Starting phenix.real_space_refine on Sun Aug 24 13:48:38 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8gpj_34194/08_2025/8gpj_34194.cif Found real_map, /net/cci-nas-00/data/ceres_data/8gpj_34194/08_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_34194/08_2025/8gpj_34194.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8gpj_34194/08_2025/8gpj_34194.map" model { file = "/net/cci-nas-00/data/ceres_data/8gpj_34194/08_2025/8gpj_34194.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8gpj_34194/08_2025/8gpj_34194.cif" } resolution = 3.5 write_initial_geo_file = False refinement { macro_cycles = 10 } 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): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/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: 5.54, per 1000 atoms: 0.27 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: 2.27 Conformation dependent library (CDL) restraints added in 674.0 milliseconds Enol-peptide restraints added in 715.3 nanoseconds 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: 0.96 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: 3.97 Time building geometry restraints manager: 2.70 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 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: 0.010 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.390 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.320 Check model and map are aligned: 0.060 Set scattering table: 0.060 Process input model: 20.210 Find NCS groups from input model: 0.500 Set up NCS constraints: 0.080 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:1.350 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 24.010 ------------------------------------------------------------------------------- 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 : 10.21 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. 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 ARG 0.009 0.001 ARG Z 304 TYR 0.035 0.002 TYR U 638 PHE 0.040 0.002 PHE X 53 TRP 0.062 0.002 TRP U 614 HIS 0.007 0.001 HIS X 374 Details of bonding type rmsd covalent geometry : bond 0.00577 (20670) covalent geometry : angle 0.85029 (28093) SS BOND : bond 0.00693 ( 38) SS BOND : angle 2.73067 ( 76) hydrogen bonds : bond 0.12920 ( 671) hydrogen bonds : angle 6.50126 ( 1950) 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) 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_NAG-ASN : bond 0.00456 ( 52) link_NAG-ASN : angle 2.60537 ( 156) *********************** 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 : 0.745 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: 0.7317 (p) REVERT: H 99 THR cc_start: 0.8406 (p) cc_final: 0.8175 (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: 0.6947 (tt0) REVERT: X 83 GLU cc_start: 0.6935 (tm-30) cc_final: 0.6570 (tm-30) REVERT: X 84 MET cc_start: 0.7082 (tmm) cc_final: 0.6143 (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: 0.7939 (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: 0.7503 (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: 0.6814 (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: 0.1553 time to fit residues: 153.1052 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 : 0.749 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 231 random chunks: chunk 216 optimal weight: 1.9990 chunk 98 optimal weight: 2.9990 chunk 194 optimal weight: 1.9990 chunk 227 optimal weight: 6.9990 chunk 107 optimal weight: 3.9990 chunk 10 optimal weight: 4.9990 chunk 66 optimal weight: 7.9990 chunk 130 optimal weight: 2.9990 chunk 124 optimal weight: 0.5980 chunk 103 optimal weight: 1.9990 chunk 200 optimal weight: 4.9990 overall best weight: 1.9188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 39 GLN A 43 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 X 203 GLN X 302 ASN X 425 ASN ** Y 94 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 203 GLN Z 33 ASN Z 348 ASN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3430 r_free = 0.3430 target = 0.112890 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3211 r_free = 0.3211 target = 0.098631 restraints weight = 32514.483| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3270 r_free = 0.3270 target = 0.102383 restraints weight = 14263.922| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3307 r_free = 0.3307 target = 0.104804 restraints weight = 8090.747| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3331 r_free = 0.3331 target = 0.106344 restraints weight = 5380.056| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3348 r_free = 0.3348 target = 0.107478 restraints weight = 3980.963| |-----------------------------------------------------------------------------| r_work (final): 0.3347 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7497 moved from start: 0.1146 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.055 20834 Z= 0.268 Angle : 0.770 10.677 28547 Z= 0.371 Chirality : 0.049 0.334 3546 Planarity : 0.005 0.069 3379 Dihedral : 12.600 85.565 5096 Min Nonbonded Distance : 2.338 Molprobity Statistics. All-atom Clashscore : 8.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.30 % Favored : 94.70 % Rotamer: Outliers : 2.02 % Allowed : 12.36 % Favored : 85.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.06 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.49 (0.18), residues: 2340 helix: 1.46 (0.28), residues: 384 sheet: 0.24 (0.19), residues: 777 loop : -1.35 (0.17), residues: 1179 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG L 50 TYR 0.028 0.002 TYR U 638 PHE 0.030 0.002 PHE Y 53 TRP 0.039 0.002 TRP U 614 HIS 0.009 0.001 HIS X 374 Details of bonding type rmsd covalent geometry : bond 0.00593 (20670) covalent geometry : angle 0.71941 (28093) SS BOND : bond 0.00663 ( 38) SS BOND : angle 2.06314 ( 76) hydrogen bonds : bond 0.05363 ( 671) hydrogen bonds : angle 5.09780 ( 1950) link_ALPHA1-2 : bond 0.00349 ( 10) link_ALPHA1-2 : angle 1.92276 ( 30) link_ALPHA1-3 : bond 0.00669 ( 12) link_ALPHA1-3 : angle 2.61460 ( 36) link_ALPHA1-6 : bond 0.00399 ( 9) link_ALPHA1-6 : angle 2.37344 ( 27) link_BETA1-4 : bond 0.00440 ( 43) link_BETA1-4 : angle 2.25479 ( 129) link_NAG-ASN : bond 0.00640 ( 52) link_NAG-ASN : angle 2.40792 ( 156) *********************** 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 706 residues out of total 2079 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 664 time to evaluate : 0.562 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: 0.8246 (mmpt) cc_final: 0.7865 (mmpt) REVERT: C 4 THR cc_start: 0.7607 (p) cc_final: 0.7399 (p) REVERT: D 22 LYS cc_start: 0.8347 (mtpp) cc_final: 0.8095 (mtpp) REVERT: H 110 LEU cc_start: 0.9011 (tt) cc_final: 0.8780 (tt) REVERT: L 32 TRP cc_start: 0.8574 (m100) cc_final: 0.7890 (m100) REVERT: U 522 PHE cc_start: 0.8844 (t80) cc_final: 0.8618 (t80) REVERT: U 577 GLN cc_start: 0.7729 (mt0) cc_final: 0.7211 (mt0) REVERT: U 647 GLU cc_start: 0.7340 (pt0) cc_final: 0.7100 (pt0) REVERT: U 650 GLN cc_start: 0.8419 (tp40) cc_final: 0.7828 (tp40) REVERT: V 542 ARG cc_start: 0.8212 (ttm110) cc_final: 0.7968 (ttm110) REVERT: V 543 GLN cc_start: 0.7786 (tp-100) cc_final: 0.7481 (tp-100) REVERT: V 579 ARG cc_start: 0.7757 (ptp-170) cc_final: 0.7257 (mtp180) REVERT: V 625 ASN cc_start: 0.8198 (t0) cc_final: 0.7870 (t0) REVERT: V 647 GLU cc_start: 0.6775 (mt-10) cc_final: 0.6454 (mt-10) REVERT: V 650 GLN cc_start: 0.8524 (tp40) cc_final: 0.8269 (tp40) REVERT: W 647 GLU cc_start: 0.7241 (tt0) cc_final: 0.6693 (tt0) REVERT: X 68 VAL cc_start: 0.8490 (m) cc_final: 0.8200 (p) REVERT: X 83 GLU cc_start: 0.7024 (tm-30) cc_final: 0.6712 (tm-30) REVERT: X 84 MET cc_start: 0.7250 (tmm) cc_final: 0.6500 (tmm) REVERT: X 97 LYS cc_start: 0.8405 (ptpp) cc_final: 0.8075 (ptpp) REVERT: X 99 GLU cc_start: 0.7023 (mp0) cc_final: 0.6783 (mp0) REVERT: X 104 MET cc_start: 0.8122 (ttt) cc_final: 0.7903 (ttt) REVERT: X 121 LYS cc_start: 0.8416 (ttmm) cc_final: 0.8197 (ttmm) REVERT: X 275 GLU cc_start: 0.7253 (tt0) cc_final: 0.6885 (tt0) REVERT: X 315 GLN cc_start: 0.8295 (mp10) cc_final: 0.7864 (mp10) REVERT: X 370 GLU cc_start: 0.7518 (mp0) cc_final: 0.7318 (mp0) REVERT: X 388 SER cc_start: 0.8201 (t) cc_final: 0.7902 (m) REVERT: X 428 GLN cc_start: 0.7958 (mp10) cc_final: 0.7563 (mp10) REVERT: X 446 LYS cc_start: 0.8073 (tttp) cc_final: 0.7854 (tttp) REVERT: Y 46 LYS cc_start: 0.8447 (mptt) cc_final: 0.8225 (mmtm) REVERT: Y 112 TRP cc_start: 0.8140 (m100) cc_final: 0.7905 (m100) REVERT: Y 190 GLU cc_start: 0.7333 (tt0) cc_final: 0.7031 (tt0) REVERT: Y 415 THR cc_start: 0.8039 (p) cc_final: 0.7832 (m) REVERT: Y 426 MET cc_start: 0.7797 (mtm) cc_final: 0.7053 (mtt) REVERT: Y 434 MET cc_start: 0.8098 (ttp) cc_final: 0.7746 (ttp) REVERT: Y 485 LYS cc_start: 0.8241 (mtmm) cc_final: 0.7686 (ptpp) REVERT: Z 66 HIS cc_start: 0.6834 (t-90) cc_final: 0.6455 (t70) REVERT: Z 97 LYS cc_start: 0.8570 (mtmm) cc_final: 0.8256 (mttt) REVERT: Z 173 TYR cc_start: 0.8586 (p90) cc_final: 0.8322 (p90) REVERT: Z 175 LEU cc_start: 0.8611 (mt) cc_final: 0.8308 (mt) REVERT: Z 199 SER cc_start: 0.8349 (m) cc_final: 0.7989 (t) REVERT: Z 388 SER cc_start: 0.8480 (t) cc_final: 0.8225 (t) outliers start: 42 outliers final: 29 residues processed: 675 average time/residue: 0.1580 time to fit residues: 157.3186 Evaluate side-chains 683 residues out of total 2079 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 654 time to evaluate : 0.736 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 26 VAL Chi-restraints excluded: chain A residue 59 SER Chi-restraints excluded: chain A residue 93 THR Chi-restraints excluded: chain D residue 51 ILE 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 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 X residue 490 GLU Chi-restraints excluded: chain Y residue 66 HIS Chi-restraints excluded: chain Y residue 84 MET Chi-restraints excluded: chain Y residue 203 GLN 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 388 SER Chi-restraints excluded: chain Y residue 413 THR 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 450 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 231 random chunks: chunk 162 optimal weight: 5.9990 chunk 102 optimal weight: 2.9990 chunk 3 optimal weight: 1.9990 chunk 11 optimal weight: 0.3980 chunk 13 optimal weight: 5.9990 chunk 18 optimal weight: 4.9990 chunk 23 optimal weight: 7.9990 chunk 184 optimal weight: 3.9990 chunk 73 optimal weight: 0.8980 chunk 87 optimal weight: 0.9990 chunk 12 optimal weight: 3.9990 overall best weight: 1.4586 ------------------------------------------------------------------------------- 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** ** L 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 X 478 ASN ** Y 94 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 203 GLN 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 = 0.3410 r_free = 0.3410 target = 0.111477 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 24)----------------| | r_work = 0.3192 r_free = 0.3192 target = 0.097120 restraints weight = 32865.190| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3250 r_free = 0.3250 target = 0.100810 restraints weight = 14845.776| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3286 r_free = 0.3286 target = 0.103237 restraints weight = 8557.382| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.3311 r_free = 0.3311 target = 0.104861 restraints weight = 5738.089| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3328 r_free = 0.3328 target = 0.105960 restraints weight = 4225.736| |-----------------------------------------------------------------------------| r_work (final): 0.3295 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7505 moved from start: 0.1375 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.047 20834 Z= 0.213 Angle : 0.708 9.637 28547 Z= 0.343 Chirality : 0.047 0.326 3546 Planarity : 0.004 0.055 3379 Dihedral : 11.051 84.035 5096 Min Nonbonded Distance : 2.369 Molprobity Statistics. All-atom Clashscore : 7.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.57 % Favored : 95.43 % Rotamer: Outliers : 3.32 % Allowed : 16.07 % Favored : 80.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.06 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.41 (0.18), residues: 2340 helix: 1.88 (0.28), residues: 366 sheet: 0.15 (0.19), residues: 792 loop : -1.29 (0.17), residues: 1182 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG W 579 TYR 0.026 0.002 TYR U 638 PHE 0.030 0.002 PHE Y 53 TRP 0.026 0.002 TRP U 614 HIS 0.008 0.001 HIS X 374 Details of bonding type rmsd covalent geometry : bond 0.00471 (20670) covalent geometry : angle 0.66032 (28093) SS BOND : bond 0.00620 ( 38) SS BOND : angle 1.96884 ( 76) hydrogen bonds : bond 0.04928 ( 671) hydrogen bonds : angle 4.92633 ( 1950) link_ALPHA1-2 : bond 0.00369 ( 10) link_ALPHA1-2 : angle 1.76563 ( 30) link_ALPHA1-3 : bond 0.00731 ( 12) link_ALPHA1-3 : angle 2.07438 ( 36) link_ALPHA1-6 : bond 0.00284 ( 9) link_ALPHA1-6 : angle 2.17662 ( 27) link_BETA1-4 : bond 0.00409 ( 43) link_BETA1-4 : angle 2.03330 ( 129) link_NAG-ASN : bond 0.00448 ( 52) link_NAG-ASN : angle 2.34584 ( 156) *********************** 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 726 residues out of total 2079 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 657 time to evaluate : 0.700 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: 0.8283 (mmpt) cc_final: 0.7864 (mmpt) REVERT: C 73 LEU cc_start: 0.8450 (tp) cc_final: 0.8230 (tp) REVERT: D 11 LYS cc_start: 0.7960 (OUTLIER) cc_final: 0.7663 (mtmm) REVERT: D 22 LYS cc_start: 0.8393 (mtpp) cc_final: 0.8047 (mtpp) REVERT: E 4 THR cc_start: 0.8279 (m) cc_final: 0.7710 (p) REVERT: H 80 ILE cc_start: 0.5456 (OUTLIER) cc_final: 0.5253 (mt) REVERT: H 110 LEU cc_start: 0.9022 (tt) cc_final: 0.8783 (tt) REVERT: L 32 TRP cc_start: 0.8562 (m100) cc_final: 0.7820 (m100) REVERT: U 522 PHE cc_start: 0.8858 (t80) cc_final: 0.8615 (t80) REVERT: U 577 GLN cc_start: 0.7723 (mt0) cc_final: 0.7212 (mt0) REVERT: U 647 GLU cc_start: 0.7364 (pt0) cc_final: 0.7089 (pt0) REVERT: V 542 ARG cc_start: 0.8206 (ttm110) cc_final: 0.7947 (ttm110) REVERT: V 577 GLN cc_start: 0.7853 (tp-100) cc_final: 0.7589 (tp40) REVERT: V 579 ARG cc_start: 0.7769 (ptp-170) cc_final: 0.7259 (mtp180) REVERT: V 625 ASN cc_start: 0.8170 (t0) cc_final: 0.7820 (t0) REVERT: V 647 GLU cc_start: 0.6822 (mt-10) cc_final: 0.6509 (mt-10) REVERT: V 650 GLN cc_start: 0.8564 (tp40) cc_final: 0.8293 (tp40) REVERT: W 647 GLU cc_start: 0.7215 (tt0) cc_final: 0.6673 (tt0) REVERT: X 68 VAL cc_start: 0.8508 (m) cc_final: 0.8216 (p) REVERT: X 83 GLU cc_start: 0.7036 (tm-30) cc_final: 0.6773 (tm-30) REVERT: X 84 MET cc_start: 0.7342 (tmm) cc_final: 0.6894 (tmm) REVERT: X 97 LYS cc_start: 0.8305 (ptpp) cc_final: 0.7871 (ptpp) REVERT: X 99 GLU cc_start: 0.6947 (mp0) cc_final: 0.6699 (mp0) REVERT: X 104 MET cc_start: 0.8098 (ttt) cc_final: 0.7866 (ttt) REVERT: X 107 ASP cc_start: 0.7376 (m-30) cc_final: 0.6923 (t0) REVERT: X 121 LYS cc_start: 0.8396 (ttmm) cc_final: 0.8160 (ttmm) REVERT: X 275 GLU cc_start: 0.7182 (tt0) cc_final: 0.6841 (tt0) REVERT: X 293 GLU cc_start: 0.6948 (tt0) cc_final: 0.6724 (tm-30) REVERT: X 315 GLN cc_start: 0.8352 (mp10) cc_final: 0.7927 (mp10) REVERT: X 428 GLN cc_start: 0.7905 (mp10) cc_final: 0.7561 (mp10) REVERT: X 482 GLU cc_start: 0.7092 (mm-30) cc_final: 0.6691 (mm-30) REVERT: Y 46 LYS cc_start: 0.8467 (mptt) cc_final: 0.8185 (mmtm) REVERT: Y 97 LYS cc_start: 0.8632 (mtmt) cc_final: 0.8202 (mtmm) REVERT: Y 190 GLU cc_start: 0.7258 (tt0) cc_final: 0.6976 (tt0) REVERT: Y 335 ARG cc_start: 0.8589 (tpp80) cc_final: 0.8308 (ttm-80) REVERT: Y 347 LYS cc_start: 0.8686 (tppt) cc_final: 0.8316 (tppt) REVERT: Y 426 MET cc_start: 0.7761 (mtm) cc_final: 0.7040 (mtm) REVERT: Y 434 MET cc_start: 0.8103 (ttp) cc_final: 0.7738 (ttp) REVERT: Z 39 TYR cc_start: 0.8566 (m-80) cc_final: 0.7640 (m-80) REVERT: Z 66 HIS cc_start: 0.6936 (t-90) cc_final: 0.6602 (t-90) REVERT: Z 97 LYS cc_start: 0.8549 (mtmm) cc_final: 0.8151 (mtmt) REVERT: Z 103 GLN cc_start: 0.7614 (tm-30) cc_final: 0.7412 (tm-30) REVERT: Z 107 ASP cc_start: 0.7468 (m-30) cc_final: 0.7033 (t0) REVERT: Z 173 TYR cc_start: 0.8566 (p90) cc_final: 0.8329 (p90) REVERT: Z 175 LEU cc_start: 0.8585 (mt) cc_final: 0.8265 (mt) REVERT: Z 199 SER cc_start: 0.8333 (m) cc_final: 0.7969 (t) REVERT: Z 208 VAL cc_start: 0.8704 (m) cc_final: 0.8278 (m) REVERT: Z 388 SER cc_start: 0.8416 (t) cc_final: 0.8168 (t) REVERT: Z 390 LEU cc_start: 0.8859 (mt) cc_final: 0.8602 (mt) REVERT: Z 474 ASP cc_start: 0.5904 (t0) cc_final: 0.5357 (t0) outliers start: 69 outliers final: 45 residues processed: 676 average time/residue: 0.1572 time to fit residues: 157.6486 Evaluate side-chains 697 residues out of total 2079 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 650 time to evaluate : 0.670 ------------------------------------------------------------------------------- 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 60 SER Chi-restraints excluded: chain C residue 88 CYS Chi-restraints excluded: chain D residue 11 LYS 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 80 ILE 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 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 568 MET Chi-restraints excluded: chain V residue 595 ILE 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 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 490 GLU Chi-restraints excluded: chain Y residue 84 MET Chi-restraints excluded: chain Y residue 120 VAL Chi-restraints excluded: chain Y residue 207 LYS 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 323 ILE Chi-restraints excluded: chain Y residue 330 HIS Chi-restraints excluded: chain Y residue 349 LEU Chi-restraints excluded: chain Z residue 111 LEU Chi-restraints excluded: chain Z residue 180 ASP Chi-restraints excluded: chain Z residue 203 GLN Chi-restraints excluded: chain Z residue 269 GLU Chi-restraints excluded: chain Z residue 295 VAL Chi-restraints excluded: chain Z residue 322 ILE Chi-restraints excluded: chain Z residue 339 GLU 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 136 optimal weight: 2.9990 chunk 155 optimal weight: 0.5980 chunk 153 optimal weight: 1.9990 chunk 101 optimal weight: 0.5980 chunk 40 optimal weight: 0.0050 chunk 209 optimal weight: 4.9990 chunk 141 optimal weight: 0.6980 chunk 9 optimal weight: 1.9990 chunk 135 optimal weight: 1.9990 chunk 140 optimal weight: 1.9990 chunk 172 optimal weight: 0.9980 overall best weight: 0.5794 ------------------------------------------------------------------------------- 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 ** 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 302 ASN ** Y 94 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Z 33 ASN Z 348 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3444 r_free = 0.3444 target = 0.113783 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3223 r_free = 0.3223 target = 0.099152 restraints weight = 32710.475| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3282 r_free = 0.3282 target = 0.102985 restraints weight = 14380.140| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3320 r_free = 0.3320 target = 0.105493 restraints weight = 8139.752| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.3345 r_free = 0.3345 target = 0.107148 restraints weight = 5400.758| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 35)----------------| | r_work = 0.3363 r_free = 0.3363 target = 0.108305 restraints weight = 3936.972| |-----------------------------------------------------------------------------| r_work (final): 0.3360 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7447 moved from start: 0.1569 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= 0.126 Angle : 0.636 9.275 28547 Z= 0.312 Chirality : 0.046 0.336 3546 Planarity : 0.004 0.043 3379 Dihedral : 9.873 80.793 5096 Min Nonbonded Distance : 2.417 Molprobity Statistics. All-atom Clashscore : 7.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.40 % Favored : 95.60 % Rotamer: Outliers : 3.70 % Allowed : 17.75 % Favored : 78.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.06 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.37 (0.17), residues: 2340 helix: 2.02 (0.28), residues: 366 sheet: 0.20 (0.19), residues: 756 loop : -1.29 (0.17), residues: 1218 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG X 469 TYR 0.028 0.001 TYR U 638 PHE 0.029 0.002 PHE Y 53 TRP 0.025 0.001 TRP Y 112 HIS 0.005 0.001 HIS Y 374 Details of bonding type rmsd covalent geometry : bond 0.00285 (20670) covalent geometry : angle 0.59566 (28093) SS BOND : bond 0.00565 ( 38) SS BOND : angle 1.79759 ( 76) hydrogen bonds : bond 0.04076 ( 671) hydrogen bonds : angle 4.74611 ( 1950) link_ALPHA1-2 : bond 0.00461 ( 10) link_ALPHA1-2 : angle 1.63523 ( 30) link_ALPHA1-3 : bond 0.00860 ( 12) link_ALPHA1-3 : angle 1.94436 ( 36) link_ALPHA1-6 : bond 0.00341 ( 9) link_ALPHA1-6 : angle 1.95118 ( 27) link_BETA1-4 : bond 0.00372 ( 43) link_BETA1-4 : angle 1.75267 ( 129) link_NAG-ASN : bond 0.00282 ( 52) link_NAG-ASN : angle 2.00394 ( 156) *********************** 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 726 residues out of total 2079 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 77 poor density : 649 time to evaluate : 0.754 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: 0.8300 (mmpt) cc_final: 0.7862 (mmpt) REVERT: C 73 LEU cc_start: 0.8429 (tp) cc_final: 0.8141 (tp) REVERT: D 22 LYS cc_start: 0.8337 (mtpp) cc_final: 0.7940 (mtpp) REVERT: E 28 ILE cc_start: 0.8796 (mm) cc_final: 0.8545 (mm) REVERT: H 106 LYS cc_start: 0.8329 (pptt) cc_final: 0.8064 (pptt) REVERT: H 110 LEU cc_start: 0.9009 (OUTLIER) cc_final: 0.8788 (tt) REVERT: L 32 TRP cc_start: 0.8553 (m100) cc_final: 0.7741 (m100) REVERT: U 522 PHE cc_start: 0.8816 (t80) cc_final: 0.8569 (t80) REVERT: U 577 GLN cc_start: 0.7699 (mt0) cc_final: 0.7256 (mt0) REVERT: U 647 GLU cc_start: 0.7358 (pt0) cc_final: 0.7030 (pt0) REVERT: V 542 ARG cc_start: 0.8182 (ttm110) cc_final: 0.7894 (ttm110) REVERT: V 579 ARG cc_start: 0.7718 (ptp-170) cc_final: 0.7158 (mtp180) REVERT: V 647 GLU cc_start: 0.6764 (mt-10) cc_final: 0.6452 (mt-10) REVERT: V 650 GLN cc_start: 0.8505 (tp40) cc_final: 0.8268 (tp-100) REVERT: W 647 GLU cc_start: 0.7239 (tt0) cc_final: 0.6688 (tt0) REVERT: X 68 VAL cc_start: 0.8470 (m) cc_final: 0.8181 (p) REVERT: X 83 GLU cc_start: 0.7070 (tm-30) cc_final: 0.6786 (tm-30) REVERT: X 84 MET cc_start: 0.7326 (tmm) cc_final: 0.6864 (tmm) REVERT: X 275 GLU cc_start: 0.7222 (tt0) cc_final: 0.6812 (tt0) REVERT: X 315 GLN cc_start: 0.8284 (mp10) cc_final: 0.7882 (mp10) REVERT: X 347 LYS cc_start: 0.8314 (ttpt) cc_final: 0.7835 (ttpt) REVERT: X 421 LYS cc_start: 0.8064 (ttpt) cc_final: 0.7785 (ttpt) REVERT: X 482 GLU cc_start: 0.7145 (mm-30) cc_final: 0.6711 (mm-30) REVERT: Y 46 LYS cc_start: 0.8449 (mptt) cc_final: 0.8139 (mmtm) REVERT: Y 97 LYS cc_start: 0.8707 (mtmt) cc_final: 0.8297 (mttp) REVERT: Y 190 GLU cc_start: 0.7226 (tt0) cc_final: 0.6908 (tt0) REVERT: Y 335 ARG cc_start: 0.8592 (tpp80) cc_final: 0.8370 (ttm-80) REVERT: Y 381 GLU cc_start: 0.7073 (tp30) cc_final: 0.6702 (tp30) REVERT: Y 423 ILE cc_start: 0.8823 (mt) cc_final: 0.8610 (mt) REVERT: Y 426 MET cc_start: 0.7545 (mtm) cc_final: 0.7163 (mtt) REVERT: Y 434 MET cc_start: 0.8096 (ttp) cc_final: 0.7857 (ttp) REVERT: Y 439 ILE cc_start: 0.8482 (mp) cc_final: 0.8116 (tp) REVERT: Z 39 TYR cc_start: 0.8522 (m-80) cc_final: 0.7575 (m-80) REVERT: Z 66 HIS cc_start: 0.6952 (t-90) cc_final: 0.6724 (t-90) REVERT: Z 97 LYS cc_start: 0.8576 (mtmm) cc_final: 0.8313 (mttt) REVERT: Z 103 GLN cc_start: 0.7561 (tm-30) cc_final: 0.7357 (tm-30) REVERT: Z 107 ASP cc_start: 0.7382 (m-30) cc_final: 0.6893 (t0) REVERT: Z 173 TYR cc_start: 0.8534 (p90) cc_final: 0.8253 (p90) REVERT: Z 175 LEU cc_start: 0.8588 (mt) cc_final: 0.8209 (mt) REVERT: Z 199 SER cc_start: 0.8292 (m) cc_final: 0.7785 (t) REVERT: Z 208 VAL cc_start: 0.8645 (m) cc_final: 0.8391 (p) REVERT: Z 231 LYS cc_start: 0.7745 (mmmt) cc_final: 0.7439 (mmmm) REVERT: Z 379 ARG cc_start: 0.8450 (mtp85) cc_final: 0.8184 (ttp80) REVERT: Z 388 SER cc_start: 0.8461 (t) cc_final: 0.8210 (t) REVERT: Z 474 ASP cc_start: 0.5862 (t0) cc_final: 0.5371 (t0) outliers start: 77 outliers final: 44 residues processed: 675 average time/residue: 0.1660 time to fit residues: 164.1864 Evaluate side-chains 673 residues out of total 2079 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 628 time to evaluate : 0.680 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 8 THR 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 37 VAL Chi-restraints excluded: chain D residue 93 THR Chi-restraints excluded: chain D residue 98 CYS Chi-restraints excluded: chain H residue 37 VAL Chi-restraints excluded: chain H residue 71 VAL 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 U residue 575 GLN Chi-restraints excluded: chain U residue 633 GLU 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 153 GLU 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 368 ASP 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 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 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 228 CYS 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 475 MET Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 231 random chunks: chunk 106 optimal weight: 0.8980 chunk 18 optimal weight: 4.9990 chunk 59 optimal weight: 7.9990 chunk 38 optimal weight: 9.9990 chunk 76 optimal weight: 0.6980 chunk 198 optimal weight: 5.9990 chunk 147 optimal weight: 0.9990 chunk 157 optimal weight: 5.9990 chunk 162 optimal weight: 1.9990 chunk 120 optimal weight: 0.9990 chunk 74 optimal weight: 3.9990 overall best weight: 1.1186 ------------------------------------------------------------------------------- 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 ** 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 Z 33 ASN Z 348 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3425 r_free = 0.3425 target = 0.112580 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 27)----------------| | r_work = 0.3204 r_free = 0.3204 target = 0.097964 restraints weight = 32925.081| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3263 r_free = 0.3263 target = 0.101778 restraints weight = 14468.508| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3301 r_free = 0.3301 target = 0.104254 restraints weight = 8195.884| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3326 r_free = 0.3326 target = 0.105906 restraints weight = 5464.168| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.3343 r_free = 0.3343 target = 0.107045 restraints weight = 3989.865| |-----------------------------------------------------------------------------| r_work (final): 0.3341 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7468 moved from start: 0.1666 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.059 20834 Z= 0.175 Angle : 0.668 10.032 28547 Z= 0.327 Chirality : 0.046 0.321 3546 Planarity : 0.004 0.038 3379 Dihedral : 9.492 77.436 5096 Min Nonbonded Distance : 2.391 Molprobity Statistics. All-atom Clashscore : 8.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.32 % Favored : 95.68 % Rotamer: Outliers : 3.56 % Allowed : 19.53 % Favored : 76.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.06 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.34 (0.18), residues: 2340 helix: 2.05 (0.28), residues: 366 sheet: 0.22 (0.19), residues: 777 loop : -1.29 (0.17), residues: 1197 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG Y 469 TYR 0.026 0.002 TYR Y 173 PHE 0.034 0.002 PHE Y 53 TRP 0.023 0.001 TRP Y 112 HIS 0.007 0.001 HIS X 374 Details of bonding type rmsd covalent geometry : bond 0.00394 (20670) covalent geometry : angle 0.62264 (28093) SS BOND : bond 0.00642 ( 38) SS BOND : angle 2.25343 ( 76) hydrogen bonds : bond 0.04389 ( 671) hydrogen bonds : angle 4.69771 ( 1950) link_ALPHA1-2 : bond 0.00354 ( 10) link_ALPHA1-2 : angle 1.71768 ( 30) link_ALPHA1-3 : bond 0.00762 ( 12) link_ALPHA1-3 : angle 2.06274 ( 36) link_ALPHA1-6 : bond 0.00313 ( 9) link_ALPHA1-6 : angle 2.06858 ( 27) link_BETA1-4 : bond 0.00346 ( 43) link_BETA1-4 : angle 1.85690 ( 129) link_NAG-ASN : bond 0.00384 ( 52) link_NAG-ASN : angle 2.08089 ( 156) *********************** 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 703 residues out of total 2079 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 74 poor density : 629 time to evaluate : 0.517 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 55 LYS cc_start: 0.8316 (mmpt) cc_final: 0.7862 (mmpt) REVERT: C 73 LEU cc_start: 0.8441 (tp) cc_final: 0.8144 (tp) REVERT: D 22 LYS cc_start: 0.8382 (mtpp) cc_final: 0.7955 (mtpp) REVERT: D 50 GLN cc_start: 0.8081 (pt0) cc_final: 0.7739 (pt0) REVERT: H 110 LEU cc_start: 0.9037 (OUTLIER) cc_final: 0.8823 (tt) REVERT: L 32 TRP cc_start: 0.8558 (m100) cc_final: 0.7622 (m100) REVERT: U 522 PHE cc_start: 0.8833 (t80) cc_final: 0.8567 (t80) REVERT: U 577 GLN cc_start: 0.7738 (mt0) cc_final: 0.7231 (mt0) REVERT: U 647 GLU cc_start: 0.7405 (pt0) cc_final: 0.7054 (pt0) REVERT: V 542 ARG cc_start: 0.8239 (ttm110) cc_final: 0.7981 (ttm110) REVERT: V 579 ARG cc_start: 0.7728 (ptp-170) cc_final: 0.7160 (mtp180) REVERT: V 647 GLU cc_start: 0.6813 (mt-10) cc_final: 0.6509 (mt-10) REVERT: V 650 GLN cc_start: 0.8528 (tp40) cc_final: 0.8287 (tp-100) REVERT: W 647 GLU cc_start: 0.7258 (tt0) cc_final: 0.6724 (tt0) REVERT: X 45 TRP cc_start: 0.8611 (p90) cc_final: 0.8207 (p90) REVERT: X 68 VAL cc_start: 0.8471 (m) cc_final: 0.8174 (p) REVERT: X 83 GLU cc_start: 0.7067 (tm-30) cc_final: 0.6814 (tm-30) REVERT: X 84 MET cc_start: 0.7356 (tmm) cc_final: 0.6952 (tmm) REVERT: X 97 LYS cc_start: 0.8391 (ptpp) cc_final: 0.8133 (ptpp) REVERT: X 104 MET cc_start: 0.8037 (ttt) cc_final: 0.7704 (ttp) REVERT: X 275 GLU cc_start: 0.7215 (tt0) cc_final: 0.6820 (tt0) REVERT: X 315 GLN cc_start: 0.8300 (mp10) cc_final: 0.7886 (mp10) REVERT: X 482 GLU cc_start: 0.7167 (mm-30) cc_final: 0.6713 (mm-30) REVERT: Y 46 LYS cc_start: 0.8441 (mptt) cc_final: 0.8020 (mmtm) REVERT: Y 97 LYS cc_start: 0.8688 (mtmt) cc_final: 0.8304 (mttp) REVERT: Y 190 GLU cc_start: 0.7236 (tt0) cc_final: 0.6918 (tt0) REVERT: Y 335 ARG cc_start: 0.8594 (tpp80) cc_final: 0.8368 (ttm-80) REVERT: Y 381 GLU cc_start: 0.7068 (tp30) cc_final: 0.6666 (tp30) REVERT: Y 434 MET cc_start: 0.8143 (ttp) cc_final: 0.7850 (ttp) REVERT: Y 439 ILE cc_start: 0.8479 (mp) cc_final: 0.8108 (tp) REVERT: Z 39 TYR cc_start: 0.8535 (m-80) cc_final: 0.7598 (m-80) REVERT: Z 53 PHE cc_start: 0.8097 (p90) cc_final: 0.7805 (p90) REVERT: Z 66 HIS cc_start: 0.7010 (t-90) cc_final: 0.6603 (t-90) REVERT: Z 97 LYS cc_start: 0.8588 (mtmm) cc_final: 0.8225 (mtmt) REVERT: Z 103 GLN cc_start: 0.7631 (tm-30) cc_final: 0.7387 (tm-30) REVERT: Z 107 ASP cc_start: 0.7377 (m-30) cc_final: 0.6884 (t0) REVERT: Z 173 TYR cc_start: 0.8580 (p90) cc_final: 0.8289 (p90) REVERT: Z 175 LEU cc_start: 0.8618 (mt) cc_final: 0.8243 (mt) REVERT: Z 208 VAL cc_start: 0.8627 (m) cc_final: 0.8299 (m) REVERT: Z 231 LYS cc_start: 0.7738 (mmmt) cc_final: 0.7511 (mmmm) REVERT: Z 347 LYS cc_start: 0.8403 (tppt) cc_final: 0.8059 (ttpt) REVERT: Z 379 ARG cc_start: 0.8449 (mtp85) cc_final: 0.8199 (ttp80) REVERT: Z 466 GLU cc_start: 0.7662 (tp30) cc_final: 0.7456 (mm-30) REVERT: Z 474 ASP cc_start: 0.5898 (t0) cc_final: 0.5412 (t0) outliers start: 74 outliers final: 55 residues processed: 654 average time/residue: 0.1515 time to fit residues: 146.5136 Evaluate side-chains 680 residues out of total 2079 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 624 time to evaluate : 0.730 ------------------------------------------------------------------------------- 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 88 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 106 LYS 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 568 MET Chi-restraints excluded: chain V residue 595 ILE 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 153 GLU 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 368 ASP Chi-restraints excluded: chain X residue 466 GLU Chi-restraints excluded: chain X residue 467 ILE Chi-restraints excluded: chain X residue 485 LYS Chi-restraints excluded: chain Y residue 84 MET Chi-restraints excluded: chain Y residue 153 GLU Chi-restraints excluded: chain Y residue 207 LYS 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 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 322 ILE Chi-restraints excluded: chain Z residue 339 GLU Chi-restraints excluded: chain Z residue 413 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 84 optimal weight: 0.7980 chunk 170 optimal weight: 2.9990 chunk 185 optimal weight: 7.9990 chunk 14 optimal weight: 9.9990 chunk 203 optimal weight: 5.9990 chunk 196 optimal weight: 0.2980 chunk 114 optimal weight: 4.9990 chunk 190 optimal weight: 0.5980 chunk 0 optimal weight: 6.9990 chunk 192 optimal weight: 0.7980 chunk 18 optimal weight: 4.9990 overall best weight: 1.0982 ------------------------------------------------------------------------------- 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 ** E 5 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 554 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** W 630 GLN X 302 ASN Y 302 ASN Z 33 ASN Z 229 ASN Z 348 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3426 r_free = 0.3426 target = 0.112601 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3207 r_free = 0.3207 target = 0.098075 restraints weight = 32730.282| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3266 r_free = 0.3266 target = 0.101885 restraints weight = 14411.062| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3303 r_free = 0.3303 target = 0.104339 restraints weight = 8167.105| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.3328 r_free = 0.3328 target = 0.105982 restraints weight = 5445.141| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 37)----------------| | r_work = 0.3345 r_free = 0.3345 target = 0.107116 restraints weight = 3979.136| |-----------------------------------------------------------------------------| r_work (final): 0.3343 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7467 moved from start: 0.1770 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.068 20834 Z= 0.172 Angle : 0.658 9.469 28547 Z= 0.324 Chirality : 0.046 0.322 3546 Planarity : 0.004 0.039 3379 Dihedral : 9.209 75.457 5096 Min Nonbonded Distance : 2.401 Molprobity Statistics. All-atom Clashscore : 8.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.36 % Favored : 95.64 % Rotamer: Outliers : 3.80 % Allowed : 19.19 % Favored : 77.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.06 % Cis-general : 0.00 % Twisted Proline : 1.01 % Twisted General : 0.09 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.38 (0.18), residues: 2340 helix: 2.06 (0.28), residues: 366 sheet: 0.13 (0.20), residues: 747 loop : -1.24 (0.17), residues: 1227 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG W 579 TYR 0.027 0.002 TYR Y 173 PHE 0.030 0.002 PHE Y 53 TRP 0.032 0.001 TRP Y 112 HIS 0.006 0.001 HIS X 374 Details of bonding type rmsd covalent geometry : bond 0.00388 (20670) covalent geometry : angle 0.61205 (28093) SS BOND : bond 0.00607 ( 38) SS BOND : angle 2.29553 ( 76) hydrogen bonds : bond 0.04364 ( 671) hydrogen bonds : angle 4.70116 ( 1950) link_ALPHA1-2 : bond 0.00359 ( 10) link_ALPHA1-2 : angle 1.69513 ( 30) link_ALPHA1-3 : bond 0.00769 ( 12) link_ALPHA1-3 : angle 2.02589 ( 36) link_ALPHA1-6 : bond 0.00355 ( 9) link_ALPHA1-6 : angle 2.06576 ( 27) link_BETA1-4 : bond 0.00341 ( 43) link_BETA1-4 : angle 1.81743 ( 129) link_NAG-ASN : bond 0.00413 ( 52) link_NAG-ASN : angle 2.04162 ( 156) *********************** 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 710 residues out of total 2079 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 79 poor density : 631 time to evaluate : 0.712 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: 0.8331 (m100) cc_final: 0.7854 (m100) REVERT: A 55 LYS cc_start: 0.8328 (mmpt) cc_final: 0.7846 (mmpt) REVERT: C 73 LEU cc_start: 0.8423 (tp) cc_final: 0.8140 (tp) REVERT: D 22 LYS cc_start: 0.8393 (mtpp) cc_final: 0.7953 (mtpp) REVERT: D 50 GLN cc_start: 0.8140 (pt0) cc_final: 0.7788 (pt0) REVERT: E 28 ILE cc_start: 0.8801 (mm) cc_final: 0.8577 (mm) REVERT: H 110 LEU cc_start: 0.9037 (OUTLIER) cc_final: 0.8828 (tt) REVERT: L 32 TRP cc_start: 0.8551 (m100) cc_final: 0.7580 (m100) REVERT: U 522 PHE cc_start: 0.8825 (t80) cc_final: 0.8540 (t80) REVERT: U 577 GLN cc_start: 0.7716 (mt0) cc_final: 0.7257 (mt0) REVERT: U 647 GLU cc_start: 0.7382 (pt0) cc_final: 0.7117 (pt0) REVERT: V 542 ARG cc_start: 0.8246 (ttm110) cc_final: 0.7976 (ttm110) REVERT: V 579 ARG cc_start: 0.7722 (ptp-170) cc_final: 0.7156 (mtp180) REVERT: V 647 GLU cc_start: 0.6828 (mt-10) cc_final: 0.6487 (mt-10) REVERT: V 650 GLN cc_start: 0.8536 (tp40) cc_final: 0.8284 (tp-100) REVERT: W 647 GLU cc_start: 0.7259 (tt0) cc_final: 0.6731 (tt0) REVERT: X 45 TRP cc_start: 0.8596 (p90) cc_final: 0.8182 (p90) REVERT: X 68 VAL cc_start: 0.8469 (m) cc_final: 0.8186 (p) REVERT: X 83 GLU cc_start: 0.7081 (tm-30) cc_final: 0.6876 (tm-30) REVERT: X 84 MET cc_start: 0.7386 (tmm) cc_final: 0.6986 (tmm) REVERT: X 97 LYS cc_start: 0.8400 (ptpp) cc_final: 0.8143 (ptpp) REVERT: X 167 ASP cc_start: 0.7953 (t0) cc_final: 0.7703 (t0) REVERT: X 275 GLU cc_start: 0.7209 (tt0) cc_final: 0.6821 (tt0) REVERT: X 315 GLN cc_start: 0.8306 (mp10) cc_final: 0.7833 (mp10) REVERT: X 482 GLU cc_start: 0.7181 (mm-30) cc_final: 0.6731 (mm-30) REVERT: Y 46 LYS cc_start: 0.8393 (mptt) cc_final: 0.8073 (mmtm) REVERT: Y 97 LYS cc_start: 0.8688 (mtmt) cc_final: 0.8393 (mttt) REVERT: Y 190 GLU cc_start: 0.7231 (tt0) cc_final: 0.6912 (tt0) REVERT: Y 293 GLU cc_start: 0.7081 (tt0) cc_final: 0.6840 (tt0) REVERT: Y 335 ARG cc_start: 0.8603 (tpp80) cc_final: 0.8382 (ttm-80) REVERT: Y 381 GLU cc_start: 0.7080 (tp30) cc_final: 0.6706 (tp30) REVERT: Y 439 ILE cc_start: 0.8478 (mp) cc_final: 0.8120 (tp) REVERT: Z 39 TYR cc_start: 0.8535 (m-80) cc_final: 0.7602 (m-80) REVERT: Z 56 SER cc_start: 0.8297 (t) cc_final: 0.8048 (p) REVERT: Z 66 HIS cc_start: 0.7036 (t-90) cc_final: 0.6698 (t-90) REVERT: Z 97 LYS cc_start: 0.8588 (mtmm) cc_final: 0.8167 (mtmt) REVERT: Z 107 ASP cc_start: 0.7369 (m-30) cc_final: 0.6950 (t0) REVERT: Z 173 TYR cc_start: 0.8593 (p90) cc_final: 0.8310 (p90) REVERT: Z 175 LEU cc_start: 0.8615 (mt) cc_final: 0.8241 (mt) REVERT: Z 208 VAL cc_start: 0.8623 (m) cc_final: 0.8305 (m) REVERT: Z 231 LYS cc_start: 0.7756 (mmmt) cc_final: 0.7555 (mmmm) REVERT: Z 317 PHE cc_start: 0.8282 (t80) cc_final: 0.8038 (t80) REVERT: Z 330 HIS cc_start: 0.8321 (p-80) cc_final: 0.8081 (p-80) REVERT: Z 379 ARG cc_start: 0.8470 (mtp85) cc_final: 0.8222 (ttp80) REVERT: Z 388 SER cc_start: 0.8407 (t) cc_final: 0.8153 (t) REVERT: Z 474 ASP cc_start: 0.5924 (t0) cc_final: 0.5441 (t0) outliers start: 79 outliers final: 61 residues processed: 657 average time/residue: 0.1673 time to fit residues: 162.1373 Evaluate side-chains 691 residues out of total 2079 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 629 time to evaluate : 0.709 ------------------------------------------------------------------------------- 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 16 SER 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 106 LYS 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 595 ILE 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 208 VAL Chi-restraints excluded: chain X residue 269 GLU Chi-restraints excluded: chain X residue 330 HIS Chi-restraints excluded: chain X residue 420 ILE Chi-restraints excluded: chain X residue 466 GLU Chi-restraints excluded: chain X residue 467 ILE Chi-restraints excluded: chain X residue 485 LYS Chi-restraints excluded: chain Y residue 84 MET Chi-restraints excluded: chain Y residue 153 GLU Chi-restraints excluded: chain Y residue 207 LYS 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 424 ILE Chi-restraints excluded: chain Y residue 425 ASN Chi-restraints excluded: chain Y residue 432 ARG Chi-restraints excluded: chain Y residue 452 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 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 322 ILE Chi-restraints excluded: chain Z residue 339 GLU Chi-restraints excluded: chain Z residue 413 THR Chi-restraints excluded: chain Z residue 429 GLU 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 44 optimal weight: 0.9990 chunk 68 optimal weight: 0.5980 chunk 98 optimal weight: 1.9990 chunk 94 optimal weight: 0.8980 chunk 204 optimal weight: 0.2980 chunk 139 optimal weight: 2.9990 chunk 113 optimal weight: 0.9980 chunk 225 optimal weight: 1.9990 chunk 206 optimal weight: 0.5980 chunk 191 optimal weight: 2.9990 chunk 11 optimal weight: 0.9990 overall best weight: 0.6780 ------------------------------------------------------------------------------- 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 ** 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 302 ASN Z 33 ASN ** Z 203 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Z 348 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3441 r_free = 0.3441 target = 0.113542 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3222 r_free = 0.3222 target = 0.098935 restraints weight = 32938.683| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3281 r_free = 0.3281 target = 0.102774 restraints weight = 14476.346| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3319 r_free = 0.3319 target = 0.105294 restraints weight = 8191.345| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.3344 r_free = 0.3344 target = 0.106946 restraints weight = 5410.796| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.3361 r_free = 0.3361 target = 0.108066 restraints weight = 3955.308| |-----------------------------------------------------------------------------| r_work (final): 0.3355 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7449 moved from start: 0.1881 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 : 0.637 9.360 28547 Z= 0.314 Chirality : 0.045 0.327 3546 Planarity : 0.004 0.037 3379 Dihedral : 8.907 74.092 5096 Min Nonbonded Distance : 2.417 Molprobity Statistics. All-atom Clashscore : 8.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.19 % Favored : 95.81 % Rotamer: Outliers : 3.08 % Allowed : 21.07 % Favored : 75.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.06 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.37 (0.17), residues: 2340 helix: 2.02 (0.29), residues: 366 sheet: 0.12 (0.20), residues: 732 loop : -1.20 (0.17), residues: 1242 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG W 579 TYR 0.028 0.001 TYR U 638 PHE 0.033 0.002 PHE Y 53 TRP 0.032 0.001 TRP Y 112 HIS 0.005 0.001 HIS X 374 Details of bonding type rmsd covalent geometry : bond 0.00305 (20670) covalent geometry : angle 0.59370 (28093) SS BOND : bond 0.00592 ( 38) SS BOND : angle 2.28412 ( 76) hydrogen bonds : bond 0.04019 ( 671) hydrogen bonds : angle 4.65562 ( 1950) link_ALPHA1-2 : bond 0.00407 ( 10) link_ALPHA1-2 : angle 1.63634 ( 30) link_ALPHA1-3 : bond 0.00826 ( 12) link_ALPHA1-3 : angle 1.92048 ( 36) link_ALPHA1-6 : bond 0.00395 ( 9) link_ALPHA1-6 : angle 1.95826 ( 27) link_BETA1-4 : bond 0.00368 ( 43) link_BETA1-4 : angle 1.72007 ( 129) link_NAG-ASN : bond 0.00306 ( 52) link_NAG-ASN : angle 1.94188 ( 156) *********************** 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 686 residues out of total 2079 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 622 time to evaluate : 0.769 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: 0.8318 (m100) cc_final: 0.7841 (m100) REVERT: A 55 LYS cc_start: 0.8305 (mmpt) cc_final: 0.7807 (mmpt) REVERT: D 22 LYS cc_start: 0.8378 (mtpp) cc_final: 0.7929 (mtpp) REVERT: D 50 GLN cc_start: 0.8128 (pt0) cc_final: 0.7759 (pt0) REVERT: E 28 ILE cc_start: 0.8788 (mm) cc_final: 0.8544 (mm) REVERT: H 110 LEU cc_start: 0.9034 (OUTLIER) cc_final: 0.8816 (tt) REVERT: L 32 TRP cc_start: 0.8529 (m100) cc_final: 0.7526 (m100) REVERT: U 522 PHE cc_start: 0.8817 (t80) cc_final: 0.8520 (t80) REVERT: U 577 GLN cc_start: 0.7783 (mt0) cc_final: 0.7287 (mt0) REVERT: U 647 GLU cc_start: 0.7366 (pt0) cc_final: 0.7095 (pt0) REVERT: V 542 ARG cc_start: 0.8231 (ttm110) cc_final: 0.7964 (ttm110) REVERT: V 579 ARG cc_start: 0.7692 (ptp-170) cc_final: 0.7109 (mtp180) REVERT: V 647 GLU cc_start: 0.6818 (mt-10) cc_final: 0.6492 (mt-10) REVERT: V 650 GLN cc_start: 0.8520 (tp40) cc_final: 0.8260 (tp-100) REVERT: W 647 GLU cc_start: 0.7251 (tt0) cc_final: 0.6721 (tt0) REVERT: X 68 VAL cc_start: 0.8472 (m) cc_final: 0.8176 (p) REVERT: X 83 GLU cc_start: 0.7080 (tm-30) cc_final: 0.6876 (tm-30) REVERT: X 84 MET cc_start: 0.7368 (tmm) cc_final: 0.7015 (tmm) REVERT: X 97 LYS cc_start: 0.8402 (ptpp) cc_final: 0.8140 (ptpp) REVERT: X 167 ASP cc_start: 0.7976 (t0) cc_final: 0.7730 (t0) REVERT: X 275 GLU cc_start: 0.7191 (tt0) cc_final: 0.6810 (tt0) REVERT: X 315 GLN cc_start: 0.8297 (mp10) cc_final: 0.7843 (mp10) REVERT: X 482 GLU cc_start: 0.7203 (mm-30) cc_final: 0.6791 (mm-30) REVERT: Y 46 LYS cc_start: 0.8367 (mptt) cc_final: 0.8095 (mmtm) REVERT: Y 97 LYS cc_start: 0.8700 (mtmt) cc_final: 0.8361 (mttp) REVERT: Y 167 ASP cc_start: 0.8154 (p0) cc_final: 0.7691 (t0) REVERT: Y 190 GLU cc_start: 0.7214 (tt0) cc_final: 0.6884 (tt0) REVERT: Y 293 GLU cc_start: 0.7123 (tt0) cc_final: 0.6853 (tt0) REVERT: Y 335 ARG cc_start: 0.8584 (tpp80) cc_final: 0.8355 (ttm-80) REVERT: Y 381 GLU cc_start: 0.7044 (tp30) cc_final: 0.6676 (tp30) REVERT: Y 439 ILE cc_start: 0.8476 (mp) cc_final: 0.8104 (tp) REVERT: Z 39 TYR cc_start: 0.8534 (m-80) cc_final: 0.7605 (m-80) REVERT: Z 56 SER cc_start: 0.8291 (t) cc_final: 0.8051 (p) REVERT: Z 66 HIS cc_start: 0.7033 (t-90) cc_final: 0.6684 (t-90) REVERT: Z 97 LYS cc_start: 0.8585 (mtmm) cc_final: 0.8160 (mtmt) REVERT: Z 107 ASP cc_start: 0.7404 (m-30) cc_final: 0.6908 (t0) REVERT: Z 173 TYR cc_start: 0.8555 (p90) cc_final: 0.8302 (p90) REVERT: Z 175 LEU cc_start: 0.8611 (mt) cc_final: 0.8234 (mt) REVERT: Z 208 VAL cc_start: 0.8619 (m) cc_final: 0.8293 (m) REVERT: Z 317 PHE cc_start: 0.8307 (t80) cc_final: 0.8100 (t80) REVERT: Z 347 LYS cc_start: 0.8371 (tppt) cc_final: 0.8035 (ttpt) REVERT: Z 379 ARG cc_start: 0.8463 (mtp85) cc_final: 0.8229 (ttp80) REVERT: Z 388 SER cc_start: 0.8398 (t) cc_final: 0.8139 (t) REVERT: Z 420 ILE cc_start: 0.8697 (OUTLIER) cc_final: 0.8483 (mm) REVERT: Z 474 ASP cc_start: 0.5954 (t0) cc_final: 0.5457 (t0) outliers start: 64 outliers final: 51 residues processed: 643 average time/residue: 0.1713 time to fit residues: 161.9880 Evaluate side-chains 666 residues out of total 2079 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 613 time to evaluate : 0.768 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 8 THR 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 90 SER Chi-restraints excluded: chain H residue 93 THR Chi-restraints excluded: chain H residue 106 LYS 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 565 LEU Chi-restraints excluded: chain V residue 568 MET Chi-restraints excluded: chain V residue 595 ILE 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 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 466 GLU Chi-restraints excluded: chain X residue 467 ILE Chi-restraints excluded: chain X residue 485 LYS Chi-restraints excluded: chain X residue 490 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 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 432 ARG Chi-restraints excluded: chain Y residue 467 ILE Chi-restraints excluded: chain Z residue 116 LEU 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 339 GLU 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 231 random chunks: chunk 209 optimal weight: 3.9990 chunk 16 optimal weight: 0.7980 chunk 89 optimal weight: 0.0000 chunk 213 optimal weight: 3.9990 chunk 119 optimal weight: 5.9990 chunk 197 optimal weight: 0.4980 chunk 88 optimal weight: 2.9990 chunk 208 optimal weight: 0.6980 chunk 204 optimal weight: 0.4980 chunk 225 optimal weight: 0.6980 chunk 132 optimal weight: 0.8980 overall best weight: 0.4784 ------------------------------------------------------------------------------- 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** ** V 554 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** W 630 GLN X 302 ASN X 360 GLN Y 302 ASN Z 33 ASN Z 94 ASN Z 203 GLN Z 348 ASN Z 478 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3450 r_free = 0.3450 target = 0.114175 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3235 r_free = 0.3235 target = 0.099783 restraints weight = 32922.142| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3292 r_free = 0.3292 target = 0.103539 restraints weight = 14835.052| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3329 r_free = 0.3329 target = 0.106002 restraints weight = 8514.284| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.3353 r_free = 0.3353 target = 0.107626 restraints weight = 5648.771| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3368 r_free = 0.3368 target = 0.108652 restraints weight = 4158.557| |-----------------------------------------------------------------------------| r_work (final): 0.3370 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7458 moved from start: 0.1979 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.070 20834 Z= 0.120 Angle : 0.629 9.273 28547 Z= 0.310 Chirality : 0.045 0.330 3546 Planarity : 0.004 0.040 3379 Dihedral : 8.683 72.611 5096 Min Nonbonded Distance : 2.402 Molprobity Statistics. All-atom Clashscore : 8.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.40 % Favored : 95.60 % Rotamer: Outliers : 3.03 % Allowed : 21.65 % Favored : 75.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.06 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.34 (0.17), residues: 2340 helix: 2.04 (0.29), residues: 366 sheet: 0.15 (0.20), residues: 732 loop : -1.18 (0.17), residues: 1242 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG Z 304 TYR 0.027 0.001 TYR Y 173 PHE 0.034 0.001 PHE Y 53 TRP 0.033 0.001 TRP Y 112 HIS 0.010 0.001 HIS Y 66 Details of bonding type rmsd covalent geometry : bond 0.00274 (20670) covalent geometry : angle 0.58657 (28093) SS BOND : bond 0.00596 ( 38) SS BOND : angle 2.24066 ( 76) hydrogen bonds : bond 0.03790 ( 671) hydrogen bonds : angle 4.61208 ( 1950) link_ALPHA1-2 : bond 0.00420 ( 10) link_ALPHA1-2 : angle 1.61329 ( 30) link_ALPHA1-3 : bond 0.00845 ( 12) link_ALPHA1-3 : angle 1.87438 ( 36) link_ALPHA1-6 : bond 0.00441 ( 9) link_ALPHA1-6 : angle 1.88128 ( 27) link_BETA1-4 : bond 0.00358 ( 43) link_BETA1-4 : angle 1.67366 ( 129) link_NAG-ASN : bond 0.00330 ( 52) link_NAG-ASN : angle 1.91436 ( 156) *********************** 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 692 residues out of total 2079 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 629 time to evaluate : 0.787 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: 0.8311 (m100) cc_final: 0.7884 (m100) REVERT: A 55 LYS cc_start: 0.8268 (mmpt) cc_final: 0.8058 (mmtt) REVERT: C 73 LEU cc_start: 0.8411 (tp) cc_final: 0.8149 (tp) REVERT: D 22 LYS cc_start: 0.8385 (mtpp) cc_final: 0.7941 (mtpp) REVERT: E 28 ILE cc_start: 0.8741 (mm) cc_final: 0.8459 (mm) REVERT: H 110 LEU cc_start: 0.9065 (OUTLIER) cc_final: 0.8837 (tt) REVERT: L 32 TRP cc_start: 0.8523 (m100) cc_final: 0.7593 (m100) REVERT: U 522 PHE cc_start: 0.8832 (t80) cc_final: 0.8527 (t80) REVERT: U 577 GLN cc_start: 0.7834 (mt0) cc_final: 0.7380 (mt0) REVERT: U 647 GLU cc_start: 0.7285 (pt0) cc_final: 0.7004 (pt0) REVERT: V 542 ARG cc_start: 0.8211 (ttm110) cc_final: 0.7929 (ttm110) REVERT: V 579 ARG cc_start: 0.7719 (ptp-170) cc_final: 0.7249 (mtp180) REVERT: V 647 GLU cc_start: 0.6845 (mt-10) cc_final: 0.6514 (mt-10) REVERT: V 650 GLN cc_start: 0.8553 (tp40) cc_final: 0.8347 (tp-100) REVERT: W 647 GLU cc_start: 0.7219 (tt0) cc_final: 0.6681 (tt0) REVERT: X 68 VAL cc_start: 0.8488 (m) cc_final: 0.8188 (p) REVERT: X 84 MET cc_start: 0.7337 (tmm) cc_final: 0.7085 (tmm) REVERT: X 167 ASP cc_start: 0.7882 (t0) cc_final: 0.7655 (t0) REVERT: X 171 LYS cc_start: 0.8415 (ttmm) cc_final: 0.8031 (ttmm) REVERT: X 275 GLU cc_start: 0.7078 (tt0) cc_final: 0.6729 (tt0) REVERT: X 305 LYS cc_start: 0.8521 (ptpt) cc_final: 0.8289 (ptmt) REVERT: X 315 GLN cc_start: 0.8312 (mp10) cc_final: 0.7897 (mp10) REVERT: X 347 LYS cc_start: 0.8277 (ttpt) cc_final: 0.7798 (ttpt) REVERT: X 482 GLU cc_start: 0.7130 (mm-30) cc_final: 0.6746 (mm-30) REVERT: Y 46 LYS cc_start: 0.8360 (mptt) cc_final: 0.8126 (mmtm) REVERT: Y 66 HIS cc_start: 0.6177 (t-90) cc_final: 0.5881 (t-90) REVERT: Y 97 LYS cc_start: 0.8625 (mtmt) cc_final: 0.8258 (mtmm) REVERT: Y 167 ASP cc_start: 0.8084 (p0) cc_final: 0.7626 (t0) REVERT: Y 190 GLU cc_start: 0.7113 (tt0) cc_final: 0.6761 (tt0) REVERT: Y 293 GLU cc_start: 0.7058 (tt0) cc_final: 0.6807 (tt0) REVERT: Y 302 ASN cc_start: 0.7592 (m-40) cc_final: 0.7368 (m110) REVERT: Y 335 ARG cc_start: 0.8552 (tpp80) cc_final: 0.8312 (ttm-80) REVERT: Y 381 GLU cc_start: 0.7002 (tp30) cc_final: 0.6660 (tp30) REVERT: Y 439 ILE cc_start: 0.8478 (mp) cc_final: 0.8094 (tp) REVERT: Z 39 TYR cc_start: 0.8551 (m-80) cc_final: 0.7680 (m-80) REVERT: Z 66 HIS cc_start: 0.7034 (t-90) cc_final: 0.6793 (t-90) REVERT: Z 97 LYS cc_start: 0.8531 (mtmm) cc_final: 0.8152 (mtmt) REVERT: Z 107 ASP cc_start: 0.7448 (m-30) cc_final: 0.6956 (t0) REVERT: Z 173 TYR cc_start: 0.8546 (p90) cc_final: 0.8325 (p90) REVERT: Z 175 LEU cc_start: 0.8554 (mt) cc_final: 0.8219 (mt) REVERT: Z 208 VAL cc_start: 0.8645 (m) cc_final: 0.8391 (p) REVERT: Z 379 ARG cc_start: 0.8405 (mtp85) cc_final: 0.8184 (ttp80) REVERT: Z 388 SER cc_start: 0.8388 (t) cc_final: 0.8142 (t) REVERT: Z 474 ASP cc_start: 0.5900 (t0) cc_final: 0.5475 (t0) outliers start: 63 outliers final: 51 residues processed: 650 average time/residue: 0.1754 time to fit residues: 166.1464 Evaluate side-chains 666 residues out of total 2079 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 614 time to evaluate : 0.605 ------------------------------------------------------------------------------- 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 90 SER Chi-restraints excluded: chain H residue 93 THR Chi-restraints excluded: chain H residue 106 LYS 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 565 LEU Chi-restraints excluded: chain V residue 568 MET Chi-restraints excluded: chain V residue 595 ILE 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 208 VAL Chi-restraints excluded: chain X residue 217 TYR 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 467 ILE Chi-restraints excluded: chain X residue 485 LYS 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 330 HIS 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 432 ARG 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 322 ILE 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 475 MET Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 231 random chunks: chunk 51 optimal weight: 0.8980 chunk 132 optimal weight: 0.8980 chunk 55 optimal weight: 3.9990 chunk 170 optimal weight: 3.9990 chunk 213 optimal weight: 3.9990 chunk 15 optimal weight: 8.9990 chunk 84 optimal weight: 0.6980 chunk 14 optimal weight: 0.4980 chunk 70 optimal weight: 5.9990 chunk 62 optimal weight: 0.9980 chunk 117 optimal weight: 1.9990 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 50 GLN ** 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 348 ASN Z 360 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3445 r_free = 0.3445 target = 0.113891 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3230 r_free = 0.3230 target = 0.099480 restraints weight = 32704.720| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3287 r_free = 0.3287 target = 0.103241 restraints weight = 14693.007| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3323 r_free = 0.3323 target = 0.105658 restraints weight = 8425.430| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3346 r_free = 0.3346 target = 0.107197 restraints weight = 5651.133| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.3363 r_free = 0.3363 target = 0.108327 restraints weight = 4204.571| |-----------------------------------------------------------------------------| r_work (final): 0.3361 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7449 moved from start: 0.2026 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.079 20834 Z= 0.145 Angle : 0.657 11.100 28547 Z= 0.321 Chirality : 0.046 0.445 3546 Planarity : 0.004 0.038 3379 Dihedral : 8.587 70.617 5096 Min Nonbonded Distance : 2.418 Molprobity Statistics. All-atom Clashscore : 8.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.23 % Favored : 95.77 % Rotamer: Outliers : 3.03 % Allowed : 22.32 % Favored : 74.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.06 % Cis-general : 0.00 % Twisted Proline : 1.01 % Twisted General : 0.04 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.34 (0.18), residues: 2340 helix: 2.03 (0.29), residues: 363 sheet: 0.13 (0.20), residues: 732 loop : -1.16 (0.17), residues: 1245 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG Z 304 TYR 0.026 0.001 TYR Y 173 PHE 0.027 0.002 PHE Y 53 TRP 0.028 0.001 TRP Y 112 HIS 0.004 0.001 HIS X 374 Details of bonding type rmsd covalent geometry : bond 0.00333 (20670) covalent geometry : angle 0.61043 (28093) SS BOND : bond 0.00615 ( 38) SS BOND : angle 2.45180 ( 76) hydrogen bonds : bond 0.03979 ( 671) hydrogen bonds : angle 4.59784 ( 1950) link_ALPHA1-2 : bond 0.00366 ( 10) link_ALPHA1-2 : angle 1.64217 ( 30) link_ALPHA1-3 : bond 0.00788 ( 12) link_ALPHA1-3 : angle 1.90847 ( 36) link_ALPHA1-6 : bond 0.00423 ( 9) link_ALPHA1-6 : angle 1.94572 ( 27) link_BETA1-4 : bond 0.00336 ( 43) link_BETA1-4 : angle 1.75817 ( 129) link_NAG-ASN : bond 0.00302 ( 52) link_NAG-ASN : angle 2.10751 ( 156) *********************** 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 676 residues out of total 2079 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 613 time to evaluate : 0.621 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 36 TRP cc_start: 0.8312 (m100) cc_final: 0.7566 (m100) REVERT: A 55 LYS cc_start: 0.8292 (mmpt) cc_final: 0.7790 (mmpt) REVERT: C 73 LEU cc_start: 0.8390 (tp) cc_final: 0.8125 (tp) REVERT: D 22 LYS cc_start: 0.8382 (mtpp) cc_final: 0.7924 (mtpp) REVERT: D 50 GLN cc_start: 0.8027 (OUTLIER) cc_final: 0.7672 (pt0) REVERT: E 28 ILE cc_start: 0.8735 (mm) cc_final: 0.8431 (mm) REVERT: H 110 LEU cc_start: 0.9077 (OUTLIER) cc_final: 0.8856 (tt) REVERT: L 32 TRP cc_start: 0.8529 (m100) cc_final: 0.7582 (m100) REVERT: U 522 PHE cc_start: 0.8818 (t80) cc_final: 0.8599 (t80) REVERT: U 577 GLN cc_start: 0.7792 (mt0) cc_final: 0.7435 (mt0) REVERT: U 647 GLU cc_start: 0.7305 (pt0) cc_final: 0.7029 (pt0) REVERT: V 542 ARG cc_start: 0.8237 (ttm110) cc_final: 0.7968 (ttm110) REVERT: V 579 ARG cc_start: 0.7691 (ptp-170) cc_final: 0.7245 (mtp180) REVERT: V 647 GLU cc_start: 0.6834 (mt-10) cc_final: 0.6463 (mt-10) REVERT: V 650 GLN cc_start: 0.8493 (tp40) cc_final: 0.8293 (tp-100) REVERT: W 647 GLU cc_start: 0.7252 (tt0) cc_final: 0.6722 (tt0) REVERT: X 45 TRP cc_start: 0.8664 (p90) cc_final: 0.8100 (p90) REVERT: X 68 VAL cc_start: 0.8457 (m) cc_final: 0.8170 (p) REVERT: X 97 LYS cc_start: 0.8407 (ptpp) cc_final: 0.8135 (ptpp) REVERT: X 167 ASP cc_start: 0.7981 (t0) cc_final: 0.7741 (t0) REVERT: X 275 GLU cc_start: 0.7175 (tt0) cc_final: 0.6796 (tt0) REVERT: X 315 GLN cc_start: 0.8302 (mp10) cc_final: 0.7840 (mp10) REVERT: X 482 GLU cc_start: 0.7208 (mm-30) cc_final: 0.6788 (mm-30) REVERT: Y 46 LYS cc_start: 0.8342 (mptt) cc_final: 0.8131 (mmtm) REVERT: Y 66 HIS cc_start: 0.6417 (t-90) cc_final: 0.6200 (t-90) REVERT: Y 97 LYS cc_start: 0.8696 (mtmt) cc_final: 0.8282 (mtmm) REVERT: Y 167 ASP cc_start: 0.8104 (p0) cc_final: 0.7699 (t0) REVERT: Y 190 GLU cc_start: 0.7350 (tt0) cc_final: 0.7076 (tt0) REVERT: Y 293 GLU cc_start: 0.7154 (tt0) cc_final: 0.6885 (tt0) REVERT: Y 335 ARG cc_start: 0.8563 (tpp80) cc_final: 0.8305 (ttm-80) REVERT: Y 381 GLU cc_start: 0.7067 (tp30) cc_final: 0.6683 (tp30) REVERT: Y 439 ILE cc_start: 0.8470 (mp) cc_final: 0.8082 (tp) REVERT: Z 39 TYR cc_start: 0.8542 (m-80) cc_final: 0.7643 (m-80) REVERT: Z 66 HIS cc_start: 0.6942 (t-90) cc_final: 0.6705 (t-90) REVERT: Z 97 LYS cc_start: 0.8592 (mtmm) cc_final: 0.8179 (mtmt) REVERT: Z 107 ASP cc_start: 0.7414 (m-30) cc_final: 0.6932 (t0) REVERT: Z 173 TYR cc_start: 0.8599 (p90) cc_final: 0.8348 (p90) REVERT: Z 175 LEU cc_start: 0.8607 (mt) cc_final: 0.8238 (mt) REVERT: Z 208 VAL cc_start: 0.8616 (m) cc_final: 0.8374 (p) REVERT: Z 330 HIS cc_start: 0.8228 (p-80) cc_final: 0.7936 (p-80) REVERT: Z 379 ARG cc_start: 0.8467 (mtp85) cc_final: 0.8237 (ttp80) REVERT: Z 388 SER cc_start: 0.8454 (t) cc_final: 0.8196 (t) REVERT: Z 474 ASP cc_start: 0.5957 (t0) cc_final: 0.5492 (t0) outliers start: 63 outliers final: 55 residues processed: 635 average time/residue: 0.1726 time to fit residues: 160.8450 Evaluate side-chains 668 residues out of total 2079 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 611 time to evaluate : 0.750 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 8 THR Chi-restraints excluded: chain A residue 37 VAL Chi-restraints excluded: chain A residue 59 SER Chi-restraints excluded: chain A residue 93 THR Chi-restraints excluded: chain D residue 50 GLN 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 90 SER Chi-restraints excluded: chain H residue 93 THR Chi-restraints excluded: chain H residue 106 LYS 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 565 LEU Chi-restraints excluded: chain V residue 568 MET Chi-restraints excluded: chain V residue 595 ILE 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 111 LEU 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 485 LYS 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 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 Y residue 427 TRP Chi-restraints excluded: chain Y residue 432 ARG 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 269 GLU Chi-restraints excluded: chain Z residue 275 GLU Chi-restraints excluded: chain Z residue 295 VAL Chi-restraints excluded: chain Z residue 322 ILE 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 475 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 231 random chunks: chunk 130 optimal weight: 0.4980 chunk 160 optimal weight: 3.9990 chunk 226 optimal weight: 6.9990 chunk 23 optimal weight: 7.9990 chunk 199 optimal weight: 0.9990 chunk 149 optimal weight: 1.9990 chunk 12 optimal weight: 2.9990 chunk 128 optimal weight: 0.9990 chunk 24 optimal weight: 0.0770 chunk 222 optimal weight: 0.4980 chunk 112 optimal weight: 2.9990 overall best weight: 0.6142 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 50 GLN ** E 5 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 554 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** W 630 GLN X 302 ASN Y 302 ASN Z 33 ASN Z 229 ASN Z 348 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3454 r_free = 0.3454 target = 0.114438 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3239 r_free = 0.3239 target = 0.100041 restraints weight = 32974.114| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3296 r_free = 0.3296 target = 0.103803 restraints weight = 14748.561| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3333 r_free = 0.3333 target = 0.106231 restraints weight = 8425.045| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3357 r_free = 0.3357 target = 0.107846 restraints weight = 5637.756| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3373 r_free = 0.3373 target = 0.108953 restraints weight = 4135.366| |-----------------------------------------------------------------------------| r_work (final): 0.3371 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7438 moved from start: 0.2111 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.080 20834 Z= 0.134 Angle : 0.684 20.288 28547 Z= 0.330 Chirality : 0.046 0.495 3546 Planarity : 0.004 0.039 3379 Dihedral : 8.504 69.686 5096 Min Nonbonded Distance : 2.492 Molprobity Statistics. All-atom Clashscore : 8.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.40 % Favored : 95.60 % Rotamer: Outliers : 2.84 % Allowed : 22.61 % Favored : 74.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.06 % Cis-general : 0.00 % Twisted Proline : 1.01 % Twisted General : 0.09 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.34 (0.18), residues: 2340 helix: 2.04 (0.29), residues: 363 sheet: 0.13 (0.20), residues: 732 loop : -1.16 (0.17), residues: 1245 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG Y 469 TYR 0.027 0.001 TYR Y 173 PHE 0.037 0.001 PHE Y 53 TRP 0.025 0.001 TRP X 45 HIS 0.004 0.001 HIS X 374 Details of bonding type rmsd covalent geometry : bond 0.00308 (20670) covalent geometry : angle 0.62572 (28093) SS BOND : bond 0.00609 ( 38) SS BOND : angle 2.44358 ( 76) hydrogen bonds : bond 0.03975 ( 671) hydrogen bonds : angle 4.62768 ( 1950) link_ALPHA1-2 : bond 0.00395 ( 10) link_ALPHA1-2 : angle 1.61285 ( 30) link_ALPHA1-3 : bond 0.00846 ( 12) link_ALPHA1-3 : angle 1.87378 ( 36) link_ALPHA1-6 : bond 0.00454 ( 9) link_ALPHA1-6 : angle 1.90000 ( 27) link_BETA1-4 : bond 0.00413 ( 43) link_BETA1-4 : angle 1.74120 ( 129) link_NAG-ASN : bond 0.00295 ( 52) link_NAG-ASN : angle 2.80225 ( 156) ********************** 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 659 residues out of total 2079 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 600 time to evaluate : 0.759 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 36 TRP cc_start: 0.8310 (m100) cc_final: 0.7567 (m100) REVERT: A 55 LYS cc_start: 0.8284 (mmpt) cc_final: 0.7780 (mmpt) REVERT: C 73 LEU cc_start: 0.8392 (tp) cc_final: 0.8118 (tp) REVERT: D 22 LYS cc_start: 0.8374 (mtpp) cc_final: 0.7918 (mtpp) REVERT: D 50 GLN cc_start: 0.7845 (OUTLIER) cc_final: 0.7593 (pt0) REVERT: E 28 ILE cc_start: 0.8719 (mm) cc_final: 0.8421 (mm) REVERT: H 110 LEU cc_start: 0.9085 (OUTLIER) cc_final: 0.8870 (tt) REVERT: L 32 TRP cc_start: 0.8518 (m100) cc_final: 0.7569 (m100) REVERT: U 522 PHE cc_start: 0.8817 (t80) cc_final: 0.8597 (t80) REVERT: U 577 GLN cc_start: 0.7781 (mt0) cc_final: 0.7429 (mt0) REVERT: U 647 GLU cc_start: 0.7297 (pt0) cc_final: 0.7024 (pt0) REVERT: V 542 ARG cc_start: 0.8243 (ttm110) cc_final: 0.7951 (ttm110) REVERT: V 579 ARG cc_start: 0.7673 (ptp-170) cc_final: 0.7231 (mtp180) REVERT: W 647 GLU cc_start: 0.7241 (tt0) cc_final: 0.6706 (tt0) REVERT: X 68 VAL cc_start: 0.8460 (m) cc_final: 0.8159 (p) REVERT: X 97 LYS cc_start: 0.8403 (ptpp) cc_final: 0.8141 (ptpp) REVERT: X 116 LEU cc_start: 0.8221 (mt) cc_final: 0.8015 (tt) REVERT: X 167 ASP cc_start: 0.7989 (t0) cc_final: 0.7754 (t0) REVERT: X 275 GLU cc_start: 0.7161 (tt0) cc_final: 0.6783 (tt0) REVERT: X 315 GLN cc_start: 0.8305 (mp10) cc_final: 0.7842 (mp10) REVERT: X 482 GLU cc_start: 0.7189 (mm-30) cc_final: 0.6771 (mm-30) REVERT: Y 46 LYS cc_start: 0.8321 (mptt) cc_final: 0.8112 (mmtm) REVERT: Y 97 LYS cc_start: 0.8682 (mtmt) cc_final: 0.8271 (mtmm) REVERT: Y 167 ASP cc_start: 0.8063 (p0) cc_final: 0.7731 (t0) REVERT: Y 190 GLU cc_start: 0.7380 (tt0) cc_final: 0.7126 (tt0) REVERT: Y 293 GLU cc_start: 0.7142 (tt0) cc_final: 0.6880 (tt0) REVERT: Y 335 ARG cc_start: 0.8528 (tpp80) cc_final: 0.8261 (ttm-80) REVERT: Y 381 GLU cc_start: 0.7056 (tp30) cc_final: 0.6677 (tp30) REVERT: Y 439 ILE cc_start: 0.8452 (mp) cc_final: 0.8060 (tp) REVERT: Z 39 TYR cc_start: 0.8539 (m-80) cc_final: 0.7646 (m-80) REVERT: Z 66 HIS cc_start: 0.6937 (t-90) cc_final: 0.6725 (t-90) REVERT: Z 97 LYS cc_start: 0.8611 (mtmm) cc_final: 0.8178 (mtmt) REVERT: Z 107 ASP cc_start: 0.7444 (m-30) cc_final: 0.6925 (t0) REVERT: Z 173 TYR cc_start: 0.8575 (p90) cc_final: 0.8288 (p90) REVERT: Z 175 LEU cc_start: 0.8607 (mt) cc_final: 0.8227 (mt) REVERT: Z 208 VAL cc_start: 0.8619 (m) cc_final: 0.8380 (p) REVERT: Z 388 SER cc_start: 0.8469 (t) cc_final: 0.8211 (t) REVERT: Z 474 ASP cc_start: 0.5930 (t0) cc_final: 0.5485 (t0) REVERT: Z 486 TYR cc_start: 0.8598 (m-80) cc_final: 0.8379 (m-80) outliers start: 59 outliers final: 50 residues processed: 622 average time/residue: 0.1696 time to fit residues: 156.0787 Evaluate side-chains 645 residues out of total 2079 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 593 time to evaluate : 0.730 ------------------------------------------------------------------------------- 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 50 GLN 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 90 SER Chi-restraints excluded: chain H residue 93 THR Chi-restraints excluded: chain H residue 106 LYS 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 595 ILE 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 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 466 GLU Chi-restraints excluded: chain X residue 467 ILE Chi-restraints excluded: chain X residue 485 LYS 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 330 HIS 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 432 ARG Chi-restraints excluded: chain Z residue 116 LEU Chi-restraints excluded: chain Z residue 128 THR Chi-restraints excluded: chain Z residue 269 GLU Chi-restraints excluded: chain Z residue 272 VAL Chi-restraints excluded: chain Z residue 275 GLU Chi-restraints excluded: chain Z residue 295 VAL Chi-restraints excluded: chain Z residue 322 ILE 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 475 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 231 random chunks: chunk 174 optimal weight: 1.9990 chunk 84 optimal weight: 0.9980 chunk 41 optimal weight: 0.0070 chunk 27 optimal weight: 1.9990 chunk 33 optimal weight: 3.9990 chunk 102 optimal weight: 1.9990 chunk 38 optimal weight: 0.4980 chunk 201 optimal weight: 2.9990 chunk 6 optimal weight: 1.9990 chunk 202 optimal weight: 0.9990 chunk 42 optimal weight: 8.9990 overall best weight: 0.9002 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 50 GLN ** E 5 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 35 ASN ** V 554 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** W 630 GLN X 302 ASN X 360 GLN Y 66 HIS Y 302 ASN Z 33 ASN Z 348 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3442 r_free = 0.3442 target = 0.113571 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3223 r_free = 0.3223 target = 0.099035 restraints weight = 32849.570| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3282 r_free = 0.3282 target = 0.102832 restraints weight = 14529.374| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3319 r_free = 0.3319 target = 0.105274 restraints weight = 8264.798| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.3344 r_free = 0.3344 target = 0.106916 restraints weight = 5520.088| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.3360 r_free = 0.3360 target = 0.108039 restraints weight = 4035.697| |-----------------------------------------------------------------------------| r_work (final): 0.3359 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7449 moved from start: 0.2126 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.079 20834 Z= 0.157 Angle : 0.685 17.234 28547 Z= 0.332 Chirality : 0.046 0.491 3546 Planarity : 0.004 0.040 3379 Dihedral : 8.448 68.098 5096 Min Nonbonded Distance : 2.498 Molprobity Statistics. All-atom Clashscore : 8.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.36 % Favored : 95.64 % Rotamer: Outliers : 2.79 % Allowed : 22.75 % Favored : 74.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.06 % Cis-general : 0.00 % Twisted Proline : 1.01 % Twisted General : 0.09 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.39 (0.18), residues: 2340 helix: 1.97 (0.29), residues: 366 sheet: 0.01 (0.20), residues: 747 loop : -1.14 (0.17), residues: 1227 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG Y 469 TYR 0.027 0.002 TYR Y 173 PHE 0.028 0.002 PHE Y 53 TRP 0.029 0.001 TRP X 45 HIS 0.005 0.001 HIS X 374 Details of bonding type rmsd covalent geometry : bond 0.00358 (20670) covalent geometry : angle 0.63281 (28093) SS BOND : bond 0.00616 ( 38) SS BOND : angle 2.44225 ( 76) hydrogen bonds : bond 0.04161 ( 671) hydrogen bonds : angle 4.61102 ( 1950) link_ALPHA1-2 : bond 0.00345 ( 10) link_ALPHA1-2 : angle 1.64270 ( 30) link_ALPHA1-3 : bond 0.00767 ( 12) link_ALPHA1-3 : angle 1.91450 ( 36) link_ALPHA1-6 : bond 0.00439 ( 9) link_ALPHA1-6 : angle 1.96220 ( 27) link_BETA1-4 : bond 0.00384 ( 43) link_BETA1-4 : angle 1.79617 ( 129) link_NAG-ASN : bond 0.00343 ( 52) link_NAG-ASN : angle 2.47470 ( 156) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3790.86 seconds wall clock time: 66 minutes 31.43 seconds (3991.43 seconds total)