Starting phenix.real_space_refine on Tue Jun 17 19:56:27 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8gpj_34194/06_2025/8gpj_34194.cif Found real_map, /net/cci-nas-00/data/ceres_data/8gpj_34194/06_2025/8gpj_34194.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.5 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8gpj_34194/06_2025/8gpj_34194.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8gpj_34194/06_2025/8gpj_34194.map" model { file = "/net/cci-nas-00/data/ceres_data/8gpj_34194/06_2025/8gpj_34194.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8gpj_34194/06_2025/8gpj_34194.cif" } resolution = 3.5 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= 0.002 sd= 0.035 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 120 5.16 5 C 12653 2.51 5 N 3319 2.21 5 O 4167 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 15 residue(s): 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/chem_data/mon_lib" Total number of atoms: 20259 Number of models: 1 Model: "" Number of chains: 48 Chain: "A" Number of atoms: 1001 Number of conformers: 1 Conformer: "" Number of residues, atoms: 130, 1001 Classifications: {'peptide': 130} Link IDs: {'PTRANS': 4, 'TRANS': 125} Chain: "C" Number of atoms: 810 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 810 Classifications: {'peptide': 107} Link IDs: {'PCIS': 2, 'PTRANS': 3, 'TRANS': 101} Chain: "D" Number of atoms: 1001 Number of conformers: 1 Conformer: "" Number of residues, atoms: 130, 1001 Classifications: {'peptide': 130} Link IDs: {'PTRANS': 4, 'TRANS': 125} Chain: "E" Number of atoms: 810 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 810 Classifications: {'peptide': 107} Link IDs: {'PCIS': 2, 'PTRANS': 3, 'TRANS': 101} Chain: "H" Number of atoms: 1001 Number of conformers: 1 Conformer: "" Number of residues, atoms: 130, 1001 Classifications: {'peptide': 130} Link IDs: {'PTRANS': 4, 'TRANS': 125} Chain: "L" Number of atoms: 810 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 810 Classifications: {'peptide': 107} Link IDs: {'PCIS': 2, 'PTRANS': 3, 'TRANS': 101} Chain: "U" Number of atoms: 1020 Number of conformers: 1 Conformer: "" Number of residues, atoms: 128, 1020 Classifications: {'peptide': 128} Link IDs: {'PTRANS': 3, 'TRANS': 124} Chain: "V" Number of atoms: 1020 Number of conformers: 1 Conformer: "" Number of residues, atoms: 128, 1020 Classifications: {'peptide': 128} Link IDs: {'PTRANS': 3, 'TRANS': 124} Chain: "W" Number of atoms: 1020 Number of conformers: 1 Conformer: "" Number of residues, atoms: 128, 1020 Classifications: {'peptide': 128} Link IDs: {'PTRANS': 3, 'TRANS': 124} Chain: "X" Number of atoms: 3378 Number of conformers: 1 Conformer: "" Number of residues, atoms: 429, 3378 Classifications: {'peptide': 429} Link IDs: {'PTRANS': 21, 'TRANS': 407} Chain breaks: 3 Chain: "Y" Number of atoms: 3378 Number of conformers: 1 Conformer: "" Number of residues, atoms: 429, 3378 Classifications: {'peptide': 429} Link IDs: {'PTRANS': 21, 'TRANS': 407} Chain breaks: 3 Chain: "Z" Number of atoms: 3378 Number of conformers: 1 Conformer: "" Number of residues, atoms: 429, 3378 Classifications: {'peptide': 429} Link IDs: {'PTRANS': 21, 'TRANS': 407} Chain breaks: 3 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: "F" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "G" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "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: 116 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 116 Unusual residues: {'BMA': 1, 'MAN': 7, 'NAG': 2} Classifications: {'undetermined': 10} Link IDs: {None: 9} Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 20 Unresolved non-hydrogen dihedrals: 30 Unresolved non-hydrogen chiralities: 10 Chain: "M" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "N" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Chain: "O" Number of atoms: 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: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "S" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "T" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "a" Number of atoms: 116 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 116 Unusual residues: {'BMA': 1, 'MAN': 7, 'NAG': 2} Classifications: {'undetermined': 10} Link IDs: {None: 9} Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 20 Unresolved non-hydrogen dihedrals: 30 Unresolved non-hydrogen chiralities: 10 Chain: "b" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "c" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Chain: "d" Number of atoms: 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: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "h" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "i" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "j" Number of atoms: 127 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 127 Unusual residues: {'BMA': 1, 'MAN': 8, 'NAG': 2} Classifications: {'undetermined': 11} Link IDs: {None: 10} Unresolved non-hydrogen bonds: 11 Unresolved non-hydrogen angles: 22 Unresolved non-hydrogen dihedrals: 33 Unresolved non-hydrogen chiralities: 11 Chain: "k" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "l" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Chain: "m" Number of atoms: 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: "n" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "o" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "p" Number of atoms: 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: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "W" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "X" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 84 Unusual residues: {'NAG': 6} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 18 Unresolved non-hydrogen chiralities: 6 Chain: "Y" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 84 Unusual residues: {'NAG': 6} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 18 Unresolved non-hydrogen chiralities: 6 Chain: "Z" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 84 Unusual residues: {'NAG': 6} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 18 Unresolved non-hydrogen chiralities: 6 Time building chain proxies: 13.06, per 1000 atoms: 0.64 Number of scatterers: 20259 At special positions: 0 Unit cell: (153.7, 149.46, 118.72, 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 120 16.00 O 4167 8.00 N 3319 7.00 C 12653 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=38, symmetry=0 Simple disulfide: pdb=" SG CYS A 21 " - pdb=" SG CYS A 98 " distance=2.03 Simple disulfide: pdb=" SG CYS C 22 " - pdb=" SG CYS C 88 " distance=2.04 Simple disulfide: pdb=" SG CYS D 21 " - pdb=" SG CYS D 98 " distance=2.03 Simple disulfide: pdb=" SG CYS E 22 " - pdb=" SG CYS E 88 " distance=2.04 Simple disulfide: pdb=" SG CYS H 21 " - pdb=" SG CYS H 98 " distance=2.03 Simple disulfide: pdb=" SG CYS U 598 " - pdb=" SG CYS U 604 " distance=2.03 Simple disulfide: pdb=" SG CYS U 605 " - pdb=" SG CYS Y 501 " distance=2.03 Simple disulfide: pdb=" SG CYS V 598 " - pdb=" SG CYS V 604 " distance=2.03 Simple disulfide: pdb=" SG CYS V 605 " - pdb=" SG CYS X 501 " distance=2.03 Simple disulfide: pdb=" SG CYS W 598 " - pdb=" SG CYS W 604 " distance=2.03 Simple disulfide: pdb=" SG CYS W 605 " - pdb=" SG CYS Z 501 " distance=2.03 Simple disulfide: pdb=" SG CYS X 54 " - pdb=" SG CYS X 74 " distance=2.03 Simple disulfide: pdb=" SG CYS X 119 " - pdb=" SG CYS X 205 " distance=2.04 Simple disulfide: pdb=" SG CYS X 126 " - pdb=" SG CYS X 196 " distance=2.03 Simple disulfide: pdb=" SG CYS X 131 " - pdb=" SG CYS X 157 " distance=2.03 Simple disulfide: pdb=" SG CYS X 218 " - pdb=" SG CYS X 247 " distance=2.02 Simple disulfide: pdb=" SG CYS X 228 " - pdb=" SG CYS X 239 " distance=2.03 Simple disulfide: pdb=" SG CYS X 296 " - pdb=" SG CYS X 331 " distance=2.05 Simple disulfide: pdb=" SG CYS X 378 " - pdb=" SG CYS X 445 " distance=2.03 Simple disulfide: pdb=" SG CYS X 385 " - pdb=" SG CYS X 418 " distance=2.03 Simple disulfide: pdb=" SG CYS Y 54 " - pdb=" SG CYS Y 74 " distance=2.03 Simple disulfide: pdb=" SG CYS Y 119 " - pdb=" SG CYS Y 205 " distance=2.04 Simple disulfide: pdb=" SG CYS Y 126 " - pdb=" SG CYS Y 196 " distance=2.03 Simple disulfide: pdb=" SG CYS Y 131 " - pdb=" SG CYS Y 157 " distance=2.03 Simple disulfide: pdb=" SG CYS Y 218 " - pdb=" SG CYS Y 247 " distance=2.03 Simple disulfide: pdb=" SG CYS Y 228 " - pdb=" SG CYS Y 239 " distance=2.03 Simple disulfide: pdb=" SG CYS Y 296 " - pdb=" SG CYS Y 331 " distance=2.05 Simple disulfide: pdb=" SG CYS Y 378 " - pdb=" SG CYS Y 445 " distance=2.03 Simple disulfide: pdb=" SG CYS Y 385 " - pdb=" SG CYS Y 418 " distance=2.03 Simple disulfide: pdb=" SG CYS Z 54 " - pdb=" SG CYS Z 74 " distance=2.03 Simple disulfide: pdb=" SG CYS Z 119 " - pdb=" SG CYS Z 205 " distance=2.04 Simple disulfide: pdb=" SG CYS Z 126 " - pdb=" SG CYS Z 196 " distance=2.03 Simple disulfide: pdb=" SG CYS Z 131 " - pdb=" SG CYS Z 157 " distance=2.03 Simple disulfide: pdb=" SG CYS Z 218 " - pdb=" SG CYS Z 247 " distance=2.05 Simple disulfide: pdb=" SG CYS Z 228 " - pdb=" SG CYS Z 239 " distance=2.03 Simple disulfide: pdb=" SG CYS Z 296 " - pdb=" SG CYS Z 331 " distance=2.05 Simple disulfide: pdb=" SG CYS Z 378 " - pdb=" SG CYS Z 445 " distance=2.03 Simple disulfide: pdb=" SG CYS Z 385 " - pdb=" SG CYS Z 418 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied ALPHA1-2 " MAN K 4 " - " MAN K 5 " " MAN K 5 " - " MAN K 6 " " MAN K 8 " - " MAN K 9 " " MAN a 4 " - " MAN a 5 " " MAN a 5 " - " MAN a 6 " " MAN a 8 " - " MAN a 9 " " MAN j 4 " - " MAN j 5 " " MAN j 5 " - " MAN j 6 " " MAN j 8 " - " MAN j 9 " " MAN j 10 " - " MAN j 11 " ALPHA1-3 " BMA K 3 " - " MAN K 4 " " MAN K 7 " - " MAN K 10 " " BMA N 3 " - " MAN N 4 " " BMA O 3 " - " MAN O 4 " " BMA a 3 " - " MAN a 4 " " MAN a 7 " - " MAN a 10 " " BMA c 3 " - " MAN c 4 " " BMA d 3 " - " MAN d 4 " " BMA j 3 " - " MAN j 4 " " MAN j 7 " - " MAN j 8 " " BMA l 3 " - " MAN l 4 " " BMA m 3 " - " MAN m 4 " ALPHA1-6 " BMA K 3 " - " MAN K 7 " " MAN K 7 " - " MAN K 8 " " BMA N 3 " - " MAN N 5 " " BMA a 3 " - " MAN a 7 " " MAN a 7 " - " MAN a 8 " " BMA c 3 " - " MAN c 5 " " BMA j 3 " - " MAN j 7 " " MAN j 7 " - " MAN j 10 " " BMA l 3 " - " MAN l 5 " BETA1-4 " NAG B 1 " - " NAG B 2 " " NAG B 2 " - " BMA B 3 " " NAG F 1 " - " NAG F 2 " " NAG F 2 " - " BMA F 3 " " NAG G 1 " - " NAG G 2 " " NAG G 2 " - " BMA G 3 " " NAG 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 M 1 " - " NAG M 2 " " NAG N 1 " - " NAG N 2 " " NAG N 2 " - " BMA N 3 " " NAG O 1 " - " NAG O 2 " " NAG O 2 " - " BMA O 3 " " NAG P 1 " - " NAG P 2 " " NAG Q 1 " - " NAG Q 2 " " NAG R 1 " - " NAG R 2 " " NAG S 1 " - " NAG S 2 " " NAG T 1 " - " NAG T 2 " " NAG a 1 " - " NAG a 2 " " NAG a 2 " - " BMA a 3 " " NAG b 1 " - " NAG b 2 " " NAG c 1 " - " NAG c 2 " " NAG c 2 " - " BMA c 3 " " NAG d 1 " - " NAG d 2 " " NAG d 2 " - " BMA d 3 " " NAG e 1 " - " NAG e 2 " " NAG f 1 " - " NAG f 2 " " NAG g 1 " - " NAG g 2 " " NAG h 1 " - " NAG h 2 " " NAG i 1 " - " NAG i 2 " " NAG j 1 " - " NAG j 2 " " NAG j 2 " - " BMA j 3 " " NAG k 1 " - " NAG k 2 " " NAG l 1 " - " NAG l 2 " " NAG l 2 " - " BMA l 3 " " NAG m 1 " - " NAG m 2 " " NAG m 2 " - " BMA m 3 " " NAG n 1 " - " NAG n 2 " " NAG o 1 " - " NAG o 2 " " NAG p 1 " - " NAG p 2 " NAG-ASN " NAG B 1 " - " ASN U 637 " " NAG F 1 " - " ASN V 637 " " NAG G 1 " - " ASN W 637 " " NAG I 1 " - " ASN X 156 " " NAG J 1 " - " ASN X 197 " " NAG K 1 " - " ASN X 234 " " NAG M 1 " - " ASN X 241 " " NAG N 1 " - " ASN X 262 " " NAG O 1 " - " ASN X 276 " " NAG P 1 " - " ASN X 289 " " NAG Q 1 " - " ASN X 332 " " NAG R 1 " - " ASN X 386 " " NAG S 1 " - " ASN Y 156 " " NAG T 1 " - " ASN Y 197 " " NAG U 701 " - " ASN U 616 " " NAG U 702 " - " ASN U 625 " " NAG V 701 " - " ASN V 616 " " NAG W 701 " - " ASN W 616 " " NAG X 701 " - " ASN X 88 " " NAG X 702 " - " ASN X 160 " " NAG X 703 " - " ASN X 448 " " NAG X 704 " - " ASN X 301 " " NAG X 705 " - " ASN X 392 " " NAG X 706 " - " ASN X 442 " " NAG Y 701 " - " ASN Y 88 " " NAG Y 702 " - " ASN Y 160 " " NAG Y 703 " - " ASN Y 301 " " NAG Y 704 " - " ASN Y 392 " " NAG Y 705 " - " ASN Y 442 " " NAG Y 706 " - " ASN Y 448 " " NAG Z 701 " - " ASN Z 88 " " NAG Z 702 " - " ASN Z 160 " " NAG Z 703 " - " ASN Z 301 " " NAG Z 704 " - " ASN Z 392 " " NAG Z 705 " - " ASN Z 442 " " NAG Z 706 " - " ASN Z 448 " " NAG a 1 " - " ASN Y 234 " " NAG b 1 " - " ASN Y 241 " " NAG c 1 " - " ASN Y 262 " " NAG d 1 " - " ASN Y 276 " " NAG e 1 " - " ASN Y 289 " " NAG f 1 " - " ASN Y 332 " " NAG g 1 " - " ASN Y 386 " " NAG h 1 " - " ASN Z 156 " " NAG i 1 " - " ASN Z 197 " " NAG j 1 " - " ASN Z 234 " " NAG k 1 " - " ASN Z 241 " " NAG l 1 " - " ASN Z 262 " " NAG m 1 " - " ASN Z 276 " " NAG n 1 " - " ASN Z 289 " " NAG o 1 " - " ASN Z 332 " " NAG p 1 " - " ASN Z 386 " Time building additional restraints: 6.93 Conformation dependent library (CDL) restraints added in 2.8 seconds 4680 Ramachandran restraints generated. 2340 Oldfield, 0 Emsley, 2340 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4410 Finding SS restraints... Secondary structure from input PDB file: 41 helices and 45 sheets defined 18.9% alpha, 34.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 3.10 Creating SS restraints... Processing helix chain 'A' and resid 60 through 63 Processing helix chain 'A' and resid 89 through 93 removed outlier: 3.695A pdb=" N THR A 93 " --> pdb=" O SER A 90 " (cutoff:3.500A) Processing helix chain 'D' and resid 60 through 63 removed outlier: 3.592A pdb=" N ARG D 63 " --> pdb=" O HIS D 60 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 60 through 63' Processing helix chain 'D' and resid 89 through 93 removed outlier: 4.063A pdb=" N THR D 93 " --> pdb=" O SER D 90 " (cutoff:3.500A) Processing helix chain 'H' and resid 60 through 63 Processing helix chain 'H' and resid 89 through 93 removed outlier: 3.756A pdb=" N THR H 93 " --> pdb=" O SER H 90 " (cutoff:3.500A) Processing helix chain 'U' and resid 529 through 534 removed outlier: 3.565A pdb=" N SER U 534 " --> pdb=" O MET U 530 " (cutoff:3.500A) Processing helix chain 'U' and resid 536 through 543 removed outlier: 4.171A pdb=" N GLN U 540 " --> pdb=" O ALA U 536 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N GLN U 543 " --> pdb=" O VAL U 539 " (cutoff:3.500A) Processing helix chain 'U' and resid 569 through 595 Processing helix chain 'U' and resid 618 through 626 removed outlier: 4.070A pdb=" N MET U 626 " --> pdb=" O ILE U 622 " (cutoff:3.500A) Processing helix chain 'U' and resid 627 through 635 Processing helix chain 'U' and resid 638 through 660 removed outlier: 3.649A pdb=" N LYS U 658 " --> pdb=" O GLU U 654 " (cutoff:3.500A) Processing helix chain 'V' and resid 529 through 534 Processing helix chain 'V' and resid 536 through 544 removed outlier: 4.658A pdb=" N GLN V 540 " --> pdb=" O ALA V 536 " (cutoff:3.500A) removed outlier: 3.797A pdb=" N LEU V 544 " --> pdb=" O GLN V 540 " (cutoff:3.500A) Processing helix chain 'V' and resid 569 through 596 removed outlier: 3.578A pdb=" N ILE V 573 " --> pdb=" O THR V 569 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N TRP V 596 " --> pdb=" O LEU V 592 " (cutoff:3.500A) Processing helix chain 'V' and resid 618 through 625 Processing helix chain 'V' and resid 627 through 635 Processing helix chain 'V' and resid 638 through 660 Processing helix chain 'W' and resid 529 through 534 Processing helix chain 'W' and resid 536 through 544 removed outlier: 4.478A pdb=" N GLN W 540 " --> pdb=" O ALA W 536 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N LEU W 544 " --> pdb=" O GLN W 540 " (cutoff:3.500A) Processing helix chain 'W' and resid 569 through 596 removed outlier: 3.555A pdb=" N TRP W 596 " --> pdb=" O LEU W 592 " (cutoff:3.500A) Processing helix chain 'W' and resid 618 through 625 Processing helix chain 'W' and resid 627 through 635 Processing helix chain 'W' and resid 638 through 660 Processing helix chain 'X' and resid 98 through 117 removed outlier: 4.208A pdb=" N ASN X 102 " --> pdb=" O ASN X 98 " (cutoff:3.500A) Processing helix chain 'X' and resid 195 through 197 No H-bonds generated for 'chain 'X' and resid 195 through 197' Processing helix chain 'X' and resid 335 through 353 removed outlier: 4.152A pdb=" N GLU X 351 " --> pdb=" O LYS X 347 " (cutoff:3.500A) removed outlier: 4.268A pdb=" N HIS X 352 " --> pdb=" O ASN X 348 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N PHE X 353 " --> pdb=" O LEU X 349 " (cutoff:3.500A) Processing helix chain 'X' and resid 368 through 373 Processing helix chain 'X' and resid 476 through 484 removed outlier: 4.237A pdb=" N SER X 481 " --> pdb=" O ASP X 477 " (cutoff:3.500A) removed outlier: 5.290A pdb=" N GLU X 482 " --> pdb=" O ASN X 478 " (cutoff:3.500A) Processing helix chain 'Y' and resid 94 through 97 removed outlier: 3.776A pdb=" N LYS Y 97 " --> pdb=" O ASN Y 94 " (cutoff:3.500A) No H-bonds generated for 'chain 'Y' and resid 94 through 97' Processing helix chain 'Y' and resid 98 through 117 removed outlier: 4.445A pdb=" N ASN Y 102 " --> pdb=" O ASN Y 98 " (cutoff:3.500A) Processing helix chain 'Y' and resid 122 through 126 Processing helix chain 'Y' and resid 335 through 350 Processing helix chain 'Y' and resid 368 through 373 Processing helix chain 'Y' and resid 474 through 479 Processing helix chain 'Z' and resid 67 through 73 Processing helix chain 'Z' and resid 94 through 97 removed outlier: 3.675A pdb=" N LYS Z 97 " --> pdb=" O ASN Z 94 " (cutoff:3.500A) No H-bonds generated for 'chain 'Z' and resid 94 through 97' Processing helix chain 'Z' and resid 98 through 117 removed outlier: 4.344A pdb=" N ASN Z 102 " --> pdb=" O ASN Z 98 " (cutoff:3.500A) Processing helix chain 'Z' and resid 336 through 353 removed outlier: 3.805A pdb=" N GLU Z 351 " --> pdb=" O LYS Z 347 " (cutoff:3.500A) removed outlier: 3.790A pdb=" N HIS Z 352 " --> pdb=" O ASN Z 348 " (cutoff:3.500A) Processing helix chain 'Z' and resid 368 through 373 Processing helix chain 'Z' and resid 476 through 481 removed outlier: 3.781A pdb=" N SER Z 481 " --> pdb=" O ASP Z 477 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 2 through 5 Processing sheet with id=AA2, first strand: chain 'A' and resid 9 through 10 removed outlier: 3.684A pdb=" N GLU A 9 " --> pdb=" O LEU A 126 " (cutoff:3.500A) removed outlier: 3.915A pdb=" N SER A 128 " --> pdb=" O GLU A 9 " (cutoff:3.500A) removed outlier: 9.357A pdb=" N TYR A 32 " --> pdb=" O TRP A 52 " (cutoff:3.500A) removed outlier: 6.382A pdb=" N TRP A 52 " --> pdb=" O TYR A 32 " (cutoff:3.500A) removed outlier: 6.790A pdb=" N VAL A 34 " --> pdb=" O GLN A 50 " (cutoff:3.500A) removed outlier: 4.407A pdb=" N GLN A 50 " --> pdb=" O VAL A 34 " (cutoff:3.500A) removed outlier: 6.677A pdb=" N TRP A 36 " --> pdb=" O ILE A 48 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N ALA A 40 " --> pdb=" O SER A 44 " (cutoff:3.500A) removed outlier: 4.495A pdb=" N SER A 44 " --> pdb=" O ALA A 40 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 9 through 10 removed outlier: 3.684A pdb=" N GLU A 9 " --> pdb=" O LEU A 126 " (cutoff:3.500A) removed outlier: 3.915A pdb=" N SER A 128 " --> pdb=" O GLU A 9 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 111 through 112 Processing sheet with id=AA5, first strand: chain 'C' and resid 3 through 6 Processing sheet with id=AA6, first strand: chain 'C' and resid 9 through 11 removed outlier: 6.441A pdb=" N TRP C 35 " --> pdb=" O LEU C 47 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'C' and resid 9 through 11 removed outlier: 3.812A pdb=" N THR C 97 " --> pdb=" O GLN C 90 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'D' and resid 2 through 5 Processing sheet with id=AA9, first strand: chain 'D' and resid 55 through 58 Processing sheet with id=AB1, first strand: chain 'D' and resid 55 through 58 Processing sheet with id=AB2, first strand: chain 'E' and resid 3 through 6 Processing sheet with id=AB3, first strand: chain 'E' and resid 9 through 11 removed outlier: 6.253A pdb=" N VAL E 33 " --> pdb=" O TYR E 49 " (cutoff:3.500A) removed outlier: 4.599A pdb=" N TYR E 49 " --> pdb=" O VAL E 33 " (cutoff:3.500A) removed outlier: 6.444A pdb=" N TRP E 35 " --> pdb=" O LEU E 47 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'E' and resid 9 through 11 removed outlier: 3.810A pdb=" N THR E 97 " --> pdb=" O GLN E 90 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'H' and resid 2 through 6 removed outlier: 4.333A pdb=" N SER H 20 " --> pdb=" O SER H 6 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'H' and resid 55 through 58 removed outlier: 4.506A pdb=" N SER H 44 " --> pdb=" O ALA H 40 " (cutoff:3.500A) removed outlier: 3.856A pdb=" N ALA H 40 " --> pdb=" O SER H 44 " (cutoff:3.500A) removed outlier: 6.654A pdb=" N TRP H 36 " --> pdb=" O ILE H 48 " (cutoff:3.500A) removed outlier: 4.489A pdb=" N GLN H 50 " --> pdb=" O VAL H 34 " (cutoff:3.500A) removed outlier: 6.935A pdb=" N VAL H 34 " --> pdb=" O GLN H 50 " (cutoff:3.500A) removed outlier: 6.491A pdb=" N TRP H 52 " --> pdb=" O TYR H 32 " (cutoff:3.500A) removed outlier: 9.334A pdb=" N TYR H 32 " --> pdb=" O TRP H 52 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'H' and resid 55 through 58 removed outlier: 4.506A pdb=" N SER H 44 " --> pdb=" O ALA H 40 " (cutoff:3.500A) removed outlier: 3.856A pdb=" N ALA H 40 " --> pdb=" O SER H 44 " (cutoff:3.500A) removed outlier: 6.654A pdb=" N TRP H 36 " --> pdb=" O ILE H 48 " (cutoff:3.500A) removed outlier: 4.489A pdb=" N GLN H 50 " --> pdb=" O VAL H 34 " (cutoff:3.500A) removed outlier: 6.935A pdb=" N VAL H 34 " --> pdb=" O GLN H 50 " (cutoff:3.500A) removed outlier: 6.491A pdb=" N TRP H 52 " --> pdb=" O TYR H 32 " (cutoff:3.500A) removed outlier: 9.334A pdb=" N TYR H 32 " --> pdb=" O TRP H 52 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'L' and resid 3 through 6 Processing sheet with id=AB9, first strand: chain 'L' and resid 9 through 11 removed outlier: 6.749A pdb=" N VAL L 33 " --> pdb=" O TYR L 49 " (cutoff:3.500A) removed outlier: 4.899A pdb=" N TYR L 49 " --> pdb=" O VAL L 33 " (cutoff:3.500A) removed outlier: 6.582A pdb=" N TRP L 35 " --> pdb=" O LEU L 47 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'U' and resid 603 through 609 removed outlier: 8.354A pdb=" N CYS U 604 " --> pdb=" O TYR Y 40 " (cutoff:3.500A) removed outlier: 8.077A pdb=" N TYR Y 40 " --> pdb=" O CYS U 604 " (cutoff:3.500A) removed outlier: 7.297A pdb=" N THR U 606 " --> pdb=" O VAL Y 38 " (cutoff:3.500A) removed outlier: 8.388A pdb=" N VAL Y 38 " --> pdb=" O THR U 606 " (cutoff:3.500A) removed outlier: 5.098A pdb=" N VAL U 608 " --> pdb=" O VAL Y 36 " (cutoff:3.500A) removed outlier: 8.857A pdb=" N ILE Y 491 " --> pdb=" O PRO Y 43 " (cutoff:3.500A) removed outlier: 7.551A pdb=" N TRP Y 45 " --> pdb=" O VAL Y 489 " (cutoff:3.500A) removed outlier: 8.184A pdb=" N VAL Y 489 " --> pdb=" O TRP Y 45 " (cutoff:3.500A) removed outlier: 8.604A pdb=" N GLU Y 47 " --> pdb=" O LYS Y 487 " (cutoff:3.500A) removed outlier: 11.182A pdb=" N LYS Y 487 " --> pdb=" O GLU Y 47 " (cutoff:3.500A) removed outlier: 4.516A pdb=" N VAL Y 242 " --> pdb=" O LEU Y 86 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'W' and resid 603 through 609 removed outlier: 8.386A pdb=" N CYS W 604 " --> pdb=" O TYR Z 40 " (cutoff:3.500A) removed outlier: 8.114A pdb=" N TYR Z 40 " --> pdb=" O CYS W 604 " (cutoff:3.500A) removed outlier: 7.215A pdb=" N THR W 606 " --> pdb=" O VAL Z 38 " (cutoff:3.500A) removed outlier: 7.869A pdb=" N VAL Z 38 " --> pdb=" O THR W 606 " (cutoff:3.500A) removed outlier: 5.345A pdb=" N VAL W 608 " --> pdb=" O VAL Z 36 " (cutoff:3.500A) removed outlier: 8.839A pdb=" N VAL Z 38 " --> pdb=" O PRO Z 498 " (cutoff:3.500A) removed outlier: 9.680A pdb=" N TYR Z 40 " --> pdb=" O VAL Z 496 " (cutoff:3.500A) removed outlier: 9.755A pdb=" N VAL Z 496 " --> pdb=" O TYR Z 40 " (cutoff:3.500A) removed outlier: 6.178A pdb=" N VAL Z 42 " --> pdb=" O LEU Z 494 " (cutoff:3.500A) removed outlier: 5.339A pdb=" N LEU Z 494 " --> pdb=" O VAL Z 42 " (cutoff:3.500A) removed outlier: 4.068A pdb=" N VAL Z 44 " --> pdb=" O LYS Z 492 " (cutoff:3.500A) removed outlier: 4.368A pdb=" N VAL Z 242 " --> pdb=" O LEU Z 86 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'X' and resid 35 through 47 removed outlier: 8.986A pdb=" N ILE X 491 " --> pdb=" O PRO X 43 " (cutoff:3.500A) removed outlier: 7.493A pdb=" N TRP X 45 " --> pdb=" O VAL X 489 " (cutoff:3.500A) removed outlier: 8.034A pdb=" N VAL X 489 " --> pdb=" O TRP X 45 " (cutoff:3.500A) removed outlier: 9.103A pdb=" N GLU X 47 " --> pdb=" O LYS X 487 " (cutoff:3.500A) removed outlier: 11.455A pdb=" N LYS X 487 " --> pdb=" O GLU X 47 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'X' and resid 53 through 55 Processing sheet with id=AC5, first strand: chain 'X' and resid 91 through 94 Processing sheet with id=AC6, first strand: chain 'X' and resid 130 through 132 Processing sheet with id=AC7, first strand: chain 'X' and resid 181 through 183 Processing sheet with id=AC8, first strand: chain 'X' and resid 200 through 203 removed outlier: 5.881A pdb=" N ALA X 200 " --> pdb=" O ALA X 433 " (cutoff:3.500A) removed outlier: 7.441A pdb=" N TYR X 435 " --> pdb=" O ALA X 200 " (cutoff:3.500A) removed outlier: 6.565A pdb=" N THR X 202 " --> pdb=" O TYR X 435 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'X' and resid 260 through 261 removed outlier: 6.493A pdb=" N LEU X 260 " --> pdb=" O THR X 450 " (cutoff:3.500A) removed outlier: 6.848A pdb=" N GLY X 451 " --> pdb=" O LYS X 290 " (cutoff:3.500A) removed outlier: 10.373A pdb=" N LYS X 290 " --> pdb=" O GLY X 451 " (cutoff:3.500A) removed outlier: 11.736A pdb=" N LEU X 453 " --> pdb=" O LEU X 288 " (cutoff:3.500A) removed outlier: 11.986A pdb=" N LEU X 288 " --> pdb=" O LEU X 453 " (cutoff:3.500A) removed outlier: 10.838A pdb=" N VAL X 455 " --> pdb=" O VAL X 286 " (cutoff:3.500A) removed outlier: 11.221A pdb=" N VAL X 286 " --> pdb=" O VAL X 455 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'X' and resid 284 through 298 current: chain 'X' and resid 358 through 361 Processing sheet with id=AD1, first strand: chain 'X' and resid 271 through 273 removed outlier: 11.221A pdb=" N VAL X 286 " --> pdb=" O VAL X 455 " (cutoff:3.500A) removed outlier: 10.838A pdb=" N VAL X 455 " --> pdb=" O VAL X 286 " (cutoff:3.500A) removed outlier: 11.986A pdb=" N LEU X 288 " --> pdb=" O LEU X 453 " (cutoff:3.500A) removed outlier: 11.736A pdb=" N LEU X 453 " --> pdb=" O LEU X 288 " (cutoff:3.500A) removed outlier: 10.373A pdb=" N LYS X 290 " --> pdb=" O GLY X 451 " (cutoff:3.500A) removed outlier: 6.848A pdb=" N GLY X 451 " --> pdb=" O LYS X 290 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'X' and resid 443 through 456 current: chain 'X' and resid 413 through 421 removed outlier: 4.085A pdb=" N PHE X 382 " --> pdb=" O LYS X 421 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'X' and resid 301 through 308 removed outlier: 7.208A pdb=" N ASN X 301 " --> pdb=" O ILE X 322 " (cutoff:3.500A) removed outlier: 4.553A pdb=" N ILE X 322 " --> pdb=" O ASN X 301 " (cutoff:3.500A) removed outlier: 6.551A pdb=" N THR X 303 " --> pdb=" O GLY X 320A" (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'Y' and resid 53 through 55 Processing sheet with id=AD4, first strand: chain 'Y' and resid 91 through 93 Processing sheet with id=AD5, first strand: chain 'Y' and resid 130 through 132 Processing sheet with id=AD6, first strand: chain 'Y' and resid 181 through 183 Processing sheet with id=AD7, first strand: chain 'Y' and resid 200 through 203 Processing sheet with id=AD8, first strand: chain 'Y' and resid 259 through 261 removed outlier: 7.017A pdb=" N GLY Y 451 " --> pdb=" O LYS Y 290 " (cutoff:3.500A) removed outlier: 10.525A pdb=" N LYS Y 290 " --> pdb=" O GLY Y 451 " (cutoff:3.500A) removed outlier: 11.826A pdb=" N LEU Y 453 " --> pdb=" O LEU Y 288 " (cutoff:3.500A) removed outlier: 11.904A pdb=" N LEU Y 288 " --> pdb=" O LEU Y 453 " (cutoff:3.500A) removed outlier: 10.955A pdb=" N VAL Y 455 " --> pdb=" O VAL Y 286 " (cutoff:3.500A) removed outlier: 11.293A pdb=" N VAL Y 286 " --> pdb=" O VAL Y 455 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'Y' and resid 284 through 298 current: chain 'Y' and resid 358 through 361 Processing sheet with id=AD9, first strand: chain 'Y' and resid 271 through 273 removed outlier: 11.293A pdb=" N VAL Y 286 " --> pdb=" O VAL Y 455 " (cutoff:3.500A) removed outlier: 10.955A pdb=" N VAL Y 455 " --> pdb=" O VAL Y 286 " (cutoff:3.500A) removed outlier: 11.904A pdb=" N LEU Y 288 " --> pdb=" O LEU Y 453 " (cutoff:3.500A) removed outlier: 11.826A pdb=" N LEU Y 453 " --> pdb=" O LEU Y 288 " (cutoff:3.500A) removed outlier: 10.525A pdb=" N LYS Y 290 " --> pdb=" O GLY Y 451 " (cutoff:3.500A) removed outlier: 7.017A pdb=" N GLY Y 451 " --> pdb=" O LYS Y 290 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'Y' and resid 443 through 456 current: chain 'Y' and resid 413 through 421 removed outlier: 3.512A pdb=" N LYS Y 421 " --> pdb=" O PHE Y 382 " (cutoff:3.500A) removed outlier: 4.354A pdb=" N PHE Y 382 " --> pdb=" O LYS Y 421 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'Y' and resid 302 through 308 removed outlier: 4.810A pdb=" N THR Y 303 " --> pdb=" O GLY Y 320A" (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'Z' and resid 53 through 55 Processing sheet with id=AE3, first strand: chain 'Z' and resid 91 through 93 Processing sheet with id=AE4, first strand: chain 'Z' and resid 130 through 133 Processing sheet with id=AE5, first strand: chain 'Z' and resid 181 through 183 Processing sheet with id=AE6, first strand: chain 'Z' and resid 200 through 203 removed outlier: 6.141A pdb=" N ALA Z 200 " --> pdb=" O ALA Z 433 " (cutoff:3.500A) removed outlier: 7.268A pdb=" N TYR Z 435 " --> pdb=" O ALA Z 200 " (cutoff:3.500A) removed outlier: 6.457A pdb=" N THR Z 202 " --> pdb=" O TYR Z 435 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'Z' and resid 259 through 261 removed outlier: 6.540A pdb=" N LEU Z 260 " --> pdb=" O THR Z 450 " (cutoff:3.500A) removed outlier: 3.757A pdb=" N ILE Z 443 " --> pdb=" O ARG Z 298 " (cutoff:3.500A) removed outlier: 6.914A pdb=" N GLY Z 451 " --> pdb=" O LYS Z 290 " (cutoff:3.500A) removed outlier: 10.474A pdb=" N LYS Z 290 " --> pdb=" O GLY Z 451 " (cutoff:3.500A) removed outlier: 11.752A pdb=" N LEU Z 453 " --> pdb=" O LEU Z 288 " (cutoff:3.500A) removed outlier: 12.011A pdb=" N LEU Z 288 " --> pdb=" O LEU Z 453 " (cutoff:3.500A) removed outlier: 10.772A pdb=" N VAL Z 455 " --> pdb=" O VAL Z 286 " (cutoff:3.500A) removed outlier: 10.514A pdb=" N VAL Z 286 " --> pdb=" O VAL Z 455 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'Z' and resid 284 through 298 current: chain 'Z' and resid 358 through 361 Processing sheet with id=AE8, first strand: chain 'Z' and resid 271 through 273 removed outlier: 10.514A pdb=" N VAL Z 286 " --> pdb=" O VAL Z 455 " (cutoff:3.500A) removed outlier: 10.772A pdb=" N VAL Z 455 " --> pdb=" O VAL Z 286 " (cutoff:3.500A) removed outlier: 12.011A pdb=" N LEU Z 288 " --> pdb=" O LEU Z 453 " (cutoff:3.500A) removed outlier: 11.752A pdb=" N LEU Z 453 " --> pdb=" O LEU Z 288 " (cutoff:3.500A) removed outlier: 10.474A pdb=" N LYS Z 290 " --> pdb=" O GLY Z 451 " (cutoff:3.500A) removed outlier: 6.914A pdb=" N GLY Z 451 " --> pdb=" O LYS Z 290 " (cutoff:3.500A) removed outlier: 3.757A pdb=" N ILE Z 443 " --> pdb=" O ARG Z 298 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'Z' and resid 443 through 456 current: chain 'Z' and resid 413 through 421 removed outlier: 4.018A pdb=" N PHE Z 382 " --> pdb=" O LYS Z 421 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'Z' and resid 304 through 308 737 hydrogen bonds defined for protein. 1950 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: 7.59 Time building geometry restraints manager: 7.84 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.35: 6277 1.35 - 1.49: 5706 1.49 - 1.62: 8525 1.62 - 1.76: 3 1.76 - 1.89: 159 Bond restraints: 20670 Sorted by residual: bond pdb=" C1 NAG b 2 " pdb=" O5 NAG b 2 " ideal model delta sigma weight residual 1.406 1.484 -0.078 2.00e-02 2.50e+03 1.51e+01 bond pdb=" CB CYS Z 218 " pdb=" SG CYS Z 218 " ideal model delta sigma weight residual 1.808 1.894 -0.086 3.30e-02 9.18e+02 6.80e+00 bond pdb=" CB CYS X 331 " pdb=" SG CYS X 331 " ideal model delta sigma weight residual 1.808 1.882 -0.074 3.30e-02 9.18e+02 4.96e+00 bond pdb=" CB CYS Y 331 " pdb=" SG CYS Y 331 " ideal model delta sigma weight residual 1.808 1.881 -0.073 3.30e-02 9.18e+02 4.84e+00 bond pdb=" CB CYS Z 331 " pdb=" SG CYS Z 331 " ideal model delta sigma weight residual 1.808 1.876 -0.068 3.30e-02 9.18e+02 4.25e+00 ... (remaining 20665 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.71: 27582 2.71 - 5.42: 429 5.42 - 8.13: 76 8.13 - 10.84: 3 10.84 - 13.55: 3 Bond angle restraints: 28093 Sorted by residual: angle pdb=" CA CYS Z 296 " pdb=" CB CYS Z 296 " pdb=" SG CYS Z 296 " ideal model delta sigma weight residual 114.40 127.95 -13.55 2.30e+00 1.89e-01 3.47e+01 angle pdb=" CA CYS Y 296 " pdb=" CB CYS Y 296 " pdb=" SG CYS Y 296 " ideal model delta sigma weight residual 114.40 127.91 -13.51 2.30e+00 1.89e-01 3.45e+01 angle pdb=" CA CYS X 296 " pdb=" CB CYS X 296 " pdb=" SG CYS X 296 " ideal model delta sigma weight residual 114.40 126.60 -12.20 2.30e+00 1.89e-01 2.81e+01 angle pdb=" CA GLN W 577 " pdb=" CB GLN W 577 " pdb=" CG GLN W 577 " ideal model delta sigma weight residual 114.10 124.63 -10.53 2.00e+00 2.50e-01 2.77e+01 angle pdb=" N CYS Z 119 " pdb=" CA CYS Z 119 " pdb=" C CYS Z 119 " ideal model delta sigma weight residual 107.73 112.99 -5.26 1.34e+00 5.57e-01 1.54e+01 ... (remaining 28088 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 23.35: 12954 23.35 - 46.69: 732 46.69 - 70.04: 89 70.04 - 93.38: 106 93.38 - 116.73: 56 Dihedral angle restraints: 13937 sinusoidal: 7091 harmonic: 6846 Sorted by residual: dihedral pdb=" CB CYS Y 119 " pdb=" SG CYS Y 119 " pdb=" SG CYS Y 205 " pdb=" CB CYS Y 205 " ideal model delta sinusoidal sigma weight residual -86.00 -167.61 81.61 1 1.00e+01 1.00e-02 8.20e+01 dihedral pdb=" CB CYS X 119 " pdb=" SG CYS X 119 " pdb=" SG CYS X 205 " pdb=" CB CYS X 205 " ideal model delta sinusoidal sigma weight residual -86.00 -161.20 75.20 1 1.00e+01 1.00e-02 7.15e+01 dihedral pdb=" CB CYS X 378 " pdb=" SG CYS X 378 " pdb=" SG CYS X 445 " pdb=" CB CYS X 445 " ideal model delta sinusoidal sigma weight residual -86.00 -155.64 69.64 1 1.00e+01 1.00e-02 6.26e+01 ... (remaining 13934 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.088: 3171 0.088 - 0.176: 347 0.176 - 0.265: 19 0.265 - 0.353: 7 0.353 - 0.441: 2 Chirality restraints: 3546 Sorted by residual: chirality pdb=" CB ILE Z 270 " pdb=" CA ILE Z 270 " pdb=" CG1 ILE Z 270 " pdb=" CG2 ILE Z 270 " both_signs ideal model delta sigma weight residual False 2.64 2.20 0.44 2.00e-01 2.50e+01 4.86e+00 chirality pdb=" C1 NAG i 1 " pdb=" ND2 ASN Z 197 " pdb=" C2 NAG i 1 " pdb=" O5 NAG i 1 " both_signs ideal model delta sigma weight residual False -2.40 -1.98 -0.42 2.00e-01 2.50e+01 4.39e+00 chirality pdb=" C1 NAG Z 705 " pdb=" ND2 ASN Z 442 " pdb=" C2 NAG Z 705 " pdb=" O5 NAG Z 705 " both_signs ideal model delta sigma weight residual False -2.40 -2.10 -0.30 2.00e-01 2.50e+01 2.28e+00 ... (remaining 3543 not shown) Planarity restraints: 3431 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LYS X 117 " -0.083 5.00e-02 4.00e+02 1.30e-01 2.69e+01 pdb=" N PRO X 118 " 0.224 5.00e-02 4.00e+02 pdb=" CA PRO X 118 " -0.072 5.00e-02 4.00e+02 pdb=" CD PRO X 118 " -0.070 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB TRP U 614 " 0.029 2.00e-02 2.50e+03 2.31e-02 1.33e+01 pdb=" CG TRP U 614 " -0.062 2.00e-02 2.50e+03 pdb=" CD1 TRP U 614 " 0.024 2.00e-02 2.50e+03 pdb=" CD2 TRP U 614 " -0.001 2.00e-02 2.50e+03 pdb=" NE1 TRP U 614 " 0.001 2.00e-02 2.50e+03 pdb=" CE2 TRP U 614 " 0.001 2.00e-02 2.50e+03 pdb=" CE3 TRP U 614 " 0.002 2.00e-02 2.50e+03 pdb=" CZ2 TRP U 614 " 0.002 2.00e-02 2.50e+03 pdb=" CZ3 TRP U 614 " 0.004 2.00e-02 2.50e+03 pdb=" CH2 TRP U 614 " 0.003 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C LYS Z 117 " 0.047 5.00e-02 4.00e+02 7.41e-02 8.80e+00 pdb=" N PRO Z 118 " -0.128 5.00e-02 4.00e+02 pdb=" CA PRO Z 118 " 0.040 5.00e-02 4.00e+02 pdb=" CD PRO Z 118 " 0.041 5.00e-02 4.00e+02 ... (remaining 3428 not shown) Histogram of nonbonded interaction distances: 2.18 - 2.72: 1010 2.72 - 3.27: 19438 3.27 - 3.81: 32250 3.81 - 4.36: 37503 4.36 - 4.90: 65330 Nonbonded interactions: 155531 Sorted by model distance: nonbonded pdb=" OG SER D 69 " pdb=" OG SER D 82 " model vdw 2.176 3.040 nonbonded pdb=" NE1 TRP H 36 " pdb=" OG SER H 81 " model vdw 2.183 3.120 nonbonded pdb=" OG SER A 69 " pdb=" OG SER A 82 " model vdw 2.190 3.040 nonbonded pdb=" O GLN D 43 " pdb=" OH TYR E 87 " model vdw 2.215 3.040 nonbonded pdb=" OH TYR C 49 " pdb=" O7 NAG G 2 " model vdw 2.230 3.040 ... (remaining 155526 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'D' selection = chain 'H' } ncs_group { reference = chain 'B' selection = chain 'F' selection = chain 'G' selection = chain 'I' } ncs_group { reference = chain 'C' selection = chain 'E' selection = chain 'L' } ncs_group { reference = chain 'J' selection = chain 'M' selection = chain 'P' selection = chain 'Q' selection = chain 'R' selection = chain 'S' selection = chain 'T' selection = chain 'b' selection = chain 'e' selection = chain 'f' selection = chain 'g' selection = chain 'h' selection = chain 'i' selection = chain 'k' selection = chain 'n' selection = chain 'o' selection = chain 'p' } ncs_group { reference = (chain 'K' and (resid 1 or resid 4 through 10)) selection = (chain 'a' and (resid 1 or resid 4 through 10)) selection = (chain 'j' and (resid 2 or resid 5 through 11)) } ncs_group { reference = chain 'N' selection = chain 'c' selection = chain 'l' } ncs_group { reference = chain 'O' selection = chain 'd' selection = chain 'm' } ncs_group { reference = (chain 'U' and (resid 520 through 660 or resid 701)) selection = chain 'V' selection = chain 'W' } ncs_group { reference = chain 'X' selection = chain 'Y' selection = chain 'Z' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.170 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.790 Check model and map are aligned: 0.130 Set scattering table: 0.200 Process input model: 50.850 Find NCS groups from input model: 1.060 Set up NCS constraints: 0.170 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:3.200 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 57.590 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7508 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 : 0.006 0.086 20834 Z= 0.268 Angle : 0.895 13.549 28547 Z= 0.408 Chirality : 0.054 0.441 3546 Planarity : 0.005 0.130 3379 Dihedral : 16.936 116.730 9413 Min Nonbonded Distance : 2.176 Molprobity Statistics. All-atom Clashscore : 10.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.66 % Favored : 95.34 % Rotamer: Outliers : 0.00 % Allowed : 0.34 % Favored : 99.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.06 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.48 (0.18), residues: 2340 helix: 1.30 (0.28), residues: 363 sheet: 0.24 (0.19), residues: 786 loop : -1.23 (0.17), residues: 1191 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.062 0.002 TRP U 614 HIS 0.007 0.001 HIS X 374 PHE 0.040 0.002 PHE X 53 TYR 0.035 0.002 TYR U 638 ARG 0.009 0.001 ARG Z 304 Details of bonding type rmsd link_NAG-ASN : bond 0.00456 ( 52) link_NAG-ASN : angle 2.60537 ( 156) link_ALPHA1-6 : bond 0.00258 ( 9) link_ALPHA1-6 : angle 2.29704 ( 27) link_BETA1-4 : bond 0.00528 ( 43) link_BETA1-4 : angle 2.07422 ( 129) link_ALPHA1-2 : bond 0.00216 ( 10) link_ALPHA1-2 : angle 2.00674 ( 30) link_ALPHA1-3 : bond 0.00228 ( 12) link_ALPHA1-3 : angle 1.93253 ( 36) hydrogen bonds : bond 0.12920 ( 671) hydrogen bonds : angle 6.50126 ( 1950) SS BOND : bond 0.00693 ( 38) SS BOND : angle 2.73067 ( 76) covalent geometry : bond 0.00577 (20670) covalent geometry : angle 0.85029 (28093) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4680 Ramachandran restraints generated. 2340 Oldfield, 0 Emsley, 2340 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4680 Ramachandran restraints generated. 2340 Oldfield, 0 Emsley, 2340 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 666 residues out of total 2079 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 666 time to evaluate : 2.088 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: C 4 THR cc_start: 0.7590 (p) cc_final: 0.7316 (p) REVERT: H 99 THR cc_start: 0.8406 (p) cc_final: 0.8174 (p) REVERT: H 110 LEU cc_start: 0.8987 (tt) cc_final: 0.8784 (tt) REVERT: U 522 PHE cc_start: 0.8669 (t80) cc_final: 0.8418 (t80) REVERT: U 577 GLN cc_start: 0.7641 (mt0) cc_final: 0.7142 (mt0) REVERT: U 647 GLU cc_start: 0.7276 (pt0) cc_final: 0.6976 (pt0) REVERT: V 625 ASN cc_start: 0.8268 (t0) cc_final: 0.7744 (t0) REVERT: W 647 GLU cc_start: 0.7156 (tt0) cc_final: 0.6948 (tt0) REVERT: X 83 GLU cc_start: 0.6935 (tm-30) cc_final: 0.6571 (tm-30) REVERT: X 84 MET cc_start: 0.7082 (tmm) cc_final: 0.6145 (tmm) REVERT: X 244 THR cc_start: 0.8492 (t) cc_final: 0.8137 (t) REVERT: X 275 GLU cc_start: 0.7221 (tt0) cc_final: 0.6792 (tt0) REVERT: X 315 GLN cc_start: 0.8306 (mp10) cc_final: 0.7938 (mp10) REVERT: X 347 LYS cc_start: 0.8286 (ttpt) cc_final: 0.7844 (tmmt) REVERT: X 370 GLU cc_start: 0.7512 (mp0) cc_final: 0.7210 (mp0) REVERT: X 424 ILE cc_start: 0.8387 (mm) cc_final: 0.8178 (mm) REVERT: X 428 GLN cc_start: 0.7884 (mp10) cc_final: 0.7504 (mp10) REVERT: X 467 ILE cc_start: 0.8166 (pt) cc_final: 0.7696 (pt) REVERT: X 482 GLU cc_start: 0.7101 (mm-30) cc_final: 0.6816 (mm-30) REVERT: Y 190 GLU cc_start: 0.7253 (tt0) cc_final: 0.7010 (tt0) REVERT: Y 359 ILE cc_start: 0.8327 (mm) cc_final: 0.8125 (mm) REVERT: Y 415 THR cc_start: 0.8039 (p) cc_final: 0.7762 (m) REVERT: Y 434 MET cc_start: 0.8066 (ttp) cc_final: 0.7695 (ttp) REVERT: Y 467 ILE cc_start: 0.8309 (mm) cc_final: 0.7812 (mm) REVERT: Y 485 LYS cc_start: 0.8272 (mtmm) cc_final: 0.7839 (ptpp) REVERT: Z 39 TYR cc_start: 0.8520 (m-80) cc_final: 0.7996 (m-80) REVERT: Z 97 LYS cc_start: 0.8506 (mtmm) cc_final: 0.8249 (mtmt) REVERT: Z 175 LEU cc_start: 0.8580 (mt) cc_final: 0.8371 (mt) REVERT: Z 199 SER cc_start: 0.8431 (m) cc_final: 0.8179 (t) REVERT: Z 388 SER cc_start: 0.8387 (t) cc_final: 0.8134 (t) REVERT: Z 448 ASN cc_start: 0.8449 (m-40) cc_final: 0.8240 (m-40) outliers start: 0 outliers final: 0 residues processed: 666 average time/residue: 0.3502 time to fit residues: 343.9878 Evaluate side-chains 638 residues out of total 2079 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 638 time to evaluate : 2.198 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 231 random chunks: chunk 195 optimal weight: 1.9990 chunk 175 optimal weight: 2.9990 chunk 97 optimal weight: 0.8980 chunk 59 optimal weight: 5.9990 chunk 118 optimal weight: 2.9990 chunk 93 optimal weight: 1.9990 chunk 181 optimal weight: 0.1980 chunk 70 optimal weight: 5.9990 chunk 110 optimal weight: 0.7980 chunk 134 optimal weight: 4.9990 chunk 209 optimal weight: 3.9990 overall best weight: 1.1784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 39 GLN C 38 GLN D 111 HIS ** D 112 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 5 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 0 GLN H 43 GLN ** L 5 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** W 630 GLN ** X 94 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** X 203 GLN X 302 ASN X 425 ASN Y 94 ASN Y 203 GLN Z 33 ASN Z 348 ASN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3434 r_free = 0.3434 target = 0.113292 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3214 r_free = 0.3214 target = 0.098744 restraints weight = 32661.082| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3273 r_free = 0.3273 target = 0.102538 restraints weight = 14383.682| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3311 r_free = 0.3311 target = 0.105013 restraints weight = 8193.140| |-----------------------------------------------------------------------------| r_work (final): 0.3306 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7506 moved from start: 0.1030 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 20834 Z= 0.185 Angle : 0.709 10.419 28547 Z= 0.343 Chirality : 0.047 0.322 3546 Planarity : 0.004 0.070 3379 Dihedral : 12.647 87.333 5096 Min Nonbonded Distance : 2.379 Molprobity Statistics. All-atom Clashscore : 8.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.49 % Favored : 95.51 % Rotamer: Outliers : 1.59 % Allowed : 12.22 % Favored : 86.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.06 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.36 (0.18), residues: 2340 helix: 1.82 (0.28), residues: 366 sheet: 0.27 (0.19), residues: 798 loop : -1.30 (0.17), residues: 1176 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.036 0.002 TRP U 614 HIS 0.006 0.001 HIS X 374 PHE 0.029 0.002 PHE Y 53 TYR 0.030 0.002 TYR U 638 ARG 0.005 0.001 ARG Z 304 Details of bonding type rmsd link_NAG-ASN : bond 0.00402 ( 52) link_NAG-ASN : angle 2.17489 ( 156) link_ALPHA1-6 : bond 0.00273 ( 9) link_ALPHA1-6 : angle 2.16924 ( 27) link_BETA1-4 : bond 0.00369 ( 43) link_BETA1-4 : angle 2.04407 ( 129) link_ALPHA1-2 : bond 0.00474 ( 10) link_ALPHA1-2 : angle 1.75746 ( 30) link_ALPHA1-3 : bond 0.00756 ( 12) link_ALPHA1-3 : angle 2.38258 ( 36) hydrogen bonds : bond 0.04773 ( 671) hydrogen bonds : angle 5.05278 ( 1950) SS BOND : bond 0.00650 ( 38) SS BOND : angle 1.86683 ( 76) covalent geometry : bond 0.00413 (20670) covalent geometry : angle 0.66434 (28093) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4680 Ramachandran restraints generated. 2340 Oldfield, 0 Emsley, 2340 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4680 Ramachandran restraints generated. 2340 Oldfield, 0 Emsley, 2340 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 684 residues out of total 2079 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 651 time to evaluate : 2.226 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 55 LYS cc_start: 0.8282 (mmpt) cc_final: 0.7911 (mmpt) REVERT: C 4 THR cc_start: 0.7531 (p) cc_final: 0.7306 (p) REVERT: D 22 LYS cc_start: 0.8362 (mtpp) cc_final: 0.8127 (mtpp) REVERT: H 110 LEU cc_start: 0.9008 (tt) cc_final: 0.8770 (tt) REVERT: L 32 TRP cc_start: 0.8550 (m100) cc_final: 0.7778 (m100) REVERT: U 522 PHE cc_start: 0.8810 (t80) cc_final: 0.8574 (t80) REVERT: U 577 GLN cc_start: 0.7732 (mt0) cc_final: 0.7188 (mt0) REVERT: U 647 GLU cc_start: 0.7391 (pt0) cc_final: 0.7098 (pt0) REVERT: U 650 GLN cc_start: 0.8380 (tp40) cc_final: 0.7853 (tp40) REVERT: V 542 ARG cc_start: 0.8179 (ttm110) cc_final: 0.7875 (ttm110) REVERT: V 579 ARG cc_start: 0.7735 (ptp-170) cc_final: 0.7243 (mtp180) REVERT: V 625 ASN cc_start: 0.8183 (t0) cc_final: 0.7846 (t0) REVERT: V 647 GLU cc_start: 0.6767 (mt-10) cc_final: 0.6450 (mt-10) REVERT: W 579 ARG cc_start: 0.7929 (mtm180) cc_final: 0.7675 (mtm110) REVERT: W 647 GLU cc_start: 0.7251 (tt0) cc_final: 0.6818 (tt0) REVERT: X 68 VAL cc_start: 0.8445 (m) cc_final: 0.8156 (p) REVERT: X 83 GLU cc_start: 0.7005 (tm-30) cc_final: 0.6683 (tm-30) REVERT: X 84 MET cc_start: 0.7186 (tmm) cc_final: 0.6440 (tmm) REVERT: X 97 LYS cc_start: 0.8395 (ptpp) cc_final: 0.8139 (ptpp) REVERT: X 121 LYS cc_start: 0.8396 (ttmm) cc_final: 0.8176 (ttmm) REVERT: X 244 THR cc_start: 0.8488 (t) cc_final: 0.8288 (t) REVERT: X 275 GLU cc_start: 0.7276 (tt0) cc_final: 0.6868 (tt0) REVERT: X 315 GLN cc_start: 0.8281 (mp10) cc_final: 0.7889 (mp10) REVERT: X 370 GLU cc_start: 0.7523 (mp0) cc_final: 0.7303 (mp0) REVERT: X 388 SER cc_start: 0.8165 (t) cc_final: 0.7870 (m) REVERT: X 428 GLN cc_start: 0.7974 (mp10) cc_final: 0.7521 (mp10) REVERT: X 467 ILE cc_start: 0.8084 (pt) cc_final: 0.7841 (pt) REVERT: X 485 LYS cc_start: 0.8379 (mttm) cc_final: 0.7832 (mtmm) REVERT: Y 112 TRP cc_start: 0.8120 (m100) cc_final: 0.7844 (m100) REVERT: Y 132 THR cc_start: 0.8244 (t) cc_final: 0.7976 (p) REVERT: Y 190 GLU cc_start: 0.7286 (tt0) cc_final: 0.6986 (tt0) REVERT: Y 217 TYR cc_start: 0.8098 (m-80) cc_final: 0.7722 (m-80) REVERT: Y 293 GLU cc_start: 0.6878 (tt0) cc_final: 0.6648 (tt0) REVERT: Y 415 THR cc_start: 0.8047 (p) cc_final: 0.7832 (m) REVERT: Y 426 MET cc_start: 0.7775 (mtm) cc_final: 0.7129 (mtt) REVERT: Y 434 MET cc_start: 0.8060 (ttp) cc_final: 0.7715 (ttp) REVERT: Y 485 LYS cc_start: 0.8236 (mtmm) cc_final: 0.7692 (ptpp) REVERT: Z 39 TYR cc_start: 0.8546 (m-80) cc_final: 0.7920 (m-80) REVERT: Z 97 LYS cc_start: 0.8560 (mtmm) cc_final: 0.8178 (mtmt) REVERT: Z 107 ASP cc_start: 0.7472 (m-30) cc_final: 0.7260 (m-30) REVERT: Z 173 TYR cc_start: 0.8547 (p90) cc_final: 0.8270 (p90) REVERT: Z 175 LEU cc_start: 0.8623 (mt) cc_final: 0.8299 (mt) REVERT: Z 199 SER cc_start: 0.8331 (m) cc_final: 0.7895 (t) REVERT: Z 388 SER cc_start: 0.8485 (t) cc_final: 0.8226 (t) outliers start: 33 outliers final: 20 residues processed: 658 average time/residue: 0.3575 time to fit residues: 347.3328 Evaluate side-chains 662 residues out of total 2079 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 642 time to evaluate : 2.288 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 93 THR Chi-restraints excluded: chain D residue 93 THR Chi-restraints excluded: chain D residue 98 CYS Chi-restraints excluded: chain H residue 90 SER Chi-restraints excluded: chain H residue 93 THR Chi-restraints excluded: chain U residue 612 SER Chi-restraints excluded: chain V residue 529 THR Chi-restraints excluded: chain W residue 573 ILE Chi-restraints excluded: chain X residue 56 SER Chi-restraints excluded: chain X residue 269 GLU Chi-restraints excluded: chain X residue 330 HIS Chi-restraints excluded: chain Y residue 66 HIS Chi-restraints excluded: chain Y residue 84 MET Chi-restraints excluded: chain Y residue 232 ARG Chi-restraints excluded: chain Y residue 265 LEU Chi-restraints excluded: chain Y residue 295 VAL Chi-restraints excluded: chain Z residue 116 LEU Chi-restraints excluded: chain Z residue 229 ASN Chi-restraints excluded: chain Z residue 295 VAL Chi-restraints excluded: chain Z residue 339 GLU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 231 random chunks: chunk 93 optimal weight: 0.7980 chunk 78 optimal weight: 3.9990 chunk 46 optimal weight: 6.9990 chunk 33 optimal weight: 4.9990 chunk 116 optimal weight: 5.9990 chunk 138 optimal weight: 1.9990 chunk 2 optimal weight: 4.9990 chunk 86 optimal weight: 0.9980 chunk 50 optimal weight: 0.9980 chunk 37 optimal weight: 10.0000 chunk 190 optimal weight: 0.5980 overall best weight: 1.0782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 39 GLN C 38 GLN ** D 112 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 5 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 5 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** U 624 ASN U 630 GLN W 630 GLN X 94 ASN X 203 GLN X 302 ASN Z 33 ASN Z 135 ASN Z 203 GLN Z 348 ASN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3432 r_free = 0.3432 target = 0.112977 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3212 r_free = 0.3212 target = 0.098377 restraints weight = 32706.851| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3270 r_free = 0.3270 target = 0.102161 restraints weight = 14400.487| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3308 r_free = 0.3308 target = 0.104628 restraints weight = 8174.617| |-----------------------------------------------------------------------------| r_work (final): 0.3300 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7503 moved from start: 0.1297 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 20834 Z= 0.171 Angle : 0.670 9.227 28547 Z= 0.326 Chirality : 0.046 0.320 3546 Planarity : 0.004 0.049 3379 Dihedral : 10.982 83.926 5096 Min Nonbonded Distance : 2.382 Molprobity Statistics. All-atom Clashscore : 8.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.57 % Favored : 95.43 % Rotamer: Outliers : 2.79 % Allowed : 14.81 % Favored : 82.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.06 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.30 (0.18), residues: 2340 helix: 2.11 (0.28), residues: 360 sheet: 0.17 (0.19), residues: 798 loop : -1.21 (0.17), residues: 1182 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.002 TRP U 614 HIS 0.007 0.001 HIS X 374 PHE 0.028 0.002 PHE Y 53 TYR 0.025 0.002 TYR Y 173 ARG 0.009 0.001 ARG W 579 Details of bonding type rmsd link_NAG-ASN : bond 0.00365 ( 52) link_NAG-ASN : angle 2.10064 ( 156) link_ALPHA1-6 : bond 0.00240 ( 9) link_ALPHA1-6 : angle 2.06981 ( 27) link_BETA1-4 : bond 0.00382 ( 43) link_BETA1-4 : angle 1.92977 ( 129) link_ALPHA1-2 : bond 0.00397 ( 10) link_ALPHA1-2 : angle 1.71014 ( 30) link_ALPHA1-3 : bond 0.00753 ( 12) link_ALPHA1-3 : angle 1.95472 ( 36) hydrogen bonds : bond 0.04494 ( 671) hydrogen bonds : angle 4.87021 ( 1950) SS BOND : bond 0.00653 ( 38) SS BOND : angle 1.79502 ( 76) covalent geometry : bond 0.00382 (20670) covalent geometry : angle 0.62724 (28093) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4680 Ramachandran restraints generated. 2340 Oldfield, 0 Emsley, 2340 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4680 Ramachandran restraints generated. 2340 Oldfield, 0 Emsley, 2340 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 697 residues out of total 2079 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 639 time to evaluate : 2.117 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 55 LYS cc_start: 0.8233 (mmpt) cc_final: 0.7814 (mmpt) REVERT: C 4 THR cc_start: 0.7485 (p) cc_final: 0.7265 (p) REVERT: C 73 LEU cc_start: 0.8385 (tp) cc_final: 0.8145 (tp) REVERT: D 22 LYS cc_start: 0.8347 (mtpp) cc_final: 0.8018 (mtpp) REVERT: D 50 GLN cc_start: 0.8209 (pt0) cc_final: 0.7983 (pt0) REVERT: H 110 LEU cc_start: 0.9056 (tt) cc_final: 0.8811 (tt) REVERT: L 32 TRP cc_start: 0.8535 (m100) cc_final: 0.7763 (m100) REVERT: U 522 PHE cc_start: 0.8812 (t80) cc_final: 0.8564 (t80) REVERT: U 577 GLN cc_start: 0.7706 (mt0) cc_final: 0.7182 (mt0) REVERT: U 647 GLU cc_start: 0.7437 (pt0) cc_final: 0.7107 (pt0) REVERT: V 542 ARG cc_start: 0.8179 (ttm110) cc_final: 0.7921 (ttm110) REVERT: V 579 ARG cc_start: 0.7761 (ptp-170) cc_final: 0.7224 (mtp180) REVERT: V 625 ASN cc_start: 0.8157 (t0) cc_final: 0.7789 (t0) REVERT: V 647 GLU cc_start: 0.6801 (mt-10) cc_final: 0.6487 (mt-10) REVERT: V 650 GLN cc_start: 0.8471 (tp40) cc_final: 0.8218 (tp40) REVERT: W 579 ARG cc_start: 0.7927 (mtm180) cc_final: 0.7623 (mtm180) REVERT: W 647 GLU cc_start: 0.7275 (tt0) cc_final: 0.6731 (tt0) REVERT: X 45 TRP cc_start: 0.8602 (p90) cc_final: 0.8189 (p90) REVERT: X 68 VAL cc_start: 0.8440 (m) cc_final: 0.8146 (p) REVERT: X 83 GLU cc_start: 0.7044 (tm-30) cc_final: 0.6724 (tm-30) REVERT: X 84 MET cc_start: 0.7277 (tmm) cc_final: 0.6677 (tmm) REVERT: X 99 GLU cc_start: 0.7034 (mp0) cc_final: 0.6776 (mp0) REVERT: X 104 MET cc_start: 0.8024 (ttt) cc_final: 0.7692 (ttp) REVERT: X 275 GLU cc_start: 0.7236 (tt0) cc_final: 0.6870 (tt0) REVERT: X 315 GLN cc_start: 0.8304 (mp10) cc_final: 0.7907 (mp10) REVERT: X 370 GLU cc_start: 0.7555 (mp0) cc_final: 0.7322 (mp0) REVERT: X 388 SER cc_start: 0.8232 (t) cc_final: 0.7963 (m) REVERT: X 424 ILE cc_start: 0.8367 (mm) cc_final: 0.8155 (mm) REVERT: X 485 LYS cc_start: 0.8313 (mttm) cc_final: 0.7773 (mtmm) REVERT: Y 47 GLU cc_start: 0.6893 (tt0) cc_final: 0.6674 (tt0) REVERT: Y 190 GLU cc_start: 0.7261 (tt0) cc_final: 0.6960 (tt0) REVERT: Y 335 ARG cc_start: 0.8528 (tpp80) cc_final: 0.8234 (ttm-80) REVERT: Y 426 MET cc_start: 0.7804 (mtm) cc_final: 0.7120 (mtt) REVERT: Y 434 MET cc_start: 0.8114 (ttp) cc_final: 0.7702 (ttp) REVERT: Y 439 ILE cc_start: 0.8482 (mp) cc_final: 0.8093 (tp) REVERT: Y 485 LYS cc_start: 0.8142 (mtmm) cc_final: 0.7599 (ptpp) REVERT: Z 97 LYS cc_start: 0.8588 (mtmm) cc_final: 0.8160 (mtmt) REVERT: Z 107 ASP cc_start: 0.7447 (m-30) cc_final: 0.7247 (m-30) REVERT: Z 173 TYR cc_start: 0.8539 (p90) cc_final: 0.8274 (p90) REVERT: Z 175 LEU cc_start: 0.8595 (mt) cc_final: 0.8226 (mt) REVERT: Z 199 SER cc_start: 0.8324 (m) cc_final: 0.7863 (t) REVERT: Z 208 VAL cc_start: 0.8613 (m) cc_final: 0.8249 (m) REVERT: Z 388 SER cc_start: 0.8465 (t) cc_final: 0.8193 (t) REVERT: Z 390 LEU cc_start: 0.8834 (mt) cc_final: 0.8617 (mt) REVERT: Z 474 ASP cc_start: 0.5976 (t0) cc_final: 0.5367 (t0) outliers start: 58 outliers final: 41 residues processed: 653 average time/residue: 0.3396 time to fit residues: 327.5376 Evaluate side-chains 674 residues out of total 2079 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 633 time to evaluate : 2.020 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 59 SER Chi-restraints excluded: chain A residue 93 THR Chi-restraints excluded: chain C residue 88 CYS Chi-restraints excluded: chain D residue 93 THR Chi-restraints excluded: chain D residue 98 CYS Chi-restraints excluded: chain H residue 71 VAL Chi-restraints excluded: chain H residue 90 SER Chi-restraints excluded: chain H residue 93 THR Chi-restraints excluded: chain L residue 104 VAL Chi-restraints excluded: chain V residue 529 THR Chi-restraints excluded: chain W residue 573 ILE Chi-restraints excluded: chain W residue 577 GLN Chi-restraints excluded: chain X residue 56 SER Chi-restraints excluded: chain X residue 134 VAL Chi-restraints excluded: chain X residue 208 VAL Chi-restraints excluded: chain X residue 269 GLU Chi-restraints excluded: chain X residue 330 HIS Chi-restraints excluded: chain X residue 466 GLU Chi-restraints excluded: chain X residue 492 LYS Chi-restraints excluded: chain Y residue 66 HIS Chi-restraints excluded: chain Y residue 84 MET Chi-restraints excluded: chain Y residue 153 GLU Chi-restraints excluded: chain Y residue 203 GLN Chi-restraints excluded: chain Y residue 208 VAL Chi-restraints excluded: chain Y residue 232 ARG Chi-restraints excluded: chain Y residue 265 LEU Chi-restraints excluded: chain Y residue 295 VAL Chi-restraints excluded: chain Y residue 330 HIS Chi-restraints excluded: chain Y residue 349 LEU Chi-restraints excluded: chain Y residue 413 THR Chi-restraints excluded: chain Z residue 116 LEU Chi-restraints excluded: chain Z residue 180 ASP Chi-restraints excluded: chain Z residue 203 GLN Chi-restraints excluded: chain Z residue 229 ASN Chi-restraints excluded: chain Z residue 275 GLU Chi-restraints excluded: chain Z residue 295 VAL Chi-restraints excluded: chain Z residue 339 GLU Chi-restraints excluded: chain Z residue 342 LEU Chi-restraints excluded: chain Z residue 429 GLU Chi-restraints excluded: chain Z residue 450 THR Chi-restraints excluded: chain Z residue 475 MET Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 231 random chunks: chunk 100 optimal weight: 3.9990 chunk 68 optimal weight: 0.9980 chunk 159 optimal weight: 0.9990 chunk 79 optimal weight: 3.9990 chunk 78 optimal weight: 2.9990 chunk 185 optimal weight: 0.0870 chunk 183 optimal weight: 0.7980 chunk 41 optimal weight: 4.9990 chunk 53 optimal weight: 3.9990 chunk 86 optimal weight: 0.9980 chunk 190 optimal weight: 0.5980 overall best weight: 0.6958 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 39 GLN C 38 GLN ** D 112 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 5 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 554 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** W 630 GLN X 302 ASN Z 33 ASN Z 258 GLN Z 348 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3446 r_free = 0.3446 target = 0.114017 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3229 r_free = 0.3229 target = 0.099539 restraints weight = 32921.656| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3287 r_free = 0.3287 target = 0.103296 restraints weight = 14625.151| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3324 r_free = 0.3324 target = 0.105769 restraints weight = 8368.636| |-----------------------------------------------------------------------------| r_work (final): 0.3318 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7504 moved from start: 0.1530 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.058 20834 Z= 0.134 Angle : 0.636 9.123 28547 Z= 0.310 Chirality : 0.046 0.333 3546 Planarity : 0.004 0.044 3379 Dihedral : 9.884 80.306 5096 Min Nonbonded Distance : 2.418 Molprobity Statistics. All-atom Clashscore : 7.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.44 % Favored : 95.56 % Rotamer: Outliers : 3.13 % Allowed : 17.36 % Favored : 79.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.06 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.27 (0.18), residues: 2340 helix: 2.09 (0.28), residues: 366 sheet: 0.21 (0.19), residues: 798 loop : -1.21 (0.17), residues: 1176 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.001 TRP Y 112 HIS 0.005 0.001 HIS X 374 PHE 0.029 0.002 PHE Y 53 TYR 0.026 0.001 TYR Y 173 ARG 0.008 0.000 ARG W 579 Details of bonding type rmsd link_NAG-ASN : bond 0.00270 ( 52) link_NAG-ASN : angle 1.99863 ( 156) link_ALPHA1-6 : bond 0.00325 ( 9) link_ALPHA1-6 : angle 1.97235 ( 27) link_BETA1-4 : bond 0.00353 ( 43) link_BETA1-4 : angle 1.76076 ( 129) link_ALPHA1-2 : bond 0.00417 ( 10) link_ALPHA1-2 : angle 1.64117 ( 30) link_ALPHA1-3 : bond 0.00841 ( 12) link_ALPHA1-3 : angle 1.94726 ( 36) hydrogen bonds : bond 0.04075 ( 671) hydrogen bonds : angle 4.75433 ( 1950) SS BOND : bond 0.00544 ( 38) SS BOND : angle 1.70708 ( 76) covalent geometry : bond 0.00304 (20670) covalent geometry : angle 0.59570 (28093) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4680 Ramachandran restraints generated. 2340 Oldfield, 0 Emsley, 2340 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4680 Ramachandran restraints generated. 2340 Oldfield, 0 Emsley, 2340 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 699 residues out of total 2079 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 634 time to evaluate : 2.261 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 55 LYS cc_start: 0.8221 (mmpt) cc_final: 0.7794 (mmpt) REVERT: C 4 THR cc_start: 0.7484 (p) cc_final: 0.7257 (p) REVERT: C 73 LEU cc_start: 0.8391 (tp) cc_final: 0.8125 (tp) REVERT: D 22 LYS cc_start: 0.8387 (mtpp) cc_final: 0.7991 (mtpp) REVERT: D 50 GLN cc_start: 0.8098 (pt0) cc_final: 0.7816 (pt0) REVERT: H 54 TRP cc_start: 0.8233 (m100) cc_final: 0.7985 (m100) REVERT: H 110 LEU cc_start: 0.9084 (OUTLIER) cc_final: 0.8851 (tt) REVERT: L 32 TRP cc_start: 0.8530 (m100) cc_final: 0.7756 (m100) REVERT: U 522 PHE cc_start: 0.8819 (t80) cc_final: 0.8563 (t80) REVERT: U 577 GLN cc_start: 0.7753 (mt0) cc_final: 0.7237 (mt0) REVERT: U 647 GLU cc_start: 0.7375 (pt0) cc_final: 0.7036 (pt0) REVERT: V 542 ARG cc_start: 0.8160 (ttm110) cc_final: 0.7894 (ttm110) REVERT: V 579 ARG cc_start: 0.7786 (ptp-170) cc_final: 0.7251 (mtp180) REVERT: V 647 GLU cc_start: 0.6799 (mt-10) cc_final: 0.6482 (mt-10) REVERT: V 650 GLN cc_start: 0.8525 (tp40) cc_final: 0.8280 (tp-100) REVERT: W 579 ARG cc_start: 0.7901 (mtm180) cc_final: 0.7534 (mtm180) REVERT: W 647 GLU cc_start: 0.7260 (tt0) cc_final: 0.6712 (tt0) REVERT: X 68 VAL cc_start: 0.8474 (m) cc_final: 0.8175 (p) REVERT: X 83 GLU cc_start: 0.7040 (tm-30) cc_final: 0.6760 (tm-30) REVERT: X 84 MET cc_start: 0.7310 (tmm) cc_final: 0.6933 (tmm) REVERT: X 97 LYS cc_start: 0.8298 (ptpp) cc_final: 0.8094 (ptpp) REVERT: X 275 GLU cc_start: 0.7152 (tt0) cc_final: 0.6769 (tt0) REVERT: X 315 GLN cc_start: 0.8304 (mp10) cc_final: 0.7964 (mp10) REVERT: X 424 ILE cc_start: 0.8233 (mm) cc_final: 0.7930 (mm) REVERT: X 482 GLU cc_start: 0.7112 (mm-30) cc_final: 0.6705 (mm-30) REVERT: Y 47 GLU cc_start: 0.6857 (tt0) cc_final: 0.6598 (tt0) REVERT: Y 190 GLU cc_start: 0.7176 (tt0) cc_final: 0.6883 (tt0) REVERT: Y 335 ARG cc_start: 0.8555 (tpp80) cc_final: 0.8333 (ttm-80) REVERT: Y 423 ILE cc_start: 0.8840 (mt) cc_final: 0.8633 (mt) REVERT: Y 426 MET cc_start: 0.7514 (mtm) cc_final: 0.7236 (mtt) REVERT: Y 434 MET cc_start: 0.8072 (ttp) cc_final: 0.7822 (ttp) REVERT: Y 439 ILE cc_start: 0.8477 (mp) cc_final: 0.8119 (tp) REVERT: Z 97 LYS cc_start: 0.8526 (mtmm) cc_final: 0.8308 (mttt) REVERT: Z 107 ASP cc_start: 0.7433 (m-30) cc_final: 0.7225 (m-30) REVERT: Z 173 TYR cc_start: 0.8520 (p90) cc_final: 0.8292 (p90) REVERT: Z 175 LEU cc_start: 0.8564 (mt) cc_final: 0.8235 (mt) REVERT: Z 199 SER cc_start: 0.8324 (m) cc_final: 0.7846 (t) REVERT: Z 208 VAL cc_start: 0.8629 (m) cc_final: 0.8387 (p) REVERT: Z 388 SER cc_start: 0.8445 (t) cc_final: 0.8185 (t) REVERT: Z 474 ASP cc_start: 0.5889 (t0) cc_final: 0.5419 (t0) REVERT: Z 486 TYR cc_start: 0.8702 (m-80) cc_final: 0.8380 (m-80) outliers start: 65 outliers final: 43 residues processed: 655 average time/residue: 0.3565 time to fit residues: 344.1840 Evaluate side-chains 670 residues out of total 2079 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 626 time to evaluate : 2.270 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 59 SER Chi-restraints excluded: chain A residue 93 THR Chi-restraints excluded: chain A residue 98 CYS Chi-restraints excluded: chain C residue 88 CYS Chi-restraints excluded: chain D residue 93 THR Chi-restraints excluded: chain D residue 98 CYS Chi-restraints excluded: chain E residue 3 MET Chi-restraints excluded: chain H residue 37 VAL Chi-restraints excluded: chain H residue 71 VAL Chi-restraints excluded: chain H residue 90 SER Chi-restraints excluded: chain H residue 93 THR Chi-restraints excluded: chain H residue 110 LEU Chi-restraints excluded: chain L residue 104 VAL Chi-restraints excluded: chain V residue 565 LEU Chi-restraints excluded: chain V residue 568 MET Chi-restraints excluded: chain W residue 573 ILE Chi-restraints excluded: chain W residue 577 GLN Chi-restraints excluded: chain X residue 52 LEU Chi-restraints excluded: chain X residue 134 VAL Chi-restraints excluded: chain X residue 269 GLU Chi-restraints excluded: chain X residue 330 HIS Chi-restraints excluded: chain X residue 466 GLU Chi-restraints excluded: chain Y residue 66 HIS Chi-restraints excluded: chain Y residue 84 MET Chi-restraints excluded: chain Y residue 153 GLU Chi-restraints excluded: chain Y residue 203 GLN Chi-restraints excluded: chain Y residue 208 VAL Chi-restraints excluded: chain Y residue 265 LEU Chi-restraints excluded: chain Y residue 295 VAL Chi-restraints excluded: chain Y residue 330 HIS Chi-restraints excluded: chain Y residue 413 THR Chi-restraints excluded: chain Y residue 425 ASN Chi-restraints excluded: chain Y residue 432 ARG Chi-restraints excluded: chain Z residue 116 LEU Chi-restraints excluded: chain Z residue 154 MET Chi-restraints excluded: chain Z residue 180 ASP Chi-restraints excluded: chain Z residue 229 ASN Chi-restraints excluded: chain Z residue 275 GLU Chi-restraints excluded: chain Z residue 295 VAL Chi-restraints excluded: chain Z residue 339 GLU Chi-restraints excluded: chain Z residue 413 THR Chi-restraints excluded: chain Z residue 443 ILE Chi-restraints excluded: chain Z residue 450 THR Chi-restraints excluded: chain Z residue 475 MET Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 231 random chunks: chunk 135 optimal weight: 3.9990 chunk 216 optimal weight: 0.7980 chunk 39 optimal weight: 2.9990 chunk 187 optimal weight: 2.9990 chunk 48 optimal weight: 1.9990 chunk 1 optimal weight: 0.8980 chunk 103 optimal weight: 3.9990 chunk 41 optimal weight: 0.5980 chunk 111 optimal weight: 2.9990 chunk 119 optimal weight: 4.9990 chunk 23 optimal weight: 7.9990 overall best weight: 1.4584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 39 GLN C 38 GLN ** D 112 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 5 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** U 624 ASN ** V 554 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** W 630 GLN X 302 ASN Z 33 ASN ** Z 203 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Z 348 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3413 r_free = 0.3413 target = 0.111755 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3195 r_free = 0.3195 target = 0.097374 restraints weight = 33152.680| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3253 r_free = 0.3253 target = 0.101054 restraints weight = 14893.188| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3289 r_free = 0.3289 target = 0.103482 restraints weight = 8602.033| |-----------------------------------------------------------------------------| r_work (final): 0.3282 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7544 moved from start: 0.1631 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.068 20834 Z= 0.214 Angle : 0.691 9.517 28547 Z= 0.337 Chirality : 0.047 0.328 3546 Planarity : 0.004 0.057 3379 Dihedral : 9.525 76.382 5096 Min Nonbonded Distance : 2.382 Molprobity Statistics. All-atom Clashscore : 8.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.66 % Favored : 95.34 % Rotamer: Outliers : 3.42 % Allowed : 18.86 % Favored : 77.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.06 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.34 (0.17), residues: 2340 helix: 2.10 (0.28), residues: 366 sheet: 0.18 (0.19), residues: 762 loop : -1.27 (0.17), residues: 1212 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP Y 112 HIS 0.008 0.001 HIS X 374 PHE 0.033 0.002 PHE Y 53 TYR 0.027 0.002 TYR Y 173 ARG 0.008 0.001 ARG W 579 Details of bonding type rmsd link_NAG-ASN : bond 0.00500 ( 52) link_NAG-ASN : angle 2.16547 ( 156) link_ALPHA1-6 : bond 0.00356 ( 9) link_ALPHA1-6 : angle 2.17521 ( 27) link_BETA1-4 : bond 0.00383 ( 43) link_BETA1-4 : angle 1.95127 ( 129) link_ALPHA1-2 : bond 0.00306 ( 10) link_ALPHA1-2 : angle 1.78580 ( 30) link_ALPHA1-3 : bond 0.00732 ( 12) link_ALPHA1-3 : angle 2.16706 ( 36) hydrogen bonds : bond 0.04655 ( 671) hydrogen bonds : angle 4.77091 ( 1950) SS BOND : bond 0.00608 ( 38) SS BOND : angle 2.22242 ( 76) covalent geometry : bond 0.00480 (20670) covalent geometry : angle 0.64360 (28093) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4680 Ramachandran restraints generated. 2340 Oldfield, 0 Emsley, 2340 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4680 Ramachandran restraints generated. 2340 Oldfield, 0 Emsley, 2340 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 716 residues out of total 2079 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 71 poor density : 645 time to evaluate : 2.110 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 55 LYS cc_start: 0.8296 (mmpt) cc_final: 0.7828 (mmpt) REVERT: C 4 THR cc_start: 0.7532 (p) cc_final: 0.7329 (p) REVERT: C 73 LEU cc_start: 0.8426 (tp) cc_final: 0.8147 (tp) REVERT: D 22 LYS cc_start: 0.8445 (mtpp) cc_final: 0.8199 (mtpp) REVERT: D 50 GLN cc_start: 0.8287 (pt0) cc_final: 0.8004 (pt0) REVERT: E 28 ILE cc_start: 0.8820 (mm) cc_final: 0.8585 (mm) REVERT: H 110 LEU cc_start: 0.9103 (OUTLIER) cc_final: 0.8872 (tt) REVERT: L 32 TRP cc_start: 0.8560 (m100) cc_final: 0.7750 (m100) REVERT: U 522 PHE cc_start: 0.8851 (t80) cc_final: 0.8569 (t80) REVERT: U 647 GLU cc_start: 0.7437 (pt0) cc_final: 0.7084 (pt0) REVERT: V 542 ARG cc_start: 0.8220 (ttm110) cc_final: 0.7977 (ttm110) REVERT: V 579 ARG cc_start: 0.7815 (ptp-170) cc_final: 0.7306 (mtp180) REVERT: V 647 GLU cc_start: 0.6850 (mt-10) cc_final: 0.6543 (mt-10) REVERT: V 650 GLN cc_start: 0.8564 (tp40) cc_final: 0.8308 (tp-100) REVERT: W 557 TRP cc_start: 0.7399 (m100) cc_final: 0.7146 (m100) REVERT: W 579 ARG cc_start: 0.8009 (mtm180) cc_final: 0.7617 (mtp-110) REVERT: W 647 GLU cc_start: 0.7281 (tt0) cc_final: 0.6741 (tt0) REVERT: X 45 TRP cc_start: 0.8637 (p90) cc_final: 0.8310 (p90) REVERT: X 68 VAL cc_start: 0.8490 (m) cc_final: 0.8204 (p) REVERT: X 83 GLU cc_start: 0.7045 (tm-30) cc_final: 0.6820 (tm-30) REVERT: X 84 MET cc_start: 0.7354 (tmm) cc_final: 0.6977 (tmm) REVERT: X 275 GLU cc_start: 0.7127 (tt0) cc_final: 0.6754 (tt0) REVERT: X 315 GLN cc_start: 0.8323 (mp10) cc_final: 0.7942 (mp10) REVERT: X 347 LYS cc_start: 0.8341 (ttpt) cc_final: 0.7890 (ttpt) REVERT: X 424 ILE cc_start: 0.8359 (mm) cc_final: 0.8131 (mm) REVERT: X 482 GLU cc_start: 0.7117 (mm-30) cc_final: 0.6700 (mm-30) REVERT: Y 47 GLU cc_start: 0.6792 (tt0) cc_final: 0.6538 (tt0) REVERT: Y 190 GLU cc_start: 0.7277 (tt0) cc_final: 0.6994 (tt0) REVERT: Y 330 HIS cc_start: 0.8515 (OUTLIER) cc_final: 0.8250 (p90) REVERT: Y 335 ARG cc_start: 0.8649 (tpp80) cc_final: 0.8421 (ttm-80) REVERT: Y 381 GLU cc_start: 0.6944 (tp30) cc_final: 0.6492 (tp30) REVERT: Y 426 MET cc_start: 0.7411 (mtm) cc_final: 0.7140 (mtt) REVERT: Y 434 MET cc_start: 0.8153 (ttp) cc_final: 0.7875 (ttp) REVERT: Y 439 ILE cc_start: 0.8513 (mp) cc_final: 0.8177 (mp) REVERT: Y 485 LYS cc_start: 0.8184 (mtmm) cc_final: 0.7982 (ptpt) REVERT: Z 39 TYR cc_start: 0.8562 (m-80) cc_final: 0.7691 (m-80) REVERT: Z 56 SER cc_start: 0.8317 (t) cc_final: 0.8043 (p) REVERT: Z 97 LYS cc_start: 0.8534 (mtmm) cc_final: 0.8211 (mtmt) REVERT: Z 107 ASP cc_start: 0.7482 (m-30) cc_final: 0.7219 (m-30) REVERT: Z 173 TYR cc_start: 0.8552 (p90) cc_final: 0.8283 (p90) REVERT: Z 175 LEU cc_start: 0.8584 (mt) cc_final: 0.8254 (mt) REVERT: Z 347 LYS cc_start: 0.8416 (tppt) cc_final: 0.8122 (ttpt) REVERT: Z 388 SER cc_start: 0.8448 (t) cc_final: 0.8199 (t) REVERT: Z 474 ASP cc_start: 0.5935 (t0) cc_final: 0.5463 (t0) outliers start: 71 outliers final: 51 residues processed: 670 average time/residue: 0.3577 time to fit residues: 350.7744 Evaluate side-chains 687 residues out of total 2079 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 634 time to evaluate : 2.102 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 8 THR Chi-restraints excluded: chain A residue 59 SER Chi-restraints excluded: chain A residue 93 THR Chi-restraints excluded: chain A residue 98 CYS Chi-restraints excluded: chain C residue 100 GLN Chi-restraints excluded: chain D residue 93 THR Chi-restraints excluded: chain D residue 98 CYS Chi-restraints excluded: chain E residue 3 MET Chi-restraints excluded: chain H residue 37 VAL Chi-restraints excluded: chain H residue 90 SER Chi-restraints excluded: chain H residue 93 THR Chi-restraints excluded: chain H residue 110 LEU Chi-restraints excluded: chain L residue 58 VAL Chi-restraints excluded: chain L residue 104 VAL Chi-restraints excluded: chain U residue 588 LYS Chi-restraints excluded: chain V residue 529 THR Chi-restraints excluded: chain V residue 568 MET Chi-restraints excluded: chain W residue 573 ILE Chi-restraints excluded: chain W residue 577 GLN Chi-restraints excluded: chain X residue 52 LEU Chi-restraints excluded: chain X residue 56 SER Chi-restraints excluded: chain X residue 111 LEU Chi-restraints excluded: chain X residue 134 VAL Chi-restraints excluded: chain X residue 269 GLU Chi-restraints excluded: chain X residue 295 VAL Chi-restraints excluded: chain X residue 297 THR Chi-restraints excluded: chain X residue 330 HIS Chi-restraints excluded: chain X residue 368 ASP Chi-restraints excluded: chain X residue 466 GLU Chi-restraints excluded: chain X residue 467 ILE Chi-restraints excluded: chain X residue 492 LYS Chi-restraints excluded: chain Y residue 84 MET Chi-restraints excluded: chain Y residue 120 VAL Chi-restraints excluded: chain Y residue 153 GLU Chi-restraints excluded: chain Y residue 203 GLN Chi-restraints excluded: chain Y residue 208 VAL Chi-restraints excluded: chain Y residue 255 VAL Chi-restraints excluded: chain Y residue 265 LEU Chi-restraints excluded: chain Y residue 295 VAL Chi-restraints excluded: chain Y residue 330 HIS Chi-restraints excluded: chain Y residue 413 THR Chi-restraints excluded: chain Y residue 425 ASN Chi-restraints excluded: chain Y residue 467 ILE Chi-restraints excluded: chain Z residue 111 LEU Chi-restraints excluded: chain Z residue 154 MET Chi-restraints excluded: chain Z residue 229 ASN Chi-restraints excluded: chain Z residue 269 GLU Chi-restraints excluded: chain Z residue 275 GLU Chi-restraints excluded: chain Z residue 295 VAL Chi-restraints excluded: chain Z residue 339 GLU Chi-restraints excluded: chain Z residue 413 THR Chi-restraints excluded: chain Z residue 450 THR Chi-restraints excluded: chain Z residue 475 MET Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 231 random chunks: chunk 212 optimal weight: 2.9990 chunk 14 optimal weight: 8.9990 chunk 192 optimal weight: 2.9990 chunk 219 optimal weight: 1.9990 chunk 218 optimal weight: 1.9990 chunk 226 optimal weight: 0.6980 chunk 184 optimal weight: 3.9990 chunk 119 optimal weight: 3.9990 chunk 179 optimal weight: 0.9990 chunk 205 optimal weight: 0.6980 chunk 8 optimal weight: 0.9990 overall best weight: 1.0786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 39 GLN C 38 GLN ** D 112 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 5 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 554 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** W 630 GLN X 302 ASN X 425 ASN Y 302 ASN Z 33 ASN ** Z 203 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Z 348 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3428 r_free = 0.3428 target = 0.112701 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3209 r_free = 0.3209 target = 0.098249 restraints weight = 32653.811| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3268 r_free = 0.3268 target = 0.102009 restraints weight = 14566.709| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3306 r_free = 0.3306 target = 0.104500 restraints weight = 8329.963| |-----------------------------------------------------------------------------| r_work (final): 0.3302 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7511 moved from start: 0.1743 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.060 20834 Z= 0.171 Angle : 0.661 9.464 28547 Z= 0.324 Chirality : 0.046 0.324 3546 Planarity : 0.004 0.058 3379 Dihedral : 9.260 75.477 5096 Min Nonbonded Distance : 2.398 Molprobity Statistics. All-atom Clashscore : 8.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.23 % Favored : 95.77 % Rotamer: Outliers : 3.46 % Allowed : 19.67 % Favored : 76.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.06 % Cis-general : 0.00 % Twisted Proline : 1.01 % Twisted General : 0.09 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.36 (0.18), residues: 2340 helix: 2.02 (0.28), residues: 366 sheet: 0.10 (0.19), residues: 762 loop : -1.19 (0.17), residues: 1212 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.001 TRP Y 112 HIS 0.006 0.001 HIS X 374 PHE 0.031 0.002 PHE Y 53 TYR 0.026 0.002 TYR U 638 ARG 0.008 0.001 ARG Y 469 Details of bonding type rmsd link_NAG-ASN : bond 0.00363 ( 52) link_NAG-ASN : angle 2.03970 ( 156) link_ALPHA1-6 : bond 0.00355 ( 9) link_ALPHA1-6 : angle 2.05662 ( 27) link_BETA1-4 : bond 0.00343 ( 43) link_BETA1-4 : angle 1.80647 ( 129) link_ALPHA1-2 : bond 0.00369 ( 10) link_ALPHA1-2 : angle 1.68482 ( 30) link_ALPHA1-3 : bond 0.00750 ( 12) link_ALPHA1-3 : angle 1.99347 ( 36) hydrogen bonds : bond 0.04355 ( 671) hydrogen bonds : angle 4.73105 ( 1950) SS BOND : bond 0.00583 ( 38) SS BOND : angle 2.20099 ( 76) covalent geometry : bond 0.00385 (20670) covalent geometry : angle 0.61716 (28093) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4680 Ramachandran restraints generated. 2340 Oldfield, 0 Emsley, 2340 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4680 Ramachandran restraints generated. 2340 Oldfield, 0 Emsley, 2340 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 708 residues out of total 2079 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 72 poor density : 636 time to evaluate : 2.146 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 55 LYS cc_start: 0.8315 (mmpt) cc_final: 0.7833 (mmpt) REVERT: C 4 THR cc_start: 0.7461 (p) cc_final: 0.7243 (p) REVERT: C 73 LEU cc_start: 0.8393 (tp) cc_final: 0.8099 (tp) REVERT: D 22 LYS cc_start: 0.8430 (mtpp) cc_final: 0.7990 (mtpp) REVERT: D 50 GLN cc_start: 0.8258 (pt0) cc_final: 0.7951 (pt0) REVERT: E 28 ILE cc_start: 0.8778 (mm) cc_final: 0.8457 (mm) REVERT: H 110 LEU cc_start: 0.9091 (OUTLIER) cc_final: 0.8887 (tt) REVERT: L 32 TRP cc_start: 0.8552 (m100) cc_final: 0.7670 (m100) REVERT: U 522 PHE cc_start: 0.8835 (t80) cc_final: 0.8545 (t80) REVERT: U 577 GLN cc_start: 0.7812 (mt0) cc_final: 0.7314 (mt0) REVERT: U 647 GLU cc_start: 0.7422 (pt0) cc_final: 0.7157 (pt0) REVERT: V 542 ARG cc_start: 0.8230 (ttm110) cc_final: 0.7970 (ttm110) REVERT: V 579 ARG cc_start: 0.7776 (ptp-170) cc_final: 0.7256 (mtp180) REVERT: V 647 GLU cc_start: 0.6846 (mt-10) cc_final: 0.6506 (mt-10) REVERT: V 650 GLN cc_start: 0.8518 (tp40) cc_final: 0.8254 (tp-100) REVERT: W 557 TRP cc_start: 0.7363 (m100) cc_final: 0.6757 (m100) REVERT: W 579 ARG cc_start: 0.7979 (mtm180) cc_final: 0.7535 (mtp-110) REVERT: W 647 GLU cc_start: 0.7290 (tt0) cc_final: 0.6762 (tt0) REVERT: X 68 VAL cc_start: 0.8462 (m) cc_final: 0.8175 (p) REVERT: X 83 GLU cc_start: 0.7089 (tm-30) cc_final: 0.6882 (tm-30) REVERT: X 84 MET cc_start: 0.7396 (tmm) cc_final: 0.6989 (tmm) REVERT: X 97 LYS cc_start: 0.8391 (ptpp) cc_final: 0.8147 (ptpp) REVERT: X 167 ASP cc_start: 0.7928 (t0) cc_final: 0.7683 (t0) REVERT: X 275 GLU cc_start: 0.7184 (tt0) cc_final: 0.6812 (tt0) REVERT: X 315 GLN cc_start: 0.8327 (mp10) cc_final: 0.7885 (mp10) REVERT: X 388 SER cc_start: 0.8355 (t) cc_final: 0.8078 (m) REVERT: X 424 ILE cc_start: 0.8337 (mm) cc_final: 0.8105 (mm) REVERT: X 482 GLU cc_start: 0.7203 (mm-30) cc_final: 0.6754 (mm-30) REVERT: Y 47 GLU cc_start: 0.6816 (tt0) cc_final: 0.6551 (tt0) REVERT: Y 190 GLU cc_start: 0.7244 (tt0) cc_final: 0.6940 (tt0) REVERT: Y 293 GLU cc_start: 0.7080 (tt0) cc_final: 0.6848 (tt0) REVERT: Y 335 ARG cc_start: 0.8600 (tpp80) cc_final: 0.8381 (ttm-80) REVERT: Y 381 GLU cc_start: 0.6964 (tp30) cc_final: 0.6639 (tp30) REVERT: Y 434 MET cc_start: 0.8171 (ttp) cc_final: 0.7816 (ttp) REVERT: Y 439 ILE cc_start: 0.8508 (mp) cc_final: 0.8248 (mp) REVERT: Z 39 TYR cc_start: 0.8556 (m-80) cc_final: 0.7632 (m-80) REVERT: Z 56 SER cc_start: 0.8287 (t) cc_final: 0.7999 (p) REVERT: Z 97 LYS cc_start: 0.8562 (mtmm) cc_final: 0.8062 (mtmm) REVERT: Z 107 ASP cc_start: 0.7490 (m-30) cc_final: 0.7204 (m-30) REVERT: Z 173 TYR cc_start: 0.8545 (p90) cc_final: 0.8275 (p90) REVERT: Z 175 LEU cc_start: 0.8626 (mt) cc_final: 0.8242 (mt) REVERT: Z 388 SER cc_start: 0.8428 (t) cc_final: 0.8180 (t) REVERT: Z 390 LEU cc_start: 0.8878 (mt) cc_final: 0.8658 (mt) REVERT: Z 474 ASP cc_start: 0.5981 (t0) cc_final: 0.5477 (t0) outliers start: 72 outliers final: 56 residues processed: 659 average time/residue: 0.3536 time to fit residues: 344.4665 Evaluate side-chains 686 residues out of total 2079 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 629 time to evaluate : 2.000 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 8 THR Chi-restraints excluded: chain A residue 59 SER Chi-restraints excluded: chain A residue 93 THR Chi-restraints excluded: chain A residue 98 CYS Chi-restraints excluded: chain D residue 93 THR Chi-restraints excluded: chain D residue 98 CYS Chi-restraints excluded: chain E residue 9 THR Chi-restraints excluded: chain H residue 37 VAL Chi-restraints excluded: chain H residue 71 VAL Chi-restraints excluded: chain H residue 90 SER Chi-restraints excluded: chain H residue 93 THR Chi-restraints excluded: chain H residue 110 LEU Chi-restraints excluded: chain L residue 58 VAL Chi-restraints excluded: chain L residue 104 VAL Chi-restraints excluded: chain U residue 588 LYS Chi-restraints excluded: chain U residue 633 GLU Chi-restraints excluded: chain V residue 529 THR Chi-restraints excluded: chain V residue 565 LEU Chi-restraints excluded: chain V residue 568 MET Chi-restraints excluded: chain V residue 604 CYS Chi-restraints excluded: chain W residue 573 ILE Chi-restraints excluded: chain W residue 577 GLN Chi-restraints excluded: chain X residue 52 LEU Chi-restraints excluded: chain X residue 56 SER Chi-restraints excluded: chain X residue 111 LEU Chi-restraints excluded: chain X residue 134 VAL Chi-restraints excluded: chain X residue 208 VAL Chi-restraints excluded: chain X residue 269 GLU Chi-restraints excluded: chain X residue 297 THR Chi-restraints excluded: chain X residue 330 HIS Chi-restraints excluded: chain X residue 467 ILE Chi-restraints excluded: chain Y residue 84 MET Chi-restraints excluded: chain Y residue 153 GLU Chi-restraints excluded: chain Y residue 208 VAL Chi-restraints excluded: chain Y residue 265 LEU Chi-restraints excluded: chain Y residue 275 GLU Chi-restraints excluded: chain Y residue 295 VAL Chi-restraints excluded: chain Y residue 330 HIS Chi-restraints excluded: chain Y residue 337 ASP Chi-restraints excluded: chain Y residue 349 LEU Chi-restraints excluded: chain Y residue 413 THR Chi-restraints excluded: chain Y residue 424 ILE Chi-restraints excluded: chain Y residue 425 ASN Chi-restraints excluded: chain Y residue 467 ILE Chi-restraints excluded: chain Z residue 116 LEU Chi-restraints excluded: chain Z residue 128 THR Chi-restraints excluded: chain Z residue 154 MET Chi-restraints excluded: chain Z residue 203 GLN Chi-restraints excluded: chain Z residue 229 ASN Chi-restraints excluded: chain Z residue 269 GLU Chi-restraints excluded: chain Z residue 275 GLU Chi-restraints excluded: chain Z residue 295 VAL Chi-restraints excluded: chain Z residue 339 GLU Chi-restraints excluded: chain Z residue 413 THR Chi-restraints excluded: chain Z residue 443 ILE Chi-restraints excluded: chain Z residue 450 THR Chi-restraints excluded: chain Z residue 475 MET Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 231 random chunks: chunk 157 optimal weight: 5.9990 chunk 126 optimal weight: 0.9990 chunk 45 optimal weight: 0.4980 chunk 20 optimal weight: 7.9990 chunk 86 optimal weight: 2.9990 chunk 199 optimal weight: 0.8980 chunk 66 optimal weight: 7.9990 chunk 151 optimal weight: 0.9990 chunk 85 optimal weight: 0.9990 chunk 16 optimal weight: 2.9990 chunk 144 optimal weight: 3.9990 overall best weight: 0.8786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 39 GLN C 38 GLN D 50 GLN ** D 112 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 5 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** U 624 ASN ** V 554 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** W 630 GLN X 302 ASN Y 66 HIS Y 203 GLN Y 302 ASN Z 33 ASN ** Z 203 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Z 229 ASN Z 348 ASN Z 478 ASN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3435 r_free = 0.3435 target = 0.113183 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3219 r_free = 0.3219 target = 0.098821 restraints weight = 32821.569| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3277 r_free = 0.3277 target = 0.102553 restraints weight = 14655.399| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3314 r_free = 0.3314 target = 0.105002 restraints weight = 8375.946| |-----------------------------------------------------------------------------| r_work (final): 0.3310 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7500 moved from start: 0.1850 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 20834 Z= 0.151 Angle : 0.646 9.415 28547 Z= 0.318 Chirality : 0.046 0.323 3546 Planarity : 0.004 0.057 3379 Dihedral : 8.972 73.585 5096 Min Nonbonded Distance : 2.385 Molprobity Statistics. All-atom Clashscore : 8.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.49 % Favored : 95.51 % Rotamer: Outliers : 3.37 % Allowed : 20.30 % Favored : 76.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.06 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.39 (0.17), residues: 2340 helix: 2.06 (0.28), residues: 366 sheet: 0.09 (0.19), residues: 732 loop : -1.21 (0.17), residues: 1242 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.001 TRP Y 112 HIS 0.005 0.001 HIS X 374 PHE 0.033 0.002 PHE Y 53 TYR 0.028 0.002 TYR U 638 ARG 0.008 0.001 ARG Y 469 Details of bonding type rmsd link_NAG-ASN : bond 0.00320 ( 52) link_NAG-ASN : angle 1.98040 ( 156) link_ALPHA1-6 : bond 0.00366 ( 9) link_ALPHA1-6 : angle 2.01277 ( 27) link_BETA1-4 : bond 0.00335 ( 43) link_BETA1-4 : angle 1.76471 ( 129) link_ALPHA1-2 : bond 0.00381 ( 10) link_ALPHA1-2 : angle 1.65389 ( 30) link_ALPHA1-3 : bond 0.00774 ( 12) link_ALPHA1-3 : angle 1.93917 ( 36) hydrogen bonds : bond 0.04137 ( 671) hydrogen bonds : angle 4.68437 ( 1950) SS BOND : bond 0.00573 ( 38) SS BOND : angle 2.09512 ( 76) covalent geometry : bond 0.00343 (20670) covalent geometry : angle 0.60392 (28093) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4680 Ramachandran restraints generated. 2340 Oldfield, 0 Emsley, 2340 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4680 Ramachandran restraints generated. 2340 Oldfield, 0 Emsley, 2340 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 705 residues out of total 2079 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 635 time to evaluate : 1.977 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 36 TRP cc_start: 0.8342 (m100) cc_final: 0.7874 (m100) REVERT: A 55 LYS cc_start: 0.8304 (mmpt) cc_final: 0.7798 (mmpt) REVERT: C 4 THR cc_start: 0.7426 (p) cc_final: 0.7209 (p) REVERT: D 22 LYS cc_start: 0.8411 (mtpp) cc_final: 0.7961 (mtpp) REVERT: D 50 GLN cc_start: 0.8078 (pt0) cc_final: 0.7819 (pt0) REVERT: E 28 ILE cc_start: 0.8743 (mm) cc_final: 0.8390 (mm) REVERT: H 110 LEU cc_start: 0.9099 (OUTLIER) cc_final: 0.8878 (tt) REVERT: L 32 TRP cc_start: 0.8548 (m100) cc_final: 0.7579 (m100) REVERT: U 522 PHE cc_start: 0.8819 (t80) cc_final: 0.8513 (t80) REVERT: U 577 GLN cc_start: 0.7810 (mt0) cc_final: 0.7270 (mt0) REVERT: U 647 GLU cc_start: 0.7418 (pt0) cc_final: 0.7134 (pt0) REVERT: V 542 ARG cc_start: 0.8228 (ttm110) cc_final: 0.7973 (ttm110) REVERT: V 579 ARG cc_start: 0.7767 (ptp-170) cc_final: 0.7212 (mtp180) REVERT: V 647 GLU cc_start: 0.6851 (mt-10) cc_final: 0.6521 (mt-10) REVERT: V 650 GLN cc_start: 0.8492 (tp40) cc_final: 0.8225 (tp-100) REVERT: W 557 TRP cc_start: 0.7306 (m100) cc_final: 0.6873 (m100) REVERT: W 647 GLU cc_start: 0.7287 (tt0) cc_final: 0.6761 (tt0) REVERT: X 68 VAL cc_start: 0.8452 (m) cc_final: 0.8164 (p) REVERT: X 83 GLU cc_start: 0.7092 (tm-30) cc_final: 0.6889 (tm-30) REVERT: X 84 MET cc_start: 0.7400 (tmm) cc_final: 0.7020 (tmm) REVERT: X 167 ASP cc_start: 0.7943 (t0) cc_final: 0.7713 (t0) REVERT: X 275 GLU cc_start: 0.7269 (tt0) cc_final: 0.6875 (tt0) REVERT: X 315 GLN cc_start: 0.8326 (mp10) cc_final: 0.7908 (mp10) REVERT: X 424 ILE cc_start: 0.8286 (mm) cc_final: 0.7964 (mm) REVERT: X 482 GLU cc_start: 0.7161 (mm-30) cc_final: 0.6703 (mm-30) REVERT: Y 47 GLU cc_start: 0.6808 (tt0) cc_final: 0.6536 (tt0) REVERT: Y 97 LYS cc_start: 0.8688 (mtmt) cc_final: 0.8286 (mtmm) REVERT: Y 190 GLU cc_start: 0.7244 (tt0) cc_final: 0.6920 (tt0) REVERT: Y 293 GLU cc_start: 0.7146 (tt0) cc_final: 0.6880 (tt0) REVERT: Y 335 ARG cc_start: 0.8594 (tpp80) cc_final: 0.8377 (ttm-80) REVERT: Y 381 GLU cc_start: 0.7088 (tp30) cc_final: 0.6670 (tp30) REVERT: Y 439 ILE cc_start: 0.8500 (mp) cc_final: 0.8295 (mp) REVERT: Y 492 LYS cc_start: 0.7968 (mtmm) cc_final: 0.7747 (mttm) REVERT: Z 39 TYR cc_start: 0.8546 (m-80) cc_final: 0.7638 (m-80) REVERT: Z 56 SER cc_start: 0.8293 (t) cc_final: 0.8016 (p) REVERT: Z 97 LYS cc_start: 0.8564 (mtmm) cc_final: 0.8159 (mtmt) REVERT: Z 107 ASP cc_start: 0.7448 (m-30) cc_final: 0.7172 (m-30) REVERT: Z 173 TYR cc_start: 0.8551 (p90) cc_final: 0.8288 (p90) REVERT: Z 175 LEU cc_start: 0.8621 (mt) cc_final: 0.8234 (mt) REVERT: Z 231 LYS cc_start: 0.7779 (mmmt) cc_final: 0.7351 (mmmm) REVERT: Z 282 LYS cc_start: 0.8411 (mmtt) cc_final: 0.8203 (mmtm) REVERT: Z 347 LYS cc_start: 0.8393 (tppt) cc_final: 0.8059 (ttpt) REVERT: Z 388 SER cc_start: 0.8414 (t) cc_final: 0.8156 (t) REVERT: Z 390 LEU cc_start: 0.8878 (mt) cc_final: 0.8643 (mt) REVERT: Z 474 ASP cc_start: 0.6031 (t0) cc_final: 0.5507 (t0) outliers start: 70 outliers final: 56 residues processed: 658 average time/residue: 0.3450 time to fit residues: 334.2749 Evaluate side-chains 681 residues out of total 2079 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 624 time to evaluate : 2.247 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 8 THR Chi-restraints excluded: chain A residue 59 SER Chi-restraints excluded: chain A residue 93 THR Chi-restraints excluded: chain D residue 93 THR Chi-restraints excluded: chain D residue 98 CYS Chi-restraints excluded: chain H residue 16 SER Chi-restraints excluded: chain H residue 37 VAL Chi-restraints excluded: chain H residue 71 VAL Chi-restraints excluded: chain H residue 90 SER Chi-restraints excluded: chain H residue 93 THR Chi-restraints excluded: chain H residue 110 LEU Chi-restraints excluded: chain L residue 58 VAL Chi-restraints excluded: chain L residue 104 VAL Chi-restraints excluded: chain U residue 633 GLU Chi-restraints excluded: chain V residue 529 THR Chi-restraints excluded: chain V residue 565 LEU Chi-restraints excluded: chain V residue 568 MET Chi-restraints excluded: chain V residue 604 CYS Chi-restraints excluded: chain W residue 573 ILE Chi-restraints excluded: chain W residue 577 GLN Chi-restraints excluded: chain X residue 52 LEU Chi-restraints excluded: chain X residue 56 SER Chi-restraints excluded: chain X residue 111 LEU Chi-restraints excluded: chain X residue 134 VAL Chi-restraints excluded: chain X residue 208 VAL Chi-restraints excluded: chain X residue 269 GLU Chi-restraints excluded: chain X residue 297 THR Chi-restraints excluded: chain X residue 330 HIS Chi-restraints excluded: chain X residue 420 ILE Chi-restraints excluded: chain X residue 467 ILE Chi-restraints excluded: chain Y residue 84 MET Chi-restraints excluded: chain Y residue 120 VAL Chi-restraints excluded: chain Y residue 153 GLU Chi-restraints excluded: chain Y residue 203 GLN Chi-restraints excluded: chain Y residue 208 VAL Chi-restraints excluded: chain Y residue 255 VAL Chi-restraints excluded: chain Y residue 265 LEU Chi-restraints excluded: chain Y residue 275 GLU Chi-restraints excluded: chain Y residue 330 HIS Chi-restraints excluded: chain Y residue 349 LEU Chi-restraints excluded: chain Y residue 413 THR Chi-restraints excluded: chain Y residue 452 LEU Chi-restraints excluded: chain Y residue 467 ILE Chi-restraints excluded: chain Z residue 111 LEU Chi-restraints excluded: chain Z residue 116 LEU Chi-restraints excluded: chain Z residue 128 THR Chi-restraints excluded: chain Z residue 154 MET Chi-restraints excluded: chain Z residue 203 GLN Chi-restraints excluded: chain Z residue 269 GLU Chi-restraints excluded: chain Z residue 275 GLU Chi-restraints excluded: chain Z residue 295 VAL Chi-restraints excluded: chain Z residue 330 HIS Chi-restraints excluded: chain Z residue 339 GLU Chi-restraints excluded: chain Z residue 413 THR Chi-restraints excluded: chain Z residue 443 ILE Chi-restraints excluded: chain Z residue 450 THR Chi-restraints excluded: chain Z residue 475 MET Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 231 random chunks: chunk 85 optimal weight: 2.9990 chunk 223 optimal weight: 0.5980 chunk 216 optimal weight: 0.9990 chunk 136 optimal weight: 0.9990 chunk 138 optimal weight: 4.9990 chunk 215 optimal weight: 0.9980 chunk 121 optimal weight: 1.9990 chunk 34 optimal weight: 0.7980 chunk 200 optimal weight: 2.9990 chunk 225 optimal weight: 1.9990 chunk 154 optimal weight: 0.0970 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 112 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 5 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 554 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** W 630 GLN X 302 ASN X 425 ASN Y 302 ASN Z 33 ASN ** Z 203 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Z 348 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3444 r_free = 0.3444 target = 0.113878 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3228 r_free = 0.3228 target = 0.099467 restraints weight = 32919.812| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3286 r_free = 0.3286 target = 0.103201 restraints weight = 14725.510| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3323 r_free = 0.3323 target = 0.105645 restraints weight = 8447.702| |-----------------------------------------------------------------------------| r_work (final): 0.3314 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7493 moved from start: 0.1921 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.063 20834 Z= 0.137 Angle : 0.643 9.358 28547 Z= 0.317 Chirality : 0.045 0.326 3546 Planarity : 0.004 0.053 3379 Dihedral : 8.799 72.326 5096 Min Nonbonded Distance : 2.374 Molprobity Statistics. All-atom Clashscore : 8.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.15 % Favored : 95.85 % Rotamer: Outliers : 3.46 % Allowed : 20.92 % Favored : 75.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.06 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.35 (0.17), residues: 2340 helix: 2.07 (0.29), residues: 366 sheet: 0.06 (0.19), residues: 747 loop : -1.16 (0.17), residues: 1227 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.035 0.001 TRP Y 112 HIS 0.005 0.001 HIS X 374 PHE 0.035 0.002 PHE Y 53 TYR 0.027 0.001 TYR U 638 ARG 0.008 0.001 ARG Y 469 Details of bonding type rmsd link_NAG-ASN : bond 0.00311 ( 52) link_NAG-ASN : angle 1.96778 ( 156) link_ALPHA1-6 : bond 0.00388 ( 9) link_ALPHA1-6 : angle 1.95408 ( 27) link_BETA1-4 : bond 0.00343 ( 43) link_BETA1-4 : angle 1.73118 ( 129) link_ALPHA1-2 : bond 0.00399 ( 10) link_ALPHA1-2 : angle 1.63277 ( 30) link_ALPHA1-3 : bond 0.00798 ( 12) link_ALPHA1-3 : angle 1.88828 ( 36) hydrogen bonds : bond 0.03972 ( 671) hydrogen bonds : angle 4.65746 ( 1950) SS BOND : bond 0.00566 ( 38) SS BOND : angle 2.29463 ( 76) covalent geometry : bond 0.00312 (20670) covalent geometry : angle 0.59922 (28093) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4680 Ramachandran restraints generated. 2340 Oldfield, 0 Emsley, 2340 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4680 Ramachandran restraints generated. 2340 Oldfield, 0 Emsley, 2340 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 703 residues out of total 2079 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 72 poor density : 631 time to evaluate : 1.992 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 36 TRP cc_start: 0.8332 (m100) cc_final: 0.7869 (m100) REVERT: A 55 LYS cc_start: 0.8295 (mmpt) cc_final: 0.7796 (mmpt) REVERT: C 73 LEU cc_start: 0.8386 (tp) cc_final: 0.8111 (tp) REVERT: D 22 LYS cc_start: 0.8402 (mtpp) cc_final: 0.7947 (mtpp) REVERT: D 50 GLN cc_start: 0.8031 (pt0) cc_final: 0.7817 (pt0) REVERT: E 28 ILE cc_start: 0.8742 (mm) cc_final: 0.8375 (mm) REVERT: H 110 LEU cc_start: 0.9078 (OUTLIER) cc_final: 0.8856 (tt) REVERT: L 32 TRP cc_start: 0.8552 (m100) cc_final: 0.7606 (m100) REVERT: U 522 PHE cc_start: 0.8818 (t80) cc_final: 0.8509 (t80) REVERT: U 577 GLN cc_start: 0.7799 (mt0) cc_final: 0.7269 (mt0) REVERT: U 647 GLU cc_start: 0.7404 (pt0) cc_final: 0.7116 (pt0) REVERT: V 542 ARG cc_start: 0.8220 (ttm110) cc_final: 0.7968 (ttm110) REVERT: V 579 ARG cc_start: 0.7736 (ptp-170) cc_final: 0.7168 (mtp180) REVERT: V 647 GLU cc_start: 0.6860 (mt-10) cc_final: 0.6535 (mt-10) REVERT: V 650 GLN cc_start: 0.8499 (tp40) cc_final: 0.8228 (tp-100) REVERT: W 557 TRP cc_start: 0.7160 (m100) cc_final: 0.6728 (m100) REVERT: W 647 GLU cc_start: 0.7280 (tt0) cc_final: 0.6760 (tt0) REVERT: X 68 VAL cc_start: 0.8460 (m) cc_final: 0.8166 (p) REVERT: X 84 MET cc_start: 0.7395 (tmm) cc_final: 0.7044 (tmm) REVERT: X 97 LYS cc_start: 0.8380 (ptpp) cc_final: 0.8122 (ptpp) REVERT: X 167 ASP cc_start: 0.7953 (t0) cc_final: 0.7733 (t0) REVERT: X 255 VAL cc_start: 0.8862 (t) cc_final: 0.8636 (p) REVERT: X 275 GLU cc_start: 0.7156 (tt0) cc_final: 0.6784 (tt0) REVERT: X 315 GLN cc_start: 0.8333 (mp10) cc_final: 0.7917 (mp10) REVERT: X 482 GLU cc_start: 0.7176 (mm-30) cc_final: 0.6756 (mm-30) REVERT: X 485 LYS cc_start: 0.8414 (mtmm) cc_final: 0.7940 (mttp) REVERT: Y 47 GLU cc_start: 0.6775 (tt0) cc_final: 0.6519 (tt0) REVERT: Y 97 LYS cc_start: 0.8631 (mtmt) cc_final: 0.8176 (mtmm) REVERT: Y 190 GLU cc_start: 0.7220 (tt0) cc_final: 0.6902 (tt0) REVERT: Y 293 GLU cc_start: 0.7162 (tt0) cc_final: 0.6897 (tt0) REVERT: Y 335 ARG cc_start: 0.8580 (tpp80) cc_final: 0.8350 (ttm-80) REVERT: Y 381 GLU cc_start: 0.7094 (tp30) cc_final: 0.6654 (tp30) REVERT: Y 439 ILE cc_start: 0.8494 (mp) cc_final: 0.8286 (mp) REVERT: Y 492 LYS cc_start: 0.8001 (mtmm) cc_final: 0.7779 (mttp) REVERT: Z 39 TYR cc_start: 0.8549 (m-80) cc_final: 0.7648 (m-80) REVERT: Z 56 SER cc_start: 0.8276 (t) cc_final: 0.8018 (p) REVERT: Z 97 LYS cc_start: 0.8564 (mtmm) cc_final: 0.8171 (mtmt) REVERT: Z 103 GLN cc_start: 0.7891 (tt0) cc_final: 0.7592 (tt0) REVERT: Z 107 ASP cc_start: 0.7440 (m-30) cc_final: 0.7174 (m-30) REVERT: Z 173 TYR cc_start: 0.8542 (p90) cc_final: 0.8290 (p90) REVERT: Z 175 LEU cc_start: 0.8564 (mt) cc_final: 0.8215 (mt) REVERT: Z 282 LYS cc_start: 0.8420 (mmtt) cc_final: 0.8216 (mmtm) REVERT: Z 388 SER cc_start: 0.8392 (t) cc_final: 0.8145 (t) REVERT: Z 390 LEU cc_start: 0.8862 (mt) cc_final: 0.8654 (mt) REVERT: Z 420 ILE cc_start: 0.8711 (OUTLIER) cc_final: 0.8501 (mm) REVERT: Z 474 ASP cc_start: 0.6006 (t0) cc_final: 0.5516 (t0) outliers start: 72 outliers final: 60 residues processed: 651 average time/residue: 0.3479 time to fit residues: 332.6227 Evaluate side-chains 682 residues out of total 2079 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 620 time to evaluate : 2.072 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 8 THR Chi-restraints excluded: chain A residue 59 SER Chi-restraints excluded: chain A residue 93 THR Chi-restraints excluded: chain D residue 93 THR Chi-restraints excluded: chain D residue 98 CYS Chi-restraints excluded: chain E residue 9 THR Chi-restraints excluded: chain H residue 16 SER Chi-restraints excluded: chain H residue 37 VAL Chi-restraints excluded: chain H residue 71 VAL Chi-restraints excluded: chain H residue 90 SER Chi-restraints excluded: chain H residue 93 THR Chi-restraints excluded: chain H residue 110 LEU Chi-restraints excluded: chain L residue 58 VAL Chi-restraints excluded: chain L residue 104 VAL Chi-restraints excluded: chain U residue 633 GLU Chi-restraints excluded: chain V residue 529 THR Chi-restraints excluded: chain V residue 565 LEU Chi-restraints excluded: chain V residue 568 MET Chi-restraints excluded: chain V residue 604 CYS Chi-restraints excluded: chain W residue 573 ILE Chi-restraints excluded: chain W residue 577 GLN Chi-restraints excluded: chain X residue 52 LEU Chi-restraints excluded: chain X residue 56 SER Chi-restraints excluded: chain X residue 111 LEU Chi-restraints excluded: chain X residue 134 VAL Chi-restraints excluded: chain X residue 208 VAL Chi-restraints excluded: chain X residue 269 GLU Chi-restraints excluded: chain X residue 297 THR Chi-restraints excluded: chain X residue 330 HIS Chi-restraints excluded: chain X residue 371 ILE Chi-restraints excluded: chain X residue 420 ILE Chi-restraints excluded: chain X residue 467 ILE Chi-restraints excluded: chain X residue 490 GLU Chi-restraints excluded: chain Y residue 84 MET Chi-restraints excluded: chain Y residue 153 GLU Chi-restraints excluded: chain Y residue 203 GLN Chi-restraints excluded: chain Y residue 208 VAL Chi-restraints excluded: chain Y residue 255 VAL Chi-restraints excluded: chain Y residue 265 LEU Chi-restraints excluded: chain Y residue 275 GLU Chi-restraints excluded: chain Y residue 330 HIS Chi-restraints excluded: chain Y residue 337 ASP Chi-restraints excluded: chain Y residue 349 LEU Chi-restraints excluded: chain Y residue 413 THR Chi-restraints excluded: chain Y residue 425 ASN Chi-restraints excluded: chain Y residue 467 ILE Chi-restraints excluded: chain Z residue 111 LEU Chi-restraints excluded: chain Z residue 116 LEU Chi-restraints excluded: chain Z residue 128 THR Chi-restraints excluded: chain Z residue 154 MET Chi-restraints excluded: chain Z residue 203 GLN Chi-restraints excluded: chain Z residue 269 GLU Chi-restraints excluded: chain Z residue 275 GLU Chi-restraints excluded: chain Z residue 295 VAL Chi-restraints excluded: chain Z residue 330 HIS Chi-restraints excluded: chain Z residue 339 GLU Chi-restraints excluded: chain Z residue 342 LEU Chi-restraints excluded: chain Z residue 413 THR Chi-restraints excluded: chain Z residue 420 ILE Chi-restraints excluded: chain Z residue 443 ILE Chi-restraints excluded: chain Z residue 450 THR Chi-restraints excluded: chain Z residue 475 MET Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 231 random chunks: chunk 53 optimal weight: 3.9990 chunk 96 optimal weight: 3.9990 chunk 211 optimal weight: 0.9990 chunk 182 optimal weight: 0.0010 chunk 114 optimal weight: 0.0980 chunk 93 optimal weight: 1.9990 chunk 177 optimal weight: 4.9990 chunk 71 optimal weight: 3.9990 chunk 188 optimal weight: 1.9990 chunk 124 optimal weight: 0.8980 chunk 154 optimal weight: 2.9990 overall best weight: 0.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 112 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 5 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 554 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** W 630 GLN X 302 ASN X 425 ASN Y 203 GLN Y 302 ASN Z 33 ASN ** Z 203 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Z 348 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3445 r_free = 0.3445 target = 0.113903 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3230 r_free = 0.3230 target = 0.099530 restraints weight = 32853.129| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3288 r_free = 0.3288 target = 0.103288 restraints weight = 14700.509| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3324 r_free = 0.3324 target = 0.105720 restraints weight = 8382.500| |-----------------------------------------------------------------------------| r_work (final): 0.3318 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7494 moved from start: 0.2001 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.074 20834 Z= 0.145 Angle : 0.660 9.906 28547 Z= 0.324 Chirality : 0.046 0.411 3546 Planarity : 0.004 0.053 3379 Dihedral : 8.657 70.747 5096 Min Nonbonded Distance : 2.332 Molprobity Statistics. All-atom Clashscore : 8.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.49 % Favored : 95.51 % Rotamer: Outliers : 3.08 % Allowed : 21.60 % Favored : 75.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.06 % Cis-general : 0.00 % Twisted Proline : 1.01 % Twisted General : 0.04 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.33 (0.18), residues: 2340 helix: 2.11 (0.29), residues: 363 sheet: 0.05 (0.19), residues: 747 loop : -1.13 (0.17), residues: 1230 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.001 TRP Y 112 HIS 0.005 0.001 HIS X 374 PHE 0.037 0.002 PHE Y 53 TYR 0.027 0.001 TYR Y 173 ARG 0.008 0.001 ARG Z 304 Details of bonding type rmsd link_NAG-ASN : bond 0.00303 ( 52) link_NAG-ASN : angle 2.11421 ( 156) link_ALPHA1-6 : bond 0.00390 ( 9) link_ALPHA1-6 : angle 1.96468 ( 27) link_BETA1-4 : bond 0.00351 ( 43) link_BETA1-4 : angle 1.77482 ( 129) link_ALPHA1-2 : bond 0.00370 ( 10) link_ALPHA1-2 : angle 1.63879 ( 30) link_ALPHA1-3 : bond 0.00759 ( 12) link_ALPHA1-3 : angle 1.88928 ( 36) hydrogen bonds : bond 0.04018 ( 671) hydrogen bonds : angle 4.64805 ( 1950) SS BOND : bond 0.00579 ( 38) SS BOND : angle 2.36962 ( 76) covalent geometry : bond 0.00334 (20670) covalent geometry : angle 0.61382 (28093) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4680 Ramachandran restraints generated. 2340 Oldfield, 0 Emsley, 2340 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4680 Ramachandran restraints generated. 2340 Oldfield, 0 Emsley, 2340 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 682 residues out of total 2079 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 618 time to evaluate : 2.127 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 36 TRP cc_start: 0.8310 (m100) cc_final: 0.7874 (m100) REVERT: A 55 LYS cc_start: 0.8295 (mmpt) cc_final: 0.7794 (mmpt) REVERT: C 73 LEU cc_start: 0.8375 (tp) cc_final: 0.8099 (tp) REVERT: D 22 LYS cc_start: 0.8410 (mtpp) cc_final: 0.7949 (mtpp) REVERT: D 50 GLN cc_start: 0.8028 (pt0) cc_final: 0.7802 (pt0) REVERT: L 32 TRP cc_start: 0.8538 (m100) cc_final: 0.7585 (m100) REVERT: U 522 PHE cc_start: 0.8819 (t80) cc_final: 0.8591 (t80) REVERT: U 577 GLN cc_start: 0.7766 (mt0) cc_final: 0.7153 (mt0) REVERT: U 647 GLU cc_start: 0.7345 (pt0) cc_final: 0.7059 (pt0) REVERT: V 542 ARG cc_start: 0.8233 (ttm110) cc_final: 0.7972 (ttm110) REVERT: V 579 ARG cc_start: 0.7753 (ptp-170) cc_final: 0.7204 (mtp180) REVERT: V 650 GLN cc_start: 0.8506 (tp40) cc_final: 0.8239 (tp-100) REVERT: W 647 GLU cc_start: 0.7276 (tt0) cc_final: 0.6752 (tt0) REVERT: X 68 VAL cc_start: 0.8455 (m) cc_final: 0.8153 (p) REVERT: X 167 ASP cc_start: 0.7953 (t0) cc_final: 0.7734 (t0) REVERT: X 255 VAL cc_start: 0.8858 (t) cc_final: 0.8649 (p) REVERT: X 275 GLU cc_start: 0.7148 (tt0) cc_final: 0.6790 (tt0) REVERT: X 315 GLN cc_start: 0.8308 (mp10) cc_final: 0.7849 (mp10) REVERT: X 482 GLU cc_start: 0.7225 (mm-30) cc_final: 0.6825 (mm-30) REVERT: X 485 LYS cc_start: 0.8500 (mtmm) cc_final: 0.8034 (mttp) REVERT: Y 47 GLU cc_start: 0.6736 (tt0) cc_final: 0.6473 (tt0) REVERT: Y 190 GLU cc_start: 0.7228 (tt0) cc_final: 0.6908 (tt0) REVERT: Y 293 GLU cc_start: 0.7169 (tt0) cc_final: 0.6906 (tt0) REVERT: Y 335 ARG cc_start: 0.8568 (tpp80) cc_final: 0.8312 (ttm-80) REVERT: Y 381 GLU cc_start: 0.7072 (tp30) cc_final: 0.6759 (tp30) REVERT: Y 492 LYS cc_start: 0.7947 (mtmm) cc_final: 0.7714 (mttp) REVERT: Z 39 TYR cc_start: 0.8551 (m-80) cc_final: 0.7664 (m-80) REVERT: Z 56 SER cc_start: 0.8281 (t) cc_final: 0.8046 (p) REVERT: Z 97 LYS cc_start: 0.8573 (mtmm) cc_final: 0.8166 (mtmt) REVERT: Z 103 GLN cc_start: 0.7883 (tt0) cc_final: 0.7582 (tt0) REVERT: Z 107 ASP cc_start: 0.7437 (m-30) cc_final: 0.7182 (m-30) REVERT: Z 173 TYR cc_start: 0.8548 (p90) cc_final: 0.8310 (p90) REVERT: Z 175 LEU cc_start: 0.8567 (mt) cc_final: 0.8214 (mt) REVERT: Z 282 LYS cc_start: 0.8397 (mmtt) cc_final: 0.8184 (mmtm) REVERT: Z 388 SER cc_start: 0.8417 (t) cc_final: 0.8176 (t) REVERT: Z 390 LEU cc_start: 0.8872 (mt) cc_final: 0.8637 (mt) REVERT: Z 474 ASP cc_start: 0.6015 (t0) cc_final: 0.5529 (t0) outliers start: 64 outliers final: 56 residues processed: 637 average time/residue: 0.3391 time to fit residues: 320.0020 Evaluate side-chains 671 residues out of total 2079 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 615 time to evaluate : 1.902 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 8 THR Chi-restraints excluded: chain A residue 59 SER Chi-restraints excluded: chain A residue 93 THR Chi-restraints excluded: chain D residue 93 THR Chi-restraints excluded: chain D residue 98 CYS Chi-restraints excluded: chain E residue 9 THR Chi-restraints excluded: chain H residue 37 VAL Chi-restraints excluded: chain H residue 71 VAL Chi-restraints excluded: chain H residue 90 SER Chi-restraints excluded: chain H residue 93 THR Chi-restraints excluded: chain L residue 58 VAL Chi-restraints excluded: chain L residue 104 VAL Chi-restraints excluded: chain U residue 633 GLU Chi-restraints excluded: chain V residue 529 THR Chi-restraints excluded: chain V residue 568 MET Chi-restraints excluded: chain V residue 604 CYS Chi-restraints excluded: chain W residue 573 ILE Chi-restraints excluded: chain W residue 577 GLN Chi-restraints excluded: chain X residue 52 LEU Chi-restraints excluded: chain X residue 56 SER Chi-restraints excluded: chain X residue 111 LEU Chi-restraints excluded: chain X residue 134 VAL Chi-restraints excluded: chain X residue 208 VAL Chi-restraints excluded: chain X residue 269 GLU Chi-restraints excluded: chain X residue 297 THR Chi-restraints excluded: chain X residue 330 HIS Chi-restraints excluded: chain X residue 420 ILE Chi-restraints excluded: chain X residue 467 ILE Chi-restraints excluded: chain X residue 490 GLU Chi-restraints excluded: chain Y residue 84 MET Chi-restraints excluded: chain Y residue 153 GLU Chi-restraints excluded: chain Y residue 203 GLN Chi-restraints excluded: chain Y residue 208 VAL Chi-restraints excluded: chain Y residue 255 VAL Chi-restraints excluded: chain Y residue 265 LEU Chi-restraints excluded: chain Y residue 275 GLU Chi-restraints excluded: chain Y residue 330 HIS Chi-restraints excluded: chain Y residue 349 LEU Chi-restraints excluded: chain Y residue 413 THR Chi-restraints excluded: chain Y residue 425 ASN Chi-restraints excluded: chain Z residue 111 LEU Chi-restraints excluded: chain Z residue 116 LEU Chi-restraints excluded: chain Z residue 128 THR Chi-restraints excluded: chain Z residue 154 MET Chi-restraints excluded: chain Z residue 203 GLN Chi-restraints excluded: chain Z residue 269 GLU Chi-restraints excluded: chain Z residue 275 GLU Chi-restraints excluded: chain Z residue 293 GLU Chi-restraints excluded: chain Z residue 295 VAL Chi-restraints excluded: chain Z residue 330 HIS Chi-restraints excluded: chain Z residue 339 GLU Chi-restraints excluded: chain Z residue 342 LEU Chi-restraints excluded: chain Z residue 413 THR Chi-restraints excluded: chain Z residue 443 ILE Chi-restraints excluded: chain Z residue 450 THR Chi-restraints excluded: chain Z residue 475 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 231 random chunks: chunk 131 optimal weight: 1.9990 chunk 162 optimal weight: 0.5980 chunk 229 optimal weight: 2.9990 chunk 135 optimal weight: 0.0000 chunk 218 optimal weight: 3.9990 chunk 68 optimal weight: 0.5980 chunk 118 optimal weight: 0.9990 chunk 4 optimal weight: 0.5980 chunk 64 optimal weight: 2.9990 chunk 8 optimal weight: 4.9990 chunk 49 optimal weight: 1.9990 overall best weight: 0.5586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 112 HIS ** E 5 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 554 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** X 302 ASN X 360 GLN X 425 ASN Y 98 ASN Y 203 GLN Y 302 ASN Z 33 ASN Z 94 ASN ** Z 203 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Z 348 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3456 r_free = 0.3456 target = 0.114745 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3238 r_free = 0.3238 target = 0.100171 restraints weight = 33055.713| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3297 r_free = 0.3297 target = 0.104000 restraints weight = 14562.609| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3334 r_free = 0.3334 target = 0.106459 restraints weight = 8249.735| |-----------------------------------------------------------------------------| r_work (final): 0.3326 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7474 moved from start: 0.2105 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.075 20834 Z= 0.129 Angle : 0.661 13.674 28547 Z= 0.323 Chirality : 0.046 0.350 3546 Planarity : 0.004 0.041 3379 Dihedral : 8.501 69.570 5096 Min Nonbonded Distance : 2.406 Molprobity Statistics. All-atom Clashscore : 8.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.15 % Favored : 95.85 % Rotamer: Outliers : 2.60 % Allowed : 22.08 % Favored : 75.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.06 % Cis-general : 0.00 % Twisted Proline : 1.01 % Twisted General : 0.04 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.37 (0.18), residues: 2340 helix: 2.06 (0.29), residues: 363 sheet: -0.07 (0.19), residues: 762 loop : -1.08 (0.17), residues: 1215 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP C 32 HIS 0.004 0.001 HIS Y 374 PHE 0.036 0.002 PHE Y 53 TYR 0.027 0.001 TYR Y 173 ARG 0.009 0.001 ARG X 469 Details of bonding type rmsd link_NAG-ASN : bond 0.00309 ( 52) link_NAG-ASN : angle 2.01132 ( 156) link_ALPHA1-6 : bond 0.00436 ( 9) link_ALPHA1-6 : angle 1.88438 ( 27) link_BETA1-4 : bond 0.00352 ( 43) link_BETA1-4 : angle 1.71423 ( 129) link_ALPHA1-2 : bond 0.00397 ( 10) link_ALPHA1-2 : angle 1.60278 ( 30) link_ALPHA1-3 : bond 0.00747 ( 12) link_ALPHA1-3 : angle 1.78978 ( 36) hydrogen bonds : bond 0.03853 ( 671) hydrogen bonds : angle 4.65886 ( 1950) SS BOND : bond 0.00561 ( 38) SS BOND : angle 2.31964 ( 76) covalent geometry : bond 0.00298 (20670) covalent geometry : angle 0.61910 (28093) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4680 Ramachandran restraints generated. 2340 Oldfield, 0 Emsley, 2340 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4680 Ramachandran restraints generated. 2340 Oldfield, 0 Emsley, 2340 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 671 residues out of total 2079 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 617 time to evaluate : 2.249 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 36 TRP cc_start: 0.8316 (m100) cc_final: 0.7574 (m100) REVERT: A 55 LYS cc_start: 0.8286 (mmpt) cc_final: 0.7783 (mmpt) REVERT: D 22 LYS cc_start: 0.8386 (mtpp) cc_final: 0.7926 (mtpp) REVERT: D 50 GLN cc_start: 0.7986 (pt0) cc_final: 0.7785 (pt0) REVERT: L 32 TRP cc_start: 0.8517 (m100) cc_final: 0.7546 (m100) REVERT: U 522 PHE cc_start: 0.8804 (t80) cc_final: 0.8581 (t80) REVERT: U 577 GLN cc_start: 0.7831 (mt0) cc_final: 0.7188 (mt0) REVERT: U 647 GLU cc_start: 0.7320 (pt0) cc_final: 0.7037 (pt0) REVERT: V 542 ARG cc_start: 0.8235 (ttm110) cc_final: 0.7966 (ttm110) REVERT: V 579 ARG cc_start: 0.7710 (ptp-170) cc_final: 0.7294 (mtp180) REVERT: W 647 GLU cc_start: 0.7282 (tt0) cc_final: 0.6752 (tt0) REVERT: X 68 VAL cc_start: 0.8449 (m) cc_final: 0.8138 (p) REVERT: X 154 MET cc_start: 0.8041 (mtt) cc_final: 0.7788 (mtm) REVERT: X 167 ASP cc_start: 0.7984 (t0) cc_final: 0.7768 (t0) REVERT: X 255 VAL cc_start: 0.8863 (t) cc_final: 0.8634 (p) REVERT: X 275 GLU cc_start: 0.7264 (tt0) cc_final: 0.6865 (tt0) REVERT: X 315 GLN cc_start: 0.8330 (mp10) cc_final: 0.7928 (mp10) REVERT: X 482 GLU cc_start: 0.7212 (mm-30) cc_final: 0.6793 (mm-30) REVERT: X 485 LYS cc_start: 0.8331 (mtmm) cc_final: 0.7839 (mttp) REVERT: Y 46 LYS cc_start: 0.8539 (mptt) cc_final: 0.7785 (tptt) REVERT: Y 47 GLU cc_start: 0.6727 (tt0) cc_final: 0.6454 (tt0) REVERT: Y 97 LYS cc_start: 0.8596 (mtmt) cc_final: 0.8205 (mtmm) REVERT: Y 190 GLU cc_start: 0.7241 (tt0) cc_final: 0.6913 (tt0) REVERT: Y 223 TYR cc_start: 0.8481 (m-80) cc_final: 0.8045 (m-80) REVERT: Y 293 GLU cc_start: 0.7204 (tt0) cc_final: 0.6921 (tt0) REVERT: Y 335 ARG cc_start: 0.8551 (tpp80) cc_final: 0.8289 (ttm-80) REVERT: Y 381 GLU cc_start: 0.7065 (tp30) cc_final: 0.6772 (tp30) REVERT: Y 492 LYS cc_start: 0.7964 (mtmm) cc_final: 0.7715 (mttm) REVERT: Z 39 TYR cc_start: 0.8546 (m-80) cc_final: 0.7643 (m-80) REVERT: Z 56 SER cc_start: 0.8270 (t) cc_final: 0.8037 (p) REVERT: Z 97 LYS cc_start: 0.8562 (mtmm) cc_final: 0.8064 (mtmm) REVERT: Z 103 GLN cc_start: 0.7886 (tt0) cc_final: 0.7587 (tt0) REVERT: Z 107 ASP cc_start: 0.7480 (m-30) cc_final: 0.7228 (m-30) REVERT: Z 173 TYR cc_start: 0.8541 (p90) cc_final: 0.8301 (p90) REVERT: Z 175 LEU cc_start: 0.8573 (mt) cc_final: 0.8280 (mt) REVERT: Z 282 LYS cc_start: 0.8426 (mmtt) cc_final: 0.8223 (mmtm) REVERT: Z 388 SER cc_start: 0.8418 (t) cc_final: 0.8171 (t) REVERT: Z 390 LEU cc_start: 0.8844 (mt) cc_final: 0.8636 (mt) REVERT: Z 474 ASP cc_start: 0.5998 (t0) cc_final: 0.5520 (t0) outliers start: 54 outliers final: 50 residues processed: 634 average time/residue: 0.3415 time to fit residues: 322.5081 Evaluate side-chains 663 residues out of total 2079 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 613 time to evaluate : 2.200 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 8 THR Chi-restraints excluded: chain A residue 59 SER Chi-restraints excluded: chain A residue 93 THR Chi-restraints excluded: chain D residue 93 THR Chi-restraints excluded: chain D residue 98 CYS Chi-restraints excluded: chain E residue 9 THR Chi-restraints excluded: chain H residue 37 VAL Chi-restraints excluded: chain H residue 71 VAL Chi-restraints excluded: chain H residue 73 LEU Chi-restraints excluded: chain H residue 90 SER Chi-restraints excluded: chain H residue 93 THR Chi-restraints excluded: chain L residue 58 VAL Chi-restraints excluded: chain L residue 104 VAL Chi-restraints excluded: chain U residue 633 GLU Chi-restraints excluded: chain V residue 568 MET Chi-restraints excluded: chain V residue 604 CYS Chi-restraints excluded: chain W residue 573 ILE Chi-restraints excluded: chain W residue 577 GLN Chi-restraints excluded: chain X residue 52 LEU Chi-restraints excluded: chain X residue 56 SER Chi-restraints excluded: chain X residue 111 LEU Chi-restraints excluded: chain X residue 134 VAL Chi-restraints excluded: chain X residue 208 VAL Chi-restraints excluded: chain X residue 269 GLU Chi-restraints excluded: chain X residue 297 THR Chi-restraints excluded: chain X residue 330 HIS Chi-restraints excluded: chain X residue 360 GLN Chi-restraints excluded: chain X residue 420 ILE Chi-restraints excluded: chain X residue 466 GLU Chi-restraints excluded: chain X residue 490 GLU Chi-restraints excluded: chain Y residue 84 MET Chi-restraints excluded: chain Y residue 153 GLU Chi-restraints excluded: chain Y residue 208 VAL Chi-restraints excluded: chain Y residue 255 VAL Chi-restraints excluded: chain Y residue 275 GLU Chi-restraints excluded: chain Y residue 349 LEU Chi-restraints excluded: chain Y residue 413 THR Chi-restraints excluded: chain Y residue 425 ASN Chi-restraints excluded: chain Y residue 427 TRP Chi-restraints excluded: chain Y residue 467 ILE Chi-restraints excluded: chain Z residue 111 LEU Chi-restraints excluded: chain Z residue 116 LEU Chi-restraints excluded: chain Z residue 269 GLU Chi-restraints excluded: chain Z residue 275 GLU Chi-restraints excluded: chain Z residue 295 VAL Chi-restraints excluded: chain Z residue 339 GLU Chi-restraints excluded: chain Z residue 443 ILE Chi-restraints excluded: chain Z residue 450 THR Chi-restraints excluded: chain Z residue 463 ASN Chi-restraints excluded: chain Z residue 475 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 231 random chunks: chunk 198 optimal weight: 4.9990 chunk 63 optimal weight: 0.0270 chunk 170 optimal weight: 1.9990 chunk 213 optimal weight: 0.6980 chunk 111 optimal weight: 0.3980 chunk 159 optimal weight: 0.0870 chunk 117 optimal weight: 0.8980 chunk 2 optimal weight: 4.9990 chunk 157 optimal weight: 6.9990 chunk 197 optimal weight: 0.7980 chunk 177 optimal weight: 2.9990 overall best weight: 0.4016 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 5 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** U 630 GLN ** V 554 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** W 630 GLN X 72 HIS ** X 258 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** X 302 ASN ** Y 203 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 302 ASN Z 33 ASN Z 94 ASN ** Z 203 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 258 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Z 348 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3455 r_free = 0.3455 target = 0.114588 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3241 r_free = 0.3241 target = 0.100238 restraints weight = 33032.922| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3298 r_free = 0.3298 target = 0.103993 restraints weight = 14720.743| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3335 r_free = 0.3335 target = 0.106405 restraints weight = 8385.620| |-----------------------------------------------------------------------------| r_work (final): 0.3328 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7479 moved from start: 0.2118 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.238 20834 Z= 0.186 Angle : 0.813 59.174 28547 Z= 0.431 Chirality : 0.048 1.023 3546 Planarity : 0.004 0.038 3379 Dihedral : 8.501 69.573 5096 Min Nonbonded Distance : 2.401 Molprobity Statistics. All-atom Clashscore : 9.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.19 % Favored : 95.81 % Rotamer: Outliers : 2.79 % Allowed : 22.51 % Favored : 74.70 % Cbeta Deviations : 0.05 % Peptide Plane: Cis-proline : 6.06 % Cis-general : 0.00 % Twisted Proline : 1.01 % Twisted General : 0.04 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.36 (0.18), residues: 2340 helix: 2.06 (0.29), residues: 363 sheet: -0.07 (0.19), residues: 762 loop : -1.08 (0.17), residues: 1215 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.001 TRP W 557 HIS 0.004 0.001 HIS Y 374 PHE 0.034 0.002 PHE Y 53 TYR 0.026 0.001 TYR Y 173 ARG 0.014 0.001 ARG W 579 Details of bonding type rmsd link_NAG-ASN : bond 0.00386 ( 52) link_NAG-ASN : angle 2.06571 ( 156) link_ALPHA1-6 : bond 0.00445 ( 9) link_ALPHA1-6 : angle 1.89521 ( 27) link_BETA1-4 : bond 0.00378 ( 43) link_BETA1-4 : angle 1.71776 ( 129) link_ALPHA1-2 : bond 0.00420 ( 10) link_ALPHA1-2 : angle 1.61225 ( 30) link_ALPHA1-3 : bond 0.00825 ( 12) link_ALPHA1-3 : angle 1.89661 ( 36) hydrogen bonds : bond 0.03840 ( 671) hydrogen bonds : angle 4.66029 ( 1950) SS BOND : bond 0.01795 ( 38) SS BOND : angle 3.25443 ( 76) covalent geometry : bond 0.00388 (20670) covalent geometry : angle 0.77170 (28093) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7584.72 seconds wall clock time: 132 minutes 4.89 seconds (7924.89 seconds total)