 GLU cc_start: 0.8040 (tm-30) cc_final: 0.7733 (tm-30) REVERT: F 651 ASN cc_start: 0.7664 (t0) cc_final: 0.7409 (t0) REVERT: G 26 GLU cc_start: 0.8067 (tm-30) cc_final: 0.7716 (tm-30) REVERT: G 33 GLU cc_start: 0.8730 (mm-30) cc_final: 0.7075 (mp0) REVERT: G 36 TRP cc_start: 0.9212 (m100) cc_final: 0.8518 (m100) REVERT: G 39 GLN cc_start: 0.8738 (tm-30) cc_final: 0.8429 (tm-30) REVERT: G 45 LEU cc_start: 0.7994 (mp) cc_final: 0.7704 (mp) REVERT: G 50 TRP cc_start: 0.9232 (p-90) cc_final: 0.8612 (p-90) REVERT: G 89 THR cc_start: 0.9100 (m) cc_final: 0.8730 (p) REVERT: G 99 THR cc_start: 0.6156 (p) cc_final: 0.5916 (p) REVERT: G 108 LEU cc_start: 0.9383 (tp) cc_final: 0.9068 (tp) REVERT: J 33 MET cc_start: 0.8199 (ttm) cc_final: 0.7942 (mtt) REVERT: J 37 GLN cc_start: 0.8503 (tm-30) cc_final: 0.8250 (pp30) REVERT: J 81 GLU cc_start: 0.9074 (tt0) cc_final: 0.8727 (tm-30) REVERT: J 96 GLU cc_start: 0.8379 (pt0) cc_final: 0.7883 (pt0) REVERT: I 9 SER cc_start: 0.8796 (m) cc_final: 0.8578 (p) REVERT: I 33 GLU cc_start: 0.8211 (mm-30) cc_final: 0.7477 (mp0) REVERT: I 50 TRP cc_start: 0.9281 (p-90) cc_final: 0.8887 (p-90) REVERT: I 89 THR cc_start: 0.9154 (m) cc_final: 0.8730 (p) REVERT: I 99 THR cc_start: 0.6349 (p) cc_final: 0.5779 (t) REVERT: I 100 GLN cc_start: 0.8203 (tt0) cc_final: 0.7741 (tt0) REVERT: I 108 LEU cc_start: 0.9430 (tp) cc_final: 0.9152 (tp) REVERT: K 5 THR cc_start: 0.7560 (m) cc_final: 0.6910 (p) REVERT: K 81 GLU cc_start: 0.8947 (tt0) cc_final: 0.8595 (tm-30) REVERT: K 82 ASP cc_start: 0.8379 (m-30) cc_final: 0.8153 (m-30) outliers start: 4 outliers final: 3 residues processed: 637 average time/residue: 0.3308 time to fit residues: 322.5210 Evaluate side-chains 463 residues out of total 2064 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 460 time to evaluate : 2.181 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 231 random chunks: chunk 116 optimal weight: 10.0000 chunk 65 optimal weight: 5.9990 chunk 174 optimal weight: 5.9990 chunk 142 optimal weight: 6.9990 chunk 57 optimal weight: 0.0770 chunk 210 optimal weight: 0.9980 chunk 227 optimal weight: 9.9990 chunk 187 optimal weight: 10.0000 chunk 208 optimal weight: 2.9990 chunk 71 optimal weight: 2.9990 chunk 168 optimal weight: 0.9990 overall best weight: 1.6144 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 99 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 203 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 328 GLN A 330 HIS A 461 ASN ** B 540 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 575 GLN ** H 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 37 GLN L 70 GLN C 328 GLN C 374 HIS ** E 540 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 575 GLN D 328 GLN D 330 HIS ** F 540 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 6 GLN J 70 GLN ** J 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 95 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7977 moved from start: 0.4801 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 20979 Z= 0.288 Angle : 0.724 10.751 28458 Z= 0.376 Chirality : 0.054 0.654 3582 Planarity : 0.005 0.058 3417 Dihedral : 9.804 72.431 5478 Min Nonbonded Distance : 2.460 Molprobity Statistics. All-atom Clashscore : 11.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.91 % Favored : 98.09 % Rotamer: Outliers : 0.24 % Allowed : 2.81 % Favored : 96.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.48 (0.17), residues: 2307 helix: 0.97 (0.24), residues: 426 sheet: 0.69 (0.18), residues: 768 loop : -0.11 (0.18), residues: 1113 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP I 36 HIS 0.007 0.001 HIS D 374 PHE 0.027 0.002 PHE A 233 TYR 0.039 0.002 TYR E 643 ARG 0.007 0.001 ARG J 103 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4614 Ramachandran restraints generated. 2307 Oldfield, 0 Emsley, 2307 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4614 Ramachandran restraints generated. 2307 Oldfield, 0 Emsley, 2307 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 573 residues out of total 2064 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 568 time to evaluate : 2.290 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: A 69 TRP cc_start: 0.6762 (p-90) cc_final: 0.6185 (p-90) REVERT: A 78 ASP cc_start: 0.8282 (m-30) cc_final: 0.7678 (p0) REVERT: A 95 MET cc_start: 0.7678 (ptm) cc_final: 0.7148 (ptm) REVERT: A 98 ASN cc_start: 0.8431 (t0) cc_final: 0.8044 (m-40) REVERT: A 460 ASN cc_start: 0.8579 (m110) cc_final: 0.7524 (m110) REVERT: B 584 GLU cc_start: 0.9073 (tt0) cc_final: 0.8758 (tt0) REVERT: B 620 ASP cc_start: 0.8894 (p0) cc_final: 0.8677 (p0) REVERT: B 634 GLU cc_start: 0.8728 (tt0) cc_final: 0.8320 (tm-30) REVERT: B 651 ASN cc_start: 0.7675 (t0) cc_final: 0.7437 (t0) REVERT: H 9 SER cc_start: 0.9252 (m) cc_final: 0.9028 (p) REVERT: H 33 GLU cc_start: 0.8062 (mm-30) cc_final: 0.7343 (mp0) REVERT: H 50 TRP cc_start: 0.9299 (p-90) cc_final: 0.8526 (p-90) REVERT: H 100 TRP cc_start: 0.8477 (m-10) cc_final: 0.7905 (m-10) REVERT: H 100 TYR cc_start: 0.5974 (m-80) cc_final: 0.5501 (m-80) REVERT: L 96 GLU cc_start: 0.8350 (pt0) cc_final: 0.8067 (pt0) REVERT: C 104 MET cc_start: 0.8603 (tpp) cc_final: 0.8367 (tpp) REVERT: C 430 VAL cc_start: 0.8678 (t) cc_final: 0.8459 (m) REVERT: E 537 LEU cc_start: 0.8386 (mt) cc_final: 0.8068 (mt) REVERT: E 601 LYS cc_start: 0.8915 (mttt) cc_final: 0.8652 (mtmm) REVERT: E 616 ASN cc_start: 0.8013 (p0) cc_final: 0.7682 (p0) REVERT: E 634 GLU cc_start: 0.8445 (tt0) cc_final: 0.7855 (tp30) REVERT: E 639 THR cc_start: 0.8997 (m) cc_final: 0.8352 (p) REVERT: E 643 TYR cc_start: 0.8927 (m-80) cc_final: 0.8707 (m-80) REVERT: D 53 PHE cc_start: 0.8732 (p90) cc_final: 0.8394 (p90) REVERT: D 69 TRP cc_start: 0.6763 (p-90) cc_final: 0.5628 (p-90) REVERT: D 98 ASN cc_start: 0.8051 (t0) cc_final: 0.7512 (m-40) REVERT: D 111 LEU cc_start: 0.9091 (tp) cc_final: 0.8644 (tp) REVERT: D 165 VAL cc_start: 0.6891 (p) cc_final: 0.6590 (p) REVERT: D 217 TYR cc_start: 0.8334 (m-80) cc_final: 0.7795 (m-80) REVERT: F 584 GLU cc_start: 0.8950 (tt0) cc_final: 0.8697 (tp30) REVERT: F 601 LYS cc_start: 0.8891 (mttt) cc_final: 0.8433 (mttm) REVERT: F 617 LYS cc_start: 0.8510 (mtpt) cc_final: 0.7907 (ttmt) REVERT: F 621 ASN cc_start: 0.8602 (t0) cc_final: 0.8243 (t0) REVERT: F 634 GLU cc_start: 0.8750 (tt0) cc_final: 0.8045 (tp30) REVERT: F 643 TYR cc_start: 0.8568 (m-80) cc_final: 0.8068 (m-10) REVERT: F 648 GLU cc_start: 0.8000 (tm-30) cc_final: 0.7570 (tm-30) REVERT: G 26 GLU cc_start: 0.8172 (tm-30) cc_final: 0.7871 (tm-30) REVERT: G 36 TRP cc_start: 0.9233 (m100) cc_final: 0.8548 (m100) REVERT: G 39 GLN cc_start: 0.8763 (tm-30) cc_final: 0.8468 (tm-30) REVERT: G 50 TRP cc_start: 0.9271 (p-90) cc_final: 0.8614 (p-90) REVERT: G 89 THR cc_start: 0.9206 (m) cc_final: 0.8767 (p) REVERT: G 96 LYS cc_start: 0.7477 (pttp) cc_final: 0.6969 (pttp) REVERT: G 99 THR cc_start: 0.6132 (p) cc_final: 0.5731 (p) REVERT: G 101 ASP cc_start: 0.8288 (t70) cc_final: 0.8016 (t70) REVERT: G 108 LEU cc_start: 0.9300 (tp) cc_final: 0.9031 (tp) REVERT: J 33 MET cc_start: 0.7973 (ttm) cc_final: 0.7744 (mtt) REVERT: J 37 GLN cc_start: 0.8307 (tm-30) cc_final: 0.8081 (tp-100) REVERT: I 9 SER cc_start: 0.9046 (m) cc_final: 0.8729 (p) REVERT: I 46 GLU cc_start: 0.8355 (tp30) cc_final: 0.7286 (mm-30) REVERT: I 89 THR cc_start: 0.9144 (m) cc_final: 0.8763 (p) REVERT: I 99 THR cc_start: 0.6680 (p) cc_final: 0.5626 (t) REVERT: I 108 LEU cc_start: 0.9505 (tp) cc_final: 0.9264 (tp) REVERT: K 5 THR cc_start: 0.7808 (m) cc_final: 0.7145 (p) REVERT: K 37 GLN cc_start: 0.8459 (tm-30) cc_final: 0.8126 (tm-30) REVERT: K 65 SER cc_start: 0.9289 (t) cc_final: 0.8799 (t) REVERT: K 81 GLU cc_start: 0.9061 (tt0) cc_final: 0.8656 (tm-30) REVERT: K 82 ASP cc_start: 0.8548 (m-30) cc_final: 0.8217 (m-30) outliers start: 5 outliers final: 0 residues processed: 571 average time/residue: 0.3442 time to fit residues: 299.9075 Evaluate side-chains 430 residues out of total 2064 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 430 time to evaluate : 2.391 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 231 random chunks: chunk 207 optimal weight: 3.9990 chunk 158 optimal weight: 6.9990 chunk 109 optimal weight: 2.9990 chunk 23 optimal weight: 2.9990 chunk 100 optimal weight: 0.7980 chunk 141 optimal weight: 7.9990 chunk 210 optimal weight: 6.9990 chunk 223 optimal weight: 10.0000 chunk 110 optimal weight: 1.9990 chunk 199 optimal weight: 2.9990 chunk 60 optimal weight: 2.9990 overall best weight: 2.3588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 203 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 330 HIS A 460 ASN ** B 540 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 653 GLN L 70 GLN ** C 203 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 540 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 653 GLN ** D 203 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 302 ASN D 330 HIS ** F 540 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 575 GLN F 656 ASN G 6 GLN J 32 HIS J 70 GLN J 90 GLN ** I 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 57 ASN ** I 95 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 32 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 70 GLN Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8099 moved from start: 0.5478 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.080 20979 Z= 0.341 Angle : 0.726 9.306 28458 Z= 0.373 Chirality : 0.054 0.582 3582 Planarity : 0.005 0.068 3417 Dihedral : 8.767 62.658 5478 Min Nonbonded Distance : 2.425 Molprobity Statistics. All-atom Clashscore : 10.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.60 % Favored : 97.40 % Rotamer: Outliers : 0.24 % Allowed : 2.03 % Favored : 97.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.22 (0.17), residues: 2307 helix: 1.02 (0.24), residues: 432 sheet: 0.61 (0.20), residues: 690 loop : -0.42 (0.17), residues: 1185 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP B 610 HIS 0.006 0.002 HIS A 330 PHE 0.024 0.002 PHE C 233 TYR 0.031 0.002 TYR E 643 ARG 0.011 0.001 ARG A 192 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4614 Ramachandran restraints generated. 2307 Oldfield, 0 Emsley, 2307 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4614 Ramachandran restraints generated. 2307 Oldfield, 0 Emsley, 2307 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 520 residues out of total 2064 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 515 time to evaluate : 2.396 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: A 373 MET cc_start: 0.8957 (mmm) cc_final: 0.8549 (tpp) REVERT: A 414 ILE cc_start: 0.8829 (mt) cc_final: 0.8571 (tp) REVERT: A 434 MET cc_start: 0.8182 (ttt) cc_final: 0.7972 (ttt) REVERT: A 460 ASN cc_start: 0.8311 (m-40) cc_final: 0.7716 (t0) REVERT: A 466 GLU cc_start: 0.8653 (mm-30) cc_final: 0.8205 (mm-30) REVERT: B 584 GLU cc_start: 0.9195 (tt0) cc_final: 0.8973 (tt0) REVERT: B 634 GLU cc_start: 0.8734 (tt0) cc_final: 0.8494 (tt0) REVERT: B 648 GLU cc_start: 0.8141 (tm-30) cc_final: 0.7908 (tm-30) REVERT: B 652 GLN cc_start: 0.9056 (tt0) cc_final: 0.8823 (tt0) REVERT: B 653 GLN cc_start: 0.8579 (OUTLIER) cc_final: 0.8123 (tm-30) REVERT: H 9 SER cc_start: 0.9585 (m) cc_final: 0.9263 (p) REVERT: H 33 GLU cc_start: 0.8127 (mm-30) cc_final: 0.7628 (mp0) REVERT: H 89 THR cc_start: 0.9257 (m) cc_final: 0.8882 (p) REVERT: H 99 THR cc_start: 0.6467 (t) cc_final: 0.5887 (t) REVERT: H 100 GLN cc_start: 0.7497 (tm-30) cc_final: 0.7127 (tm-30) REVERT: H 100 TYR cc_start: 0.6058 (m-80) cc_final: 0.5553 (m-80) REVERT: L 46 LEU cc_start: 0.8224 (pt) cc_final: 0.7953 (pp) REVERT: C 348 LYS cc_start: 0.9058 (mmmt) cc_final: 0.8364 (mmtm) REVERT: C 373 MET cc_start: 0.8909 (mtm) cc_final: 0.8686 (mtm) REVERT: C 430 VAL cc_start: 0.8818 (t) cc_final: 0.8590 (m) REVERT: E 601 LYS cc_start: 0.8878 (mttt) cc_final: 0.8495 (mtmm) REVERT: E 634 GLU cc_start: 0.8503 (tt0) cc_final: 0.8041 (tp30) REVERT: E 639 THR cc_start: 0.9080 (m) cc_final: 0.8400 (p) REVERT: E 651 ASN cc_start: 0.7802 (t0) cc_final: 0.7462 (t0) REVERT: D 466 GLU cc_start: 0.8858 (mm-30) cc_final: 0.8353 (mm-30) REVERT: F 584 GLU cc_start: 0.9128 (tt0) cc_final: 0.8611 (tp30) REVERT: F 601 LYS cc_start: 0.8974 (mttt) cc_final: 0.8761 (mtpt) REVERT: F 617 LYS cc_start: 0.8589 (mtpt) cc_final: 0.7905 (ttmt) REVERT: F 621 ASN cc_start: 0.8600 (t0) cc_final: 0.8184 (t0) REVERT: F 634 GLU cc_start: 0.8675 (tt0) cc_final: 0.7993 (tp30) REVERT: F 648 GLU cc_start: 0.8152 (tm-30) cc_final: 0.7786 (tm-30) REVERT: G 26 GLU cc_start: 0.8038 (tm-30) cc_final: 0.7775 (tm-30) REVERT: G 36 TRP cc_start: 0.9239 (m100) cc_final: 0.8509 (m100) REVERT: G 39 GLN cc_start: 0.8806 (tm-30) cc_final: 0.8481 (tm-30) REVERT: G 46 GLU cc_start: 0.8504 (tp30) cc_final: 0.7477 (mm-30) REVERT: G 72 ASP cc_start: 0.8518 (t0) cc_final: 0.8104 (t0) REVERT: G 89 THR cc_start: 0.9127 (m) cc_final: 0.8622 (p) REVERT: G 98 TYR cc_start: 0.5063 (t80) cc_final: 0.4633 (t80) REVERT: G 108 LEU cc_start: 0.9106 (tp) cc_final: 0.8830 (tp) REVERT: J 5 THR cc_start: 0.7938 (m) cc_final: 0.7223 (p) REVERT: J 30 TYR cc_start: 0.7573 (m-80) cc_final: 0.7366 (m-10) REVERT: J 33 MET cc_start: 0.7697 (ttm) cc_final: 0.7428 (mtt) REVERT: J 34 THR cc_start: 0.9245 (m) cc_final: 0.8998 (p) REVERT: J 37 GLN cc_start: 0.8439 (tm-30) cc_final: 0.8150 (pp30) REVERT: J 96 GLU cc_start: 0.8410 (pt0) cc_final: 0.8199 (pt0) REVERT: I 9 SER cc_start: 0.9258 (m) cc_final: 0.8912 (p) REVERT: I 81 ASP cc_start: 0.8412 (m-30) cc_final: 0.8131 (m-30) REVERT: I 89 THR cc_start: 0.9212 (m) cc_final: 0.8734 (p) REVERT: I 107 THR cc_start: 0.9490 (t) cc_final: 0.9238 (m) REVERT: I 108 LEU cc_start: 0.9459 (tp) cc_final: 0.9155 (tp) REVERT: K 17 GLU cc_start: 0.8994 (pt0) cc_final: 0.8703 (pm20) REVERT: K 37 GLN cc_start: 0.8136 (tm-30) cc_final: 0.7743 (tm-30) REVERT: K 65 SER cc_start: 0.9120 (t) cc_final: 0.8639 (t) REVERT: K 81 GLU cc_start: 0.9321 (tt0) cc_final: 0.8897 (tm-30) REVERT: K 82 ASP cc_start: 0.8701 (m-30) cc_final: 0.8133 (m-30) outliers start: 5 outliers final: 0 residues processed: 518 average time/residue: 0.3284 time to fit residues: 263.2074 Evaluate side-chains 408 residues out of total 2064 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 407 time to evaluate : 2.326 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 231 random chunks: chunk 185 optimal weight: 2.9990 chunk 126 optimal weight: 0.9980 chunk 3 optimal weight: 8.9990 chunk 166 optimal weight: 3.9990 chunk 92 optimal weight: 0.8980 chunk 190 optimal weight: 0.7980 chunk 154 optimal weight: 0.8980 chunk 0 optimal weight: 5.9990 chunk 114 optimal weight: 4.9990 chunk 200 optimal weight: 8.9990 chunk 56 optimal weight: 5.9990 overall best weight: 1.3182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 460 ASN ** A 461 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 540 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 651 ASN L 32 HIS L 70 GLN C 203 GLN ** E 540 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 203 GLN F 651 ASN ** I 95 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 32 HIS K 70 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8073 moved from start: 0.5789 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.058 20979 Z= 0.233 Angle : 0.644 7.792 28458 Z= 0.331 Chirality : 0.048 0.306 3582 Planarity : 0.005 0.068 3417 Dihedral : 7.963 57.557 5478 Min Nonbonded Distance : 2.341 Molprobity Statistics. All-atom Clashscore : 10.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.43 % Favored : 97.57 % Rotamer: Outliers : 0.24 % Allowed : 2.03 % Favored : 97.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.15 (0.17), residues: 2307 helix: 1.19 (0.25), residues: 426 sheet: 0.41 (0.19), residues: 768 loop : -0.49 (0.18), residues: 1113 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.035 0.002 TRP I 36 HIS 0.006 0.001 HIS C 105 PHE 0.025 0.002 PHE H 58 TYR 0.019 0.002 TYR D 384 ARG 0.010 0.001 ARG K 103 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4614 Ramachandran restraints generated. 2307 Oldfield, 0 Emsley, 2307 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4614 Ramachandran restraints generated. 2307 Oldfield, 0 Emsley, 2307 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 500 residues out of total 2064 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 495 time to evaluate : 2.084 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: A 78 ASP cc_start: 0.8329 (m-30) cc_final: 0.7802 (p0) REVERT: A 373 MET cc_start: 0.8954 (mmm) cc_final: 0.8615 (tpp) REVERT: A 425 ASN cc_start: 0.8201 (t0) cc_final: 0.7931 (t0) REVERT: A 460 ASN cc_start: 0.8332 (m110) cc_final: 0.7714 (t0) REVERT: A 466 GLU cc_start: 0.8567 (mm-30) cc_final: 0.8094 (mm-30) REVERT: B 543 GLN cc_start: 0.8560 (mt0) cc_final: 0.8342 (mt0) REVERT: B 584 GLU cc_start: 0.9221 (tt0) cc_final: 0.8636 (tp30) REVERT: B 634 GLU cc_start: 0.8797 (tt0) cc_final: 0.8518 (tt0) REVERT: B 648 GLU cc_start: 0.8296 (tm-30) cc_final: 0.7889 (tm-30) REVERT: B 651 ASN cc_start: 0.7701 (t0) cc_final: 0.7409 (t0) REVERT: H 9 SER cc_start: 0.9535 (m) cc_final: 0.9229 (p) REVERT: H 33 GLU cc_start: 0.8041 (mm-30) cc_final: 0.7519 (mp0) REVERT: H 89 THR cc_start: 0.9216 (m) cc_final: 0.8860 (p) REVERT: H 100 GLN cc_start: 0.7308 (tm-30) cc_final: 0.7078 (tm-30) REVERT: H 100 TYR cc_start: 0.6002 (m-80) cc_final: 0.5635 (m-80) REVERT: H 107 THR cc_start: 0.9337 (t) cc_final: 0.9015 (t) REVERT: C 373 MET cc_start: 0.8899 (mtm) cc_final: 0.8668 (mtm) REVERT: E 545 LEU cc_start: 0.8498 (tp) cc_final: 0.8289 (tt) REVERT: E 601 LYS cc_start: 0.8850 (mttt) cc_final: 0.8476 (mtmm) REVERT: E 616 ASN cc_start: 0.8090 (p0) cc_final: 0.7815 (p0) REVERT: E 634 GLU cc_start: 0.8627 (tt0) cc_final: 0.8158 (tp30) REVERT: E 639 THR cc_start: 0.9162 (m) cc_final: 0.8913 (p) REVERT: D 466 GLU cc_start: 0.8773 (mm-30) cc_final: 0.8262 (mm-30) REVERT: F 543 GLN cc_start: 0.8748 (mt0) cc_final: 0.8537 (mt0) REVERT: F 584 GLU cc_start: 0.9113 (tt0) cc_final: 0.8576 (tp30) REVERT: F 634 GLU cc_start: 0.8818 (tt0) cc_final: 0.8078 (tp30) REVERT: F 648 GLU cc_start: 0.8162 (tm-30) cc_final: 0.7804 (tm-30) REVERT: G 26 GLU cc_start: 0.8111 (tm-30) cc_final: 0.7831 (tm-30) REVERT: G 31 ARG cc_start: 0.8993 (mtt-85) cc_final: 0.8739 (ttm110) REVERT: G 36 TRP cc_start: 0.9204 (m100) cc_final: 0.8424 (m100) REVERT: G 39 GLN cc_start: 0.8799 (tm-30) cc_final: 0.8346 (tm-30) REVERT: G 47 TRP cc_start: 0.8953 (t60) cc_final: 0.8627 (t60) REVERT: G 72 ASP cc_start: 0.8463 (t0) cc_final: 0.8010 (t0) REVERT: G 89 THR cc_start: 0.9082 (m) cc_final: 0.8599 (p) REVERT: G 99 THR cc_start: 0.6353 (p) cc_final: 0.5753 (p) REVERT: G 108 LEU cc_start: 0.9255 (tp) cc_final: 0.9022 (tp) REVERT: J 5 THR cc_start: 0.7796 (m) cc_final: 0.7201 (p) REVERT: J 30 TYR cc_start: 0.7336 (m-80) cc_final: 0.7096 (m-10) REVERT: J 33 MET cc_start: 0.7675 (ttm) cc_final: 0.7406 (mtt) REVERT: J 34 THR cc_start: 0.9070 (m) cc_final: 0.8762 (p) REVERT: J 47 LEU cc_start: 0.8863 (mp) cc_final: 0.8558 (mm) REVERT: J 96 GLU cc_start: 0.8395 (pt0) cc_final: 0.8065 (pt0) REVERT: I 9 SER cc_start: 0.9267 (m) cc_final: 0.8985 (p) REVERT: I 89 THR cc_start: 0.9059 (m) cc_final: 0.8615 (p) REVERT: I 108 LEU cc_start: 0.9501 (tp) cc_final: 0.9262 (tp) REVERT: K 5 THR cc_start: 0.7662 (m) cc_final: 0.6968 (p) REVERT: K 17 GLU cc_start: 0.8898 (pt0) cc_final: 0.8536 (pm20) REVERT: K 65 SER cc_start: 0.9144 (t) cc_final: 0.8725 (t) REVERT: K 81 GLU cc_start: 0.9359 (tt0) cc_final: 0.9017 (tm-30) REVERT: K 82 ASP cc_start: 0.8667 (m-30) cc_final: 0.8184 (t0) outliers start: 5 outliers final: 0 residues processed: 498 average time/residue: 0.3028 time to fit residues: 236.3235 Evaluate side-chains 401 residues out of total 2064 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 401 time to evaluate : 2.287 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 231 random chunks: chunk 75 optimal weight: 7.9990 chunk 201 optimal weight: 20.0000 chunk 44 optimal weight: 6.9990 chunk 131 optimal weight: 3.9990 chunk 55 optimal weight: 0.4980 chunk 223 optimal weight: 10.0000 chunk 185 optimal weight: 1.9990 chunk 103 optimal weight: 6.9990 chunk 18 optimal weight: 3.9990 chunk 73 optimal weight: 7.9990 chunk 117 optimal weight: 3.9990 overall best weight: 2.8988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 203 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 575 GLN B 653 GLN L 70 GLN ** E 540 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 653 GLN ** F 540 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 70 GLN I 57 ASN I 95 GLN K 70 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8181 moved from start: 0.6228 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.067 20979 Z= 0.405 Angle : 0.750 7.186 28458 Z= 0.389 Chirality : 0.050 0.329 3582 Planarity : 0.006 0.081 3417 Dihedral : 8.043 56.790 5478 Min Nonbonded Distance : 2.340 Molprobity Statistics. All-atom Clashscore : 12.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.03 % Favored : 95.97 % Rotamer: Outliers : 0.10 % Allowed : 2.18 % Favored : 97.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % 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: -0.04 (0.17), residues: 2307 helix: 1.17 (0.25), residues: 411 sheet: 0.24 (0.19), residues: 699 loop : -0.57 (0.18), residues: 1197 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.033 0.002 TRP I 36 HIS 0.007 0.001 HIS G 35A PHE 0.023 0.003 PHE H 58 TYR 0.022 0.002 TYR I 100E ARG 0.011 0.001 ARG J 103 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4614 Ramachandran restraints generated. 2307 Oldfield, 0 Emsley, 2307 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4614 Ramachandran restraints generated. 2307 Oldfield, 0 Emsley, 2307 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 473 residues out of total 2064 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 471 time to evaluate : 2.305 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: A 69 TRP cc_start: 0.7198 (p-90) cc_final: 0.6807 (p-90) REVERT: A 95 MET cc_start: 0.8353 (ptm) cc_final: 0.7989 (ppp) REVERT: A 211 GLU cc_start: 0.8891 (mp0) cc_final: 0.8661 (mp0) REVERT: A 373 MET cc_start: 0.9046 (mmm) cc_final: 0.8569 (tpp) REVERT: A 425 ASN cc_start: 0.8472 (t0) cc_final: 0.8223 (t0) REVERT: A 460 ASN cc_start: 0.8187 (m110) cc_final: 0.7729 (m110) REVERT: A 466 GLU cc_start: 0.8714 (mm-30) cc_final: 0.8272 (mp0) REVERT: A 474 ASP cc_start: 0.8206 (t0) cc_final: 0.7493 (p0) REVERT: B 584 GLU cc_start: 0.9327 (tt0) cc_final: 0.8830 (tp30) REVERT: B 634 GLU cc_start: 0.8794 (tt0) cc_final: 0.8470 (tt0) REVERT: B 648 GLU cc_start: 0.8068 (tm-30) cc_final: 0.7763 (tm-30) REVERT: B 650 GLN cc_start: 0.7790 (tm-30) cc_final: 0.7523 (tm-30) REVERT: B 651 ASN cc_start: 0.7636 (t0) cc_final: 0.7217 (t0) REVERT: B 652 GLN cc_start: 0.9062 (tt0) cc_final: 0.8839 (tt0) REVERT: H 9 SER cc_start: 0.9499 (m) cc_final: 0.9123 (p) REVERT: H 31 ARG cc_start: 0.8765 (ptp-110) cc_final: 0.8396 (ptp-110) REVERT: H 89 THR cc_start: 0.9272 (m) cc_final: 0.8923 (p) REVERT: H 95 GLN cc_start: 0.8564 (tm-30) cc_final: 0.8318 (tm-30) REVERT: H 107 THR cc_start: 0.9423 (t) cc_final: 0.9061 (t) REVERT: C 333 ILE cc_start: 0.9110 (mm) cc_final: 0.8796 (tp) REVERT: C 373 MET cc_start: 0.9009 (mtm) cc_final: 0.8757 (mtm) REVERT: C 460 ASN cc_start: 0.8437 (m110) cc_final: 0.7863 (m110) REVERT: E 584 GLU cc_start: 0.9249 (tt0) cc_final: 0.8787 (tp30) REVERT: E 601 LYS cc_start: 0.8914 (mttt) cc_final: 0.8536 (mtmm) REVERT: E 616 ASN cc_start: 0.8148 (p0) cc_final: 0.7926 (p0) REVERT: D 466 GLU cc_start: 0.8917 (mm-30) cc_final: 0.8524 (mm-30) REVERT: F 584 GLU cc_start: 0.9192 (tt0) cc_final: 0.8695 (tp30) REVERT: F 617 LYS cc_start: 0.8546 (mtpt) cc_final: 0.8191 (ttmt) REVERT: F 621 ASN cc_start: 0.8585 (t0) cc_final: 0.8243 (t0) REVERT: F 634 GLU cc_start: 0.8699 (tt0) cc_final: 0.8047 (tp30) REVERT: F 648 GLU cc_start: 0.8117 (tm-30) cc_final: 0.7807 (tm-30) REVERT: F 651 ASN cc_start: 0.7872 (t0) cc_final: 0.7632 (t0) REVERT: G 26 GLU cc_start: 0.8161 (tm-30) cc_final: 0.7898 (tm-30) REVERT: G 36 TRP cc_start: 0.9211 (m100) cc_final: 0.8497 (m100) REVERT: G 39 GLN cc_start: 0.8814 (tm-30) cc_final: 0.8549 (tm-30) REVERT: G 72 ASP cc_start: 0.8733 (t0) cc_final: 0.8257 (t0) REVERT: G 89 THR cc_start: 0.9128 (m) cc_final: 0.8645 (p) REVERT: G 98 TYR cc_start: 0.6037 (t80) cc_final: 0.5402 (t80) REVERT: G 108 LEU cc_start: 0.9286 (tp) cc_final: 0.9039 (tp) REVERT: J 30 TYR cc_start: 0.7396 (m-80) cc_final: 0.7170 (m-10) REVERT: J 33 MET cc_start: 0.7784 (ttm) cc_final: 0.6691 (tpt) REVERT: J 34 THR cc_start: 0.9178 (m) cc_final: 0.8861 (p) REVERT: I 9 SER cc_start: 0.9150 (m) cc_final: 0.8835 (p) REVERT: I 65 GLN cc_start: 0.8760 (tt0) cc_final: 0.8558 (mt0) REVERT: I 89 THR cc_start: 0.9256 (m) cc_final: 0.8828 (p) REVERT: I 102 LEU cc_start: 0.9191 (mt) cc_final: 0.8953 (mt) REVERT: I 107 THR cc_start: 0.9505 (t) cc_final: 0.9217 (t) outliers start: 2 outliers final: 0 residues processed: 471 average time/residue: 0.3187 time to fit residues: 234.5952 Evaluate side-chains 382 residues out of total 2064 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 382 time to evaluate : 2.320 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 231 random chunks: chunk 215 optimal weight: 0.8980 chunk 25 optimal weight: 0.6980 chunk 127 optimal weight: 8.9990 chunk 163 optimal weight: 7.9990 chunk 126 optimal weight: 3.9990 chunk 188 optimal weight: 3.9990 chunk 124 optimal weight: 0.9990 chunk 222 optimal weight: 10.0000 chunk 139 optimal weight: 0.9990 chunk 135 optimal weight: 0.0060 chunk 102 optimal weight: 0.8980 overall best weight: 0.6998 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 203 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 287 GLN L 32 HIS L 70 GLN C 460 ASN ** E 540 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 575 GLN ** E 653 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 658 GLN D 99 ASN ** D 203 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 540 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 575 GLN G 95 GLN J 32 HIS J 70 GLN K 70 GLN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8085 moved from start: 0.6391 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 20979 Z= 0.205 Angle : 0.660 8.048 28458 Z= 0.343 Chirality : 0.052 0.772 3582 Planarity : 0.005 0.065 3417 Dihedral : 7.552 58.556 5478 Min Nonbonded Distance : 2.362 Molprobity Statistics. All-atom Clashscore : 10.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.99 % Favored : 97.01 % Rotamer: Outliers : 0.15 % Allowed : 0.87 % Favored : 98.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.01 (0.17), residues: 2307 helix: 1.44 (0.26), residues: 408 sheet: 0.20 (0.19), residues: 738 loop : -0.60 (0.18), residues: 1161 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.049 0.002 TRP C 45 HIS 0.005 0.001 HIS A 374 PHE 0.031 0.002 PHE G 58 TYR 0.024 0.001 TYR F 643 ARG 0.014 0.001 ARG G 31 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4614 Ramachandran restraints generated. 2307 Oldfield, 0 Emsley, 2307 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4614 Ramachandran restraints generated. 2307 Oldfield, 0 Emsley, 2307 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 504 residues out of total 2064 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 501 time to evaluate : 2.214 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: A 78 ASP cc_start: 0.8503 (m-30) cc_final: 0.7842 (p0) REVERT: A 211 GLU cc_start: 0.8871 (mp0) cc_final: 0.8657 (mp0) REVERT: A 373 MET cc_start: 0.8736 (mmm) cc_final: 0.8403 (tpp) REVERT: A 425 ASN cc_start: 0.8076 (t0) cc_final: 0.7837 (t0) REVERT: A 466 GLU cc_start: 0.8575 (mm-30) cc_final: 0.8180 (mm-30) REVERT: B 584 GLU cc_start: 0.9207 (tt0) cc_final: 0.8679 (tp30) REVERT: B 629 MET cc_start: 0.8136 (mtp) cc_final: 0.7906 (mtp) REVERT: B 634 GLU cc_start: 0.8753 (tt0) cc_final: 0.8461 (tt0) REVERT: B 648 GLU cc_start: 0.8235 (tm-30) cc_final: 0.7825 (tm-30) REVERT: H 9 SER cc_start: 0.9426 (m) cc_final: 0.9174 (p) REVERT: H 31 ARG cc_start: 0.8738 (ptp-110) cc_final: 0.8529 (ttp-110) REVERT: H 89 THR cc_start: 0.9225 (m) cc_final: 0.8829 (p) REVERT: H 100 GLN cc_start: 0.6950 (tm-30) cc_final: 0.5993 (tm-30) REVERT: H 107 THR cc_start: 0.9330 (t) cc_final: 0.8996 (t) REVERT: L 46 LEU cc_start: 0.8094 (pt) cc_final: 0.7771 (pp) REVERT: L 65 SER cc_start: 0.9429 (t) cc_final: 0.9142 (t) REVERT: C 69 TRP cc_start: 0.6335 (p-90) cc_final: 0.5994 (p-90) REVERT: C 370 GLU cc_start: 0.7727 (mp0) cc_final: 0.7392 (pt0) REVERT: E 543 GLN cc_start: 0.8740 (mt0) cc_final: 0.8380 (mt0) REVERT: E 584 GLU cc_start: 0.9078 (tt0) cc_final: 0.8813 (tp30) REVERT: E 601 LYS cc_start: 0.8882 (mttt) cc_final: 0.8529 (mtmm) REVERT: E 653 GLN cc_start: 0.8476 (pp30) cc_final: 0.8258 (tm-30) REVERT: E 659 GLU cc_start: 0.7471 (mp0) cc_final: 0.6795 (tp30) REVERT: D 466 GLU cc_start: 0.8758 (mm-30) cc_final: 0.8386 (mm-30) REVERT: F 584 GLU cc_start: 0.9056 (tt0) cc_final: 0.8617 (tp30) REVERT: F 617 LYS cc_start: 0.8465 (mtpt) cc_final: 0.8163 (ttmt) REVERT: F 621 ASN cc_start: 0.8572 (t0) cc_final: 0.8276 (t0) REVERT: F 634 GLU cc_start: 0.8635 (tt0) cc_final: 0.8013 (tp30) REVERT: F 648 GLU cc_start: 0.8244 (tm-30) cc_final: 0.7887 (tm-30) REVERT: G 26 GLU cc_start: 0.8087 (tm-30) cc_final: 0.7785 (tm-30) REVERT: G 36 TRP cc_start: 0.9272 (m100) cc_final: 0.8509 (m100) REVERT: G 39 GLN cc_start: 0.8747 (tm-30) cc_final: 0.8440 (tm-30) REVERT: G 47 TRP cc_start: 0.8966 (t60) cc_final: 0.8641 (t60) REVERT: G 50 TRP cc_start: 0.9296 (p-90) cc_final: 0.8926 (p-90) REVERT: G 72 ASP cc_start: 0.8542 (t0) cc_final: 0.8053 (t0) REVERT: G 89 THR cc_start: 0.9109 (m) cc_final: 0.8623 (p) REVERT: G 94 ARG cc_start: 0.7541 (tmm-80) cc_final: 0.7195 (tmm160) REVERT: G 98 TYR cc_start: 0.5719 (t80) cc_final: 0.5096 (t80) REVERT: G 108 LEU cc_start: 0.9239 (tp) cc_final: 0.9029 (tp) REVERT: J 34 THR cc_start: 0.8919 (m) cc_final: 0.8706 (p) REVERT: J 96 GLU cc_start: 0.8378 (pt0) cc_final: 0.8074 (pt0) REVERT: I 9 SER cc_start: 0.9078 (m) cc_final: 0.8840 (p) REVERT: I 31 ARG cc_start: 0.8939 (ttm110) cc_final: 0.8587 (ttm-80) REVERT: I 65 GLN cc_start: 0.8762 (tt0) cc_final: 0.8536 (mt0) REVERT: I 75 LEU cc_start: 0.8167 (mt) cc_final: 0.7807 (tp) REVERT: I 89 THR cc_start: 0.9162 (m) cc_final: 0.8681 (p) REVERT: I 107 THR cc_start: 0.9459 (t) cc_final: 0.9164 (t) REVERT: K 5 THR cc_start: 0.7726 (m) cc_final: 0.7120 (p) REVERT: K 65 SER cc_start: 0.9307 (t) cc_final: 0.9051 (t) REVERT: K 82 ASP cc_start: 0.8683 (m-30) cc_final: 0.8134 (t0) outliers start: 3 outliers final: 0 residues processed: 502 average time/residue: 0.3080 time to fit residues: 241.5997 Evaluate side-chains 398 residues out of total 2064 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 398 time to evaluate : 2.367 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 231 random chunks: chunk 137 optimal weight: 5.9990 chunk 88 optimal weight: 0.2980 chunk 132 optimal weight: 0.8980 chunk 67 optimal weight: 10.0000 chunk 43 optimal weight: 0.8980 chunk 141 optimal weight: 8.9990 chunk 151 optimal weight: 2.9990 chunk 110 optimal weight: 1.9990 chunk 20 optimal weight: 5.9990 chunk 175 optimal weight: 0.7980 chunk 202 optimal weight: 0.6980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 374 HIS B 543 GLN B 651 ASN B 653 GLN L 32 HIS L 70 GLN C 460 ASN ** E 540 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 653 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 203 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 540 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 35AHIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 57 ASN ** I 95 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 70 GLN K 90 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8065 moved from start: 0.6553 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 20979 Z= 0.202 Angle : 0.649 7.791 28458 Z= 0.337 Chirality : 0.051 0.690 3582 Planarity : 0.005 0.064 3417 Dihedral : 7.257 54.010 5478 Min Nonbonded Distance : 2.296 Molprobity Statistics. All-atom Clashscore : 10.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.60 % Favored : 96.40 % Rotamer: Outliers : 0.10 % Allowed : 0.97 % Favored : 98.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.05 (0.17), residues: 2307 helix: 1.50 (0.26), residues: 405 sheet: 0.28 (0.19), residues: 735 loop : -0.62 (0.18), residues: 1167 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.038 0.002 TRP I 36 HIS 0.002 0.001 HIS I 35A PHE 0.030 0.002 PHE I 58 TYR 0.010 0.001 TYR K 71 ARG 0.013 0.001 ARG J 103 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4614 Ramachandran restraints generated. 2307 Oldfield, 0 Emsley, 2307 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4614 Ramachandran restraints generated. 2307 Oldfield, 0 Emsley, 2307 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 502 residues out of total 2064 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 500 time to evaluate : 2.357 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: A 78 ASP cc_start: 0.8472 (m-30) cc_final: 0.7837 (p0) REVERT: A 104 MET cc_start: 0.8587 (ttm) cc_final: 0.8125 (tpp) REVERT: A 205 CYS cc_start: 0.7843 (m) cc_final: 0.7365 (m) REVERT: A 373 MET cc_start: 0.8798 (mmm) cc_final: 0.8478 (tpp) REVERT: A 425 ASN cc_start: 0.8133 (t0) cc_final: 0.7878 (t0) REVERT: A 466 GLU cc_start: 0.8537 (mm-30) cc_final: 0.8160 (mm-30) REVERT: B 584 GLU cc_start: 0.9203 (tt0) cc_final: 0.8658 (tp30) REVERT: B 629 MET cc_start: 0.7955 (mtp) cc_final: 0.7718 (mtp) REVERT: B 634 GLU cc_start: 0.8733 (tt0) cc_final: 0.8466 (tt0) REVERT: B 648 GLU cc_start: 0.8186 (tm-30) cc_final: 0.7876 (tm-30) REVERT: H 31 ARG cc_start: 0.8677 (ptp-110) cc_final: 0.8329 (ttp-110) REVERT: H 47 TRP cc_start: 0.9107 (t60) cc_final: 0.8384 (t60) REVERT: H 89 THR cc_start: 0.9177 (m) cc_final: 0.8780 (p) REVERT: H 95 GLN cc_start: 0.8303 (tm-30) cc_final: 0.8068 (tm-30) REVERT: H 108 LEU cc_start: 0.9460 (tp) cc_final: 0.9244 (tp) REVERT: L 46 LEU cc_start: 0.8193 (pt) cc_final: 0.7922 (pp) REVERT: L 65 SER cc_start: 0.9413 (t) cc_final: 0.9144 (t) REVERT: L 96 GLU cc_start: 0.8284 (pt0) cc_final: 0.7569 (pt0) REVERT: C 370 GLU cc_start: 0.7751 (mp0) cc_final: 0.7368 (pt0) REVERT: C 474 ASP cc_start: 0.8206 (t0) cc_final: 0.7859 (t0) REVERT: E 543 GLN cc_start: 0.8703 (mt0) cc_final: 0.8407 (mt0) REVERT: E 584 GLU cc_start: 0.9127 (tt0) cc_final: 0.8784 (tp30) REVERT: E 601 LYS cc_start: 0.8875 (mttt) cc_final: 0.8513 (mtmm) REVERT: E 657 GLU cc_start: 0.8683 (pm20) cc_final: 0.8388 (tm-30) REVERT: E 659 GLU cc_start: 0.7441 (mp0) cc_final: 0.6789 (tp30) REVERT: D 69 TRP cc_start: 0.6566 (p-90) cc_final: 0.6251 (p-90) REVERT: D 466 GLU cc_start: 0.8675 (mm-30) cc_final: 0.8373 (mm-30) REVERT: F 584 GLU cc_start: 0.9048 (tt0) cc_final: 0.8607 (tp30) REVERT: F 617 LYS cc_start: 0.8462 (mtpt) cc_final: 0.8077 (ttmt) REVERT: F 621 ASN cc_start: 0.8568 (t0) cc_final: 0.8253 (t0) REVERT: F 634 GLU cc_start: 0.8651 (tt0) cc_final: 0.8428 (tm-30) REVERT: F 648 GLU cc_start: 0.8237 (tm-30) cc_final: 0.7936 (tm-30) REVERT: F 651 ASN cc_start: 0.7906 (t0) cc_final: 0.7586 (t0) REVERT: G 26 GLU cc_start: 0.8156 (tm-30) cc_final: 0.7808 (tm-30) REVERT: G 36 TRP cc_start: 0.9170 (m100) cc_final: 0.8508 (m100) REVERT: G 47 TRP cc_start: 0.8979 (t60) cc_final: 0.8584 (t60) REVERT: G 50 TRP cc_start: 0.9338 (p-90) cc_final: 0.8924 (p-90) REVERT: G 72 ASP cc_start: 0.8587 (t0) cc_final: 0.8136 (t0) REVERT: G 98 TYR cc_start: 0.5478 (t80) cc_final: 0.5061 (t80) REVERT: G 108 LEU cc_start: 0.9204 (tp) cc_final: 0.8997 (tp) REVERT: J 5 THR cc_start: 0.7707 (m) cc_final: 0.7114 (p) REVERT: J 96 GLU cc_start: 0.8379 (pt0) cc_final: 0.8073 (pt0) REVERT: I 31 ARG cc_start: 0.9004 (ttm110) cc_final: 0.8650 (ttm-80) REVERT: I 65 GLN cc_start: 0.8771 (tt0) cc_final: 0.8507 (mt0) REVERT: I 75 LEU cc_start: 0.8144 (mt) cc_final: 0.7916 (tp) REVERT: I 89 THR cc_start: 0.9155 (m) cc_final: 0.8663 (p) REVERT: K 5 THR cc_start: 0.7718 (m) cc_final: 0.7076 (p) REVERT: K 65 SER cc_start: 0.9333 (t) cc_final: 0.9101 (t) REVERT: K 82 ASP cc_start: 0.8746 (m-30) cc_final: 0.8261 (t0) outliers start: 2 outliers final: 0 residues processed: 500 average time/residue: 0.3118 time to fit residues: 244.6118 Evaluate side-chains 390 residues out of total 2064 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 390 time to evaluate : 2.275 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 231 random chunks: chunk 213 optimal weight: 0.2980 chunk 194 optimal weight: 4.9990 chunk 207 optimal weight: 7.9990 chunk 124 optimal weight: 0.6980 chunk 90 optimal weight: 4.9990 chunk 162 optimal weight: 2.9990 chunk 63 optimal weight: 6.9990 chunk 187 optimal weight: 0.5980 chunk 196 optimal weight: 1.9990 chunk 206 optimal weight: 8.9990 chunk 136 optimal weight: 0.0000 overall best weight: 0.7186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 650 GLN L 32 HIS L 70 GLN ** C 203 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 540 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 203 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 540 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 575 GLN J 32 HIS J 70 GLN I 95 GLN K 70 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8054 moved from start: 0.6712 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 20979 Z= 0.200 Angle : 0.654 8.307 28458 Z= 0.341 Chirality : 0.050 0.638 3582 Planarity : 0.005 0.083 3417 Dihedral : 7.002 59.576 5478 Min Nonbonded Distance : 2.292 Molprobity Statistics. All-atom Clashscore : 9.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.38 % Favored : 96.62 % Rotamer: Outliers : 0.10 % Allowed : 0.53 % Favored : 99.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % 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: -0.02 (0.17), residues: 2307 helix: 1.32 (0.26), residues: 408 sheet: 0.43 (0.19), residues: 768 loop : -0.80 (0.18), residues: 1131 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.035 0.002 TRP H 36 HIS 0.002 0.001 HIS C 216 PHE 0.021 0.002 PHE A 233 TYR 0.036 0.001 TYR A 217 ARG 0.010 0.001 ARG J 77 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4614 Ramachandran restraints generated. 2307 Oldfield, 0 Emsley, 2307 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4614 Ramachandran restraints generated. 2307 Oldfield, 0 Emsley, 2307 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 505 residues out of total 2064 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 503 time to evaluate : 2.600 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: A 78 ASP cc_start: 0.8489 (m-30) cc_final: 0.7847 (p0) REVERT: A 373 MET cc_start: 0.8807 (mmm) cc_final: 0.8521 (tpp) REVERT: A 425 ASN cc_start: 0.8149 (t0) cc_final: 0.7870 (t0) REVERT: A 466 GLU cc_start: 0.8495 (mm-30) cc_final: 0.8128 (mm-30) REVERT: B 584 GLU cc_start: 0.9163 (tt0) cc_final: 0.8639 (tp30) REVERT: B 629 MET cc_start: 0.8014 (mtp) cc_final: 0.7680 (mtp) REVERT: B 634 GLU cc_start: 0.8697 (tt0) cc_final: 0.8446 (tt0) REVERT: B 648 GLU cc_start: 0.8188 (tm-30) cc_final: 0.7890 (tm-30) REVERT: H 31 ARG cc_start: 0.8747 (ptp-110) cc_final: 0.8478 (ttp-110) REVERT: H 47 TRP cc_start: 0.9126 (t60) cc_final: 0.8445 (t60) REVERT: H 89 THR cc_start: 0.9160 (m) cc_final: 0.8758 (p) REVERT: H 99 THR cc_start: 0.7033 (t) cc_final: 0.6476 (t) REVERT: H 108 LEU cc_start: 0.9476 (tp) cc_final: 0.9226 (tp) REVERT: L 46 LEU cc_start: 0.8070 (pt) cc_final: 0.7837 (pp) REVERT: L 65 SER cc_start: 0.9403 (t) cc_final: 0.9073 (t) REVERT: L 66 GLN cc_start: 0.6823 (tt0) cc_final: 0.6291 (tp40) REVERT: L 96 GLU cc_start: 0.8277 (pt0) cc_final: 0.7422 (pt0) REVERT: C 370 GLU cc_start: 0.7540 (mp0) cc_final: 0.7327 (pt0) REVERT: E 543 GLN cc_start: 0.8664 (mt0) cc_final: 0.8381 (mt0) REVERT: E 584 GLU cc_start: 0.9092 (tt0) cc_final: 0.8826 (tp30) REVERT: E 601 LYS cc_start: 0.8878 (mttt) cc_final: 0.8503 (mtmm) REVERT: E 659 GLU cc_start: 0.7301 (mp0) cc_final: 0.6775 (tp30) REVERT: D 354 ARG cc_start: 0.8580 (tpm170) cc_final: 0.8253 (tpm170) REVERT: D 395 TRP cc_start: 0.7601 (m100) cc_final: 0.7223 (m100) REVERT: D 466 GLU cc_start: 0.8618 (mm-30) cc_final: 0.8287 (mm-30) REVERT: F 584 GLU cc_start: 0.9047 (tt0) cc_final: 0.8611 (tp30) REVERT: F 617 LYS cc_start: 0.8440 (mtpt) cc_final: 0.8198 (ttmt) REVERT: F 621 ASN cc_start: 0.8427 (t0) cc_final: 0.7983 (t0) REVERT: F 626 MET cc_start: 0.6808 (ttm) cc_final: 0.5940 (ttm) REVERT: F 634 GLU cc_start: 0.8638 (tt0) cc_final: 0.8344 (tm-30) REVERT: F 648 GLU cc_start: 0.8184 (tm-30) cc_final: 0.7875 (tm-30) REVERT: G 36 TRP cc_start: 0.9214 (m100) cc_final: 0.8422 (m100) REVERT: G 39 GLN cc_start: 0.8671 (tm-30) cc_final: 0.8393 (tm-30) REVERT: G 47 TRP cc_start: 0.8975 (t60) cc_final: 0.8615 (t60) REVERT: G 72 ASP cc_start: 0.8574 (t0) cc_final: 0.8130 (t0) REVERT: G 89 THR cc_start: 0.9020 (m) cc_final: 0.8521 (p) REVERT: J 5 THR cc_start: 0.7622 (m) cc_final: 0.6990 (p) REVERT: J 96 GLU cc_start: 0.8417 (pt0) cc_final: 0.8059 (pt0) REVERT: I 31 ARG cc_start: 0.9020 (ttm110) cc_final: 0.8670 (ttm-80) REVERT: I 65 GLN cc_start: 0.8778 (tt0) cc_final: 0.8530 (mt0) REVERT: I 75 LEU cc_start: 0.8141 (mt) cc_final: 0.7869 (tp) REVERT: I 89 THR cc_start: 0.9141 (m) cc_final: 0.8641 (p) REVERT: K 5 THR cc_start: 0.7691 (m) cc_final: 0.7057 (p) REVERT: K 33 MET cc_start: 0.6740 (pmm) cc_final: 0.6456 (pmm) outliers start: 2 outliers final: 0 residues processed: 503 average time/residue: 0.3230 time to fit residues: 258.3376 Evaluate side-chains 396 residues out of total 2064 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 396 time to evaluate : 2.240 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 231 random chunks: chunk 219 optimal weight: 0.9990 chunk 133 optimal weight: 0.9990 chunk 104 optimal weight: 6.9990 chunk 152 optimal weight: 1.9990 chunk 230 optimal weight: 2.9990 chunk 211 optimal weight: 4.9990 chunk 183 optimal weight: 0.8980 chunk 19 optimal weight: 4.9990 chunk 141 optimal weight: 0.0570 chunk 112 optimal weight: 2.9990 chunk 145 optimal weight: 0.8980 overall best weight: 0.7702 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L 32 HIS L 70 GLN ** C 203 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 540 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 203 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 540 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 57 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 32 HIS J 70 GLN I 95 GLN K 70 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8051 moved from start: 0.6867 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 20979 Z= 0.209 Angle : 0.651 7.397 28458 Z= 0.340 Chirality : 0.050 0.597 3582 Planarity : 0.005 0.063 3417 Dihedral : 6.764 54.229 5478 Min Nonbonded Distance : 2.337 Molprobity Statistics. All-atom Clashscore : 10.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.99 % Favored : 96.01 % Rotamer: Outliers : 0.10 % Allowed : 0.19 % Favored : 99.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % 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: -0.06 (0.17), residues: 2307 helix: 1.29 (0.26), residues: 408 sheet: 0.39 (0.19), residues: 738 loop : -0.79 (0.18), residues: 1161 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.032 0.002 TRP I 36 HIS 0.002 0.001 HIS H 79 PHE 0.024 0.002 PHE I 58 TYR 0.024 0.001 TYR A 217 ARG 0.011 0.001 ARG G 31 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4614 Ramachandran restraints generated. 2307 Oldfield, 0 Emsley, 2307 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4614 Ramachandran restraints generated. 2307 Oldfield, 0 Emsley, 2307 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 498 residues out of total 2064 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 496 time to evaluate : 2.036 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: A 78 ASP cc_start: 0.8470 (m-30) cc_final: 0.7846 (p0) REVERT: A 211 GLU cc_start: 0.8918 (mp0) cc_final: 0.8314 (tp30) REVERT: A 373 MET cc_start: 0.8835 (mmm) cc_final: 0.8452 (mmt) REVERT: A 425 ASN cc_start: 0.8163 (t0) cc_final: 0.7878 (t0) REVERT: A 466 GLU cc_start: 0.8458 (mm-30) cc_final: 0.8102 (mm-30) REVERT: B 584 GLU cc_start: 0.9160 (tt0) cc_final: 0.8649 (tp30) REVERT: B 621 ASN cc_start: 0.8154 (p0) cc_final: 0.7811 (t0) REVERT: B 629 MET cc_start: 0.8026 (mtp) cc_final: 0.7706 (mtp) REVERT: B 634 GLU cc_start: 0.8685 (tt0) cc_final: 0.8437 (tt0) REVERT: H 31 ARG cc_start: 0.8868 (ptp-110) cc_final: 0.8529 (ttp-110) REVERT: H 47 TRP cc_start: 0.9116 (t60) cc_final: 0.8505 (t60) REVERT: H 89 THR cc_start: 0.9145 (m) cc_final: 0.8724 (p) REVERT: H 99 THR cc_start: 0.7097 (t) cc_final: 0.6529 (t) REVERT: H 108 LEU cc_start: 0.9475 (tp) cc_final: 0.9210 (tp) REVERT: L 65 SER cc_start: 0.9382 (t) cc_final: 0.9071 (t) REVERT: L 70 GLN cc_start: 0.7925 (OUTLIER) cc_final: 0.7711 (pp30) REVERT: E 543 GLN cc_start: 0.8678 (mt0) cc_final: 0.8374 (mt0) REVERT: E 584 GLU cc_start: 0.9076 (tt0) cc_final: 0.8816 (tp30) REVERT: E 601 LYS cc_start: 0.8949 (mttt) cc_final: 0.8623 (mtmm) REVERT: E 617 LYS cc_start: 0.8027 (mtpt) cc_final: 0.7754 (ttmt) REVERT: E 659 GLU cc_start: 0.7522 (mp0) cc_final: 0.6856 (tp30) REVERT: D 69 TRP cc_start: 0.6679 (p-90) cc_final: 0.6450 (p-90) REVERT: D 95 MET cc_start: 0.8170 (ppp) cc_final: 0.7863 (ppp) REVERT: D 104 MET cc_start: 0.8869 (ttm) cc_final: 0.8229 (ttm) REVERT: D 354 ARG cc_start: 0.8525 (tpm170) cc_final: 0.8201 (tpm170) REVERT: D 395 TRP cc_start: 0.7654 (m100) cc_final: 0.7246 (m100) REVERT: D 466 GLU cc_start: 0.8606 (mm-30) cc_final: 0.8204 (mm-30) REVERT: F 584 GLU cc_start: 0.9110 (tt0) cc_final: 0.8607 (tp30) REVERT: F 617 LYS cc_start: 0.8422 (mtpt) cc_final: 0.7999 (ttmt) REVERT: F 621 ASN cc_start: 0.8316 (t0) cc_final: 0.7958 (t0) REVERT: F 626 MET cc_start: 0.6661 (ttm) cc_final: 0.6344 (ttt) REVERT: F 643 TYR cc_start: 0.8818 (m-80) cc_final: 0.8577 (m-80) REVERT: F 648 GLU cc_start: 0.8191 (tm-30) cc_final: 0.7888 (tm-30) REVERT: G 36 TRP cc_start: 0.9156 (m100) cc_final: 0.8468 (m100) REVERT: G 39 GLN cc_start: 0.8669 (tm-30) cc_final: 0.8352 (tm-30) REVERT: G 47 TRP cc_start: 0.9033 (t60) cc_final: 0.8618 (t60) REVERT: G 50 TRP cc_start: 0.9310 (p-90) cc_final: 0.9014 (p-90) REVERT: G 72 ASP cc_start: 0.8558 (t0) cc_final: 0.8097 (t0) REVERT: G 89 THR cc_start: 0.8979 (m) cc_final: 0.8503 (p) REVERT: G 95 GLN cc_start: 0.7816 (tm-30) cc_final: 0.7481 (tm-30) REVERT: J 5 THR cc_start: 0.7723 (m) cc_final: 0.7109 (p) REVERT: J 96 GLU cc_start: 0.8290 (pt0) cc_final: 0.7926 (pt0) REVERT: I 31 ARG cc_start: 0.9037 (ttm110) cc_final: 0.8730 (ttm-80) REVERT: I 65 GLN cc_start: 0.8726 (tt0) cc_final: 0.8519 (mt0) REVERT: I 75 LEU cc_start: 0.8028 (mt) cc_final: 0.7817 (tp) REVERT: I 89 THR cc_start: 0.9151 (m) cc_final: 0.8649 (p) REVERT: I 100 GLN cc_start: 0.7569 (tm-30) cc_final: 0.7061 (tm-30) REVERT: I 100 TYR cc_start: 0.5404 (m-80) cc_final: 0.5000 (m-80) REVERT: K 5 THR cc_start: 0.7782 (m) cc_final: 0.7158 (p) REVERT: K 33 MET cc_start: 0.6527 (pmm) cc_final: 0.6088 (pmm) REVERT: K 65 SER cc_start: 0.9321 (t) cc_final: 0.9116 (t) REVERT: K 82 ASP cc_start: 0.8655 (m-30) cc_final: 0.8227 (t0) outliers start: 2 outliers final: 0 residues processed: 496 average time/residue: 0.3066 time to fit residues: 239.1044 Evaluate side-chains 405 residues out of total 2064 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 404 time to evaluate : 2.355 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 231 random chunks: chunk 195 optimal weight: 0.0570 chunk 56 optimal weight: 8.9990 chunk 168 optimal weight: 2.9990 chunk 27 optimal weight: 0.9990 chunk 50 optimal weight: 0.9980 chunk 183 optimal weight: 6.9990 chunk 76 optimal weight: 2.9990 chunk 188 optimal weight: 0.7980 chunk 23 optimal weight: 0.9980 chunk 33 optimal weight: 4.9990 chunk 161 optimal weight: 4.9990 overall best weight: 0.7700 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 651 ASN L 32 HIS L 70 GLN ** C 203 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 540 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 203 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 540 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 575 GLN J 32 HIS J 70 GLN I 95 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3672 r_free = 0.3672 target = 0.119555 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3256 r_free = 0.3256 target = 0.092319 restraints weight = 44239.358| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.3302 r_free = 0.3302 target = 0.095110 restraints weight = 29102.766| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.3333 r_free = 0.3333 target = 0.096970 restraints weight = 22380.680| |-----------------------------------------------------------------------------| r_work (final): 0.3335 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7895 moved from start: 0.7012 Sorry: Reduce crashed with command 'molprobity.reduce -quiet -trim -'. Dumping stdin to file 'reduce_fail.pdb'. Return code: -15 Dumping stderr: