Starting phenix.real_space_refine on Mon Feb 19 22:00:53 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6ozc_20224/02_2024/6ozc_20224.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6ozc_20224/02_2024/6ozc_20224.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.79 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6ozc_20224/02_2024/6ozc_20224.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6ozc_20224/02_2024/6ozc_20224.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6ozc_20224/02_2024/6ozc_20224.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6ozc_20224/02_2024/6ozc_20224.pdb" } resolution = 3.79 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= 0.061 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 150 5.16 5 C 16083 2.51 5 N 4164 2.21 5 O 5424 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 381": "OE1" <-> "OE2" Residue "L PHE 62": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 80": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 91": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E GLU 381": "OE1" <-> "OE2" Residue "Q PHE 62": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M PHE 80": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F GLU 381": "OE1" <-> "OE2" Residue "R PHE 62": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N PHE 80": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.07s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 25821 Number of models: 1 Model: "" Number of chains: 54 Chain: "A" Number of atoms: 3416 Number of conformers: 1 Conformer: "" Number of residues, atoms: 435, 3416 Classifications: {'peptide': 435} Link IDs: {'PTRANS': 22, 'TRANS': 412} Chain breaks: 3 Chain: "B" Number of atoms: 956 Number of conformers: 1 Conformer: "" Number of residues, atoms: 120, 956 Classifications: {'peptide': 120} Link IDs: {'PTRANS': 1, 'TRANS': 118} Chain breaks: 1 Chain: "L" Number of atoms: 798 Number of conformers: 1 Conformer: "" Number of residues, atoms: 105, 798 Classifications: {'peptide': 105} Link IDs: {'PCIS': 1, 'PTRANS': 3, 'TRANS': 100} Chain: "H" Number of atoms: 938 Number of conformers: 1 Conformer: "" Number of residues, atoms: 122, 938 Classifications: {'peptide': 122} Link IDs: {'PTRANS': 3, 'TRANS': 118} Chain: "D" Number of atoms: 798 Number of conformers: 1 Conformer: "" Number of residues, atoms: 105, 798 Classifications: {'peptide': 105} Link IDs: {'PCIS': 1, 'PTRANS': 3, 'TRANS': 100} Chain: "C" Number of atoms: 938 Number of conformers: 1 Conformer: "" Number of residues, atoms: 122, 938 Classifications: {'peptide': 122} Link IDs: {'PTRANS': 3, 'TRANS': 118} Chain: "E" Number of atoms: 3416 Number of conformers: 1 Conformer: "" Number of residues, atoms: 435, 3416 Classifications: {'peptide': 435} Link IDs: {'PTRANS': 22, 'TRANS': 412} Chain breaks: 3 Chain: "G" Number of atoms: 956 Number of conformers: 1 Conformer: "" Number of residues, atoms: 120, 956 Classifications: {'peptide': 120} Link IDs: {'PTRANS': 1, 'TRANS': 118} Chain breaks: 1 Chain: "Q" Number of atoms: 798 Number of conformers: 1 Conformer: "" Number of residues, atoms: 105, 798 Classifications: {'peptide': 105} Link IDs: {'PCIS': 1, 'PTRANS': 3, 'TRANS': 100} Chain: "O" Number of atoms: 938 Number of conformers: 1 Conformer: "" Number of residues, atoms: 122, 938 Classifications: {'peptide': 122} Link IDs: {'PTRANS': 3, 'TRANS': 118} Chain: "M" Number of atoms: 798 Number of conformers: 1 Conformer: "" Number of residues, atoms: 105, 798 Classifications: {'peptide': 105} Link IDs: {'PCIS': 1, 'PTRANS': 3, 'TRANS': 100} Chain: "J" Number of atoms: 938 Number of conformers: 1 Conformer: "" Number of residues, atoms: 122, 938 Classifications: {'peptide': 122} Link IDs: {'PTRANS': 3, 'TRANS': 118} Chain: "F" Number of atoms: 3416 Number of conformers: 1 Conformer: "" Number of residues, atoms: 435, 3416 Classifications: {'peptide': 435} Link IDs: {'PTRANS': 22, 'TRANS': 412} Chain breaks: 3 Chain: "I" Number of atoms: 956 Number of conformers: 1 Conformer: "" Number of residues, atoms: 120, 956 Classifications: {'peptide': 120} Link IDs: {'PTRANS': 1, 'TRANS': 118} Chain breaks: 1 Chain: "R" Number of atoms: 798 Number of conformers: 1 Conformer: "" Number of residues, atoms: 105, 798 Classifications: {'peptide': 105} Link IDs: {'PCIS': 1, 'PTRANS': 3, 'TRANS': 100} Chain: "P" Number of atoms: 938 Number of conformers: 1 Conformer: "" Number of residues, atoms: 122, 938 Classifications: {'peptide': 122} Link IDs: {'PTRANS': 3, 'TRANS': 118} Chain: "N" Number of atoms: 798 Number of conformers: 1 Conformer: "" Number of residues, atoms: 105, 798 Classifications: {'peptide': 105} Link IDs: {'PCIS': 1, 'PTRANS': 3, 'TRANS': 100} Chain: "K" Number of atoms: 938 Number of conformers: 1 Conformer: "" Number of residues, atoms: 122, 938 Classifications: {'peptide': 122} Link IDs: {'PTRANS': 3, 'TRANS': 118} Chain: "S" 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: "T" 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: "U" Number of atoms: 105 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 105 Unusual residues: {'BMA': 1, 'MAN': 6, 'NAG': 2} Classifications: {'undetermined': 9} Link IDs: {None: 8} Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 18 Unresolved non-hydrogen dihedrals: 27 Unresolved non-hydrogen chiralities: 9 Chain: "V" 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: "W" Number of atoms: 94 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 94 Unusual residues: {'BMA': 1, 'MAN': 5, 'NAG': 2} Classifications: {'undetermined': 8} Link IDs: {None: 7} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen dihedrals: 24 Unresolved non-hydrogen chiralities: 8 Chain: "X" Number of atoms: 83 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 83 Unusual residues: {'BMA': 1, 'MAN': 4, 'NAG': 2} Classifications: {'undetermined': 7} Link IDs: {None: 6} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 21 Unresolved non-hydrogen chiralities: 7 Chain: "Y" Number of atoms: 105 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 105 Unusual residues: {'BMA': 1, 'MAN': 6, 'NAG': 2} Classifications: {'undetermined': 9} Link IDs: {None: 8} Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 18 Unresolved non-hydrogen dihedrals: 27 Unresolved non-hydrogen chiralities: 9 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: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "b" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "c" Number of atoms: 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: "d" 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: "e" Number of atoms: 105 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 105 Unusual residues: {'BMA': 1, 'MAN': 6, 'NAG': 2} Classifications: {'undetermined': 9} Link IDs: {None: 8} Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 18 Unresolved non-hydrogen dihedrals: 27 Unresolved non-hydrogen chiralities: 9 Chain: "f" 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: "g" Number of atoms: 94 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 94 Unusual residues: {'BMA': 1, 'MAN': 5, 'NAG': 2} Classifications: {'undetermined': 8} Link IDs: {None: 7} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen dihedrals: 24 Unresolved non-hydrogen chiralities: 8 Chain: "h" Number of atoms: 83 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 83 Unusual residues: {'BMA': 1, 'MAN': 4, 'NAG': 2} Classifications: {'undetermined': 7} Link IDs: {None: 6} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 21 Unresolved non-hydrogen chiralities: 7 Chain: "i" Number of atoms: 105 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 105 Unusual residues: {'BMA': 1, 'MAN': 6, 'NAG': 2} Classifications: {'undetermined': 9} Link IDs: {None: 8} Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 18 Unresolved non-hydrogen dihedrals: 27 Unresolved non-hydrogen chiralities: 9 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: 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: "n" 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: "o" Number of atoms: 105 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 105 Unusual residues: {'BMA': 1, 'MAN': 6, 'NAG': 2} Classifications: {'undetermined': 9} Link IDs: {None: 8} Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 18 Unresolved non-hydrogen dihedrals: 27 Unresolved non-hydrogen chiralities: 9 Chain: "p" 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: "q" Number of atoms: 94 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 94 Unusual residues: {'BMA': 1, 'MAN': 5, 'NAG': 2} Classifications: {'undetermined': 8} Link IDs: {None: 7} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen dihedrals: 24 Unresolved non-hydrogen chiralities: 8 Chain: "r" Number of atoms: 83 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 83 Unusual residues: {'BMA': 1, 'MAN': 4, 'NAG': 2} Classifications: {'undetermined': 7} Link IDs: {None: 6} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 21 Unresolved non-hydrogen chiralities: 7 Chain: "s" Number of atoms: 105 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 105 Unusual residues: {'BMA': 1, 'MAN': 6, 'NAG': 2} Classifications: {'undetermined': 9} Link IDs: {None: 8} Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 18 Unresolved non-hydrogen dihedrals: 27 Unresolved non-hydrogen chiralities: 9 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: "A" Number of atoms: 56 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 56 Unusual residues: {'NAG': 4} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 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: "E" Number of atoms: 56 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 56 Unusual residues: {'NAG': 4} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Chain: "G" 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: "F" Number of atoms: 56 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 56 Unusual residues: {'NAG': 4} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Chain: "I" 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: 14.40, per 1000 atoms: 0.56 Number of scatterers: 25821 At special positions: 0 Unit cell: (188.64, 197.81, 137.55, 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 150 16.00 O 5424 8.00 N 4164 7.00 C 16083 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=42, symmetry=0 Simple disulfide: pdb=" SG CYS A 54 " - pdb=" SG CYS A 74 " distance=2.03 Simple disulfide: pdb=" SG CYS A 119 " - pdb=" SG CYS A 205 " distance=2.12 Simple disulfide: pdb=" SG CYS A 126 " - pdb=" SG CYS A 196 " distance=2.04 Simple disulfide: pdb=" SG CYS A 131 " - pdb=" SG CYS A 157 " distance=2.03 Simple disulfide: pdb=" SG CYS A 218 " - pdb=" SG CYS A 247 " distance=2.03 Simple disulfide: pdb=" SG CYS A 228 " - pdb=" SG CYS A 239 " distance=2.03 Simple disulfide: pdb=" SG CYS A 296 " - pdb=" SG CYS A 331 " distance=2.03 Simple disulfide: pdb=" SG CYS A 378 " - pdb=" SG CYS A 445 " distance=2.04 Simple disulfide: pdb=" SG CYS A 385 " - pdb=" SG CYS A 418 " distance=2.02 Simple disulfide: pdb=" SG CYS B 598 " - pdb=" SG CYS B 604 " distance=2.03 Simple disulfide: pdb=" SG CYS L 23 " - pdb=" SG CYS L 88 " distance=2.07 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 92 " distance=2.02 Simple disulfide: pdb=" SG CYS D 23 " - pdb=" SG CYS D 88 " distance=2.03 Simple disulfide: pdb=" SG CYS C 22 " - pdb=" SG CYS C 92 " distance=2.02 Simple disulfide: pdb=" SG CYS E 54 " - pdb=" SG CYS E 74 " distance=2.03 Simple disulfide: pdb=" SG CYS E 119 " - pdb=" SG CYS E 205 " distance=2.12 Simple disulfide: pdb=" SG CYS E 126 " - pdb=" SG CYS E 196 " distance=2.04 Simple disulfide: pdb=" SG CYS E 131 " - pdb=" SG CYS E 157 " distance=2.03 Simple disulfide: pdb=" SG CYS E 218 " - pdb=" SG CYS E 247 " distance=2.03 Simple disulfide: pdb=" SG CYS E 228 " - pdb=" SG CYS E 239 " distance=2.03 Simple disulfide: pdb=" SG CYS E 296 " - pdb=" SG CYS E 331 " distance=2.03 Simple disulfide: pdb=" SG CYS E 378 " - pdb=" SG CYS E 445 " distance=2.04 Simple disulfide: pdb=" SG CYS E 385 " - pdb=" SG CYS E 418 " distance=2.02 Simple disulfide: pdb=" SG CYS G 598 " - pdb=" SG CYS G 604 " distance=2.03 Simple disulfide: pdb=" SG CYS Q 23 " - pdb=" SG CYS Q 88 " distance=2.07 Simple disulfide: pdb=" SG CYS O 22 " - pdb=" SG CYS O 92 " distance=2.02 Simple disulfide: pdb=" SG CYS M 23 " - pdb=" SG CYS M 88 " distance=2.03 Simple disulfide: pdb=" SG CYS J 22 " - pdb=" SG CYS J 92 " distance=2.02 Simple disulfide: pdb=" SG CYS F 54 " - pdb=" SG CYS F 74 " distance=2.03 Simple disulfide: pdb=" SG CYS F 119 " - pdb=" SG CYS F 205 " distance=2.12 Simple disulfide: pdb=" SG CYS F 126 " - pdb=" SG CYS F 196 " distance=2.04 Simple disulfide: pdb=" SG CYS F 131 " - pdb=" SG CYS F 157 " distance=2.03 Simple disulfide: pdb=" SG CYS F 218 " - pdb=" SG CYS F 247 " distance=2.03 Simple disulfide: pdb=" SG CYS F 228 " - pdb=" SG CYS F 239 " distance=2.03 Simple disulfide: pdb=" SG CYS F 296 " - pdb=" SG CYS F 331 " distance=2.03 Simple disulfide: pdb=" SG CYS F 378 " - pdb=" SG CYS F 445 " distance=2.04 Simple disulfide: pdb=" SG CYS F 385 " - pdb=" SG CYS F 418 " distance=2.02 Simple disulfide: pdb=" SG CYS I 598 " - pdb=" SG CYS I 604 " distance=2.03 Simple disulfide: pdb=" SG CYS R 23 " - pdb=" SG CYS R 88 " distance=2.07 Simple disulfide: pdb=" SG CYS P 22 " - pdb=" SG CYS P 92 " distance=2.02 Simple disulfide: pdb=" SG CYS N 23 " - pdb=" SG CYS N 88 " distance=2.03 Simple disulfide: pdb=" SG CYS K 22 " - pdb=" SG CYS K 92 " distance=2.02 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied ALPHA1-2 " MAN S 4 " - " MAN S 5 " " MAN U 4 " - " MAN U 5 " " MAN U 5 " - " MAN U 6 " " MAN W 5 " - " MAN W 6 " " MAN X 4 " - " MAN X 5 " " MAN X 5 " - " MAN X 6 " " MAN Y 5 " - " MAN Y 6 " " MAN Y 8 " - " MAN Y 9 " " MAN c 4 " - " MAN c 5 " " MAN e 4 " - " MAN e 5 " " MAN e 5 " - " MAN e 6 " " MAN g 5 " - " MAN g 6 " " MAN h 4 " - " MAN h 5 " " MAN h 5 " - " MAN h 6 " " MAN i 5 " - " MAN i 6 " " MAN i 8 " - " MAN i 9 " " MAN m 4 " - " MAN m 5 " " MAN o 4 " - " MAN o 5 " " MAN o 5 " - " MAN o 6 " " MAN q 5 " - " MAN q 6 " " MAN r 4 " - " MAN r 5 " " MAN r 5 " - " MAN r 6 " " MAN s 5 " - " MAN s 6 " " MAN s 8 " - " MAN s 9 " ALPHA1-3 " BMA S 3 " - " MAN S 4 " " BMA T 3 " - " MAN T 4 " " BMA U 3 " - " MAN U 4 " " MAN U 7 " - " MAN U 8 " " BMA V 3 " - " MAN V 4 " " BMA W 3 " - " MAN W 8 " " MAN W 4 " - " MAN W 5 " " BMA X 3 " - " MAN X 4 " " BMA Y 3 " - " MAN Y 8 " " MAN Y 4 " - " MAN Y 5 " " BMA c 3 " - " MAN c 4 " " BMA d 3 " - " MAN d 4 " " BMA e 3 " - " MAN e 4 " " MAN e 7 " - " MAN e 8 " " BMA f 3 " - " MAN f 4 " " BMA g 3 " - " MAN g 8 " " MAN g 4 " - " MAN g 5 " " BMA h 3 " - " MAN h 4 " " BMA i 3 " - " MAN i 8 " " MAN i 4 " - " MAN i 5 " " BMA m 3 " - " MAN m 4 " " BMA n 3 " - " MAN n 4 " " BMA o 3 " - " MAN o 4 " " MAN o 7 " - " MAN o 8 " " BMA p 3 " - " MAN p 4 " " BMA q 3 " - " MAN q 8 " " MAN q 4 " - " MAN q 5 " " BMA r 3 " - " MAN r 4 " " BMA s 3 " - " MAN s 8 " " MAN s 4 " - " MAN s 5 " ALPHA1-6 " BMA S 3 " - " MAN S 6 " " BMA T 3 " - " MAN T 5 " " BMA U 3 " - " MAN U 7 " " MAN U 7 " - " MAN U 9 " " BMA V 3 " - " MAN V 5 " " BMA W 3 " - " MAN W 4 " " MAN W 4 " - " MAN W 7 " " BMA X 3 " - " MAN X 7 " " BMA Y 3 " - " MAN Y 4 " " MAN Y 4 " - " MAN Y 7 " " BMA c 3 " - " MAN c 6 " " BMA d 3 " - " MAN d 5 " " BMA e 3 " - " MAN e 7 " " MAN e 7 " - " MAN e 9 " " BMA f 3 " - " MAN f 5 " " BMA g 3 " - " MAN g 4 " " MAN g 4 " - " MAN g 7 " " BMA h 3 " - " MAN h 7 " " BMA i 3 " - " MAN i 4 " " MAN i 4 " - " MAN i 7 " " BMA m 3 " - " MAN m 6 " " BMA n 3 " - " MAN n 5 " " BMA o 3 " - " MAN o 7 " " MAN o 7 " - " MAN o 9 " " BMA p 3 " - " MAN p 5 " " BMA q 3 " - " MAN q 4 " " MAN q 4 " - " MAN q 7 " " BMA r 3 " - " MAN r 7 " " BMA s 3 " - " MAN s 4 " " MAN s 4 " - " MAN s 7 " BETA1-4 " NAG S 1 " - " NAG S 2 " " NAG S 2 " - " BMA S 3 " " NAG T 1 " - " NAG T 2 " " NAG T 2 " - " BMA T 3 " " NAG U 1 " - " NAG U 2 " " NAG U 2 " - " BMA U 3 " " NAG V 1 " - " NAG V 2 " " NAG V 2 " - " BMA V 3 " " NAG W 1 " - " NAG W 2 " " NAG W 2 " - " BMA W 3 " " NAG X 1 " - " NAG X 2 " " NAG X 2 " - " BMA X 3 " " NAG Y 1 " - " NAG Y 2 " " NAG Y 2 " - " BMA Y 3 " " NAG Z 1 " - " NAG Z 2 " " NAG a 1 " - " NAG a 2 " " NAG b 1 " - " NAG b 2 " " NAG c 1 " - " NAG c 2 " " NAG c 2 " - " BMA c 3 " " NAG d 1 " - " NAG d 2 " " NAG d 2 " - " BMA d 3 " " NAG e 1 " - " NAG e 2 " " NAG e 2 " - " BMA e 3 " " NAG f 1 " - " NAG f 2 " " NAG f 2 " - " BMA f 3 " " NAG g 1 " - " NAG g 2 " " NAG g 2 " - " BMA g 3 " " NAG h 1 " - " NAG h 2 " " NAG h 2 " - " BMA h 3 " " 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 p 2 " - " BMA p 3 " " NAG q 1 " - " NAG q 2 " " NAG q 2 " - " BMA q 3 " " NAG r 1 " - " NAG r 2 " " NAG r 2 " - " BMA r 3 " " NAG s 1 " - " NAG s 2 " " NAG s 2 " - " BMA s 3 " " NAG t 1 " - " NAG t 2 " " NAG u 1 " - " NAG u 2 " " NAG v 1 " - " NAG v 2 " NAG-ASN " NAG A 626 " - " ASN A 133 " " NAG A 653 " - " ASN A 234 " " NAG A 656 " - " ASN A 160 " " NAG A 659 " - " ASN A 197 " " NAG B 701 " - " ASN B 611 " " NAG B 702 " - " ASN B 618 " " NAG B 703 " - " ASN B 637 " " NAG E 626 " - " ASN E 133 " " NAG E 653 " - " ASN E 234 " " NAG E 656 " - " ASN E 160 " " NAG E 659 " - " ASN E 197 " " NAG F 626 " - " ASN F 133 " " NAG F 653 " - " ASN F 234 " " NAG F 656 " - " ASN F 160 " " NAG F 659 " - " ASN F 197 " " NAG G 701 " - " ASN G 611 " " NAG G 702 " - " ASN G 618 " " NAG G 703 " - " ASN G 637 " " NAG I 701 " - " ASN I 611 " " NAG I 702 " - " ASN I 618 " " NAG I 703 " - " ASN I 637 " " NAG S 1 " - " ASN A 262 " " NAG T 1 " - " ASN A 363 " " NAG U 1 " - " ASN A 392 " " NAG V 1 " - " ASN A 386 " " NAG W 1 " - " ASN A 332 " " NAG X 1 " - " ASN A 295 " " NAG Y 1 " - " ASN A 339 " " NAG Z 1 " - " ASN A 448 " " NAG a 1 " - " ASN A 301 " " NAG b 1 " - " ASN A 156 " " NAG c 1 " - " ASN E 262 " " NAG d 1 " - " ASN E 363 " " NAG e 1 " - " ASN E 392 " " NAG f 1 " - " ASN E 386 " " NAG g 1 " - " ASN E 332 " " NAG h 1 " - " ASN E 295 " " NAG i 1 " - " ASN E 339 " " NAG j 1 " - " ASN E 448 " " NAG k 1 " - " ASN E 301 " " NAG l 1 " - " ASN E 156 " " NAG m 1 " - " ASN F 262 " " NAG n 1 " - " ASN F 363 " " NAG o 1 " - " ASN F 392 " " NAG p 1 " - " ASN F 386 " " NAG q 1 " - " ASN F 332 " " NAG r 1 " - " ASN F 295 " " NAG s 1 " - " ASN F 339 " " NAG t 1 " - " ASN F 448 " " NAG u 1 " - " ASN F 301 " " NAG v 1 " - " ASN F 156 " Time building additional restraints: 13.39 Conformation dependent library (CDL) restraints added in 4.9 seconds 5934 Ramachandran restraints generated. 2967 Oldfield, 0 Emsley, 2967 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5562 Finding SS restraints... Secondary structure from input PDB file: 66 helices and 66 sheets defined 18.1% alpha, 39.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 3.38 Creating SS restraints... Processing helix chain 'A' and resid 98 through 116 removed outlier: 4.174A pdb=" N GLU A 102 " --> pdb=" O ASN A 98 " (cutoff:3.500A) Processing helix chain 'A' and resid 122 through 126 Processing helix chain 'A' and resid 335 through 350 Processing helix chain 'A' and resid 351 through 353 No H-bonds generated for 'chain 'A' and resid 351 through 353' Processing helix chain 'A' and resid 368 through 373 Processing helix chain 'A' and resid 425 through 429 removed outlier: 3.817A pdb=" N GLN A 428 " --> pdb=" O ASN A 425 " (cutoff:3.500A) removed outlier: 3.829A pdb=" N ARG A 429 " --> pdb=" O MET A 426 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 425 through 429' Processing helix chain 'A' and resid 475 through 484 removed outlier: 3.786A pdb=" N GLU A 482 " --> pdb=" O ASN A 478 " (cutoff:3.500A) Processing helix chain 'B' and resid 531 through 535 Processing helix chain 'B' and resid 536 through 543 removed outlier: 3.947A pdb=" N ASN B 543 " --> pdb=" O VAL B 539 " (cutoff:3.500A) Processing helix chain 'B' and resid 568 through 596 removed outlier: 3.548A pdb=" N GLY B 572 " --> pdb=" O LEU B 568 " (cutoff:3.500A) removed outlier: 6.453A pdb=" N LYS B 574 " --> pdb=" O VAL B 570 " (cutoff:3.500A) removed outlier: 4.057A pdb=" N LEU B 592 " --> pdb=" O ARG B 588 " (cutoff:3.500A) Processing helix chain 'B' and resid 618 through 623 Processing helix chain 'B' and resid 627 through 636 removed outlier: 3.819A pdb=" N GLU B 634 " --> pdb=" O GLN B 630 " (cutoff:3.500A) Processing helix chain 'B' and resid 638 through 655 removed outlier: 4.063A pdb=" N GLN B 650 " --> pdb=" O LEU B 646 " (cutoff:3.500A) Processing helix chain 'B' and resid 656 through 661 Processing helix chain 'L' and resid 79 through 83 Processing helix chain 'H' and resid 28 through 32 Processing helix chain 'H' and resid 52A through 55 Processing helix chain 'H' and resid 61 through 64 Processing helix chain 'H' and resid 83 through 87 Processing helix chain 'D' and resid 79 through 83 Processing helix chain 'C' and resid 52A through 55 Processing helix chain 'C' and resid 83 through 87 Processing helix chain 'E' and resid 98 through 116 removed outlier: 4.174A pdb=" N GLU E 102 " --> pdb=" O ASN E 98 " (cutoff:3.500A) Processing helix chain 'E' and resid 122 through 126 Processing helix chain 'E' and resid 335 through 350 Processing helix chain 'E' and resid 351 through 353 No H-bonds generated for 'chain 'E' and resid 351 through 353' Processing helix chain 'E' and resid 368 through 373 Processing helix chain 'E' and resid 425 through 429 removed outlier: 3.817A pdb=" N GLN E 428 " --> pdb=" O ASN E 425 " (cutoff:3.500A) removed outlier: 3.829A pdb=" N ARG E 429 " --> pdb=" O MET E 426 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 425 through 429' Processing helix chain 'E' and resid 475 through 484 removed outlier: 3.786A pdb=" N GLU E 482 " --> pdb=" O ASN E 478 " (cutoff:3.500A) Processing helix chain 'G' and resid 531 through 535 Processing helix chain 'G' and resid 536 through 543 removed outlier: 3.947A pdb=" N ASN G 543 " --> pdb=" O VAL G 539 " (cutoff:3.500A) Processing helix chain 'G' and resid 568 through 596 removed outlier: 3.548A pdb=" N GLY G 572 " --> pdb=" O LEU G 568 " (cutoff:3.500A) removed outlier: 6.453A pdb=" N LYS G 574 " --> pdb=" O VAL G 570 " (cutoff:3.500A) removed outlier: 4.057A pdb=" N LEU G 592 " --> pdb=" O ARG G 588 " (cutoff:3.500A) Processing helix chain 'G' and resid 618 through 623 Processing helix chain 'G' and resid 627 through 636 removed outlier: 3.819A pdb=" N GLU G 634 " --> pdb=" O GLN G 630 " (cutoff:3.500A) Processing helix chain 'G' and resid 638 through 655 removed outlier: 4.062A pdb=" N GLN G 650 " --> pdb=" O LEU G 646 " (cutoff:3.500A) Processing helix chain 'G' and resid 656 through 661 Processing helix chain 'Q' and resid 79 through 83 Processing helix chain 'O' and resid 28 through 32 Processing helix chain 'O' and resid 52A through 55 Processing helix chain 'O' and resid 61 through 64 Processing helix chain 'O' and resid 83 through 87 Processing helix chain 'M' and resid 79 through 83 Processing helix chain 'J' and resid 52A through 55 Processing helix chain 'J' and resid 83 through 87 Processing helix chain 'F' and resid 98 through 116 removed outlier: 4.174A pdb=" N GLU F 102 " --> pdb=" O ASN F 98 " (cutoff:3.500A) Processing helix chain 'F' and resid 122 through 126 Processing helix chain 'F' and resid 335 through 350 Processing helix chain 'F' and resid 351 through 353 No H-bonds generated for 'chain 'F' and resid 351 through 353' Processing helix chain 'F' and resid 368 through 373 Processing helix chain 'F' and resid 425 through 429 removed outlier: 3.817A pdb=" N GLN F 428 " --> pdb=" O ASN F 425 " (cutoff:3.500A) removed outlier: 3.829A pdb=" N ARG F 429 " --> pdb=" O MET F 426 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 425 through 429' Processing helix chain 'F' and resid 475 through 484 removed outlier: 3.786A pdb=" N GLU F 482 " --> pdb=" O ASN F 478 " (cutoff:3.500A) Processing helix chain 'I' and resid 531 through 535 Processing helix chain 'I' and resid 536 through 543 removed outlier: 3.947A pdb=" N ASN I 543 " --> pdb=" O VAL I 539 " (cutoff:3.500A) Processing helix chain 'I' and resid 568 through 596 removed outlier: 3.548A pdb=" N GLY I 572 " --> pdb=" O LEU I 568 " (cutoff:3.500A) removed outlier: 6.452A pdb=" N LYS I 574 " --> pdb=" O VAL I 570 " (cutoff:3.500A) removed outlier: 4.057A pdb=" N LEU I 592 " --> pdb=" O ARG I 588 " (cutoff:3.500A) Processing helix chain 'I' and resid 618 through 623 Processing helix chain 'I' and resid 627 through 636 removed outlier: 3.819A pdb=" N GLU I 634 " --> pdb=" O GLN I 630 " (cutoff:3.500A) Processing helix chain 'I' and resid 638 through 655 removed outlier: 4.062A pdb=" N GLN I 650 " --> pdb=" O LEU I 646 " (cutoff:3.500A) Processing helix chain 'I' and resid 656 through 661 Processing helix chain 'R' and resid 79 through 83 Processing helix chain 'P' and resid 28 through 32 Processing helix chain 'P' and resid 52A through 55 Processing helix chain 'P' and resid 61 through 64 Processing helix chain 'P' and resid 83 through 87 Processing helix chain 'N' and resid 79 through 83 Processing helix chain 'K' and resid 52A through 55 Processing helix chain 'K' and resid 83 through 87 Processing sheet with id=AA1, first strand: chain 'A' and resid 495 through 498 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 92 through 94 Processing sheet with id=AA5, first strand: chain 'A' and resid 169 through 177 Processing sheet with id=AA6, first strand: chain 'A' and resid 201 through 203 removed outlier: 6.635A pdb=" N THR A 202 " --> pdb=" O TYR A 435 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 259 through 261 removed outlier: 6.535A pdb=" N LEU A 260 " --> pdb=" O THR A 450 " (cutoff:3.500A) removed outlier: 9.993A pdb=" N ARG A 444 " --> pdb=" O ILE A 294 " (cutoff:3.500A) removed outlier: 11.502A pdb=" N ILE A 294 " --> pdb=" O ARG A 444 " (cutoff:3.500A) removed outlier: 9.562A pdb=" N VAL A 446 " --> pdb=" O VAL A 292 " (cutoff:3.500A) removed outlier: 10.231A pdb=" N VAL A 292 " --> pdb=" O VAL A 446 " (cutoff:3.500A) removed outlier: 9.110A pdb=" N ASN A 448 " --> pdb=" O THR A 290 " (cutoff:3.500A) removed outlier: 9.759A pdb=" N THR A 290 " --> pdb=" O ASN A 448 " (cutoff:3.500A) removed outlier: 6.964A pdb=" N THR A 450 " --> pdb=" O PHE A 288 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 284 through 298 current: chain 'A' and resid 358 through 361 Processing sheet with id=AA8, first strand: chain 'A' and resid 271 through 274 removed outlier: 6.964A pdb=" N THR A 450 " --> pdb=" O PHE A 288 " (cutoff:3.500A) removed outlier: 9.759A pdb=" N THR A 290 " --> pdb=" O ASN A 448 " (cutoff:3.500A) removed outlier: 9.110A pdb=" N ASN A 448 " --> pdb=" O THR A 290 " (cutoff:3.500A) removed outlier: 10.231A pdb=" N VAL A 292 " --> pdb=" O VAL A 446 " (cutoff:3.500A) removed outlier: 9.562A pdb=" N VAL A 446 " --> pdb=" O VAL A 292 " (cutoff:3.500A) removed outlier: 11.502A pdb=" N ILE A 294 " --> pdb=" O ARG A 444 " (cutoff:3.500A) removed outlier: 9.993A pdb=" N ARG A 444 " --> pdb=" O ILE A 294 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 443 through 456 current: chain 'A' and resid 413 through 416 Processing sheet with id=AA9, first strand: chain 'A' and resid 304 through 312 removed outlier: 6.632A pdb=" N GLN A 315 " --> pdb=" O ILE A 309 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 374 through 378 Processing sheet with id=AB2, first strand: chain 'L' and resid 4 through 7 Processing sheet with id=AB3, first strand: chain 'L' and resid 10 through 12 removed outlier: 6.333A pdb=" N LEU L 11 " --> pdb=" O GLU L 105 " (cutoff:3.500A) removed outlier: 6.595A pdb=" N LEU L 33 " --> pdb=" O TYR L 49 " (cutoff:3.500A) removed outlier: 4.616A pdb=" N TYR L 49 " --> pdb=" O LEU L 33 " (cutoff:3.500A) removed outlier: 6.451A pdb=" N TRP L 35 " --> pdb=" O LEU L 47 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'L' and resid 10 through 12 removed outlier: 6.333A pdb=" N LEU L 11 " --> pdb=" O GLU L 105 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'H' and resid 3 through 7 Processing sheet with id=AB6, first strand: chain 'H' and resid 10 through 13 removed outlier: 6.480A pdb=" N GLY H 10 " --> pdb=" O THR H 110 " (cutoff:3.500A) removed outlier: 7.831A pdb=" N SER H 112 " --> pdb=" O GLY H 10 " (cutoff:3.500A) removed outlier: 7.191A pdb=" N VAL H 12 " --> pdb=" O SER H 112 " (cutoff:3.500A) removed outlier: 5.989A pdb=" N ARG H 38 " --> pdb=" O TRP H 47 " (cutoff:3.500A) removed outlier: 5.497A pdb=" N TRP H 47 " --> pdb=" O ARG H 38 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'H' and resid 10 through 13 removed outlier: 6.480A pdb=" N GLY H 10 " --> pdb=" O THR H 110 " (cutoff:3.500A) removed outlier: 7.831A pdb=" N SER H 112 " --> pdb=" O GLY H 10 " (cutoff:3.500A) removed outlier: 7.191A pdb=" N VAL H 12 " --> pdb=" O SER H 112 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N ALA H 102 " --> pdb=" O ARG H 94 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'D' and resid 4 through 7 Processing sheet with id=AB9, first strand: chain 'D' and resid 10 through 12 removed outlier: 6.664A pdb=" N LEU D 33 " --> pdb=" O TYR D 49 " (cutoff:3.500A) removed outlier: 4.362A pdb=" N TYR D 49 " --> pdb=" O LEU D 33 " (cutoff:3.500A) removed outlier: 6.425A pdb=" N TRP D 35 " --> pdb=" O LEU D 47 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'D' and resid 10 through 12 Processing sheet with id=AC2, first strand: chain 'C' and resid 3 through 7 Processing sheet with id=AC3, first strand: chain 'C' and resid 10 through 13 removed outlier: 6.877A pdb=" N MET C 34 " --> pdb=" O SER C 50 " (cutoff:3.500A) removed outlier: 4.643A pdb=" N SER C 50 " --> pdb=" O MET C 34 " (cutoff:3.500A) removed outlier: 6.451A pdb=" N TRP C 36 " --> pdb=" O VAL C 48 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'C' and resid 10 through 13 removed outlier: 3.505A pdb=" N ALA C 102 " --> pdb=" O ARG C 94 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'E' and resid 495 through 498 Processing sheet with id=AC6, first strand: chain 'E' and resid 45 through 47 Processing sheet with id=AC7, first strand: chain 'E' and resid 53 through 55 Processing sheet with id=AC8, first strand: chain 'E' and resid 92 through 94 Processing sheet with id=AC9, first strand: chain 'E' and resid 169 through 177 Processing sheet with id=AD1, first strand: chain 'E' and resid 201 through 203 removed outlier: 6.636A pdb=" N THR E 202 " --> pdb=" O TYR E 435 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'E' and resid 259 through 261 removed outlier: 6.536A pdb=" N LEU E 260 " --> pdb=" O THR E 450 " (cutoff:3.500A) removed outlier: 9.992A pdb=" N ARG E 444 " --> pdb=" O ILE E 294 " (cutoff:3.500A) removed outlier: 11.501A pdb=" N ILE E 294 " --> pdb=" O ARG E 444 " (cutoff:3.500A) removed outlier: 9.561A pdb=" N VAL E 446 " --> pdb=" O VAL E 292 " (cutoff:3.500A) removed outlier: 10.231A pdb=" N VAL E 292 " --> pdb=" O VAL E 446 " (cutoff:3.500A) removed outlier: 9.111A pdb=" N ASN E 448 " --> pdb=" O THR E 290 " (cutoff:3.500A) removed outlier: 9.759A pdb=" N THR E 290 " --> pdb=" O ASN E 448 " (cutoff:3.500A) removed outlier: 6.964A pdb=" N THR E 450 " --> pdb=" O PHE E 288 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'E' and resid 284 through 298 current: chain 'E' and resid 358 through 361 Processing sheet with id=AD3, first strand: chain 'E' and resid 271 through 274 removed outlier: 6.964A pdb=" N THR E 450 " --> pdb=" O PHE E 288 " (cutoff:3.500A) removed outlier: 9.759A pdb=" N THR E 290 " --> pdb=" O ASN E 448 " (cutoff:3.500A) removed outlier: 9.111A pdb=" N ASN E 448 " --> pdb=" O THR E 290 " (cutoff:3.500A) removed outlier: 10.231A pdb=" N VAL E 292 " --> pdb=" O VAL E 446 " (cutoff:3.500A) removed outlier: 9.561A pdb=" N VAL E 446 " --> pdb=" O VAL E 292 " (cutoff:3.500A) removed outlier: 11.501A pdb=" N ILE E 294 " --> pdb=" O ARG E 444 " (cutoff:3.500A) removed outlier: 9.992A pdb=" N ARG E 444 " --> pdb=" O ILE E 294 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'E' and resid 443 through 456 current: chain 'E' and resid 413 through 416 Processing sheet with id=AD4, first strand: chain 'E' and resid 304 through 312 removed outlier: 6.632A pdb=" N GLN E 315 " --> pdb=" O ILE E 309 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'E' and resid 374 through 378 Processing sheet with id=AD6, first strand: chain 'Q' and resid 4 through 7 Processing sheet with id=AD7, first strand: chain 'Q' and resid 10 through 12 removed outlier: 6.333A pdb=" N LEU Q 11 " --> pdb=" O GLU Q 105 " (cutoff:3.500A) removed outlier: 6.595A pdb=" N LEU Q 33 " --> pdb=" O TYR Q 49 " (cutoff:3.500A) removed outlier: 4.616A pdb=" N TYR Q 49 " --> pdb=" O LEU Q 33 " (cutoff:3.500A) removed outlier: 6.451A pdb=" N TRP Q 35 " --> pdb=" O LEU Q 47 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'Q' and resid 10 through 12 removed outlier: 6.333A pdb=" N LEU Q 11 " --> pdb=" O GLU Q 105 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'O' and resid 3 through 7 Processing sheet with id=AE1, first strand: chain 'O' and resid 10 through 13 removed outlier: 6.480A pdb=" N GLY O 10 " --> pdb=" O THR O 110 " (cutoff:3.500A) removed outlier: 7.831A pdb=" N SER O 112 " --> pdb=" O GLY O 10 " (cutoff:3.500A) removed outlier: 7.192A pdb=" N VAL O 12 " --> pdb=" O SER O 112 " (cutoff:3.500A) removed outlier: 5.989A pdb=" N ARG O 38 " --> pdb=" O TRP O 47 " (cutoff:3.500A) removed outlier: 5.497A pdb=" N TRP O 47 " --> pdb=" O ARG O 38 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'O' and resid 10 through 13 removed outlier: 6.480A pdb=" N GLY O 10 " --> pdb=" O THR O 110 " (cutoff:3.500A) removed outlier: 7.831A pdb=" N SER O 112 " --> pdb=" O GLY O 10 " (cutoff:3.500A) removed outlier: 7.192A pdb=" N VAL O 12 " --> pdb=" O SER O 112 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N ALA O 102 " --> pdb=" O ARG O 94 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'M' and resid 4 through 7 Processing sheet with id=AE4, first strand: chain 'M' and resid 10 through 12 removed outlier: 6.664A pdb=" N LEU M 33 " --> pdb=" O TYR M 49 " (cutoff:3.500A) removed outlier: 4.362A pdb=" N TYR M 49 " --> pdb=" O LEU M 33 " (cutoff:3.500A) removed outlier: 6.425A pdb=" N TRP M 35 " --> pdb=" O LEU M 47 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'M' and resid 10 through 12 Processing sheet with id=AE6, first strand: chain 'J' and resid 3 through 7 Processing sheet with id=AE7, first strand: chain 'J' and resid 10 through 13 removed outlier: 6.877A pdb=" N MET J 34 " --> pdb=" O SER J 50 " (cutoff:3.500A) removed outlier: 4.643A pdb=" N SER J 50 " --> pdb=" O MET J 34 " (cutoff:3.500A) removed outlier: 6.451A pdb=" N TRP J 36 " --> pdb=" O VAL J 48 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'J' and resid 10 through 13 removed outlier: 3.505A pdb=" N ALA J 102 " --> pdb=" O ARG J 94 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'F' and resid 495 through 498 Processing sheet with id=AF1, first strand: chain 'F' and resid 45 through 47 Processing sheet with id=AF2, first strand: chain 'F' and resid 53 through 55 Processing sheet with id=AF3, first strand: chain 'F' and resid 92 through 94 Processing sheet with id=AF4, first strand: chain 'F' and resid 169 through 177 Processing sheet with id=AF5, first strand: chain 'F' and resid 201 through 203 removed outlier: 6.635A pdb=" N THR F 202 " --> pdb=" O TYR F 435 " (cutoff:3.500A) Processing sheet with id=AF6, first strand: chain 'F' and resid 259 through 261 removed outlier: 6.535A pdb=" N LEU F 260 " --> pdb=" O THR F 450 " (cutoff:3.500A) removed outlier: 9.992A pdb=" N ARG F 444 " --> pdb=" O ILE F 294 " (cutoff:3.500A) removed outlier: 11.501A pdb=" N ILE F 294 " --> pdb=" O ARG F 444 " (cutoff:3.500A) removed outlier: 9.561A pdb=" N VAL F 446 " --> pdb=" O VAL F 292 " (cutoff:3.500A) removed outlier: 10.231A pdb=" N VAL F 292 " --> pdb=" O VAL F 446 " (cutoff:3.500A) removed outlier: 9.110A pdb=" N ASN F 448 " --> pdb=" O THR F 290 " (cutoff:3.500A) removed outlier: 9.759A pdb=" N THR F 290 " --> pdb=" O ASN F 448 " (cutoff:3.500A) removed outlier: 6.964A pdb=" N THR F 450 " --> pdb=" O PHE F 288 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'F' and resid 284 through 298 current: chain 'F' and resid 358 through 361 Processing sheet with id=AF7, first strand: chain 'F' and resid 271 through 274 removed outlier: 6.964A pdb=" N THR F 450 " --> pdb=" O PHE F 288 " (cutoff:3.500A) removed outlier: 9.759A pdb=" N THR F 290 " --> pdb=" O ASN F 448 " (cutoff:3.500A) removed outlier: 9.110A pdb=" N ASN F 448 " --> pdb=" O THR F 290 " (cutoff:3.500A) removed outlier: 10.231A pdb=" N VAL F 292 " --> pdb=" O VAL F 446 " (cutoff:3.500A) removed outlier: 9.561A pdb=" N VAL F 446 " --> pdb=" O VAL F 292 " (cutoff:3.500A) removed outlier: 11.501A pdb=" N ILE F 294 " --> pdb=" O ARG F 444 " (cutoff:3.500A) removed outlier: 9.992A pdb=" N ARG F 444 " --> pdb=" O ILE F 294 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'F' and resid 443 through 456 current: chain 'F' and resid 413 through 416 Processing sheet with id=AF8, first strand: chain 'F' and resid 304 through 312 removed outlier: 6.632A pdb=" N GLN F 315 " --> pdb=" O ILE F 309 " (cutoff:3.500A) Processing sheet with id=AF9, first strand: chain 'F' and resid 374 through 378 Processing sheet with id=AG1, first strand: chain 'R' and resid 4 through 7 Processing sheet with id=AG2, first strand: chain 'R' and resid 10 through 12 removed outlier: 6.333A pdb=" N LEU R 11 " --> pdb=" O GLU R 105 " (cutoff:3.500A) removed outlier: 6.595A pdb=" N LEU R 33 " --> pdb=" O TYR R 49 " (cutoff:3.500A) removed outlier: 4.616A pdb=" N TYR R 49 " --> pdb=" O LEU R 33 " (cutoff:3.500A) removed outlier: 6.451A pdb=" N TRP R 35 " --> pdb=" O LEU R 47 " (cutoff:3.500A) Processing sheet with id=AG3, first strand: chain 'R' and resid 10 through 12 removed outlier: 6.333A pdb=" N LEU R 11 " --> pdb=" O GLU R 105 " (cutoff:3.500A) Processing sheet with id=AG4, first strand: chain 'P' and resid 3 through 7 Processing sheet with id=AG5, first strand: chain 'P' and resid 10 through 13 removed outlier: 6.480A pdb=" N GLY P 10 " --> pdb=" O THR P 110 " (cutoff:3.500A) removed outlier: 7.831A pdb=" N SER P 112 " --> pdb=" O GLY P 10 " (cutoff:3.500A) removed outlier: 7.191A pdb=" N VAL P 12 " --> pdb=" O SER P 112 " (cutoff:3.500A) removed outlier: 5.989A pdb=" N ARG P 38 " --> pdb=" O TRP P 47 " (cutoff:3.500A) removed outlier: 5.497A pdb=" N TRP P 47 " --> pdb=" O ARG P 38 " (cutoff:3.500A) Processing sheet with id=AG6, first strand: chain 'P' and resid 10 through 13 removed outlier: 6.480A pdb=" N GLY P 10 " --> pdb=" O THR P 110 " (cutoff:3.500A) removed outlier: 7.831A pdb=" N SER P 112 " --> pdb=" O GLY P 10 " (cutoff:3.500A) removed outlier: 7.191A pdb=" N VAL P 12 " --> pdb=" O SER P 112 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N ALA P 102 " --> pdb=" O ARG P 94 " (cutoff:3.500A) Processing sheet with id=AG7, first strand: chain 'N' and resid 4 through 7 Processing sheet with id=AG8, first strand: chain 'N' and resid 10 through 12 removed outlier: 6.663A pdb=" N LEU N 33 " --> pdb=" O TYR N 49 " (cutoff:3.500A) removed outlier: 4.362A pdb=" N TYR N 49 " --> pdb=" O LEU N 33 " (cutoff:3.500A) removed outlier: 6.425A pdb=" N TRP N 35 " --> pdb=" O LEU N 47 " (cutoff:3.500A) Processing sheet with id=AG9, first strand: chain 'N' and resid 10 through 12 Processing sheet with id=AH1, first strand: chain 'K' and resid 3 through 7 Processing sheet with id=AH2, first strand: chain 'K' and resid 10 through 13 removed outlier: 6.877A pdb=" N MET K 34 " --> pdb=" O SER K 50 " (cutoff:3.500A) removed outlier: 4.643A pdb=" N SER K 50 " --> pdb=" O MET K 34 " (cutoff:3.500A) removed outlier: 6.451A pdb=" N TRP K 36 " --> pdb=" O VAL K 48 " (cutoff:3.500A) Processing sheet with id=AH3, first strand: chain 'K' and resid 10 through 13 removed outlier: 3.505A pdb=" N ALA K 102 " --> pdb=" O ARG K 94 " (cutoff:3.500A) 978 hydrogen bonds defined for protein. 2421 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: 12.07 Time building geometry restraints manager: 14.04 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.32: 5455 1.32 - 1.45: 8504 1.45 - 1.59: 12135 1.59 - 1.72: 21 1.72 - 1.86: 198 Bond restraints: 26313 Sorted by residual: bond pdb=" C1 NAG F 659 " pdb=" O5 NAG F 659 " ideal model delta sigma weight residual 1.406 1.547 -0.141 2.00e-02 2.50e+03 4.98e+01 bond pdb=" C1 NAG A 659 " pdb=" O5 NAG A 659 " ideal model delta sigma weight residual 1.406 1.547 -0.141 2.00e-02 2.50e+03 4.97e+01 bond pdb=" C1 NAG E 659 " pdb=" O5 NAG E 659 " ideal model delta sigma weight residual 1.406 1.547 -0.141 2.00e-02 2.50e+03 4.95e+01 bond pdb=" C THR B 627 " pdb=" N TRP B 628 " ideal model delta sigma weight residual 1.335 1.247 0.087 1.25e-02 6.40e+03 4.90e+01 bond pdb=" CB TYR L 91 " pdb=" CG TYR L 91 " ideal model delta sigma weight residual 1.512 1.358 0.154 2.20e-02 2.07e+03 4.89e+01 ... (remaining 26308 not shown) Histogram of bond angle deviations from ideal: 98.98 - 106.05: 855 106.05 - 113.13: 14743 113.13 - 120.20: 10030 120.20 - 127.27: 9753 127.27 - 134.34: 331 Bond angle restraints: 35712 Sorted by residual: angle pdb=" N ARG J 66 " pdb=" CA ARG J 66 " pdb=" C ARG J 66 " ideal model delta sigma weight residual 113.88 101.37 12.51 1.23e+00 6.61e-01 1.03e+02 angle pdb=" N ARG C 66 " pdb=" CA ARG C 66 " pdb=" C ARG C 66 " ideal model delta sigma weight residual 113.88 101.38 12.50 1.23e+00 6.61e-01 1.03e+02 angle pdb=" N ARG K 66 " pdb=" CA ARG K 66 " pdb=" C ARG K 66 " ideal model delta sigma weight residual 113.88 101.40 12.48 1.23e+00 6.61e-01 1.03e+02 angle pdb=" N HIS E 72 " pdb=" CA HIS E 72 " pdb=" C HIS E 72 " ideal model delta sigma weight residual 114.56 102.85 11.71 1.27e+00 6.20e-01 8.51e+01 angle pdb=" N HIS F 72 " pdb=" CA HIS F 72 " pdb=" C HIS F 72 " ideal model delta sigma weight residual 114.56 102.85 11.71 1.27e+00 6.20e-01 8.51e+01 ... (remaining 35707 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 21.93: 17157 21.93 - 43.86: 489 43.86 - 65.79: 150 65.79 - 87.73: 135 87.73 - 109.66: 87 Dihedral angle restraints: 18018 sinusoidal: 9357 harmonic: 8661 Sorted by residual: dihedral pdb=" CB CYS A 126 " pdb=" SG CYS A 126 " pdb=" SG CYS A 196 " pdb=" CB CYS A 196 " ideal model delta sinusoidal sigma weight residual 93.00 133.36 -40.36 1 1.00e+01 1.00e-02 2.28e+01 dihedral pdb=" CB CYS F 126 " pdb=" SG CYS F 126 " pdb=" SG CYS F 196 " pdb=" CB CYS F 196 " ideal model delta sinusoidal sigma weight residual 93.00 133.35 -40.35 1 1.00e+01 1.00e-02 2.28e+01 dihedral pdb=" CB CYS E 126 " pdb=" SG CYS E 126 " pdb=" SG CYS E 196 " pdb=" CB CYS E 196 " ideal model delta sinusoidal sigma weight residual 93.00 133.34 -40.34 1 1.00e+01 1.00e-02 2.28e+01 ... (remaining 18015 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.115: 3436 0.115 - 0.229: 1000 0.229 - 0.344: 127 0.344 - 0.459: 18 0.459 - 0.573: 21 Chirality restraints: 4602 Sorted by residual: chirality pdb=" C1 NAG Y 2 " pdb=" O4 NAG Y 1 " pdb=" C2 NAG Y 2 " pdb=" O5 NAG Y 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.64 0.24 2.00e-02 2.50e+03 1.48e+02 chirality pdb=" C1 NAG i 2 " pdb=" O4 NAG i 1 " pdb=" C2 NAG i 2 " pdb=" O5 NAG i 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.64 0.24 2.00e-02 2.50e+03 1.46e+02 chirality pdb=" C1 NAG s 2 " pdb=" O4 NAG s 1 " pdb=" C2 NAG s 2 " pdb=" O5 NAG s 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.64 0.24 2.00e-02 2.50e+03 1.46e+02 ... (remaining 4599 not shown) Planarity restraints: 4284 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C2 NAG Z 1 " -0.064 2.00e-02 2.50e+03 5.23e-02 3.42e+01 pdb=" C7 NAG Z 1 " 0.016 2.00e-02 2.50e+03 pdb=" C8 NAG Z 1 " -0.048 2.00e-02 2.50e+03 pdb=" N2 NAG Z 1 " 0.083 2.00e-02 2.50e+03 pdb=" O7 NAG Z 1 " 0.012 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG t 1 " -0.064 2.00e-02 2.50e+03 5.23e-02 3.41e+01 pdb=" C7 NAG t 1 " 0.016 2.00e-02 2.50e+03 pdb=" C8 NAG t 1 " -0.048 2.00e-02 2.50e+03 pdb=" N2 NAG t 1 " 0.083 2.00e-02 2.50e+03 pdb=" O7 NAG t 1 " 0.012 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG j 1 " 0.063 2.00e-02 2.50e+03 5.21e-02 3.40e+01 pdb=" C7 NAG j 1 " -0.016 2.00e-02 2.50e+03 pdb=" C8 NAG j 1 " 0.048 2.00e-02 2.50e+03 pdb=" N2 NAG j 1 " -0.083 2.00e-02 2.50e+03 pdb=" O7 NAG j 1 " -0.012 2.00e-02 2.50e+03 ... (remaining 4281 not shown) Histogram of nonbonded interaction distances: 2.30 - 2.82: 8160 2.82 - 3.34: 23259 3.34 - 3.86: 43967 3.86 - 4.38: 51813 4.38 - 4.90: 83268 Nonbonded interactions: 210467 Sorted by model distance: nonbonded pdb=" O4 NAG A 659 " pdb=" O6 NAG A 659 " model vdw 2.303 2.440 nonbonded pdb=" O4 NAG E 659 " pdb=" O6 NAG E 659 " model vdw 2.304 2.440 nonbonded pdb=" O4 NAG F 659 " pdb=" O6 NAG F 659 " model vdw 2.304 2.440 nonbonded pdb=" O LEU G 568 " pdb=" OG1 THR G 569 " model vdw 2.340 2.440 nonbonded pdb=" O LEU I 568 " pdb=" OG1 THR I 569 " model vdw 2.341 2.440 ... (remaining 210462 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'E' selection = chain 'F' } ncs_group { reference = chain 'B' selection = chain 'G' selection = chain 'I' } ncs_group { reference = chain 'C' selection = chain 'H' selection = chain 'J' selection = chain 'K' selection = chain 'O' selection = chain 'P' } ncs_group { reference = chain 'D' selection = chain 'L' selection = chain 'M' selection = chain 'N' selection = chain 'Q' selection = chain 'R' } ncs_group { reference = (chain 'S' and (resid 1 or resid 4 through 6)) selection = (chain 'X' and (resid 2 or resid 5 through 7)) selection = (chain 'c' and (resid 1 or resid 4 through 6)) selection = (chain 'h' and (resid 2 or resid 5 through 7)) selection = (chain 'm' and (resid 1 or resid 4 through 6)) selection = (chain 'r' and (resid 2 or resid 5 through 7)) } ncs_group { reference = chain 'T' selection = chain 'V' selection = chain 'd' selection = chain 'f' selection = chain 'n' selection = chain 'p' } ncs_group { reference = (chain 'U' and (resid 2 or resid 5 through 9)) selection = (chain 'W' and (resid 1 or resid 4 through 8)) selection = (chain 'Y' and (resid 2 or resid 5 through 9)) selection = (chain 'e' and (resid 2 or resid 5 through 9)) selection = (chain 'g' and (resid 1 or resid 4 through 8)) selection = (chain 'i' and (resid 2 or resid 5 through 9)) selection = (chain 'o' and (resid 2 or resid 5 through 9)) selection = (chain 'q' and (resid 1 or resid 4 through 8)) selection = (chain 's' and (resid 2 or resid 5 through 9)) } ncs_group { reference = chain 'Z' selection = chain 'a' selection = chain 'b' selection = chain 'j' selection = chain 'k' selection = chain 'l' selection = chain 't' selection = chain 'u' selection = chain 'v' } 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: 0.020 Extract box with map and model: 5.220 Check model and map are aligned: 0.420 Set scattering table: 0.260 Process input model: 75.580 Find NCS groups from input model: 1.840 Set up NCS constraints: 0.380 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.880 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 87.350 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8115 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 0.212 26313 Z= 1.441 Angle : 1.840 12.505 35712 Z= 1.153 Chirality : 0.110 0.573 4602 Planarity : 0.009 0.052 4233 Dihedral : 15.750 109.656 12330 Min Nonbonded Distance : 2.303 Molprobity Statistics. All-atom Clashscore : 1.05 Ramachandran Plot: Outliers : 0.71 % Allowed : 3.13 % Favored : 96.16 % Rotamer: Outliers : 0.00 % Allowed : 0.23 % Favored : 99.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.41 % 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: 0.38 (0.15), residues: 2967 helix: -1.25 (0.22), residues: 393 sheet: 0.81 (0.14), residues: 1107 loop : 0.41 (0.16), residues: 1467 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.061 0.009 TRP D 35 HIS 0.011 0.003 HIS F 374 PHE 0.047 0.007 PHE D 71 TYR 0.077 0.010 TYR K 91 ARG 0.007 0.001 ARG J 38 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5934 Ramachandran restraints generated. 2967 Oldfield, 0 Emsley, 2967 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5934 Ramachandran restraints generated. 2967 Oldfield, 0 Emsley, 2967 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 725 residues out of total 2604 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 725 time to evaluate : 3.672 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 161 MET cc_start: 0.9309 (tpp) cc_final: 0.8880 (tpt) REVERT: A 377 ASN cc_start: 0.8428 (t0) cc_final: 0.7972 (p0) REVERT: A 491 ILE cc_start: 0.8624 (mp) cc_final: 0.8374 (tp) REVERT: B 535 MET cc_start: 0.8445 (mtt) cc_final: 0.7980 (tpt) REVERT: L 42 LYS cc_start: 0.8660 (mmtt) cc_final: 0.8413 (mmtt) REVERT: L 55 LYS cc_start: 0.8089 (tttm) cc_final: 0.7759 (tttt) REVERT: L 79 GLN cc_start: 0.7599 (mm-40) cc_final: 0.7231 (tm-30) REVERT: H 2 VAL cc_start: 0.7847 (t) cc_final: 0.7539 (p) REVERT: H 26 ASN cc_start: 0.8214 (m-40) cc_final: 0.7700 (m-40) REVERT: D 33 LEU cc_start: 0.6981 (tt) cc_final: 0.6470 (tt) REVERT: D 61 ARG cc_start: 0.8535 (mtm-85) cc_final: 0.8139 (mtm-85) REVERT: D 82 ASP cc_start: 0.8349 (m-30) cc_final: 0.7568 (m-30) REVERT: C 26 ASN cc_start: 0.8534 (m-40) cc_final: 0.8058 (m-40) REVERT: C 34 MET cc_start: 0.8751 (mmm) cc_final: 0.8313 (mmm) REVERT: E 377 ASN cc_start: 0.8469 (t0) cc_final: 0.8086 (p0) REVERT: G 601 LYS cc_start: 0.8702 (pttm) cc_final: 0.8290 (pttm) REVERT: G 615 SER cc_start: 0.8873 (m) cc_final: 0.8630 (t) REVERT: Q 42 LYS cc_start: 0.8781 (mmtt) cc_final: 0.8515 (mmtp) REVERT: Q 79 GLN cc_start: 0.7472 (mm-40) cc_final: 0.7035 (tm-30) REVERT: O 26 ASN cc_start: 0.8248 (m-40) cc_final: 0.8003 (m-40) REVERT: M 33 LEU cc_start: 0.7093 (tt) cc_final: 0.6674 (tt) REVERT: M 82 ASP cc_start: 0.8624 (m-30) cc_final: 0.8246 (m-30) REVERT: J 26 ASN cc_start: 0.7912 (m-40) cc_final: 0.7526 (m-40) REVERT: J 34 MET cc_start: 0.8666 (mmm) cc_final: 0.8372 (mmm) REVERT: J 72 ASP cc_start: 0.6786 (t0) cc_final: 0.5483 (t70) REVERT: F 122 LEU cc_start: 0.9254 (mt) cc_final: 0.9039 (mm) REVERT: F 125 LEU cc_start: 0.9153 (mp) cc_final: 0.8939 (tp) REVERT: F 161 MET cc_start: 0.9213 (tpp) cc_final: 0.8485 (tpt) REVERT: F 491 ILE cc_start: 0.8790 (mp) cc_final: 0.8513 (tp) REVERT: R 42 LYS cc_start: 0.8472 (mmtt) cc_final: 0.8136 (mmtp) REVERT: R 75 ILE cc_start: 0.7475 (mt) cc_final: 0.7129 (tp) REVERT: R 78 LEU cc_start: 0.8553 (tp) cc_final: 0.8276 (tp) REVERT: R 79 GLN cc_start: 0.7244 (mm-40) cc_final: 0.6917 (tm-30) REVERT: P 26 ASN cc_start: 0.8142 (m-40) cc_final: 0.7799 (m-40) REVERT: P 72 ASP cc_start: 0.6683 (t0) cc_final: 0.6398 (t0) REVERT: N 73 LEU cc_start: 0.8631 (mt) cc_final: 0.8150 (tp) REVERT: N 80 PHE cc_start: 0.8797 (m-80) cc_final: 0.8506 (m-80) REVERT: N 91 TYR cc_start: 0.4513 (p90) cc_final: 0.4081 (p90) REVERT: N 100 GLN cc_start: 0.9065 (pm20) cc_final: 0.8767 (pm20) REVERT: K 26 ASN cc_start: 0.7822 (m-40) cc_final: 0.7460 (m-40) REVERT: K 34 MET cc_start: 0.8601 (mmm) cc_final: 0.8160 (mmm) REVERT: K 72 ASP cc_start: 0.7018 (t0) cc_final: 0.4980 (t0) outliers start: 0 outliers final: 0 residues processed: 725 average time/residue: 0.4439 time to fit residues: 477.2181 Evaluate side-chains 341 residues out of total 2604 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 341 time to evaluate : 2.974 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 297 random chunks: chunk 250 optimal weight: 7.9990 chunk 225 optimal weight: 2.9990 chunk 124 optimal weight: 0.9990 chunk 76 optimal weight: 6.9990 chunk 151 optimal weight: 3.9990 chunk 120 optimal weight: 3.9990 chunk 232 optimal weight: 0.9990 chunk 90 optimal weight: 2.9990 chunk 141 optimal weight: 1.9990 chunk 173 optimal weight: 7.9990 chunk 269 optimal weight: 3.9990 overall best weight: 1.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 195 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 543 ASN B 590 GLN B 616 ASN ** B 651 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 89 GLN ** L 100 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 81 GLN ** E 195 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 425 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 616 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 656 ASN Q 37 GLN ** Q 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 100 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 82AHIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 195 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 328 GLN ** F 425 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 575 GLN I 616 ASN ** I 651 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 37 GLN ** R 100 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8207 moved from start: 0.3139 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.051 26313 Z= 0.303 Angle : 0.796 8.717 35712 Z= 0.413 Chirality : 0.049 0.231 4602 Planarity : 0.005 0.072 4233 Dihedral : 13.031 84.861 6939 Min Nonbonded Distance : 2.137 Molprobity Statistics. All-atom Clashscore : 11.95 Ramachandran Plot: Outliers : 0.40 % Allowed : 4.92 % Favored : 94.67 % Rotamer: Outliers : 2.73 % Allowed : 9.25 % Favored : 88.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.41 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.10 % 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: 0.28 (0.15), residues: 2967 helix: 0.09 (0.27), residues: 372 sheet: 0.62 (0.15), residues: 1056 loop : 0.02 (0.16), residues: 1539 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.002 TRP M 35 HIS 0.007 0.002 HIS Q 90 PHE 0.025 0.002 PHE D 71 TYR 0.026 0.002 TYR Q 49 ARG 0.013 0.001 ARG M 24 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5934 Ramachandran restraints generated. 2967 Oldfield, 0 Emsley, 2967 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5934 Ramachandran restraints generated. 2967 Oldfield, 0 Emsley, 2967 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 468 residues out of total 2604 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 71 poor density : 397 time to evaluate : 3.062 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 104 MET cc_start: 0.8660 (tpp) cc_final: 0.8110 (tpp) REVERT: A 161 MET cc_start: 0.9243 (tpp) cc_final: 0.8930 (tpt) REVERT: A 377 ASN cc_start: 0.8488 (t0) cc_final: 0.8121 (p0) REVERT: B 543 ASN cc_start: 0.7653 (OUTLIER) cc_final: 0.7401 (t0) REVERT: B 626 MET cc_start: 0.8162 (ttp) cc_final: 0.7690 (tmm) REVERT: B 641 ILE cc_start: 0.8691 (mp) cc_final: 0.8467 (pt) REVERT: L 4 MET cc_start: 0.7484 (ttp) cc_final: 0.7267 (ttt) REVERT: L 42 LYS cc_start: 0.8754 (mmtt) cc_final: 0.8475 (mmtp) REVERT: L 79 GLN cc_start: 0.7908 (mm-40) cc_final: 0.7588 (tm-30) REVERT: D 33 LEU cc_start: 0.6168 (tt) cc_final: 0.5808 (tt) REVERT: D 62 PHE cc_start: 0.6707 (m-80) cc_final: 0.6369 (m-80) REVERT: D 103 ARG cc_start: 0.8232 (ptp90) cc_final: 0.7903 (mpp-170) REVERT: C 34 MET cc_start: 0.8666 (mmm) cc_final: 0.8230 (mmm) REVERT: C 99 ARG cc_start: 0.9154 (mmm160) cc_final: 0.8860 (tmm-80) REVERT: E 377 ASN cc_start: 0.8528 (t0) cc_final: 0.8165 (p0) REVERT: E 434 MET cc_start: 0.8788 (ttp) cc_final: 0.8454 (ttp) REVERT: G 615 SER cc_start: 0.8935 (m) cc_final: 0.8662 (t) REVERT: Q 58 VAL cc_start: 0.7546 (t) cc_final: 0.7142 (t) REVERT: Q 79 GLN cc_start: 0.7343 (mm-40) cc_final: 0.7137 (tm-30) REVERT: O 26 ASN cc_start: 0.7722 (m-40) cc_final: 0.7449 (m110) REVERT: M 21 ILE cc_start: 0.7842 (OUTLIER) cc_final: 0.7563 (tp) REVERT: M 82 ASP cc_start: 0.8507 (m-30) cc_final: 0.7849 (m-30) REVERT: M 91 TYR cc_start: 0.5845 (p90) cc_final: 0.5614 (p90) REVERT: J 34 MET cc_start: 0.8664 (mmm) cc_final: 0.8366 (mmm) REVERT: J 82 LYS cc_start: 0.9422 (mmmt) cc_final: 0.9165 (mtmm) REVERT: J 100 ASP cc_start: 0.8110 (OUTLIER) cc_final: 0.7908 (m-30) REVERT: F 104 MET cc_start: 0.8528 (tpp) cc_final: 0.8273 (tpp) REVERT: F 161 MET cc_start: 0.9158 (tpp) cc_final: 0.8861 (tpp) REVERT: F 377 ASN cc_start: 0.8472 (t0) cc_final: 0.8164 (p0) REVERT: I 538 THR cc_start: 0.7913 (m) cc_final: 0.7660 (m) REVERT: I 649 SER cc_start: 0.8886 (m) cc_final: 0.8443 (p) REVERT: R 42 LYS cc_start: 0.8641 (mmtt) cc_final: 0.8397 (mmtp) REVERT: R 78 LEU cc_start: 0.8920 (tp) cc_final: 0.8674 (tp) REVERT: P 79 TYR cc_start: 0.7354 (m-80) cc_final: 0.7043 (m-10) REVERT: P 82 MET cc_start: 0.7749 (mtm) cc_final: 0.7540 (mtp) REVERT: N 23 CYS cc_start: 0.3371 (p) cc_final: 0.1274 (p) REVERT: N 61 ARG cc_start: 0.8581 (ptp-110) cc_final: 0.7628 (ptp-110) REVERT: N 75 ILE cc_start: 0.8225 (mt) cc_final: 0.7870 (mm) REVERT: N 82 ASP cc_start: 0.8925 (m-30) cc_final: 0.8412 (m-30) REVERT: N 91 TYR cc_start: 0.4980 (p90) cc_final: 0.4347 (p90) REVERT: K 34 MET cc_start: 0.8577 (mmm) cc_final: 0.8183 (mmm) REVERT: K 74 LEU cc_start: 0.9077 (mt) cc_final: 0.8871 (mt) outliers start: 71 outliers final: 38 residues processed: 439 average time/residue: 0.4083 time to fit residues: 271.4057 Evaluate side-chains 346 residues out of total 2604 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 305 time to evaluate : 2.980 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 137 ASN Chi-restraints excluded: chain A residue 194 ILE Chi-restraints excluded: chain A residue 373 THR Chi-restraints excluded: chain A residue 450 THR Chi-restraints excluded: chain B residue 543 ASN Chi-restraints excluded: chain B residue 570 VAL Chi-restraints excluded: chain B residue 603 ILE Chi-restraints excluded: chain B residue 616 ASN Chi-restraints excluded: chain B residue 659 ASP Chi-restraints excluded: chain L residue 73 LEU Chi-restraints excluded: chain L residue 78 LEU Chi-restraints excluded: chain L residue 82 ASP Chi-restraints excluded: chain H residue 66 ARG Chi-restraints excluded: chain C residue 61 ASP Chi-restraints excluded: chain C residue 82 HIS Chi-restraints excluded: chain C residue 100 ASP Chi-restraints excluded: chain Q residue 24 ARG Chi-restraints excluded: chain Q residue 37 GLN Chi-restraints excluded: chain Q residue 82 ASP Chi-restraints excluded: chain O residue 73 ASP Chi-restraints excluded: chain M residue 19 ILE Chi-restraints excluded: chain M residue 21 ILE Chi-restraints excluded: chain M residue 47 LEU Chi-restraints excluded: chain M residue 87 HIS Chi-restraints excluded: chain M residue 103 ARG Chi-restraints excluded: chain J residue 11 LEU Chi-restraints excluded: chain J residue 100 ASP Chi-restraints excluded: chain J residue 100 ASP Chi-restraints excluded: chain F residue 137 ASN Chi-restraints excluded: chain F residue 328 GLN Chi-restraints excluded: chain F residue 371 VAL Chi-restraints excluded: chain F residue 450 THR Chi-restraints excluded: chain F residue 488 VAL Chi-restraints excluded: chain I residue 623 TRP Chi-restraints excluded: chain I residue 652 GLN Chi-restraints excluded: chain R residue 82 ASP Chi-restraints excluded: chain N residue 60 SER Chi-restraints excluded: chain N residue 87 HIS Chi-restraints excluded: chain K residue 11 LEU Chi-restraints excluded: chain K residue 61 ASP Chi-restraints excluded: chain K residue 100 ASP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 297 random chunks: chunk 149 optimal weight: 8.9990 chunk 83 optimal weight: 20.0000 chunk 224 optimal weight: 0.9990 chunk 183 optimal weight: 50.0000 chunk 74 optimal weight: 10.0000 chunk 270 optimal weight: 0.9990 chunk 291 optimal weight: 10.0000 chunk 240 optimal weight: 2.9990 chunk 267 optimal weight: 0.5980 chunk 92 optimal weight: 10.0000 chunk 216 optimal weight: 6.9990 overall best weight: 2.5188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 195 ASN A 425 ASN ** B 590 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 100 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 81 GLN ** D 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 170 GLN ** E 195 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 328 GLN ** E 425 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 616 ASN ** Q 100 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 81 GLN J 81 GLN ** J 82AHIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 195 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 328 GLN ** F 425 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 652 GLN I 653 GLN ** R 79 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 100 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 81 GLN K 26 ASN K 81 GLN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8285 moved from start: 0.3883 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.058 26313 Z= 0.312 Angle : 0.730 9.402 35712 Z= 0.370 Chirality : 0.047 0.258 4602 Planarity : 0.004 0.065 4233 Dihedral : 11.177 78.712 6939 Min Nonbonded Distance : 2.084 Molprobity Statistics. All-atom Clashscore : 13.04 Ramachandran Plot: Outliers : 0.10 % Allowed : 5.73 % Favored : 94.17 % Rotamer: Outliers : 3.30 % Allowed : 10.71 % Favored : 85.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.41 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % 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: 0.14 (0.15), residues: 2967 helix: 0.32 (0.28), residues: 357 sheet: 0.51 (0.15), residues: 1050 loop : -0.16 (0.16), residues: 1560 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP F 112 HIS 0.008 0.001 HIS F 330 PHE 0.025 0.002 PHE M 98 TYR 0.021 0.002 TYR Q 49 ARG 0.007 0.001 ARG D 61 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5934 Ramachandran restraints generated. 2967 Oldfield, 0 Emsley, 2967 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5934 Ramachandran restraints generated. 2967 Oldfield, 0 Emsley, 2967 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 414 residues out of total 2604 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 86 poor density : 328 time to evaluate : 3.020 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 104 MET cc_start: 0.8752 (tpp) cc_final: 0.8242 (tpp) REVERT: A 161 MET cc_start: 0.9277 (tpp) cc_final: 0.8974 (tpt) REVERT: A 271 MET cc_start: 0.8598 (mmm) cc_final: 0.8170 (mmm) REVERT: B 641 ILE cc_start: 0.8794 (mp) cc_final: 0.8581 (pt) REVERT: L 79 GLN cc_start: 0.7910 (mm-40) cc_final: 0.7578 (tm-30) REVERT: H 100 ASN cc_start: 0.7943 (m-40) cc_final: 0.7695 (t0) REVERT: D 54 LEU cc_start: 0.8770 (pp) cc_final: 0.8478 (tt) REVERT: D 103 ARG cc_start: 0.8305 (ptp90) cc_final: 0.7983 (mpp-170) REVERT: C 26 ASN cc_start: 0.8312 (m110) cc_final: 0.8096 (m110) REVERT: C 34 MET cc_start: 0.8749 (mmm) cc_final: 0.8268 (mmm) REVERT: C 99 ARG cc_start: 0.9143 (mmm160) cc_final: 0.8604 (tpp-160) REVERT: E 434 MET cc_start: 0.8781 (ttp) cc_final: 0.8528 (ttp) REVERT: G 535 MET cc_start: 0.7004 (OUTLIER) cc_final: 0.6775 (tpt) REVERT: G 601 LYS cc_start: 0.8903 (pttm) cc_final: 0.8654 (pttt) REVERT: G 649 SER cc_start: 0.8593 (m) cc_final: 0.8360 (p) REVERT: Q 48 ILE cc_start: 0.7963 (OUTLIER) cc_final: 0.7556 (mm) REVERT: Q 105 GLU cc_start: 0.7435 (mt-10) cc_final: 0.6724 (pm20) REVERT: O 26 ASN cc_start: 0.7570 (m-40) cc_final: 0.7276 (m110) REVERT: M 54 LEU cc_start: 0.8602 (pp) cc_final: 0.8360 (tt) REVERT: M 82 ASP cc_start: 0.8442 (m-30) cc_final: 0.7988 (m-30) REVERT: J 100 ASP cc_start: 0.8355 (OUTLIER) cc_final: 0.7601 (m-30) REVERT: F 104 MET cc_start: 0.8688 (tpp) cc_final: 0.8217 (tpp) REVERT: I 530 MET cc_start: 0.7680 (mmt) cc_final: 0.7457 (mmt) REVERT: I 626 MET cc_start: 0.7998 (ttp) cc_final: 0.7558 (ttm) REVERT: I 649 SER cc_start: 0.8862 (m) cc_final: 0.8492 (p) REVERT: I 652 GLN cc_start: 0.9176 (OUTLIER) cc_final: 0.8836 (tm-30) REVERT: P 34 MET cc_start: 0.8771 (mpp) cc_final: 0.8512 (mmm) REVERT: K 34 MET cc_start: 0.8654 (mmm) cc_final: 0.8381 (mmm) outliers start: 86 outliers final: 51 residues processed: 385 average time/residue: 0.3928 time to fit residues: 238.7078 Evaluate side-chains 326 residues out of total 2604 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 55 poor density : 271 time to evaluate : 2.942 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 50 THR Chi-restraints excluded: chain A residue 75 VAL Chi-restraints excluded: chain A residue 137 ASN Chi-restraints excluded: chain A residue 373 THR Chi-restraints excluded: chain A residue 450 THR Chi-restraints excluded: chain A residue 491 ILE Chi-restraints excluded: chain B residue 538 THR Chi-restraints excluded: chain B residue 616 ASN Chi-restraints excluded: chain B residue 623 TRP Chi-restraints excluded: chain B residue 647 GLU Chi-restraints excluded: chain B residue 659 ASP Chi-restraints excluded: chain L residue 73 LEU Chi-restraints excluded: chain L residue 78 LEU Chi-restraints excluded: chain L residue 82 ASP Chi-restraints excluded: chain H residue 18 LEU Chi-restraints excluded: chain H residue 66 ARG Chi-restraints excluded: chain H residue 73 ASP Chi-restraints excluded: chain D residue 19 ILE Chi-restraints excluded: chain D residue 87 HIS Chi-restraints excluded: chain C residue 82 HIS Chi-restraints excluded: chain C residue 100 ASP Chi-restraints excluded: chain E residue 75 VAL Chi-restraints excluded: chain E residue 491 ILE Chi-restraints excluded: chain G residue 535 MET Chi-restraints excluded: chain G residue 538 THR Chi-restraints excluded: chain G residue 570 VAL Chi-restraints excluded: chain Q residue 48 ILE Chi-restraints excluded: chain Q residue 49 TYR Chi-restraints excluded: chain Q residue 73 LEU Chi-restraints excluded: chain O residue 73 ASP Chi-restraints excluded: chain O residue 74 LEU Chi-restraints excluded: chain M residue 19 ILE Chi-restraints excluded: chain M residue 47 LEU Chi-restraints excluded: chain M residue 60 SER Chi-restraints excluded: chain M residue 87 HIS Chi-restraints excluded: chain M residue 103 ARG Chi-restraints excluded: chain J residue 11 LEU Chi-restraints excluded: chain J residue 100 ASP Chi-restraints excluded: chain J residue 100 ASP Chi-restraints excluded: chain F residue 137 ASN Chi-restraints excluded: chain F residue 450 THR Chi-restraints excluded: chain F residue 488 VAL Chi-restraints excluded: chain F residue 491 ILE Chi-restraints excluded: chain I residue 535 MET Chi-restraints excluded: chain I residue 623 TRP Chi-restraints excluded: chain I residue 652 GLN Chi-restraints excluded: chain R residue 47 LEU Chi-restraints excluded: chain P residue 74 LEU Chi-restraints excluded: chain P residue 76 ASP Chi-restraints excluded: chain N residue 47 LEU Chi-restraints excluded: chain N residue 87 HIS Chi-restraints excluded: chain K residue 11 LEU Chi-restraints excluded: chain K residue 38 ARG Chi-restraints excluded: chain K residue 100 ASP Chi-restraints excluded: chain K residue 107 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 297 random chunks: chunk 266 optimal weight: 0.9990 chunk 203 optimal weight: 8.9990 chunk 140 optimal weight: 0.6980 chunk 29 optimal weight: 4.9990 chunk 128 optimal weight: 4.9990 chunk 181 optimal weight: 0.2980 chunk 271 optimal weight: 8.9990 chunk 287 optimal weight: 1.9990 chunk 141 optimal weight: 4.9990 chunk 256 optimal weight: 8.9990 chunk 77 optimal weight: 30.0000 overall best weight: 1.7986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 170 GLN B 590 GLN B 616 ASN ** L 100 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 328 GLN Q 79 GLN ** Q 100 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 79 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 82AHIS ** F 195 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 425 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 590 GLN I 652 GLN ** R 79 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 100 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 79 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8289 moved from start: 0.4322 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 26313 Z= 0.239 Angle : 0.693 12.704 35712 Z= 0.344 Chirality : 0.047 0.282 4602 Planarity : 0.004 0.060 4233 Dihedral : 9.943 72.389 6939 Min Nonbonded Distance : 2.017 Molprobity Statistics. All-atom Clashscore : 12.33 Ramachandran Plot: Outliers : 0.10 % Allowed : 5.16 % Favored : 94.74 % Rotamer: Outliers : 3.57 % Allowed : 11.94 % Favored : 84.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.41 % 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: 0.07 (0.15), residues: 2967 helix: 0.62 (0.29), residues: 339 sheet: 0.36 (0.16), residues: 1026 loop : -0.20 (0.15), residues: 1602 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP E 112 HIS 0.006 0.001 HIS D 87 PHE 0.030 0.002 PHE D 71 TYR 0.019 0.002 TYR R 49 ARG 0.007 0.000 ARG L 24 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5934 Ramachandran restraints generated. 2967 Oldfield, 0 Emsley, 2967 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5934 Ramachandran restraints generated. 2967 Oldfield, 0 Emsley, 2967 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 400 residues out of total 2604 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 93 poor density : 307 time to evaluate : 3.056 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 104 MET cc_start: 0.8731 (tpp) cc_final: 0.8137 (tpp) REVERT: A 161 MET cc_start: 0.9218 (tpp) cc_final: 0.8917 (tpt) REVERT: A 271 MET cc_start: 0.8623 (mmm) cc_final: 0.8213 (mmm) REVERT: B 584 GLU cc_start: 0.8799 (tt0) cc_final: 0.8562 (tm-30) REVERT: B 649 SER cc_start: 0.8861 (m) cc_final: 0.8564 (p) REVERT: L 79 GLN cc_start: 0.7841 (mm-40) cc_final: 0.7548 (tm-30) REVERT: H 36 TRP cc_start: 0.8487 (m100) cc_final: 0.8235 (m100) REVERT: D 33 LEU cc_start: 0.5955 (tp) cc_final: 0.5406 (tp) REVERT: D 54 LEU cc_start: 0.8838 (pp) cc_final: 0.8544 (tt) REVERT: D 82 ASP cc_start: 0.8003 (m-30) cc_final: 0.7493 (m-30) REVERT: D 103 ARG cc_start: 0.8433 (ptp90) cc_final: 0.8112 (mpp-170) REVERT: C 34 MET cc_start: 0.8698 (mmm) cc_final: 0.8422 (mmm) REVERT: C 75 GLU cc_start: 0.7492 (mm-30) cc_final: 0.7266 (mm-30) REVERT: C 99 ARG cc_start: 0.9124 (mmm160) cc_final: 0.8622 (tpp-160) REVERT: E 423 ILE cc_start: 0.9431 (OUTLIER) cc_final: 0.9144 (mp) REVERT: E 434 MET cc_start: 0.8728 (ttp) cc_final: 0.8453 (ttp) REVERT: Q 4 MET cc_start: 0.7713 (ttp) cc_final: 0.7441 (tmm) REVERT: Q 58 VAL cc_start: 0.7707 (t) cc_final: 0.7135 (t) REVERT: O 26 ASN cc_start: 0.7464 (m-40) cc_final: 0.7205 (m110) REVERT: J 100 ASP cc_start: 0.8410 (OUTLIER) cc_final: 0.7648 (m-30) REVERT: I 649 SER cc_start: 0.8876 (m) cc_final: 0.8411 (p) REVERT: I 652 GLN cc_start: 0.9169 (OUTLIER) cc_final: 0.8840 (tm-30) REVERT: R 24 ARG cc_start: 0.8185 (tpt90) cc_final: 0.7964 (tpt90) REVERT: N 23 CYS cc_start: 0.4054 (t) cc_final: 0.2783 (t) REVERT: N 54 LEU cc_start: 0.8873 (pp) cc_final: 0.8606 (tt) REVERT: N 61 ARG cc_start: 0.8878 (OUTLIER) cc_final: 0.8340 (mtm110) REVERT: N 79 GLN cc_start: 0.7093 (OUTLIER) cc_final: 0.6821 (tm-30) REVERT: K 34 MET cc_start: 0.8656 (mmm) cc_final: 0.8382 (mmm) REVERT: K 38 ARG cc_start: 0.7386 (OUTLIER) cc_final: 0.6038 (ttm-80) REVERT: K 100 ASN cc_start: 0.7411 (OUTLIER) cc_final: 0.6896 (t0) REVERT: K 100 ASP cc_start: 0.8367 (OUTLIER) cc_final: 0.7854 (t0) REVERT: K 107 THR cc_start: 0.7491 (OUTLIER) cc_final: 0.7198 (m) outliers start: 93 outliers final: 63 residues processed: 366 average time/residue: 0.3688 time to fit residues: 212.3994 Evaluate side-chains 346 residues out of total 2604 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 72 poor density : 274 time to evaluate : 2.696 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 75 VAL Chi-restraints excluded: chain A residue 137 ASN Chi-restraints excluded: chain A residue 373 THR Chi-restraints excluded: chain A residue 450 THR Chi-restraints excluded: chain A residue 491 ILE Chi-restraints excluded: chain B residue 570 VAL Chi-restraints excluded: chain B residue 616 ASN Chi-restraints excluded: chain B residue 623 TRP Chi-restraints excluded: chain B residue 625 ASN Chi-restraints excluded: chain B residue 647 GLU Chi-restraints excluded: chain L residue 58 VAL Chi-restraints excluded: chain L residue 67 SER Chi-restraints excluded: chain L residue 73 LEU Chi-restraints excluded: chain H residue 52 THR Chi-restraints excluded: chain H residue 66 ARG Chi-restraints excluded: chain H residue 73 ASP Chi-restraints excluded: chain H residue 76 ASP Chi-restraints excluded: chain H residue 108 VAL Chi-restraints excluded: chain D residue 11 LEU Chi-restraints excluded: chain D residue 19 ILE Chi-restraints excluded: chain D residue 87 HIS Chi-restraints excluded: chain C residue 82 HIS Chi-restraints excluded: chain C residue 100 ASP Chi-restraints excluded: chain C residue 107 THR Chi-restraints excluded: chain C residue 108 VAL Chi-restraints excluded: chain E residue 38 VAL Chi-restraints excluded: chain E residue 75 VAL Chi-restraints excluded: chain E residue 423 ILE Chi-restraints excluded: chain E residue 491 ILE Chi-restraints excluded: chain G residue 570 VAL Chi-restraints excluded: chain G residue 647 GLU Chi-restraints excluded: chain O residue 18 LEU Chi-restraints excluded: chain O residue 52 THR Chi-restraints excluded: chain O residue 74 LEU Chi-restraints excluded: chain O residue 76 ASP Chi-restraints excluded: chain O residue 108 VAL Chi-restraints excluded: chain M residue 47 LEU Chi-restraints excluded: chain M residue 62 PHE Chi-restraints excluded: chain M residue 87 HIS Chi-restraints excluded: chain J residue 11 LEU Chi-restraints excluded: chain J residue 82 HIS Chi-restraints excluded: chain J residue 100 ASP Chi-restraints excluded: chain J residue 100 ASP Chi-restraints excluded: chain J residue 107 THR Chi-restraints excluded: chain J residue 108 VAL Chi-restraints excluded: chain F residue 100 MET Chi-restraints excluded: chain F residue 137 ASN Chi-restraints excluded: chain F residue 347 LYS Chi-restraints excluded: chain F residue 450 THR Chi-restraints excluded: chain F residue 488 VAL Chi-restraints excluded: chain F residue 491 ILE Chi-restraints excluded: chain I residue 538 THR Chi-restraints excluded: chain I residue 570 VAL Chi-restraints excluded: chain I residue 623 TRP Chi-restraints excluded: chain I residue 652 GLN Chi-restraints excluded: chain I residue 659 ASP Chi-restraints excluded: chain R residue 73 LEU Chi-restraints excluded: chain P residue 73 ASP Chi-restraints excluded: chain P residue 74 LEU Chi-restraints excluded: chain P residue 76 ASP Chi-restraints excluded: chain P residue 95 LYS Chi-restraints excluded: chain P residue 108 VAL Chi-restraints excluded: chain N residue 61 ARG Chi-restraints excluded: chain N residue 79 GLN Chi-restraints excluded: chain N residue 82 ASP Chi-restraints excluded: chain N residue 87 HIS Chi-restraints excluded: chain K residue 38 ARG Chi-restraints excluded: chain K residue 100 ASP Chi-restraints excluded: chain K residue 100 ASN Chi-restraints excluded: chain K residue 100 ASP Chi-restraints excluded: chain K residue 107 THR Chi-restraints excluded: chain K residue 108 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 297 random chunks: chunk 239 optimal weight: 0.7980 chunk 162 optimal weight: 8.9990 chunk 4 optimal weight: 0.9980 chunk 213 optimal weight: 5.9990 chunk 118 optimal weight: 4.9990 chunk 244 optimal weight: 0.9990 chunk 198 optimal weight: 5.9990 chunk 0 optimal weight: 6.9990 chunk 146 optimal weight: 4.9990 chunk 257 optimal weight: 0.7980 chunk 72 optimal weight: 0.9990 overall best weight: 0.9184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 195 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 348 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 425 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 616 ASN B 656 ASN ** L 100 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 100 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 90 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 82AHIS F 130 GLN ** F 195 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 328 GLN ** F 425 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 79 GLN ** R 100 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 79 GLN N 90 HIS K 82AHIS Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8271 moved from start: 0.4592 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.061 26313 Z= 0.189 Angle : 0.657 10.371 35712 Z= 0.323 Chirality : 0.046 0.293 4602 Planarity : 0.004 0.056 4233 Dihedral : 9.294 68.453 6939 Min Nonbonded Distance : 2.110 Molprobity Statistics. All-atom Clashscore : 12.37 Ramachandran Plot: Outliers : 0.10 % Allowed : 5.06 % Favored : 94.84 % Rotamer: Outliers : 3.30 % Allowed : 13.40 % Favored : 83.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.41 % 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: 0.06 (0.15), residues: 2967 helix: 0.75 (0.29), residues: 339 sheet: 0.35 (0.16), residues: 1026 loop : -0.24 (0.15), residues: 1602 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.036 0.001 TRP D 35 HIS 0.014 0.001 HIS J 82A PHE 0.016 0.002 PHE D 71 TYR 0.020 0.001 TYR R 91 ARG 0.003 0.000 ARG D 61 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5934 Ramachandran restraints generated. 2967 Oldfield, 0 Emsley, 2967 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5934 Ramachandran restraints generated. 2967 Oldfield, 0 Emsley, 2967 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 398 residues out of total 2604 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 86 poor density : 312 time to evaluate : 2.765 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: A 104 MET cc_start: 0.8695 (tpp) cc_final: 0.8061 (tpp) REVERT: A 161 MET cc_start: 0.9124 (tpp) cc_final: 0.8832 (tpt) REVERT: A 271 MET cc_start: 0.8517 (mmm) cc_final: 0.8140 (mmm) REVERT: A 377 ASN cc_start: 0.8695 (t0) cc_final: 0.8070 (p0) REVERT: B 649 SER cc_start: 0.8855 (m) cc_final: 0.8555 (p) REVERT: L 79 GLN cc_start: 0.7803 (mm-40) cc_final: 0.7495 (tm-30) REVERT: L 105 GLU cc_start: 0.6895 (tp30) cc_final: 0.6663 (tp30) REVERT: D 103 ARG cc_start: 0.8461 (ptp90) cc_final: 0.8124 (mpp-170) REVERT: C 34 MET cc_start: 0.8682 (mmm) cc_final: 0.8419 (mmm) REVERT: C 85 GLU cc_start: 0.8750 (tm-30) cc_final: 0.8458 (tp30) REVERT: C 99 ARG cc_start: 0.9098 (mmm160) cc_final: 0.8606 (tpp-160) REVERT: G 530 MET cc_start: 0.8445 (mmm) cc_final: 0.8132 (mmm) REVERT: G 601 LYS cc_start: 0.8624 (pttp) cc_final: 0.8220 (mptt) REVERT: G 649 SER cc_start: 0.8677 (m) cc_final: 0.8365 (p) REVERT: Q 4 MET cc_start: 0.7785 (ttp) cc_final: 0.7542 (tmm) REVERT: Q 58 VAL cc_start: 0.7556 (t) cc_final: 0.7290 (t) REVERT: O 26 ASN cc_start: 0.7433 (m-40) cc_final: 0.7155 (m110) REVERT: M 54 LEU cc_start: 0.8751 (pp) cc_final: 0.8521 (tt) REVERT: M 82 ASP cc_start: 0.8529 (m-30) cc_final: 0.7512 (m-30) REVERT: M 103 ARG cc_start: 0.8244 (mpp-170) cc_final: 0.7594 (tpp80) REVERT: J 11 LEU cc_start: 0.8614 (OUTLIER) cc_final: 0.8290 (tp) REVERT: J 100 ASP cc_start: 0.8367 (OUTLIER) cc_final: 0.7605 (m-30) REVERT: I 601 LYS cc_start: 0.8764 (pttm) cc_final: 0.8220 (pttt) REVERT: I 649 SER cc_start: 0.9053 (m) cc_final: 0.8546 (p) REVERT: R 24 ARG cc_start: 0.8349 (tpt90) cc_final: 0.8064 (tpt90) REVERT: P 20 LEU cc_start: 0.8042 (OUTLIER) cc_final: 0.7742 (mm) REVERT: N 54 LEU cc_start: 0.8937 (pp) cc_final: 0.8716 (tt) REVERT: K 34 MET cc_start: 0.8627 (mmm) cc_final: 0.8393 (mmm) REVERT: K 38 ARG cc_start: 0.7363 (OUTLIER) cc_final: 0.5951 (ttm-80) REVERT: K 82 MET cc_start: 0.7477 (mtp) cc_final: 0.6559 (ptp) REVERT: K 100 ASN cc_start: 0.7351 (OUTLIER) cc_final: 0.6833 (t0) REVERT: K 107 THR cc_start: 0.7316 (OUTLIER) cc_final: 0.7007 (m) REVERT: K 110 THR cc_start: 0.8430 (m) cc_final: 0.8046 (p) outliers start: 86 outliers final: 56 residues processed: 367 average time/residue: 0.3710 time to fit residues: 214.1608 Evaluate side-chains 339 residues out of total 2604 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 62 poor density : 277 time to evaluate : 3.185 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 75 VAL Chi-restraints excluded: chain A residue 137 ASN Chi-restraints excluded: chain A residue 373 THR Chi-restraints excluded: chain A residue 491 ILE Chi-restraints excluded: chain B residue 570 VAL Chi-restraints excluded: chain B residue 606 THR Chi-restraints excluded: chain B residue 616 ASN Chi-restraints excluded: chain B residue 623 TRP Chi-restraints excluded: chain B residue 625 ASN Chi-restraints excluded: chain B residue 647 GLU Chi-restraints excluded: chain L residue 73 LEU Chi-restraints excluded: chain L residue 78 LEU Chi-restraints excluded: chain H residue 73 ASP Chi-restraints excluded: chain D residue 11 LEU Chi-restraints excluded: chain D residue 19 ILE Chi-restraints excluded: chain D residue 62 PHE Chi-restraints excluded: chain D residue 87 HIS Chi-restraints excluded: chain C residue 11 LEU Chi-restraints excluded: chain C residue 82 HIS Chi-restraints excluded: chain C residue 100 ASP Chi-restraints excluded: chain C residue 107 THR Chi-restraints excluded: chain C residue 108 VAL Chi-restraints excluded: chain E residue 38 VAL Chi-restraints excluded: chain E residue 75 VAL Chi-restraints excluded: chain E residue 491 ILE Chi-restraints excluded: chain G residue 570 VAL Chi-restraints excluded: chain G residue 647 GLU Chi-restraints excluded: chain G residue 659 ASP Chi-restraints excluded: chain Q residue 47 LEU Chi-restraints excluded: chain Q residue 73 LEU Chi-restraints excluded: chain O residue 73 ASP Chi-restraints excluded: chain O residue 74 LEU Chi-restraints excluded: chain O residue 76 ASP Chi-restraints excluded: chain M residue 47 LEU Chi-restraints excluded: chain M residue 60 SER Chi-restraints excluded: chain M residue 87 HIS Chi-restraints excluded: chain J residue 11 LEU Chi-restraints excluded: chain J residue 82 HIS Chi-restraints excluded: chain J residue 100 ASP Chi-restraints excluded: chain J residue 100 ASP Chi-restraints excluded: chain J residue 107 THR Chi-restraints excluded: chain J residue 108 VAL Chi-restraints excluded: chain F residue 137 ASN Chi-restraints excluded: chain F residue 347 LYS Chi-restraints excluded: chain F residue 371 VAL Chi-restraints excluded: chain F residue 373 THR Chi-restraints excluded: chain F residue 491 ILE Chi-restraints excluded: chain I residue 538 THR Chi-restraints excluded: chain I residue 570 VAL Chi-restraints excluded: chain I residue 623 TRP Chi-restraints excluded: chain I residue 659 ASP Chi-restraints excluded: chain R residue 47 LEU Chi-restraints excluded: chain R residue 73 LEU Chi-restraints excluded: chain P residue 20 LEU Chi-restraints excluded: chain P residue 73 ASP Chi-restraints excluded: chain P residue 76 ASP Chi-restraints excluded: chain N residue 87 HIS Chi-restraints excluded: chain K residue 38 ARG Chi-restraints excluded: chain K residue 100 ASP Chi-restraints excluded: chain K residue 100 ASN Chi-restraints excluded: chain K residue 107 THR Chi-restraints excluded: chain K residue 108 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 297 random chunks: chunk 96 optimal weight: 20.0000 chunk 258 optimal weight: 3.9990 chunk 56 optimal weight: 0.5980 chunk 168 optimal weight: 10.0000 chunk 70 optimal weight: 0.9990 chunk 287 optimal weight: 5.9990 chunk 238 optimal weight: 9.9990 chunk 133 optimal weight: 6.9990 chunk 23 optimal weight: 3.9990 chunk 95 optimal weight: 10.0000 chunk 150 optimal weight: 7.9990 overall best weight: 3.1188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 195 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 328 GLN ** A 348 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 425 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 100 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 89 GLN D 90 HIS ** E 195 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 425 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 100 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 79 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 90 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 195 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 425 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 575 GLN R 89 GLN ** R 100 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 89 GLN K 82AHIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8358 moved from start: 0.4928 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.063 26313 Z= 0.332 Angle : 0.707 8.296 35712 Z= 0.349 Chirality : 0.048 0.304 4602 Planarity : 0.004 0.057 4233 Dihedral : 9.044 62.604 6939 Min Nonbonded Distance : 2.074 Molprobity Statistics. All-atom Clashscore : 14.10 Ramachandran Plot: Outliers : 0.10 % Allowed : 6.07 % Favored : 93.83 % Rotamer: Outliers : 4.11 % Allowed : 13.56 % Favored : 82.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.41 % 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: -0.08 (0.15), residues: 2967 helix: 0.55 (0.29), residues: 345 sheet: 0.31 (0.16), residues: 1050 loop : -0.36 (0.16), residues: 1572 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.002 TRP D 35 HIS 0.017 0.001 HIS J 82A PHE 0.015 0.002 PHE D 71 TYR 0.015 0.002 TYR R 49 ARG 0.005 0.001 ARG A 500 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5934 Ramachandran restraints generated. 2967 Oldfield, 0 Emsley, 2967 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5934 Ramachandran restraints generated. 2967 Oldfield, 0 Emsley, 2967 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 386 residues out of total 2604 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 107 poor density : 279 time to evaluate : 3.003 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 104 MET cc_start: 0.8735 (tpp) cc_final: 0.8209 (tpp) REVERT: A 161 MET cc_start: 0.9145 (tpp) cc_final: 0.8831 (tpt) REVERT: L 4 MET cc_start: 0.8124 (tpp) cc_final: 0.7601 (tpp) REVERT: L 42 LYS cc_start: 0.8728 (mmtt) cc_final: 0.8378 (mmmt) REVERT: L 79 GLN cc_start: 0.7830 (mm-40) cc_final: 0.7490 (tm-30) REVERT: D 39 LYS cc_start: 0.7771 (OUTLIER) cc_final: 0.7227 (mmtm) REVERT: D 103 ARG cc_start: 0.8572 (ptp90) cc_final: 0.8269 (mpp-170) REVERT: C 11 LEU cc_start: 0.8684 (OUTLIER) cc_final: 0.8480 (tp) REVERT: C 34 MET cc_start: 0.8713 (mmm) cc_final: 0.8445 (mmm) REVERT: C 99 ARG cc_start: 0.9141 (mmm160) cc_final: 0.8891 (tpp-160) REVERT: E 434 MET cc_start: 0.8763 (ttp) cc_final: 0.8502 (ttp) REVERT: G 530 MET cc_start: 0.8323 (mmm) cc_final: 0.8072 (mmm) REVERT: G 601 LYS cc_start: 0.8768 (pttp) cc_final: 0.8460 (pttt) REVERT: G 649 SER cc_start: 0.8785 (m) cc_final: 0.8478 (p) REVERT: Q 55 LYS cc_start: 0.8339 (tttt) cc_final: 0.7723 (ttmt) REVERT: Q 58 VAL cc_start: 0.7717 (t) cc_final: 0.7241 (t) REVERT: Q 105 GLU cc_start: 0.7122 (mt-10) cc_final: 0.6417 (pm20) REVERT: O 26 ASN cc_start: 0.7426 (m-40) cc_final: 0.7142 (m110) REVERT: O 72 ASP cc_start: 0.8176 (OUTLIER) cc_final: 0.7827 (m-30) REVERT: M 42 LYS cc_start: 0.9096 (mmtt) cc_final: 0.8888 (mmmm) REVERT: M 54 LEU cc_start: 0.8806 (pp) cc_final: 0.8550 (tt) REVERT: M 103 ARG cc_start: 0.8156 (mpp-170) cc_final: 0.7620 (tpp80) REVERT: J 11 LEU cc_start: 0.8707 (OUTLIER) cc_final: 0.8379 (tp) REVERT: J 100 ASN cc_start: 0.7448 (OUTLIER) cc_final: 0.6307 (t0) REVERT: I 535 MET cc_start: 0.8054 (mmt) cc_final: 0.7744 (mmt) REVERT: I 601 LYS cc_start: 0.8909 (pttm) cc_final: 0.8450 (pttt) REVERT: I 649 SER cc_start: 0.9046 (m) cc_final: 0.8626 (p) REVERT: P 100 ASP cc_start: 0.8548 (m-30) cc_final: 0.8301 (m-30) REVERT: N 54 LEU cc_start: 0.9124 (pp) cc_final: 0.8916 (tt) REVERT: K 34 MET cc_start: 0.8688 (mmm) cc_final: 0.8415 (mmm) REVERT: K 38 ARG cc_start: 0.7327 (OUTLIER) cc_final: 0.6045 (ttm-80) REVERT: K 100 ASP cc_start: 0.8762 (OUTLIER) cc_final: 0.8298 (t0) REVERT: K 107 THR cc_start: 0.7036 (OUTLIER) cc_final: 0.6757 (m) REVERT: K 110 THR cc_start: 0.8569 (m) cc_final: 0.8124 (p) outliers start: 107 outliers final: 79 residues processed: 357 average time/residue: 0.3958 time to fit residues: 222.0439 Evaluate side-chains 344 residues out of total 2604 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 87 poor density : 257 time to evaluate : 2.887 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 50 THR Chi-restraints excluded: chain A residue 75 VAL Chi-restraints excluded: chain A residue 137 ASN Chi-restraints excluded: chain A residue 328 GLN Chi-restraints excluded: chain A residue 373 THR Chi-restraints excluded: chain A residue 450 THR Chi-restraints excluded: chain A residue 475 MET Chi-restraints excluded: chain A residue 491 ILE Chi-restraints excluded: chain B residue 570 VAL Chi-restraints excluded: chain B residue 599 SER Chi-restraints excluded: chain B residue 606 THR Chi-restraints excluded: chain B residue 623 TRP Chi-restraints excluded: chain B residue 625 ASN Chi-restraints excluded: chain B residue 647 GLU Chi-restraints excluded: chain B residue 659 ASP Chi-restraints excluded: chain L residue 73 LEU Chi-restraints excluded: chain L residue 78 LEU Chi-restraints excluded: chain H residue 18 LEU Chi-restraints excluded: chain H residue 52 THR Chi-restraints excluded: chain H residue 66 ARG Chi-restraints excluded: chain H residue 73 ASP Chi-restraints excluded: chain H residue 76 ASP Chi-restraints excluded: chain H residue 108 VAL Chi-restraints excluded: chain D residue 11 LEU Chi-restraints excluded: chain D residue 19 ILE Chi-restraints excluded: chain D residue 23 CYS Chi-restraints excluded: chain D residue 39 LYS Chi-restraints excluded: chain D residue 47 LEU Chi-restraints excluded: chain D residue 58 VAL Chi-restraints excluded: chain D residue 62 PHE Chi-restraints excluded: chain D residue 87 HIS Chi-restraints excluded: chain C residue 11 LEU Chi-restraints excluded: chain C residue 33 THR Chi-restraints excluded: chain C residue 82 HIS Chi-restraints excluded: chain C residue 100 ASP Chi-restraints excluded: chain C residue 107 THR Chi-restraints excluded: chain C residue 108 VAL Chi-restraints excluded: chain E residue 50 THR Chi-restraints excluded: chain E residue 75 VAL Chi-restraints excluded: chain E residue 373 THR Chi-restraints excluded: chain E residue 491 ILE Chi-restraints excluded: chain G residue 570 VAL Chi-restraints excluded: chain G residue 599 SER Chi-restraints excluded: chain G residue 647 GLU Chi-restraints excluded: chain G residue 659 ASP Chi-restraints excluded: chain Q residue 47 LEU Chi-restraints excluded: chain O residue 52 THR Chi-restraints excluded: chain O residue 72 ASP Chi-restraints excluded: chain O residue 73 ASP Chi-restraints excluded: chain O residue 74 LEU Chi-restraints excluded: chain O residue 76 ASP Chi-restraints excluded: chain O residue 108 VAL Chi-restraints excluded: chain M residue 19 ILE Chi-restraints excluded: chain M residue 47 LEU Chi-restraints excluded: chain M residue 87 HIS Chi-restraints excluded: chain J residue 11 LEU Chi-restraints excluded: chain J residue 82 HIS Chi-restraints excluded: chain J residue 100 ASP Chi-restraints excluded: chain J residue 100 ASN Chi-restraints excluded: chain J residue 107 THR Chi-restraints excluded: chain J residue 108 VAL Chi-restraints excluded: chain F residue 137 ASN Chi-restraints excluded: chain F residue 347 LYS Chi-restraints excluded: chain F residue 373 THR Chi-restraints excluded: chain F residue 450 THR Chi-restraints excluded: chain F residue 488 VAL Chi-restraints excluded: chain F residue 491 ILE Chi-restraints excluded: chain I residue 538 THR Chi-restraints excluded: chain I residue 570 VAL Chi-restraints excluded: chain I residue 599 SER Chi-restraints excluded: chain I residue 623 TRP Chi-restraints excluded: chain I residue 647 GLU Chi-restraints excluded: chain I residue 659 ASP Chi-restraints excluded: chain R residue 47 LEU Chi-restraints excluded: chain R residue 73 LEU Chi-restraints excluded: chain P residue 73 ASP Chi-restraints excluded: chain P residue 74 LEU Chi-restraints excluded: chain P residue 76 ASP Chi-restraints excluded: chain P residue 108 VAL Chi-restraints excluded: chain N residue 87 HIS Chi-restraints excluded: chain K residue 11 LEU Chi-restraints excluded: chain K residue 38 ARG Chi-restraints excluded: chain K residue 82 HIS Chi-restraints excluded: chain K residue 100 ASP Chi-restraints excluded: chain K residue 100 ASP Chi-restraints excluded: chain K residue 107 THR Chi-restraints excluded: chain K residue 108 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 297 random chunks: chunk 277 optimal weight: 3.9990 chunk 32 optimal weight: 6.9990 chunk 163 optimal weight: 9.9990 chunk 209 optimal weight: 0.9990 chunk 162 optimal weight: 7.9990 chunk 241 optimal weight: 9.9990 chunk 160 optimal weight: 10.0000 chunk 286 optimal weight: 4.9990 chunk 179 optimal weight: 9.9990 chunk 174 optimal weight: 8.9990 chunk 132 optimal weight: 0.6980 overall best weight: 3.5388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 195 ASN ** A 328 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 425 ASN B 543 ASN L 38 GLN ** L 100 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 590 GLN ** Q 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 100 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 79 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 90 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 82AHIS F 170 GLN ** F 195 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 425 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 652 GLN I 653 GLN ** R 100 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 82AHIS Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8394 moved from start: 0.5246 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.068 26313 Z= 0.360 Angle : 0.732 9.538 35712 Z= 0.360 Chirality : 0.048 0.312 4602 Planarity : 0.005 0.070 4233 Dihedral : 8.891 59.216 6939 Min Nonbonded Distance : 2.070 Molprobity Statistics. All-atom Clashscore : 14.57 Ramachandran Plot: Outliers : 0.10 % Allowed : 6.20 % Favored : 93.70 % Rotamer: Outliers : 4.15 % Allowed : 13.98 % Favored : 81.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.41 % 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: -0.28 (0.15), residues: 2967 helix: 0.42 (0.29), residues: 345 sheet: 0.14 (0.16), residues: 1050 loop : -0.48 (0.16), residues: 1572 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.002 TRP D 35 HIS 0.032 0.002 HIS K 82A PHE 0.017 0.002 PHE E 376 TYR 0.017 0.002 TYR R 91 ARG 0.005 0.001 ARG F 192 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5934 Ramachandran restraints generated. 2967 Oldfield, 0 Emsley, 2967 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5934 Ramachandran restraints generated. 2967 Oldfield, 0 Emsley, 2967 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 377 residues out of total 2604 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 108 poor density : 269 time to evaluate : 2.861 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: A 104 MET cc_start: 0.8743 (tpp) cc_final: 0.8231 (tpp) REVERT: A 161 MET cc_start: 0.9166 (tpp) cc_final: 0.8859 (tpt) REVERT: L 4 MET cc_start: 0.8294 (tpp) cc_final: 0.7691 (tpp) REVERT: L 79 GLN cc_start: 0.7886 (mm-40) cc_final: 0.7585 (tm-30) REVERT: D 39 LYS cc_start: 0.7698 (OUTLIER) cc_final: 0.7398 (mmtm) REVERT: D 103 ARG cc_start: 0.8585 (ptp90) cc_final: 0.8282 (mpp-170) REVERT: C 34 MET cc_start: 0.8788 (mmm) cc_final: 0.8326 (mmm) REVERT: C 99 ARG cc_start: 0.9122 (mmm160) cc_final: 0.8908 (tpp-160) REVERT: E 434 MET cc_start: 0.8785 (ttp) cc_final: 0.8480 (ttp) REVERT: G 601 LYS cc_start: 0.8778 (pttp) cc_final: 0.8575 (pttt) REVERT: G 649 SER cc_start: 0.8830 (m) cc_final: 0.8516 (p) REVERT: Q 55 LYS cc_start: 0.7563 (tttt) cc_final: 0.7343 (ttmt) REVERT: Q 58 VAL cc_start: 0.7539 (t) cc_final: 0.7017 (t) REVERT: Q 105 GLU cc_start: 0.7149 (mt-10) cc_final: 0.6560 (pm20) REVERT: O 26 ASN cc_start: 0.7234 (m-40) cc_final: 0.6982 (m110) REVERT: O 72 ASP cc_start: 0.8175 (OUTLIER) cc_final: 0.7886 (m-30) REVERT: M 39 LYS cc_start: 0.7623 (OUTLIER) cc_final: 0.7129 (mmtm) REVERT: M 54 LEU cc_start: 0.8897 (pp) cc_final: 0.8656 (tt) REVERT: M 80 PHE cc_start: 0.9288 (m-80) cc_final: 0.8995 (m-80) REVERT: M 103 ARG cc_start: 0.8473 (mpp-170) cc_final: 0.7905 (tpp80) REVERT: J 11 LEU cc_start: 0.8719 (OUTLIER) cc_final: 0.8428 (tp) REVERT: F 91 GLU cc_start: 0.6520 (mm-30) cc_final: 0.6279 (mm-30) REVERT: I 601 LYS cc_start: 0.9018 (pttm) cc_final: 0.8540 (pttt) REVERT: I 649 SER cc_start: 0.9210 (m) cc_final: 0.8801 (p) REVERT: N 54 LEU cc_start: 0.9135 (pp) cc_final: 0.8927 (tt) REVERT: K 34 MET cc_start: 0.8780 (mmm) cc_final: 0.8077 (mmm) REVERT: K 38 ARG cc_start: 0.7401 (OUTLIER) cc_final: 0.6138 (ttm-80) REVERT: K 100 ASP cc_start: 0.8939 (OUTLIER) cc_final: 0.8458 (t0) REVERT: K 110 THR cc_start: 0.8596 (m) cc_final: 0.8121 (p) outliers start: 108 outliers final: 85 residues processed: 345 average time/residue: 0.3830 time to fit residues: 209.6187 Evaluate side-chains 349 residues out of total 2604 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 91 poor density : 258 time to evaluate : 2.919 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 50 THR Chi-restraints excluded: chain A residue 75 VAL Chi-restraints excluded: chain A residue 137 ASN Chi-restraints excluded: chain A residue 195 ASN Chi-restraints excluded: chain A residue 373 THR Chi-restraints excluded: chain A residue 450 THR Chi-restraints excluded: chain A residue 475 MET Chi-restraints excluded: chain A residue 491 ILE Chi-restraints excluded: chain B residue 570 VAL Chi-restraints excluded: chain B residue 599 SER Chi-restraints excluded: chain B residue 606 THR Chi-restraints excluded: chain B residue 623 TRP Chi-restraints excluded: chain B residue 625 ASN Chi-restraints excluded: chain B residue 647 GLU Chi-restraints excluded: chain B residue 659 ASP Chi-restraints excluded: chain L residue 58 VAL Chi-restraints excluded: chain L residue 78 LEU Chi-restraints excluded: chain H residue 18 LEU Chi-restraints excluded: chain H residue 52 THR Chi-restraints excluded: chain H residue 66 ARG Chi-restraints excluded: chain H residue 73 ASP Chi-restraints excluded: chain H residue 76 ASP Chi-restraints excluded: chain H residue 108 VAL Chi-restraints excluded: chain D residue 11 LEU Chi-restraints excluded: chain D residue 19 ILE Chi-restraints excluded: chain D residue 33 LEU Chi-restraints excluded: chain D residue 39 LYS Chi-restraints excluded: chain D residue 58 VAL Chi-restraints excluded: chain D residue 87 HIS Chi-restraints excluded: chain C residue 33 THR Chi-restraints excluded: chain C residue 72 ASP Chi-restraints excluded: chain C residue 82 HIS Chi-restraints excluded: chain C residue 100 ASP Chi-restraints excluded: chain C residue 107 THR Chi-restraints excluded: chain C residue 108 VAL Chi-restraints excluded: chain E residue 50 THR Chi-restraints excluded: chain E residue 75 VAL Chi-restraints excluded: chain E residue 373 THR Chi-restraints excluded: chain E residue 491 ILE Chi-restraints excluded: chain G residue 570 VAL Chi-restraints excluded: chain G residue 599 SER Chi-restraints excluded: chain G residue 647 GLU Chi-restraints excluded: chain G residue 659 ASP Chi-restraints excluded: chain Q residue 19 ILE Chi-restraints excluded: chain Q residue 47 LEU Chi-restraints excluded: chain Q residue 73 LEU Chi-restraints excluded: chain O residue 52 THR Chi-restraints excluded: chain O residue 72 ASP Chi-restraints excluded: chain O residue 73 ASP Chi-restraints excluded: chain O residue 74 LEU Chi-restraints excluded: chain O residue 76 ASP Chi-restraints excluded: chain O residue 108 VAL Chi-restraints excluded: chain M residue 19 ILE Chi-restraints excluded: chain M residue 39 LYS Chi-restraints excluded: chain M residue 47 LEU Chi-restraints excluded: chain M residue 87 HIS Chi-restraints excluded: chain J residue 11 LEU Chi-restraints excluded: chain J residue 82 HIS Chi-restraints excluded: chain J residue 100 ASP Chi-restraints excluded: chain J residue 107 THR Chi-restraints excluded: chain J residue 108 VAL Chi-restraints excluded: chain F residue 50 THR Chi-restraints excluded: chain F residue 137 ASN Chi-restraints excluded: chain F residue 347 LYS Chi-restraints excluded: chain F residue 373 THR Chi-restraints excluded: chain F residue 450 THR Chi-restraints excluded: chain F residue 488 VAL Chi-restraints excluded: chain F residue 491 ILE Chi-restraints excluded: chain I residue 538 THR Chi-restraints excluded: chain I residue 570 VAL Chi-restraints excluded: chain I residue 599 SER Chi-restraints excluded: chain I residue 623 TRP Chi-restraints excluded: chain I residue 647 GLU Chi-restraints excluded: chain I residue 659 ASP Chi-restraints excluded: chain R residue 47 LEU Chi-restraints excluded: chain R residue 73 LEU Chi-restraints excluded: chain P residue 34 MET Chi-restraints excluded: chain P residue 73 ASP Chi-restraints excluded: chain P residue 74 LEU Chi-restraints excluded: chain P residue 76 ASP Chi-restraints excluded: chain P residue 108 VAL Chi-restraints excluded: chain N residue 87 HIS Chi-restraints excluded: chain K residue 11 LEU Chi-restraints excluded: chain K residue 38 ARG Chi-restraints excluded: chain K residue 72 ASP Chi-restraints excluded: chain K residue 82 MET Chi-restraints excluded: chain K residue 82 HIS Chi-restraints excluded: chain K residue 100 ASP Chi-restraints excluded: chain K residue 100 ASP Chi-restraints excluded: chain K residue 107 THR Chi-restraints excluded: chain K residue 108 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 297 random chunks: chunk 177 optimal weight: 9.9990 chunk 114 optimal weight: 3.9990 chunk 170 optimal weight: 5.9990 chunk 86 optimal weight: 9.9990 chunk 56 optimal weight: 10.0000 chunk 55 optimal weight: 9.9990 chunk 181 optimal weight: 20.0000 chunk 195 optimal weight: 6.9990 chunk 141 optimal weight: 0.7980 chunk 26 optimal weight: 7.9990 chunk 225 optimal weight: 5.9990 overall best weight: 4.7588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 195 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 328 GLN ** A 425 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 616 ASN ** L 100 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 100 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 100CASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 79 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 90 HIS J 82AHIS ** F 195 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 328 GLN ** F 425 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 100 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 82AHIS ** K 100CASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8439 moved from start: 0.5499 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.077 26313 Z= 0.464 Angle : 0.803 11.184 35712 Z= 0.393 Chirality : 0.050 0.322 4602 Planarity : 0.005 0.069 4233 Dihedral : 9.046 58.963 6939 Min Nonbonded Distance : 2.049 Molprobity Statistics. All-atom Clashscore : 16.50 Ramachandran Plot: Outliers : 0.10 % Allowed : 6.84 % Favored : 93.06 % Rotamer: Outliers : 3.88 % Allowed : 15.36 % Favored : 80.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.41 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % 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: -0.57 (0.16), residues: 2967 helix: 0.13 (0.28), residues: 351 sheet: -0.08 (0.16), residues: 1023 loop : -0.62 (0.16), residues: 1593 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP P 36 HIS 0.027 0.002 HIS J 82A PHE 0.022 0.003 PHE E 376 TYR 0.023 0.002 TYR O 79 ARG 0.008 0.001 ARG A 192 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5934 Ramachandran restraints generated. 2967 Oldfield, 0 Emsley, 2967 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5934 Ramachandran restraints generated. 2967 Oldfield, 0 Emsley, 2967 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 366 residues out of total 2604 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 101 poor density : 265 time to evaluate : 3.072 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 104 MET cc_start: 0.8828 (tpp) cc_final: 0.8396 (tpp) REVERT: A 161 MET cc_start: 0.9229 (tpp) cc_final: 0.8913 (tpt) REVERT: L 4 MET cc_start: 0.8416 (tpp) cc_final: 0.7736 (tpp) REVERT: L 79 GLN cc_start: 0.7889 (mm-40) cc_final: 0.7601 (tm-30) REVERT: D 39 LYS cc_start: 0.7749 (OUTLIER) cc_final: 0.6618 (mmtm) REVERT: D 42 LYS cc_start: 0.8837 (mmmm) cc_final: 0.8455 (pttt) REVERT: D 103 ARG cc_start: 0.8541 (ptp90) cc_final: 0.8174 (mpp-170) REVERT: C 34 MET cc_start: 0.8844 (mmm) cc_final: 0.8344 (mmm) REVERT: C 99 ARG cc_start: 0.9101 (mmm160) cc_final: 0.8887 (tpp-160) REVERT: E 434 MET cc_start: 0.8818 (ttp) cc_final: 0.8475 (ttp) REVERT: G 601 LYS cc_start: 0.8865 (pttp) cc_final: 0.8553 (pttt) REVERT: Q 55 LYS cc_start: 0.7577 (tttt) cc_final: 0.7296 (ttmt) REVERT: Q 58 VAL cc_start: 0.7602 (t) cc_final: 0.7114 (t) REVERT: Q 105 GLU cc_start: 0.6835 (mt-10) cc_final: 0.6300 (pm20) REVERT: O 72 ASP cc_start: 0.8096 (OUTLIER) cc_final: 0.7808 (m-30) REVERT: O 100 ASN cc_start: 0.8873 (OUTLIER) cc_final: 0.8661 (t0) REVERT: M 54 LEU cc_start: 0.8982 (pp) cc_final: 0.8744 (tt) REVERT: M 80 PHE cc_start: 0.9307 (m-80) cc_final: 0.9018 (m-80) REVERT: M 103 ARG cc_start: 0.8606 (mpp-170) cc_final: 0.7979 (tpp80) REVERT: J 11 LEU cc_start: 0.8757 (OUTLIER) cc_final: 0.8474 (tp) REVERT: I 601 LYS cc_start: 0.9045 (pttm) cc_final: 0.8621 (pttt) REVERT: I 649 SER cc_start: 0.9183 (m) cc_final: 0.8786 (p) REVERT: P 61 ASP cc_start: 0.8338 (p0) cc_final: 0.8058 (p0) REVERT: K 34 MET cc_start: 0.8813 (mmm) cc_final: 0.8094 (mmm) REVERT: K 100 ASP cc_start: 0.9019 (OUTLIER) cc_final: 0.8535 (t0) REVERT: K 110 THR cc_start: 0.8637 (m) cc_final: 0.8134 (p) outliers start: 101 outliers final: 86 residues processed: 338 average time/residue: 0.3655 time to fit residues: 196.8884 Evaluate side-chains 346 residues out of total 2604 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 91 poor density : 255 time to evaluate : 2.912 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 50 THR Chi-restraints excluded: chain A residue 75 VAL Chi-restraints excluded: chain A residue 137 ASN Chi-restraints excluded: chain A residue 373 THR Chi-restraints excluded: chain A residue 450 THR Chi-restraints excluded: chain A residue 475 MET Chi-restraints excluded: chain A residue 491 ILE Chi-restraints excluded: chain B residue 570 VAL Chi-restraints excluded: chain B residue 599 SER Chi-restraints excluded: chain B residue 606 THR Chi-restraints excluded: chain B residue 616 ASN Chi-restraints excluded: chain B residue 623 TRP Chi-restraints excluded: chain B residue 625 ASN Chi-restraints excluded: chain B residue 647 GLU Chi-restraints excluded: chain B residue 659 ASP Chi-restraints excluded: chain L residue 58 VAL Chi-restraints excluded: chain L residue 73 LEU Chi-restraints excluded: chain L residue 78 LEU Chi-restraints excluded: chain H residue 18 LEU Chi-restraints excluded: chain H residue 52 THR Chi-restraints excluded: chain H residue 66 ARG Chi-restraints excluded: chain H residue 73 ASP Chi-restraints excluded: chain H residue 76 ASP Chi-restraints excluded: chain H residue 100 ASN Chi-restraints excluded: chain H residue 108 VAL Chi-restraints excluded: chain D residue 11 LEU Chi-restraints excluded: chain D residue 19 ILE Chi-restraints excluded: chain D residue 33 LEU Chi-restraints excluded: chain D residue 39 LYS Chi-restraints excluded: chain D residue 47 LEU Chi-restraints excluded: chain D residue 62 PHE Chi-restraints excluded: chain D residue 87 HIS Chi-restraints excluded: chain C residue 100 ASP Chi-restraints excluded: chain C residue 107 THR Chi-restraints excluded: chain C residue 108 VAL Chi-restraints excluded: chain E residue 50 THR Chi-restraints excluded: chain E residue 75 VAL Chi-restraints excluded: chain E residue 373 THR Chi-restraints excluded: chain E residue 491 ILE Chi-restraints excluded: chain G residue 570 VAL Chi-restraints excluded: chain G residue 647 GLU Chi-restraints excluded: chain G residue 659 ASP Chi-restraints excluded: chain Q residue 19 ILE Chi-restraints excluded: chain Q residue 73 LEU Chi-restraints excluded: chain O residue 52 THR Chi-restraints excluded: chain O residue 72 ASP Chi-restraints excluded: chain O residue 73 ASP Chi-restraints excluded: chain O residue 74 LEU Chi-restraints excluded: chain O residue 76 ASP Chi-restraints excluded: chain O residue 100 ASN Chi-restraints excluded: chain O residue 108 VAL Chi-restraints excluded: chain M residue 19 ILE Chi-restraints excluded: chain M residue 47 LEU Chi-restraints excluded: chain M residue 87 HIS Chi-restraints excluded: chain J residue 11 LEU Chi-restraints excluded: chain J residue 82 HIS Chi-restraints excluded: chain J residue 100 ASP Chi-restraints excluded: chain J residue 107 THR Chi-restraints excluded: chain J residue 108 VAL Chi-restraints excluded: chain F residue 50 THR Chi-restraints excluded: chain F residue 137 ASN Chi-restraints excluded: chain F residue 328 GLN Chi-restraints excluded: chain F residue 373 THR Chi-restraints excluded: chain F residue 434 MET Chi-restraints excluded: chain F residue 450 THR Chi-restraints excluded: chain F residue 488 VAL Chi-restraints excluded: chain F residue 491 ILE Chi-restraints excluded: chain I residue 538 THR Chi-restraints excluded: chain I residue 570 VAL Chi-restraints excluded: chain I residue 623 TRP Chi-restraints excluded: chain I residue 647 GLU Chi-restraints excluded: chain I residue 659 ASP Chi-restraints excluded: chain R residue 19 ILE Chi-restraints excluded: chain R residue 47 LEU Chi-restraints excluded: chain R residue 73 LEU Chi-restraints excluded: chain P residue 73 ASP Chi-restraints excluded: chain P residue 74 LEU Chi-restraints excluded: chain P residue 76 ASP Chi-restraints excluded: chain P residue 108 VAL Chi-restraints excluded: chain N residue 87 HIS Chi-restraints excluded: chain N residue 90 HIS Chi-restraints excluded: chain K residue 11 LEU Chi-restraints excluded: chain K residue 18 LEU Chi-restraints excluded: chain K residue 38 ARG Chi-restraints excluded: chain K residue 72 ASP Chi-restraints excluded: chain K residue 82 MET Chi-restraints excluded: chain K residue 82 HIS Chi-restraints excluded: chain K residue 100 ASP Chi-restraints excluded: chain K residue 100 ASP Chi-restraints excluded: chain K residue 107 THR Chi-restraints excluded: chain K residue 108 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 297 random chunks: chunk 260 optimal weight: 30.0000 chunk 274 optimal weight: 0.9990 chunk 250 optimal weight: 1.9990 chunk 266 optimal weight: 1.9990 chunk 160 optimal weight: 10.0000 chunk 116 optimal weight: 3.9990 chunk 209 optimal weight: 2.9990 chunk 81 optimal weight: 0.9990 chunk 241 optimal weight: 20.0000 chunk 252 optimal weight: 0.0060 chunk 265 optimal weight: 0.8980 overall best weight: 0.9802 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** L 100 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 100 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 79 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 82AHIS ** F 195 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 425 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 100 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 82AHIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8351 moved from start: 0.5587 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.059 26313 Z= 0.192 Angle : 0.679 8.785 35712 Z= 0.333 Chirality : 0.047 0.319 4602 Planarity : 0.004 0.056 4233 Dihedral : 8.191 59.399 6939 Min Nonbonded Distance : 2.107 Molprobity Statistics. All-atom Clashscore : 13.29 Ramachandran Plot: Outliers : 0.10 % Allowed : 5.43 % Favored : 94.47 % Rotamer: Outliers : 3.07 % Allowed : 15.98 % Favored : 80.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.41 % 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: -0.33 (0.16), residues: 2967 helix: 0.58 (0.29), residues: 345 sheet: 0.06 (0.16), residues: 1023 loop : -0.51 (0.16), residues: 1599 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.060 0.002 TRP D 35 HIS 0.020 0.001 HIS K 82A PHE 0.015 0.002 PHE M 62 TYR 0.024 0.002 TYR O 79 ARG 0.008 0.000 ARG B 617 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5934 Ramachandran restraints generated. 2967 Oldfield, 0 Emsley, 2967 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5934 Ramachandran restraints generated. 2967 Oldfield, 0 Emsley, 2967 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 366 residues out of total 2604 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 80 poor density : 286 time to evaluate : 3.265 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: A 104 MET cc_start: 0.8654 (tpp) cc_final: 0.8184 (tpp) REVERT: A 161 MET cc_start: 0.9132 (tpp) cc_final: 0.8859 (tpt) REVERT: L 4 MET cc_start: 0.8352 (tpp) cc_final: 0.7740 (tpp) REVERT: L 79 GLN cc_start: 0.7949 (mm-40) cc_final: 0.7694 (tm-30) REVERT: H 68 THR cc_start: 0.8949 (m) cc_final: 0.8683 (p) REVERT: D 30 GLU cc_start: 0.8980 (mp0) cc_final: 0.8555 (pm20) REVERT: D 39 LYS cc_start: 0.7697 (OUTLIER) cc_final: 0.7407 (mmtm) REVERT: D 103 ARG cc_start: 0.8547 (ptp90) cc_final: 0.8176 (mpp-170) REVERT: C 34 MET cc_start: 0.8787 (mmm) cc_final: 0.8310 (mmm) REVERT: C 99 ARG cc_start: 0.9098 (mmm160) cc_final: 0.8650 (tpp-160) REVERT: E 434 MET cc_start: 0.8764 (ttp) cc_final: 0.8526 (ttp) REVERT: G 530 MET cc_start: 0.6833 (mmt) cc_final: 0.6005 (mmm) REVERT: G 601 LYS cc_start: 0.8670 (pttp) cc_final: 0.8398 (pttt) REVERT: G 649 SER cc_start: 0.8806 (m) cc_final: 0.8504 (p) REVERT: Q 55 LYS cc_start: 0.7618 (tttt) cc_final: 0.7289 (ttmt) REVERT: Q 58 VAL cc_start: 0.7600 (t) cc_final: 0.7105 (t) REVERT: Q 105 GLU cc_start: 0.7222 (mt-10) cc_final: 0.6519 (pm20) REVERT: O 72 ASP cc_start: 0.8124 (OUTLIER) cc_final: 0.7685 (m-30) REVERT: O 100 ASN cc_start: 0.8285 (OUTLIER) cc_final: 0.8027 (t0) REVERT: M 54 LEU cc_start: 0.8983 (pp) cc_final: 0.8759 (tt) REVERT: M 103 ARG cc_start: 0.8642 (mpp-170) cc_final: 0.8020 (tpp80) REVERT: J 11 LEU cc_start: 0.8693 (OUTLIER) cc_final: 0.8446 (tp) REVERT: I 601 LYS cc_start: 0.8861 (pttm) cc_final: 0.8420 (ptpp) REVERT: I 649 SER cc_start: 0.9152 (m) cc_final: 0.8734 (p) REVERT: K 34 MET cc_start: 0.8717 (mmm) cc_final: 0.8040 (mmm) REVERT: K 38 ARG cc_start: 0.7380 (OUTLIER) cc_final: 0.5994 (ttm-80) REVERT: K 100 ASN cc_start: 0.6880 (OUTLIER) cc_final: 0.6301 (t0) REVERT: K 100 ASP cc_start: 0.8834 (OUTLIER) cc_final: 0.8331 (t0) REVERT: K 107 THR cc_start: 0.7112 (OUTLIER) cc_final: 0.6657 (m) REVERT: K 110 THR cc_start: 0.8543 (m) cc_final: 0.8041 (p) outliers start: 80 outliers final: 60 residues processed: 340 average time/residue: 0.3873 time to fit residues: 205.6675 Evaluate side-chains 329 residues out of total 2604 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 68 poor density : 261 time to evaluate : 3.057 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 75 VAL Chi-restraints excluded: chain A residue 137 ASN Chi-restraints excluded: chain A residue 475 MET Chi-restraints excluded: chain A residue 491 ILE Chi-restraints excluded: chain B residue 539 VAL Chi-restraints excluded: chain B residue 599 SER Chi-restraints excluded: chain B residue 606 THR Chi-restraints excluded: chain B residue 616 ASN Chi-restraints excluded: chain B residue 623 TRP Chi-restraints excluded: chain B residue 625 ASN Chi-restraints excluded: chain B residue 659 ASP Chi-restraints excluded: chain L residue 67 SER Chi-restraints excluded: chain L residue 73 LEU Chi-restraints excluded: chain L residue 78 LEU Chi-restraints excluded: chain H residue 73 ASP Chi-restraints excluded: chain H residue 76 ASP Chi-restraints excluded: chain H residue 108 VAL Chi-restraints excluded: chain D residue 11 LEU Chi-restraints excluded: chain D residue 19 ILE Chi-restraints excluded: chain D residue 23 CYS Chi-restraints excluded: chain D residue 33 LEU Chi-restraints excluded: chain D residue 39 LYS Chi-restraints excluded: chain D residue 47 LEU Chi-restraints excluded: chain D residue 48 ILE Chi-restraints excluded: chain D residue 62 PHE Chi-restraints excluded: chain D residue 87 HIS Chi-restraints excluded: chain C residue 33 THR Chi-restraints excluded: chain C residue 100 ASP Chi-restraints excluded: chain E residue 75 VAL Chi-restraints excluded: chain E residue 491 ILE Chi-restraints excluded: chain G residue 570 VAL Chi-restraints excluded: chain G residue 647 GLU Chi-restraints excluded: chain G residue 659 ASP Chi-restraints excluded: chain Q residue 47 LEU Chi-restraints excluded: chain Q residue 73 LEU Chi-restraints excluded: chain O residue 72 ASP Chi-restraints excluded: chain O residue 73 ASP Chi-restraints excluded: chain O residue 76 ASP Chi-restraints excluded: chain O residue 100 ASN Chi-restraints excluded: chain M residue 87 HIS Chi-restraints excluded: chain J residue 11 LEU Chi-restraints excluded: chain J residue 100 ASP Chi-restraints excluded: chain J residue 107 THR Chi-restraints excluded: chain J residue 108 VAL Chi-restraints excluded: chain F residue 100 MET Chi-restraints excluded: chain F residue 137 ASN Chi-restraints excluded: chain F residue 373 THR Chi-restraints excluded: chain F residue 488 VAL Chi-restraints excluded: chain F residue 491 ILE Chi-restraints excluded: chain I residue 538 THR Chi-restraints excluded: chain I residue 570 VAL Chi-restraints excluded: chain I residue 599 SER Chi-restraints excluded: chain I residue 623 TRP Chi-restraints excluded: chain I residue 647 GLU Chi-restraints excluded: chain I residue 659 ASP Chi-restraints excluded: chain R residue 73 LEU Chi-restraints excluded: chain P residue 73 ASP Chi-restraints excluded: chain P residue 74 LEU Chi-restraints excluded: chain P residue 76 ASP Chi-restraints excluded: chain P residue 108 VAL Chi-restraints excluded: chain N residue 87 HIS Chi-restraints excluded: chain K residue 11 LEU Chi-restraints excluded: chain K residue 38 ARG Chi-restraints excluded: chain K residue 82 HIS Chi-restraints excluded: chain K residue 100 ASP Chi-restraints excluded: chain K residue 100 ASN Chi-restraints excluded: chain K residue 100 ASP Chi-restraints excluded: chain K residue 107 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 297 random chunks: chunk 175 optimal weight: 10.0000 chunk 282 optimal weight: 30.0000 chunk 172 optimal weight: 0.7980 chunk 133 optimal weight: 2.9990 chunk 196 optimal weight: 9.9990 chunk 295 optimal weight: 9.9990 chunk 272 optimal weight: 8.9990 chunk 235 optimal weight: 0.5980 chunk 24 optimal weight: 0.8980 chunk 181 optimal weight: 30.0000 chunk 144 optimal weight: 2.9990 overall best weight: 1.6584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** L 100 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 130 GLN ** Q 100 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 79 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 195 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 425 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 616 ASN ** R 100 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 82AHIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8362 moved from start: 0.5689 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.056 26313 Z= 0.226 Angle : 0.681 11.305 35712 Z= 0.333 Chirality : 0.046 0.316 4602 Planarity : 0.004 0.058 4233 Dihedral : 7.813 59.870 6939 Min Nonbonded Distance : 2.096 Molprobity Statistics. All-atom Clashscore : 12.92 Ramachandran Plot: Outliers : 0.10 % Allowed : 5.46 % Favored : 94.44 % Rotamer: Outliers : 2.69 % Allowed : 16.55 % Favored : 80.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.41 % 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: -0.32 (0.16), residues: 2967 helix: 0.64 (0.29), residues: 351 sheet: 0.05 (0.16), residues: 1023 loop : -0.51 (0.16), residues: 1593 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.093 0.002 TRP M 35 HIS 0.008 0.001 HIS K 82A PHE 0.017 0.002 PHE M 62 TYR 0.017 0.001 TYR Q 91 ARG 0.016 0.001 ARG C 83 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5934 Ramachandran restraints generated. 2967 Oldfield, 0 Emsley, 2967 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5934 Ramachandran restraints generated. 2967 Oldfield, 0 Emsley, 2967 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 345 residues out of total 2604 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 70 poor density : 275 time to evaluate : 3.183 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 104 MET cc_start: 0.8628 (tpp) cc_final: 0.8155 (tpp) REVERT: A 161 MET cc_start: 0.9203 (tpp) cc_final: 0.8896 (tpt) REVERT: B 530 MET cc_start: 0.7709 (mtm) cc_final: 0.7211 (mtm) REVERT: L 4 MET cc_start: 0.8376 (tpp) cc_final: 0.7752 (tpp) REVERT: L 55 LYS cc_start: 0.8012 (tttt) cc_final: 0.7203 (ttpt) REVERT: L 79 GLN cc_start: 0.8033 (mm-40) cc_final: 0.7778 (tm-30) REVERT: H 68 THR cc_start: 0.8938 (m) cc_final: 0.8702 (p) REVERT: D 30 GLU cc_start: 0.8979 (mp0) cc_final: 0.8548 (pm20) REVERT: D 39 LYS cc_start: 0.7741 (OUTLIER) cc_final: 0.6559 (mmtm) REVERT: D 42 LYS cc_start: 0.8914 (mmmm) cc_final: 0.8578 (pttt) REVERT: C 34 MET cc_start: 0.8758 (mmm) cc_final: 0.8298 (mmm) REVERT: C 82 MET cc_start: 0.7212 (ptp) cc_final: 0.7002 (ptp) REVERT: C 99 ARG cc_start: 0.9101 (mmm160) cc_final: 0.8665 (tpp-160) REVERT: E 434 MET cc_start: 0.8763 (ttp) cc_final: 0.8503 (ttp) REVERT: G 530 MET cc_start: 0.6580 (mmt) cc_final: 0.5929 (mmm) REVERT: G 601 LYS cc_start: 0.8713 (pttp) cc_final: 0.8406 (pttt) REVERT: G 649 SER cc_start: 0.8848 (m) cc_final: 0.8531 (p) REVERT: Q 55 LYS cc_start: 0.7463 (tttt) cc_final: 0.7058 (ttmt) REVERT: Q 58 VAL cc_start: 0.7581 (t) cc_final: 0.7094 (t) REVERT: Q 105 GLU cc_start: 0.6797 (mt-10) cc_final: 0.6259 (pm20) REVERT: O 100 ASN cc_start: 0.8498 (OUTLIER) cc_final: 0.8261 (t0) REVERT: M 54 LEU cc_start: 0.9014 (pp) cc_final: 0.8794 (tt) REVERT: M 103 ARG cc_start: 0.8647 (mpp-170) cc_final: 0.8038 (tpp80) REVERT: J 11 LEU cc_start: 0.8664 (OUTLIER) cc_final: 0.8443 (tp) REVERT: I 601 LYS cc_start: 0.8895 (pttm) cc_final: 0.8473 (ptpp) REVERT: I 649 SER cc_start: 0.9179 (m) cc_final: 0.8767 (p) REVERT: R 4 MET cc_start: 0.8152 (ttt) cc_final: 0.7773 (tmm) REVERT: K 34 MET cc_start: 0.8753 (mmm) cc_final: 0.8117 (mmm) REVERT: K 38 ARG cc_start: 0.7263 (OUTLIER) cc_final: 0.5736 (ttm-80) REVERT: K 100 ASN cc_start: 0.7063 (OUTLIER) cc_final: 0.6551 (t0) REVERT: K 100 ASP cc_start: 0.8816 (OUTLIER) cc_final: 0.8310 (t0) REVERT: K 107 THR cc_start: 0.7154 (OUTLIER) cc_final: 0.6942 (m) REVERT: K 110 THR cc_start: 0.8538 (m) cc_final: 0.8029 (p) outliers start: 70 outliers final: 60 residues processed: 326 average time/residue: 0.3712 time to fit residues: 191.9628 Evaluate side-chains 323 residues out of total 2604 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 67 poor density : 256 time to evaluate : 3.181 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 75 VAL Chi-restraints excluded: chain A residue 137 ASN Chi-restraints excluded: chain A residue 475 MET Chi-restraints excluded: chain A residue 491 ILE Chi-restraints excluded: chain B residue 539 VAL Chi-restraints excluded: chain B residue 570 VAL Chi-restraints excluded: chain B residue 599 SER Chi-restraints excluded: chain B residue 606 THR Chi-restraints excluded: chain B residue 623 TRP Chi-restraints excluded: chain B residue 625 ASN Chi-restraints excluded: chain B residue 659 ASP Chi-restraints excluded: chain L residue 67 SER Chi-restraints excluded: chain L residue 73 LEU Chi-restraints excluded: chain L residue 78 LEU Chi-restraints excluded: chain H residue 66 ARG Chi-restraints excluded: chain H residue 73 ASP Chi-restraints excluded: chain H residue 76 ASP Chi-restraints excluded: chain H residue 108 VAL Chi-restraints excluded: chain D residue 11 LEU Chi-restraints excluded: chain D residue 19 ILE Chi-restraints excluded: chain D residue 23 CYS Chi-restraints excluded: chain D residue 33 LEU Chi-restraints excluded: chain D residue 39 LYS Chi-restraints excluded: chain D residue 47 LEU Chi-restraints excluded: chain D residue 62 PHE Chi-restraints excluded: chain D residue 87 HIS Chi-restraints excluded: chain C residue 33 THR Chi-restraints excluded: chain C residue 100 ASP Chi-restraints excluded: chain E residue 75 VAL Chi-restraints excluded: chain E residue 373 THR Chi-restraints excluded: chain E residue 491 ILE Chi-restraints excluded: chain G residue 570 VAL Chi-restraints excluded: chain G residue 647 GLU Chi-restraints excluded: chain G residue 659 ASP Chi-restraints excluded: chain Q residue 47 LEU Chi-restraints excluded: chain Q residue 73 LEU Chi-restraints excluded: chain O residue 34 MET Chi-restraints excluded: chain O residue 73 ASP Chi-restraints excluded: chain O residue 76 ASP Chi-restraints excluded: chain O residue 100 ASN Chi-restraints excluded: chain O residue 108 VAL Chi-restraints excluded: chain M residue 87 HIS Chi-restraints excluded: chain J residue 11 LEU Chi-restraints excluded: chain J residue 100 ASP Chi-restraints excluded: chain J residue 108 VAL Chi-restraints excluded: chain F residue 137 ASN Chi-restraints excluded: chain F residue 373 THR Chi-restraints excluded: chain F residue 488 VAL Chi-restraints excluded: chain F residue 491 ILE Chi-restraints excluded: chain I residue 538 THR Chi-restraints excluded: chain I residue 570 VAL Chi-restraints excluded: chain I residue 623 TRP Chi-restraints excluded: chain I residue 647 GLU Chi-restraints excluded: chain I residue 659 ASP Chi-restraints excluded: chain R residue 73 LEU Chi-restraints excluded: chain P residue 73 ASP Chi-restraints excluded: chain P residue 74 LEU Chi-restraints excluded: chain P residue 76 ASP Chi-restraints excluded: chain P residue 108 VAL Chi-restraints excluded: chain N residue 87 HIS Chi-restraints excluded: chain K residue 11 LEU Chi-restraints excluded: chain K residue 38 ARG Chi-restraints excluded: chain K residue 82 HIS Chi-restraints excluded: chain K residue 100 ASP Chi-restraints excluded: chain K residue 100 ASN Chi-restraints excluded: chain K residue 100 ASP Chi-restraints excluded: chain K residue 107 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 297 random chunks: chunk 187 optimal weight: 0.0870 chunk 250 optimal weight: 10.0000 chunk 72 optimal weight: 2.9990 chunk 217 optimal weight: 0.8980 chunk 34 optimal weight: 5.9990 chunk 65 optimal weight: 8.9990 chunk 235 optimal weight: 0.9980 chunk 98 optimal weight: 8.9990 chunk 242 optimal weight: 8.9990 chunk 29 optimal weight: 0.6980 chunk 43 optimal weight: 9.9990 overall best weight: 1.1360 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** L 100 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 100 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 79 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 195 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 425 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 89 GLN ** R 100 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3646 r_free = 0.3646 target = 0.084549 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3143 r_free = 0.3143 target = 0.059739 restraints weight = 91384.136| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3197 r_free = 0.3197 target = 0.062117 restraints weight = 45213.481| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3232 r_free = 0.3232 target = 0.063661 restraints weight = 30298.213| |-----------------------------------------------------------------------------| r_work (final): 0.3214 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7933 moved from start: 0.5786 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.055 26313 Z= 0.194 Angle : 0.670 9.980 35712 Z= 0.327 Chirality : 0.046 0.309 4602 Planarity : 0.004 0.058 4233 Dihedral : 7.464 59.350 6939 Min Nonbonded Distance : 2.095 Molprobity Statistics. All-atom Clashscore : 12.50 Ramachandran Plot: Outliers : 0.10 % Allowed : 5.43 % Favored : 94.47 % Rotamer: Outliers : 2.42 % Allowed : 16.74 % Favored : 80.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.41 % 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: -0.27 (0.16), residues: 2967 helix: 0.78 (0.29), residues: 348 sheet: 0.08 (0.16), residues: 1023 loop : -0.50 (0.16), residues: 1596 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.079 0.002 TRP M 35 HIS 0.010 0.001 HIS K 82A PHE 0.017 0.001 PHE M 62 TYR 0.017 0.001 TYR R 49 ARG 0.014 0.000 ARG C 83 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5273.32 seconds wall clock time: 97 minutes 51.76 seconds (5871.76 seconds total)