Starting phenix.real_space_refine on Thu Mar 5 07:24:06 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8gpj_34194/03_2026/8gpj_34194.cif Found real_map, /net/cci-nas-00/data/ceres_data/8gpj_34194/03_2026/8gpj_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 { model { file = "/net/cci-nas-00/data/ceres_data/8gpj_34194/03_2026/8gpj_34194.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8gpj_34194/03_2026/8gpj_34194.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8gpj_34194/03_2026/8gpj_34194.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8gpj_34194/03_2026/8gpj_34194.map" } 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-dev-5986/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: 4.72, per 1000 atoms: 0.23 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: 1.86 Conformation dependent library (CDL) restraints added in 889.6 milliseconds 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: 0.97 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: 3.38 Time building geometry restraints manager: 2.31 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: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.910 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.370 Check model and map are aligned: 0.060 Set scattering table: 0.050 Process input model: 18.500 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:1.490 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 22.980 ------------------------------------------------------------------------------- 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 are 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 : 0.565 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: 0.8783 (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: 0.6791 (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: 0.8328 (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: 0.1493 time to fit residues: 147.6255 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 : 0.696 ------------------------------------------------------------------------------- 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 are 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 : 0.632 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: 0.7606 (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: 0.6692 (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 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: 0.8139 (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: 0.8348 (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: 0.1503 time to fit residues: 150.4451 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 : 0.522 ------------------------------------------------------------------------------- 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 Y 425 ASN Z 33 ASN Z 135 ASN Z 203 GLN Z 348 ASN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3407 r_free = 0.3407 target = 0.111259 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3188 r_free = 0.3188 target = 0.096870 restraints weight = 32895.578| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3246 r_free = 0.3246 target = 0.100581 restraints weight = 14862.630| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3283 r_free = 0.3283 target = 0.103016 restraints weight = 8556.532| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 40)----------------| | r_work = 0.3308 r_free = 0.3308 target = 0.104621 restraints weight = 5740.808| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.3324 r_free = 0.3324 target = 0.105724 restraints weight = 4236.424| |-----------------------------------------------------------------------------| r_work (final): 0.3323 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7506 moved from start: 0.1365 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 : 0.710 9.724 28547 Z= 0.344 Chirality : 0.047 0.327 3546 Planarity : 0.004 0.052 3379 Dihedral : 11.104 84.085 5096 Min Nonbonded Distance : 2.367 Molprobity Statistics. All-atom Clashscore : 8.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.79 % Favored : 95.21 % Rotamer: Outliers : 3.17 % Allowed : 16.31 % Favored : 80.52 % 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 are 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 0.008 0.001 ARG W 579 TYR 0.026 0.002 TYR C 49 PHE 0.029 0.002 PHE Y 53 TRP 0.027 0.002 TRP U 614 HIS 0.007 0.001 HIS X 374 Details of bonding type rmsd covalent geometry : bond 0.00471 (20670) covalent geometry : angle 0.66130 (28093) SS BOND : bond 0.00583 ( 38) SS BOND : angle 2.00316 ( 76) hydrogen bonds : bond 0.04927 ( 671) hydrogen bonds : angle 4.92656 ( 1950) link_ALPHA1-2 : bond 0.00395 ( 10) link_ALPHA1-2 : angle 1.78630 ( 30) link_ALPHA1-3 : bond 0.00732 ( 12) link_ALPHA1-3 : angle 2.09736 ( 36) link_ALPHA1-6 : bond 0.00290 ( 9) link_ALPHA1-6 : angle 2.18473 ( 27) link_BETA1-4 : bond 0.00392 ( 43) link_BETA1-4 : angle 2.05351 ( 129) link_NAG-ASN : bond 0.00459 ( 52) link_NAG-ASN : angle 2.35778 ( 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 722 residues out of total 2079 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 656 time to evaluate : 0.660 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 55 LYS cc_start: 0.8283 (mmpt) cc_final: 0.7867 (mmpt) REVERT: C 73 LEU cc_start: 0.8451 (tp) cc_final: 0.8228 (tp) REVERT: D 11 LYS cc_start: 0.7949 (OUTLIER) cc_final: 0.7678 (mtmm) REVERT: D 22 LYS cc_start: 0.8390 (mtpp) cc_final: 0.8046 (mtpp) REVERT: E 4 THR cc_start: 0.8274 (m) cc_final: 0.7706 (p) REVERT: H 110 LEU cc_start: 0.9022 (tt) cc_final: 0.8781 (tt) REVERT: L 32 TRP cc_start: 0.8567 (m100) cc_final: 0.7836 (m100) REVERT: U 522 PHE cc_start: 0.8866 (t80) cc_final: 0.8620 (t80) REVERT: U 577 GLN cc_start: 0.7718 (mt0) cc_final: 0.7207 (mt0) REVERT: U 647 GLU cc_start: 0.7363 (pt0) cc_final: 0.7092 (pt0) REVERT: V 542 ARG cc_start: 0.8207 (ttm110) cc_final: 0.7946 (ttm110) REVERT: V 577 GLN cc_start: 0.7854 (tp-100) cc_final: 0.7588 (tp40) REVERT: V 579 ARG cc_start: 0.7769 (ptp-170) cc_final: 0.7260 (mtp180) REVERT: V 625 ASN cc_start: 0.8171 (t0) cc_final: 0.7821 (t0) REVERT: V 647 GLU cc_start: 0.6823 (mt-10) cc_final: 0.6511 (mt-10) REVERT: V 650 GLN cc_start: 0.8570 (tp40) cc_final: 0.8304 (tp40) REVERT: W 647 GLU cc_start: 0.7220 (tt0) cc_final: 0.6674 (tt0) REVERT: X 68 VAL cc_start: 0.8508 (m) cc_final: 0.8214 (p) REVERT: X 83 GLU cc_start: 0.7034 (tm-30) cc_final: 0.6765 (tm-30) REVERT: X 84 MET cc_start: 0.7335 (tmm) cc_final: 0.6874 (tmm) REVERT: X 97 LYS cc_start: 0.8310 (ptpp) cc_final: 0.7891 (ptpp) REVERT: X 99 GLU cc_start: 0.6951 (mp0) cc_final: 0.6707 (mp0) REVERT: X 104 MET cc_start: 0.8100 (ttt) cc_final: 0.7867 (ttt) REVERT: X 107 ASP cc_start: 0.7375 (m-30) cc_final: 0.6916 (t0) REVERT: X 121 LYS cc_start: 0.8405 (ttmm) cc_final: 0.8158 (ttmm) REVERT: X 275 GLU cc_start: 0.7185 (tt0) cc_final: 0.6845 (tt0) REVERT: X 293 GLU cc_start: 0.6935 (tt0) cc_final: 0.6720 (tm-30) REVERT: X 315 GLN cc_start: 0.8351 (mp10) cc_final: 0.7923 (mp10) REVERT: X 428 GLN cc_start: 0.7913 (mp10) cc_final: 0.7527 (mp10) REVERT: X 482 GLU cc_start: 0.7096 (mm-30) cc_final: 0.6698 (mm-30) REVERT: Y 46 LYS cc_start: 0.8491 (mptt) cc_final: 0.8150 (mmtm) REVERT: Y 97 LYS cc_start: 0.8627 (mtmt) cc_final: 0.8173 (mtmm) REVERT: Y 190 GLU cc_start: 0.7263 (tt0) cc_final: 0.6983 (tt0) REVERT: Y 335 ARG cc_start: 0.8586 (tpp80) cc_final: 0.8305 (ttm-80) REVERT: Y 347 LYS cc_start: 0.8690 (tppt) cc_final: 0.8322 (tppt) REVERT: Y 426 MET cc_start: 0.7765 (mtm) cc_final: 0.7030 (mtt) REVERT: Y 434 MET cc_start: 0.8101 (ttp) cc_final: 0.7728 (ttp) REVERT: Z 39 TYR cc_start: 0.8564 (m-80) cc_final: 0.7639 (m-80) REVERT: Z 66 HIS cc_start: 0.6933 (t-90) cc_final: 0.6595 (t-90) REVERT: Z 97 LYS cc_start: 0.8553 (mtmm) cc_final: 0.8166 (mtmt) REVERT: Z 107 ASP cc_start: 0.7441 (m-30) cc_final: 0.7018 (t0) REVERT: Z 173 TYR cc_start: 0.8569 (p90) cc_final: 0.8343 (p90) REVERT: Z 175 LEU cc_start: 0.8586 (mt) cc_final: 0.8264 (mt) REVERT: Z 199 SER cc_start: 0.8333 (m) cc_final: 0.7966 (t) REVERT: Z 208 VAL cc_start: 0.8706 (m) cc_final: 0.8278 (m) REVERT: Z 388 SER cc_start: 0.8423 (t) cc_final: 0.8170 (t) REVERT: Z 390 LEU cc_start: 0.8855 (mt) cc_final: 0.8613 (mt) REVERT: Z 474 ASP cc_start: 0.5910 (t0) cc_final: 0.5377 (t0) outliers start: 66 outliers final: 44 residues processed: 674 average time/residue: 0.1522 time to fit residues: 152.9013 Evaluate side-chains 695 residues out of total 2079 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 650 time to evaluate : 0.534 ------------------------------------------------------------------------------- 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 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 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: 0.6980 chunk 153 optimal weight: 3.9990 chunk 101 optimal weight: 1.9990 chunk 40 optimal weight: 0.0670 chunk 209 optimal weight: 2.9990 chunk 141 optimal weight: 0.6980 chunk 9 optimal weight: 0.7980 chunk 135 optimal weight: 2.9990 chunk 140 optimal weight: 1.9990 chunk 172 optimal weight: 0.9980 overall best weight: 0.6518 ------------------------------------------------------------------------------- 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** 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** Y 203 GLN Z 33 ASN Z 258 GLN Z 348 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3439 r_free = 0.3439 target = 0.113537 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3219 r_free = 0.3219 target = 0.098914 restraints weight = 32712.004| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 24)----------------| | r_work = 0.3278 r_free = 0.3278 target = 0.102734 restraints weight = 14388.091| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3316 r_free = 0.3316 target = 0.105271 restraints weight = 8147.273| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3341 r_free = 0.3341 target = 0.106934 restraints weight = 5375.099| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 41)----------------| | r_work = 0.3359 r_free = 0.3359 target = 0.108069 restraints weight = 3914.863| |-----------------------------------------------------------------------------| r_work (final): 0.3355 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7451 moved from start: 0.1550 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 20834 Z= 0.132 Angle : 0.641 9.300 28547 Z= 0.314 Chirality : 0.046 0.333 3546 Planarity : 0.004 0.043 3379 Dihedral : 9.943 81.038 5096 Min Nonbonded Distance : 2.413 Molprobity Statistics. All-atom Clashscore : 7.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.57 % Favored : 95.43 % Rotamer: Outliers : 3.70 % Allowed : 17.60 % Favored : 78.69 % 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 are not related in a simple way. whole: -0.36 (0.17), residues: 2340 helix: 1.99 (0.28), residues: 366 sheet: 0.17 (0.19), residues: 771 loop : -1.24 (0.17), residues: 1203 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG Z 304 TYR 0.028 0.001 TYR U 638 PHE 0.030 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 0.00297 (20670) covalent geometry : angle 0.60003 (28093) SS BOND : bond 0.00555 ( 38) SS BOND : angle 1.79805 ( 76) hydrogen bonds : bond 0.04159 ( 671) hydrogen bonds : angle 4.75800 ( 1950) link_ALPHA1-2 : bond 0.00455 ( 10) link_ALPHA1-2 : angle 1.64101 ( 30) link_ALPHA1-3 : bond 0.00814 ( 12) link_ALPHA1-3 : angle 1.93051 ( 36) link_ALPHA1-6 : bond 0.00326 ( 9) link_ALPHA1-6 : angle 1.97018 ( 27) link_BETA1-4 : bond 0.00364 ( 43) link_BETA1-4 : angle 1.76987 ( 129) link_NAG-ASN : bond 0.00274 ( 52) link_NAG-ASN : angle 2.02336 ( 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 723 residues out of total 2079 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 77 poor density : 646 time to evaluate : 0.573 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 55 LYS cc_start: 0.8300 (mmpt) cc_final: 0.7857 (mmpt) REVERT: C 73 LEU cc_start: 0.8433 (tp) cc_final: 0.8147 (tp) REVERT: D 22 LYS cc_start: 0.8344 (mtpp) cc_final: 0.8075 (mtpp) REVERT: E 28 ILE cc_start: 0.8797 (mm) cc_final: 0.8551 (mm) REVERT: H 110 LEU cc_start: 0.8992 (OUTLIER) cc_final: 0.8775 (tt) REVERT: L 32 TRP cc_start: 0.8558 (m100) cc_final: 0.7739 (m100) REVERT: U 522 PHE cc_start: 0.8817 (t80) cc_final: 0.8571 (t80) REVERT: U 577 GLN cc_start: 0.7680 (mt0) cc_final: 0.7140 (mt0) REVERT: U 647 GLU cc_start: 0.7364 (pt0) cc_final: 0.7037 (pt0) REVERT: V 542 ARG cc_start: 0.8185 (ttm110) cc_final: 0.7899 (ttm110) REVERT: V 579 ARG cc_start: 0.7679 (ptp-170) cc_final: 0.7100 (mtp180) REVERT: V 647 GLU cc_start: 0.6773 (mt-10) cc_final: 0.6466 (mt-10) REVERT: V 650 GLN cc_start: 0.8506 (tp40) cc_final: 0.8265 (tp-100) REVERT: W 647 GLU cc_start: 0.7239 (tt0) cc_final: 0.6689 (tt0) REVERT: X 46 LYS cc_start: 0.7971 (mmtm) cc_final: 0.7662 (mmtt) REVERT: X 68 VAL cc_start: 0.8469 (m) cc_final: 0.8183 (p) REVERT: X 83 GLU cc_start: 0.7059 (tm-30) cc_final: 0.6779 (tm-30) REVERT: X 84 MET cc_start: 0.7318 (tmm) cc_final: 0.6852 (tmm) REVERT: X 99 GLU cc_start: 0.6979 (mp0) cc_final: 0.6711 (mp0) REVERT: X 104 MET cc_start: 0.7994 (ttt) cc_final: 0.7793 (ttt) REVERT: X 275 GLU cc_start: 0.7225 (tt0) cc_final: 0.6825 (tt0) REVERT: X 315 GLN cc_start: 0.8285 (mp10) cc_final: 0.7878 (mp10) REVERT: X 347 LYS cc_start: 0.8322 (ttpt) cc_final: 0.7844 (ttpt) REVERT: X 421 LYS cc_start: 0.8077 (ttpt) cc_final: 0.7801 (ttpt) REVERT: X 482 GLU cc_start: 0.7137 (mm-30) cc_final: 0.6704 (mm-30) REVERT: Y 46 LYS cc_start: 0.8448 (mptt) cc_final: 0.8112 (mmtm) REVERT: Y 97 LYS cc_start: 0.8703 (mtmt) cc_final: 0.8307 (mttp) REVERT: Y 112 TRP cc_start: 0.8170 (m100) cc_final: 0.7967 (m100) REVERT: Y 190 GLU cc_start: 0.7227 (tt0) cc_final: 0.6910 (tt0) REVERT: Y 335 ARG cc_start: 0.8558 (tpp80) cc_final: 0.8337 (ttm-80) REVERT: Y 347 LYS cc_start: 0.8717 (tppt) cc_final: 0.8347 (tppt) REVERT: Y 381 GLU cc_start: 0.7077 (tp30) cc_final: 0.6706 (tp30) REVERT: Y 423 ILE cc_start: 0.8861 (mt) cc_final: 0.8655 (mt) REVERT: Y 426 MET cc_start: 0.7518 (mtm) cc_final: 0.7212 (mtt) REVERT: Y 434 MET cc_start: 0.8103 (ttp) cc_final: 0.7865 (ttp) REVERT: Y 439 ILE cc_start: 0.8488 (mp) cc_final: 0.8123 (tp) REVERT: Z 39 TYR cc_start: 0.8525 (m-80) cc_final: 0.7581 (m-80) REVERT: Z 66 HIS cc_start: 0.6947 (t-90) cc_final: 0.6725 (t-90) REVERT: Z 97 LYS cc_start: 0.8579 (mtmm) cc_final: 0.8318 (mttt) REVERT: Z 107 ASP cc_start: 0.7410 (m-30) cc_final: 0.6886 (t0) REVERT: Z 173 TYR cc_start: 0.8537 (p90) cc_final: 0.8249 (p90) REVERT: Z 175 LEU cc_start: 0.8588 (mt) cc_final: 0.8206 (mt) REVERT: Z 199 SER cc_start: 0.8294 (m) cc_final: 0.7792 (t) REVERT: Z 208 VAL cc_start: 0.8638 (m) cc_final: 0.8411 (p) REVERT: Z 388 SER cc_start: 0.8460 (t) cc_final: 0.8212 (t) REVERT: Z 390 LEU cc_start: 0.8813 (mt) cc_final: 0.8575 (mt) REVERT: Z 474 ASP cc_start: 0.5867 (t0) cc_final: 0.5383 (t0) outliers start: 77 outliers final: 44 residues processed: 670 average time/residue: 0.1515 time to fit residues: 149.7885 Evaluate side-chains 674 residues out of total 2079 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 629 time to evaluate : 0.660 ------------------------------------------------------------------------------- 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 90 SER Chi-restraints excluded: chain H residue 93 THR Chi-restraints excluded: chain H residue 110 LEU Chi-restraints excluded: chain L residue 104 VAL Chi-restraints excluded: chain 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 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 X residue 492 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 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: 1.9990 chunk 18 optimal weight: 4.9990 chunk 59 optimal weight: 7.9990 chunk 38 optimal weight: 9.9990 chunk 76 optimal weight: 0.9990 chunk 198 optimal weight: 5.9990 chunk 147 optimal weight: 0.9980 chunk 157 optimal weight: 5.9990 chunk 162 optimal weight: 2.9990 chunk 120 optimal weight: 1.9990 chunk 74 optimal weight: 3.9990 overall best weight: 1.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 39 GLN C 38 GLN ** D 112 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 5 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** U 624 ASN ** V 554 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** W 630 GLN X 302 ASN Y 66 HIS Y 425 ASN Z 33 ASN ** Z 203 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Z 348 ASN Z 360 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3419 r_free = 0.3419 target = 0.112159 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3198 r_free = 0.3198 target = 0.097755 restraints weight = 32699.732| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3258 r_free = 0.3258 target = 0.101546 restraints weight = 14352.682| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3295 r_free = 0.3295 target = 0.103963 restraints weight = 8135.299| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3321 r_free = 0.3321 target = 0.105600 restraints weight = 5436.590| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.3338 r_free = 0.3338 target = 0.106708 restraints weight = 3974.873| |-----------------------------------------------------------------------------| r_work (final): 0.3309 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7498 moved from start: 0.1670 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.076 20834 Z= 0.256 Angle : 0.726 10.700 28547 Z= 0.354 Chirality : 0.048 0.333 3546 Planarity : 0.004 0.044 3379 Dihedral : 9.709 76.899 5096 Min Nonbonded Distance : 2.347 Molprobity Statistics. All-atom Clashscore : 8.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.96 % Favored : 95.04 % Rotamer: Outliers : 3.90 % Allowed : 18.90 % Favored : 77.20 % 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 are not related in a simple way. whole: -0.44 (0.17), residues: 2340 helix: 1.97 (0.28), residues: 366 sheet: 0.21 (0.20), residues: 735 loop : -1.35 (0.17), residues: 1239 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG X 469 TYR 0.028 0.002 TYR C 49 PHE 0.035 0.002 PHE Y 53 TRP 0.024 0.002 TRP U 614 HIS 0.008 0.001 HIS X 374 Details of bonding type rmsd covalent geometry : bond 0.00566 (20670) covalent geometry : angle 0.67610 (28093) SS BOND : bond 0.00689 ( 38) SS BOND : angle 2.38835 ( 76) hydrogen bonds : bond 0.04985 ( 671) hydrogen bonds : angle 4.79429 ( 1950) link_ALPHA1-2 : bond 0.00310 ( 10) link_ALPHA1-2 : angle 1.86454 ( 30) link_ALPHA1-3 : bond 0.00722 ( 12) link_ALPHA1-3 : angle 2.27158 ( 36) link_ALPHA1-6 : bond 0.00366 ( 9) link_ALPHA1-6 : angle 2.23646 ( 27) link_BETA1-4 : bond 0.00424 ( 43) link_BETA1-4 : angle 2.06289 ( 129) link_NAG-ASN : bond 0.00563 ( 52) link_NAG-ASN : angle 2.26595 ( 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 726 residues out of total 2079 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 81 poor density : 645 time to evaluate : 0.686 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 55 LYS cc_start: 0.8336 (mmpt) cc_final: 0.7871 (mmpt) REVERT: C 73 LEU cc_start: 0.8448 (tp) cc_final: 0.8156 (tp) REVERT: D 22 LYS cc_start: 0.8418 (mtpp) cc_final: 0.7999 (mtpp) REVERT: D 50 GLN cc_start: 0.8169 (pt0) cc_final: 0.7830 (pt0) REVERT: H 110 LEU cc_start: 0.9038 (OUTLIER) cc_final: 0.8812 (tt) REVERT: L 32 TRP cc_start: 0.8576 (m100) cc_final: 0.7612 (m100) REVERT: U 522 PHE cc_start: 0.8854 (t80) cc_final: 0.8579 (t80) REVERT: U 577 GLN cc_start: 0.7766 (mt0) cc_final: 0.7279 (mt0) REVERT: U 647 GLU cc_start: 0.7427 (pt0) cc_final: 0.7090 (pt0) REVERT: V 542 ARG cc_start: 0.8267 (ttm110) cc_final: 0.8034 (ttm110) REVERT: V 543 GLN cc_start: 0.7821 (tp-100) cc_final: 0.7501 (tp-100) REVERT: V 577 GLN cc_start: 0.7839 (tp-100) cc_final: 0.7495 (tp40) REVERT: V 579 ARG cc_start: 0.7728 (ptp-170) cc_final: 0.7209 (mtp180) REVERT: V 625 ASN cc_start: 0.8205 (t0) cc_final: 0.7834 (t0) REVERT: V 647 GLU cc_start: 0.6845 (mt-10) cc_final: 0.6546 (mt-10) REVERT: W 579 ARG cc_start: 0.7862 (mtm180) cc_final: 0.7592 (mtm110) REVERT: W 647 GLU cc_start: 0.7255 (tt0) cc_final: 0.6748 (tt0) REVERT: X 45 TRP cc_start: 0.8674 (p90) cc_final: 0.8342 (p90) REVERT: X 68 VAL cc_start: 0.8495 (m) cc_final: 0.8212 (p) REVERT: X 84 MET cc_start: 0.7385 (tmm) cc_final: 0.6949 (tmm) REVERT: X 97 LYS cc_start: 0.8381 (ptpp) cc_final: 0.8114 (ptpp) REVERT: X 275 GLU cc_start: 0.7211 (tt0) cc_final: 0.6820 (tt0) REVERT: X 315 GLN cc_start: 0.8308 (mp10) cc_final: 0.7807 (mp10) REVERT: X 428 GLN cc_start: 0.7943 (mp10) cc_final: 0.7556 (mp10) REVERT: X 482 GLU cc_start: 0.7166 (mm-30) cc_final: 0.6715 (mm-30) REVERT: Y 46 LYS cc_start: 0.8429 (mptt) cc_final: 0.8184 (mmtm) REVERT: Y 97 LYS cc_start: 0.8700 (mtmt) cc_final: 0.8319 (mttp) REVERT: Y 190 GLU cc_start: 0.7326 (tt0) cc_final: 0.7015 (tt0) REVERT: Y 293 GLU cc_start: 0.7050 (tt0) cc_final: 0.6830 (tt0) REVERT: Y 335 ARG cc_start: 0.8638 (tpp80) cc_final: 0.8400 (ttm-80) REVERT: Y 381 GLU cc_start: 0.7082 (tp30) cc_final: 0.6696 (tp30) REVERT: Y 426 MET cc_start: 0.7759 (mtm) cc_final: 0.7083 (mtt) REVERT: Y 434 MET cc_start: 0.8184 (ttp) cc_final: 0.7666 (ttp) REVERT: Y 439 ILE cc_start: 0.8499 (mp) cc_final: 0.8110 (tp) REVERT: Z 56 SER cc_start: 0.8335 (t) cc_final: 0.8092 (p) REVERT: Z 66 HIS cc_start: 0.7023 (t-90) cc_final: 0.6634 (t-90) REVERT: Z 97 LYS cc_start: 0.8586 (mtmm) cc_final: 0.8225 (mtmt) REVERT: Z 107 ASP cc_start: 0.7437 (m-30) cc_final: 0.6881 (t0) REVERT: Z 173 TYR cc_start: 0.8583 (p90) cc_final: 0.8309 (p90) REVERT: Z 175 LEU cc_start: 0.8601 (mt) cc_final: 0.8225 (mt) REVERT: Z 208 VAL cc_start: 0.8667 (m) cc_final: 0.8390 (m) REVERT: Z 347 LYS cc_start: 0.8458 (tppt) cc_final: 0.8128 (ttpt) REVERT: Z 379 ARG cc_start: 0.8434 (mtp85) cc_final: 0.8196 (ttp80) REVERT: Z 388 SER cc_start: 0.8424 (t) cc_final: 0.8165 (t) REVERT: Z 474 ASP cc_start: 0.5932 (t0) cc_final: 0.5455 (t0) outliers start: 81 outliers final: 58 residues processed: 675 average time/residue: 0.1466 time to fit residues: 147.2933 Evaluate side-chains 702 residues out of total 2079 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 643 time to evaluate : 0.551 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 8 THR Chi-restraints excluded: chain A residue 59 SER Chi-restraints excluded: chain A residue 93 THR Chi-restraints excluded: chain A residue 98 CYS Chi-restraints excluded: chain C residue 100 GLN Chi-restraints excluded: chain D residue 93 THR Chi-restraints excluded: chain D residue 98 CYS Chi-restraints excluded: chain E residue 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 208 VAL Chi-restraints excluded: chain X residue 269 GLU Chi-restraints excluded: chain X residue 295 VAL Chi-restraints excluded: chain X residue 297 THR Chi-restraints excluded: chain X residue 330 HIS Chi-restraints excluded: chain X residue 466 GLU Chi-restraints excluded: chain X residue 467 ILE Chi-restraints excluded: chain Y residue 84 MET Chi-restraints excluded: chain Y residue 120 VAL Chi-restraints excluded: chain Y residue 153 GLU Chi-restraints excluded: chain Y residue 201 ILE 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 349 LEU Chi-restraints excluded: chain Y residue 413 THR Chi-restraints excluded: chain Y residue 467 ILE Chi-restraints excluded: chain Z residue 111 LEU Chi-restraints excluded: chain Z residue 128 THR Chi-restraints excluded: chain Z residue 154 MET Chi-restraints excluded: chain Z residue 229 ASN Chi-restraints excluded: chain Z residue 269 GLU Chi-restraints excluded: chain Z residue 275 GLU Chi-restraints excluded: chain Z residue 295 VAL Chi-restraints excluded: chain Z residue 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 450 THR Chi-restraints excluded: chain Z residue 475 MET Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 231 random chunks: chunk 84 optimal weight: 0.9990 chunk 170 optimal weight: 0.8980 chunk 185 optimal weight: 9.9990 chunk 14 optimal weight: 0.9980 chunk 203 optimal weight: 0.9980 chunk 196 optimal weight: 0.7980 chunk 114 optimal weight: 0.8980 chunk 190 optimal weight: 0.5980 chunk 0 optimal weight: 6.9990 chunk 192 optimal weight: 2.9990 chunk 18 optimal weight: 3.9990 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 39 GLN C 38 GLN ** D 112 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 5 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 554 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** W 630 GLN X 302 ASN Y 302 ASN Z 33 ASN ** Z 203 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 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 = 0.3432 r_free = 0.3432 target = 0.113041 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3214 r_free = 0.3214 target = 0.098631 restraints weight = 32724.670| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3273 r_free = 0.3273 target = 0.102388 restraints weight = 14682.582| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3310 r_free = 0.3310 target = 0.104854 restraints weight = 8410.753| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.3335 r_free = 0.3335 target = 0.106479 restraints weight = 5616.082| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3350 r_free = 0.3350 target = 0.107524 restraints weight = 4120.113| |-----------------------------------------------------------------------------| r_work (final): 0.3346 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7465 moved from start: 0.1794 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 20834 Z= 0.148 Angle : 0.655 9.511 28547 Z= 0.323 Chirality : 0.046 0.326 3546 Planarity : 0.004 0.040 3379 Dihedral : 9.271 76.651 5096 Min Nonbonded Distance : 2.395 Molprobity Statistics. All-atom Clashscore : 8.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.06 % Favored : 95.94 % Rotamer: Outliers : 3.46 % Allowed : 20.01 % Favored : 76.53 % 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 are not related in a simple way. whole: -0.45 (0.17), residues: 2340 helix: 1.93 (0.28), residues: 366 sheet: 0.07 (0.20), residues: 732 loop : -1.24 (0.17), residues: 1242 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG X 469 TYR 0.028 0.002 TYR U 638 PHE 0.031 0.002 PHE Y 53 TRP 0.025 0.001 TRP Y 112 HIS 0.005 0.001 HIS X 374 Details of bonding type rmsd covalent geometry : bond 0.00336 (20670) covalent geometry : angle 0.61147 (28093) SS BOND : bond 0.00605 ( 38) SS BOND : angle 2.21505 ( 76) hydrogen bonds : bond 0.04241 ( 671) hydrogen bonds : angle 4.71255 ( 1950) link_ALPHA1-2 : bond 0.00417 ( 10) link_ALPHA1-2 : angle 1.66159 ( 30) link_ALPHA1-3 : bond 0.00806 ( 12) link_ALPHA1-3 : angle 1.95104 ( 36) link_ALPHA1-6 : bond 0.00371 ( 9) link_ALPHA1-6 : angle 2.01499 ( 27) link_BETA1-4 : bond 0.00342 ( 43) link_BETA1-4 : angle 1.75873 ( 129) link_NAG-ASN : bond 0.00334 ( 52) link_NAG-ASN : angle 2.00670 ( 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 702 residues out of total 2079 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 72 poor density : 630 time to evaluate : 0.713 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 55 LYS cc_start: 0.8296 (mmpt) cc_final: 0.7848 (mmpt) REVERT: C 73 LEU cc_start: 0.8437 (tp) cc_final: 0.8159 (tp) REVERT: D 22 LYS cc_start: 0.8391 (mtpp) cc_final: 0.7960 (mtpp) REVERT: D 50 GLN cc_start: 0.8150 (pt0) cc_final: 0.7924 (pt0) REVERT: E 28 ILE cc_start: 0.8802 (mm) cc_final: 0.8579 (mm) REVERT: H 110 LEU cc_start: 0.9027 (OUTLIER) cc_final: 0.8812 (tt) REVERT: L 32 TRP cc_start: 0.8531 (m100) cc_final: 0.7607 (m100) REVERT: U 522 PHE cc_start: 0.8826 (t80) cc_final: 0.8539 (t80) REVERT: U 577 GLN cc_start: 0.7817 (mt0) cc_final: 0.7186 (mt0) REVERT: U 647 GLU cc_start: 0.7381 (pt0) cc_final: 0.7116 (pt0) REVERT: V 542 ARG cc_start: 0.8240 (ttm110) cc_final: 0.7967 (ttm110) REVERT: V 579 ARG cc_start: 0.7724 (ptp-170) cc_final: 0.7171 (mtp180) REVERT: V 647 GLU cc_start: 0.6829 (mt-10) cc_final: 0.6488 (mt-10) REVERT: V 650 GLN cc_start: 0.8494 (tp40) cc_final: 0.8240 (tp40) REVERT: W 647 GLU cc_start: 0.7253 (tt0) cc_final: 0.6728 (tt0) REVERT: X 45 TRP cc_start: 0.8602 (p90) cc_final: 0.8201 (p90) REVERT: X 68 VAL cc_start: 0.8475 (m) cc_final: 0.8181 (p) REVERT: X 84 MET cc_start: 0.7321 (tmm) cc_final: 0.7025 (tmm) REVERT: X 97 LYS cc_start: 0.8389 (ptpp) cc_final: 0.8125 (ptpp) REVERT: X 167 ASP cc_start: 0.7941 (t0) cc_final: 0.7682 (t0) REVERT: X 275 GLU cc_start: 0.7209 (tt0) cc_final: 0.6809 (tt0) REVERT: X 305 LYS cc_start: 0.8530 (OUTLIER) cc_final: 0.8308 (ptmt) REVERT: X 315 GLN cc_start: 0.8331 (mp10) cc_final: 0.7854 (mp10) REVERT: X 482 GLU cc_start: 0.7180 (mm-30) cc_final: 0.6743 (mm-30) REVERT: Y 46 LYS cc_start: 0.8409 (mptt) cc_final: 0.8091 (mmtm) REVERT: Y 97 LYS cc_start: 0.8672 (mtmt) cc_final: 0.8224 (mtmm) REVERT: Y 167 ASP cc_start: 0.8105 (p0) cc_final: 0.7765 (t0) REVERT: Y 190 GLU cc_start: 0.7211 (tt0) cc_final: 0.6893 (tt0) REVERT: Y 293 GLU cc_start: 0.7081 (tt0) cc_final: 0.6839 (tt0) REVERT: Y 302 ASN cc_start: 0.7683 (m-40) cc_final: 0.7462 (m110) REVERT: Y 335 ARG cc_start: 0.8593 (tpp80) cc_final: 0.8356 (ttm-80) REVERT: Y 381 GLU cc_start: 0.7079 (tp30) cc_final: 0.6680 (tp30) REVERT: Y 434 MET cc_start: 0.8096 (ttp) cc_final: 0.7820 (ttp) REVERT: Y 439 ILE cc_start: 0.8490 (mp) cc_final: 0.8120 (tp) REVERT: Z 39 TYR cc_start: 0.8542 (m-80) cc_final: 0.7608 (m-80) REVERT: Z 56 SER cc_start: 0.8286 (t) cc_final: 0.8036 (p) REVERT: Z 66 HIS cc_start: 0.7019 (t-90) cc_final: 0.6626 (t-90) REVERT: Z 97 LYS cc_start: 0.8580 (mtmm) cc_final: 0.8161 (mtmt) REVERT: Z 107 ASP cc_start: 0.7396 (m-30) cc_final: 0.6919 (t0) REVERT: Z 173 TYR cc_start: 0.8544 (p90) cc_final: 0.8276 (p90) REVERT: Z 175 LEU cc_start: 0.8629 (mt) cc_final: 0.8240 (mt) REVERT: Z 208 VAL cc_start: 0.8628 (m) cc_final: 0.8314 (m) REVERT: Z 231 LYS cc_start: 0.7740 (mmmt) cc_final: 0.7431 (mmmm) REVERT: Z 379 ARG cc_start: 0.8463 (mtp85) cc_final: 0.8208 (ttp80) REVERT: Z 388 SER cc_start: 0.8393 (t) cc_final: 0.8136 (t) REVERT: Z 390 LEU cc_start: 0.8872 (mt) cc_final: 0.8626 (mt) REVERT: Z 474 ASP cc_start: 0.5944 (t0) cc_final: 0.5451 (t0) outliers start: 72 outliers final: 55 residues processed: 655 average time/residue: 0.1529 time to fit residues: 147.6581 Evaluate side-chains 683 residues out of total 2079 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 626 time to evaluate : 0.682 ------------------------------------------------------------------------------- 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 37 VAL Chi-restraints excluded: chain D residue 93 THR Chi-restraints excluded: chain D residue 98 CYS Chi-restraints excluded: chain E residue 9 THR Chi-restraints excluded: chain H residue 16 SER Chi-restraints excluded: chain H residue 37 VAL Chi-restraints excluded: chain H residue 71 VAL Chi-restraints excluded: chain H residue 90 SER Chi-restraints excluded: chain H residue 93 THR Chi-restraints excluded: chain H residue 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 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 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 305 LYS Chi-restraints excluded: chain X residue 330 HIS 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 425 ASN Chi-restraints excluded: chain Y residue 452 LEU Chi-restraints excluded: chain Y residue 467 ILE Chi-restraints excluded: chain Z residue 111 LEU Chi-restraints excluded: chain Z residue 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 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: 2.9990 chunk 98 optimal weight: 1.9990 chunk 94 optimal weight: 0.9990 chunk 204 optimal weight: 0.9990 chunk 139 optimal weight: 0.7980 chunk 113 optimal weight: 0.6980 chunk 225 optimal weight: 2.9990 chunk 206 optimal weight: 2.9990 chunk 191 optimal weight: 2.9990 chunk 11 optimal weight: 0.7980 overall best weight: 0.8584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 39 GLN C 38 GLN ** D 112 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 5 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** U 624 ASN ** V 554 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** W 630 GLN X 302 ASN X 360 GLN Y 66 HIS 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 = 0.3431 r_free = 0.3431 target = 0.112919 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3213 r_free = 0.3213 target = 0.098519 restraints weight = 32985.413| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3271 r_free = 0.3271 target = 0.102262 restraints weight = 14863.754| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3308 r_free = 0.3308 target = 0.104672 restraints weight = 8543.048| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 22)----------------| | r_work = 0.3331 r_free = 0.3331 target = 0.106246 restraints weight = 5753.840| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3349 r_free = 0.3349 target = 0.107385 restraints weight = 4268.659| |-----------------------------------------------------------------------------| r_work (final): 0.3338 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7482 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 0.059 20834 Z= 0.150 Angle : 0.651 9.464 28547 Z= 0.320 Chirality : 0.046 0.320 3546 Planarity : 0.004 0.037 3379 Dihedral : 8.957 73.933 5096 Min Nonbonded Distance : 2.405 Molprobity Statistics. All-atom Clashscore : 8.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.44 % Favored : 95.56 % Rotamer: Outliers : 3.51 % Allowed : 21.02 % Favored : 75.47 % 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 are not related in a simple way. whole: -0.46 (0.17), residues: 2340 helix: 1.97 (0.28), residues: 366 sheet: -0.04 (0.20), residues: 747 loop : -1.20 (0.17), residues: 1227 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG X 469 TYR 0.030 0.002 TYR U 638 PHE 0.034 0.002 PHE Y 53 TRP 0.038 0.001 TRP Y 112 HIS 0.005 0.001 HIS X 374 Details of bonding type rmsd covalent geometry : bond 0.00341 (20670) covalent geometry : angle 0.60662 (28093) SS BOND : bond 0.00614 ( 38) SS BOND : angle 2.28350 ( 76) hydrogen bonds : bond 0.04185 ( 671) hydrogen bonds : angle 4.65500 ( 1950) link_ALPHA1-2 : bond 0.00363 ( 10) link_ALPHA1-2 : angle 1.67799 ( 30) link_ALPHA1-3 : bond 0.00773 ( 12) link_ALPHA1-3 : angle 1.97136 ( 36) link_ALPHA1-6 : bond 0.00381 ( 9) link_ALPHA1-6 : angle 2.00014 ( 27) link_BETA1-4 : bond 0.00338 ( 43) link_BETA1-4 : angle 1.77677 ( 129) link_NAG-ASN : bond 0.00327 ( 52) link_NAG-ASN : angle 1.98851 ( 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 705 residues out of total 2079 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 73 poor density : 632 time to evaluate : 0.653 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: 0.8347 (m100) cc_final: 0.7907 (m100) REVERT: A 55 LYS cc_start: 0.8279 (mmpt) cc_final: 0.8066 (mmtt) REVERT: D 22 LYS cc_start: 0.8409 (mtpp) cc_final: 0.7973 (mtpp) REVERT: D 50 GLN cc_start: 0.8157 (pt0) cc_final: 0.7954 (pt0) REVERT: E 28 ILE cc_start: 0.8779 (mm) cc_final: 0.8501 (mm) REVERT: H 110 LEU cc_start: 0.9036 (OUTLIER) cc_final: 0.8811 (tt) REVERT: L 32 TRP cc_start: 0.8552 (m100) cc_final: 0.7643 (m100) REVERT: U 522 PHE cc_start: 0.8841 (t80) cc_final: 0.8536 (t80) REVERT: U 577 GLN cc_start: 0.7807 (mt0) cc_final: 0.7478 (mt0) REVERT: U 647 GLU cc_start: 0.7350 (pt0) cc_final: 0.7089 (pt0) REVERT: V 542 ARG cc_start: 0.8241 (ttm110) cc_final: 0.7970 (ttm110) REVERT: V 579 ARG cc_start: 0.7759 (ptp-170) cc_final: 0.7207 (mtp180) REVERT: V 647 GLU cc_start: 0.6862 (mt-10) cc_final: 0.6527 (mt-10) REVERT: V 650 GLN cc_start: 0.8563 (tp40) cc_final: 0.8302 (tp40) REVERT: W 647 GLU cc_start: 0.7230 (tt0) cc_final: 0.6713 (tt0) REVERT: X 45 TRP cc_start: 0.8587 (p90) cc_final: 0.8204 (p90) REVERT: X 68 VAL cc_start: 0.8496 (m) cc_final: 0.8220 (p) REVERT: X 97 LYS cc_start: 0.8368 (ptpp) cc_final: 0.8102 (ptpp) REVERT: X 99 GLU cc_start: 0.6931 (mp0) cc_final: 0.6682 (mp0) REVERT: X 167 ASP cc_start: 0.7887 (t0) cc_final: 0.7659 (t0) REVERT: X 275 GLU cc_start: 0.7112 (tt0) cc_final: 0.6760 (tt0) REVERT: X 315 GLN cc_start: 0.8325 (mp10) cc_final: 0.7866 (mp10) REVERT: X 388 SER cc_start: 0.8311 (t) cc_final: 0.8064 (m) REVERT: X 482 GLU cc_start: 0.7097 (mm-30) cc_final: 0.6702 (mm-30) REVERT: Y 46 LYS cc_start: 0.8393 (mptt) cc_final: 0.8154 (mmtm) REVERT: Y 97 LYS cc_start: 0.8623 (mtmt) cc_final: 0.8342 (mttp) REVERT: Y 167 ASP cc_start: 0.7996 (p0) cc_final: 0.7706 (t0) REVERT: Y 190 GLU cc_start: 0.7136 (tt0) cc_final: 0.6841 (tt0) REVERT: Y 293 GLU cc_start: 0.7052 (tt0) cc_final: 0.6819 (tt0) REVERT: Y 335 ARG cc_start: 0.8584 (tpp80) cc_final: 0.8358 (ttm-80) REVERT: Y 381 GLU cc_start: 0.7001 (tp30) cc_final: 0.6688 (tp30) REVERT: Y 439 ILE cc_start: 0.8511 (mp) cc_final: 0.8107 (tp) REVERT: Z 39 TYR cc_start: 0.8555 (m-80) cc_final: 0.7677 (m-80) REVERT: Z 56 SER cc_start: 0.8270 (t) cc_final: 0.8063 (p) REVERT: Z 66 HIS cc_start: 0.7036 (t-90) cc_final: 0.6726 (t-90) REVERT: Z 97 LYS cc_start: 0.8547 (mtmm) cc_final: 0.8161 (mtmt) REVERT: Z 107 ASP cc_start: 0.7388 (m-30) cc_final: 0.6920 (t0) REVERT: Z 173 TYR cc_start: 0.8541 (p90) cc_final: 0.8316 (p90) REVERT: Z 175 LEU cc_start: 0.8607 (mt) cc_final: 0.8260 (mt) REVERT: Z 208 VAL cc_start: 0.8642 (m) cc_final: 0.8319 (m) REVERT: Z 347 LYS cc_start: 0.8386 (tppt) cc_final: 0.8096 (ttpt) REVERT: Z 379 ARG cc_start: 0.8413 (mtp85) cc_final: 0.8184 (ttp80) REVERT: Z 388 SER cc_start: 0.8328 (t) cc_final: 0.8083 (t) REVERT: Z 390 LEU cc_start: 0.8875 (mt) cc_final: 0.8638 (mt) REVERT: Z 474 ASP cc_start: 0.5915 (t0) cc_final: 0.5470 (t0) outliers start: 73 outliers final: 56 residues processed: 657 average time/residue: 0.1488 time to fit residues: 144.4369 Evaluate side-chains 684 residues out of total 2079 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 627 time to evaluate : 0.650 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 8 THR Chi-restraints excluded: chain A residue 59 SER Chi-restraints excluded: chain A residue 93 THR Chi-restraints excluded: chain D residue 93 THR Chi-restraints excluded: chain D residue 98 CYS Chi-restraints excluded: chain E residue 9 THR Chi-restraints excluded: chain H residue 16 SER Chi-restraints excluded: chain H residue 37 VAL Chi-restraints excluded: chain H residue 71 VAL Chi-restraints excluded: chain H residue 90 SER Chi-restraints excluded: chain H residue 93 THR Chi-restraints excluded: chain H residue 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 208 VAL Chi-restraints excluded: chain X residue 217 TYR Chi-restraints excluded: chain X residue 269 GLU Chi-restraints excluded: chain X residue 295 VAL Chi-restraints excluded: chain X residue 297 THR Chi-restraints excluded: chain X residue 330 HIS Chi-restraints excluded: chain X residue 360 GLN 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 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 452 LEU Chi-restraints excluded: chain Y residue 467 ILE 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 443 ILE 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: 0.9980 chunk 89 optimal weight: 0.8980 chunk 213 optimal weight: 3.9990 chunk 119 optimal weight: 3.9990 chunk 197 optimal weight: 0.9980 chunk 88 optimal weight: 2.9990 chunk 208 optimal weight: 0.6980 chunk 204 optimal weight: 0.0970 chunk 225 optimal weight: 0.0060 chunk 132 optimal weight: 1.9990 overall best weight: 0.5394 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 112 HIS ** E 5 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 554 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** W 630 GLN X 302 ASN 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 = 0.114227 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3236 r_free = 0.3236 target = 0.099914 restraints weight = 32838.494| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 24)----------------| | r_work = 0.3293 r_free = 0.3293 target = 0.103681 restraints weight = 14640.686| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3330 r_free = 0.3330 target = 0.106121 restraints weight = 8336.852| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.3355 r_free = 0.3355 target = 0.107753 restraints weight = 5543.301| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 36)----------------| | r_work = 0.3371 r_free = 0.3371 target = 0.108859 restraints weight = 4049.426| |-----------------------------------------------------------------------------| r_work (final): 0.3366 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7443 moved from start: 0.1984 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.059 20834 Z= 0.126 Angle : 0.644 12.490 28547 Z= 0.317 Chirality : 0.045 0.329 3546 Planarity : 0.004 0.039 3379 Dihedral : 8.722 72.853 5096 Min Nonbonded Distance : 2.420 Molprobity Statistics. All-atom Clashscore : 8.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.10 % Favored : 95.90 % Rotamer: Outliers : 3.03 % Allowed : 22.13 % Favored : 74.84 % 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 are not related in a simple way. whole: -0.39 (0.17), residues: 2340 helix: 2.02 (0.29), residues: 366 sheet: 0.08 (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 X 469 TYR 0.030 0.001 TYR U 638 PHE 0.034 0.002 PHE Y 53 TRP 0.034 0.001 TRP Y 112 HIS 0.005 0.001 HIS Y 374 Details of bonding type rmsd covalent geometry : bond 0.00289 (20670) covalent geometry : angle 0.60335 (28093) SS BOND : bond 0.00572 ( 38) SS BOND : angle 2.29813 ( 76) hydrogen bonds : bond 0.03867 ( 671) hydrogen bonds : angle 4.62971 ( 1950) link_ALPHA1-2 : bond 0.00419 ( 10) link_ALPHA1-2 : angle 1.62396 ( 30) link_ALPHA1-3 : bond 0.00857 ( 12) link_ALPHA1-3 : angle 1.88263 ( 36) link_ALPHA1-6 : bond 0.00431 ( 9) link_ALPHA1-6 : angle 1.89696 ( 27) link_BETA1-4 : bond 0.00363 ( 43) link_BETA1-4 : angle 1.68218 ( 129) link_NAG-ASN : bond 0.00286 ( 52) link_NAG-ASN : angle 1.89508 ( 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 693 residues out of total 2079 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 630 time to evaluate : 0.539 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: 0.8303 (m100) cc_final: 0.7857 (m100) REVERT: A 55 LYS cc_start: 0.8292 (mmpt) cc_final: 0.8089 (mmtt) REVERT: C 73 LEU cc_start: 0.8419 (tp) cc_final: 0.8147 (tp) REVERT: D 22 LYS cc_start: 0.8375 (mtpp) cc_final: 0.7930 (mtpp) REVERT: D 50 GLN cc_start: 0.8077 (pt0) cc_final: 0.7867 (pt0) REVERT: E 28 ILE cc_start: 0.8744 (mm) cc_final: 0.8444 (mm) REVERT: H 110 LEU cc_start: 0.9033 (OUTLIER) cc_final: 0.8819 (tt) REVERT: L 32 TRP cc_start: 0.8528 (m100) cc_final: 0.7585 (m100) REVERT: U 522 PHE cc_start: 0.8816 (t80) cc_final: 0.8598 (t80) REVERT: U 577 GLN cc_start: 0.7761 (mt0) cc_final: 0.7419 (mt0) REVERT: U 647 GLU cc_start: 0.7301 (pt0) cc_final: 0.7031 (pt0) REVERT: V 542 ARG cc_start: 0.8234 (ttm110) cc_final: 0.7955 (ttm110) REVERT: V 579 ARG cc_start: 0.7678 (ptp-170) cc_final: 0.7201 (mtp180) REVERT: V 647 GLU cc_start: 0.6839 (mt-10) cc_final: 0.6512 (mt-10) REVERT: V 650 GLN cc_start: 0.8492 (tp40) cc_final: 0.8228 (tp40) REVERT: W 647 GLU cc_start: 0.7249 (tt0) cc_final: 0.6724 (tt0) REVERT: X 68 VAL cc_start: 0.8472 (m) cc_final: 0.8180 (p) REVERT: X 99 GLU cc_start: 0.6981 (mp0) cc_final: 0.6715 (mp0) REVERT: X 167 ASP cc_start: 0.7979 (t0) cc_final: 0.7742 (t0) REVERT: X 171 LYS cc_start: 0.8432 (ttmm) cc_final: 0.8030 (ttmm) REVERT: X 275 GLU cc_start: 0.7175 (tt0) cc_final: 0.6802 (tt0) REVERT: X 305 LYS cc_start: 0.8520 (ptpt) cc_final: 0.8278 (ptmt) REVERT: X 315 GLN cc_start: 0.8325 (mp10) cc_final: 0.7864 (mp10) REVERT: X 482 GLU cc_start: 0.7154 (mm-30) cc_final: 0.6710 (mm-30) REVERT: Y 46 LYS cc_start: 0.8368 (mptt) cc_final: 0.8141 (mmtm) REVERT: Y 97 LYS cc_start: 0.8709 (mtmt) cc_final: 0.8278 (mtmm) REVERT: Y 190 GLU cc_start: 0.7192 (tt0) cc_final: 0.6871 (tt0) REVERT: Y 293 GLU cc_start: 0.7148 (tt0) cc_final: 0.6879 (tt0) REVERT: Y 302 ASN cc_start: 0.7671 (m-40) cc_final: 0.7441 (m110) REVERT: Y 335 ARG cc_start: 0.8554 (tpp80) cc_final: 0.8301 (ttm-80) REVERT: Y 381 GLU cc_start: 0.7065 (tp30) cc_final: 0.6664 (tp30) REVERT: Y 439 ILE cc_start: 0.8484 (mp) cc_final: 0.8104 (tp) REVERT: Z 39 TYR cc_start: 0.8534 (m-80) cc_final: 0.7614 (m-80) REVERT: Z 56 SER cc_start: 0.8281 (t) cc_final: 0.8063 (p) REVERT: Z 66 HIS cc_start: 0.7029 (t-90) cc_final: 0.6686 (t-90) REVERT: Z 97 LYS cc_start: 0.8572 (mtmm) cc_final: 0.8168 (mtmt) REVERT: Z 103 GLN cc_start: 0.7871 (tt0) cc_final: 0.7581 (tt0) REVERT: Z 107 ASP cc_start: 0.7412 (m-30) cc_final: 0.6920 (t0) REVERT: Z 173 TYR cc_start: 0.8549 (p90) cc_final: 0.8310 (p90) REVERT: Z 175 LEU cc_start: 0.8611 (mt) cc_final: 0.8227 (mt) REVERT: Z 208 VAL cc_start: 0.8618 (m) cc_final: 0.8282 (m) REVERT: Z 231 LYS cc_start: 0.7755 (mmmt) cc_final: 0.7437 (mmmm) REVERT: Z 379 ARG cc_start: 0.8462 (mtp85) cc_final: 0.8248 (ttp80) REVERT: Z 388 SER cc_start: 0.8408 (t) cc_final: 0.8148 (t) REVERT: Z 474 ASP cc_start: 0.5951 (t0) cc_final: 0.5457 (t0) outliers start: 63 outliers final: 52 residues processed: 651 average time/residue: 0.1563 time to fit residues: 149.5496 Evaluate side-chains 662 residues out of total 2079 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 609 time to evaluate : 0.480 ------------------------------------------------------------------------------- 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 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 568 MET Chi-restraints excluded: chain V residue 604 CYS Chi-restraints excluded: chain W residue 573 ILE Chi-restraints excluded: chain W residue 577 GLN Chi-restraints excluded: chain X residue 52 LEU Chi-restraints excluded: chain X residue 56 SER Chi-restraints excluded: chain X residue 111 LEU Chi-restraints excluded: chain X residue 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 429 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 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 Y residue 475 MET Chi-restraints excluded: chain Z residue 111 LEU Chi-restraints excluded: chain Z residue 128 THR Chi-restraints excluded: chain Z residue 203 GLN 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 293 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 475 MET Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 231 random chunks: chunk 51 optimal weight: 0.9980 chunk 132 optimal weight: 1.9990 chunk 55 optimal weight: 1.9990 chunk 170 optimal weight: 0.8980 chunk 213 optimal weight: 3.9990 chunk 15 optimal weight: 8.9990 chunk 84 optimal weight: 2.9990 chunk 14 optimal weight: 8.9990 chunk 70 optimal weight: 5.9990 chunk 62 optimal weight: 0.9990 chunk 117 optimal weight: 2.9990 overall best weight: 1.3786 ------------------------------------------------------------------------------- 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 258 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** X 302 ASN Z 33 ASN Z 348 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3422 r_free = 0.3422 target = 0.112322 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3206 r_free = 0.3206 target = 0.098034 restraints weight = 32732.724| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3263 r_free = 0.3263 target = 0.101751 restraints weight = 14691.773| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3300 r_free = 0.3300 target = 0.104172 restraints weight = 8418.886| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3324 r_free = 0.3324 target = 0.105771 restraints weight = 5621.893| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3340 r_free = 0.3340 target = 0.106839 restraints weight = 4136.786| |-----------------------------------------------------------------------------| r_work (final): 0.3335 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7475 moved from start: 0.2007 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.077 20834 Z= 0.204 Angle : 0.702 11.338 28547 Z= 0.344 Chirality : 0.047 0.329 3546 Planarity : 0.004 0.049 3379 Dihedral : 8.760 70.189 5096 Min Nonbonded Distance : 2.283 Molprobity Statistics. All-atom Clashscore : 8.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.57 % Favored : 95.43 % Rotamer: Outliers : 3.32 % Allowed : 22.37 % Favored : 74.31 % 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 are not related in a simple way. whole: -0.41 (0.18), residues: 2340 helix: 1.95 (0.29), residues: 366 sheet: 0.00 (0.19), residues: 765 loop : -1.18 (0.17), residues: 1209 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG X 469 TYR 0.026 0.002 TYR Y 173 PHE 0.028 0.002 PHE Y 53 TRP 0.036 0.002 TRP Z 112 HIS 0.006 0.001 HIS X 374 Details of bonding type rmsd covalent geometry : bond 0.00459 (20670) covalent geometry : angle 0.65442 (28093) SS BOND : bond 0.00644 ( 38) SS BOND : angle 2.65242 ( 76) hydrogen bonds : bond 0.04485 ( 671) hydrogen bonds : angle 4.66535 ( 1950) link_ALPHA1-2 : bond 0.00299 ( 10) link_ALPHA1-2 : angle 1.74651 ( 30) link_ALPHA1-3 : bond 0.00741 ( 12) link_ALPHA1-3 : angle 2.06405 ( 36) link_ALPHA1-6 : bond 0.00408 ( 9) link_ALPHA1-6 : angle 2.09748 ( 27) link_BETA1-4 : bond 0.00360 ( 43) link_BETA1-4 : angle 1.89543 ( 129) link_NAG-ASN : bond 0.00438 ( 52) link_NAG-ASN : angle 2.10134 ( 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 706 residues out of total 2079 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 637 time to evaluate : 0.728 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: 0.8306 (mmpt) cc_final: 0.8096 (mmtt) REVERT: C 73 LEU cc_start: 0.8441 (tp) cc_final: 0.8180 (tp) REVERT: D 22 LYS cc_start: 0.8408 (mtpp) cc_final: 0.7965 (mtpp) REVERT: D 50 GLN cc_start: 0.8185 (pt0) cc_final: 0.7950 (pt0) REVERT: E 28 ILE cc_start: 0.8757 (mm) cc_final: 0.8455 (mm) REVERT: H 110 LEU cc_start: 0.9055 (OUTLIER) cc_final: 0.8838 (tt) REVERT: L 32 TRP cc_start: 0.8567 (m100) cc_final: 0.7577 (m100) REVERT: U 522 PHE cc_start: 0.8856 (t80) cc_final: 0.8536 (t80) REVERT: U 577 GLN cc_start: 0.7802 (mt0) cc_final: 0.7421 (mt0) REVERT: U 647 GLU cc_start: 0.7319 (pt0) cc_final: 0.7063 (pt0) REVERT: V 542 ARG cc_start: 0.8276 (ttm110) cc_final: 0.8028 (ttm110) REVERT: V 543 GLN cc_start: 0.7826 (tp-100) cc_final: 0.7596 (tp-100) REVERT: V 579 ARG cc_start: 0.7690 (ptp-170) cc_final: 0.7160 (mtp180) REVERT: V 647 GLU cc_start: 0.6870 (mt-10) cc_final: 0.6506 (mt-10) REVERT: V 650 GLN cc_start: 0.8496 (tp40) cc_final: 0.8243 (tp40) REVERT: W 647 GLU cc_start: 0.7262 (tt0) cc_final: 0.6762 (tt0) REVERT: X 45 TRP cc_start: 0.8688 (p90) cc_final: 0.8154 (p90) REVERT: X 68 VAL cc_start: 0.8482 (m) cc_final: 0.8192 (p) REVERT: X 97 LYS cc_start: 0.8395 (ptpp) cc_final: 0.8022 (mtmm) REVERT: X 167 ASP cc_start: 0.7984 (t0) cc_final: 0.7758 (t0) REVERT: X 275 GLU cc_start: 0.7198 (tt0) cc_final: 0.6828 (tt0) REVERT: X 279 ASN cc_start: 0.8020 (t0) cc_final: 0.7786 (t0) REVERT: X 305 LYS cc_start: 0.8527 (OUTLIER) cc_final: 0.8295 (ptmt) REVERT: X 315 GLN cc_start: 0.8320 (mp10) cc_final: 0.7805 (mp10) REVERT: X 482 GLU cc_start: 0.7178 (mm-30) cc_final: 0.6727 (mm-30) REVERT: Y 46 LYS cc_start: 0.8354 (mptt) cc_final: 0.8143 (mmtm) REVERT: Y 97 LYS cc_start: 0.8703 (mtmt) cc_final: 0.8279 (mtmm) REVERT: Y 190 GLU cc_start: 0.7237 (tt0) cc_final: 0.6915 (tt0) REVERT: Y 293 GLU cc_start: 0.7153 (tt0) cc_final: 0.6885 (tt0) REVERT: Y 335 ARG cc_start: 0.8561 (tpp80) cc_final: 0.8293 (ttm-80) REVERT: Y 381 GLU cc_start: 0.7095 (tp30) cc_final: 0.6610 (tp30) REVERT: Z 39 TYR cc_start: 0.8537 (m-80) cc_final: 0.7636 (m-80) REVERT: Z 56 SER cc_start: 0.8297 (t) cc_final: 0.8078 (p) REVERT: Z 66 HIS cc_start: 0.7012 (t-90) cc_final: 0.6664 (t-90) REVERT: Z 97 LYS cc_start: 0.8606 (mtmm) cc_final: 0.8219 (mtpt) REVERT: Z 107 ASP cc_start: 0.7438 (m-30) cc_final: 0.6965 (t0) REVERT: Z 173 TYR cc_start: 0.8592 (p90) cc_final: 0.8355 (p90) REVERT: Z 175 LEU cc_start: 0.8607 (mt) cc_final: 0.8208 (mt) REVERT: Z 208 VAL cc_start: 0.8617 (m) cc_final: 0.8361 (m) REVERT: Z 231 LYS cc_start: 0.7790 (mmmt) cc_final: 0.7492 (mmmm) REVERT: Z 379 ARG cc_start: 0.8484 (mtp85) cc_final: 0.8256 (ttp80) REVERT: Z 474 ASP cc_start: 0.5984 (t0) cc_final: 0.5525 (t0) outliers start: 69 outliers final: 60 residues processed: 661 average time/residue: 0.1536 time to fit residues: 150.1643 Evaluate side-chains 694 residues out of total 2079 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 632 time to evaluate : 0.585 ------------------------------------------------------------------------------- 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 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 588 LYS Chi-restraints excluded: chain U residue 633 GLU Chi-restraints excluded: chain V residue 568 MET Chi-restraints excluded: chain V residue 604 CYS Chi-restraints excluded: chain W residue 573 ILE Chi-restraints excluded: chain W residue 577 GLN Chi-restraints excluded: chain X residue 52 LEU Chi-restraints excluded: chain X residue 56 SER Chi-restraints excluded: chain X residue 111 LEU Chi-restraints excluded: chain X residue 208 VAL Chi-restraints excluded: chain X residue 269 GLU Chi-restraints excluded: chain X residue 297 THR Chi-restraints excluded: chain X residue 305 LYS Chi-restraints excluded: chain X residue 330 HIS Chi-restraints excluded: chain X residue 359 ILE Chi-restraints excluded: chain X residue 420 ILE Chi-restraints excluded: chain X residue 429 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 120 VAL 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 452 LEU Chi-restraints excluded: chain Y residue 467 ILE Chi-restraints excluded: chain Y residue 475 MET Chi-restraints excluded: chain Z residue 111 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 272 VAL Chi-restraints excluded: chain Z residue 275 GLU Chi-restraints excluded: chain Z residue 293 GLU Chi-restraints excluded: chain Z residue 295 VAL Chi-restraints excluded: chain Z residue 322 ILE Chi-restraints excluded: chain Z residue 339 GLU Chi-restraints excluded: chain Z residue 360 GLN Chi-restraints excluded: chain Z residue 443 ILE 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: 2.9990 chunk 23 optimal weight: 7.9990 chunk 199 optimal weight: 0.8980 chunk 149 optimal weight: 0.8980 chunk 12 optimal weight: 5.9990 chunk 128 optimal weight: 0.6980 chunk 24 optimal weight: 0.0980 chunk 222 optimal weight: 3.9990 chunk 112 optimal weight: 3.9990 overall best weight: 0.6180 ------------------------------------------------------------------------------- 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** V 619 GLN W 630 GLN ** X 258 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** X 302 ASN X 360 GLN X 425 ASN Y 302 ASN Z 33 ASN Z 203 GLN Z 348 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3451 r_free = 0.3451 target = 0.114168 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3234 r_free = 0.3234 target = 0.099777 restraints weight = 32981.987| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3292 r_free = 0.3292 target = 0.103545 restraints weight = 14679.197| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3329 r_free = 0.3329 target = 0.105994 restraints weight = 8368.843| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3353 r_free = 0.3353 target = 0.107598 restraints weight = 5570.123| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.3370 r_free = 0.3370 target = 0.108714 restraints weight = 4089.194| |-----------------------------------------------------------------------------| r_work (final): 0.3366 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7443 moved from start: 0.2128 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.069 20834 Z= 0.132 Angle : 0.661 10.914 28547 Z= 0.325 Chirality : 0.046 0.415 3546 Planarity : 0.004 0.042 3379 Dihedral : 8.534 70.330 5096 Min Nonbonded Distance : 2.324 Molprobity Statistics. All-atom Clashscore : 8.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.02 % Favored : 95.98 % Rotamer: Outliers : 2.69 % Allowed : 23.18 % Favored : 74.12 % 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 are not related in a simple way. whole: -0.39 (0.18), residues: 2340 helix: 2.01 (0.29), residues: 363 sheet: 0.02 (0.19), residues: 747 loop : -1.15 (0.17), residues: 1230 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG Y 469 TYR 0.027 0.001 TYR Y 173 PHE 0.036 0.002 PHE Y 53 TRP 0.044 0.002 TRP Z 112 HIS 0.005 0.001 HIS Y 374 Details of bonding type rmsd covalent geometry : bond 0.00304 (20670) covalent geometry : angle 0.61955 (28093) SS BOND : bond 0.00612 ( 38) SS BOND : angle 2.24752 ( 76) hydrogen bonds : bond 0.03941 ( 671) hydrogen bonds : angle 4.64968 ( 1950) link_ALPHA1-2 : bond 0.00402 ( 10) link_ALPHA1-2 : angle 1.61101 ( 30) link_ALPHA1-3 : bond 0.00789 ( 12) link_ALPHA1-3 : angle 1.84069 ( 36) link_ALPHA1-6 : bond 0.00460 ( 9) link_ALPHA1-6 : angle 1.90581 ( 27) link_BETA1-4 : bond 0.00359 ( 43) link_BETA1-4 : angle 1.70416 ( 129) link_NAG-ASN : bond 0.00338 ( 52) link_NAG-ASN : angle 2.00979 ( 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 669 residues out of total 2079 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 613 time to evaluate : 0.576 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 55 LYS cc_start: 0.8291 (mmpt) cc_final: 0.8078 (mmtt) REVERT: C 73 LEU cc_start: 0.8411 (tp) cc_final: 0.8135 (tp) REVERT: D 22 LYS cc_start: 0.8234 (mtpp) cc_final: 0.7761 (mtpp) REVERT: D 50 GLN cc_start: 0.8085 (pt0) cc_final: 0.7858 (pt0) REVERT: E 28 ILE cc_start: 0.8745 (mm) cc_final: 0.8426 (mm) REVERT: H 110 LEU cc_start: 0.9046 (OUTLIER) cc_final: 0.8829 (tt) REVERT: L 32 TRP cc_start: 0.8506 (m100) cc_final: 0.7540 (m100) REVERT: U 522 PHE cc_start: 0.8836 (t80) cc_final: 0.8556 (t80) REVERT: U 577 GLN cc_start: 0.7835 (mt0) cc_final: 0.7476 (mt0) REVERT: U 647 GLU cc_start: 0.7298 (pt0) cc_final: 0.7046 (pt0) REVERT: V 542 ARG cc_start: 0.8254 (ttm110) cc_final: 0.7957 (ttm110) REVERT: V 579 ARG cc_start: 0.7685 (ptp-170) cc_final: 0.7224 (mtp180) REVERT: V 650 GLN cc_start: 0.8501 (tp40) cc_final: 0.8242 (tp40) REVERT: W 647 GLU cc_start: 0.7246 (tt0) cc_final: 0.6713 (tt0) REVERT: X 68 VAL cc_start: 0.8492 (m) cc_final: 0.8199 (p) REVERT: X 97 LYS cc_start: 0.8405 (ptpp) cc_final: 0.8027 (mtmm) REVERT: X 167 ASP cc_start: 0.7971 (t0) cc_final: 0.7753 (t0) REVERT: X 255 VAL cc_start: 0.8853 (t) cc_final: 0.8619 (p) REVERT: X 275 GLU cc_start: 0.7182 (tt0) cc_final: 0.6789 (tt0) REVERT: X 315 GLN cc_start: 0.8342 (mp10) cc_final: 0.7877 (mp10) REVERT: X 482 GLU cc_start: 0.7183 (mm-30) cc_final: 0.6773 (mm-30) REVERT: Y 46 LYS cc_start: 0.8342 (mptt) cc_final: 0.8132 (mmtm) REVERT: Y 97 LYS cc_start: 0.8671 (mtmt) cc_final: 0.8356 (mttp) REVERT: Y 190 GLU cc_start: 0.7191 (tt0) cc_final: 0.6867 (tt0) REVERT: Y 293 GLU cc_start: 0.7139 (tt0) cc_final: 0.6875 (tt0) REVERT: Y 335 ARG cc_start: 0.8535 (tpp80) cc_final: 0.8263 (ttm-80) REVERT: Y 381 GLU cc_start: 0.7067 (tp30) cc_final: 0.6699 (tp30) REVERT: Y 439 ILE cc_start: 0.8438 (mp) cc_final: 0.8054 (tp) REVERT: Y 490 GLU cc_start: 0.7171 (mt-10) cc_final: 0.6927 (mt-10) REVERT: Z 39 TYR cc_start: 0.8534 (m-80) cc_final: 0.7630 (m-80) REVERT: Z 56 SER cc_start: 0.8310 (t) cc_final: 0.8079 (p) REVERT: Z 66 HIS cc_start: 0.6912 (t-90) cc_final: 0.6684 (t-90) REVERT: Z 97 LYS cc_start: 0.8609 (mtmm) cc_final: 0.8171 (mtmt) REVERT: Z 103 GLN cc_start: 0.7854 (tt0) cc_final: 0.7560 (tt0) REVERT: Z 107 ASP cc_start: 0.7446 (m-30) cc_final: 0.6941 (t0) REVERT: Z 173 TYR cc_start: 0.8552 (p90) cc_final: 0.8288 (p90) REVERT: Z 175 LEU cc_start: 0.8617 (mt) cc_final: 0.8219 (mt) REVERT: Z 208 VAL cc_start: 0.8622 (m) cc_final: 0.8413 (p) REVERT: Z 282 LYS cc_start: 0.8360 (mmtm) cc_final: 0.7925 (mmtp) REVERT: Z 388 SER cc_start: 0.8402 (t) cc_final: 0.8160 (t) REVERT: Z 474 ASP cc_start: 0.6004 (t0) cc_final: 0.5506 (t0) outliers start: 56 outliers final: 51 residues processed: 628 average time/residue: 0.1541 time to fit residues: 144.9582 Evaluate side-chains 662 residues out of total 2079 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 610 time to evaluate : 0.701 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 8 THR Chi-restraints excluded: chain A residue 59 SER Chi-restraints excluded: chain A residue 93 THR Chi-restraints excluded: chain D residue 93 THR Chi-restraints excluded: chain D residue 98 CYS Chi-restraints excluded: chain E residue 9 THR Chi-restraints excluded: chain H residue 37 VAL Chi-restraints excluded: chain H residue 71 VAL Chi-restraints excluded: chain H residue 90 SER Chi-restraints excluded: chain H residue 93 THR Chi-restraints excluded: chain 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 568 MET Chi-restraints excluded: chain V residue 604 CYS Chi-restraints excluded: chain W residue 573 ILE Chi-restraints excluded: chain W residue 577 GLN Chi-restraints excluded: chain X residue 52 LEU Chi-restraints excluded: chain X residue 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 360 GLN Chi-restraints excluded: chain X residue 429 GLU 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 349 LEU Chi-restraints excluded: chain Y residue 425 ASN Chi-restraints excluded: chain Y residue 427 TRP Chi-restraints excluded: chain Y residue 467 ILE Chi-restraints excluded: chain Y residue 475 MET Chi-restraints excluded: chain Z residue 128 THR Chi-restraints excluded: chain Z residue 203 GLN 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 293 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: 0.6980 chunk 84 optimal weight: 0.8980 chunk 41 optimal weight: 0.0040 chunk 27 optimal weight: 0.0370 chunk 33 optimal weight: 2.9990 chunk 102 optimal weight: 1.9990 chunk 38 optimal weight: 0.6980 chunk 201 optimal weight: 2.9990 chunk 6 optimal weight: 3.9990 chunk 202 optimal weight: 0.8980 chunk 42 optimal weight: 8.9990 overall best weight: 0.4670 ------------------------------------------------------------------------------- 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** V 619 GLN W 630 GLN X 302 ASN X 360 GLN Z 33 ASN Z 203 GLN Z 348 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3453 r_free = 0.3453 target = 0.114346 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3237 r_free = 0.3237 target = 0.100003 restraints weight = 32716.930| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3295 r_free = 0.3295 target = 0.103764 restraints weight = 14618.095| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3332 r_free = 0.3332 target = 0.106187 restraints weight = 8359.473| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.3356 r_free = 0.3356 target = 0.107815 restraints weight = 5581.778| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3372 r_free = 0.3372 target = 0.108885 restraints weight = 4082.317| |-----------------------------------------------------------------------------| r_work (final): 0.3369 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7442 moved from start: 0.2144 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.148 20834 Z= 0.186 Angle : 0.921 59.183 28547 Z= 0.512 Chirality : 0.046 0.544 3546 Planarity : 0.004 0.102 3379 Dihedral : 8.553 70.324 5096 Min Nonbonded Distance : 2.321 Molprobity Statistics. All-atom Clashscore : 9.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.10 % Favored : 95.90 % Rotamer: Outliers : 2.74 % Allowed : 23.67 % Favored : 73.59 % Cbeta Deviations : 0.09 % 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 are not related in a simple way. whole: -0.38 (0.17), residues: 2340 helix: 2.02 (0.29), residues: 363 sheet: 0.02 (0.19), residues: 747 loop : -1.15 (0.17), residues: 1230 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG X 456 TYR 0.025 0.001 TYR Y 173 PHE 0.033 0.002 PHE Y 53 TRP 0.038 0.002 TRP Z 112 HIS 0.005 0.001 HIS Y 374 Details of bonding type rmsd covalent geometry : bond 0.00394 (20670) covalent geometry : angle 0.86859 (28093) SS BOND : bond 0.00645 ( 38) SS BOND : angle 2.68400 ( 76) hydrogen bonds : bond 0.03923 ( 671) hydrogen bonds : angle 4.65209 ( 1950) link_ALPHA1-2 : bond 0.00384 ( 10) link_ALPHA1-2 : angle 1.61592 ( 30) link_ALPHA1-3 : bond 0.00719 ( 12) link_ALPHA1-3 : angle 1.82453 ( 36) link_ALPHA1-6 : bond 0.00454 ( 9) link_ALPHA1-6 : angle 1.89465 ( 27) link_BETA1-4 : bond 0.00365 ( 43) link_BETA1-4 : angle 1.70195 ( 129) link_NAG-ASN : bond 0.00272 ( 52) link_NAG-ASN : angle 3.38510 ( 156) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3544.37 seconds wall clock time: 62 minutes 1.23 seconds (3721.23 seconds total)