Starting phenix.real_space_refine on Sun Sep 13 10:50:44 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/6okp_20100/09_2026/6okp_20100.cif Found real_map, /net/cci-nas-00/data/ceres_data/6okp_20100/09_2026/6okp_20100.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.28 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/6okp_20100/09_2026/6okp_20100.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6okp_20100/09_2026/6okp_20100.map" restraint_files = "/net/cci-nas-00/data/ceres_data/6okp_20100/09_2026/6okp_20100.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/6okp_20100/09_2026/6okp_20100.cif" model { file = "/net/cci-nas-00/data/ceres_data/6okp_20100/09_2026/6okp_20100.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6okp_20100/09_2026/6okp_20100.cif" } resolution = 3.28 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= -0.000 sd= 0.005 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 121 5.16 5 C 14261 2.51 5 N 3750 2.21 5 O 4725 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 32 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2.1-6174/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 22857 Number of models: 1 Model: "" Number of chains: 51 Chain: "A" Number of atoms: 960 Number of conformers: 1 Conformer: "" Number of residues, atoms: 118, 960 Classifications: {'peptide': 118} Link IDs: {'PTRANS': 1, 'TRANS': 116} Chain breaks: 1 Chain: "B" Number of atoms: 960 Number of conformers: 1 Conformer: "" Number of residues, atoms: 118, 960 Classifications: {'peptide': 118} Link IDs: {'PTRANS': 1, 'TRANS': 116} Chain breaks: 1 Chain: "C" Number of atoms: 960 Number of conformers: 1 Conformer: "" Number of residues, atoms: 118, 960 Classifications: {'peptide': 118} Link IDs: {'PTRANS': 1, 'TRANS': 116} Chain breaks: 1 Chain: "D" Number of atoms: 3569 Number of conformers: 1 Conformer: "" Number of residues, atoms: 456, 3569 Classifications: {'peptide': 456} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 24, 'TRANS': 431} Chain breaks: 2 Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "E" Number of atoms: 3559 Number of conformers: 1 Conformer: "" Number of residues, atoms: 455, 3559 Classifications: {'peptide': 455} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 24, 'TRANS': 430} Chain breaks: 2 Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 9 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'ASN:plan1': 1, 'GLU:plan': 1} Unresolved non-hydrogen planarities: 7 Chain: "F" Number of atoms: 3569 Number of conformers: 1 Conformer: "" Number of residues, atoms: 456, 3569 Classifications: {'peptide': 456} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 24, 'TRANS': 431} Chain breaks: 2 Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "K" Number of atoms: 1041 Number of conformers: 1 Conformer: "" Number of residues, atoms: 133, 1041 Classifications: {'peptide': 133} Link IDs: {'PTRANS': 5, 'TRANS': 127} Chain: "L" Number of atoms: 779 Number of conformers: 1 Conformer: "" Number of residues, atoms: 101, 779 Classifications: {'peptide': 101} Link IDs: {'PTRANS': 6, 'TRANS': 94} Chain: "M" Number of atoms: 1019 Number of conformers: 1 Conformer: "" Number of residues, atoms: 131, 1019 Classifications: {'peptide': 131} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 8, 'TRANS': 122} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "N" Number of atoms: 797 Number of conformers: 1 Conformer: "" Number of residues, atoms: 104, 797 Classifications: {'peptide': 104} Link IDs: {'PCIS': 1, 'PTRANS': 4, 'TRANS': 98} Chain: "O" Number of atoms: 1019 Number of conformers: 1 Conformer: "" Number of residues, atoms: 131, 1019 Classifications: {'peptide': 131} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 8, 'TRANS': 122} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "P" Number of atoms: 797 Number of conformers: 1 Conformer: "" Number of residues, atoms: 104, 797 Classifications: {'peptide': 104} Link IDs: {'PCIS': 1, 'PTRANS': 4, 'TRANS': 98} Chain: "Q" Number of atoms: 1019 Number of conformers: 1 Conformer: "" Number of residues, atoms: 131, 1019 Classifications: {'peptide': 131} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 8, 'TRANS': 122} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "R" Number of atoms: 797 Number of conformers: 1 Conformer: "" Number of residues, atoms: 104, 797 Classifications: {'peptide': 104} Link IDs: {'PCIS': 1, 'PTRANS': 4, 'TRANS': 98} Chain: "G" Number of atoms: 94 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 94 Unusual residues: {'BMA': 1, 'MAN': 5, 'NAG': 2} Classifications: {'undetermined': 8} Link IDs: {None: 7} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen chiralities: 8 Chain: "H" Number of atoms: 105 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 105 Unusual residues: {'BMA': 1, 'MAN': 6, 'NAG': 2} Classifications: {'undetermined': 9} Link IDs: {None: 8} Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 18 Unresolved non-hydrogen chiralities: 9 Chain: "I" Number of atoms: 83 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 83 Unusual residues: {'BMA': 1, 'MAN': 4, 'NAG': 2} Classifications: {'undetermined': 7} Link IDs: {None: 6} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen chiralities: 7 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 chiralities: 2 Chain: "S" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen chiralities: 3 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 chiralities: 2 Chain: "U" 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 chiralities: 3 Chain: "V" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "W" 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 chiralities: 2 Chain: "X" 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 chiralities: 2 Chain: "Y" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "Z" Number of atoms: 83 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 83 Unusual residues: {'BMA': 1, 'MAN': 4, 'NAG': 2} Classifications: {'undetermined': 7} Link IDs: {None: 6} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen chiralities: 7 Chain: "a" 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 chiralities: 3 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 chiralities: 2 Chain: "c" 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 chiralities: 3 Chain: "d" 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 chiralities: 2 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 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 chiralities: 2 Chain: "g" Number of atoms: 83 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 83 Unusual residues: {'BMA': 1, 'MAN': 4, 'NAG': 2} Classifications: {'undetermined': 7} Link IDs: {None: 6} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen chiralities: 7 Chain: "h" Number of atoms: 72 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 72 Unusual residues: {'BMA': 1, 'MAN': 3, 'NAG': 2} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen chiralities: 6 Chain: "i" Number of atoms: 83 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 83 Unusual residues: {'BMA': 1, 'MAN': 4, 'NAG': 2} Classifications: {'undetermined': 7} Link IDs: {None: 6} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen chiralities: 7 Chain: "j" Number of atoms: 83 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 83 Unusual residues: {'BMA': 1, 'MAN': 4, 'NAG': 2} Classifications: {'undetermined': 7} Link IDs: {None: 6} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen chiralities: 7 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 chiralities: 2 Chain: "l" 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 chiralities: 3 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 chiralities: 2 Chain: "n" 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 chiralities: 3 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 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 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 chiralities: 2 Chain: "r" Number of atoms: 105 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 105 Unusual residues: {'BMA': 1, 'MAN': 6, 'NAG': 2} Classifications: {'undetermined': 9} Link IDs: {None: 8} Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 18 Unresolved non-hydrogen chiralities: 9 Chain: "s" Number of atoms: 105 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 105 Unusual residues: {'BMA': 1, 'MAN': 6, 'NAG': 2} Classifications: {'undetermined': 9} Link IDs: {None: 8} Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 18 Unresolved non-hydrogen chiralities: 9 Chain: "A" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "B" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "C" 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 chiralities: 2 Chain: "D" Number of atoms: 126 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 126 Unusual residues: {'NAG': 9} Classifications: {'undetermined': 9} Link IDs: {None: 8} Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 18 Unresolved non-hydrogen chiralities: 9 Chain: "E" Number of atoms: 126 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 126 Unusual residues: {'NAG': 9} Classifications: {'undetermined': 9} Link IDs: {None: 8} Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 18 Unresolved non-hydrogen chiralities: 9 Chain: "F" Number of atoms: 126 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 126 Unusual residues: {'NAG': 9} Classifications: {'undetermined': 9} Link IDs: {None: 8} Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 18 Unresolved non-hydrogen chiralities: 9 Time building chain proxies: 5.62, per 1000 atoms: 0.25 Number of scatterers: 22857 At special positions: 0 Unit cell: (154.78, 166.77, 166.77, 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 121 16.00 O 4725 8.00 N 3750 7.00 C 14261 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=27, symmetry=0 Simple disulfide: pdb=" SG CYS A 598 " - pdb=" SG CYS A 604 " distance=2.02 Simple disulfide: pdb=" SG CYS A 605 " - pdb=" SG CYS D 501 " distance=2.03 Simple disulfide: pdb=" SG CYS B 598 " - pdb=" SG CYS B 604 " distance=2.02 Simple disulfide: pdb=" SG CYS B 605 " - pdb=" SG CYS E 501 " distance=2.03 Simple disulfide: pdb=" SG CYS C 598 " - pdb=" SG CYS C 604 " distance=2.02 Simple disulfide: pdb=" SG CYS C 605 " - pdb=" SG CYS F 501 " distance=2.03 Simple disulfide: pdb=" SG CYS D 54 " - pdb=" SG CYS D 74 " distance=2.04 Simple disulfide: pdb=" SG CYS D 119 " - pdb=" SG CYS D 205 " distance=2.03 Simple disulfide: pdb=" SG CYS D 126 " - pdb=" SG CYS D 196 " distance=2.03 Simple disulfide: pdb=" SG CYS D 296 " - pdb=" SG CYS D 331 " distance=2.03 Simple disulfide: pdb=" SG CYS D 378 " - pdb=" SG CYS D 445 " distance=2.02 Simple disulfide: pdb=" SG CYS E 54 " - pdb=" SG CYS E 74 " distance=2.04 Simple disulfide: pdb=" SG CYS E 126 " - pdb=" SG CYS E 196 " distance=2.03 Simple disulfide: pdb=" SG CYS E 296 " - pdb=" SG CYS E 331 " distance=2.04 Simple disulfide: pdb=" SG CYS E 378 " - pdb=" SG CYS E 445 " distance=2.01 Simple disulfide: pdb=" SG CYS F 54 " - pdb=" SG CYS F 74 " distance=2.04 Simple disulfide: pdb=" SG CYS F 126 " - pdb=" SG CYS F 196 " distance=2.03 Simple disulfide: pdb=" SG CYS F 296 " - pdb=" SG CYS F 331 " distance=2.02 Simple disulfide: pdb=" SG CYS F 378 " - pdb=" SG CYS F 445 " distance=2.01 Simple disulfide: pdb=" SG CYS K 22 " - pdb=" SG CYS K 92 " distance=2.03 Simple disulfide: pdb=" SG CYS L 23 " - pdb=" SG CYS L 88 " distance=2.03 Simple disulfide: pdb=" SG CYS M 22 " - pdb=" SG CYS M 92 " distance=2.03 Simple disulfide: pdb=" SG CYS N 23 " - pdb=" SG CYS N 88 " distance=2.03 Simple disulfide: pdb=" SG CYS O 22 " - pdb=" SG CYS O 92 " distance=2.03 Simple disulfide: pdb=" SG CYS P 23 " - pdb=" SG CYS P 88 " distance=2.03 Simple disulfide: pdb=" SG CYS Q 22 " - pdb=" SG CYS Q 92 " distance=2.03 Simple disulfide: pdb=" SG CYS R 23 " - pdb=" SG CYS R 88 " 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=3, symmetry=0 Links applied ALPHA1-2 " MAN G 4 " - " MAN G 5 " " MAN H 5 " - " MAN H 6 " " MAN g 4 " - " MAN g 5 " " MAN h 4 " - " MAN h 5 " " MAN r 5 " - " MAN r 6 " " MAN s 5 " - " MAN s 6 " ALPHA1-3 " BMA G 3 " - " MAN G 4 " " MAN G 6 " - " MAN G 7 " " BMA H 3 " - " MAN H 8 " " MAN H 4 " - " MAN H 7 " " MAN H 8 " - " MAN H 9 " " BMA I 3 " - " MAN I 7 " " MAN I 4 " - " MAN I 5 " " BMA Z 3 " - " MAN Z 7 " " MAN Z 4 " - " MAN Z 5 " " BMA g 3 " - " MAN g 4 " " MAN g 6 " - " MAN g 7 " " BMA h 3 " - " MAN h 4 " " BMA i 3 " - " MAN i 7 " " MAN i 4 " - " MAN i 5 " " BMA j 3 " - " MAN j 7 " " MAN j 4 " - " MAN j 5 " " BMA r 3 " - " MAN r 8 " " MAN r 4 " - " MAN r 7 " " MAN r 8 " - " MAN r 9 " " BMA s 3 " - " MAN s 8 " " MAN s 4 " - " MAN s 7 " " MAN s 8 " - " MAN s 9 " ALPHA1-6 " BMA G 3 " - " MAN G 6 " " MAN G 6 " - " MAN G 8 " " BMA H 3 " - " MAN H 4 " " MAN H 4 " - " MAN H 5 " " BMA I 3 " - " MAN I 4 " " MAN I 4 " - " MAN I 6 " " BMA Z 3 " - " MAN Z 4 " " MAN Z 4 " - " MAN Z 6 " " BMA g 3 " - " MAN g 6 " " BMA h 3 " - " MAN h 6 " " BMA i 3 " - " MAN i 4 " " MAN i 4 " - " MAN i 6 " " BMA j 3 " - " MAN j 4 " " MAN j 4 " - " MAN j 6 " " BMA r 3 " - " MAN r 4 " " MAN r 4 " - " MAN r 5 " " BMA s 3 " - " MAN s 4 " " MAN s 4 " - " MAN s 5 " BETA1-4 " NAG G 1 " - " NAG G 2 " " NAG G 2 " - " BMA G 3 " " NAG H 1 " - " NAG H 2 " " NAG H 2 " - " BMA H 3 " " NAG I 1 " - " NAG I 2 " " NAG I 2 " - " BMA I 3 " " NAG J 1 " - " NAG J 2 " " NAG S 1 " - " NAG S 2 " " NAG S 2 " - " BMA S 3 " " NAG T 1 " - " NAG T 2 " " NAG U 1 " - " NAG U 2 " " NAG U 2 " - " BMA U 3 " " NAG V 1 " - " NAG V 2 " " NAG W 1 " - " NAG W 2 " " NAG X 1 " - " NAG X 2 " " NAG Y 1 " - " NAG Y 2 " " NAG Z 1 " - " NAG Z 2 " " NAG Z 2 " - " BMA Z 3 " " NAG a 1 " - " NAG a 2 " " NAG 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 e 1 " - " NAG e 2 " " NAG f 1 " - " NAG f 2 " " NAG g 1 " - " NAG g 2 " " NAG g 2 " - " BMA g 3 " " NAG h 1 " - " NAG h 2 " " NAG h 2 " - " BMA h 3 " " NAG i 1 " - " NAG i 2 " " NAG i 2 " - " BMA i 3 " " NAG j 1 " - " NAG j 2 " " NAG 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 n 1 " - " NAG n 2 " " NAG n 2 " - " BMA n 3 " " NAG o 1 " - " NAG o 2 " " NAG p 1 " - " NAG p 2 " " NAG q 1 " - " NAG q 2 " " NAG r 1 " - " NAG r 2 " " NAG r 2 " - " BMA r 3 " " NAG s 1 " - " NAG s 2 " " NAG s 2 " - " BMA s 3 " NAG-ASN " NAG A 701 " - " ASN A 616 " " NAG A 702 " - " ASN A 637 " " NAG B 701 " - " ASN B 616 " " NAG B 702 " - " ASN B 637 " " NAG C 701 " - " ASN C 616 " " NAG C 702 " - " ASN C 637 " " NAG D 627 " - " ASN D 301 " " NAG D 631 " - " ASN D 88 " " NAG D 632 " - " ASN D 241 " " NAG D 635 " - " ASN D 276 " " NAG D 636 " - " ASN D 339 " " NAG D 640 " - " ASN D 396 " " NAG D 647 " - " ASN D 413 " " NAG D 648 " - " ASN D 355 " " NAG D 649 " - " ASN D 197 " " NAG E 610 " - " ASN E 301 " " NAG E 614 " - " ASN E 88 " " NAG E 615 " - " ASN E 241 " " NAG E 618 " - " ASN E 276 " " NAG E 619 " - " ASN E 339 " " NAG E 623 " - " ASN E 396 " " NAG E 630 " - " ASN E 413 " " NAG E 631 " - " ASN E 355 " " NAG E 639 " - " ASN E 197 " " NAG F 617 " - " ASN F 301 " " NAG F 621 " - " ASN F 88 " " NAG F 622 " - " ASN F 241 " " NAG F 625 " - " ASN F 276 " " NAG F 626 " - " ASN F 339 " " NAG F 630 " - " ASN F 396 " " NAG F 637 " - " ASN F 413 " " NAG F 638 " - " ASN F 355 " " NAG F 639 " - " ASN F 197 " " NAG G 1 " - " ASN D 295 " " NAG H 1 " - " ASN D 262 " " NAG I 1 " - " ASN D 448 " " NAG J 1 " - " ASN D 332 " " NAG S 1 " - " ASN D 160 " " NAG T 1 " - " ASN D 234 " " NAG U 1 " - " ASN D 392 " " NAG V 1 " - " ASN D 362 " " NAG W 1 " - " ASN D 386 " " NAG X 1 " - " ASN D 156 " " NAG Y 1 " - " ASN E 295 " " NAG Z 1 " - " ASN E 448 " " NAG a 1 " - " ASN E 160 " " NAG b 1 " - " ASN E 234 " " NAG c 1 " - " ASN E 392 " " NAG d 1 " - " ASN E 362 " " NAG e 1 " - " ASN E 386 " " NAG f 1 " - " ASN E 156 " " NAG g 1 " - " ASN E 332 " " NAG h 1 " - " ASN E 137 " " NAG i 1 " - " ASN F 295 " " NAG j 1 " - " ASN F 448 " " NAG k 1 " - " ASN F 332 " " NAG l 1 " - " ASN F 160 " " NAG m 1 " - " ASN F 234 " " NAG n 1 " - " ASN F 392 " " NAG o 1 " - " ASN F 362 " " NAG p 1 " - " ASN F 386 " " NAG q 1 " - " ASN F 156 " " NAG r 1 " - " ASN E 262 " " NAG s 1 " - " ASN F 262 " Number of additional bonds: simple=3, symmetry=0 Coordination: Other bonds: Time building additional restraints: 2.36 Conformation dependent library (CDL) restraints added in 1.1 seconds 5228 Ramachandran restraints generated. 2614 Oldfield, 0 Emsley, 2614 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4896 Finding SS restraints... Secondary structure from input PDB file: 39 helices and 54 sheets defined 14.1% alpha, 24.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.77 Creating SS restraints... Processing helix chain 'A' and resid 571 through 595 removed outlier: 3.734A pdb=" N GLN A 575 " --> pdb=" O TRP A 571 " (cutoff:3.500A) removed outlier: 4.077A pdb=" N ASP A 589 " --> pdb=" O ARG A 585 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N ILE A 595 " --> pdb=" O GLN A 591 " (cutoff:3.500A) Processing helix chain 'A' and resid 618 through 623 Processing helix chain 'A' and resid 628 through 635 Processing helix chain 'A' and resid 638 through 648 Processing helix chain 'A' and resid 651 through 663 removed outlier: 3.715A pdb=" N ASN A 656 " --> pdb=" O GLN A 652 " (cutoff:3.500A) removed outlier: 4.079A pdb=" N GLU A 657 " --> pdb=" O GLN A 653 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N LEU A 663 " --> pdb=" O GLU A 659 " (cutoff:3.500A) Processing helix chain 'B' and resid 571 through 595 removed outlier: 3.733A pdb=" N GLN B 575 " --> pdb=" O TRP B 571 " (cutoff:3.500A) removed outlier: 4.077A pdb=" N ASP B 589 " --> pdb=" O ARG B 585 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N ILE B 595 " --> pdb=" O GLN B 591 " (cutoff:3.500A) Processing helix chain 'B' and resid 618 through 623 Processing helix chain 'B' and resid 628 through 635 Processing helix chain 'B' and resid 638 through 648 Processing helix chain 'B' and resid 651 through 663 removed outlier: 3.715A pdb=" N ASN B 656 " --> pdb=" O GLN B 652 " (cutoff:3.500A) removed outlier: 4.079A pdb=" N GLU B 657 " --> pdb=" O GLN B 653 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N LEU B 663 " --> pdb=" O GLU B 659 " (cutoff:3.500A) Processing helix chain 'C' and resid 571 through 595 removed outlier: 3.733A pdb=" N GLN C 575 " --> pdb=" O TRP C 571 " (cutoff:3.500A) removed outlier: 4.077A pdb=" N ASP C 589 " --> pdb=" O ARG C 585 " (cutoff:3.500A) removed outlier: 3.733A pdb=" N ILE C 595 " --> pdb=" O GLN C 591 " (cutoff:3.500A) Processing helix chain 'C' and resid 618 through 623 Processing helix chain 'C' and resid 628 through 635 Processing helix chain 'C' and resid 638 through 648 Processing helix chain 'C' and resid 651 through 663 removed outlier: 3.714A pdb=" N ASN C 656 " --> pdb=" O GLN C 652 " (cutoff:3.500A) removed outlier: 4.079A pdb=" N GLU C 657 " --> pdb=" O GLN C 653 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N LEU C 663 " --> pdb=" O GLU C 659 " (cutoff:3.500A) Processing helix chain 'D' and resid 99 through 110 removed outlier: 3.611A pdb=" N ILE D 109 " --> pdb=" O HIS D 105 " (cutoff:3.500A) Processing helix chain 'D' and resid 122 through 126 removed outlier: 3.626A pdb=" N LEU D 125 " --> pdb=" O LEU D 122 " (cutoff:3.500A) Processing helix chain 'D' and resid 335 through 353 removed outlier: 3.526A pdb=" N GLU D 340 " --> pdb=" O ALA D 336 " (cutoff:3.500A) removed outlier: 3.838A pdb=" N THR D 341 " --> pdb=" O ARG D 337 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N VAL D 346 " --> pdb=" O LEU D 342 " (cutoff:3.500A) removed outlier: 3.866A pdb=" N ALA D 347 " --> pdb=" O GLY D 343 " (cutoff:3.500A) removed outlier: 4.082A pdb=" N LYS D 348 " --> pdb=" O GLN D 344 " (cutoff:3.500A) removed outlier: 4.225A pdb=" N GLU D 351 " --> pdb=" O ALA D 347 " (cutoff:3.500A) removed outlier: 4.161A pdb=" N GLN D 352 " --> pdb=" O LYS D 348 " (cutoff:3.500A) Processing helix chain 'D' and resid 475 through 479 removed outlier: 3.519A pdb=" N ASN D 478 " --> pdb=" O MET D 475 " (cutoff:3.500A) Processing helix chain 'E' and resid 98 through 115 removed outlier: 4.298A pdb=" N GLU E 102 " --> pdb=" O ASN E 98 " (cutoff:3.500A) removed outlier: 3.781A pdb=" N SER E 115 " --> pdb=" O LEU E 111 " (cutoff:3.500A) Processing helix chain 'E' and resid 123 through 126 removed outlier: 3.650A pdb=" N CYS E 126 " --> pdb=" O THR E 123 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 123 through 126' Processing helix chain 'E' and resid 334 through 353 removed outlier: 3.621A pdb=" N TRP E 338 " --> pdb=" O SER E 334 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N VAL E 346 " --> pdb=" O LEU E 342 " (cutoff:3.500A) removed outlier: 3.752A pdb=" N ALA E 347 " --> pdb=" O GLY E 343 " (cutoff:3.500A) removed outlier: 4.133A pdb=" N LYS E 348 " --> pdb=" O GLN E 344 " (cutoff:3.500A) removed outlier: 4.133A pdb=" N GLU E 351 " --> pdb=" O ALA E 347 " (cutoff:3.500A) removed outlier: 4.204A pdb=" N GLN E 352 " --> pdb=" O LYS E 348 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N PHE E 353 " --> pdb=" O LEU E 349 " (cutoff:3.500A) Processing helix chain 'E' and resid 368 through 373 removed outlier: 3.580A pdb=" N VAL E 372 " --> pdb=" O ASP E 368 " (cutoff:3.500A) removed outlier: 3.802A pdb=" N THR E 373 " --> pdb=" O PRO E 369 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 368 through 373' Processing helix chain 'E' and resid 475 through 479 Processing helix chain 'F' and resid 98 through 112 removed outlier: 4.308A pdb=" N GLU F 102 " --> pdb=" O ASN F 98 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N GLU F 106 " --> pdb=" O GLU F 102 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N ILE F 109 " --> pdb=" O HIS F 105 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N LEU F 111 " --> pdb=" O ASP F 107 " (cutoff:3.500A) Processing helix chain 'F' and resid 123 through 126 Processing helix chain 'F' and resid 335 through 353 removed outlier: 3.971A pdb=" N GLU F 340 " --> pdb=" O ALA F 336 " (cutoff:3.500A) removed outlier: 3.922A pdb=" N THR F 341 " --> pdb=" O ARG F 337 " (cutoff:3.500A) removed outlier: 3.731A pdb=" N VAL F 346 " --> pdb=" O LEU F 342 " (cutoff:3.500A) removed outlier: 3.861A pdb=" N ALA F 347 " --> pdb=" O GLY F 343 " (cutoff:3.500A) removed outlier: 4.047A pdb=" N LYS F 348 " --> pdb=" O GLN F 344 " (cutoff:3.500A) removed outlier: 4.263A pdb=" N GLU F 351 " --> pdb=" O ALA F 347 " (cutoff:3.500A) removed outlier: 4.045A pdb=" N GLN F 352 " --> pdb=" O LYS F 348 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N PHE F 353 " --> pdb=" O LEU F 349 " (cutoff:3.500A) Processing helix chain 'F' and resid 425 through 429 removed outlier: 4.443A pdb=" N GLY F 429 " --> pdb=" O MET F 426 " (cutoff:3.500A) Processing helix chain 'F' and resid 476 through 481 removed outlier: 3.759A pdb=" N SER F 481 " --> pdb=" O ASP F 477 " (cutoff:3.500A) Processing helix chain 'K' and resid 28 through 32 removed outlier: 3.868A pdb=" N ASN K 31 " --> pdb=" O SER K 28 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N TYR K 32 " --> pdb=" O MET K 29 " (cutoff:3.500A) No H-bonds generated for 'chain 'K' and resid 28 through 32' Processing helix chain 'K' and resid 83 through 87 removed outlier: 3.673A pdb=" N THR K 87 " --> pdb=" O PRO K 84 " (cutoff:3.500A) Processing helix chain 'K' and resid 100D through 100H removed outlier: 3.638A pdb=" N PHE K 100G" --> pdb=" O VAL K 100D" (cutoff:3.500A) Processing helix chain 'L' and resid 79 through 83 removed outlier: 4.353A pdb=" N GLU L 83 " --> pdb=" O ALA L 80 " (cutoff:3.500A) Processing helix chain 'M' and resid 63 through 65 No H-bonds generated for 'chain 'M' and resid 63 through 65' Processing helix chain 'M' and resid 83 through 87 Processing helix chain 'O' and resid 63 through 65 No H-bonds generated for 'chain 'O' and resid 63 through 65' Processing helix chain 'O' and resid 83 through 87 Processing helix chain 'Q' and resid 63 through 65 No H-bonds generated for 'chain 'Q' and resid 63 through 65' Processing helix chain 'Q' and resid 83 through 87 Processing sheet with id=AA1, first strand: chain 'A' and resid 603 through 609 removed outlier: 8.529A pdb=" N CYS A 604 " --> pdb=" O TYR D 40 " (cutoff:3.500A) removed outlier: 8.213A pdb=" N TYR D 40 " --> pdb=" O CYS A 604 " (cutoff:3.500A) removed outlier: 7.722A pdb=" N THR A 606 " --> pdb=" O VAL D 38 " (cutoff:3.500A) removed outlier: 8.494A pdb=" N VAL D 38 " --> pdb=" O THR A 606 " (cutoff:3.500A) removed outlier: 5.528A pdb=" N VAL A 608 " --> pdb=" O VAL D 36 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 603 through 609 removed outlier: 8.435A pdb=" N CYS B 604 " --> pdb=" O TYR E 40 " (cutoff:3.500A) removed outlier: 8.152A pdb=" N TYR E 40 " --> pdb=" O CYS B 604 " (cutoff:3.500A) removed outlier: 7.684A pdb=" N THR B 606 " --> pdb=" O VAL E 38 " (cutoff:3.500A) removed outlier: 8.451A pdb=" N VAL E 38 " --> pdb=" O THR B 606 " (cutoff:3.500A) removed outlier: 5.616A pdb=" N VAL B 608 " --> pdb=" O VAL E 36 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'C' and resid 603 through 609 removed outlier: 5.608A pdb=" N VAL F 36 " --> pdb=" O THR C 606 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'D' and resid 45 through 47 removed outlier: 3.550A pdb=" N ALA D 224 " --> pdb=" O VAL D 489 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'D' and resid 53 through 54 Processing sheet with id=AA6, first strand: chain 'D' and resid 170 through 177 Processing sheet with id=AA7, first strand: chain 'D' and resid 271 through 273 Processing sheet with id=AA8, first strand: chain 'D' and resid 292 through 293 Processing sheet with id=AA9, first strand: chain 'D' and resid 320 through 322 removed outlier: 5.344A pdb=" N ASP D 321A" --> pdb=" O THR D 303 " (cutoff:3.500A) removed outlier: 3.775A pdb=" N ILE D 443 " --> pdb=" O ARG D 298 " (cutoff:3.500A) removed outlier: 5.146A pdb=" N ASN D 300 " --> pdb=" O GLY D 441 " (cutoff:3.500A) removed outlier: 5.213A pdb=" N GLY D 441 " --> pdb=" O ASN D 300 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'D' and resid 307 through 308 Processing sheet with id=AB2, first strand: chain 'D' and resid 394 through 395 removed outlier: 6.474A pdb=" N THR D 357 " --> pdb=" O GLU D 466 " (cutoff:3.500A) removed outlier: 7.974A pdb=" N PHE D 468 " --> pdb=" O THR D 357 " (cutoff:3.500A) removed outlier: 6.595A pdb=" N ILE D 360 " --> pdb=" O PHE D 468 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'D' and resid 374 through 378 removed outlier: 3.617A pdb=" N GLU D 381 " --> pdb=" O CYS D 378 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'E' and resid 45 through 47 removed outlier: 3.518A pdb=" N LYS E 487 " --> pdb=" O LEU E 226 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'E' and resid 53 through 55 Processing sheet with id=AB6, first strand: chain 'E' and resid 92 through 93 Processing sheet with id=AB7, first strand: chain 'E' and resid 120 through 121 removed outlier: 4.026A pdb=" N VAL E 120 " --> pdb=" O GLN E 203 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'E' and resid 129 through 130 Processing sheet with id=AB9, first strand: chain 'E' and resid 154 through 162 Processing sheet with id=AC1, first strand: chain 'E' and resid 259 through 260 removed outlier: 6.732A pdb=" N LEU E 260 " --> pdb=" O THR E 450 " (cutoff:3.500A) removed outlier: 10.029A pdb=" N ASN E 448 " --> pdb=" O GLU E 290 " (cutoff:3.500A) removed outlier: 8.818A pdb=" N GLU E 290 " --> pdb=" O ASN E 448 " (cutoff:3.500A) removed outlier: 7.635A pdb=" N THR E 450 " --> pdb=" O LEU E 288 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'E' and resid 322 through 323 removed outlier: 4.335A pdb=" N ASN E 301 " --> pdb=" O ILE E 323 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N ILE E 443 " --> pdb=" O ARG E 298 " (cutoff:3.500A) removed outlier: 5.029A pdb=" N ASN E 300 " --> pdb=" O GLY E 441 " (cutoff:3.500A) removed outlier: 5.201A pdb=" N GLY E 441 " --> pdb=" O ASN E 300 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'E' and resid 307 through 308 Processing sheet with id=AC4, first strand: chain 'E' and resid 394 through 395 removed outlier: 6.626A pdb=" N THR E 357 " --> pdb=" O GLU E 466 " (cutoff:3.500A) removed outlier: 8.143A pdb=" N PHE E 468 " --> pdb=" O THR E 357 " (cutoff:3.500A) removed outlier: 6.672A pdb=" N ILE E 360 " --> pdb=" O PHE E 468 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'E' and resid 374 through 378 removed outlier: 3.642A pdb=" N GLU E 381 " --> pdb=" O CYS E 378 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'F' and resid 45 through 47 removed outlier: 3.543A pdb=" N ALA F 224 " --> pdb=" O VAL F 489 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'F' and resid 53 through 55 Processing sheet with id=AC8, first strand: chain 'F' and resid 120 through 121 removed outlier: 3.899A pdb=" N VAL F 120 " --> pdb=" O GLN F 203 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'F' and resid 169 through 177 Processing sheet with id=AD1, first strand: chain 'F' and resid 271 through 274 removed outlier: 6.733A pdb=" N THR F 357 " --> pdb=" O GLU F 466 " (cutoff:3.500A) removed outlier: 7.984A pdb=" N PHE F 468 " --> pdb=" O THR F 357 " (cutoff:3.500A) removed outlier: 6.629A pdb=" N ILE F 360 " --> pdb=" O PHE F 468 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'F' and resid 292 through 294 Processing sheet with id=AD3, first strand: chain 'F' and resid 297 through 298 removed outlier: 3.712A pdb=" N ILE F 443 " --> pdb=" O ARG F 298 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'F' and resid 302 through 304 removed outlier: 5.060A pdb=" N ASP F 321A" --> pdb=" O THR F 303 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'F' and resid 307 through 308 Processing sheet with id=AD6, first strand: chain 'F' and resid 374 through 378 removed outlier: 3.513A pdb=" N GLU F 381 " --> pdb=" O CYS F 378 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'K' and resid 3 through 7 Processing sheet with id=AD8, first strand: chain 'K' and resid 11 through 12 removed outlier: 3.623A pdb=" N VAL K 12 " --> pdb=" O THR K 110 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N VAL K 109 " --> pdb=" O ALA K 88 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N ALA K 88 " --> pdb=" O VAL K 109 " (cutoff:3.500A) removed outlier: 3.826A pdb=" N TYR K 33 " --> pdb=" O ALA K 95 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'K' and resid 11 through 12 removed outlier: 3.623A pdb=" N VAL K 12 " --> pdb=" O THR K 110 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N VAL K 109 " --> pdb=" O ALA K 88 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N ALA K 88 " --> pdb=" O VAL K 109 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N SER K 100O" --> pdb=" O ARG K 96 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'K' and resid 67 through 68 Processing sheet with id=AE2, first strand: chain 'L' and resid 18 through 22 Processing sheet with id=AE3, first strand: chain 'L' and resid 44 through 46 removed outlier: 3.701A pdb=" N TYR L 36 " --> pdb=" O TYR L 87 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N TYR L 87 " --> pdb=" O TYR L 36 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'M' and resid 4 through 7 removed outlier: 3.573A pdb=" N GLN M 77 " --> pdb=" O ASP M 72 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'M' and resid 11 through 12 removed outlier: 3.612A pdb=" N ALA M 93 " --> pdb=" O SER M 35 " (cutoff:3.500A) removed outlier: 6.352A pdb=" N TRP M 34 " --> pdb=" O PHE M 50 " (cutoff:3.500A) removed outlier: 4.469A pdb=" N PHE M 50 " --> pdb=" O TRP M 34 " (cutoff:3.500A) removed outlier: 6.829A pdb=" N TRP M 36 " --> pdb=" O ILE M 48 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'N' and resid 4 through 7 Processing sheet with id=AE7, first strand: chain 'N' and resid 4 through 7 Processing sheet with id=AE8, first strand: chain 'N' and resid 10 through 13 removed outlier: 6.387A pdb=" N LEU N 11 " --> pdb=" O GLU N 102 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N TYR N 87 " --> pdb=" O TYR N 36 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N GLN N 89 " --> pdb=" O ALA N 34 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N ALA N 34 " --> pdb=" O GLN N 89 " (cutoff:3.500A) removed outlier: 6.363A pdb=" N TRP N 35 " --> pdb=" O LEU N 47 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N ARG N 45 " --> pdb=" O GLN N 37 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'O' and resid 4 through 7 removed outlier: 3.573A pdb=" N GLN O 77 " --> pdb=" O ASP O 72 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'O' and resid 11 through 12 removed outlier: 3.612A pdb=" N ALA O 93 " --> pdb=" O SER O 35 " (cutoff:3.500A) removed outlier: 6.351A pdb=" N TRP O 34 " --> pdb=" O PHE O 50 " (cutoff:3.500A) removed outlier: 4.469A pdb=" N PHE O 50 " --> pdb=" O TRP O 34 " (cutoff:3.500A) removed outlier: 6.830A pdb=" N TRP O 36 " --> pdb=" O ILE O 48 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'P' and resid 4 through 7 Processing sheet with id=AF3, first strand: chain 'P' and resid 4 through 7 Processing sheet with id=AF4, first strand: chain 'P' and resid 10 through 13 removed outlier: 6.387A pdb=" N LEU P 11 " --> pdb=" O GLU P 102 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N TYR P 87 " --> pdb=" O TYR P 36 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N GLN P 89 " --> pdb=" O ALA P 34 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N ALA P 34 " --> pdb=" O GLN P 89 " (cutoff:3.500A) removed outlier: 6.363A pdb=" N TRP P 35 " --> pdb=" O LEU P 47 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N ARG P 45 " --> pdb=" O GLN P 37 " (cutoff:3.500A) Processing sheet with id=AF5, first strand: chain 'Q' and resid 4 through 7 removed outlier: 3.573A pdb=" N GLN Q 77 " --> pdb=" O ASP Q 72 " (cutoff:3.500A) Processing sheet with id=AF6, first strand: chain 'Q' and resid 11 through 12 removed outlier: 3.611A pdb=" N ALA Q 93 " --> pdb=" O SER Q 35 " (cutoff:3.500A) removed outlier: 6.353A pdb=" N TRP Q 34 " --> pdb=" O PHE Q 50 " (cutoff:3.500A) removed outlier: 4.468A pdb=" N PHE Q 50 " --> pdb=" O TRP Q 34 " (cutoff:3.500A) removed outlier: 6.830A pdb=" N TRP Q 36 " --> pdb=" O ILE Q 48 " (cutoff:3.500A) Processing sheet with id=AF7, first strand: chain 'R' and resid 4 through 7 Processing sheet with id=AF8, first strand: chain 'R' and resid 4 through 7 Processing sheet with id=AF9, first strand: chain 'R' and resid 10 through 13 removed outlier: 6.388A pdb=" N LEU R 11 " --> pdb=" O GLU R 102 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N TYR R 87 " --> pdb=" O TYR R 36 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N GLN R 89 " --> pdb=" O ALA R 34 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N ALA R 34 " --> pdb=" O GLN R 89 " (cutoff:3.500A) removed outlier: 6.363A pdb=" N TRP R 35 " --> pdb=" O LEU R 47 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N ARG R 45 " --> pdb=" O GLN R 37 " (cutoff:3.500A) 575 hydrogen bonds defined for protein. 1470 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: 4.35 Time building geometry restraints manager: 3.08 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.34: 6778 1.34 - 1.46: 5637 1.46 - 1.58: 10743 1.58 - 1.70: 5 1.70 - 1.82: 160 Bond restraints: 23323 Sorted by residual: bond pdb=" C1 NAG J 2 " pdb=" O5 NAG J 2 " ideal model delta sigma weight residual 1.406 1.482 -0.076 2.00e-02 2.50e+03 1.43e+01 bond pdb=" C1 NAG E 614 " pdb=" O5 NAG E 614 " ideal model delta sigma weight residual 1.406 1.476 -0.070 2.00e-02 2.50e+03 1.21e+01 bond pdb=" C1 MAN j 6 " pdb=" C2 MAN j 6 " ideal model delta sigma weight residual 1.526 1.593 -0.067 2.00e-02 2.50e+03 1.12e+01 bond pdb=" C1 MAN I 6 " pdb=" C2 MAN I 6 " ideal model delta sigma weight residual 1.526 1.590 -0.064 2.00e-02 2.50e+03 1.03e+01 bond pdb=" C3 MAN i 4 " pdb=" O3 MAN i 4 " ideal model delta sigma weight residual 1.408 1.472 -0.064 2.00e-02 2.50e+03 1.02e+01 ... (remaining 23318 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.37: 30911 3.37 - 6.75: 706 6.75 - 10.12: 69 10.12 - 13.50: 12 13.50 - 16.87: 6 Bond angle restraints: 31704 Sorted by residual: angle pdb=" N ASN F 332 " pdb=" CA ASN F 332 " pdb=" C ASN F 332 " ideal model delta sigma weight residual 111.02 119.54 -8.52 1.25e+00 6.40e-01 4.64e+01 angle pdb=" C GLU D 411 " pdb=" N GLN D 412 " pdb=" CA GLN D 412 " ideal model delta sigma weight residual 121.54 133.48 -11.94 1.91e+00 2.74e-01 3.91e+01 angle pdb=" C PRO D 407 " pdb=" N THR D 408 " pdb=" CA THR D 408 " ideal model delta sigma weight residual 121.54 132.44 -10.90 1.91e+00 2.74e-01 3.25e+01 angle pdb=" CA LEU F 116 " pdb=" CB LEU F 116 " pdb=" CG LEU F 116 " ideal model delta sigma weight residual 116.30 133.17 -16.87 3.50e+00 8.16e-02 2.32e+01 angle pdb=" C PRO F 407 " pdb=" N THR F 408 " pdb=" CA THR F 408 " ideal model delta sigma weight residual 126.45 134.87 -8.42 1.77e+00 3.19e-01 2.26e+01 ... (remaining 31699 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.22: 11991 16.22 - 32.43: 547 32.43 - 48.65: 144 48.65 - 64.87: 15 64.87 - 81.08: 16 Dihedral angle restraints: 12713 sinusoidal: 5085 harmonic: 7628 Sorted by residual: dihedral pdb=" CA ASP O 101 " pdb=" C ASP O 101 " pdb=" N PRO O 102 " pdb=" CA PRO O 102 " ideal model delta harmonic sigma weight residual -180.00 -119.65 -60.35 0 5.00e+00 4.00e-02 1.46e+02 dihedral pdb=" CA ASP Q 101 " pdb=" C ASP Q 101 " pdb=" N PRO Q 102 " pdb=" CA PRO Q 102 " ideal model delta harmonic sigma weight residual -180.00 -119.68 -60.32 0 5.00e+00 4.00e-02 1.46e+02 dihedral pdb=" CA ASP M 101 " pdb=" C ASP M 101 " pdb=" N PRO M 102 " pdb=" CA PRO M 102 " ideal model delta harmonic sigma weight residual -180.00 -119.69 -60.31 0 5.00e+00 4.00e-02 1.45e+02 ... (remaining 12710 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.259: 3971 0.259 - 0.518: 25 0.518 - 0.777: 3 0.777 - 1.036: 1 1.036 - 1.295: 2 Chirality restraints: 4002 Sorted by residual: chirality pdb=" C1 NAG U 1 " pdb=" ND2 ASN D 392 " pdb=" C2 NAG U 1 " pdb=" O5 NAG U 1 " both_signs ideal model delta sigma weight residual False -2.40 -1.11 -1.29 2.00e-01 2.50e+01 4.19e+01 chirality pdb=" C1 NAG c 1 " pdb=" ND2 ASN E 392 " pdb=" C2 NAG c 1 " pdb=" O5 NAG c 1 " both_signs ideal model delta sigma weight residual False -2.40 -1.19 -1.21 2.00e-01 2.50e+01 3.64e+01 chirality pdb=" C1 NAG e 1 " pdb=" ND2 ASN E 386 " pdb=" C2 NAG e 1 " pdb=" O5 NAG e 1 " both_signs ideal model delta sigma weight residual False -2.40 -1.58 -0.82 2.00e-01 2.50e+01 1.70e+01 ... (remaining 3999 not shown) Planarity restraints: 3887 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C2 NAG r 2 " -0.040 2.00e-02 2.50e+03 3.32e-02 1.37e+01 pdb=" C7 NAG r 2 " 0.007 2.00e-02 2.50e+03 pdb=" C8 NAG r 2 " -0.029 2.00e-02 2.50e+03 pdb=" N2 NAG r 2 " 0.054 2.00e-02 2.50e+03 pdb=" O7 NAG r 2 " 0.009 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ASP M 101 " 0.055 5.00e-02 4.00e+02 8.45e-02 1.14e+01 pdb=" N PRO M 102 " -0.146 5.00e-02 4.00e+02 pdb=" CA PRO M 102 " 0.045 5.00e-02 4.00e+02 pdb=" CD PRO M 102 " 0.046 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASP O 101 " -0.055 5.00e-02 4.00e+02 8.44e-02 1.14e+01 pdb=" N PRO O 102 " 0.146 5.00e-02 4.00e+02 pdb=" CA PRO O 102 " -0.045 5.00e-02 4.00e+02 pdb=" CD PRO O 102 " -0.046 5.00e-02 4.00e+02 ... (remaining 3884 not shown) Histogram of nonbonded interaction distances: 2.22 - 2.76: 3110 2.76 - 3.29: 19609 3.29 - 3.83: 34443 3.83 - 4.36: 39237 4.36 - 4.90: 69517 Nonbonded interactions: 165916 Sorted by model distance: nonbonded pdb=" O TRP F 69 " pdb=" OG1 THR F 71 " model vdw 2.222 3.040 nonbonded pdb=" O TRP E 69 " pdb=" OG1 THR E 71 " model vdw 2.245 3.040 nonbonded pdb=" OD1 ASP Q 100B" pdb=" O6 NAG s 1 " model vdw 2.258 3.040 nonbonded pdb=" OG SER D 447 " pdb=" O7 NAG H 1 " model vdw 2.276 3.040 nonbonded pdb=" O PRO E 369 " pdb=" OG1 THR E 373 " model vdw 2.294 3.040 ... (remaining 165911 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 'B' selection = chain 'C' } ncs_group { reference = (chain 'D' and (resid 32 through 137 or (resid 138 and (name N or name CA or nam \ e C or name O or name CB )) or resid 152 through 649)) selection = chain 'E' selection = (chain 'F' and (resid 32 through 137 or (resid 138 and (name N or name CA or nam \ e C or name O or name CB )) or resid 152 through 639)) } ncs_group { reference = (chain 'G' and resid 5 through 8) selection = (chain 'H' and resid 6 through 9) selection = (chain 'I' and resid 4 through 7) selection = (chain 'Z' and resid 4 through 7) selection = (chain 'g' and resid 4 through 7) selection = (chain 'i' and resid 4 through 7) selection = (chain 'j' and resid 4 through 7) selection = (chain 'r' and resid 6 through 9) selection = (chain 's' and resid 6 through 9) } ncs_group { reference = chain 'J' selection = chain 'T' selection = chain 'V' selection = chain 'W' selection = chain 'X' selection = chain 'Y' selection = chain 'b' selection = chain 'd' selection = chain 'e' selection = chain 'f' selection = chain 'k' selection = chain 'm' selection = chain 'o' selection = chain 'p' selection = chain 'q' } ncs_group { reference = chain 'M' selection = chain 'O' selection = chain 'Q' } ncs_group { reference = chain 'N' selection = chain 'P' selection = chain 'R' } ncs_group { reference = chain 'S' selection = chain 'U' selection = chain 'a' selection = chain 'c' selection = chain 'l' selection = chain 'n' } 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 individual isotropic 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: 1.440 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.410 Check model and map are aligned: 0.070 Set scattering table: 0.060 Process input model: 22.500 Find NCS groups from input model: 0.670 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: 0.000 Load rotamer database and sin/cos tables:1.020 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 26.270 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8118 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 : 0.009 0.090 23510 Z= 0.409 Angle : 1.343 20.086 32229 Z= 0.635 Chirality : 0.079 1.295 4002 Planarity : 0.008 0.085 3823 Dihedral : 10.602 81.081 7736 Min Nonbonded Distance : 2.222 Molprobity Statistics. All-atom Clashscore : 3.72 Ramachandran Plot: Outliers : 0.31 % Allowed : 11.09 % Favored : 88.60 % Rotamer: Outliers : 0.57 % Allowed : 2.62 % Favored : 96.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.40 % Cis-general : 0.00 % Twisted Proline : 2.40 % Twisted General : 0.48 % 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: -3.85 (0.14), residues: 2614 helix: -2.87 (0.21), residues: 301 sheet: -1.54 (0.17), residues: 835 loop : -3.23 (0.13), residues: 1478 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.021 0.001 ARG F 273 TYR 0.033 0.003 TYR M 52 PHE 0.035 0.005 PHE O 100A TRP 0.036 0.004 TRP Q 103 HIS 0.012 0.002 HIS M 100G Details of bonding type rmsd/Z covalent geometry : bond 0.00914 / 0.41 (23323) covalent geometry : angle 1.22786 / 0.61 (31704) SS BOND : bond 0.00696 / 0.46 ( 27) SS BOND : angle 1.74095 / 1.25 ( 54) hydrogen bonds : bond 0.18872 / 12.50 ( 555) hydrogen bonds : angle 7.81313 / 5.52 ( 1470) Misc. bond : bond 0.00725 / 0.36 ( 3) link_ALPHA1-2 : bond 0.01049 / 0.52 ( 6) link_ALPHA1-2 : angle 3.45395 / 2.03 ( 18) link_ALPHA1-3 : bond 0.00682 / 0.39 ( 22) link_ALPHA1-3 : angle 3.32936 / 2.07 ( 66) link_ALPHA1-6 : bond 0.01569 / 0.88 ( 18) link_ALPHA1-6 : angle 3.09388 / 2.21 ( 54) link_BETA1-4 : bond 0.01161 / 0.67 ( 47) link_BETA1-4 : angle 4.41800 / 2.72 ( 141) link_NAG-ASN : bond 0.00654 / 0.45 ( 64) link_NAG-ASN : angle 5.55299 / 3.79 ( 192) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5228 Ramachandran restraints generated. 2614 Oldfield, 0 Emsley, 2614 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5228 Ramachandran restraints generated. 2614 Oldfield, 0 Emsley, 2614 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 615 residues out of total 2301 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 602 time to evaluate : 0.829 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 647 GLU cc_start: 0.8091 (tm-30) cc_final: 0.7757 (tt0) REVERT: D 78 ASP cc_start: 0.7965 (t70) cc_final: 0.7311 (t0) REVERT: E 80 ASN cc_start: 0.7723 (m-40) cc_final: 0.7480 (p0) REVERT: E 432 LYS cc_start: 0.7791 (mmtt) cc_final: 0.7384 (tttm) REVERT: F 78 ASP cc_start: 0.7460 (t70) cc_final: 0.7092 (t0) REVERT: F 325 ASN cc_start: 0.7869 (m-40) cc_final: 0.7654 (m-40) REVERT: F 358 ILE cc_start: 0.8421 (OUTLIER) cc_final: 0.8151 (pp) REVERT: F 432 LYS cc_start: 0.7727 (mmtt) cc_final: 0.7182 (ptmm) REVERT: F 443 ILE cc_start: 0.8523 (mm) cc_final: 0.8138 (mm) REVERT: K 81 LYS cc_start: 0.7910 (mmtp) cc_final: 0.7666 (tmtt) REVERT: K 99 GLN cc_start: 0.6985 (tt0) cc_final: 0.6738 (tt0) REVERT: L 34 GLN cc_start: 0.7396 (mp-120) cc_final: 0.6928 (mp10) REVERT: L 35 TRP cc_start: 0.7515 (m100) cc_final: 0.7010 (m100) REVERT: L 49 TYR cc_start: 0.7255 (p90) cc_final: 0.6867 (p90) REVERT: N 53 THR cc_start: 0.7902 (m) cc_final: 0.7502 (p) REVERT: O 36 TRP cc_start: 0.7722 (m100) cc_final: 0.7502 (m100) REVERT: P 48 LEU cc_start: 0.7009 (tp) cc_final: 0.6797 (tp) REVERT: Q 5 GLN cc_start: 0.6546 (tt0) cc_final: 0.6225 (pp30) REVERT: R 45 ARG cc_start: 0.6264 (ptt180) cc_final: 0.6011 (mtp180) REVERT: R 53 THR cc_start: 0.7125 (m) cc_final: 0.6908 (p) REVERT: R 63 ILE cc_start: 0.6996 (mt) cc_final: 0.6464 (mt) REVERT: R 65 SER cc_start: 0.8090 (p) cc_final: 0.7770 (m) outliers start: 13 outliers final: 1 residues processed: 613 average time/residue: 0.1856 time to fit residues: 168.9783 Evaluate side-chains 343 residues out of total 2301 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 341 time to evaluate : 0.838 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 98 ASN Chi-restraints excluded: chain F residue 358 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 260 random chunks: chunk 197 optimal weight: 6.9990 chunk 215 optimal weight: 3.9990 chunk 20 optimal weight: 1.9990 chunk 132 optimal weight: 2.9990 chunk 248 optimal weight: 1.9990 chunk 207 optimal weight: 8.9990 chunk 155 optimal weight: 5.9990 chunk 244 optimal weight: 10.0000 chunk 183 optimal weight: 9.9990 chunk 111 optimal weight: 0.8980 chunk 258 optimal weight: 10.0000 overall best weight: 2.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 577 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 650 GLN A 658 GLN B 650 GLN ** C 577 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 656 ASN D 98 ASN D 114 GLN D 397 ASN E 66 HIS E 98 ASN E 114 GLN E 397 ASN E 417 GLN F 98 ASN F 114 GLN F 397 ASN L 42 GLN L 66CASN ** R 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3957 r_free = 0.3957 target = 0.161686 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3426 r_free = 0.3426 target = 0.116657 restraints weight = 34578.703| |-----------------------------------------------------------------------------| r_work (start): 0.3393 rms_B_bonded: 2.99 r_work: 0.3198 rms_B_bonded: 3.16 restraints_weight: 0.5000 r_work (final): 0.3198 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8363 moved from start: 0.2211 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.061 23510 Z= 0.200 Angle : 0.960 17.759 32229 Z= 0.441 Chirality : 0.056 0.730 4002 Planarity : 0.006 0.088 3823 Dihedral : 6.917 49.648 2869 Min Nonbonded Distance : 2.338 Molprobity Statistics. All-atom Clashscore : 6.45 Ramachandran Plot: Outliers : 0.15 % Allowed : 9.14 % Favored : 90.70 % Rotamer: Outliers : 2.53 % Allowed : 10.37 % Favored : 87.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.40 % Cis-general : 0.00 % Twisted Proline : 2.40 % Twisted General : 0.28 % 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: -3.13 (0.15), residues: 2614 helix: -1.41 (0.27), residues: 336 sheet: -1.02 (0.19), residues: 810 loop : -3.00 (0.13), residues: 1468 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG L 31 TYR 0.022 0.002 TYR M 52 PHE 0.031 0.002 PHE P 71 TRP 0.030 0.002 TRP E 395 HIS 0.006 0.002 HIS C 641 Details of bonding type rmsd/Z covalent geometry : bond 0.00463 / 0.20 (23323) covalent geometry : angle 0.86034 / 0.42 (31704) SS BOND : bond 0.00804 / 0.37 ( 27) SS BOND : angle 2.01204 / 1.35 ( 54) hydrogen bonds : bond 0.05673 / 3.78 ( 555) hydrogen bonds : angle 6.20547 / 4.35 ( 1470) Misc. bond : bond 0.00230 / 0.11 ( 3) link_ALPHA1-2 : bond 0.00741 / 0.39 ( 6) link_ALPHA1-2 : angle 2.34619 / 1.37 ( 18) link_ALPHA1-3 : bond 0.00559 / 0.35 ( 22) link_ALPHA1-3 : angle 2.44644 / 1.48 ( 66) link_ALPHA1-6 : bond 0.00972 / 0.57 ( 18) link_ALPHA1-6 : angle 2.15244 / 1.52 ( 54) link_BETA1-4 : bond 0.00783 / 0.47 ( 47) link_BETA1-4 : angle 2.90286 / 1.79 ( 141) link_NAG-ASN : bond 0.00763 / 0.54 ( 64) link_NAG-ASN : angle 4.62367 / 3.21 ( 192) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5228 Ramachandran restraints generated. 2614 Oldfield, 0 Emsley, 2614 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5228 Ramachandran restraints generated. 2614 Oldfield, 0 Emsley, 2614 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 427 residues out of total 2301 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 369 time to evaluate : 0.856 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 650 GLN cc_start: 0.4787 (OUTLIER) cc_final: 0.3926 (tm-30) REVERT: C 647 GLU cc_start: 0.8725 (tm-30) cc_final: 0.8146 (tt0) REVERT: D 104 MET cc_start: 0.9164 (ttt) cc_final: 0.8853 (ttt) REVERT: D 208 VAL cc_start: 0.8570 (OUTLIER) cc_final: 0.8315 (t) REVERT: E 80 ASN cc_start: 0.7928 (m-40) cc_final: 0.7477 (p0) REVERT: E 213 ILE cc_start: 0.8940 (pt) cc_final: 0.8716 (mt) REVERT: E 432 LYS cc_start: 0.8039 (mmtt) cc_final: 0.7557 (tttm) REVERT: F 78 ASP cc_start: 0.7773 (t70) cc_final: 0.7371 (t0) REVERT: F 325 ASN cc_start: 0.8198 (m-40) cc_final: 0.7850 (m-40) REVERT: F 432 LYS cc_start: 0.7863 (mmtt) cc_final: 0.7047 (ptmm) REVERT: K 81 LYS cc_start: 0.8093 (mmtp) cc_final: 0.7754 (tmtt) REVERT: L 34 GLN cc_start: 0.7429 (mp-120) cc_final: 0.6810 (mp10) REVERT: L 35 TRP cc_start: 0.7404 (m100) cc_final: 0.6845 (m100) REVERT: L 49 TYR cc_start: 0.7064 (p90) cc_final: 0.6549 (p90) REVERT: L 50 ASN cc_start: 0.7711 (t0) cc_final: 0.7006 (t0) REVERT: M 109 VAL cc_start: 0.7810 (t) cc_final: 0.7499 (p) REVERT: N 35 TRP cc_start: 0.7900 (m100) cc_final: 0.7477 (m100) REVERT: N 69 ARG cc_start: 0.7664 (mtp180) cc_final: 0.7355 (mtp180) REVERT: O 36 TRP cc_start: 0.7903 (m100) cc_final: 0.7537 (m100) REVERT: O 43 LYS cc_start: 0.7421 (mtmm) cc_final: 0.6311 (pttp) REVERT: O 47 TRP cc_start: 0.7773 (t60) cc_final: 0.7161 (t60) REVERT: P 24 ARG cc_start: 0.7333 (ttt90) cc_final: 0.6668 (ttm-80) REVERT: P 69 ARG cc_start: 0.7124 (ptp-170) cc_final: 0.6883 (ptp-110) REVERT: Q 5 GLN cc_start: 0.6419 (tt0) cc_final: 0.5927 (pp30) REVERT: R 45 ARG cc_start: 0.6164 (ptt180) cc_final: 0.5689 (ptt-90) REVERT: R 54 ARG cc_start: 0.7491 (ttm170) cc_final: 0.7189 (ttm170) REVERT: R 69 ARG cc_start: 0.6907 (ptp90) cc_final: 0.6686 (ptp-170) outliers start: 58 outliers final: 28 residues processed: 408 average time/residue: 0.1805 time to fit residues: 110.3684 Evaluate side-chains 355 residues out of total 2301 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 325 time to evaluate : 0.812 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 650 GLN Chi-restraints excluded: chain B residue 613 SER Chi-restraints excluded: chain C residue 613 SER Chi-restraints excluded: chain C residue 644 THR Chi-restraints excluded: chain D residue 96 TRP Chi-restraints excluded: chain D residue 112 TRP Chi-restraints excluded: chain D residue 126 CYS Chi-restraints excluded: chain D residue 208 VAL Chi-restraints excluded: chain D residue 236 SER Chi-restraints excluded: chain D residue 331 CYS Chi-restraints excluded: chain D residue 424 ILE Chi-restraints excluded: chain E residue 88 ASN Chi-restraints excluded: chain E residue 112 TRP Chi-restraints excluded: chain E residue 116 LEU Chi-restraints excluded: chain E residue 165 ILE Chi-restraints excluded: chain E residue 424 ILE Chi-restraints excluded: chain F residue 96 TRP Chi-restraints excluded: chain F residue 191 TYR Chi-restraints excluded: chain K residue 73 THR Chi-restraints excluded: chain K residue 83 THR Chi-restraints excluded: chain M residue 100 PHE Chi-restraints excluded: chain N residue 74 THR Chi-restraints excluded: chain O residue 100 PHE Chi-restraints excluded: chain P residue 10 THR Chi-restraints excluded: chain P residue 27 SER Chi-restraints excluded: chain Q residue 19 SER Chi-restraints excluded: chain Q residue 28 SER Chi-restraints excluded: chain Q residue 100 PHE Chi-restraints excluded: chain Q residue 100 ASP Chi-restraints excluded: chain R residue 33 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 260 random chunks: chunk 131 optimal weight: 0.1980 chunk 20 optimal weight: 1.9990 chunk 9 optimal weight: 5.9990 chunk 219 optimal weight: 1.9990 chunk 85 optimal weight: 0.7980 chunk 28 optimal weight: 7.9990 chunk 258 optimal weight: 9.9990 chunk 242 optimal weight: 0.9980 chunk 175 optimal weight: 6.9990 chunk 253 optimal weight: 6.9990 chunk 164 optimal weight: 10.0000 overall best weight: 1.1984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 650 GLN ** C 577 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 80 ASN D 132 ASN E 72 HIS E 425 ASN L 42 GLN ** R 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3973 r_free = 0.3973 target = 0.163084 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3520 r_free = 0.3520 target = 0.123873 restraints weight = 34500.197| |-----------------------------------------------------------------------------| r_work (start): 0.3492 rms_B_bonded: 4.04 r_work: 0.3177 rms_B_bonded: 3.77 restraints_weight: 0.5000 r_work (final): 0.3177 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8368 moved from start: 0.2570 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.057 23510 Z= 0.143 Angle : 0.841 16.813 32229 Z= 0.385 Chirality : 0.051 0.615 4002 Planarity : 0.005 0.086 3823 Dihedral : 6.252 47.638 2865 Min Nonbonded Distance : 2.367 Molprobity Statistics. All-atom Clashscore : 6.41 Ramachandran Plot: Outliers : 0.11 % Allowed : 8.99 % Favored : 90.90 % Rotamer: Outliers : 2.79 % Allowed : 12.16 % Favored : 85.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.40 % Cis-general : 0.00 % Twisted Proline : 2.40 % Twisted General : 0.20 % 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: -2.66 (0.15), residues: 2614 helix: -0.50 (0.30), residues: 313 sheet: -0.73 (0.19), residues: 801 loop : -2.78 (0.13), residues: 1500 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG L 31 TYR 0.017 0.001 TYR Q 52 PHE 0.022 0.002 PHE P 71 TRP 0.016 0.001 TRP A 628 HIS 0.007 0.001 HIS L 38 Details of bonding type rmsd/Z covalent geometry : bond 0.00313 / 0.14 (23323) covalent geometry : angle 0.75171 / 0.36 (31704) SS BOND : bond 0.00369 / 0.22 ( 27) SS BOND : angle 1.50137 / 0.94 ( 54) hydrogen bonds : bond 0.04681 / 3.12 ( 555) hydrogen bonds : angle 5.69730 / 4.00 ( 1470) Misc. bond : bond 0.00354 / 0.18 ( 3) link_ALPHA1-2 : bond 0.00879 / 0.46 ( 6) link_ALPHA1-2 : angle 2.30207 / 1.34 ( 18) link_ALPHA1-3 : bond 0.00632 / 0.40 ( 22) link_ALPHA1-3 : angle 2.27596 / 1.38 ( 66) link_ALPHA1-6 : bond 0.00950 / 0.56 ( 18) link_ALPHA1-6 : angle 2.01527 / 1.43 ( 54) link_BETA1-4 : bond 0.00701 / 0.42 ( 47) link_BETA1-4 : angle 2.66476 / 1.64 ( 141) link_NAG-ASN : bond 0.00421 / 0.29 ( 64) link_NAG-ASN : angle 4.00384 / 2.70 ( 192) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5228 Ramachandran restraints generated. 2614 Oldfield, 0 Emsley, 2614 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5228 Ramachandran restraints generated. 2614 Oldfield, 0 Emsley, 2614 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 419 residues out of total 2301 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 355 time to evaluate : 0.844 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 650 GLN cc_start: 0.5078 (OUTLIER) cc_final: 0.4227 (tm-30) REVERT: A 659 GLU cc_start: 0.8158 (tt0) cc_final: 0.7942 (tt0) REVERT: C 647 GLU cc_start: 0.8860 (tm-30) cc_final: 0.8232 (tt0) REVERT: D 104 MET cc_start: 0.9167 (ttt) cc_final: 0.8797 (ttt) REVERT: E 80 ASN cc_start: 0.7965 (m-40) cc_final: 0.7542 (p0) REVERT: E 432 LYS cc_start: 0.8074 (mmtt) cc_final: 0.7608 (tttm) REVERT: F 78 ASP cc_start: 0.7858 (t70) cc_final: 0.7457 (t0) REVERT: F 432 LYS cc_start: 0.7863 (mmtt) cc_final: 0.7092 (ptmm) REVERT: K 81 LYS cc_start: 0.8177 (mmtp) cc_final: 0.7801 (tmtt) REVERT: K 100 VAL cc_start: 0.8779 (OUTLIER) cc_final: 0.8522 (t) REVERT: L 34 GLN cc_start: 0.7415 (mp-120) cc_final: 0.6822 (mp10) REVERT: L 35 TRP cc_start: 0.7328 (m100) cc_final: 0.6766 (m100) REVERT: L 50 ASN cc_start: 0.7646 (t0) cc_final: 0.6907 (t0) REVERT: M 109 VAL cc_start: 0.7865 (t) cc_final: 0.7577 (p) REVERT: N 35 TRP cc_start: 0.7908 (m100) cc_final: 0.7589 (m100) REVERT: N 42 GLN cc_start: 0.6734 (tp40) cc_final: 0.5768 (mt0) REVERT: N 100 LYS cc_start: 0.7663 (tttt) cc_final: 0.6772 (mttp) REVERT: O 36 TRP cc_start: 0.7838 (m100) cc_final: 0.7609 (m100) REVERT: O 47 TRP cc_start: 0.7709 (t60) cc_final: 0.7176 (t60) REVERT: P 24 ARG cc_start: 0.7286 (ttt90) cc_final: 0.6908 (ttm-80) REVERT: Q 5 GLN cc_start: 0.6539 (tt0) cc_final: 0.6100 (pp30) REVERT: R 45 ARG cc_start: 0.6188 (ptt180) cc_final: 0.5717 (ptt-90) REVERT: R 60 ASP cc_start: 0.7079 (t0) cc_final: 0.6507 (t0) REVERT: R 99 THR cc_start: 0.5900 (m) cc_final: 0.5463 (m) outliers start: 64 outliers final: 37 residues processed: 400 average time/residue: 0.1682 time to fit residues: 102.0506 Evaluate side-chains 363 residues out of total 2301 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 324 time to evaluate : 0.865 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 650 GLN Chi-restraints excluded: chain B residue 612 ASP Chi-restraints excluded: chain B residue 613 SER Chi-restraints excluded: chain B residue 644 THR Chi-restraints excluded: chain B residue 650 GLN Chi-restraints excluded: chain B residue 664 ASP Chi-restraints excluded: chain D residue 96 TRP Chi-restraints excluded: chain D residue 112 TRP Chi-restraints excluded: chain D residue 126 CYS Chi-restraints excluded: chain D residue 189 THR Chi-restraints excluded: chain D residue 208 VAL Chi-restraints excluded: chain D residue 244 THR Chi-restraints excluded: chain D residue 424 ILE Chi-restraints excluded: chain E residue 88 ASN Chi-restraints excluded: chain E residue 112 TRP Chi-restraints excluded: chain E residue 116 LEU Chi-restraints excluded: chain E residue 165 ILE Chi-restraints excluded: chain E residue 208 VAL Chi-restraints excluded: chain E residue 209 SER Chi-restraints excluded: chain E residue 236 SER Chi-restraints excluded: chain E residue 424 ILE Chi-restraints excluded: chain E residue 425 ASN Chi-restraints excluded: chain E residue 452 LEU Chi-restraints excluded: chain F residue 89 VAL Chi-restraints excluded: chain F residue 96 TRP Chi-restraints excluded: chain F residue 191 TYR Chi-restraints excluded: chain F residue 365 SER Chi-restraints excluded: chain K residue 73 THR Chi-restraints excluded: chain K residue 83 THR Chi-restraints excluded: chain K residue 100 VAL Chi-restraints excluded: chain M residue 100 PHE Chi-restraints excluded: chain M residue 100 ASP Chi-restraints excluded: chain N residue 53 THR Chi-restraints excluded: chain O residue 100 PHE Chi-restraints excluded: chain P residue 10 THR Chi-restraints excluded: chain P residue 88 CYS Chi-restraints excluded: chain Q residue 19 SER Chi-restraints excluded: chain Q residue 28 SER Chi-restraints excluded: chain Q residue 100 PHE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 260 random chunks: chunk 81 optimal weight: 2.9990 chunk 118 optimal weight: 5.9990 chunk 123 optimal weight: 6.9990 chunk 22 optimal weight: 8.9990 chunk 240 optimal weight: 6.9990 chunk 120 optimal weight: 0.9980 chunk 241 optimal weight: 5.9990 chunk 189 optimal weight: 10.0000 chunk 224 optimal weight: 10.0000 chunk 237 optimal weight: 20.0000 chunk 222 optimal weight: 20.0000 overall best weight: 4.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 650 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 577 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 650 GLN D 374 HIS E 308 HIS E 374 HIS L 42 GLN P 6 GLN ** P 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 6 GLN ** R 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3891 r_free = 0.3891 target = 0.156098 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3353 r_free = 0.3353 target = 0.111667 restraints weight = 34712.523| |-----------------------------------------------------------------------------| r_work (start): 0.3327 rms_B_bonded: 3.02 r_work: 0.3101 rms_B_bonded: 3.16 restraints_weight: 0.5000 r_work (final): 0.3101 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8470 moved from start: 0.3005 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.089 23510 Z= 0.312 Angle : 1.039 19.881 32229 Z= 0.479 Chirality : 0.059 0.716 4002 Planarity : 0.006 0.090 3823 Dihedral : 6.707 46.506 2865 Min Nonbonded Distance : 2.279 Molprobity Statistics. All-atom Clashscore : 6.99 Ramachandran Plot: Outliers : 0.15 % Allowed : 11.59 % Favored : 88.26 % Rotamer: Outliers : 4.23 % Allowed : 12.64 % Favored : 83.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.40 % Cis-general : 0.00 % Twisted Proline : 2.40 % Twisted General : 0.16 % 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: -2.69 (0.15), residues: 2614 helix: -0.75 (0.28), residues: 330 sheet: -0.83 (0.19), residues: 815 loop : -2.72 (0.14), residues: 1469 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG D 480 TYR 0.030 0.002 TYR E 39 PHE 0.031 0.003 PHE M 100A TRP 0.024 0.002 TRP D 112 HIS 0.008 0.003 HIS F 330 Details of bonding type rmsd/Z covalent geometry : bond 0.00769 / 0.31 (23323) covalent geometry : angle 0.94990 / 0.46 (31704) SS BOND : bond 0.00602 / 0.33 ( 27) SS BOND : angle 2.15161 / 1.31 ( 54) hydrogen bonds : bond 0.06232 / 4.15 ( 555) hydrogen bonds : angle 5.84930 / 4.14 ( 1470) Misc. bond : bond 0.00691 / 0.35 ( 3) link_ALPHA1-2 : bond 0.00851 / 0.44 ( 6) link_ALPHA1-2 : angle 2.29573 / 1.34 ( 18) link_ALPHA1-3 : bond 0.00611 / 0.36 ( 22) link_ALPHA1-3 : angle 2.53165 / 1.57 ( 66) link_ALPHA1-6 : bond 0.00934 / 0.53 ( 18) link_ALPHA1-6 : angle 2.21190 / 1.55 ( 54) link_BETA1-4 : bond 0.00738 / 0.44 ( 47) link_BETA1-4 : angle 2.99873 / 1.84 ( 141) link_NAG-ASN : bond 0.00642 / 0.43 ( 64) link_NAG-ASN : angle 4.50559 / 2.96 ( 192) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5228 Ramachandran restraints generated. 2614 Oldfield, 0 Emsley, 2614 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5228 Ramachandran restraints generated. 2614 Oldfield, 0 Emsley, 2614 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 419 residues out of total 2301 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 97 poor density : 322 time to evaluate : 0.865 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 599 SER cc_start: 0.8838 (p) cc_final: 0.8572 (t) REVERT: D 104 MET cc_start: 0.9207 (ttt) cc_final: 0.8828 (ttt) REVERT: E 80 ASN cc_start: 0.8121 (m-40) cc_final: 0.7730 (p0) REVERT: E 113 ASP cc_start: 0.8531 (m-30) cc_final: 0.8318 (m-30) REVERT: E 396 ASN cc_start: 0.5877 (OUTLIER) cc_final: 0.5654 (p0) REVERT: E 432 LYS cc_start: 0.8093 (mmtt) cc_final: 0.7706 (tttm) REVERT: F 78 ASP cc_start: 0.7820 (t70) cc_final: 0.7438 (t0) REVERT: F 176 PHE cc_start: 0.8495 (OUTLIER) cc_final: 0.7906 (p90) REVERT: F 432 LYS cc_start: 0.7913 (mmtt) cc_final: 0.7190 (ptmm) REVERT: K 81 LYS cc_start: 0.8228 (mmtp) cc_final: 0.7784 (tmtt) REVERT: L 34 GLN cc_start: 0.7577 (mp-120) cc_final: 0.7043 (mp10) REVERT: L 35 TRP cc_start: 0.7470 (m100) cc_final: 0.6903 (m100) REVERT: L 49 TYR cc_start: 0.6558 (p90) cc_final: 0.6311 (p90) REVERT: M 64 ARG cc_start: 0.7372 (ttm110) cc_final: 0.7132 (tpt90) REVERT: M 109 VAL cc_start: 0.7787 (t) cc_final: 0.7509 (p) REVERT: N 42 GLN cc_start: 0.6498 (tp40) cc_final: 0.5601 (mt0) REVERT: N 100 LYS cc_start: 0.7618 (tttt) cc_final: 0.6765 (mttp) REVERT: O 36 TRP cc_start: 0.7925 (m100) cc_final: 0.7637 (m100) REVERT: O 47 TRP cc_start: 0.7976 (t60) cc_final: 0.7503 (t60) REVERT: O 72 ASP cc_start: 0.8211 (t0) cc_final: 0.7922 (t0) REVERT: P 37 GLN cc_start: 0.7273 (tt0) cc_final: 0.6865 (tt0) REVERT: Q 5 GLN cc_start: 0.6574 (tt0) cc_final: 0.6244 (pp30) REVERT: Q 23 ARG cc_start: 0.8162 (tpt-90) cc_final: 0.7694 (tpt90) REVERT: R 45 ARG cc_start: 0.6395 (ptt180) cc_final: 0.5969 (ptt-90) outliers start: 97 outliers final: 65 residues processed: 394 average time/residue: 0.1733 time to fit residues: 103.8786 Evaluate side-chains 374 residues out of total 2301 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 307 time to evaluate : 0.813 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 613 SER Chi-restraints excluded: chain B residue 622 ILE Chi-restraints excluded: chain B residue 644 THR Chi-restraints excluded: chain B residue 664 ASP Chi-restraints excluded: chain C residue 528 SER Chi-restraints excluded: chain C residue 613 SER Chi-restraints excluded: chain C residue 644 THR Chi-restraints excluded: chain D residue 96 TRP Chi-restraints excluded: chain D residue 112 TRP Chi-restraints excluded: chain D residue 176 PHE Chi-restraints excluded: chain D residue 189 THR Chi-restraints excluded: chain D residue 207 LYS Chi-restraints excluded: chain D residue 208 VAL Chi-restraints excluded: chain D residue 228 CYS Chi-restraints excluded: chain D residue 236 SER Chi-restraints excluded: chain D residue 244 THR Chi-restraints excluded: chain D residue 331 CYS Chi-restraints excluded: chain D residue 346 VAL Chi-restraints excluded: chain D residue 370 GLU Chi-restraints excluded: chain D residue 424 ILE Chi-restraints excluded: chain E residue 88 ASN Chi-restraints excluded: chain E residue 95 MET Chi-restraints excluded: chain E residue 112 TRP Chi-restraints excluded: chain E residue 116 LEU Chi-restraints excluded: chain E residue 165 ILE Chi-restraints excluded: chain E residue 191 TYR Chi-restraints excluded: chain E residue 209 SER Chi-restraints excluded: chain E residue 236 SER Chi-restraints excluded: chain E residue 346 VAL Chi-restraints excluded: chain E residue 396 ASN Chi-restraints excluded: chain E residue 424 ILE Chi-restraints excluded: chain E residue 452 LEU Chi-restraints excluded: chain F residue 89 VAL Chi-restraints excluded: chain F residue 96 TRP Chi-restraints excluded: chain F residue 176 PHE Chi-restraints excluded: chain F residue 184 LEU Chi-restraints excluded: chain F residue 191 TYR Chi-restraints excluded: chain F residue 198 THR Chi-restraints excluded: chain F residue 270 ILE Chi-restraints excluded: chain F residue 333 ILE Chi-restraints excluded: chain F residue 365 SER Chi-restraints excluded: chain F residue 386 ASN Chi-restraints excluded: chain K residue 83 THR Chi-restraints excluded: chain M residue 83 THR Chi-restraints excluded: chain M residue 100 PHE Chi-restraints excluded: chain M residue 100 ASP Chi-restraints excluded: chain N residue 20 THR Chi-restraints excluded: chain N residue 53 THR Chi-restraints excluded: chain N residue 74 THR Chi-restraints excluded: chain N residue 101 VAL Chi-restraints excluded: chain O residue 68 THR Chi-restraints excluded: chain O residue 82 VAL Chi-restraints excluded: chain O residue 100 PHE Chi-restraints excluded: chain O residue 100 ASP Chi-restraints excluded: chain P residue 10 THR Chi-restraints excluded: chain P residue 27 SER Chi-restraints excluded: chain P residue 95 LEU Chi-restraints excluded: chain Q residue 19 SER Chi-restraints excluded: chain Q residue 28 SER Chi-restraints excluded: chain Q residue 68 THR Chi-restraints excluded: chain Q residue 92 CYS Chi-restraints excluded: chain Q residue 95 LEU Chi-restraints excluded: chain Q residue 100 PHE Chi-restraints excluded: chain Q residue 100 ASP Chi-restraints excluded: chain R residue 5 THR Chi-restraints excluded: chain R residue 33 LEU Chi-restraints excluded: chain R residue 52 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 260 random chunks: chunk 143 optimal weight: 0.8980 chunk 85 optimal weight: 0.9980 chunk 242 optimal weight: 0.6980 chunk 116 optimal weight: 4.9990 chunk 126 optimal weight: 3.9990 chunk 189 optimal weight: 7.9990 chunk 95 optimal weight: 0.9980 chunk 97 optimal weight: 0.9990 chunk 36 optimal weight: 0.6980 chunk 167 optimal weight: 1.9990 chunk 71 optimal weight: 0.8980 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 650 GLN ** C 577 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 425 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3958 r_free = 0.3958 target = 0.161965 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3496 r_free = 0.3496 target = 0.122290 restraints weight = 34364.612| |-----------------------------------------------------------------------------| r_work (start): 0.3468 rms_B_bonded: 4.11 r_work: 0.3157 rms_B_bonded: 3.76 restraints_weight: 0.5000 r_work (final): 0.3157 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8393 moved from start: 0.3219 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.067 23510 Z= 0.135 Angle : 0.822 17.707 32229 Z= 0.376 Chirality : 0.052 0.627 4002 Planarity : 0.005 0.090 3823 Dihedral : 5.973 43.529 2865 Min Nonbonded Distance : 2.381 Molprobity Statistics. All-atom Clashscore : 6.43 Ramachandran Plot: Outliers : 0.15 % Allowed : 8.22 % Favored : 91.62 % Rotamer: Outliers : 2.83 % Allowed : 14.60 % Favored : 82.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.40 % Cis-general : 0.00 % Twisted Proline : 2.40 % Twisted General : 0.12 % 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: -2.40 (0.16), residues: 2614 helix: -0.27 (0.29), residues: 328 sheet: -0.54 (0.19), residues: 808 loop : -2.65 (0.14), residues: 1478 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG L 31 TYR 0.016 0.001 TYR E 191 PHE 0.020 0.002 PHE O 50 TRP 0.024 0.001 TRP F 395 HIS 0.003 0.001 HIS R 49 Details of bonding type rmsd/Z covalent geometry : bond 0.00284 / 0.13 (23323) covalent geometry : angle 0.73226 / 0.36 (31704) SS BOND : bond 0.00786 / 0.39 ( 27) SS BOND : angle 1.35083 / 0.89 ( 54) hydrogen bonds : bond 0.04252 / 2.84 ( 555) hydrogen bonds : angle 5.42129 / 3.84 ( 1470) Misc. bond : bond 0.00118 / 0.06 ( 3) link_ALPHA1-2 : bond 0.00806 / 0.42 ( 6) link_ALPHA1-2 : angle 2.18635 / 1.27 ( 18) link_ALPHA1-3 : bond 0.00614 / 0.39 ( 22) link_ALPHA1-3 : angle 2.12956 / 1.28 ( 66) link_ALPHA1-6 : bond 0.00930 / 0.54 ( 18) link_ALPHA1-6 : angle 1.92216 / 1.36 ( 54) link_BETA1-4 : bond 0.00655 / 0.38 ( 47) link_BETA1-4 : angle 2.48750 / 1.52 ( 141) link_NAG-ASN : bond 0.00708 / 0.45 ( 64) link_NAG-ASN : angle 4.10233 / 2.65 ( 192) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5228 Ramachandran restraints generated. 2614 Oldfield, 0 Emsley, 2614 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5228 Ramachandran restraints generated. 2614 Oldfield, 0 Emsley, 2614 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 406 residues out of total 2301 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 341 time to evaluate : 0.731 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: C 647 GLU cc_start: 0.8863 (tm-30) cc_final: 0.8376 (tt0) REVERT: D 104 MET cc_start: 0.9174 (ttt) cc_final: 0.8823 (ttt) REVERT: D 208 VAL cc_start: 0.8180 (OUTLIER) cc_final: 0.7945 (t) REVERT: E 80 ASN cc_start: 0.8128 (m-40) cc_final: 0.7512 (p0) REVERT: E 113 ASP cc_start: 0.8353 (m-30) cc_final: 0.8067 (m-30) REVERT: E 176 PHE cc_start: 0.8204 (OUTLIER) cc_final: 0.7302 (p90) REVERT: E 432 LYS cc_start: 0.8163 (mmtt) cc_final: 0.7777 (tttm) REVERT: F 78 ASP cc_start: 0.7874 (t70) cc_final: 0.7474 (t0) REVERT: F 432 LYS cc_start: 0.7833 (mmtt) cc_final: 0.7092 (ptmm) REVERT: K 81 LYS cc_start: 0.8295 (mmtp) cc_final: 0.7838 (tmtt) REVERT: L 31 ARG cc_start: 0.6422 (mmt90) cc_final: 0.5953 (tpp80) REVERT: L 34 GLN cc_start: 0.7443 (mp-120) cc_final: 0.7072 (mp10) REVERT: L 35 TRP cc_start: 0.7344 (m100) cc_final: 0.6758 (m100) REVERT: L 87 TYR cc_start: 0.6264 (m-80) cc_final: 0.5868 (m-80) REVERT: M 109 VAL cc_start: 0.7813 (t) cc_final: 0.7571 (p) REVERT: N 35 TRP cc_start: 0.7967 (m100) cc_final: 0.7642 (m100) REVERT: N 42 GLN cc_start: 0.6594 (tp40) cc_final: 0.5733 (mt0) REVERT: N 63 ILE cc_start: 0.8534 (mp) cc_final: 0.8327 (tt) REVERT: O 36 TRP cc_start: 0.7869 (m100) cc_final: 0.7610 (m100) REVERT: O 47 TRP cc_start: 0.7788 (t60) cc_final: 0.7474 (t60) REVERT: O 72 ASP cc_start: 0.8186 (t0) cc_final: 0.7884 (t0) REVERT: P 24 ARG cc_start: 0.7180 (ttt90) cc_final: 0.6861 (ttm-80) REVERT: Q 5 GLN cc_start: 0.6554 (tt0) cc_final: 0.6139 (pp30) REVERT: Q 23 ARG cc_start: 0.8167 (tpt-90) cc_final: 0.7785 (tpt90) REVERT: Q 91 TYR cc_start: 0.7668 (m-80) cc_final: 0.7103 (m-80) REVERT: R 45 ARG cc_start: 0.6348 (ptt180) cc_final: 0.5941 (ptt-90) REVERT: R 69 ARG cc_start: 0.6612 (ttm110) cc_final: 0.6314 (ttm110) outliers start: 65 outliers final: 41 residues processed: 389 average time/residue: 0.1732 time to fit residues: 102.3665 Evaluate side-chains 364 residues out of total 2301 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 321 time to evaluate : 0.817 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 612 ASP Chi-restraints excluded: chain B residue 612 ASP Chi-restraints excluded: chain B residue 613 SER Chi-restraints excluded: chain B residue 650 GLN Chi-restraints excluded: chain B residue 664 ASP Chi-restraints excluded: chain C residue 618 THR Chi-restraints excluded: chain D residue 96 TRP Chi-restraints excluded: chain D residue 112 TRP Chi-restraints excluded: chain D residue 208 VAL Chi-restraints excluded: chain D residue 244 THR Chi-restraints excluded: chain D residue 331 CYS Chi-restraints excluded: chain D residue 346 VAL Chi-restraints excluded: chain D residue 370 GLU Chi-restraints excluded: chain D residue 424 ILE Chi-restraints excluded: chain E residue 88 ASN Chi-restraints excluded: chain E residue 95 MET Chi-restraints excluded: chain E residue 112 TRP Chi-restraints excluded: chain E residue 176 PHE Chi-restraints excluded: chain E residue 209 SER Chi-restraints excluded: chain E residue 236 SER Chi-restraints excluded: chain E residue 424 ILE Chi-restraints excluded: chain E residue 445 CYS Chi-restraints excluded: chain E residue 452 LEU Chi-restraints excluded: chain F residue 69 TRP Chi-restraints excluded: chain F residue 89 VAL Chi-restraints excluded: chain F residue 96 TRP Chi-restraints excluded: chain F residue 191 TYR Chi-restraints excluded: chain F residue 365 SER Chi-restraints excluded: chain K residue 73 THR Chi-restraints excluded: chain K residue 83 THR Chi-restraints excluded: chain M residue 100 PHE Chi-restraints excluded: chain N residue 77 SER Chi-restraints excluded: chain O residue 100 PHE Chi-restraints excluded: chain P residue 10 THR Chi-restraints excluded: chain P residue 48 LEU Chi-restraints excluded: chain P residue 58 ILE Chi-restraints excluded: chain P residue 95 LEU Chi-restraints excluded: chain Q residue 19 SER Chi-restraints excluded: chain Q residue 28 SER Chi-restraints excluded: chain Q residue 92 CYS Chi-restraints excluded: chain Q residue 100 PHE Chi-restraints excluded: chain Q residue 100 ASP Chi-restraints excluded: chain R residue 33 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 260 random chunks: chunk 13 optimal weight: 4.9990 chunk 123 optimal weight: 5.9990 chunk 70 optimal weight: 5.9990 chunk 226 optimal weight: 5.9990 chunk 211 optimal weight: 0.0070 chunk 14 optimal weight: 0.9980 chunk 202 optimal weight: 5.9990 chunk 137 optimal weight: 4.9990 chunk 243 optimal weight: 0.5980 chunk 255 optimal weight: 1.9990 chunk 212 optimal weight: 8.9990 overall best weight: 1.7202 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 658 GLN ** C 577 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 114 GLN E 425 ASN F 462 GLN ** P 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3941 r_free = 0.3941 target = 0.160239 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3407 r_free = 0.3407 target = 0.115190 restraints weight = 34665.637| |-----------------------------------------------------------------------------| r_work (start): 0.3369 rms_B_bonded: 3.01 r_work: 0.3171 rms_B_bonded: 3.23 restraints_weight: 0.5000 r_work (final): 0.3171 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8399 moved from start: 0.3349 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 23510 Z= 0.155 Angle : 0.835 16.966 32229 Z= 0.380 Chirality : 0.053 0.848 4002 Planarity : 0.005 0.091 3823 Dihedral : 5.828 42.883 2865 Min Nonbonded Distance : 2.348 Molprobity Statistics. All-atom Clashscore : 6.21 Ramachandran Plot: Outliers : 0.15 % Allowed : 9.64 % Favored : 90.21 % Rotamer: Outliers : 3.53 % Allowed : 14.47 % Favored : 82.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.40 % Cis-general : 0.00 % Twisted Proline : 2.40 % Twisted General : 0.08 % 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: -2.29 (0.16), residues: 2614 helix: 0.03 (0.30), residues: 323 sheet: -0.60 (0.19), residues: 809 loop : -2.54 (0.14), residues: 1482 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG O 81 TYR 0.020 0.001 TYR E 191 PHE 0.027 0.002 PHE O 50 TRP 0.017 0.001 TRP F 96 HIS 0.005 0.001 HIS E 330 Details of bonding type rmsd/Z covalent geometry : bond 0.00359 / 0.15 (23323) covalent geometry : angle 0.74918 / 0.36 (31704) SS BOND : bond 0.00408 / 0.23 ( 27) SS BOND : angle 1.25822 / 0.79 ( 54) hydrogen bonds : bond 0.04498 / 3.00 ( 555) hydrogen bonds : angle 5.31696 / 3.77 ( 1470) Misc. bond : bond 0.00215 / 0.10 ( 3) link_ALPHA1-2 : bond 0.00826 / 0.43 ( 6) link_ALPHA1-2 : angle 2.14698 / 1.24 ( 18) link_ALPHA1-3 : bond 0.00580 / 0.35 ( 22) link_ALPHA1-3 : angle 2.19706 / 1.34 ( 66) link_ALPHA1-6 : bond 0.00905 / 0.53 ( 18) link_ALPHA1-6 : angle 1.99077 / 1.41 ( 54) link_BETA1-4 : bond 0.00669 / 0.38 ( 47) link_BETA1-4 : angle 2.52399 / 1.53 ( 141) link_NAG-ASN : bond 0.00539 / 0.36 ( 64) link_NAG-ASN : angle 3.98577 / 2.63 ( 192) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5228 Ramachandran restraints generated. 2614 Oldfield, 0 Emsley, 2614 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5228 Ramachandran restraints generated. 2614 Oldfield, 0 Emsley, 2614 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 404 residues out of total 2301 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 81 poor density : 323 time to evaluate : 0.910 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: C 647 GLU cc_start: 0.8902 (tm-30) cc_final: 0.8371 (tt0) REVERT: D 104 MET cc_start: 0.9164 (ttt) cc_final: 0.8831 (ttt) REVERT: E 80 ASN cc_start: 0.8144 (m-40) cc_final: 0.7617 (p0) REVERT: E 113 ASP cc_start: 0.8297 (m-30) cc_final: 0.8048 (m-30) REVERT: E 176 PHE cc_start: 0.8255 (OUTLIER) cc_final: 0.7487 (p90) REVERT: E 432 LYS cc_start: 0.8159 (mmtt) cc_final: 0.7793 (tttm) REVERT: E 446 SER cc_start: 0.9147 (t) cc_final: 0.8876 (p) REVERT: F 78 ASP cc_start: 0.7796 (t70) cc_final: 0.7447 (t0) REVERT: F 432 LYS cc_start: 0.7863 (mmtt) cc_final: 0.7189 (ptmm) REVERT: K 81 LYS cc_start: 0.8270 (mmtp) cc_final: 0.7808 (tmtt) REVERT: L 31 ARG cc_start: 0.6416 (mmt90) cc_final: 0.5858 (mmt-90) REVERT: L 34 GLN cc_start: 0.7527 (mp-120) cc_final: 0.7185 (mp10) REVERT: L 35 TRP cc_start: 0.7393 (m100) cc_final: 0.6854 (m100) REVERT: M 109 VAL cc_start: 0.7888 (t) cc_final: 0.7678 (p) REVERT: N 35 TRP cc_start: 0.7901 (m100) cc_final: 0.7614 (m100) REVERT: N 42 GLN cc_start: 0.6537 (tp40) cc_final: 0.5714 (mt0) REVERT: N 63 ILE cc_start: 0.8602 (mp) cc_final: 0.8358 (tt) REVERT: O 36 TRP cc_start: 0.7852 (m100) cc_final: 0.7600 (m100) REVERT: O 47 TRP cc_start: 0.7840 (t60) cc_final: 0.7412 (t60) REVERT: P 24 ARG cc_start: 0.7247 (ttt90) cc_final: 0.6994 (ttm-80) REVERT: Q 5 GLN cc_start: 0.6707 (tt0) cc_final: 0.6290 (pp30) REVERT: Q 23 ARG cc_start: 0.8197 (tpt-90) cc_final: 0.7768 (tpt90) REVERT: Q 91 TYR cc_start: 0.7693 (m-80) cc_final: 0.7158 (m-80) REVERT: R 45 ARG cc_start: 0.6332 (ptt180) cc_final: 0.5912 (ptt-90) REVERT: R 69 ARG cc_start: 0.6679 (ttm110) cc_final: 0.6472 (ttm110) REVERT: R 99 THR cc_start: 0.6108 (m) cc_final: 0.5903 (m) outliers start: 81 outliers final: 54 residues processed: 384 average time/residue: 0.1758 time to fit residues: 102.6394 Evaluate side-chains 370 residues out of total 2301 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 315 time to evaluate : 0.936 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 612 ASP Chi-restraints excluded: chain B residue 612 ASP Chi-restraints excluded: chain B residue 613 SER Chi-restraints excluded: chain B residue 664 ASP Chi-restraints excluded: chain C residue 618 THR Chi-restraints excluded: chain D residue 96 TRP Chi-restraints excluded: chain D residue 112 TRP Chi-restraints excluded: chain D residue 125 LEU Chi-restraints excluded: chain D residue 205 CYS Chi-restraints excluded: chain D residue 209 SER Chi-restraints excluded: chain D residue 244 THR Chi-restraints excluded: chain D residue 331 CYS Chi-restraints excluded: chain D residue 346 VAL Chi-restraints excluded: chain D residue 370 GLU Chi-restraints excluded: chain D residue 424 ILE Chi-restraints excluded: chain E residue 88 ASN Chi-restraints excluded: chain E residue 95 MET Chi-restraints excluded: chain E residue 112 TRP Chi-restraints excluded: chain E residue 134 VAL Chi-restraints excluded: chain E residue 176 PHE Chi-restraints excluded: chain E residue 191 TYR Chi-restraints excluded: chain E residue 209 SER Chi-restraints excluded: chain E residue 236 SER Chi-restraints excluded: chain E residue 424 ILE Chi-restraints excluded: chain E residue 425 ASN Chi-restraints excluded: chain E residue 445 CYS Chi-restraints excluded: chain E residue 452 LEU Chi-restraints excluded: chain F residue 69 TRP Chi-restraints excluded: chain F residue 89 VAL Chi-restraints excluded: chain F residue 96 TRP Chi-restraints excluded: chain F residue 116 LEU Chi-restraints excluded: chain F residue 165 ILE Chi-restraints excluded: chain F residue 191 TYR Chi-restraints excluded: chain F residue 198 THR Chi-restraints excluded: chain F residue 365 SER Chi-restraints excluded: chain K residue 83 THR Chi-restraints excluded: chain M residue 83 THR Chi-restraints excluded: chain M residue 100 PHE Chi-restraints excluded: chain N residue 77 SER Chi-restraints excluded: chain N residue 88 CYS Chi-restraints excluded: chain O residue 53 ASP Chi-restraints excluded: chain O residue 100 PHE Chi-restraints excluded: chain O residue 100 ASP Chi-restraints excluded: chain P residue 10 THR Chi-restraints excluded: chain P residue 27 SER Chi-restraints excluded: chain P residue 48 LEU Chi-restraints excluded: chain P residue 58 ILE Chi-restraints excluded: chain P residue 95 LEU Chi-restraints excluded: chain Q residue 19 SER Chi-restraints excluded: chain Q residue 28 SER Chi-restraints excluded: chain Q residue 92 CYS Chi-restraints excluded: chain Q residue 100 PHE Chi-restraints excluded: chain Q residue 100 ASP Chi-restraints excluded: chain R residue 33 LEU Chi-restraints excluded: chain R residue 52 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 260 random chunks: chunk 210 optimal weight: 20.0000 chunk 146 optimal weight: 0.8980 chunk 230 optimal weight: 4.9990 chunk 144 optimal weight: 4.9990 chunk 195 optimal weight: 2.9990 chunk 34 optimal weight: 0.5980 chunk 188 optimal weight: 20.0000 chunk 157 optimal weight: 1.9990 chunk 100 optimal weight: 2.9990 chunk 30 optimal weight: 0.9990 chunk 125 optimal weight: 4.9990 overall best weight: 1.4986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C 577 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 46 GLN ** P 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3948 r_free = 0.3948 target = 0.160975 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3497 r_free = 0.3497 target = 0.122282 restraints weight = 34485.954| |-----------------------------------------------------------------------------| r_work (start): 0.3469 rms_B_bonded: 4.09 r_work: 0.3133 rms_B_bonded: 3.82 restraints_weight: 0.5000 r_work (final): 0.3133 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8420 moved from start: 0.3475 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 23510 Z= 0.146 Angle : 0.824 16.806 32229 Z= 0.376 Chirality : 0.053 0.760 4002 Planarity : 0.005 0.090 3823 Dihedral : 5.720 43.704 2865 Min Nonbonded Distance : 2.360 Molprobity Statistics. All-atom Clashscore : 6.03 Ramachandran Plot: Outliers : 0.15 % Allowed : 8.91 % Favored : 90.93 % Rotamer: Outliers : 3.23 % Allowed : 14.82 % Favored : 81.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.40 % Cis-general : 0.00 % Twisted Proline : 2.40 % Twisted General : 0.12 % 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: -2.22 (0.16), residues: 2614 helix: 0.23 (0.30), residues: 320 sheet: -0.55 (0.19), residues: 791 loop : -2.50 (0.14), residues: 1503 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG O 81 TYR 0.019 0.001 TYR E 191 PHE 0.026 0.002 PHE O 50 TRP 0.016 0.001 TRP F 96 HIS 0.004 0.001 HIS E 330 Details of bonding type rmsd/Z covalent geometry : bond 0.00331 / 0.14 (23323) covalent geometry : angle 0.73978 / 0.36 (31704) SS BOND : bond 0.00380 / 0.21 ( 27) SS BOND : angle 1.26905 / 0.77 ( 54) hydrogen bonds : bond 0.04319 / 2.89 ( 555) hydrogen bonds : angle 5.24764 / 3.73 ( 1470) Misc. bond : bond 0.00164 / 0.08 ( 3) link_ALPHA1-2 : bond 0.00823 / 0.43 ( 6) link_ALPHA1-2 : angle 2.11348 / 1.22 ( 18) link_ALPHA1-3 : bond 0.00579 / 0.36 ( 22) link_ALPHA1-3 : angle 2.12567 / 1.30 ( 66) link_ALPHA1-6 : bond 0.00896 / 0.52 ( 18) link_ALPHA1-6 : angle 1.93733 / 1.37 ( 54) link_BETA1-4 : bond 0.00650 / 0.38 ( 47) link_BETA1-4 : angle 2.44428 / 1.48 ( 141) link_NAG-ASN : bond 0.00565 / 0.38 ( 64) link_NAG-ASN : angle 3.96924 / 2.62 ( 192) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5228 Ramachandran restraints generated. 2614 Oldfield, 0 Emsley, 2614 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5228 Ramachandran restraints generated. 2614 Oldfield, 0 Emsley, 2614 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 398 residues out of total 2301 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 74 poor density : 324 time to evaluate : 0.860 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 647 GLU cc_start: 0.8965 (tm-30) cc_final: 0.8426 (tt0) REVERT: D 104 MET cc_start: 0.9193 (ttt) cc_final: 0.8865 (ttt) REVERT: D 228 CYS cc_start: 0.8896 (OUTLIER) cc_final: 0.8339 (t) REVERT: E 80 ASN cc_start: 0.8210 (m-40) cc_final: 0.7609 (p0) REVERT: E 113 ASP cc_start: 0.8359 (m-30) cc_final: 0.8090 (m-30) REVERT: E 176 PHE cc_start: 0.8205 (OUTLIER) cc_final: 0.7472 (p90) REVERT: E 425 ASN cc_start: 0.8514 (p0) cc_final: 0.8132 (t0) REVERT: E 432 LYS cc_start: 0.8193 (mmtt) cc_final: 0.7849 (tttm) REVERT: E 446 SER cc_start: 0.9136 (t) cc_final: 0.8880 (p) REVERT: F 78 ASP cc_start: 0.7849 (t70) cc_final: 0.7455 (t0) REVERT: F 432 LYS cc_start: 0.7889 (mmtt) cc_final: 0.7202 (ptmm) REVERT: K 81 LYS cc_start: 0.8252 (mmtp) cc_final: 0.7801 (tmtt) REVERT: L 31 ARG cc_start: 0.6410 (mmt90) cc_final: 0.6016 (tpp80) REVERT: L 34 GLN cc_start: 0.7511 (mp-120) cc_final: 0.7162 (mp10) REVERT: L 35 TRP cc_start: 0.7306 (m100) cc_final: 0.6749 (m100) REVERT: M 109 VAL cc_start: 0.7866 (t) cc_final: 0.7656 (p) REVERT: N 35 TRP cc_start: 0.7902 (m100) cc_final: 0.7634 (m100) REVERT: N 42 GLN cc_start: 0.6423 (tp40) cc_final: 0.5619 (mt0) REVERT: N 63 ILE cc_start: 0.8577 (mp) cc_final: 0.8347 (tt) REVERT: O 36 TRP cc_start: 0.7839 (m100) cc_final: 0.7589 (m100) REVERT: O 47 TRP cc_start: 0.7869 (t60) cc_final: 0.7536 (t60) REVERT: P 24 ARG cc_start: 0.7270 (ttt90) cc_final: 0.6898 (ttm-80) REVERT: Q 5 GLN cc_start: 0.6778 (tt0) cc_final: 0.6326 (pp30) REVERT: Q 23 ARG cc_start: 0.8312 (tpt-90) cc_final: 0.7897 (tpt90) REVERT: Q 91 TYR cc_start: 0.7704 (m-80) cc_final: 0.7050 (m-80) REVERT: Q 101 ASP cc_start: 0.8195 (OUTLIER) cc_final: 0.7914 (t0) REVERT: R 45 ARG cc_start: 0.6325 (ptt180) cc_final: 0.5902 (ptt-90) REVERT: R 99 THR cc_start: 0.6076 (m) cc_final: 0.5610 (m) outliers start: 74 outliers final: 57 residues processed: 380 average time/residue: 0.1791 time to fit residues: 103.1729 Evaluate side-chains 377 residues out of total 2301 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 317 time to evaluate : 0.856 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 612 ASP Chi-restraints excluded: chain A residue 618 THR Chi-restraints excluded: chain B residue 612 ASP Chi-restraints excluded: chain B residue 613 SER Chi-restraints excluded: chain B residue 664 ASP Chi-restraints excluded: chain C residue 618 THR Chi-restraints excluded: chain D residue 96 TRP Chi-restraints excluded: chain D residue 112 TRP Chi-restraints excluded: chain D residue 125 LEU Chi-restraints excluded: chain D residue 189 THR Chi-restraints excluded: chain D residue 205 CYS Chi-restraints excluded: chain D residue 209 SER Chi-restraints excluded: chain D residue 228 CYS Chi-restraints excluded: chain D residue 244 THR Chi-restraints excluded: chain D residue 331 CYS Chi-restraints excluded: chain D residue 346 VAL Chi-restraints excluded: chain D residue 370 GLU Chi-restraints excluded: chain D residue 424 ILE Chi-restraints excluded: chain E residue 88 ASN Chi-restraints excluded: chain E residue 95 MET Chi-restraints excluded: chain E residue 112 TRP Chi-restraints excluded: chain E residue 134 VAL Chi-restraints excluded: chain E residue 166 ARG Chi-restraints excluded: chain E residue 176 PHE Chi-restraints excluded: chain E residue 208 VAL Chi-restraints excluded: chain E residue 209 SER Chi-restraints excluded: chain E residue 236 SER Chi-restraints excluded: chain E residue 424 ILE Chi-restraints excluded: chain E residue 445 CYS Chi-restraints excluded: chain E residue 452 LEU Chi-restraints excluded: chain F residue 69 TRP Chi-restraints excluded: chain F residue 89 VAL Chi-restraints excluded: chain F residue 96 TRP Chi-restraints excluded: chain F residue 116 LEU Chi-restraints excluded: chain F residue 165 ILE Chi-restraints excluded: chain F residue 191 TYR Chi-restraints excluded: chain F residue 198 THR Chi-restraints excluded: chain F residue 365 SER Chi-restraints excluded: chain K residue 83 THR Chi-restraints excluded: chain M residue 83 THR Chi-restraints excluded: chain M residue 100 PHE Chi-restraints excluded: chain N residue 27 SER Chi-restraints excluded: chain N residue 53 THR Chi-restraints excluded: chain N residue 77 SER Chi-restraints excluded: chain N residue 88 CYS Chi-restraints excluded: chain O residue 53 ASP Chi-restraints excluded: chain O residue 100 PHE Chi-restraints excluded: chain P residue 10 THR Chi-restraints excluded: chain P residue 27 SER Chi-restraints excluded: chain P residue 48 LEU Chi-restraints excluded: chain P residue 58 ILE Chi-restraints excluded: chain P residue 95 LEU Chi-restraints excluded: chain Q residue 19 SER Chi-restraints excluded: chain Q residue 28 SER Chi-restraints excluded: chain Q residue 92 CYS Chi-restraints excluded: chain Q residue 100 PHE Chi-restraints excluded: chain Q residue 100 ASP Chi-restraints excluded: chain Q residue 101 ASP Chi-restraints excluded: chain R residue 33 LEU Chi-restraints excluded: chain R residue 52 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 260 random chunks: chunk 142 optimal weight: 1.9990 chunk 223 optimal weight: 1.9990 chunk 192 optimal weight: 0.0170 chunk 228 optimal weight: 9.9990 chunk 207 optimal weight: 10.0000 chunk 126 optimal weight: 0.8980 chunk 107 optimal weight: 2.9990 chunk 54 optimal weight: 0.0980 chunk 247 optimal weight: 3.9990 chunk 34 optimal weight: 4.9990 chunk 224 optimal weight: 4.9990 overall best weight: 1.0022 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C 577 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 46 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3970 r_free = 0.3970 target = 0.162907 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3515 r_free = 0.3515 target = 0.123468 restraints weight = 34294.383| |-----------------------------------------------------------------------------| r_work (start): 0.3481 rms_B_bonded: 3.91 r_work: 0.3183 rms_B_bonded: 3.62 restraints_weight: 0.5000 r_work (final): 0.3183 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8386 moved from start: 0.3678 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 23510 Z= 0.127 Angle : 0.785 16.324 32229 Z= 0.358 Chirality : 0.050 0.540 4002 Planarity : 0.005 0.116 3823 Dihedral : 5.491 43.757 2865 Min Nonbonded Distance : 2.376 Molprobity Statistics. All-atom Clashscore : 6.10 Ramachandran Plot: Outliers : 0.15 % Allowed : 8.38 % Favored : 91.47 % Rotamer: Outliers : 2.92 % Allowed : 15.17 % Favored : 81.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.40 % Cis-general : 0.00 % Twisted Proline : 2.40 % Twisted General : 0.08 % 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: -2.07 (0.16), residues: 2614 helix: 0.42 (0.31), residues: 320 sheet: -0.44 (0.19), residues: 807 loop : -2.45 (0.14), residues: 1487 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.001 ARG R 69 TYR 0.018 0.001 TYR E 191 PHE 0.027 0.002 PHE O 50 TRP 0.018 0.001 TRP C 628 HIS 0.004 0.001 HIS E 330 Details of bonding type rmsd/Z covalent geometry : bond 0.00276 / 0.13 (23323) covalent geometry : angle 0.70725 / 0.34 (31704) SS BOND : bond 0.00341 / 0.19 ( 27) SS BOND : angle 1.08705 / 0.67 ( 54) hydrogen bonds : bond 0.03856 / 2.59 ( 555) hydrogen bonds : angle 5.09127 / 3.62 ( 1470) Misc. bond : bond 0.00122 / 0.06 ( 3) link_ALPHA1-2 : bond 0.00812 / 0.42 ( 6) link_ALPHA1-2 : angle 2.08475 / 1.20 ( 18) link_ALPHA1-3 : bond 0.00577 / 0.36 ( 22) link_ALPHA1-3 : angle 2.01661 / 1.26 ( 66) link_ALPHA1-6 : bond 0.00878 / 0.52 ( 18) link_ALPHA1-6 : angle 1.87332 / 1.32 ( 54) link_BETA1-4 : bond 0.00637 / 0.37 ( 47) link_BETA1-4 : angle 2.34759 / 1.43 ( 141) link_NAG-ASN : bond 0.00548 / 0.36 ( 64) link_NAG-ASN : angle 3.70623 / 2.47 ( 192) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5228 Ramachandran restraints generated. 2614 Oldfield, 0 Emsley, 2614 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5228 Ramachandran restraints generated. 2614 Oldfield, 0 Emsley, 2614 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 400 residues out of total 2301 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 333 time to evaluate : 0.873 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 664 ASP cc_start: 0.7061 (OUTLIER) cc_final: 0.6790 (p0) REVERT: C 647 GLU cc_start: 0.8901 (tm-30) cc_final: 0.8401 (tt0) REVERT: D 104 MET cc_start: 0.9146 (ttt) cc_final: 0.8833 (ttt) REVERT: E 80 ASN cc_start: 0.8038 (m-40) cc_final: 0.7483 (p0) REVERT: E 113 ASP cc_start: 0.8288 (m-30) cc_final: 0.8023 (m-30) REVERT: E 176 PHE cc_start: 0.8205 (OUTLIER) cc_final: 0.7556 (p90) REVERT: E 425 ASN cc_start: 0.8361 (p0) cc_final: 0.8004 (t0) REVERT: E 432 LYS cc_start: 0.8112 (mmtt) cc_final: 0.7839 (tttm) REVERT: E 446 SER cc_start: 0.9037 (t) cc_final: 0.8675 (p) REVERT: F 78 ASP cc_start: 0.7793 (t70) cc_final: 0.7441 (t0) REVERT: F 432 LYS cc_start: 0.7917 (mmtt) cc_final: 0.7227 (ptmm) REVERT: K 81 LYS cc_start: 0.8205 (mmtp) cc_final: 0.7782 (tmtt) REVERT: L 34 GLN cc_start: 0.7509 (mp-120) cc_final: 0.7282 (mp10) REVERT: L 35 TRP cc_start: 0.7306 (m100) cc_final: 0.6764 (m100) REVERT: N 35 TRP cc_start: 0.7870 (m100) cc_final: 0.7626 (m100) REVERT: N 42 GLN cc_start: 0.6366 (tp40) cc_final: 0.5609 (mt0) REVERT: N 63 ILE cc_start: 0.8584 (mp) cc_final: 0.8330 (tt) REVERT: O 36 TRP cc_start: 0.7797 (m100) cc_final: 0.7552 (m100) REVERT: P 24 ARG cc_start: 0.7248 (ttt90) cc_final: 0.6932 (ttm-80) REVERT: Q 5 GLN cc_start: 0.7005 (tt0) cc_final: 0.6461 (pp30) REVERT: Q 23 ARG cc_start: 0.8374 (tpt-90) cc_final: 0.8024 (tpt90) REVERT: Q 91 TYR cc_start: 0.7689 (m-80) cc_final: 0.7134 (m-80) REVERT: R 45 ARG cc_start: 0.6254 (ptt180) cc_final: 0.5783 (ptt-90) REVERT: R 99 THR cc_start: 0.6254 (m) cc_final: 0.5735 (m) outliers start: 67 outliers final: 53 residues processed: 377 average time/residue: 0.1810 time to fit residues: 103.2101 Evaluate side-chains 376 residues out of total 2301 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 321 time to evaluate : 0.946 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 616 ASN Chi-restraints excluded: chain A residue 618 THR Chi-restraints excluded: chain B residue 613 SER Chi-restraints excluded: chain B residue 664 ASP Chi-restraints excluded: chain C residue 618 THR Chi-restraints excluded: chain D residue 96 TRP Chi-restraints excluded: chain D residue 112 TRP Chi-restraints excluded: chain D residue 125 LEU Chi-restraints excluded: chain D residue 205 CYS Chi-restraints excluded: chain D residue 209 SER Chi-restraints excluded: chain D residue 244 THR Chi-restraints excluded: chain D residue 331 CYS Chi-restraints excluded: chain D residue 370 GLU Chi-restraints excluded: chain D residue 424 ILE Chi-restraints excluded: chain E residue 88 ASN Chi-restraints excluded: chain E residue 95 MET Chi-restraints excluded: chain E residue 112 TRP Chi-restraints excluded: chain E residue 166 ARG Chi-restraints excluded: chain E residue 176 PHE Chi-restraints excluded: chain E residue 208 VAL Chi-restraints excluded: chain E residue 209 SER Chi-restraints excluded: chain E residue 424 ILE Chi-restraints excluded: chain E residue 445 CYS Chi-restraints excluded: chain E residue 452 LEU Chi-restraints excluded: chain F residue 69 TRP Chi-restraints excluded: chain F residue 89 VAL Chi-restraints excluded: chain F residue 96 TRP Chi-restraints excluded: chain F residue 116 LEU Chi-restraints excluded: chain F residue 165 ILE Chi-restraints excluded: chain F residue 191 TYR Chi-restraints excluded: chain F residue 198 THR Chi-restraints excluded: chain F residue 358 ILE Chi-restraints excluded: chain K residue 73 THR Chi-restraints excluded: chain K residue 83 THR Chi-restraints excluded: chain M residue 53 ASP Chi-restraints excluded: chain M residue 100 PHE Chi-restraints excluded: chain N residue 53 THR Chi-restraints excluded: chain N residue 77 SER Chi-restraints excluded: chain N residue 88 CYS Chi-restraints excluded: chain O residue 82 VAL Chi-restraints excluded: chain O residue 100 PHE Chi-restraints excluded: chain P residue 10 THR Chi-restraints excluded: chain P residue 27 SER Chi-restraints excluded: chain P residue 48 LEU Chi-restraints excluded: chain P residue 58 ILE Chi-restraints excluded: chain P residue 95 LEU Chi-restraints excluded: chain Q residue 19 SER Chi-restraints excluded: chain Q residue 28 SER Chi-restraints excluded: chain Q residue 92 CYS Chi-restraints excluded: chain Q residue 100 PHE Chi-restraints excluded: chain Q residue 100 ASP Chi-restraints excluded: chain Q residue 101 ASP Chi-restraints excluded: chain R residue 26 SER Chi-restraints excluded: chain R residue 33 LEU Chi-restraints excluded: chain R residue 52 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 260 random chunks: chunk 11 optimal weight: 8.9990 chunk 87 optimal weight: 0.6980 chunk 220 optimal weight: 9.9990 chunk 254 optimal weight: 8.9990 chunk 49 optimal weight: 0.9980 chunk 195 optimal weight: 4.9990 chunk 217 optimal weight: 0.9980 chunk 89 optimal weight: 2.9990 chunk 127 optimal weight: 3.9990 chunk 169 optimal weight: 7.9990 chunk 238 optimal weight: 7.9990 overall best weight: 1.9384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 650 GLN ** B 650 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 577 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 46 GLN ** P 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 97 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3942 r_free = 0.3942 target = 0.160490 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3473 r_free = 0.3473 target = 0.120354 restraints weight = 34385.386| |-----------------------------------------------------------------------------| r_work (start): 0.3442 rms_B_bonded: 4.00 r_work: 0.3134 rms_B_bonded: 3.65 restraints_weight: 0.5000 r_work (final): 0.3134 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8422 moved from start: 0.3721 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 23510 Z= 0.161 Angle : 0.830 16.672 32229 Z= 0.379 Chirality : 0.052 0.547 4002 Planarity : 0.005 0.092 3823 Dihedral : 5.640 44.655 2865 Min Nonbonded Distance : 2.345 Molprobity Statistics. All-atom Clashscore : 6.43 Ramachandran Plot: Outliers : 0.15 % Allowed : 9.53 % Favored : 90.32 % Rotamer: Outliers : 3.18 % Allowed : 15.39 % Favored : 81.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.40 % Cis-general : 0.00 % Twisted Proline : 2.40 % Twisted General : 0.12 % 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: -2.05 (0.16), residues: 2614 helix: 0.46 (0.31), residues: 316 sheet: -0.48 (0.19), residues: 813 loop : -2.41 (0.14), residues: 1485 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG R 69 TYR 0.019 0.001 TYR E 191 PHE 0.029 0.002 PHE P 71 TRP 0.026 0.002 TRP O 47 HIS 0.005 0.001 HIS E 330 Details of bonding type rmsd/Z covalent geometry : bond 0.00375 / 0.16 (23323) covalent geometry : angle 0.75338 / 0.36 (31704) SS BOND : bond 0.00309 / 0.20 ( 27) SS BOND : angle 1.30192 / 0.80 ( 54) hydrogen bonds : bond 0.04518 / 3.03 ( 555) hydrogen bonds : angle 5.17373 / 3.68 ( 1470) Misc. bond : bond 0.00253 / 0.12 ( 3) link_ALPHA1-2 : bond 0.00829 / 0.43 ( 6) link_ALPHA1-2 : angle 2.05296 / 1.18 ( 18) link_ALPHA1-3 : bond 0.00559 / 0.34 ( 22) link_ALPHA1-3 : angle 2.09207 / 1.31 ( 66) link_ALPHA1-6 : bond 0.00871 / 0.51 ( 18) link_ALPHA1-6 : angle 1.92766 / 1.36 ( 54) link_BETA1-4 : bond 0.00644 / 0.36 ( 47) link_BETA1-4 : angle 2.42711 / 1.47 ( 141) link_NAG-ASN : bond 0.00483 / 0.32 ( 64) link_NAG-ASN : angle 3.77201 / 2.52 ( 192) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5228 Ramachandran restraints generated. 2614 Oldfield, 0 Emsley, 2614 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5228 Ramachandran restraints generated. 2614 Oldfield, 0 Emsley, 2614 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 394 residues out of total 2301 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 73 poor density : 321 time to evaluate : 0.887 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 664 ASP cc_start: 0.6939 (OUTLIER) cc_final: 0.6660 (p0) REVERT: D 104 MET cc_start: 0.9182 (ttt) cc_final: 0.8857 (ttt) REVERT: D 168 LYS cc_start: 0.8279 (mmmm) cc_final: 0.7445 (ptmm) REVERT: D 228 CYS cc_start: 0.8957 (OUTLIER) cc_final: 0.8386 (t) REVERT: D 358 ILE cc_start: 0.8202 (OUTLIER) cc_final: 0.7943 (pp) REVERT: D 423 ILE cc_start: 0.9114 (OUTLIER) cc_final: 0.8565 (mm) REVERT: E 80 ASN cc_start: 0.8068 (m-40) cc_final: 0.7602 (p0) REVERT: E 113 ASP cc_start: 0.8335 (m-30) cc_final: 0.8087 (m-30) REVERT: E 176 PHE cc_start: 0.8200 (OUTLIER) cc_final: 0.7582 (p90) REVERT: E 425 ASN cc_start: 0.8491 (p0) cc_final: 0.8094 (t0) REVERT: E 432 LYS cc_start: 0.8155 (mmtt) cc_final: 0.7839 (tttm) REVERT: E 446 SER cc_start: 0.9129 (t) cc_final: 0.8847 (p) REVERT: F 33 LYS cc_start: 0.8133 (mtpt) cc_final: 0.7593 (mmmt) REVERT: F 78 ASP cc_start: 0.7787 (t70) cc_final: 0.7402 (t0) REVERT: F 432 LYS cc_start: 0.7922 (mmtt) cc_final: 0.7232 (ptmm) REVERT: K 81 LYS cc_start: 0.8217 (mmtp) cc_final: 0.7757 (tmtt) REVERT: L 34 GLN cc_start: 0.7527 (mp-120) cc_final: 0.7280 (mp10) REVERT: L 35 TRP cc_start: 0.7294 (m100) cc_final: 0.6764 (m100) REVERT: N 24 ARG cc_start: 0.6694 (mtp-110) cc_final: 0.6351 (mtp-110) REVERT: N 35 TRP cc_start: 0.7905 (m100) cc_final: 0.7657 (m100) REVERT: N 42 GLN cc_start: 0.6131 (tp40) cc_final: 0.5427 (mt0) REVERT: N 63 ILE cc_start: 0.8621 (mp) cc_final: 0.8390 (tt) REVERT: O 36 TRP cc_start: 0.7819 (m100) cc_final: 0.7568 (m100) REVERT: O 47 TRP cc_start: 0.7588 (t60) cc_final: 0.7101 (t60) REVERT: P 24 ARG cc_start: 0.7280 (ttt90) cc_final: 0.6978 (ttm-80) REVERT: Q 5 GLN cc_start: 0.6854 (tt0) cc_final: 0.6467 (pp30) REVERT: Q 23 ARG cc_start: 0.8345 (tpt-90) cc_final: 0.7919 (tpt90) REVERT: Q 91 TYR cc_start: 0.7727 (m-80) cc_final: 0.7163 (m-80) outliers start: 73 outliers final: 57 residues processed: 375 average time/residue: 0.1839 time to fit residues: 103.8680 Evaluate side-chains 378 residues out of total 2301 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 316 time to evaluate : 0.942 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 616 ASN Chi-restraints excluded: chain A residue 618 THR Chi-restraints excluded: chain B residue 613 SER Chi-restraints excluded: chain B residue 664 ASP Chi-restraints excluded: chain D residue 96 TRP Chi-restraints excluded: chain D residue 112 TRP Chi-restraints excluded: chain D residue 125 LEU Chi-restraints excluded: chain D residue 205 CYS Chi-restraints excluded: chain D residue 209 SER Chi-restraints excluded: chain D residue 228 CYS Chi-restraints excluded: chain D residue 244 THR Chi-restraints excluded: chain D residue 331 CYS Chi-restraints excluded: chain D residue 358 ILE Chi-restraints excluded: chain D residue 370 GLU Chi-restraints excluded: chain D residue 423 ILE Chi-restraints excluded: chain D residue 424 ILE Chi-restraints excluded: chain D residue 440 ARG Chi-restraints excluded: chain E residue 88 ASN Chi-restraints excluded: chain E residue 95 MET Chi-restraints excluded: chain E residue 112 TRP Chi-restraints excluded: chain E residue 134 VAL Chi-restraints excluded: chain E residue 166 ARG Chi-restraints excluded: chain E residue 176 PHE Chi-restraints excluded: chain E residue 191 TYR Chi-restraints excluded: chain E residue 209 SER Chi-restraints excluded: chain E residue 236 SER Chi-restraints excluded: chain E residue 424 ILE Chi-restraints excluded: chain E residue 445 CYS Chi-restraints excluded: chain E residue 452 LEU Chi-restraints excluded: chain F residue 69 TRP Chi-restraints excluded: chain F residue 89 VAL Chi-restraints excluded: chain F residue 96 TRP Chi-restraints excluded: chain F residue 116 LEU Chi-restraints excluded: chain F residue 165 ILE Chi-restraints excluded: chain F residue 191 TYR Chi-restraints excluded: chain F residue 198 THR Chi-restraints excluded: chain F residue 365 SER Chi-restraints excluded: chain K residue 73 THR Chi-restraints excluded: chain K residue 83 THR Chi-restraints excluded: chain M residue 53 ASP Chi-restraints excluded: chain M residue 83 THR Chi-restraints excluded: chain M residue 100 PHE Chi-restraints excluded: chain N residue 27 SER Chi-restraints excluded: chain N residue 53 THR Chi-restraints excluded: chain N residue 77 SER Chi-restraints excluded: chain N residue 88 CYS Chi-restraints excluded: chain O residue 82 VAL Chi-restraints excluded: chain O residue 100 PHE Chi-restraints excluded: chain P residue 10 THR Chi-restraints excluded: chain P residue 27 SER Chi-restraints excluded: chain P residue 48 LEU Chi-restraints excluded: chain P residue 58 ILE Chi-restraints excluded: chain P residue 95 LEU Chi-restraints excluded: chain Q residue 19 SER Chi-restraints excluded: chain Q residue 28 SER Chi-restraints excluded: chain Q residue 92 CYS Chi-restraints excluded: chain Q residue 95 LEU Chi-restraints excluded: chain Q residue 100 PHE Chi-restraints excluded: chain Q residue 100 ASP Chi-restraints excluded: chain Q residue 101 ASP Chi-restraints excluded: chain R residue 33 LEU Chi-restraints excluded: chain R residue 52 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 260 random chunks: chunk 172 optimal weight: 10.0000 chunk 151 optimal weight: 2.9990 chunk 184 optimal weight: 30.0000 chunk 226 optimal weight: 5.9990 chunk 49 optimal weight: 0.0870 chunk 230 optimal weight: 6.9990 chunk 183 optimal weight: 3.9990 chunk 213 optimal weight: 0.9990 chunk 42 optimal weight: 0.7980 chunk 16 optimal weight: 7.9990 chunk 157 optimal weight: 0.9990 overall best weight: 1.1764 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 650 GLN B 658 GLN ** C 577 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 46 GLN ** R 97 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3963 r_free = 0.3963 target = 0.162366 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3503 r_free = 0.3503 target = 0.122556 restraints weight = 34371.416| |-----------------------------------------------------------------------------| r_work (start): 0.3473 rms_B_bonded: 4.01 r_work: 0.3170 rms_B_bonded: 3.64 restraints_weight: 0.5000 r_work (final): 0.3170 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8388 moved from start: 0.3851 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 23510 Z= 0.133 Angle : 0.791 16.420 32229 Z= 0.361 Chirality : 0.051 0.517 4002 Planarity : 0.005 0.091 3823 Dihedral : 5.504 43.499 2865 Min Nonbonded Distance : 2.374 Molprobity Statistics. All-atom Clashscore : 6.58 Ramachandran Plot: Outliers : 0.15 % Allowed : 8.30 % Favored : 91.55 % Rotamer: Outliers : 2.66 % Allowed : 16.00 % Favored : 81.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.40 % Cis-general : 0.00 % Twisted Proline : 2.40 % Twisted General : 0.12 % 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: -2.00 (0.16), residues: 2614 helix: 0.54 (0.31), residues: 316 sheet: -0.43 (0.19), residues: 807 loop : -2.39 (0.14), residues: 1491 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.016 0.001 ARG R 69 TYR 0.021 0.001 TYR C 638 PHE 0.030 0.002 PHE P 71 TRP 0.018 0.001 TRP C 628 HIS 0.004 0.001 HIS E 330 Details of bonding type rmsd/Z covalent geometry : bond 0.00292 / 0.13 (23323) covalent geometry : angle 0.71578 / 0.34 (31704) SS BOND : bond 0.00345 / 0.19 ( 27) SS BOND : angle 1.09403 / 0.68 ( 54) hydrogen bonds : bond 0.04035 / 2.71 ( 555) hydrogen bonds : angle 5.09272 / 3.63 ( 1470) Misc. bond : bond 0.00462 / 0.22 ( 3) link_ALPHA1-2 : bond 0.00795 / 0.41 ( 6) link_ALPHA1-2 : angle 2.04205 / 1.18 ( 18) link_ALPHA1-3 : bond 0.00569 / 0.35 ( 22) link_ALPHA1-3 : angle 1.95015 / 1.24 ( 66) link_ALPHA1-6 : bond 0.00854 / 0.50 ( 18) link_ALPHA1-6 : angle 1.84424 / 1.30 ( 54) link_BETA1-4 : bond 0.00629 / 0.36 ( 47) link_BETA1-4 : angle 2.34583 / 1.43 ( 141) link_NAG-ASN : bond 0.00506 / 0.33 ( 64) link_NAG-ASN : angle 3.67416 / 2.47 ( 192) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5228 Ramachandran restraints generated. 2614 Oldfield, 0 Emsley, 2614 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5228 Ramachandran restraints generated. 2614 Oldfield, 0 Emsley, 2614 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 384 residues out of total 2301 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 323 time to evaluate : 0.905 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 621 GLU cc_start: 0.7891 (tt0) cc_final: 0.7500 (tt0) REVERT: B 650 GLN cc_start: 0.5883 (OUTLIER) cc_final: 0.5640 (tm-30) REVERT: B 664 ASP cc_start: 0.6862 (OUTLIER) cc_final: 0.6597 (p0) REVERT: C 647 GLU cc_start: 0.8930 (tm-30) cc_final: 0.8387 (tt0) REVERT: D 104 MET cc_start: 0.9164 (ttt) cc_final: 0.8844 (ttt) REVERT: D 168 LYS cc_start: 0.8226 (mmmm) cc_final: 0.7454 (ptmm) REVERT: D 228 CYS cc_start: 0.8867 (OUTLIER) cc_final: 0.8335 (t) REVERT: D 445 CYS cc_start: 0.7785 (OUTLIER) cc_final: 0.7480 (m) REVERT: E 80 ASN cc_start: 0.8043 (m-40) cc_final: 0.7472 (p0) REVERT: E 113 ASP cc_start: 0.8288 (m-30) cc_final: 0.8005 (m-30) REVERT: E 176 PHE cc_start: 0.8223 (OUTLIER) cc_final: 0.7657 (p90) REVERT: E 425 ASN cc_start: 0.8360 (p0) cc_final: 0.7944 (t0) REVERT: E 432 LYS cc_start: 0.8155 (mmtt) cc_final: 0.7870 (tttm) REVERT: E 446 SER cc_start: 0.9030 (t) cc_final: 0.8654 (p) REVERT: F 33 LYS cc_start: 0.8053 (mtpt) cc_final: 0.7609 (mmmt) REVERT: F 78 ASP cc_start: 0.7773 (t70) cc_final: 0.7443 (t0) REVERT: F 432 LYS cc_start: 0.7913 (mmtt) cc_final: 0.7250 (ptmm) REVERT: K 81 LYS cc_start: 0.8212 (mmtp) cc_final: 0.7752 (tmtt) REVERT: N 24 ARG cc_start: 0.6729 (mtp-110) cc_final: 0.6464 (mtp-110) REVERT: N 35 TRP cc_start: 0.7879 (m100) cc_final: 0.7633 (m100) REVERT: N 42 GLN cc_start: 0.5912 (tp40) cc_final: 0.5256 (mt0) REVERT: N 63 ILE cc_start: 0.8619 (mp) cc_final: 0.8378 (tt) REVERT: O 36 TRP cc_start: 0.7794 (m100) cc_final: 0.7540 (m100) REVERT: P 24 ARG cc_start: 0.7270 (ttt90) cc_final: 0.6967 (ttm-80) REVERT: Q 5 GLN cc_start: 0.6760 (tt0) cc_final: 0.6393 (pp30) REVERT: Q 23 ARG cc_start: 0.8355 (tpt-90) cc_final: 0.7992 (tpt90) REVERT: Q 91 TYR cc_start: 0.7674 (m-80) cc_final: 0.7126 (m-80) REVERT: R 45 ARG cc_start: 0.6180 (ptt180) cc_final: 0.5739 (ptt-90) outliers start: 61 outliers final: 48 residues processed: 368 average time/residue: 0.1813 time to fit residues: 100.1195 Evaluate side-chains 364 residues out of total 2301 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 311 time to evaluate : 0.830 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 618 THR Chi-restraints excluded: chain B residue 613 SER Chi-restraints excluded: chain B residue 650 GLN Chi-restraints excluded: chain B residue 664 ASP Chi-restraints excluded: chain D residue 96 TRP Chi-restraints excluded: chain D residue 112 TRP Chi-restraints excluded: chain D residue 125 LEU Chi-restraints excluded: chain D residue 205 CYS Chi-restraints excluded: chain D residue 228 CYS Chi-restraints excluded: chain D residue 244 THR Chi-restraints excluded: chain D residue 331 CYS Chi-restraints excluded: chain D residue 370 GLU Chi-restraints excluded: chain D residue 424 ILE Chi-restraints excluded: chain D residue 445 CYS Chi-restraints excluded: chain E residue 88 ASN Chi-restraints excluded: chain E residue 95 MET Chi-restraints excluded: chain E residue 112 TRP Chi-restraints excluded: chain E residue 134 VAL Chi-restraints excluded: chain E residue 166 ARG Chi-restraints excluded: chain E residue 176 PHE Chi-restraints excluded: chain E residue 209 SER Chi-restraints excluded: chain E residue 424 ILE Chi-restraints excluded: chain E residue 445 CYS Chi-restraints excluded: chain E residue 452 LEU Chi-restraints excluded: chain F residue 69 TRP Chi-restraints excluded: chain F residue 89 VAL Chi-restraints excluded: chain F residue 96 TRP Chi-restraints excluded: chain F residue 116 LEU Chi-restraints excluded: chain F residue 165 ILE Chi-restraints excluded: chain F residue 191 TYR Chi-restraints excluded: chain F residue 198 THR Chi-restraints excluded: chain K residue 73 THR Chi-restraints excluded: chain K residue 83 THR Chi-restraints excluded: chain M residue 53 ASP Chi-restraints excluded: chain M residue 83 THR Chi-restraints excluded: chain M residue 100 PHE Chi-restraints excluded: chain N residue 27 SER Chi-restraints excluded: chain N residue 77 SER Chi-restraints excluded: chain N residue 88 CYS Chi-restraints excluded: chain O residue 100 PHE Chi-restraints excluded: chain P residue 10 THR Chi-restraints excluded: chain P residue 27 SER Chi-restraints excluded: chain P residue 48 LEU Chi-restraints excluded: chain P residue 58 ILE Chi-restraints excluded: chain P residue 95 LEU Chi-restraints excluded: chain Q residue 19 SER Chi-restraints excluded: chain Q residue 28 SER Chi-restraints excluded: chain Q residue 92 CYS Chi-restraints excluded: chain Q residue 100 PHE Chi-restraints excluded: chain Q residue 100 ASP Chi-restraints excluded: chain Q residue 101 ASP Chi-restraints excluded: chain R residue 33 LEU Chi-restraints excluded: chain R residue 52 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 260 random chunks: chunk 73 optimal weight: 0.8980 chunk 160 optimal weight: 0.9990 chunk 242 optimal weight: 2.9990 chunk 157 optimal weight: 0.8980 chunk 29 optimal weight: 3.9990 chunk 169 optimal weight: 0.7980 chunk 235 optimal weight: 8.9990 chunk 36 optimal weight: 7.9990 chunk 66 optimal weight: 2.9990 chunk 155 optimal weight: 2.9990 chunk 107 optimal weight: 0.8980 overall best weight: 0.8982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 658 GLN ** C 577 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 89 HIS ** N 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 46 GLN ** R 97 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3971 r_free = 0.3971 target = 0.163130 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3512 r_free = 0.3512 target = 0.123555 restraints weight = 34438.926| |-----------------------------------------------------------------------------| r_work (start): 0.3485 rms_B_bonded: 4.03 r_work: 0.3183 rms_B_bonded: 3.67 restraints_weight: 0.5000 r_work (final): 0.3183 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8368 moved from start: 0.3949 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 23510 Z= 0.125 Angle : 0.777 16.211 32229 Z= 0.353 Chirality : 0.050 0.510 4002 Planarity : 0.005 0.090 3823 Dihedral : 5.387 43.305 2865 Min Nonbonded Distance : 2.374 Molprobity Statistics. All-atom Clashscore : 6.32 Ramachandran Plot: Outliers : 0.15 % Allowed : 8.49 % Favored : 91.35 % Rotamer: Outliers : 2.44 % Allowed : 16.52 % Favored : 81.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.40 % Cis-general : 0.00 % Twisted Proline : 2.40 % Twisted General : 0.12 % 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: -1.91 (0.16), residues: 2614 helix: 0.66 (0.31), residues: 314 sheet: -0.38 (0.20), residues: 795 loop : -2.31 (0.14), residues: 1505 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG O 81 TYR 0.019 0.001 TYR E 191 PHE 0.029 0.002 PHE O 50 TRP 0.016 0.001 TRP C 628 HIS 0.004 0.001 HIS E 330 Details of bonding type rmsd/Z covalent geometry : bond 0.00268 / 0.12 (23323) covalent geometry : angle 0.70268 / 0.34 (31704) SS BOND : bond 0.00324 / 0.18 ( 27) SS BOND : angle 1.07266 / 0.68 ( 54) hydrogen bonds : bond 0.03862 / 2.59 ( 555) hydrogen bonds : angle 5.01331 / 3.57 ( 1470) Misc. bond : bond 0.00093 / 0.05 ( 3) link_ALPHA1-2 : bond 0.00739 / 0.39 ( 6) link_ALPHA1-2 : angle 2.00484 / 1.16 ( 18) link_ALPHA1-3 : bond 0.00578 / 0.35 ( 22) link_ALPHA1-3 : angle 1.89549 / 1.22 ( 66) link_ALPHA1-6 : bond 0.00843 / 0.50 ( 18) link_ALPHA1-6 : angle 1.82467 / 1.28 ( 54) link_BETA1-4 : bond 0.00614 / 0.36 ( 47) link_BETA1-4 : angle 2.28854 / 1.39 ( 141) link_NAG-ASN : bond 0.00508 / 0.33 ( 64) link_NAG-ASN : angle 3.60833 / 2.43 ( 192) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5659.66 seconds wall clock time: 97 minutes 55.28 seconds (5875.28 seconds total)