Starting phenix.real_space_refine on Mon Feb 19 04:53:34 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5vn3_8713/02_2024/5vn3_8713.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5vn3_8713/02_2024/5vn3_8713.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.7 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5vn3_8713/02_2024/5vn3_8713.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5vn3_8713/02_2024/5vn3_8713.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5vn3_8713/02_2024/5vn3_8713.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5vn3_8713/02_2024/5vn3_8713.pdb" } resolution = 3.7 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.010 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 123 5.16 5 C 14808 2.51 5 N 3936 2.21 5 O 4860 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "L TYR 49": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L TYR 96": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 522": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G TYR 61": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 98": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H PHE 91": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N TYR 49": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N TYR 96": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 522": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I TYR 61": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 98": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K PHE 91": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "O TYR 49": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "O TYR 96": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 522": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J TYR 61": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 98": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M PHE 91": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.06s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 23727 Number of models: 1 Model: "" Number of chains: 54 Chain: "L" Number of atoms: 849 Number of conformers: 1 Conformer: "" Number of residues, atoms: 110, 849 Classifications: {'peptide': 110} Link IDs: {'PCIS': 1, 'PTRANS': 6, 'TRANS': 102} Chain: "A" Number of atoms: 1090 Number of conformers: 1 Conformer: "" Number of residues, atoms: 136, 1090 Classifications: {'peptide': 136} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 134} Chain breaks: 1 Chain: "G" Number of atoms: 3050 Number of conformers: 1 Conformer: "" Number of residues, atoms: 389, 3050 Classifications: {'peptide': 389} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 21, 'TRANS': 367} Chain breaks: 3 Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 1 Chain: "C" Number of atoms: 1370 Number of conformers: 1 Conformer: "" Number of residues, atoms: 176, 1370 Classifications: {'peptide': 176} Link IDs: {'PTRANS': 6, 'TRANS': 169} Chain: "H" Number of atoms: 987 Number of conformers: 1 Conformer: "" Number of residues, atoms: 127, 987 Classifications: {'peptide': 127} Link IDs: {'PTRANS': 3, 'TRANS': 123} Chain: "N" Number of atoms: 849 Number of conformers: 1 Conformer: "" Number of residues, atoms: 110, 849 Classifications: {'peptide': 110} Link IDs: {'PCIS': 1, 'PTRANS': 6, 'TRANS': 102} Chain: "B" Number of atoms: 1090 Number of conformers: 1 Conformer: "" Number of residues, atoms: 136, 1090 Classifications: {'peptide': 136} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 134} Chain breaks: 1 Chain: "I" Number of atoms: 3050 Number of conformers: 1 Conformer: "" Number of residues, atoms: 389, 3050 Classifications: {'peptide': 389} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 21, 'TRANS': 367} Chain breaks: 3 Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 1 Chain: "E" Number of atoms: 1370 Number of conformers: 1 Conformer: "" Number of residues, atoms: 176, 1370 Classifications: {'peptide': 176} Link IDs: {'PTRANS': 6, 'TRANS': 169} Chain: "K" Number of atoms: 987 Number of conformers: 1 Conformer: "" Number of residues, atoms: 127, 987 Classifications: {'peptide': 127} Link IDs: {'PTRANS': 3, 'TRANS': 123} Chain: "O" Number of atoms: 849 Number of conformers: 1 Conformer: "" Number of residues, atoms: 110, 849 Classifications: {'peptide': 110} Link IDs: {'PCIS': 1, 'PTRANS': 6, 'TRANS': 102} Chain: "D" Number of atoms: 1090 Number of conformers: 1 Conformer: "" Number of residues, atoms: 136, 1090 Classifications: {'peptide': 136} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 134} Chain breaks: 1 Chain: "J" Number of atoms: 3050 Number of conformers: 1 Conformer: "" Number of residues, atoms: 389, 3050 Classifications: {'peptide': 389} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 21, 'TRANS': 367} Chain breaks: 3 Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 1 Chain: "F" Number of atoms: 1370 Number of conformers: 1 Conformer: "" Number of residues, atoms: 176, 1370 Classifications: {'peptide': 176} Link IDs: {'PTRANS': 6, 'TRANS': 169} Chain: "M" Number of atoms: 987 Number of conformers: 1 Conformer: "" Number of residues, atoms: 127, 987 Classifications: {'peptide': 127} Link IDs: {'PTRANS': 3, 'TRANS': 123} Chain: "P" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "Q" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "R" Number of atoms: 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: 50 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 50 Unusual residues: {'BMA': 1, 'MAN': 1, 'NAG': 2} 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: "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: 50 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 50 Unusual residues: {'BMA': 1, 'MAN': 1, 'NAG': 2} 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: "W" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "X" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "Y" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "Z" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "a" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "b" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "c" 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: "d" Number of atoms: 50 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 50 Unusual residues: {'BMA': 1, 'MAN': 1, 'NAG': 2} 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: "e" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "f" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "g" Number of atoms: 50 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 50 Unusual residues: {'BMA': 1, 'MAN': 1, 'NAG': 2} 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: "h" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "i" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "j" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "k" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "l" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "m" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "n" Number of atoms: 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: "o" Number of atoms: 50 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 50 Unusual residues: {'BMA': 1, 'MAN': 1, 'NAG': 2} 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: "p" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "q" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "r" Number of atoms: 50 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 50 Unusual residues: {'BMA': 1, 'MAN': 1, 'NAG': 2} 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: "s" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "t" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "u" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "v" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "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: "G" 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: 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: 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: "D" 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: "J" 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 Time building chain proxies: 13.16, per 1000 atoms: 0.55 Number of scatterers: 23727 At special positions: 0 Unit cell: (192.57, 188.64, 146.72, 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 123 16.00 O 4860 8.00 N 3936 7.00 C 14808 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=42, symmetry=0 Simple disulfide: pdb=" SG CYS L 23 " - pdb=" SG CYS L 88 " distance=2.04 Simple disulfide: pdb=" SG CYS A 598 " - pdb=" SG CYS A 604 " distance=2.02 Simple disulfide: pdb=" SG CYS A 605 " - pdb=" SG CYS G 501 " distance=1.98 Simple disulfide: pdb=" SG CYS G 54 " - pdb=" SG CYS G 74 " distance=2.03 Simple disulfide: pdb=" SG CYS G 119 " - pdb=" SG CYS G 205 " distance=2.03 Simple disulfide: pdb=" SG CYS G 126 " - pdb=" SG CYS G 196 " distance=2.03 Simple disulfide: pdb=" SG CYS G 218 " - pdb=" SG CYS G 247 " distance=2.02 Simple disulfide: pdb=" SG CYS G 228 " - pdb=" SG CYS G 239 " distance=2.02 Simple disulfide: pdb=" SG CYS G 296 " - pdb=" SG CYS G 331 " distance=2.01 Simple disulfide: pdb=" SG CYS G 378 " - pdb=" SG CYS G 445 " distance=2.02 Simple disulfide: pdb=" SG CYS G 385 " - pdb=" SG CYS G 418 " distance=2.02 Simple disulfide: pdb=" SG CYS C 16 " - pdb=" SG CYS C 84 " distance=2.04 Simple disulfide: pdb=" SG CYS C 130 " - pdb=" SG CYS C 159 " distance=2.04 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 92 " distance=2.02 Simple disulfide: pdb=" SG CYS N 23 " - pdb=" SG CYS N 88 " distance=2.04 Simple disulfide: pdb=" SG CYS B 598 " - pdb=" SG CYS B 604 " distance=2.02 Simple disulfide: pdb=" SG CYS B 605 " - pdb=" SG CYS I 501 " distance=2.04 Simple disulfide: pdb=" SG CYS I 54 " - pdb=" SG CYS I 74 " distance=2.03 Simple disulfide: pdb=" SG CYS I 119 " - pdb=" SG CYS I 205 " distance=2.03 Simple disulfide: pdb=" SG CYS I 126 " - pdb=" SG CYS I 196 " distance=2.03 Simple disulfide: pdb=" SG CYS I 218 " - pdb=" SG CYS I 247 " distance=2.02 Simple disulfide: pdb=" SG CYS I 228 " - pdb=" SG CYS I 239 " distance=2.02 Simple disulfide: pdb=" SG CYS I 296 " - pdb=" SG CYS I 331 " distance=2.01 Simple disulfide: pdb=" SG CYS I 378 " - pdb=" SG CYS I 445 " distance=2.02 Simple disulfide: pdb=" SG CYS I 385 " - pdb=" SG CYS I 418 " distance=2.02 Simple disulfide: pdb=" SG CYS E 16 " - pdb=" SG CYS E 84 " distance=2.04 Simple disulfide: pdb=" SG CYS E 130 " - pdb=" SG CYS E 159 " distance=2.04 Simple disulfide: pdb=" SG CYS K 22 " - pdb=" SG CYS K 92 " distance=2.02 Simple disulfide: pdb=" SG CYS O 23 " - pdb=" SG CYS O 88 " distance=2.04 Simple disulfide: pdb=" SG CYS D 598 " - pdb=" SG CYS D 604 " distance=2.02 Simple disulfide: pdb=" SG CYS D 605 " - pdb=" SG CYS J 501 " distance=2.09 Simple disulfide: pdb=" SG CYS J 54 " - pdb=" SG CYS J 74 " distance=2.03 Simple disulfide: pdb=" SG CYS J 119 " - pdb=" SG CYS J 205 " distance=2.03 Simple disulfide: pdb=" SG CYS J 126 " - pdb=" SG CYS J 196 " distance=2.03 Simple disulfide: pdb=" SG CYS J 218 " - pdb=" SG CYS J 247 " distance=2.02 Simple disulfide: pdb=" SG CYS J 228 " - pdb=" SG CYS J 239 " distance=2.02 Simple disulfide: pdb=" SG CYS J 296 " - pdb=" SG CYS J 331 " distance=2.01 Simple disulfide: pdb=" SG CYS J 378 " - pdb=" SG CYS J 445 " distance=2.02 Simple disulfide: pdb=" SG CYS J 385 " - pdb=" SG CYS J 418 " distance=2.02 Simple disulfide: pdb=" SG CYS F 16 " - pdb=" SG CYS F 84 " distance=2.04 Simple disulfide: pdb=" SG CYS F 130 " - pdb=" SG CYS F 159 " distance=2.04 Simple disulfide: pdb=" SG CYS M 22 " - pdb=" SG CYS M 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=7, symmetry=0 Links applied ALPHA1-2 " MAN R 4 " - " MAN R 5 " " MAN R 5 " - " MAN R 6 " " MAN c 4 " - " MAN c 5 " " MAN c 5 " - " MAN c 6 " " MAN n 4 " - " MAN n 5 " " MAN n 5 " - " MAN n 6 " ALPHA1-3 " BMA R 3 " - " MAN R 4 " " BMA V 3 " - " MAN V 4 " " BMA c 3 " - " MAN c 4 " " BMA g 3 " - " MAN g 4 " " BMA n 3 " - " MAN n 4 " " BMA r 3 " - " MAN r 4 " ALPHA1-6 " BMA R 3 " - " MAN R 7 " " BMA S 3 " - " MAN S 4 " " BMA c 3 " - " MAN c 7 " " BMA d 3 " - " MAN d 4 " " BMA n 3 " - " MAN n 7 " " BMA o 3 " - " MAN o 4 " BETA1-4 " NAG P 1 " - " NAG P 2 " " 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 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 Z 1 " - " NAG Z 2 " " NAG Z 2 " - " BMA Z 3 " " NAG a 1 " - " NAG a 2 " " NAG b 1 " - " NAG b 2 " " NAG b 2 " - " BMA b 3 " " NAG c 1 " - " NAG c 2 " " NAG c 2 " - " BMA c 3 " " NAG d 1 " - " NAG d 2 " " NAG d 2 " - " BMA d 3 " " NAG e 1 " - " NAG e 2 " " NAG f 1 " - " NAG f 2 " " 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 k 2 " - " BMA k 3 " " NAG l 1 " - " NAG l 2 " " NAG m 1 " - " NAG m 2 " " NAG m 2 " - " BMA m 3 " " NAG n 1 " - " NAG n 2 " " NAG n 2 " - " BMA n 3 " " NAG o 1 " - " NAG o 2 " " NAG o 2 " - " BMA o 3 " " NAG p 1 " - " NAG p 2 " " NAG q 1 " - " NAG q 2 " " NAG r 1 " - " NAG r 2 " " NAG r 2 " - " BMA r 3 " " 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 v 1 " - " NAG v 2 " " NAG v 2 " - " BMA v 3 " NAG-ASN " NAG A 701 " - " ASN A 611 " " NAG A 702 " - " ASN A 616 " " NAG A 703 " - " ASN A 625 " " NAG A 704 " - " ASN A 637 " " NAG B 701 " - " ASN B 611 " " NAG B 702 " - " ASN B 616 " " NAG B 703 " - " ASN B 625 " " NAG B 704 " - " ASN B 637 " " NAG D 701 " - " ASN D 611 " " NAG D 702 " - " ASN D 616 " " NAG D 703 " - " ASN D 625 " " NAG D 704 " - " ASN D 637 " " NAG G 601 " - " ASN G 88 " " NAG G 622 " - " ASN G 339 " " NAG G 623 " - " ASN G 355 " " NAG G 631 " - " ASN G 397 " " NAG I 601 " - " ASN I 88 " " NAG I 622 " - " ASN I 339 " " NAG I 623 " - " ASN I 355 " " NAG I 631 " - " ASN I 397 " " NAG J 601 " - " ASN J 88 " " NAG J 622 " - " ASN J 339 " " NAG J 623 " - " ASN J 355 " " NAG J 631 " - " ASN J 397 " " NAG P 1 " - " ASN G 234 " " NAG Q 1 " - " ASN G 241 " " NAG R 1 " - " ASN G 262 " " NAG S 1 " - " ASN G 276 " " NAG T 1 " - " ASN G 295 " " NAG U 1 " - " ASN G 332 " " NAG V 1 " - " ASN G 362 " " NAG W 1 " - " ASN G 386 " " NAG X 1 " - " ASN G 413 " " NAG Y 1 " - " ASN G 448 " " NAG Z 1 " - " ASN G 392 " " NAG a 1 " - " ASN I 234 " " NAG b 1 " - " ASN I 241 " " NAG c 1 " - " ASN I 262 " " NAG d 1 " - " ASN I 276 " " NAG e 1 " - " ASN I 295 " " NAG f 1 " - " ASN I 332 " " NAG g 1 " - " ASN I 362 " " NAG h 1 " - " ASN I 386 " " NAG i 1 " - " ASN I 413 " " NAG j 1 " - " ASN I 448 " " NAG k 1 " - " ASN I 392 " " NAG l 1 " - " ASN J 234 " " NAG m 1 " - " ASN J 241 " " NAG n 1 " - " ASN J 262 " " NAG o 1 " - " ASN J 276 " " NAG p 1 " - " ASN J 295 " " NAG q 1 " - " ASN J 332 " " NAG r 1 " - " ASN J 362 " " NAG s 1 " - " ASN J 386 " " NAG t 1 " - " ASN J 413 " " NAG u 1 " - " ASN J 448 " " NAG v 1 " - " ASN J 392 " Number of additional bonds: simple=7, symmetry=0 Coordination: Other bonds: Time building additional restraints: 11.75 Conformation dependent library (CDL) restraints added in 4.2 seconds 5520 Ramachandran restraints generated. 2760 Oldfield, 0 Emsley, 2760 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5220 Finding SS restraints... Secondary structure from input PDB file: 48 helices and 54 sheets defined 17.7% alpha, 23.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.72 Creating SS restraints... Processing helix chain 'A' and resid 529 through 547 removed outlier: 3.820A pdb=" N THR A 538 " --> pdb=" O SER A 534 " (cutoff:3.500A) removed outlier: 3.854A pdb=" N VAL A 539 " --> pdb=" O MET A 535 " (cutoff:3.500A) Processing helix chain 'A' and resid 565 through 568 Processing helix chain 'A' and resid 569 through 593 removed outlier: 3.718A pdb=" N LEU A 576 " --> pdb=" O GLY A 572 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N ALA A 578 " --> pdb=" O LYS A 574 " (cutoff:3.500A) removed outlier: 3.833A pdb=" N ARG A 579 " --> pdb=" O GLN A 575 " (cutoff:3.500A) Processing helix chain 'A' and resid 594 through 596 No H-bonds generated for 'chain 'A' and resid 594 through 596' Processing helix chain 'A' and resid 618 through 625 removed outlier: 3.768A pdb=" N TRP A 623 " --> pdb=" O ILE A 619 " (cutoff:3.500A) Processing helix chain 'A' and resid 627 through 635 removed outlier: 3.733A pdb=" N LYS A 633 " --> pdb=" O MET A 629 " (cutoff:3.500A) Processing helix chain 'A' and resid 641 through 662 removed outlier: 3.580A pdb=" N GLU A 647 " --> pdb=" O TYR A 643 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N LEU A 660 " --> pdb=" O ASN A 656 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N GLU A 662 " --> pdb=" O GLN A 658 " (cutoff:3.500A) Processing helix chain 'G' and resid 64 through 73 Processing helix chain 'G' and resid 100 through 113 removed outlier: 3.803A pdb=" N GLU G 106 " --> pdb=" O GLU G 102 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N ILE G 109 " --> pdb=" O HIS G 105 " (cutoff:3.500A) removed outlier: 3.996A pdb=" N SER G 110 " --> pdb=" O GLU G 106 " (cutoff:3.500A) removed outlier: 3.967A pdb=" N LEU G 111 " --> pdb=" O ASP G 107 " (cutoff:3.500A) Processing helix chain 'G' and resid 334 through 350 removed outlier: 4.822A pdb=" N GLU G 340 " --> pdb=" O ALA G 336 " (cutoff:3.500A) removed outlier: 3.799A pdb=" N THR G 341 " --> pdb=" O ARG G 337 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N ALA G 347 " --> pdb=" O GLY G 343 " (cutoff:3.500A) Processing helix chain 'G' and resid 368 through 373 removed outlier: 3.821A pdb=" N THR G 373 " --> pdb=" O PRO G 369 " (cutoff:3.500A) Processing helix chain 'G' and resid 387 through 392 removed outlier: 3.726A pdb=" N PHE G 391 " --> pdb=" O THR G 387 " (cutoff:3.500A) Processing helix chain 'G' and resid 474 through 481 removed outlier: 3.501A pdb=" N ASN G 478 " --> pdb=" O ASN G 474 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N SER G 481 " --> pdb=" O ASP G 477 " (cutoff:3.500A) Processing helix chain 'C' and resid 58 through 62 Processing helix chain 'C' and resid 75 through 79 Processing helix chain 'H' and resid 28 through 32 removed outlier: 4.276A pdb=" N TYR H 32 " --> pdb=" O PHE H 29 " (cutoff:3.500A) Processing helix chain 'B' and resid 529 through 547 removed outlier: 3.820A pdb=" N THR B 538 " --> pdb=" O SER B 534 " (cutoff:3.500A) removed outlier: 3.853A pdb=" N VAL B 539 " --> pdb=" O MET B 535 " (cutoff:3.500A) Processing helix chain 'B' and resid 565 through 568 Processing helix chain 'B' and resid 569 through 593 removed outlier: 3.718A pdb=" N LEU B 576 " --> pdb=" O GLY B 572 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N ALA B 578 " --> pdb=" O LYS B 574 " (cutoff:3.500A) removed outlier: 3.833A pdb=" N ARG B 579 " --> pdb=" O GLN B 575 " (cutoff:3.500A) Processing helix chain 'B' and resid 594 through 596 No H-bonds generated for 'chain 'B' and resid 594 through 596' Processing helix chain 'B' and resid 618 through 625 removed outlier: 3.768A pdb=" N TRP B 623 " --> pdb=" O ILE B 619 " (cutoff:3.500A) Processing helix chain 'B' and resid 627 through 635 removed outlier: 3.734A pdb=" N LYS B 633 " --> pdb=" O MET B 629 " (cutoff:3.500A) Processing helix chain 'B' and resid 641 through 662 removed outlier: 3.581A pdb=" N GLU B 647 " --> pdb=" O TYR B 643 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N LEU B 660 " --> pdb=" O ASN B 656 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N GLU B 662 " --> pdb=" O GLN B 658 " (cutoff:3.500A) Processing helix chain 'I' and resid 64 through 73 Processing helix chain 'I' and resid 100 through 113 removed outlier: 3.803A pdb=" N GLU I 106 " --> pdb=" O GLU I 102 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N ILE I 109 " --> pdb=" O HIS I 105 " (cutoff:3.500A) removed outlier: 3.996A pdb=" N SER I 110 " --> pdb=" O GLU I 106 " (cutoff:3.500A) removed outlier: 3.967A pdb=" N LEU I 111 " --> pdb=" O ASP I 107 " (cutoff:3.500A) Processing helix chain 'I' and resid 334 through 350 removed outlier: 4.822A pdb=" N GLU I 340 " --> pdb=" O ALA I 336 " (cutoff:3.500A) removed outlier: 3.799A pdb=" N THR I 341 " --> pdb=" O ARG I 337 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N ALA I 347 " --> pdb=" O GLY I 343 " (cutoff:3.500A) Processing helix chain 'I' and resid 368 through 373 removed outlier: 3.822A pdb=" N THR I 373 " --> pdb=" O PRO I 369 " (cutoff:3.500A) Processing helix chain 'I' and resid 387 through 392 removed outlier: 3.726A pdb=" N PHE I 391 " --> pdb=" O THR I 387 " (cutoff:3.500A) Processing helix chain 'I' and resid 474 through 481 removed outlier: 3.500A pdb=" N ASN I 478 " --> pdb=" O ASN I 474 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N SER I 481 " --> pdb=" O ASP I 477 " (cutoff:3.500A) Processing helix chain 'E' and resid 58 through 62 Processing helix chain 'E' and resid 75 through 79 Processing helix chain 'K' and resid 28 through 32 removed outlier: 4.276A pdb=" N TYR K 32 " --> pdb=" O PHE K 29 " (cutoff:3.500A) Processing helix chain 'D' and resid 529 through 547 removed outlier: 3.821A pdb=" N THR D 538 " --> pdb=" O SER D 534 " (cutoff:3.500A) removed outlier: 3.855A pdb=" N VAL D 539 " --> pdb=" O MET D 535 " (cutoff:3.500A) Processing helix chain 'D' and resid 565 through 568 Processing helix chain 'D' and resid 569 through 593 removed outlier: 3.719A pdb=" N LEU D 576 " --> pdb=" O GLY D 572 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N ALA D 578 " --> pdb=" O LYS D 574 " (cutoff:3.500A) removed outlier: 3.834A pdb=" N ARG D 579 " --> pdb=" O GLN D 575 " (cutoff:3.500A) Processing helix chain 'D' and resid 594 through 596 No H-bonds generated for 'chain 'D' and resid 594 through 596' Processing helix chain 'D' and resid 618 through 625 removed outlier: 3.768A pdb=" N TRP D 623 " --> pdb=" O ILE D 619 " (cutoff:3.500A) Processing helix chain 'D' and resid 627 through 635 removed outlier: 3.734A pdb=" N LYS D 633 " --> pdb=" O MET D 629 " (cutoff:3.500A) Processing helix chain 'D' and resid 641 through 662 removed outlier: 3.581A pdb=" N GLU D 647 " --> pdb=" O TYR D 643 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N LEU D 660 " --> pdb=" O ASN D 656 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N GLU D 662 " --> pdb=" O GLN D 658 " (cutoff:3.500A) Processing helix chain 'J' and resid 64 through 73 Processing helix chain 'J' and resid 100 through 113 removed outlier: 3.803A pdb=" N GLU J 106 " --> pdb=" O GLU J 102 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N ILE J 109 " --> pdb=" O HIS J 105 " (cutoff:3.500A) removed outlier: 3.995A pdb=" N SER J 110 " --> pdb=" O GLU J 106 " (cutoff:3.500A) removed outlier: 3.967A pdb=" N LEU J 111 " --> pdb=" O ASP J 107 " (cutoff:3.500A) Processing helix chain 'J' and resid 334 through 350 removed outlier: 4.822A pdb=" N GLU J 340 " --> pdb=" O ALA J 336 " (cutoff:3.500A) removed outlier: 3.798A pdb=" N THR J 341 " --> pdb=" O ARG J 337 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N ALA J 347 " --> pdb=" O GLY J 343 " (cutoff:3.500A) Processing helix chain 'J' and resid 368 through 373 removed outlier: 3.821A pdb=" N THR J 373 " --> pdb=" O PRO J 369 " (cutoff:3.500A) Processing helix chain 'J' and resid 387 through 392 removed outlier: 3.726A pdb=" N PHE J 391 " --> pdb=" O THR J 387 " (cutoff:3.500A) Processing helix chain 'J' and resid 474 through 481 removed outlier: 3.500A pdb=" N ASN J 478 " --> pdb=" O ASN J 474 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N SER J 481 " --> pdb=" O ASP J 477 " (cutoff:3.500A) Processing helix chain 'F' and resid 58 through 62 Processing helix chain 'F' and resid 75 through 79 Processing helix chain 'M' and resid 28 through 32 removed outlier: 4.276A pdb=" N TYR M 32 " --> pdb=" O PHE M 29 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'L' and resid 4 through 6 removed outlier: 3.585A pdb=" N ALA L 25 " --> pdb=" O ALA L 69 " (cutoff:3.500A) removed outlier: 6.405A pdb=" N ALA L 69 " --> pdb=" O ALA L 25 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'L' and resid 53 through 54 removed outlier: 3.569A pdb=" N THR L 53 " --> pdb=" O TYR L 49 " (cutoff:3.500A) removed outlier: 6.483A pdb=" N TRP L 35 " --> pdb=" O LEU L 47 " (cutoff:3.500A) removed outlier: 4.908A pdb=" N TYR L 49 " --> pdb=" O LEU L 33 " (cutoff:3.500A) removed outlier: 6.795A pdb=" N LEU L 33 " --> pdb=" O TYR L 49 " (cutoff:3.500A) removed outlier: 3.846A pdb=" N ALA L 34 " --> pdb=" O GLN L 89 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N GLN L 89 " --> pdb=" O ALA L 34 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'G' and resid 35 through 45 removed outlier: 5.267A pdb=" N VAL G 36 " --> pdb=" O THR G 499 " (cutoff:3.500A) removed outlier: 6.049A pdb=" N THR G 499 " --> pdb=" O VAL G 36 " (cutoff:3.500A) removed outlier: 5.400A pdb=" N VAL G 38 " --> pdb=" O ALA G 497 " (cutoff:3.500A) removed outlier: 7.082A pdb=" N ALA G 497 " --> pdb=" O VAL G 38 " (cutoff:3.500A) removed outlier: 5.280A pdb=" N TYR G 40 " --> pdb=" O GLY G 495 " (cutoff:3.500A) removed outlier: 6.946A pdb=" N GLY G 495 " --> pdb=" O TYR G 40 " (cutoff:3.500A) removed outlier: 6.622A pdb=" N VAL G 44 " --> pdb=" O ILE G 491 " (cutoff:3.500A) removed outlier: 4.535A pdb=" N ILE G 491 " --> pdb=" O VAL G 44 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'G' and resid 53 through 54 Processing sheet with id=AA5, first strand: chain 'G' and resid 84 through 85 removed outlier: 3.557A pdb=" N ILE G 225 " --> pdb=" O VAL G 245 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N LYS G 487 " --> pdb=" O LEU G 226 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'G' and resid 271 through 273 removed outlier: 3.501A pdb=" N VAL G 271 " --> pdb=" O GLN G 287 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N ASN G 295 " --> pdb=" O ASN G 332 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'G' and resid 271 through 273 removed outlier: 3.501A pdb=" N VAL G 271 " --> pdb=" O GLN G 287 " (cutoff:3.500A) removed outlier: 6.664A pdb=" N THR G 450 " --> pdb=" O LEU G 288 " (cutoff:3.500A) removed outlier: 11.010A pdb=" N GLU G 290 " --> pdb=" O ASN G 448 " (cutoff:3.500A) removed outlier: 9.422A pdb=" N ASN G 448 " --> pdb=" O GLU G 290 " (cutoff:3.500A) removed outlier: 10.547A pdb=" N VAL G 292 " --> pdb=" O SER G 446 " (cutoff:3.500A) removed outlier: 10.253A pdb=" N SER G 446 " --> pdb=" O VAL G 292 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'G' and resid 357 through 361 Processing sheet with id=AA9, first strand: chain 'G' and resid 374 through 378 Processing sheet with id=AB1, first strand: chain 'G' and resid 423 through 425 Processing sheet with id=AB2, first strand: chain 'C' and resid 2 through 6 removed outlier: 4.076A pdb=" N LYS C 2 " --> pdb=" O GLU C 92 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'C' and resid 13 through 14 Processing sheet with id=AB4, first strand: chain 'C' and resid 39 through 40 removed outlier: 3.825A pdb=" N GLN C 40 " --> pdb=" O PHE C 43 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'C' and resid 99 through 102 removed outlier: 3.886A pdb=" N GLY C 99 " --> pdb=" O GLU C 119 " (cutoff:3.500A) removed outlier: 6.407A pdb=" N GLN C 112 " --> pdb=" O GLN C 148 " (cutoff:3.500A) removed outlier: 3.891A pdb=" N GLN C 148 " --> pdb=" O GLN C 112 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'C' and resid 127 through 129 removed outlier: 3.510A pdb=" N VAL C 168 " --> pdb=" O VAL C 161 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'H' and resid 18 through 23 Processing sheet with id=AB8, first strand: chain 'H' and resid 57 through 59 removed outlier: 6.664A pdb=" N TRP H 36 " --> pdb=" O MET H 48 " (cutoff:3.500A) removed outlier: 4.797A pdb=" N ARG H 50 " --> pdb=" O PHE H 34 " (cutoff:3.500A) removed outlier: 7.044A pdb=" N PHE H 34 " --> pdb=" O ARG H 50 " (cutoff:3.500A) removed outlier: 3.737A pdb=" N VAL H 37 " --> pdb=" O PHE H 91 " (cutoff:3.500A) removed outlier: 3.985A pdb=" N PHE H 91 " --> pdb=" O VAL H 37 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'H' and resid 57 through 59 removed outlier: 6.664A pdb=" N TRP H 36 " --> pdb=" O MET H 48 " (cutoff:3.500A) removed outlier: 4.797A pdb=" N ARG H 50 " --> pdb=" O PHE H 34 " (cutoff:3.500A) removed outlier: 7.044A pdb=" N PHE H 34 " --> pdb=" O ARG H 50 " (cutoff:3.500A) removed outlier: 3.737A pdb=" N VAL H 37 " --> pdb=" O PHE H 91 " (cutoff:3.500A) removed outlier: 3.985A pdb=" N PHE H 91 " --> pdb=" O VAL H 37 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'N' and resid 4 through 6 removed outlier: 3.586A pdb=" N ALA N 25 " --> pdb=" O ALA N 69 " (cutoff:3.500A) removed outlier: 6.405A pdb=" N ALA N 69 " --> pdb=" O ALA N 25 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'N' and resid 53 through 54 removed outlier: 3.569A pdb=" N THR N 53 " --> pdb=" O TYR N 49 " (cutoff:3.500A) removed outlier: 6.483A pdb=" N TRP N 35 " --> pdb=" O LEU N 47 " (cutoff:3.500A) removed outlier: 4.908A pdb=" N TYR N 49 " --> pdb=" O LEU N 33 " (cutoff:3.500A) removed outlier: 6.795A pdb=" N LEU N 33 " --> pdb=" O TYR N 49 " (cutoff:3.500A) removed outlier: 3.846A pdb=" N ALA N 34 " --> pdb=" O GLN N 89 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N GLN N 89 " --> pdb=" O ALA N 34 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'I' and resid 35 through 45 removed outlier: 5.267A pdb=" N VAL I 36 " --> pdb=" O THR I 499 " (cutoff:3.500A) removed outlier: 6.050A pdb=" N THR I 499 " --> pdb=" O VAL I 36 " (cutoff:3.500A) removed outlier: 5.399A pdb=" N VAL I 38 " --> pdb=" O ALA I 497 " (cutoff:3.500A) removed outlier: 7.082A pdb=" N ALA I 497 " --> pdb=" O VAL I 38 " (cutoff:3.500A) removed outlier: 5.280A pdb=" N TYR I 40 " --> pdb=" O GLY I 495 " (cutoff:3.500A) removed outlier: 6.946A pdb=" N GLY I 495 " --> pdb=" O TYR I 40 " (cutoff:3.500A) removed outlier: 6.621A pdb=" N VAL I 44 " --> pdb=" O ILE I 491 " (cutoff:3.500A) removed outlier: 4.537A pdb=" N ILE I 491 " --> pdb=" O VAL I 44 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'I' and resid 53 through 54 Processing sheet with id=AC5, first strand: chain 'I' and resid 84 through 85 removed outlier: 3.556A pdb=" N ILE I 225 " --> pdb=" O VAL I 245 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N LYS I 487 " --> pdb=" O LEU I 226 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'I' and resid 271 through 273 removed outlier: 3.501A pdb=" N VAL I 271 " --> pdb=" O GLN I 287 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N ASN I 295 " --> pdb=" O ASN I 332 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'I' and resid 271 through 273 removed outlier: 3.501A pdb=" N VAL I 271 " --> pdb=" O GLN I 287 " (cutoff:3.500A) removed outlier: 6.665A pdb=" N THR I 450 " --> pdb=" O LEU I 288 " (cutoff:3.500A) removed outlier: 11.010A pdb=" N GLU I 290 " --> pdb=" O ASN I 448 " (cutoff:3.500A) removed outlier: 9.422A pdb=" N ASN I 448 " --> pdb=" O GLU I 290 " (cutoff:3.500A) removed outlier: 10.548A pdb=" N VAL I 292 " --> pdb=" O SER I 446 " (cutoff:3.500A) removed outlier: 10.252A pdb=" N SER I 446 " --> pdb=" O VAL I 292 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'I' and resid 357 through 361 Processing sheet with id=AC9, first strand: chain 'I' and resid 374 through 378 Processing sheet with id=AD1, first strand: chain 'I' and resid 423 through 425 Processing sheet with id=AD2, first strand: chain 'E' and resid 2 through 6 removed outlier: 4.076A pdb=" N LYS E 2 " --> pdb=" O GLU E 92 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'E' and resid 13 through 14 Processing sheet with id=AD4, first strand: chain 'E' and resid 39 through 40 removed outlier: 3.825A pdb=" N GLN E 40 " --> pdb=" O PHE E 43 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'E' and resid 99 through 102 removed outlier: 3.886A pdb=" N GLY E 99 " --> pdb=" O GLU E 119 " (cutoff:3.500A) removed outlier: 6.406A pdb=" N GLN E 112 " --> pdb=" O GLN E 148 " (cutoff:3.500A) removed outlier: 3.891A pdb=" N GLN E 148 " --> pdb=" O GLN E 112 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'E' and resid 127 through 129 removed outlier: 3.510A pdb=" N VAL E 168 " --> pdb=" O VAL E 161 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'K' and resid 18 through 23 Processing sheet with id=AD8, first strand: chain 'K' and resid 57 through 59 removed outlier: 6.664A pdb=" N TRP K 36 " --> pdb=" O MET K 48 " (cutoff:3.500A) removed outlier: 4.797A pdb=" N ARG K 50 " --> pdb=" O PHE K 34 " (cutoff:3.500A) removed outlier: 7.044A pdb=" N PHE K 34 " --> pdb=" O ARG K 50 " (cutoff:3.500A) removed outlier: 3.736A pdb=" N VAL K 37 " --> pdb=" O PHE K 91 " (cutoff:3.500A) removed outlier: 3.984A pdb=" N PHE K 91 " --> pdb=" O VAL K 37 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'K' and resid 57 through 59 removed outlier: 6.664A pdb=" N TRP K 36 " --> pdb=" O MET K 48 " (cutoff:3.500A) removed outlier: 4.797A pdb=" N ARG K 50 " --> pdb=" O PHE K 34 " (cutoff:3.500A) removed outlier: 7.044A pdb=" N PHE K 34 " --> pdb=" O ARG K 50 " (cutoff:3.500A) removed outlier: 3.736A pdb=" N VAL K 37 " --> pdb=" O PHE K 91 " (cutoff:3.500A) removed outlier: 3.984A pdb=" N PHE K 91 " --> pdb=" O VAL K 37 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'O' and resid 4 through 6 removed outlier: 3.585A pdb=" N ALA O 25 " --> pdb=" O ALA O 69 " (cutoff:3.500A) removed outlier: 6.404A pdb=" N ALA O 69 " --> pdb=" O ALA O 25 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'O' and resid 53 through 54 removed outlier: 3.569A pdb=" N THR O 53 " --> pdb=" O TYR O 49 " (cutoff:3.500A) removed outlier: 6.483A pdb=" N TRP O 35 " --> pdb=" O LEU O 47 " (cutoff:3.500A) removed outlier: 4.908A pdb=" N TYR O 49 " --> pdb=" O LEU O 33 " (cutoff:3.500A) removed outlier: 6.795A pdb=" N LEU O 33 " --> pdb=" O TYR O 49 " (cutoff:3.500A) removed outlier: 3.847A pdb=" N ALA O 34 " --> pdb=" O GLN O 89 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N GLN O 89 " --> pdb=" O ALA O 34 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'J' and resid 35 through 45 removed outlier: 5.267A pdb=" N VAL J 36 " --> pdb=" O THR J 499 " (cutoff:3.500A) removed outlier: 6.050A pdb=" N THR J 499 " --> pdb=" O VAL J 36 " (cutoff:3.500A) removed outlier: 5.399A pdb=" N VAL J 38 " --> pdb=" O ALA J 497 " (cutoff:3.500A) removed outlier: 7.081A pdb=" N ALA J 497 " --> pdb=" O VAL J 38 " (cutoff:3.500A) removed outlier: 5.280A pdb=" N TYR J 40 " --> pdb=" O GLY J 495 " (cutoff:3.500A) removed outlier: 6.946A pdb=" N GLY J 495 " --> pdb=" O TYR J 40 " (cutoff:3.500A) removed outlier: 6.622A pdb=" N VAL J 44 " --> pdb=" O ILE J 491 " (cutoff:3.500A) removed outlier: 4.536A pdb=" N ILE J 491 " --> pdb=" O VAL J 44 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'J' and resid 53 through 54 Processing sheet with id=AE5, first strand: chain 'J' and resid 84 through 85 removed outlier: 3.557A pdb=" N ILE J 225 " --> pdb=" O VAL J 245 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N LYS J 487 " --> pdb=" O LEU J 226 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'J' and resid 271 through 273 removed outlier: 3.502A pdb=" N VAL J 271 " --> pdb=" O GLN J 287 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N ASN J 295 " --> pdb=" O ASN J 332 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'J' and resid 271 through 273 removed outlier: 3.502A pdb=" N VAL J 271 " --> pdb=" O GLN J 287 " (cutoff:3.500A) removed outlier: 6.665A pdb=" N THR J 450 " --> pdb=" O LEU J 288 " (cutoff:3.500A) removed outlier: 11.010A pdb=" N GLU J 290 " --> pdb=" O ASN J 448 " (cutoff:3.500A) removed outlier: 9.422A pdb=" N ASN J 448 " --> pdb=" O GLU J 290 " (cutoff:3.500A) removed outlier: 10.547A pdb=" N VAL J 292 " --> pdb=" O SER J 446 " (cutoff:3.500A) removed outlier: 10.252A pdb=" N SER J 446 " --> pdb=" O VAL J 292 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'J' and resid 357 through 361 Processing sheet with id=AE9, first strand: chain 'J' and resid 374 through 378 Processing sheet with id=AF1, first strand: chain 'J' and resid 423 through 425 Processing sheet with id=AF2, first strand: chain 'F' and resid 2 through 6 removed outlier: 4.077A pdb=" N LYS F 2 " --> pdb=" O GLU F 92 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'F' and resid 13 through 14 Processing sheet with id=AF4, first strand: chain 'F' and resid 39 through 40 removed outlier: 3.825A pdb=" N GLN F 40 " --> pdb=" O PHE F 43 " (cutoff:3.500A) Processing sheet with id=AF5, first strand: chain 'F' and resid 99 through 102 removed outlier: 3.886A pdb=" N GLY F 99 " --> pdb=" O GLU F 119 " (cutoff:3.500A) removed outlier: 6.406A pdb=" N GLN F 112 " --> pdb=" O GLN F 148 " (cutoff:3.500A) removed outlier: 3.891A pdb=" N GLN F 148 " --> pdb=" O GLN F 112 " (cutoff:3.500A) Processing sheet with id=AF6, first strand: chain 'F' and resid 127 through 129 removed outlier: 3.510A pdb=" N VAL F 168 " --> pdb=" O VAL F 161 " (cutoff:3.500A) Processing sheet with id=AF7, first strand: chain 'M' and resid 18 through 23 Processing sheet with id=AF8, first strand: chain 'M' and resid 57 through 59 removed outlier: 6.664A pdb=" N TRP M 36 " --> pdb=" O MET M 48 " (cutoff:3.500A) removed outlier: 4.796A pdb=" N ARG M 50 " --> pdb=" O PHE M 34 " (cutoff:3.500A) removed outlier: 7.044A pdb=" N PHE M 34 " --> pdb=" O ARG M 50 " (cutoff:3.500A) removed outlier: 3.737A pdb=" N VAL M 37 " --> pdb=" O PHE M 91 " (cutoff:3.500A) removed outlier: 3.984A pdb=" N PHE M 91 " --> pdb=" O VAL M 37 " (cutoff:3.500A) Processing sheet with id=AF9, first strand: chain 'M' and resid 57 through 59 removed outlier: 6.664A pdb=" N TRP M 36 " --> pdb=" O MET M 48 " (cutoff:3.500A) removed outlier: 4.796A pdb=" N ARG M 50 " --> pdb=" O PHE M 34 " (cutoff:3.500A) removed outlier: 7.044A pdb=" N PHE M 34 " --> pdb=" O ARG M 50 " (cutoff:3.500A) removed outlier: 3.737A pdb=" N VAL M 37 " --> pdb=" O PHE M 91 " (cutoff:3.500A) removed outlier: 3.984A pdb=" N PHE M 91 " --> pdb=" O VAL M 37 " (cutoff:3.500A) 600 hydrogen bonds defined for protein. 1566 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 7.75 Time building geometry restraints manager: 12.47 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 7422 1.34 - 1.46: 5788 1.46 - 1.58: 10792 1.58 - 1.70: 1 1.70 - 1.82: 159 Bond restraints: 24162 Sorted by residual: bond pdb=" C GLN L 38 " pdb=" N LYS L 39 " ideal model delta sigma weight residual 1.333 1.238 0.094 2.74e-02 1.33e+03 1.18e+01 bond pdb=" C GLN O 38 " pdb=" N LYS O 39 " ideal model delta sigma weight residual 1.333 1.238 0.094 2.74e-02 1.33e+03 1.18e+01 bond pdb=" C GLN N 38 " pdb=" N LYS N 39 " ideal model delta sigma weight residual 1.333 1.239 0.093 2.74e-02 1.33e+03 1.16e+01 bond pdb=" C1 MAN r 4 " pdb=" O5 MAN r 4 " ideal model delta sigma weight residual 1.399 1.458 -0.059 2.00e-02 2.50e+03 8.72e+00 bond pdb=" C1 NAG A 703 " pdb=" O5 NAG A 703 " ideal model delta sigma weight residual 1.406 1.463 -0.057 2.00e-02 2.50e+03 8.26e+00 ... (remaining 24157 not shown) Histogram of bond angle deviations from ideal: 97.38 - 104.74: 381 104.74 - 112.11: 12814 112.11 - 119.47: 8059 119.47 - 126.83: 11147 126.83 - 134.20: 389 Bond angle restraints: 32790 Sorted by residual: angle pdb=" C ASN G 300 " pdb=" N ASN G 301 " pdb=" CA ASN G 301 " ideal model delta sigma weight residual 121.54 133.08 -11.54 1.91e+00 2.74e-01 3.65e+01 angle pdb=" C ASN J 300 " pdb=" N ASN J 301 " pdb=" CA ASN J 301 " ideal model delta sigma weight residual 121.54 133.07 -11.53 1.91e+00 2.74e-01 3.64e+01 angle pdb=" C ASN I 300 " pdb=" N ASN I 301 " pdb=" CA ASN I 301 " ideal model delta sigma weight residual 121.54 133.04 -11.50 1.91e+00 2.74e-01 3.62e+01 angle pdb=" N ASN I 301 " pdb=" CA ASN I 301 " pdb=" C ASN I 301 " ideal model delta sigma weight residual 110.80 120.95 -10.15 2.13e+00 2.20e-01 2.27e+01 angle pdb=" N ASN G 301 " pdb=" CA ASN G 301 " pdb=" C ASN G 301 " ideal model delta sigma weight residual 110.80 120.90 -10.10 2.13e+00 2.20e-01 2.25e+01 ... (remaining 32785 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 22.30: 15337 22.30 - 44.59: 572 44.59 - 66.89: 70 66.89 - 89.19: 140 89.19 - 111.48: 84 Dihedral angle restraints: 16203 sinusoidal: 8121 harmonic: 8082 Sorted by residual: dihedral pdb=" CB CYS I 119 " pdb=" SG CYS I 119 " pdb=" SG CYS I 205 " pdb=" CB CYS I 205 " ideal model delta sinusoidal sigma weight residual -86.00 -163.85 77.85 1 1.00e+01 1.00e-02 7.58e+01 dihedral pdb=" CB CYS G 119 " pdb=" SG CYS G 119 " pdb=" SG CYS G 205 " pdb=" CB CYS G 205 " ideal model delta sinusoidal sigma weight residual -86.00 -163.85 77.85 1 1.00e+01 1.00e-02 7.58e+01 dihedral pdb=" CB CYS J 119 " pdb=" SG CYS J 119 " pdb=" SG CYS J 205 " pdb=" CB CYS J 205 " ideal model delta sinusoidal sigma weight residual -86.00 -163.84 77.84 1 1.00e+01 1.00e-02 7.58e+01 ... (remaining 16200 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.072: 3129 0.072 - 0.144: 809 0.144 - 0.216: 120 0.216 - 0.289: 28 0.289 - 0.361: 6 Chirality restraints: 4092 Sorted by residual: chirality pdb=" CB ILE B 603 " pdb=" CA ILE B 603 " pdb=" CG1 ILE B 603 " pdb=" CG2 ILE B 603 " both_signs ideal model delta sigma weight residual False 2.64 2.28 0.36 2.00e-01 2.50e+01 3.25e+00 chirality pdb=" CB ILE D 603 " pdb=" CA ILE D 603 " pdb=" CG1 ILE D 603 " pdb=" CG2 ILE D 603 " both_signs ideal model delta sigma weight residual False 2.64 2.28 0.36 2.00e-01 2.50e+01 3.25e+00 chirality pdb=" CB ILE A 603 " pdb=" CA ILE A 603 " pdb=" CG1 ILE A 603 " pdb=" CG2 ILE A 603 " both_signs ideal model delta sigma weight residual False 2.64 2.29 0.36 2.00e-01 2.50e+01 3.21e+00 ... (remaining 4089 not shown) Planarity restraints: 4068 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB ASN A 625 " 0.024 2.00e-02 2.50e+03 2.36e-02 6.97e+00 pdb=" CG ASN A 625 " -0.021 2.00e-02 2.50e+03 pdb=" OD1 ASN A 625 " 0.002 2.00e-02 2.50e+03 pdb=" ND2 ASN A 625 " -0.032 2.00e-02 2.50e+03 pdb=" C1 NAG A 703 " 0.027 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN G 276 " 0.023 2.00e-02 2.50e+03 2.29e-02 6.55e+00 pdb=" CG ASN G 276 " -0.012 2.00e-02 2.50e+03 pdb=" OD1 ASN G 276 " -0.006 2.00e-02 2.50e+03 pdb=" ND2 ASN G 276 " -0.034 2.00e-02 2.50e+03 pdb=" C1 NAG S 1 " 0.029 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN I 276 " 0.022 2.00e-02 2.50e+03 2.23e-02 6.24e+00 pdb=" CG ASN I 276 " -0.011 2.00e-02 2.50e+03 pdb=" OD1 ASN I 276 " -0.006 2.00e-02 2.50e+03 pdb=" ND2 ASN I 276 " -0.033 2.00e-02 2.50e+03 pdb=" C1 NAG d 1 " 0.028 2.00e-02 2.50e+03 ... (remaining 4065 not shown) Histogram of nonbonded interaction distances: 2.24 - 2.77: 4503 2.77 - 3.30: 21149 3.30 - 3.83: 37189 3.83 - 4.37: 41954 4.37 - 4.90: 73821 Nonbonded interactions: 178616 Sorted by model distance: nonbonded pdb=" O GLY J 441 " pdb=" O6 MAN n 5 " model vdw 2.235 2.440 nonbonded pdb=" O GLY I 441 " pdb=" O6 MAN c 5 " model vdw 2.247 2.440 nonbonded pdb=" O CYS D 604 " pdb=" OG1 THR J 37 " model vdw 2.256 2.440 nonbonded pdb=" NE2 GLN L 38 " pdb=" O LYS L 39 " model vdw 2.294 2.520 nonbonded pdb=" NE2 GLN O 38 " pdb=" O LYS O 39 " model vdw 2.295 2.520 ... (remaining 178611 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 'B' selection = chain 'D' } ncs_group { reference = chain 'C' selection = chain 'E' selection = chain 'F' } ncs_group { reference = chain 'G' selection = chain 'I' selection = chain 'J' } ncs_group { reference = chain 'H' selection = chain 'K' selection = chain 'M' } ncs_group { reference = chain 'L' selection = chain 'N' selection = chain 'O' } ncs_group { reference = chain 'P' selection = chain 'T' selection = chain 'U' selection = chain 'Y' selection = chain 'a' selection = chain 'e' selection = chain 'f' selection = chain 'j' selection = chain 'l' selection = chain 'p' selection = chain 'q' selection = chain 'u' } ncs_group { reference = chain 'Q' selection = chain 'W' selection = chain 'X' selection = chain 'Z' selection = chain 'b' selection = chain 'h' selection = chain 'i' selection = chain 'k' selection = chain 'm' selection = chain 's' selection = chain 't' selection = chain 'v' } ncs_group { reference = chain 'R' selection = chain 'c' selection = chain 'n' } ncs_group { reference = chain 'S' selection = chain 'V' selection = chain 'd' selection = chain 'g' selection = chain 'o' selection = chain 'r' } 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: 5.120 Check model and map are aligned: 0.340 Set scattering table: 0.210 Process input model: 64.320 Find NCS groups from input model: 1.780 Set up NCS constraints: 0.490 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.890 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 75.910 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7768 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 : 0.010 0.094 24162 Z= 0.635 Angle : 1.234 11.544 32790 Z= 0.658 Chirality : 0.067 0.361 4092 Planarity : 0.006 0.062 4011 Dihedral : 16.113 111.482 10857 Min Nonbonded Distance : 2.235 Molprobity Statistics. All-atom Clashscore : 6.36 Ramachandran Plot: Outliers : 0.43 % Allowed : 10.76 % Favored : 88.80 % Rotamer: Outliers : 0.12 % Allowed : 2.33 % Favored : 97.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.63 % 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: -5.03 (0.12), residues: 2760 helix: -4.37 (0.10), residues: 444 sheet: -2.51 (0.18), residues: 720 loop : -3.56 (0.12), residues: 1596 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.037 0.004 TRP G 45 HIS 0.009 0.003 HIS B 641 PHE 0.042 0.004 PHE G 382 TYR 0.029 0.004 TYR I 384 ARG 0.007 0.001 ARG H 83 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5520 Ramachandran restraints generated. 2760 Oldfield, 0 Emsley, 2760 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5520 Ramachandran restraints generated. 2760 Oldfield, 0 Emsley, 2760 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 517 residues out of total 2454 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 514 time to evaluate : 2.749 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: A 629 MET cc_start: 0.8653 (mmm) cc_final: 0.8430 (mmm) REVERT: A 657 GLU cc_start: 0.8432 (tp30) cc_final: 0.8214 (tm-30) REVERT: G 61 TYR cc_start: 0.8224 (p90) cc_final: 0.8012 (p90) REVERT: G 426 MET cc_start: 0.9157 (mtm) cc_final: 0.8664 (mtm) REVERT: H 1 GLN cc_start: 0.6871 (mt0) cc_final: 0.5321 (pm20) REVERT: H 13 LYS cc_start: 0.7438 (mmtt) cc_final: 0.6937 (ptmm) REVERT: B 624 ASP cc_start: 0.7446 (m-30) cc_final: 0.7195 (m-30) REVERT: B 629 MET cc_start: 0.8482 (mmm) cc_final: 0.8094 (mmm) REVERT: B 657 GLU cc_start: 0.8507 (tp30) cc_final: 0.7578 (tm-30) REVERT: I 61 TYR cc_start: 0.8322 (p90) cc_final: 0.8099 (p90) REVERT: E 70 ILE cc_start: 0.9078 (mt) cc_final: 0.8369 (mt) REVERT: E 130 CYS cc_start: 0.3801 (m) cc_final: 0.3216 (t) REVERT: E 137 ASN cc_start: 0.7553 (m-40) cc_final: 0.6667 (t0) REVERT: K 1 GLN cc_start: 0.6268 (mt0) cc_final: 0.5557 (pm20) REVERT: K 13 LYS cc_start: 0.7215 (mmtt) cc_final: 0.6696 (ptmm) REVERT: O 46 LEU cc_start: 0.8300 (tp) cc_final: 0.8085 (tt) REVERT: O 70 GLU cc_start: 0.8238 (tt0) cc_final: 0.7849 (tm-30) REVERT: D 629 MET cc_start: 0.8543 (mmm) cc_final: 0.8215 (mmm) REVERT: D 657 GLU cc_start: 0.8675 (tp30) cc_final: 0.8410 (tm-30) REVERT: J 426 MET cc_start: 0.8896 (mtm) cc_final: 0.8616 (mtm) REVERT: M 1 GLN cc_start: 0.6429 (mt0) cc_final: 0.5370 (pm20) REVERT: M 13 LYS cc_start: 0.7364 (mmtt) cc_final: 0.7153 (ptmm) REVERT: M 101 LYS cc_start: 0.8331 (tttm) cc_final: 0.8121 (tptt) outliers start: 3 outliers final: 0 residues processed: 514 average time/residue: 0.4105 time to fit residues: 308.9359 Evaluate side-chains 282 residues out of total 2454 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 282 time to evaluate : 2.888 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 273 random chunks: chunk 230 optimal weight: 0.6980 chunk 206 optimal weight: 0.9990 chunk 114 optimal weight: 4.9990 chunk 70 optimal weight: 3.9990 chunk 139 optimal weight: 2.9990 chunk 110 optimal weight: 2.9990 chunk 213 optimal weight: 0.8980 chunk 82 optimal weight: 1.9990 chunk 130 optimal weight: 1.9990 chunk 159 optimal weight: 0.6980 chunk 247 optimal weight: 0.8980 overall best weight: 0.8382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** L 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 92 ASN ** A 653 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 103 GLN G 197 ASN G 308 HIS ** G 398 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 422 GLN G 462 GLN C 25 GLN C 163 GLN H 82BASN ** N 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 92 ASN B 653 GLN I 103 GLN I 197 ASN ** I 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 377 ASN ** I 398 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 422 GLN I 462 GLN E 25 GLN E 163 GLN O 6 GLN ** O 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 92 ASN ** D 567 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 653 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 103 GLN J 197 ASN ** J 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 377 ASN ** J 398 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 422 GLN F 25 GLN F 163 GLN Total number of N/Q/H flips: 26 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7745 moved from start: 0.2354 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 24162 Z= 0.190 Angle : 0.696 10.051 32790 Z= 0.343 Chirality : 0.047 0.224 4092 Planarity : 0.005 0.049 4011 Dihedral : 13.932 87.460 5619 Min Nonbonded Distance : 2.158 Molprobity Statistics. All-atom Clashscore : 9.64 Ramachandran Plot: Outliers : 0.22 % Allowed : 7.86 % Favored : 91.92 % Rotamer: Outliers : 1.84 % Allowed : 8.32 % Favored : 89.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.63 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.91 (0.14), residues: 2760 helix: -2.18 (0.20), residues: 435 sheet: -1.93 (0.18), residues: 690 loop : -3.15 (0.13), residues: 1635 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP K 36 HIS 0.005 0.001 HIS G 308 PHE 0.014 0.001 PHE G 382 TYR 0.022 0.002 TYR H 79 ARG 0.005 0.001 ARG O 24 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5520 Ramachandran restraints generated. 2760 Oldfield, 0 Emsley, 2760 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5520 Ramachandran restraints generated. 2760 Oldfield, 0 Emsley, 2760 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 397 residues out of total 2454 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 352 time to evaluate : 2.748 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: L 1 GLU cc_start: 0.7664 (mt-10) cc_final: 0.7352 (mm-30) REVERT: L 92 ASN cc_start: 0.8820 (OUTLIER) cc_final: 0.8208 (t0) REVERT: A 629 MET cc_start: 0.8526 (mmm) cc_final: 0.8018 (mtp) REVERT: A 659 GLU cc_start: 0.8538 (mm-30) cc_final: 0.8238 (tt0) REVERT: G 61 TYR cc_start: 0.8456 (p90) cc_final: 0.8190 (p90) REVERT: G 376 PHE cc_start: 0.8186 (p90) cc_final: 0.7927 (p90) REVERT: G 457 ASP cc_start: 0.7497 (t0) cc_final: 0.7161 (t0) REVERT: C 169 GLU cc_start: 0.7123 (mm-30) cc_final: 0.6888 (mm-30) REVERT: H 1 GLN cc_start: 0.6697 (mt0) cc_final: 0.6398 (pt0) REVERT: H 13 LYS cc_start: 0.7557 (mmtt) cc_final: 0.6926 (ptmm) REVERT: N 92 ASN cc_start: 0.8625 (OUTLIER) cc_final: 0.8111 (t0) REVERT: B 566 LEU cc_start: 0.8218 (OUTLIER) cc_final: 0.7923 (tt) REVERT: B 624 ASP cc_start: 0.7194 (m-30) cc_final: 0.6934 (m-30) REVERT: B 629 MET cc_start: 0.8317 (mmm) cc_final: 0.7818 (mmm) REVERT: B 657 GLU cc_start: 0.8069 (tp30) cc_final: 0.7702 (tm-30) REVERT: I 61 TYR cc_start: 0.8467 (p90) cc_final: 0.8203 (p90) REVERT: E 10 ASP cc_start: 0.6591 (p0) cc_final: 0.6118 (p0) REVERT: E 130 CYS cc_start: 0.4363 (m) cc_final: 0.3833 (t) REVERT: E 137 ASN cc_start: 0.7372 (m-40) cc_final: 0.6649 (t0) REVERT: K 13 LYS cc_start: 0.7189 (mmtt) cc_final: 0.6710 (ptmm) REVERT: K 81 GLU cc_start: 0.7867 (tm-30) cc_final: 0.7620 (tm-30) REVERT: O 92 ASN cc_start: 0.8612 (OUTLIER) cc_final: 0.8081 (t0) REVERT: D 629 MET cc_start: 0.8397 (mmm) cc_final: 0.8022 (mmm) REVERT: D 638 TYR cc_start: 0.8486 (m-80) cc_final: 0.8226 (m-10) REVERT: D 659 GLU cc_start: 0.8622 (mm-30) cc_final: 0.8403 (tt0) REVERT: F 169 GLU cc_start: 0.7498 (mm-30) cc_final: 0.7291 (mm-30) REVERT: M 13 LYS cc_start: 0.7473 (mmtt) cc_final: 0.7195 (ptmm) REVERT: M 100 GLU cc_start: 0.6878 (mt-10) cc_final: 0.6463 (mt-10) outliers start: 45 outliers final: 16 residues processed: 384 average time/residue: 0.3387 time to fit residues: 205.1399 Evaluate side-chains 277 residues out of total 2454 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 257 time to evaluate : 2.803 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 92 ASN Chi-restraints excluded: chain A residue 615 SER Chi-restraints excluded: chain G residue 49 THR Chi-restraints excluded: chain G residue 63 THR Chi-restraints excluded: chain G residue 373 THR Chi-restraints excluded: chain C residue 87 GLU Chi-restraints excluded: chain H residue 73 LYS Chi-restraints excluded: chain H residue 82 LEU Chi-restraints excluded: chain N residue 92 ASN Chi-restraints excluded: chain B residue 566 LEU Chi-restraints excluded: chain B residue 595 ILE Chi-restraints excluded: chain B residue 615 SER Chi-restraints excluded: chain I residue 300 ASN Chi-restraints excluded: chain I residue 401 THR Chi-restraints excluded: chain E residue 87 GLU Chi-restraints excluded: chain K residue 95 VAL Chi-restraints excluded: chain O residue 92 ASN Chi-restraints excluded: chain F residue 87 GLU Chi-restraints excluded: chain M residue 28 THR Chi-restraints excluded: chain M residue 82 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 273 random chunks: chunk 137 optimal weight: 5.9990 chunk 76 optimal weight: 20.0000 chunk 206 optimal weight: 0.6980 chunk 168 optimal weight: 6.9990 chunk 68 optimal weight: 1.9990 chunk 248 optimal weight: 0.9990 chunk 268 optimal weight: 9.9990 chunk 221 optimal weight: 0.4980 chunk 246 optimal weight: 7.9990 chunk 84 optimal weight: 7.9990 chunk 199 optimal weight: 0.9990 overall best weight: 1.0386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** L 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 92 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 653 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 197 ASN ** G 398 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 92 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 398 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 39 ASN O 6 GLN ** O 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 92 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 567 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 398 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7764 moved from start: 0.2707 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 24162 Z= 0.185 Angle : 0.659 8.229 32790 Z= 0.321 Chirality : 0.047 0.371 4092 Planarity : 0.004 0.032 4011 Dihedral : 12.039 84.093 5619 Min Nonbonded Distance : 2.154 Molprobity Statistics. All-atom Clashscore : 10.24 Ramachandran Plot: Outliers : 0.22 % Allowed : 8.33 % Favored : 91.45 % Rotamer: Outliers : 1.92 % Allowed : 9.96 % Favored : 88.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.63 % 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: -3.24 (0.14), residues: 2760 helix: -1.18 (0.23), residues: 456 sheet: -1.65 (0.19), residues: 693 loop : -2.79 (0.13), residues: 1611 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.001 TRP M 36 HIS 0.003 0.001 HIS G 374 PHE 0.014 0.001 PHE G 382 TYR 0.017 0.001 TYR N 91 ARG 0.005 0.000 ARG K 82A *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5520 Ramachandran restraints generated. 2760 Oldfield, 0 Emsley, 2760 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5520 Ramachandran restraints generated. 2760 Oldfield, 0 Emsley, 2760 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 327 residues out of total 2454 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 47 poor density : 280 time to evaluate : 2.604 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: L 18 ARG cc_start: 0.7676 (mmm-85) cc_final: 0.7405 (tpp80) REVERT: L 70 GLU cc_start: 0.8140 (tm-30) cc_final: 0.7914 (tm-30) REVERT: A 629 MET cc_start: 0.8561 (mmm) cc_final: 0.8010 (mtp) REVERT: A 659 GLU cc_start: 0.8580 (mm-30) cc_final: 0.8250 (tt0) REVERT: G 61 TYR cc_start: 0.8413 (p90) cc_final: 0.8165 (p90) REVERT: G 376 PHE cc_start: 0.8181 (p90) cc_final: 0.7862 (p90) REVERT: G 377 ASN cc_start: 0.8517 (m-40) cc_final: 0.7970 (t0) REVERT: G 457 ASP cc_start: 0.7484 (t0) cc_final: 0.7052 (t0) REVERT: H 13 LYS cc_start: 0.7543 (mmtt) cc_final: 0.6855 (ptmm) REVERT: H 100 TYR cc_start: 0.7042 (t80) cc_final: 0.6531 (t80) REVERT: B 624 ASP cc_start: 0.7516 (m-30) cc_final: 0.7144 (m-30) REVERT: B 629 MET cc_start: 0.8310 (mmm) cc_final: 0.7882 (mmm) REVERT: B 657 GLU cc_start: 0.8132 (tp30) cc_final: 0.7738 (tm-30) REVERT: I 61 TYR cc_start: 0.8470 (p90) cc_final: 0.8204 (p90) REVERT: E 10 ASP cc_start: 0.6521 (p0) cc_final: 0.6289 (p0) REVERT: E 85 GLU cc_start: 0.7214 (mp0) cc_final: 0.6487 (mp0) REVERT: E 130 CYS cc_start: 0.4358 (m) cc_final: 0.3824 (t) REVERT: E 137 ASN cc_start: 0.7457 (m-40) cc_final: 0.6765 (t0) REVERT: K 13 LYS cc_start: 0.7168 (mmtt) cc_final: 0.6715 (ptmm) REVERT: K 81 GLU cc_start: 0.8012 (tm-30) cc_final: 0.7728 (tm-30) REVERT: D 629 MET cc_start: 0.8478 (mmm) cc_final: 0.8138 (mmm) REVERT: D 638 TYR cc_start: 0.8444 (m-80) cc_final: 0.8197 (m-10) REVERT: J 95 MET cc_start: 0.8499 (OUTLIER) cc_final: 0.8032 (ttp) REVERT: J 434 MET cc_start: 0.8053 (tmm) cc_final: 0.7832 (ppp) REVERT: F 10 ASP cc_start: 0.6615 (p0) cc_final: 0.6354 (p0) REVERT: M 13 LYS cc_start: 0.7566 (mmtt) cc_final: 0.7085 (ptmm) outliers start: 47 outliers final: 32 residues processed: 311 average time/residue: 0.3188 time to fit residues: 161.3273 Evaluate side-chains 286 residues out of total 2454 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 253 time to evaluate : 2.721 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 612 ASP Chi-restraints excluded: chain A residue 615 SER Chi-restraints excluded: chain A residue 622 ILE Chi-restraints excluded: chain G residue 49 THR Chi-restraints excluded: chain G residue 63 THR Chi-restraints excluded: chain G residue 355 ASN Chi-restraints excluded: chain G residue 373 THR Chi-restraints excluded: chain C residue 24 ILE Chi-restraints excluded: chain C residue 87 GLU Chi-restraints excluded: chain C residue 138 ILE Chi-restraints excluded: chain H residue 73 LYS Chi-restraints excluded: chain H residue 82 LEU Chi-restraints excluded: chain H residue 95 VAL Chi-restraints excluded: chain B residue 615 SER Chi-restraints excluded: chain I residue 300 ASN Chi-restraints excluded: chain I residue 309 ILE Chi-restraints excluded: chain I residue 373 THR Chi-restraints excluded: chain I residue 401 THR Chi-restraints excluded: chain I residue 426 MET Chi-restraints excluded: chain E residue 39 ASN Chi-restraints excluded: chain E residue 87 GLU Chi-restraints excluded: chain D residue 615 SER Chi-restraints excluded: chain D residue 622 ILE Chi-restraints excluded: chain D residue 649 SER Chi-restraints excluded: chain J residue 95 MET Chi-restraints excluded: chain J residue 355 ASN Chi-restraints excluded: chain F residue 24 ILE Chi-restraints excluded: chain F residue 87 GLU Chi-restraints excluded: chain F residue 91 GLU Chi-restraints excluded: chain M residue 16 SER Chi-restraints excluded: chain M residue 28 THR Chi-restraints excluded: chain M residue 82 LEU Chi-restraints excluded: chain M residue 95 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 273 random chunks: chunk 245 optimal weight: 5.9990 chunk 186 optimal weight: 4.9990 chunk 128 optimal weight: 4.9990 chunk 27 optimal weight: 5.9990 chunk 118 optimal weight: 1.9990 chunk 166 optimal weight: 10.0000 chunk 249 optimal weight: 8.9990 chunk 263 optimal weight: 10.0000 chunk 130 optimal weight: 5.9990 chunk 236 optimal weight: 5.9990 chunk 71 optimal weight: 7.9990 overall best weight: 4.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L 92 ASN G 229 ASN G 301 ASN ** G 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 398 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 92 ASN B 564 HIS I 197 ASN ** I 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 398 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 92 ASN ** J 66 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 197 ASN ** J 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 398 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 462 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 100HASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7911 moved from start: 0.3220 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.065 24162 Z= 0.494 Angle : 0.844 12.686 32790 Z= 0.406 Chirality : 0.051 0.482 4092 Planarity : 0.005 0.050 4011 Dihedral : 10.548 79.231 5619 Min Nonbonded Distance : 2.035 Molprobity Statistics. All-atom Clashscore : 14.59 Ramachandran Plot: Outliers : 0.22 % Allowed : 10.91 % Favored : 88.88 % Rotamer: Outliers : 3.06 % Allowed : 11.18 % Favored : 85.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.63 % 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: -3.23 (0.14), residues: 2760 helix: -1.24 (0.23), residues: 459 sheet: -1.50 (0.19), residues: 735 loop : -2.86 (0.14), residues: 1566 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.003 TRP J 112 HIS 0.007 0.002 HIS J 105 PHE 0.019 0.002 PHE G 233 TYR 0.023 0.003 TYR I 484 ARG 0.007 0.001 ARG M 31 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5520 Ramachandran restraints generated. 2760 Oldfield, 0 Emsley, 2760 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5520 Ramachandran restraints generated. 2760 Oldfield, 0 Emsley, 2760 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 338 residues out of total 2454 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 75 poor density : 263 time to evaluate : 2.779 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: L 70 GLU cc_start: 0.8245 (tm-30) cc_final: 0.7944 (tm-30) REVERT: L 92 ASN cc_start: 0.8872 (OUTLIER) cc_final: 0.8272 (t0) REVERT: A 629 MET cc_start: 0.8873 (mmm) cc_final: 0.8654 (mmm) REVERT: A 659 GLU cc_start: 0.8717 (mm-30) cc_final: 0.8413 (tt0) REVERT: G 61 TYR cc_start: 0.8582 (p90) cc_final: 0.8238 (p90) REVERT: G 457 ASP cc_start: 0.7907 (t0) cc_final: 0.7507 (t0) REVERT: H 1 GLN cc_start: 0.6909 (mt0) cc_final: 0.5996 (pt0) REVERT: H 13 LYS cc_start: 0.7701 (mmtt) cc_final: 0.6875 (ptmm) REVERT: N 33 LEU cc_start: 0.7128 (tp) cc_final: 0.6841 (tp) REVERT: N 92 ASN cc_start: 0.8732 (OUTLIER) cc_final: 0.8252 (t0) REVERT: B 566 LEU cc_start: 0.8422 (OUTLIER) cc_final: 0.8158 (tt) REVERT: B 629 MET cc_start: 0.8645 (mmm) cc_final: 0.8213 (mmm) REVERT: B 657 GLU cc_start: 0.8001 (tp30) cc_final: 0.7600 (tm-30) REVERT: I 49 THR cc_start: 0.8089 (p) cc_final: 0.7806 (p) REVERT: I 61 TYR cc_start: 0.8515 (p90) cc_final: 0.8215 (p90) REVERT: I 482 GLU cc_start: 0.8032 (tp30) cc_final: 0.7807 (tp30) REVERT: E 85 GLU cc_start: 0.7563 (mp0) cc_final: 0.6855 (mp0) REVERT: E 88 ASP cc_start: 0.8603 (m-30) cc_final: 0.8400 (m-30) REVERT: E 130 CYS cc_start: 0.5035 (m) cc_final: 0.4722 (t) REVERT: K 1 GLN cc_start: 0.6626 (mt0) cc_final: 0.5725 (pm20) REVERT: K 13 LYS cc_start: 0.7393 (mmtt) cc_final: 0.7057 (ptmm) REVERT: K 38 ARG cc_start: 0.6726 (OUTLIER) cc_final: 0.5389 (ttm170) REVERT: K 46 GLU cc_start: 0.7159 (mt-10) cc_final: 0.6860 (mt-10) REVERT: K 81 GLU cc_start: 0.8183 (tm-30) cc_final: 0.7878 (tm-30) REVERT: O 92 ASN cc_start: 0.8619 (OUTLIER) cc_final: 0.7912 (t0) REVERT: D 565 MET cc_start: 0.4799 (OUTLIER) cc_final: 0.4431 (mmm) REVERT: D 624 ASP cc_start: 0.7288 (m-30) cc_final: 0.6934 (m-30) REVERT: D 629 MET cc_start: 0.8579 (mmm) cc_final: 0.8015 (mmm) REVERT: J 434 MET cc_start: 0.8262 (tmm) cc_final: 0.8021 (ppp) REVERT: F 136 LYS cc_start: 0.5102 (OUTLIER) cc_final: 0.4702 (tmmt) REVERT: F 169 GLU cc_start: 0.7503 (mm-30) cc_final: 0.7199 (mm-30) REVERT: M 13 LYS cc_start: 0.7768 (mmtt) cc_final: 0.7162 (ptmm) REVERT: M 46 GLU cc_start: 0.6903 (mt-10) cc_final: 0.6562 (mt-10) outliers start: 75 outliers final: 51 residues processed: 317 average time/residue: 0.3206 time to fit residues: 165.1043 Evaluate side-chains 296 residues out of total 2454 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 58 poor density : 238 time to evaluate : 2.967 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 92 ASN Chi-restraints excluded: chain A residue 615 SER Chi-restraints excluded: chain A residue 622 ILE Chi-restraints excluded: chain G residue 49 THR Chi-restraints excluded: chain G residue 63 THR Chi-restraints excluded: chain G residue 68 VAL Chi-restraints excluded: chain G residue 208 VAL Chi-restraints excluded: chain G residue 239 CYS Chi-restraints excluded: chain G residue 244 THR Chi-restraints excluded: chain G residue 355 ASN Chi-restraints excluded: chain G residue 373 THR Chi-restraints excluded: chain C residue 24 ILE Chi-restraints excluded: chain C residue 53 ASP Chi-restraints excluded: chain C residue 56 ASP Chi-restraints excluded: chain C residue 87 GLU Chi-restraints excluded: chain C residue 138 ILE Chi-restraints excluded: chain H residue 16 SER Chi-restraints excluded: chain H residue 78 VAL Chi-restraints excluded: chain H residue 82 LEU Chi-restraints excluded: chain H residue 95 VAL Chi-restraints excluded: chain N residue 92 ASN Chi-restraints excluded: chain B residue 566 LEU Chi-restraints excluded: chain B residue 615 SER Chi-restraints excluded: chain I residue 44 VAL Chi-restraints excluded: chain I residue 239 CYS Chi-restraints excluded: chain I residue 244 THR Chi-restraints excluded: chain I residue 300 ASN Chi-restraints excluded: chain I residue 373 THR Chi-restraints excluded: chain I residue 401 THR Chi-restraints excluded: chain I residue 426 MET Chi-restraints excluded: chain E residue 16 CYS Chi-restraints excluded: chain E residue 87 GLU Chi-restraints excluded: chain K residue 2 VAL Chi-restraints excluded: chain K residue 38 ARG Chi-restraints excluded: chain K residue 55 ASP Chi-restraints excluded: chain K residue 95 VAL Chi-restraints excluded: chain O residue 92 ASN Chi-restraints excluded: chain D residue 565 MET Chi-restraints excluded: chain D residue 615 SER Chi-restraints excluded: chain D residue 622 ILE Chi-restraints excluded: chain D residue 649 SER Chi-restraints excluded: chain D residue 659 GLU Chi-restraints excluded: chain J residue 95 MET Chi-restraints excluded: chain J residue 104 MET Chi-restraints excluded: chain J residue 208 VAL Chi-restraints excluded: chain J residue 239 CYS Chi-restraints excluded: chain J residue 244 THR Chi-restraints excluded: chain J residue 300 ASN Chi-restraints excluded: chain J residue 355 ASN Chi-restraints excluded: chain F residue 16 CYS Chi-restraints excluded: chain F residue 24 ILE Chi-restraints excluded: chain F residue 83 ILE Chi-restraints excluded: chain F residue 87 GLU Chi-restraints excluded: chain F residue 136 LYS Chi-restraints excluded: chain M residue 16 SER Chi-restraints excluded: chain M residue 28 THR Chi-restraints excluded: chain M residue 82 LEU Chi-restraints excluded: chain M residue 95 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 273 random chunks: chunk 219 optimal weight: 0.8980 chunk 149 optimal weight: 8.9990 chunk 3 optimal weight: 10.0000 chunk 196 optimal weight: 0.8980 chunk 108 optimal weight: 0.5980 chunk 225 optimal weight: 1.9990 chunk 182 optimal weight: 10.0000 chunk 0 optimal weight: 9.9990 chunk 134 optimal weight: 0.9990 chunk 236 optimal weight: 0.9980 chunk 66 optimal weight: 1.9990 overall best weight: 0.8782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** L 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 92 ASN ** G 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 398 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 92 ASN I 72 HIS ** I 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 398 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 39 ASN ** O 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 92 ASN ** J 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 398 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 462 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7820 moved from start: 0.3327 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 24162 Z= 0.177 Angle : 0.639 10.359 32790 Z= 0.311 Chirality : 0.046 0.414 4092 Planarity : 0.003 0.033 4011 Dihedral : 9.121 73.064 5619 Min Nonbonded Distance : 2.170 Molprobity Statistics. All-atom Clashscore : 10.96 Ramachandran Plot: Outliers : 0.22 % Allowed : 7.54 % Favored : 92.25 % Rotamer: Outliers : 2.37 % Allowed : 12.61 % Favored : 85.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.63 % 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: -2.78 (0.15), residues: 2760 helix: -0.60 (0.24), residues: 459 sheet: -1.26 (0.19), residues: 714 loop : -2.62 (0.14), residues: 1587 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP G 69 HIS 0.003 0.001 HIS K 102 PHE 0.014 0.001 PHE I 53 TYR 0.019 0.001 TYR B 638 ARG 0.004 0.000 ARG L 18 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5520 Ramachandran restraints generated. 2760 Oldfield, 0 Emsley, 2760 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5520 Ramachandran restraints generated. 2760 Oldfield, 0 Emsley, 2760 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 330 residues out of total 2454 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 58 poor density : 272 time to evaluate : 2.580 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: L 70 GLU cc_start: 0.8197 (tm-30) cc_final: 0.7837 (tm-30) REVERT: A 629 MET cc_start: 0.8639 (mmm) cc_final: 0.8169 (mtp) REVERT: A 659 GLU cc_start: 0.8619 (mm-30) cc_final: 0.8400 (tt0) REVERT: G 61 TYR cc_start: 0.8586 (p90) cc_final: 0.8306 (p90) REVERT: G 95 MET cc_start: 0.8062 (ttp) cc_final: 0.7711 (ttp) REVERT: G 377 ASN cc_start: 0.8456 (OUTLIER) cc_final: 0.7961 (t0) REVERT: G 457 ASP cc_start: 0.7819 (t0) cc_final: 0.7454 (t0) REVERT: C 85 GLU cc_start: 0.7380 (mp0) cc_final: 0.7167 (mp0) REVERT: H 1 GLN cc_start: 0.7025 (mt0) cc_final: 0.5304 (pm20) REVERT: H 13 LYS cc_start: 0.7553 (mmtt) cc_final: 0.6738 (ptmm) REVERT: H 81 GLU cc_start: 0.8104 (tm-30) cc_final: 0.7699 (tm-30) REVERT: H 99 GLU cc_start: 0.7351 (mm-30) cc_final: 0.7029 (mm-30) REVERT: N 33 LEU cc_start: 0.7147 (tp) cc_final: 0.6934 (tp) REVERT: B 624 ASP cc_start: 0.7651 (m-30) cc_final: 0.7287 (m-30) REVERT: B 629 MET cc_start: 0.8381 (mmm) cc_final: 0.8072 (mmm) REVERT: B 657 GLU cc_start: 0.7914 (tp30) cc_final: 0.7689 (tm-30) REVERT: I 49 THR cc_start: 0.7747 (p) cc_final: 0.7453 (p) REVERT: I 61 TYR cc_start: 0.8505 (p90) cc_final: 0.8187 (p90) REVERT: E 85 GLU cc_start: 0.7222 (mp0) cc_final: 0.6947 (mp0) REVERT: K 13 LYS cc_start: 0.7287 (mmtt) cc_final: 0.6721 (ptmm) REVERT: K 38 ARG cc_start: 0.6597 (OUTLIER) cc_final: 0.5554 (ttm170) REVERT: K 46 GLU cc_start: 0.7161 (mt-10) cc_final: 0.6493 (mt-10) REVERT: K 81 GLU cc_start: 0.8123 (tm-30) cc_final: 0.7815 (tm-30) REVERT: D 624 ASP cc_start: 0.7295 (m-30) cc_final: 0.6931 (m-30) REVERT: D 629 MET cc_start: 0.8383 (mmm) cc_final: 0.8021 (mmm) REVERT: J 95 MET cc_start: 0.8442 (OUTLIER) cc_final: 0.7857 (ttp) REVERT: F 85 GLU cc_start: 0.7476 (mp0) cc_final: 0.7198 (mp0) REVERT: F 169 GLU cc_start: 0.7470 (mm-30) cc_final: 0.7123 (mm-30) REVERT: M 13 LYS cc_start: 0.7772 (mmtt) cc_final: 0.7265 (ptmm) REVERT: M 46 GLU cc_start: 0.6909 (mt-10) cc_final: 0.6555 (mt-10) outliers start: 58 outliers final: 38 residues processed: 311 average time/residue: 0.3170 time to fit residues: 161.6102 Evaluate side-chains 286 residues out of total 2454 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 245 time to evaluate : 2.824 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 47 LEU Chi-restraints excluded: chain A residue 615 SER Chi-restraints excluded: chain G residue 49 THR Chi-restraints excluded: chain G residue 74 CYS Chi-restraints excluded: chain G residue 239 CYS Chi-restraints excluded: chain G residue 355 ASN Chi-restraints excluded: chain G residue 373 THR Chi-restraints excluded: chain G residue 377 ASN Chi-restraints excluded: chain C residue 24 ILE Chi-restraints excluded: chain C residue 53 ASP Chi-restraints excluded: chain C residue 87 GLU Chi-restraints excluded: chain C residue 92 GLU Chi-restraints excluded: chain C residue 138 ILE Chi-restraints excluded: chain H residue 78 VAL Chi-restraints excluded: chain H residue 82 LEU Chi-restraints excluded: chain H residue 95 VAL Chi-restraints excluded: chain B residue 615 SER Chi-restraints excluded: chain I residue 123 THR Chi-restraints excluded: chain I residue 239 CYS Chi-restraints excluded: chain I residue 300 ASN Chi-restraints excluded: chain I residue 373 THR Chi-restraints excluded: chain I residue 401 THR Chi-restraints excluded: chain I residue 426 MET Chi-restraints excluded: chain E residue 16 CYS Chi-restraints excluded: chain E residue 87 GLU Chi-restraints excluded: chain K residue 2 VAL Chi-restraints excluded: chain K residue 38 ARG Chi-restraints excluded: chain K residue 84 SER Chi-restraints excluded: chain K residue 95 VAL Chi-restraints excluded: chain D residue 530 MET Chi-restraints excluded: chain D residue 615 SER Chi-restraints excluded: chain D residue 622 ILE Chi-restraints excluded: chain J residue 95 MET Chi-restraints excluded: chain J residue 239 CYS Chi-restraints excluded: chain J residue 355 ASN Chi-restraints excluded: chain F residue 16 CYS Chi-restraints excluded: chain F residue 87 GLU Chi-restraints excluded: chain M residue 2 VAL Chi-restraints excluded: chain M residue 28 THR Chi-restraints excluded: chain M residue 82 LEU Chi-restraints excluded: chain M residue 95 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 273 random chunks: chunk 88 optimal weight: 6.9990 chunk 237 optimal weight: 7.9990 chunk 52 optimal weight: 3.9990 chunk 154 optimal weight: 9.9990 chunk 65 optimal weight: 9.9990 chunk 264 optimal weight: 0.7980 chunk 219 optimal weight: 3.9990 chunk 122 optimal weight: 6.9990 chunk 21 optimal weight: 0.5980 chunk 87 optimal weight: 9.9990 chunk 138 optimal weight: 0.8980 overall best weight: 2.0584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** G 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 398 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 607 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 653 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 398 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 39 ASN ** J 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 398 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 462 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 474 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7849 moved from start: 0.3510 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 24162 Z= 0.248 Angle : 0.660 10.788 32790 Z= 0.319 Chirality : 0.046 0.406 4092 Planarity : 0.003 0.035 4011 Dihedral : 8.688 70.389 5619 Min Nonbonded Distance : 2.106 Molprobity Statistics. All-atom Clashscore : 11.35 Ramachandran Plot: Outliers : 0.22 % Allowed : 9.02 % Favored : 90.76 % Rotamer: Outliers : 2.94 % Allowed : 12.85 % Favored : 84.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.63 % 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: -2.64 (0.15), residues: 2760 helix: -0.46 (0.24), residues: 468 sheet: -1.14 (0.19), residues: 720 loop : -2.56 (0.14), residues: 1572 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.001 TRP M 36 HIS 0.004 0.001 HIS G 66 PHE 0.013 0.001 PHE G 382 TYR 0.025 0.002 TYR B 638 ARG 0.004 0.000 ARG H 31 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5520 Ramachandran restraints generated. 2760 Oldfield, 0 Emsley, 2760 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5520 Ramachandran restraints generated. 2760 Oldfield, 0 Emsley, 2760 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 329 residues out of total 2454 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 72 poor density : 257 time to evaluate : 2.621 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: L 70 GLU cc_start: 0.8253 (tm-30) cc_final: 0.7884 (tm-30) REVERT: A 612 ASP cc_start: 0.7320 (OUTLIER) cc_final: 0.7098 (t0) REVERT: A 629 MET cc_start: 0.8720 (mmm) cc_final: 0.8174 (mtp) REVERT: A 659 GLU cc_start: 0.8628 (mm-30) cc_final: 0.8427 (tt0) REVERT: G 61 TYR cc_start: 0.8558 (p90) cc_final: 0.8301 (p90) REVERT: G 95 MET cc_start: 0.8033 (ttp) cc_final: 0.7675 (ttp) REVERT: G 377 ASN cc_start: 0.8551 (OUTLIER) cc_final: 0.8015 (t0) REVERT: G 457 ASP cc_start: 0.7900 (t0) cc_final: 0.7548 (t0) REVERT: C 85 GLU cc_start: 0.7577 (mp0) cc_final: 0.7201 (mp0) REVERT: H 1 GLN cc_start: 0.6977 (mt0) cc_final: 0.5452 (pm20) REVERT: H 13 LYS cc_start: 0.7602 (mmtt) cc_final: 0.6747 (ptmm) REVERT: H 81 GLU cc_start: 0.8159 (tm-30) cc_final: 0.7699 (tm-30) REVERT: B 624 ASP cc_start: 0.7653 (m-30) cc_final: 0.7297 (m-30) REVERT: B 629 MET cc_start: 0.8512 (mmm) cc_final: 0.8135 (mmm) REVERT: B 657 GLU cc_start: 0.8054 (tp30) cc_final: 0.7668 (tm-30) REVERT: I 49 THR cc_start: 0.7956 (p) cc_final: 0.7659 (p) REVERT: I 61 TYR cc_start: 0.8533 (p90) cc_final: 0.8225 (p90) REVERT: E 10 ASP cc_start: 0.6713 (p0) cc_final: 0.6170 (p0) REVERT: E 85 GLU cc_start: 0.7433 (mp0) cc_final: 0.6663 (mp0) REVERT: K 13 LYS cc_start: 0.7527 (mmtt) cc_final: 0.6784 (ptmm) REVERT: K 38 ARG cc_start: 0.6608 (OUTLIER) cc_final: 0.6025 (ttm170) REVERT: K 81 GLU cc_start: 0.8097 (tm-30) cc_final: 0.7780 (tm-30) REVERT: D 624 ASP cc_start: 0.7239 (m-30) cc_final: 0.6877 (m-30) REVERT: D 629 MET cc_start: 0.8423 (mmm) cc_final: 0.7970 (mmm) REVERT: J 95 MET cc_start: 0.8566 (OUTLIER) cc_final: 0.8134 (ttp) REVERT: F 136 LYS cc_start: 0.4769 (OUTLIER) cc_final: 0.4449 (ttpt) REVERT: F 169 GLU cc_start: 0.7468 (mm-30) cc_final: 0.7098 (mm-30) REVERT: M 13 LYS cc_start: 0.7971 (mmtt) cc_final: 0.7463 (ptmm) REVERT: M 46 GLU cc_start: 0.7088 (mt-10) cc_final: 0.6742 (mt-10) REVERT: M 82 LEU cc_start: 0.7612 (OUTLIER) cc_final: 0.7389 (mt) outliers start: 72 outliers final: 50 residues processed: 307 average time/residue: 0.3113 time to fit residues: 156.6694 Evaluate side-chains 300 residues out of total 2454 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 56 poor density : 244 time to evaluate : 2.897 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 32 ASP Chi-restraints excluded: chain L residue 47 LEU Chi-restraints excluded: chain A residue 612 ASP Chi-restraints excluded: chain A residue 615 SER Chi-restraints excluded: chain A residue 622 ILE Chi-restraints excluded: chain G residue 49 THR Chi-restraints excluded: chain G residue 63 THR Chi-restraints excluded: chain G residue 74 CYS Chi-restraints excluded: chain G residue 123 THR Chi-restraints excluded: chain G residue 239 CYS Chi-restraints excluded: chain G residue 355 ASN Chi-restraints excluded: chain G residue 373 THR Chi-restraints excluded: chain G residue 377 ASN Chi-restraints excluded: chain C residue 24 ILE Chi-restraints excluded: chain C residue 39 ASN Chi-restraints excluded: chain C residue 87 GLU Chi-restraints excluded: chain C residue 138 ILE Chi-restraints excluded: chain H residue 2 VAL Chi-restraints excluded: chain H residue 16 SER Chi-restraints excluded: chain H residue 78 VAL Chi-restraints excluded: chain H residue 82 LEU Chi-restraints excluded: chain H residue 84 SER Chi-restraints excluded: chain H residue 95 VAL Chi-restraints excluded: chain B residue 615 SER Chi-restraints excluded: chain I residue 74 CYS Chi-restraints excluded: chain I residue 123 THR Chi-restraints excluded: chain I residue 239 CYS Chi-restraints excluded: chain I residue 300 ASN Chi-restraints excluded: chain I residue 355 ASN Chi-restraints excluded: chain I residue 373 THR Chi-restraints excluded: chain I residue 401 THR Chi-restraints excluded: chain I residue 426 MET Chi-restraints excluded: chain E residue 16 CYS Chi-restraints excluded: chain E residue 87 GLU Chi-restraints excluded: chain K residue 2 VAL Chi-restraints excluded: chain K residue 38 ARG Chi-restraints excluded: chain K residue 84 SER Chi-restraints excluded: chain K residue 95 VAL Chi-restraints excluded: chain D residue 530 MET Chi-restraints excluded: chain D residue 615 SER Chi-restraints excluded: chain D residue 622 ILE Chi-restraints excluded: chain D residue 649 SER Chi-restraints excluded: chain J residue 49 THR Chi-restraints excluded: chain J residue 74 CYS Chi-restraints excluded: chain J residue 95 MET Chi-restraints excluded: chain J residue 239 CYS Chi-restraints excluded: chain J residue 300 ASN Chi-restraints excluded: chain J residue 355 ASN Chi-restraints excluded: chain F residue 16 CYS Chi-restraints excluded: chain F residue 83 ILE Chi-restraints excluded: chain F residue 87 GLU Chi-restraints excluded: chain F residue 136 LYS Chi-restraints excluded: chain M residue 2 VAL Chi-restraints excluded: chain M residue 28 THR Chi-restraints excluded: chain M residue 82 LEU Chi-restraints excluded: chain M residue 95 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 273 random chunks: chunk 254 optimal weight: 0.0070 chunk 29 optimal weight: 0.0270 chunk 150 optimal weight: 5.9990 chunk 192 optimal weight: 1.9990 chunk 149 optimal weight: 0.0030 chunk 222 optimal weight: 5.9990 chunk 147 optimal weight: 10.0000 chunk 263 optimal weight: 20.0000 chunk 164 optimal weight: 0.0980 chunk 160 optimal weight: 7.9990 chunk 121 optimal weight: 4.9990 overall best weight: 0.4268 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** G 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 398 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 607 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 653 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 398 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 39 ASN ** D 567 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 308 HIS ** J 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 398 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 462 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 474 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7786 moved from start: 0.3663 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.040 24162 Z= 0.155 Angle : 0.607 11.446 32790 Z= 0.295 Chirality : 0.045 0.432 4092 Planarity : 0.003 0.033 4011 Dihedral : 7.970 65.694 5619 Min Nonbonded Distance : 2.169 Molprobity Statistics. All-atom Clashscore : 9.73 Ramachandran Plot: Outliers : 0.22 % Allowed : 6.78 % Favored : 93.01 % Rotamer: Outliers : 2.08 % Allowed : 13.67 % Favored : 84.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.63 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.11 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.22 (0.15), residues: 2760 helix: 0.09 (0.25), residues: 459 sheet: -0.92 (0.19), residues: 723 loop : -2.32 (0.14), residues: 1578 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP M 36 HIS 0.003 0.001 HIS I 374 PHE 0.013 0.001 PHE I 53 TYR 0.017 0.001 TYR B 638 ARG 0.017 0.000 ARG K 38 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5520 Ramachandran restraints generated. 2760 Oldfield, 0 Emsley, 2760 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5520 Ramachandran restraints generated. 2760 Oldfield, 0 Emsley, 2760 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 327 residues out of total 2454 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 51 poor density : 276 time to evaluate : 2.890 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: L 70 GLU cc_start: 0.8212 (tm-30) cc_final: 0.7764 (tm-30) REVERT: A 647 GLU cc_start: 0.8162 (tm-30) cc_final: 0.7917 (tm-30) REVERT: G 61 TYR cc_start: 0.8476 (p90) cc_final: 0.8228 (p90) REVERT: G 95 MET cc_start: 0.7854 (ttp) cc_final: 0.7288 (ttp) REVERT: G 377 ASN cc_start: 0.8546 (OUTLIER) cc_final: 0.8277 (t0) REVERT: G 457 ASP cc_start: 0.7871 (t0) cc_final: 0.7537 (t0) REVERT: C 10 ASP cc_start: 0.7768 (m-30) cc_final: 0.7520 (p0) REVERT: C 77 GLU cc_start: 0.7544 (mp0) cc_final: 0.7316 (mp0) REVERT: C 85 GLU cc_start: 0.7272 (mp0) cc_final: 0.7009 (mp0) REVERT: H 13 LYS cc_start: 0.7599 (mmtt) cc_final: 0.6792 (ptmm) REVERT: H 81 GLU cc_start: 0.8161 (tm-30) cc_final: 0.7688 (tm-30) REVERT: H 82 LEU cc_start: 0.7629 (OUTLIER) cc_final: 0.7248 (mt) REVERT: H 99 GLU cc_start: 0.7394 (mm-30) cc_final: 0.7139 (mm-30) REVERT: B 624 ASP cc_start: 0.7545 (m-30) cc_final: 0.7185 (m-30) REVERT: B 629 MET cc_start: 0.8409 (mmm) cc_final: 0.8086 (mmm) REVERT: B 657 GLU cc_start: 0.8030 (tp30) cc_final: 0.7663 (tm-30) REVERT: I 49 THR cc_start: 0.7680 (p) cc_final: 0.7397 (p) REVERT: I 61 TYR cc_start: 0.8512 (p90) cc_final: 0.8192 (p90) REVERT: I 440 ARG cc_start: 0.7531 (mmm-85) cc_final: 0.7159 (mmm160) REVERT: E 10 ASP cc_start: 0.6571 (p0) cc_final: 0.6026 (p0) REVERT: K 13 LYS cc_start: 0.7505 (mmtt) cc_final: 0.6814 (ptmm) REVERT: K 48 MET cc_start: 0.8768 (tpp) cc_final: 0.8378 (mtp) REVERT: K 81 GLU cc_start: 0.8174 (tm-30) cc_final: 0.7876 (tm-30) REVERT: D 624 ASP cc_start: 0.7121 (m-30) cc_final: 0.6765 (m-30) REVERT: D 629 MET cc_start: 0.8372 (mmm) cc_final: 0.8028 (mmm) REVERT: J 95 MET cc_start: 0.8455 (OUTLIER) cc_final: 0.8039 (ttp) REVERT: F 136 LYS cc_start: 0.4622 (OUTLIER) cc_final: 0.4270 (ttpt) REVERT: F 169 GLU cc_start: 0.7393 (mm-30) cc_final: 0.7030 (mm-30) REVERT: M 13 LYS cc_start: 0.7992 (mmtt) cc_final: 0.7433 (ptmm) REVERT: M 46 GLU cc_start: 0.7019 (mt-10) cc_final: 0.6672 (mt-10) outliers start: 51 outliers final: 38 residues processed: 306 average time/residue: 0.3155 time to fit residues: 159.4426 Evaluate side-chains 280 residues out of total 2454 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 238 time to evaluate : 3.084 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 47 LEU Chi-restraints excluded: chain A residue 615 SER Chi-restraints excluded: chain G residue 49 THR Chi-restraints excluded: chain G residue 63 THR Chi-restraints excluded: chain G residue 74 CYS Chi-restraints excluded: chain G residue 239 CYS Chi-restraints excluded: chain G residue 355 ASN Chi-restraints excluded: chain G residue 377 ASN Chi-restraints excluded: chain C residue 24 ILE Chi-restraints excluded: chain C residue 84 CYS Chi-restraints excluded: chain C residue 87 GLU Chi-restraints excluded: chain H residue 2 VAL Chi-restraints excluded: chain H residue 78 VAL Chi-restraints excluded: chain H residue 82 LEU Chi-restraints excluded: chain H residue 95 VAL Chi-restraints excluded: chain B residue 615 SER Chi-restraints excluded: chain I residue 74 CYS Chi-restraints excluded: chain I residue 239 CYS Chi-restraints excluded: chain I residue 300 ASN Chi-restraints excluded: chain I residue 355 ASN Chi-restraints excluded: chain I residue 401 THR Chi-restraints excluded: chain I residue 426 MET Chi-restraints excluded: chain E residue 16 CYS Chi-restraints excluded: chain E residue 87 GLU Chi-restraints excluded: chain K residue 2 VAL Chi-restraints excluded: chain K residue 84 SER Chi-restraints excluded: chain K residue 95 VAL Chi-restraints excluded: chain O residue 18 ARG Chi-restraints excluded: chain D residue 530 MET Chi-restraints excluded: chain J residue 49 THR Chi-restraints excluded: chain J residue 74 CYS Chi-restraints excluded: chain J residue 95 MET Chi-restraints excluded: chain J residue 239 CYS Chi-restraints excluded: chain J residue 355 ASN Chi-restraints excluded: chain F residue 16 CYS Chi-restraints excluded: chain F residue 83 ILE Chi-restraints excluded: chain F residue 87 GLU Chi-restraints excluded: chain F residue 91 GLU Chi-restraints excluded: chain F residue 136 LYS Chi-restraints excluded: chain M residue 2 VAL Chi-restraints excluded: chain M residue 28 THR Chi-restraints excluded: chain M residue 95 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 273 random chunks: chunk 162 optimal weight: 10.0000 chunk 105 optimal weight: 2.9990 chunk 157 optimal weight: 2.9990 chunk 79 optimal weight: 6.9990 chunk 51 optimal weight: 6.9990 chunk 50 optimal weight: 0.8980 chunk 167 optimal weight: 20.0000 chunk 179 optimal weight: 6.9990 chunk 130 optimal weight: 0.5980 chunk 24 optimal weight: 0.0370 chunk 206 optimal weight: 5.9990 overall best weight: 1.5062 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** G 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 398 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 422 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 607 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 653 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 398 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 39 ASN ** J 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 398 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 462 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 474 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7816 moved from start: 0.3775 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.070 24162 Z= 0.210 Angle : 0.622 11.385 32790 Z= 0.303 Chirality : 0.045 0.393 4092 Planarity : 0.003 0.033 4011 Dihedral : 7.750 63.642 5619 Min Nonbonded Distance : 2.129 Molprobity Statistics. All-atom Clashscore : 10.30 Ramachandran Plot: Outliers : 0.22 % Allowed : 7.72 % Favored : 92.07 % Rotamer: Outliers : 2.61 % Allowed : 13.87 % Favored : 83.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.63 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.11 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.12 (0.15), residues: 2760 helix: 0.15 (0.25), residues: 459 sheet: -0.83 (0.20), residues: 678 loop : -2.24 (0.14), residues: 1623 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.001 TRP M 36 HIS 0.003 0.001 HIS G 374 PHE 0.050 0.002 PHE H 29 TYR 0.019 0.001 TYR H 100E ARG 0.004 0.000 ARG H 31 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5520 Ramachandran restraints generated. 2760 Oldfield, 0 Emsley, 2760 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5520 Ramachandran restraints generated. 2760 Oldfield, 0 Emsley, 2760 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 315 residues out of total 2454 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 64 poor density : 251 time to evaluate : 3.730 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: L 70 GLU cc_start: 0.8219 (tm-30) cc_final: 0.7728 (tm-30) REVERT: A 629 MET cc_start: 0.8684 (mmm) cc_final: 0.8158 (mtp) REVERT: A 647 GLU cc_start: 0.8262 (tm-30) cc_final: 0.7981 (tm-30) REVERT: G 61 TYR cc_start: 0.8493 (p90) cc_final: 0.8240 (p90) REVERT: G 95 MET cc_start: 0.8030 (ttp) cc_final: 0.7529 (ttp) REVERT: G 457 ASP cc_start: 0.7942 (t0) cc_final: 0.7612 (t0) REVERT: C 10 ASP cc_start: 0.7831 (m-30) cc_final: 0.7535 (p0) REVERT: C 77 GLU cc_start: 0.7876 (mp0) cc_final: 0.7431 (mp0) REVERT: C 85 GLU cc_start: 0.7396 (mp0) cc_final: 0.7053 (mp0) REVERT: H 13 LYS cc_start: 0.7696 (mmtt) cc_final: 0.6793 (ptmm) REVERT: H 81 GLU cc_start: 0.8154 (tm-30) cc_final: 0.7658 (tm-30) REVERT: H 82 LEU cc_start: 0.7652 (OUTLIER) cc_final: 0.7268 (mt) REVERT: H 99 GLU cc_start: 0.7557 (mm-30) cc_final: 0.7079 (mm-30) REVERT: B 624 ASP cc_start: 0.7580 (m-30) cc_final: 0.7203 (m-30) REVERT: B 629 MET cc_start: 0.8485 (mmm) cc_final: 0.8106 (mmm) REVERT: B 657 GLU cc_start: 0.8044 (tp30) cc_final: 0.7684 (tm-30) REVERT: I 61 TYR cc_start: 0.8468 (p90) cc_final: 0.8184 (p90) REVERT: I 440 ARG cc_start: 0.7588 (mmm-85) cc_final: 0.7231 (mmm160) REVERT: E 10 ASP cc_start: 0.6723 (p0) cc_final: 0.6495 (p0) REVERT: K 13 LYS cc_start: 0.7538 (mmtt) cc_final: 0.6765 (ptmm) REVERT: K 48 MET cc_start: 0.8756 (tpp) cc_final: 0.8389 (mtp) REVERT: K 81 GLU cc_start: 0.8151 (tm-30) cc_final: 0.7862 (tm-30) REVERT: D 565 MET cc_start: 0.4871 (OUTLIER) cc_final: 0.4627 (mmm) REVERT: D 624 ASP cc_start: 0.7142 (m-30) cc_final: 0.6775 (m-30) REVERT: D 629 MET cc_start: 0.8363 (mmm) cc_final: 0.7890 (mmm) REVERT: J 95 MET cc_start: 0.8433 (OUTLIER) cc_final: 0.8038 (ttp) REVERT: F 136 LYS cc_start: 0.4770 (OUTLIER) cc_final: 0.4382 (ttpt) REVERT: F 169 GLU cc_start: 0.7474 (mm-30) cc_final: 0.7200 (mm-30) REVERT: M 13 LYS cc_start: 0.8022 (mmtt) cc_final: 0.7416 (ptmm) outliers start: 64 outliers final: 48 residues processed: 291 average time/residue: 0.3263 time to fit residues: 154.7417 Evaluate side-chains 288 residues out of total 2454 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 52 poor density : 236 time to evaluate : 2.556 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 47 LEU Chi-restraints excluded: chain A residue 615 SER Chi-restraints excluded: chain A residue 622 ILE Chi-restraints excluded: chain G residue 49 THR Chi-restraints excluded: chain G residue 63 THR Chi-restraints excluded: chain G residue 74 CYS Chi-restraints excluded: chain G residue 123 THR Chi-restraints excluded: chain G residue 239 CYS Chi-restraints excluded: chain G residue 355 ASN Chi-restraints excluded: chain G residue 373 THR Chi-restraints excluded: chain C residue 24 ILE Chi-restraints excluded: chain C residue 87 GLU Chi-restraints excluded: chain C residue 138 ILE Chi-restraints excluded: chain H residue 2 VAL Chi-restraints excluded: chain H residue 16 SER Chi-restraints excluded: chain H residue 78 VAL Chi-restraints excluded: chain H residue 82 LEU Chi-restraints excluded: chain H residue 84 SER Chi-restraints excluded: chain H residue 95 VAL Chi-restraints excluded: chain B residue 523 LEU Chi-restraints excluded: chain B residue 615 SER Chi-restraints excluded: chain I residue 74 CYS Chi-restraints excluded: chain I residue 123 THR Chi-restraints excluded: chain I residue 239 CYS Chi-restraints excluded: chain I residue 300 ASN Chi-restraints excluded: chain I residue 355 ASN Chi-restraints excluded: chain I residue 373 THR Chi-restraints excluded: chain I residue 401 THR Chi-restraints excluded: chain I residue 426 MET Chi-restraints excluded: chain E residue 16 CYS Chi-restraints excluded: chain E residue 87 GLU Chi-restraints excluded: chain K residue 2 VAL Chi-restraints excluded: chain K residue 67 VAL Chi-restraints excluded: chain K residue 84 SER Chi-restraints excluded: chain K residue 95 VAL Chi-restraints excluded: chain O residue 18 ARG Chi-restraints excluded: chain D residue 530 MET Chi-restraints excluded: chain D residue 565 MET Chi-restraints excluded: chain J residue 49 THR Chi-restraints excluded: chain J residue 74 CYS Chi-restraints excluded: chain J residue 95 MET Chi-restraints excluded: chain J residue 123 THR Chi-restraints excluded: chain J residue 239 CYS Chi-restraints excluded: chain J residue 355 ASN Chi-restraints excluded: chain F residue 16 CYS Chi-restraints excluded: chain F residue 24 ILE Chi-restraints excluded: chain F residue 87 GLU Chi-restraints excluded: chain F residue 136 LYS Chi-restraints excluded: chain M residue 2 VAL Chi-restraints excluded: chain M residue 28 THR Chi-restraints excluded: chain M residue 82 LEU Chi-restraints excluded: chain M residue 95 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 273 random chunks: chunk 239 optimal weight: 9.9990 chunk 252 optimal weight: 8.9990 chunk 229 optimal weight: 6.9990 chunk 245 optimal weight: 7.9990 chunk 147 optimal weight: 5.9990 chunk 106 optimal weight: 0.0170 chunk 192 optimal weight: 20.0000 chunk 75 optimal weight: 7.9990 chunk 221 optimal weight: 0.0270 chunk 231 optimal weight: 3.9990 chunk 244 optimal weight: 9.9990 overall best weight: 3.4082 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** L 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 398 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 422 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 607 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 653 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 66 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 398 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 39 ASN ** J 66 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 328 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 398 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 462 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 474 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7881 moved from start: 0.3882 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.067 24162 Z= 0.363 Angle : 0.708 12.253 32790 Z= 0.343 Chirality : 0.048 0.403 4092 Planarity : 0.004 0.034 4011 Dihedral : 8.076 61.467 5619 Min Nonbonded Distance : 2.062 Molprobity Statistics. All-atom Clashscore : 12.37 Ramachandran Plot: Outliers : 0.22 % Allowed : 9.64 % Favored : 90.14 % Rotamer: Outliers : 2.86 % Allowed : 13.91 % Favored : 83.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.63 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.11 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.33 (0.15), residues: 2760 helix: -0.28 (0.24), residues: 468 sheet: -1.00 (0.19), residues: 738 loop : -2.31 (0.14), residues: 1554 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP M 36 HIS 0.004 0.001 HIS J 105 PHE 0.042 0.002 PHE H 29 TYR 0.018 0.002 TYR I 484 ARG 0.006 0.001 ARG M 31 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5520 Ramachandran restraints generated. 2760 Oldfield, 0 Emsley, 2760 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5520 Ramachandran restraints generated. 2760 Oldfield, 0 Emsley, 2760 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 310 residues out of total 2454 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 70 poor density : 240 time to evaluate : 2.830 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: L 70 GLU cc_start: 0.8249 (tm-30) cc_final: 0.7811 (tm-30) REVERT: L 81 GLU cc_start: 0.7873 (pt0) cc_final: 0.7558 (pm20) REVERT: G 61 TYR cc_start: 0.8686 (p90) cc_final: 0.8408 (p90) REVERT: G 95 MET cc_start: 0.8336 (ttp) cc_final: 0.7991 (ttp) REVERT: G 457 ASP cc_start: 0.7916 (t0) cc_final: 0.7605 (t0) REVERT: C 77 GLU cc_start: 0.7995 (mp0) cc_final: 0.7556 (mp0) REVERT: C 85 GLU cc_start: 0.7555 (mp0) cc_final: 0.7241 (mp0) REVERT: H 1 GLN cc_start: 0.7116 (mt0) cc_final: 0.5923 (pm20) REVERT: H 13 LYS cc_start: 0.7814 (mmtt) cc_final: 0.6860 (ptmm) REVERT: H 81 GLU cc_start: 0.8201 (tm-30) cc_final: 0.7714 (tm-30) REVERT: H 82 LEU cc_start: 0.7730 (OUTLIER) cc_final: 0.7246 (mt) REVERT: H 99 GLU cc_start: 0.7637 (mm-30) cc_final: 0.7175 (mm-30) REVERT: B 620 ASN cc_start: 0.8334 (t0) cc_final: 0.7707 (t0) REVERT: B 629 MET cc_start: 0.8587 (mmm) cc_final: 0.8218 (mmm) REVERT: B 657 GLU cc_start: 0.8094 (tp30) cc_final: 0.7766 (tm-30) REVERT: I 61 TYR cc_start: 0.8527 (p90) cc_final: 0.8204 (p90) REVERT: I 208 VAL cc_start: 0.8882 (p) cc_final: 0.8642 (m) REVERT: I 440 ARG cc_start: 0.7746 (mmm-85) cc_final: 0.7409 (mmm160) REVERT: E 10 ASP cc_start: 0.6864 (p0) cc_final: 0.6503 (p0) REVERT: K 13 LYS cc_start: 0.7414 (mmtt) cc_final: 0.6684 (ptmm) REVERT: K 38 ARG cc_start: 0.6227 (OUTLIER) cc_final: 0.5014 (ttt180) REVERT: K 48 MET cc_start: 0.8708 (tpp) cc_final: 0.8434 (mtp) REVERT: K 81 GLU cc_start: 0.8139 (tm-30) cc_final: 0.7835 (tm-30) REVERT: D 565 MET cc_start: 0.4907 (OUTLIER) cc_final: 0.4686 (mmm) REVERT: D 624 ASP cc_start: 0.7185 (m-30) cc_final: 0.6833 (m-30) REVERT: D 629 MET cc_start: 0.8442 (mmm) cc_final: 0.8029 (mmm) REVERT: F 169 GLU cc_start: 0.7454 (mm-30) cc_final: 0.7194 (mm-30) REVERT: M 13 LYS cc_start: 0.7998 (mmtt) cc_final: 0.7337 (ptmm) REVERT: M 81 GLU cc_start: 0.8072 (tm-30) cc_final: 0.6977 (tm-30) outliers start: 70 outliers final: 58 residues processed: 289 average time/residue: 0.3246 time to fit residues: 153.3093 Evaluate side-chains 296 residues out of total 2454 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 61 poor density : 235 time to evaluate : 2.668 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 47 LEU Chi-restraints excluded: chain A residue 615 SER Chi-restraints excluded: chain A residue 622 ILE Chi-restraints excluded: chain G residue 49 THR Chi-restraints excluded: chain G residue 63 THR Chi-restraints excluded: chain G residue 74 CYS Chi-restraints excluded: chain G residue 123 THR Chi-restraints excluded: chain G residue 239 CYS Chi-restraints excluded: chain G residue 244 THR Chi-restraints excluded: chain G residue 355 ASN Chi-restraints excluded: chain G residue 373 THR Chi-restraints excluded: chain C residue 24 ILE Chi-restraints excluded: chain C residue 39 ASN Chi-restraints excluded: chain C residue 83 ILE Chi-restraints excluded: chain C residue 87 GLU Chi-restraints excluded: chain C residue 138 ILE Chi-restraints excluded: chain C residue 169 GLU Chi-restraints excluded: chain H residue 2 VAL Chi-restraints excluded: chain H residue 16 SER Chi-restraints excluded: chain H residue 78 VAL Chi-restraints excluded: chain H residue 82 LEU Chi-restraints excluded: chain H residue 84 SER Chi-restraints excluded: chain H residue 95 VAL Chi-restraints excluded: chain B residue 523 LEU Chi-restraints excluded: chain B residue 615 SER Chi-restraints excluded: chain I residue 74 CYS Chi-restraints excluded: chain I residue 123 THR Chi-restraints excluded: chain I residue 239 CYS Chi-restraints excluded: chain I residue 244 THR Chi-restraints excluded: chain I residue 300 ASN Chi-restraints excluded: chain I residue 355 ASN Chi-restraints excluded: chain I residue 373 THR Chi-restraints excluded: chain I residue 401 THR Chi-restraints excluded: chain I residue 419 ARG Chi-restraints excluded: chain I residue 426 MET Chi-restraints excluded: chain E residue 16 CYS Chi-restraints excluded: chain E residue 87 GLU Chi-restraints excluded: chain E residue 130 CYS Chi-restraints excluded: chain K residue 2 VAL Chi-restraints excluded: chain K residue 38 ARG Chi-restraints excluded: chain K residue 67 VAL Chi-restraints excluded: chain K residue 84 SER Chi-restraints excluded: chain K residue 95 VAL Chi-restraints excluded: chain O residue 18 ARG Chi-restraints excluded: chain D residue 530 MET Chi-restraints excluded: chain D residue 565 MET Chi-restraints excluded: chain D residue 615 SER Chi-restraints excluded: chain D residue 622 ILE Chi-restraints excluded: chain J residue 49 THR Chi-restraints excluded: chain J residue 74 CYS Chi-restraints excluded: chain J residue 123 THR Chi-restraints excluded: chain J residue 239 CYS Chi-restraints excluded: chain J residue 355 ASN Chi-restraints excluded: chain F residue 16 CYS Chi-restraints excluded: chain F residue 24 ILE Chi-restraints excluded: chain F residue 83 ILE Chi-restraints excluded: chain F residue 87 GLU Chi-restraints excluded: chain M residue 2 VAL Chi-restraints excluded: chain M residue 28 THR Chi-restraints excluded: chain M residue 82 LEU Chi-restraints excluded: chain M residue 95 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 273 random chunks: chunk 161 optimal weight: 9.9990 chunk 259 optimal weight: 20.0000 chunk 158 optimal weight: 6.9990 chunk 123 optimal weight: 0.3980 chunk 180 optimal weight: 2.9990 chunk 271 optimal weight: 3.9990 chunk 250 optimal weight: 7.9990 chunk 216 optimal weight: 10.0000 chunk 22 optimal weight: 0.9980 chunk 167 optimal weight: 0.0010 chunk 132 optimal weight: 10.0000 overall best weight: 1.6790 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** L 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 229 ASN ** G 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 398 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 422 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 607 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 653 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 328 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 398 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 39 ASN ** J 328 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 398 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 462 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 474 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7843 moved from start: 0.3954 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.066 24162 Z= 0.225 Angle : 0.641 13.134 32790 Z= 0.311 Chirality : 0.046 0.385 4092 Planarity : 0.003 0.032 4011 Dihedral : 7.811 59.789 5619 Min Nonbonded Distance : 2.128 Molprobity Statistics. All-atom Clashscore : 10.84 Ramachandran Plot: Outliers : 0.22 % Allowed : 7.79 % Favored : 91.99 % Rotamer: Outliers : 2.61 % Allowed : 14.08 % Favored : 83.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.63 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.11 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.16 (0.15), residues: 2760 helix: -0.02 (0.25), residues: 468 sheet: -0.94 (0.19), residues: 741 loop : -2.21 (0.15), residues: 1551 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP M 36 HIS 0.003 0.001 HIS E 27 PHE 0.038 0.002 PHE H 29 TYR 0.014 0.001 TYR B 638 ARG 0.004 0.000 ARG M 31 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5520 Ramachandran restraints generated. 2760 Oldfield, 0 Emsley, 2760 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5520 Ramachandran restraints generated. 2760 Oldfield, 0 Emsley, 2760 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 311 residues out of total 2454 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 64 poor density : 247 time to evaluate : 2.996 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: L 70 GLU cc_start: 0.8220 (tm-30) cc_final: 0.7739 (tm-30) REVERT: L 81 GLU cc_start: 0.7890 (pt0) cc_final: 0.7554 (pm20) REVERT: A 629 MET cc_start: 0.8649 (mmm) cc_final: 0.8123 (mtp) REVERT: A 647 GLU cc_start: 0.8339 (tm-30) cc_final: 0.8021 (tm-30) REVERT: G 61 TYR cc_start: 0.8607 (p90) cc_final: 0.8317 (p90) REVERT: G 95 MET cc_start: 0.8204 (ttp) cc_final: 0.7810 (ttp) REVERT: G 457 ASP cc_start: 0.7884 (t0) cc_final: 0.7595 (t0) REVERT: C 77 GLU cc_start: 0.7925 (mp0) cc_final: 0.7544 (mp0) REVERT: C 85 GLU cc_start: 0.7488 (mp0) cc_final: 0.7109 (mp0) REVERT: H 1 GLN cc_start: 0.7137 (mt0) cc_final: 0.5975 (pm20) REVERT: H 13 LYS cc_start: 0.7783 (mmtt) cc_final: 0.6823 (ptmm) REVERT: H 81 GLU cc_start: 0.8176 (tm-30) cc_final: 0.7684 (tm-30) REVERT: H 82 LEU cc_start: 0.7763 (OUTLIER) cc_final: 0.7310 (mt) REVERT: H 99 GLU cc_start: 0.7624 (mm-30) cc_final: 0.7216 (mm-30) REVERT: B 620 ASN cc_start: 0.8417 (t0) cc_final: 0.7833 (t0) REVERT: B 629 MET cc_start: 0.8499 (mmm) cc_final: 0.8160 (mmm) REVERT: B 661 LEU cc_start: 0.7533 (mt) cc_final: 0.7332 (pp) REVERT: I 61 TYR cc_start: 0.8562 (p90) cc_final: 0.8235 (p90) REVERT: I 440 ARG cc_start: 0.7693 (mmm-85) cc_final: 0.7362 (mmm160) REVERT: E 10 ASP cc_start: 0.6573 (p0) cc_final: 0.6272 (p0) REVERT: K 13 LYS cc_start: 0.7319 (mmtt) cc_final: 0.6649 (ptmm) REVERT: K 48 MET cc_start: 0.8682 (OUTLIER) cc_final: 0.8414 (mtp) REVERT: K 81 GLU cc_start: 0.8142 (tm-30) cc_final: 0.7850 (tm-30) REVERT: D 565 MET cc_start: 0.4739 (OUTLIER) cc_final: 0.4504 (mmm) REVERT: D 624 ASP cc_start: 0.7107 (m-30) cc_final: 0.6730 (m-30) REVERT: D 629 MET cc_start: 0.8295 (mmm) cc_final: 0.7999 (mmm) REVERT: F 85 GLU cc_start: 0.7474 (mp0) cc_final: 0.7254 (mp0) REVERT: M 13 LYS cc_start: 0.8037 (mmtt) cc_final: 0.7392 (ptmm) REVERT: M 46 GLU cc_start: 0.7123 (mt-10) cc_final: 0.6873 (mt-10) REVERT: M 81 GLU cc_start: 0.8145 (tm-30) cc_final: 0.7059 (tm-30) REVERT: M 99 GLU cc_start: 0.6811 (mm-30) cc_final: 0.6570 (mm-30) outliers start: 64 outliers final: 56 residues processed: 290 average time/residue: 0.3252 time to fit residues: 153.4442 Evaluate side-chains 298 residues out of total 2454 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 59 poor density : 239 time to evaluate : 2.566 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 47 LEU Chi-restraints excluded: chain A residue 615 SER Chi-restraints excluded: chain A residue 622 ILE Chi-restraints excluded: chain G residue 49 THR Chi-restraints excluded: chain G residue 63 THR Chi-restraints excluded: chain G residue 74 CYS Chi-restraints excluded: chain G residue 123 THR Chi-restraints excluded: chain G residue 239 CYS Chi-restraints excluded: chain G residue 355 ASN Chi-restraints excluded: chain G residue 373 THR Chi-restraints excluded: chain C residue 16 CYS Chi-restraints excluded: chain C residue 24 ILE Chi-restraints excluded: chain C residue 53 ASP Chi-restraints excluded: chain C residue 83 ILE Chi-restraints excluded: chain C residue 87 GLU Chi-restraints excluded: chain C residue 138 ILE Chi-restraints excluded: chain C residue 169 GLU Chi-restraints excluded: chain H residue 2 VAL Chi-restraints excluded: chain H residue 16 SER Chi-restraints excluded: chain H residue 78 VAL Chi-restraints excluded: chain H residue 82 LEU Chi-restraints excluded: chain H residue 84 SER Chi-restraints excluded: chain H residue 95 VAL Chi-restraints excluded: chain B residue 523 LEU Chi-restraints excluded: chain B residue 615 SER Chi-restraints excluded: chain I residue 74 CYS Chi-restraints excluded: chain I residue 123 THR Chi-restraints excluded: chain I residue 239 CYS Chi-restraints excluded: chain I residue 300 ASN Chi-restraints excluded: chain I residue 355 ASN Chi-restraints excluded: chain I residue 373 THR Chi-restraints excluded: chain I residue 401 THR Chi-restraints excluded: chain I residue 419 ARG Chi-restraints excluded: chain I residue 426 MET Chi-restraints excluded: chain E residue 16 CYS Chi-restraints excluded: chain E residue 87 GLU Chi-restraints excluded: chain K residue 2 VAL Chi-restraints excluded: chain K residue 48 MET Chi-restraints excluded: chain K residue 67 VAL Chi-restraints excluded: chain K residue 84 SER Chi-restraints excluded: chain K residue 95 VAL Chi-restraints excluded: chain O residue 18 ARG Chi-restraints excluded: chain D residue 530 MET Chi-restraints excluded: chain D residue 565 MET Chi-restraints excluded: chain D residue 615 SER Chi-restraints excluded: chain J residue 49 THR Chi-restraints excluded: chain J residue 74 CYS Chi-restraints excluded: chain J residue 123 THR Chi-restraints excluded: chain J residue 239 CYS Chi-restraints excluded: chain J residue 355 ASN Chi-restraints excluded: chain J residue 373 THR Chi-restraints excluded: chain F residue 16 CYS Chi-restraints excluded: chain F residue 24 ILE Chi-restraints excluded: chain F residue 83 ILE Chi-restraints excluded: chain F residue 87 GLU Chi-restraints excluded: chain M residue 2 VAL Chi-restraints excluded: chain M residue 28 THR Chi-restraints excluded: chain M residue 82 LEU Chi-restraints excluded: chain M residue 95 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 273 random chunks: chunk 172 optimal weight: 9.9990 chunk 230 optimal weight: 0.9980 chunk 66 optimal weight: 4.9990 chunk 199 optimal weight: 2.9990 chunk 31 optimal weight: 0.5980 chunk 60 optimal weight: 3.9990 chunk 216 optimal weight: 10.0000 chunk 90 optimal weight: 9.9990 chunk 222 optimal weight: 2.9990 chunk 27 optimal weight: 1.9990 chunk 39 optimal weight: 5.9990 overall best weight: 1.9186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** L 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 398 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 422 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 607 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 653 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 66 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 398 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 328 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 398 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 462 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 474 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3700 r_free = 0.3700 target = 0.096410 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3233 r_free = 0.3233 target = 0.072112 restraints weight = 68816.394| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3240 r_free = 0.3240 target = 0.072698 restraints weight = 42864.516| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3244 r_free = 0.3244 target = 0.072972 restraints weight = 34802.169| |-----------------------------------------------------------------------------| r_work (final): 0.3226 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8100 moved from start: 0.4043 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.058 24162 Z= 0.239 Angle : 0.646 13.118 32790 Z= 0.313 Chirality : 0.046 0.384 4092 Planarity : 0.003 0.032 4011 Dihedral : 7.470 59.909 5619 Min Nonbonded Distance : 2.121 Molprobity Statistics. All-atom Clashscore : 10.60 Ramachandran Plot: Outliers : 0.22 % Allowed : 8.70 % Favored : 91.09 % Rotamer: Outliers : 2.69 % Allowed : 14.20 % Favored : 83.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.63 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.11 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.09 (0.15), residues: 2760 helix: -0.04 (0.25), residues: 471 sheet: -0.88 (0.19), residues: 741 loop : -2.15 (0.15), residues: 1548 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP M 36 HIS 0.003 0.001 HIS G 66 PHE 0.038 0.002 PHE H 29 TYR 0.015 0.001 TYR I 484 ARG 0.004 0.000 ARG M 31 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4360.71 seconds wall clock time: 81 minutes 6.85 seconds (4866.85 seconds total)