Starting phenix.real_space_refine on Sat Jul 4 03:25:16 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9zrx_74654/07_2026/9zrx_74654.cif Found real_map, /net/cci-nas-00/data/ceres_data/9zrx_74654/07_2026/9zrx_74654.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9zrx_74654/07_2026/9zrx_74654.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9zrx_74654/07_2026/9zrx_74654.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9zrx_74654/07_2026/9zrx_74654.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9zrx_74654/07_2026/9zrx_74654.map" } resolution = 3.3 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= 0.001 sd= 0.011 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 108 5.16 5 C 10779 2.51 5 N 2850 2.21 5 O 3554 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 34 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 17291 Number of models: 1 Model: "" Number of chains: 53 Chain: "A" Number of atoms: 1036 Number of conformers: 1 Conformer: "" Number of residues, atoms: 135, 1036 Classifications: {'peptide': 135} Link IDs: {'PTRANS': 5, 'TRANS': 129} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'TYS:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "B" Number of atoms: 873 Number of conformers: 1 Conformer: "" Number of residues, atoms: 114, 873 Classifications: {'peptide': 114} Link IDs: {'PCIS': 2, 'PTRANS': 7, 'TRANS': 104} Chain: "b" Number of atoms: 3525 Number of conformers: 1 Conformer: "" Number of residues, atoms: 445, 3525 Classifications: {'peptide': 445} Link IDs: {'PTRANS': 22, 'TRANS': 422} Chain breaks: 3 Chain: "c" Number of atoms: 1026 Number of conformers: 1 Conformer: "" Number of residues, atoms: 127, 1026 Classifications: {'peptide': 127} Link IDs: {'PTRANS': 1, 'TRANS': 125} Chain breaks: 1 Chain: "d" Number of atoms: 3525 Number of conformers: 1 Conformer: "" Number of residues, atoms: 445, 3525 Classifications: {'peptide': 445} Link IDs: {'PTRANS': 22, 'TRANS': 422} Chain breaks: 3 Chain: "e" Number of atoms: 1026 Number of conformers: 1 Conformer: "" Number of residues, atoms: 127, 1026 Classifications: {'peptide': 127} Link IDs: {'PTRANS': 1, 'TRANS': 125} Chain breaks: 1 Chain: "f" Number of atoms: 3525 Number of conformers: 1 Conformer: "" Number of residues, atoms: 445, 3525 Classifications: {'peptide': 445} Link IDs: {'PTRANS': 22, 'TRANS': 422} Chain breaks: 3 Chain: "g" Number of atoms: 1026 Number of conformers: 1 Conformer: "" Number of residues, atoms: 127, 1026 Classifications: {'peptide': 127} Link IDs: {'PTRANS': 1, 'TRANS': 125} Chain breaks: 1 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 dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "D" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "E" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Chain: "F" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "G" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "H" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "I" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "J" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "K" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "L" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "M" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "N" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "O" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "P" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "Q" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Chain: "R" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "S" Number of atoms: 50 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 50 Unusual residues: {'BMA': 1, 'MAN': 1, 'NAG': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Chain: "T" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "U" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "V" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "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 dihedrals: 6 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 dihedrals: 6 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 dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "Z" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "a" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "h" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "i" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 33 Unusual residues: {'MAN': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "j" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "k" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "l" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Chain: "m" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "n" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Chain: "o" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "p" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "q" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "r" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "s" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "t" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "u" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "b" Number of atoms: 112 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 112 Unusual residues: {'NAG': 8} Classifications: {'undetermined': 8} Link IDs: {None: 7} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen dihedrals: 24 Unresolved non-hydrogen chiralities: 8 Chain: "c" Number of atoms: 42 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 42 Unusual residues: {'NAG': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "d" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 84 Unusual residues: {'NAG': 6} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 18 Unresolved non-hydrogen chiralities: 6 Chain: "e" Number of atoms: 42 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 42 Unusual residues: {'NAG': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "f" Number of atoms: 112 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 112 Unusual residues: {'NAG': 8} Classifications: {'undetermined': 8} Link IDs: {None: 7} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen dihedrals: 24 Unresolved non-hydrogen chiralities: 8 Chain: "g" Number of atoms: 42 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 42 Unusual residues: {'NAG': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Time building chain proxies: 3.94, per 1000 atoms: 0.23 Number of scatterers: 17291 At special positions: 0 Unit cell: (129.48, 133.63, 170.15, 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 108 16.00 O 3554 8.00 N 2850 7.00 C 10779 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=38, symmetry=0 Simple disulfide: pdb=" SG CYS A 22 " - pdb=" SG CYS A 97 " distance=2.03 Simple disulfide: pdb=" SG CYS B 23 " - pdb=" SG CYS B 93 " distance=2.04 Simple disulfide: pdb=" SG CYS b 54 " - pdb=" SG CYS b 74 " distance=2.03 Simple disulfide: pdb=" SG CYS b 119 " - pdb=" SG CYS b 205 " distance=2.03 Simple disulfide: pdb=" SG CYS b 126 " - pdb=" SG CYS b 196 " distance=2.03 Simple disulfide: pdb=" SG CYS b 131 " - pdb=" SG CYS b 157 " distance=2.03 Simple disulfide: pdb=" SG CYS b 201 " - pdb=" SG CYS b 433 " distance=2.03 Simple disulfide: pdb=" SG CYS b 218 " - pdb=" SG CYS b 247 " distance=2.03 Simple disulfide: pdb=" SG CYS b 228 " - pdb=" SG CYS b 239 " distance=2.03 Simple disulfide: pdb=" SG CYS b 296 " - pdb=" SG CYS b 331 " distance=2.03 Simple disulfide: pdb=" SG CYS b 378 " - pdb=" SG CYS b 445 " distance=2.04 Simple disulfide: pdb=" SG CYS b 385 " - pdb=" SG CYS b 418 " distance=2.03 Simple disulfide: pdb=" SG CYS b 501 " - pdb=" SG CYS c 605 " distance=2.03 Simple disulfide: pdb=" SG CYS c 598 " - pdb=" SG CYS c 604 " 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 131 " - pdb=" SG CYS d 157 " distance=2.03 Simple disulfide: pdb=" SG CYS d 201 " - pdb=" SG CYS d 433 " distance=2.03 Simple disulfide: pdb=" SG CYS d 218 " - pdb=" SG CYS d 247 " distance=2.03 Simple disulfide: pdb=" SG CYS d 228 " - pdb=" SG CYS d 239 " 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=2.04 Simple disulfide: pdb=" SG CYS d 385 " - pdb=" SG CYS d 418 " distance=2.03 Simple disulfide: pdb=" SG CYS d 501 " - pdb=" SG CYS e 605 " distance=2.03 Simple disulfide: pdb=" SG CYS e 598 " - pdb=" SG CYS e 604 " distance=2.03 Simple disulfide: pdb=" SG CYS f 54 " - pdb=" SG CYS f 74 " distance=2.04 Simple disulfide: pdb=" SG CYS f 119 " - pdb=" SG CYS f 205 " distance=2.03 Simple disulfide: pdb=" SG CYS f 126 " - pdb=" SG CYS f 196 " distance=2.03 Simple disulfide: pdb=" SG CYS f 131 " - pdb=" SG CYS f 157 " distance=2.03 Simple disulfide: pdb=" SG CYS f 201 " - pdb=" SG CYS f 433 " distance=2.03 Simple disulfide: pdb=" SG CYS f 218 " - pdb=" SG CYS f 247 " distance=2.03 Simple disulfide: pdb=" SG CYS f 228 " - pdb=" SG CYS f 239 " distance=2.03 Simple disulfide: pdb=" SG CYS f 296 " - pdb=" SG CYS f 331 " distance=2.03 Simple disulfide: pdb=" SG CYS f 378 " - pdb=" SG CYS f 445 " distance=2.04 Simple disulfide: pdb=" SG CYS f 385 " - pdb=" SG CYS f 418 " distance=2.03 Simple disulfide: pdb=" SG CYS f 501 " - pdb=" SG CYS g 605 " distance=2.03 Simple disulfide: pdb=" SG CYS g 598 " - pdb=" SG CYS g 604 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied ALPHA1-3 " BMA E 3 " - " MAN E 4 " " BMA Q 3 " - " MAN Q 4 " " BMA S 3 " - " MAN S 4 " " MAN i 1 " - " MAN i 2 " " BMA l 3 " - " MAN l 4 " " BMA n 3 " - " MAN n 4 " ALPHA1-6 " BMA E 3 " - " MAN E 5 " " BMA Q 3 " - " MAN Q 5 " " MAN i 1 " - " MAN i 3 " " BMA l 3 " - " MAN l 5 " " BMA n 3 " - " MAN n 5 " BETA1-4 " NAG C 1 " - " NAG C 2 " " NAG D 1 " - " NAG D 2 " " NAG D 2 " - " BMA D 3 " " NAG E 1 " - " NAG E 2 " " NAG E 2 " - " BMA E 3 " " NAG F 1 " - " NAG F 2 " " NAG G 1 " - " NAG G 2 " " NAG H 1 " - " NAG H 2 " " NAG I 1 " - " NAG I 2 " " NAG J 1 " - " NAG J 2 " " NAG J 2 " - " BMA J 3 " " NAG K 1 " - " NAG K 2 " " NAG L 1 " - " NAG L 2 " " NAG M 1 " - " NAG M 2 " " NAG N 1 " - " NAG N 2 " " NAG O 1 " - " NAG O 2 " " NAG P 1 " - " NAG P 2 " " NAG P 2 " - " BMA P 3 " " NAG Q 1 " - " NAG Q 2 " " NAG Q 2 " - " BMA Q 3 " " NAG R 1 " - " NAG R 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 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 a 1 " - " NAG a 2 " " NAG h 1 " - " NAG h 2 " " NAG j 1 " - " NAG j 2 " " NAG k 1 " - " NAG k 2 " " NAG k 2 " - " BMA k 3 " " NAG l 1 " - " NAG l 2 " " NAG 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 s 1 " - " NAG s 2 " " NAG t 1 " - " NAG t 2 " " NAG u 1 " - " NAG u 2 " NAG-ASN " NAG C 1 " - " ASN b 392 " " NAG D 1 " - " ASN b 332 " " NAG E 1 " - " ASN b 262 " " NAG F 1 " - " ASN b 156 " " NAG G 1 " - " ASN b 160 " " NAG H 1 " - " ASN b 197 " " NAG I 1 " - " ASN b 234 " " NAG J 1 " - " ASN b 241 " " NAG K 1 " - " ASN b 276 " " NAG L 1 " - " ASN b 301 " " NAG M 1 " - " ASN b 448 " " NAG N 1 " - " ASN b 465 " " NAG O 1 " - " ASN d 392 " " NAG P 1 " - " ASN d 332 " " NAG Q 1 " - " ASN d 262 " " NAG R 1 " - " ASN d 156 " " NAG S 1 " - " ASN d 160 " " NAG T 1 " - " ASN d 197 " " NAG U 1 " - " ASN d 234 " " NAG V 1 " - " ASN d 241 " " NAG W 1 " - " ASN d 276 " " NAG X 1 " - " ASN d 301 " " NAG Y 1 " - " ASN d 363 " " NAG Z 1 " - " ASN d 386 " " NAG a 1 " - " ASN d 448 " " NAG b 601 " - " ASN b 88 " " NAG b 602 " - " ASN b 133 " " NAG b 603 " - " ASN b 339 " " NAG b 604 " - " ASN b 355 " " NAG b 605 " - " ASN b 269 " " NAG b 606 " - " ASN b 363 " " NAG b 607 " - " ASN b 386 " " NAG c 701 " - " ASN c 611 " " NAG c 702 " - " ASN c 637 " " NAG c 703 " - " ASN c 625 " " NAG d 601 " - " ASN d 88 " " NAG d 602 " - " ASN d 133 " " NAG d 603 " - " ASN d 355 " " NAG d 604 " - " ASN d 269 " " NAG e 701 " - " ASN e 611 " " NAG e 702 " - " ASN e 637 " " NAG e 703 " - " ASN e 625 " " NAG f 601 " - " ASN f 88 " " NAG f 602 " - " ASN f 133 " " NAG f 603 " - " ASN f 339 " " NAG f 604 " - " ASN f 355 " " NAG f 605 " - " ASN f 269 " " NAG f 607 " - " ASN f 386 " " NAG f 608 " - " ASN f 363 " " NAG g 701 " - " ASN g 611 " " NAG g 702 " - " ASN g 637 " " NAG g 703 " - " ASN g 625 " " NAG h 1 " - " ASN d 465 " " NAG j 1 " - " ASN f 392 " " NAG k 1 " - " ASN f 332 " " NAG l 1 " - " ASN f 262 " " NAG m 1 " - " ASN f 156 " " NAG n 1 " - " ASN f 160 " " NAG o 1 " - " ASN f 197 " " NAG p 1 " - " ASN f 234 " " NAG q 1 " - " ASN f 241 " " NAG r 1 " - " ASN f 276 " " NAG s 1 " - " ASN f 301 " " NAG t 1 " - " ASN f 448 " " NAG u 1 " - " ASN f 465 " Time building additional restraints: 1.63 Conformation dependent library (CDL) restraints added in 677.0 milliseconds 3844 Ramachandran restraints generated. 1922 Oldfield, 0 Emsley, 1922 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3656 Finding SS restraints... Secondary structure from input PDB file: 46 helices and 35 sheets defined 23.4% alpha, 31.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.41 Creating SS restraints... Processing helix chain 'A' and resid 88 through 92 Processing helix chain 'B' and resid 84 through 88 removed outlier: 3.970A pdb=" N VAL B 88 " --> pdb=" O ALA B 85 " (cutoff:3.500A) Processing helix chain 'b' and resid 70 through 74 Processing helix chain 'b' and resid 99 through 117 Processing helix chain 'b' and resid 122 through 126 Processing helix chain 'b' and resid 334 through 351 removed outlier: 3.703A pdb=" N LYS b 340 " --> pdb=" O SER b 336 " (cutoff:3.500A) removed outlier: 4.114A pdb=" N THR b 341 " --> pdb=" O ARG b 337 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N LEU b 342 " --> pdb=" O TRP b 338 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N THR b 351 " --> pdb=" O GLU b 347 " (cutoff:3.500A) Processing helix chain 'b' and resid 368 through 373 Processing helix chain 'b' and resid 387 through 390 Processing helix chain 'b' and resid 475 through 481 removed outlier: 4.169A pdb=" N TRP b 479 " --> pdb=" O MET b 475 " (cutoff:3.500A) Processing helix chain 'b' and resid 482 through 484 No H-bonds generated for 'chain 'b' and resid 482 through 484' Processing helix chain 'c' and resid 529 through 534 Processing helix chain 'c' and resid 536 through 543 removed outlier: 3.996A pdb=" N GLN c 540 " --> pdb=" O THR c 536 " (cutoff:3.500A) Processing helix chain 'c' and resid 544 through 546 No H-bonds generated for 'chain 'c' and resid 544 through 546' Processing helix chain 'c' and resid 569 through 596 removed outlier: 3.570A pdb=" N ASP c 589 " --> pdb=" O ARG c 585 " (cutoff:3.500A) removed outlier: 3.874A pdb=" N LEU c 592 " --> pdb=" O ARG c 588 " (cutoff:3.500A) removed outlier: 3.843A pdb=" N LEU c 593 " --> pdb=" O ASP c 589 " (cutoff:3.500A) Processing helix chain 'c' and resid 619 through 625 Processing helix chain 'c' and resid 627 through 636 removed outlier: 3.599A pdb=" N TRP c 631 " --> pdb=" O THR c 627 " (cutoff:3.500A) removed outlier: 4.243A pdb=" N LYS c 633 " --> pdb=" O LEU c 629 " (cutoff:3.500A) removed outlier: 4.804A pdb=" N GLU c 634 " --> pdb=" O GLN c 630 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N ILE c 635 " --> pdb=" O TRP c 631 " (cutoff:3.500A) Processing helix chain 'c' and resid 638 through 658 removed outlier: 3.572A pdb=" N GLU c 647 " --> pdb=" O TYR c 643 " (cutoff:3.500A) removed outlier: 3.880A pdb=" N GLU c 648 " --> pdb=" O ARG c 644 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N SER c 649 " --> pdb=" O LEU c 645 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N GLN c 650 " --> pdb=" O ILE c 646 " (cutoff:3.500A) removed outlier: 4.076A pdb=" N GLN c 653 " --> pdb=" O SER c 649 " (cutoff:3.500A) Processing helix chain 'd' and resid 70 through 74 Processing helix chain 'd' and resid 99 through 117 Processing helix chain 'd' and resid 334 through 351 removed outlier: 3.594A pdb=" N THR d 341 " --> pdb=" O ARG d 337 " (cutoff:3.500A) Processing helix chain 'd' and resid 368 through 373 Processing helix chain 'd' and resid 387 through 390 Processing helix chain 'd' and resid 475 through 481 removed outlier: 4.065A pdb=" N TRP d 479 " --> pdb=" O MET d 475 " (cutoff:3.500A) Processing helix chain 'd' and resid 482 through 484 No H-bonds generated for 'chain 'd' and resid 482 through 484' Processing helix chain 'e' and resid 529 through 534 Processing helix chain 'e' and resid 536 through 543 removed outlier: 3.754A pdb=" N GLN e 540 " --> pdb=" O THR e 536 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N GLN e 543 " --> pdb=" O VAL e 539 " (cutoff:3.500A) Processing helix chain 'e' and resid 544 through 546 No H-bonds generated for 'chain 'e' and resid 544 through 546' Processing helix chain 'e' and resid 569 through 596 removed outlier: 4.026A pdb=" N LEU e 592 " --> pdb=" O ARG e 588 " (cutoff:3.500A) removed outlier: 4.101A pdb=" N LEU e 593 " --> pdb=" O ASP e 589 " (cutoff:3.500A) Processing helix chain 'e' and resid 618 through 625 removed outlier: 3.632A pdb=" N ILE e 622 " --> pdb=" O SER e 618 " (cutoff:3.500A) Processing helix chain 'e' and resid 627 through 636 removed outlier: 4.380A pdb=" N LYS e 633 " --> pdb=" O LEU e 629 " (cutoff:3.500A) removed outlier: 3.863A pdb=" N GLU e 634 " --> pdb=" O GLN e 630 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N ILE e 635 " --> pdb=" O TRP e 631 " (cutoff:3.500A) Processing helix chain 'e' and resid 638 through 658 removed outlier: 3.659A pdb=" N GLN e 653 " --> pdb=" O SER e 649 " (cutoff:3.500A) Processing helix chain 'f' and resid 70 through 74 Processing helix chain 'f' and resid 99 through 117 Processing helix chain 'f' and resid 122 through 126 removed outlier: 3.600A pdb=" N LEU f 125 " --> pdb=" O LEU f 122 " (cutoff:3.500A) removed outlier: 3.791A pdb=" N CYS f 126 " --> pdb=" O THR f 123 " (cutoff:3.500A) No H-bonds generated for 'chain 'f' and resid 122 through 126' Processing helix chain 'f' and resid 150 through 152 No H-bonds generated for 'chain 'f' and resid 150 through 152' Processing helix chain 'f' and resid 334 through 351 removed outlier: 3.948A pdb=" N LYS f 340 " --> pdb=" O SER f 336 " (cutoff:3.500A) removed outlier: 3.934A pdb=" N GLN f 343 " --> pdb=" O ASN f 339 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N THR f 351 " --> pdb=" O GLU f 347 " (cutoff:3.500A) Processing helix chain 'f' and resid 368 through 373 Processing helix chain 'f' and resid 387 through 390 Processing helix chain 'f' and resid 475 through 481 removed outlier: 4.191A pdb=" N TRP f 479 " --> pdb=" O MET f 475 " (cutoff:3.500A) Processing helix chain 'f' and resid 482 through 484 No H-bonds generated for 'chain 'f' and resid 482 through 484' Processing helix chain 'g' and resid 529 through 534 Processing helix chain 'g' and resid 536 through 543 removed outlier: 3.936A pdb=" N GLN g 540 " --> pdb=" O THR g 536 " (cutoff:3.500A) Processing helix chain 'g' and resid 544 through 546 No H-bonds generated for 'chain 'g' and resid 544 through 546' Processing helix chain 'g' and resid 569 through 596 removed outlier: 3.601A pdb=" N LYS g 574 " --> pdb=" O VAL g 570 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N ASP g 589 " --> pdb=" O ARG g 585 " (cutoff:3.500A) removed outlier: 4.417A pdb=" N LEU g 592 " --> pdb=" O ARG g 588 " (cutoff:3.500A) removed outlier: 4.088A pdb=" N LEU g 593 " --> pdb=" O ASP g 589 " (cutoff:3.500A) Processing helix chain 'g' and resid 620 through 625 Processing helix chain 'g' and resid 627 through 658 removed outlier: 4.065A pdb=" N LYS g 633 " --> pdb=" O LEU g 629 " (cutoff:3.500A) removed outlier: 3.789A pdb=" N GLU g 634 " --> pdb=" O GLN g 630 " (cutoff:3.500A) removed outlier: 5.868A pdb=" N ASN g 637 " --> pdb=" O LYS g 633 " (cutoff:3.500A) removed outlier: 5.195A pdb=" N TYR g 638 " --> pdb=" O GLU g 634 " (cutoff:3.500A) removed outlier: 4.758A pdb=" N GLN g 640 " --> pdb=" O GLY g 636 " (cutoff:3.500A) removed outlier: 5.376A pdb=" N LEU g 641 " --> pdb=" O ASN g 637 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N SER g 649 " --> pdb=" O LEU g 645 " (cutoff:3.500A) removed outlier: 3.818A pdb=" N GLN g 652 " --> pdb=" O GLU g 648 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 3 through 7 removed outlier: 3.628A pdb=" N GLN A 79 " --> pdb=" O ASP A 74 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 11 through 12 Processing sheet with id=AA3, first strand: chain 'A' and resid 59 through 61 removed outlier: 5.504A pdb=" N TRP A 48 " --> pdb=" O ARG A 39 " (cutoff:3.500A) removed outlier: 6.978A pdb=" N ARG A 39 " --> pdb=" O TRP A 48 " (cutoff:3.500A) removed outlier: 3.948A pdb=" N GLY A 50 " --> pdb=" O TRP A 37 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 102 through 105 removed outlier: 3.551A pdb=" N THR A 118 " --> pdb=" O SER A 103 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 4 through 7 Processing sheet with id=AA6, first strand: chain 'B' and resid 10 through 13 removed outlier: 3.969A pdb=" N GLU B 110 " --> pdb=" O LEU B 11 " (cutoff:3.500A) removed outlier: 6.579A pdb=" N LEU B 38 " --> pdb=" O TYR B 54 " (cutoff:3.500A) removed outlier: 4.736A pdb=" N TYR B 54 " --> pdb=" O LEU B 38 " (cutoff:3.500A) removed outlier: 6.720A pdb=" N TRP B 40 " --> pdb=" O LEU B 52 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 10 through 13 removed outlier: 3.969A pdb=" N GLU B 110 " --> pdb=" O LEU B 11 " (cutoff:3.500A) removed outlier: 3.999A pdb=" N THR B 102 " --> pdb=" O GLN B 95 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'b' and resid 495 through 499 removed outlier: 5.537A pdb=" N VAL c 608 " --> pdb=" O VAL b 36 " (cutoff:3.500A) removed outlier: 8.343A pdb=" N VAL b 38 " --> pdb=" O THR c 606 " (cutoff:3.500A) removed outlier: 7.763A pdb=" N THR c 606 " --> pdb=" O VAL b 38 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'b' and resid 45 through 47 Processing sheet with id=AB1, first strand: chain 'b' and resid 66 through 67 removed outlier: 7.188A pdb=" N HIS b 66 " --> pdb=" O SER b 209 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB1 Processing sheet with id=AB2, first strand: chain 'b' and resid 91 through 94 Processing sheet with id=AB3, first strand: chain 'b' and resid 169 through 177 Processing sheet with id=AB4, first strand: chain 'b' and resid 202 through 203 removed outlier: 6.270A pdb=" N THR b 202 " --> pdb=" O TYR b 435 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'b' and resid 259 through 261 removed outlier: 3.654A pdb=" N GLY b 451 " --> pdb=" O LEU b 260 " (cutoff:3.500A) removed outlier: 10.317A pdb=" N LYS b 444 " --> pdb=" O ILE b 294 " (cutoff:3.500A) removed outlier: 11.568A pdb=" N ILE b 294 " --> pdb=" O LYS b 444 " (cutoff:3.500A) removed outlier: 9.959A pdb=" N GLU b 446 " --> pdb=" O VAL b 292 " (cutoff:3.500A) removed outlier: 10.953A pdb=" N VAL b 292 " --> pdb=" O GLU b 446 " (cutoff:3.500A) removed outlier: 9.189A pdb=" N ASN b 448 " --> pdb=" O GLN b 290 " (cutoff:3.500A) removed outlier: 10.073A pdb=" N GLN b 290 " --> pdb=" O ASN b 448 " (cutoff:3.500A) removed outlier: 6.628A pdb=" N THR b 450 " --> pdb=" O LEU b 288 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N HIS b 330 " --> pdb=" O ILE b 297 " (cutoff:3.500A) removed outlier: 3.789A pdb=" N LYS b 421 " --> pdb=" O PHE b 382 " (cutoff:3.500A) removed outlier: 4.706A pdb=" N PHE b 382 " --> pdb=" O LYS b 421 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'b' and resid 271 through 273 removed outlier: 6.628A pdb=" N THR b 450 " --> pdb=" O LEU b 288 " (cutoff:3.500A) removed outlier: 10.073A pdb=" N GLN b 290 " --> pdb=" O ASN b 448 " (cutoff:3.500A) removed outlier: 9.189A pdb=" N ASN b 448 " --> pdb=" O GLN b 290 " (cutoff:3.500A) removed outlier: 10.953A pdb=" N VAL b 292 " --> pdb=" O GLU b 446 " (cutoff:3.500A) removed outlier: 9.959A pdb=" N GLU b 446 " --> pdb=" O VAL b 292 " (cutoff:3.500A) removed outlier: 11.568A pdb=" N ILE b 294 " --> pdb=" O LYS b 444 " (cutoff:3.500A) removed outlier: 10.317A pdb=" N LYS b 444 " --> pdb=" O ILE b 294 " (cutoff:3.500A) removed outlier: 6.847A pdb=" N THR b 357 " --> pdb=" O GLU b 466 " (cutoff:3.500A) removed outlier: 8.011A pdb=" N PHE b 468 " --> pdb=" O THR b 357 " (cutoff:3.500A) removed outlier: 6.760A pdb=" N ILE b 359 " --> pdb=" O PHE b 468 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'b' and resid 301 through 312 removed outlier: 7.412A pdb=" N ASN b 301 " --> pdb=" O ILE b 323 " (cutoff:3.500A) removed outlier: 5.372A pdb=" N ILE b 323 " --> pdb=" O ASN b 301 " (cutoff:3.500A) removed outlier: 4.906A pdb=" N THR b 303 " --> pdb=" O GLY b 321 " (cutoff:3.500A) removed outlier: 7.178A pdb=" N GLN b 315 " --> pdb=" O ILE b 309 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'd' and resid 494 through 499 removed outlier: 5.546A pdb=" N VAL e 608 " --> pdb=" O VAL d 36 " (cutoff:3.500A) removed outlier: 8.241A pdb=" N VAL d 38 " --> pdb=" O THR e 606 " (cutoff:3.500A) removed outlier: 7.741A pdb=" N THR e 606 " --> pdb=" O VAL d 38 " (cutoff:3.500A) removed outlier: 8.061A pdb=" N TYR d 40 " --> pdb=" O CYS e 604 " (cutoff:3.500A) removed outlier: 8.747A pdb=" N CYS e 604 " --> pdb=" O TYR d 40 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'd' and resid 45 through 47 Processing sheet with id=AC1, first strand: chain 'd' and resid 66 through 67 removed outlier: 7.331A pdb=" N HIS d 66 " --> pdb=" O SER d 209 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC1 Processing sheet with id=AC2, first strand: chain 'd' and resid 91 through 94 Processing sheet with id=AC3, first strand: chain 'd' and resid 130 through 132 Processing sheet with id=AC4, first strand: chain 'd' and resid 181 through 183 Processing sheet with id=AC5, first strand: chain 'd' and resid 202 through 203 removed outlier: 6.206A pdb=" N THR d 202 " --> pdb=" O TYR d 435 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'd' and resid 259 through 261 removed outlier: 3.509A pdb=" N GLY d 451 " --> pdb=" O LEU d 260 " (cutoff:3.500A) removed outlier: 3.903A pdb=" N ILE d 443 " --> pdb=" O ARG d 298 " (cutoff:3.500A) removed outlier: 7.720A pdb=" N GLY d 451 " --> pdb=" O GLN d 290 " (cutoff:3.500A) removed outlier: 10.999A pdb=" N GLN d 290 " --> pdb=" O GLY d 451 " (cutoff:3.500A) removed outlier: 12.041A pdb=" N LEU d 453 " --> pdb=" O LEU d 288 " (cutoff:3.500A) removed outlier: 12.038A pdb=" N LEU d 288 " --> pdb=" O LEU d 453 " (cutoff:3.500A) removed outlier: 10.673A pdb=" N THR d 455 " --> pdb=" O VAL d 286 " (cutoff:3.500A) removed outlier: 10.996A pdb=" N VAL d 286 " --> pdb=" O THR d 455 " (cutoff:3.500A) removed outlier: 4.234A pdb=" N ALA d 329 " --> pdb=" O CYS d 418 " (cutoff:3.500A) removed outlier: 3.805A pdb=" N LYS d 421 " --> pdb=" O PHE d 382 " (cutoff:3.500A) removed outlier: 4.755A pdb=" N PHE d 382 " --> pdb=" O LYS d 421 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N PHE d 376 " --> pdb=" O PHE d 383 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'd' and resid 271 through 273 removed outlier: 10.996A pdb=" N VAL d 286 " --> pdb=" O THR d 455 " (cutoff:3.500A) removed outlier: 10.673A pdb=" N THR d 455 " --> pdb=" O VAL d 286 " (cutoff:3.500A) removed outlier: 12.038A pdb=" N LEU d 288 " --> pdb=" O LEU d 453 " (cutoff:3.500A) removed outlier: 12.041A pdb=" N LEU d 453 " --> pdb=" O LEU d 288 " (cutoff:3.500A) removed outlier: 10.999A pdb=" N GLN d 290 " --> pdb=" O GLY d 451 " (cutoff:3.500A) removed outlier: 7.720A pdb=" N GLY d 451 " --> pdb=" O GLN d 290 " (cutoff:3.500A) removed outlier: 3.903A pdb=" N ILE d 443 " --> pdb=" O ARG d 298 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'd' and resid 301 through 312 removed outlier: 7.028A pdb=" N ASN d 301 " --> pdb=" O ILE d 323 " (cutoff:3.500A) removed outlier: 4.871A pdb=" N ILE d 323 " --> pdb=" O ASN d 301 " (cutoff:3.500A) removed outlier: 4.990A pdb=" N THR d 303 " --> pdb=" O GLY d 321 " (cutoff:3.500A) removed outlier: 7.063A pdb=" N GLN d 315 " --> pdb=" O ILE d 309 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'f' and resid 495 through 499 removed outlier: 5.482A pdb=" N VAL g 608 " --> pdb=" O VAL f 36 " (cutoff:3.500A) removed outlier: 8.163A pdb=" N VAL f 38 " --> pdb=" O THR g 606 " (cutoff:3.500A) removed outlier: 7.767A pdb=" N THR g 606 " --> pdb=" O VAL f 38 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'f' and resid 45 through 47 Processing sheet with id=AD2, first strand: chain 'f' and resid 53 through 55 Processing sheet with id=AD3, first strand: chain 'f' and resid 91 through 94 Processing sheet with id=AD4, first strand: chain 'f' and resid 169 through 177 Processing sheet with id=AD5, first strand: chain 'f' and resid 202 through 203 removed outlier: 6.317A pdb=" N THR f 202 " --> pdb=" O TYR f 435 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'f' and resid 259 through 261 removed outlier: 3.542A pdb=" N GLY f 451 " --> pdb=" O LEU f 260 " (cutoff:3.500A) removed outlier: 10.143A pdb=" N LYS f 444 " --> pdb=" O ILE f 294 " (cutoff:3.500A) removed outlier: 11.394A pdb=" N ILE f 294 " --> pdb=" O LYS f 444 " (cutoff:3.500A) removed outlier: 9.800A pdb=" N GLU f 446 " --> pdb=" O VAL f 292 " (cutoff:3.500A) removed outlier: 10.837A pdb=" N VAL f 292 " --> pdb=" O GLU f 446 " (cutoff:3.500A) removed outlier: 9.416A pdb=" N ASN f 448 " --> pdb=" O GLN f 290 " (cutoff:3.500A) removed outlier: 10.067A pdb=" N GLN f 290 " --> pdb=" O ASN f 448 " (cutoff:3.500A) removed outlier: 6.829A pdb=" N THR f 450 " --> pdb=" O LEU f 288 " (cutoff:3.500A) removed outlier: 4.476A pdb=" N ALA f 329 " --> pdb=" O CYS f 418 " (cutoff:3.500A) removed outlier: 3.733A pdb=" N LYS f 421 " --> pdb=" O PHE f 382 " (cutoff:3.500A) removed outlier: 4.670A pdb=" N PHE f 382 " --> pdb=" O LYS f 421 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'f' and resid 271 through 273 removed outlier: 6.829A pdb=" N THR f 450 " --> pdb=" O LEU f 288 " (cutoff:3.500A) removed outlier: 10.067A pdb=" N GLN f 290 " --> pdb=" O ASN f 448 " (cutoff:3.500A) removed outlier: 9.416A pdb=" N ASN f 448 " --> pdb=" O GLN f 290 " (cutoff:3.500A) removed outlier: 10.837A pdb=" N VAL f 292 " --> pdb=" O GLU f 446 " (cutoff:3.500A) removed outlier: 9.800A pdb=" N GLU f 446 " --> pdb=" O VAL f 292 " (cutoff:3.500A) removed outlier: 11.394A pdb=" N ILE f 294 " --> pdb=" O LYS f 444 " (cutoff:3.500A) removed outlier: 10.143A pdb=" N LYS f 444 " --> pdb=" O ILE f 294 " (cutoff:3.500A) removed outlier: 6.499A pdb=" N THR f 357 " --> pdb=" O GLU f 466 " (cutoff:3.500A) removed outlier: 7.887A pdb=" N PHE f 468 " --> pdb=" O THR f 357 " (cutoff:3.500A) removed outlier: 6.751A pdb=" N ILE f 359 " --> pdb=" O PHE f 468 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N SER f 393 " --> pdb=" O PHE f 361 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'f' and resid 301 through 312 removed outlier: 6.929A pdb=" N ASN f 301 " --> pdb=" O ILE f 323 " (cutoff:3.500A) removed outlier: 4.807A pdb=" N ILE f 323 " --> pdb=" O ASN f 301 " (cutoff:3.500A) removed outlier: 6.389A pdb=" N THR f 303 " --> pdb=" O GLY f 321 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N LYS f 305 " --> pdb=" O ALA f 319 " (cutoff:3.500A) removed outlier: 7.100A pdb=" N GLN f 315 " --> pdb=" O ILE f 309 " (cutoff:3.500A) 570 hydrogen bonds defined for protein. 1533 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: 2.93 Time building geometry restraints manager: 2.05 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 5199 1.34 - 1.46: 4511 1.46 - 1.58: 7771 1.58 - 1.70: 1 1.70 - 1.83: 138 Bond restraints: 17620 Sorted by residual: bond pdb=" CB GLU c 659 " pdb=" CG GLU c 659 " ideal model delta sigma weight residual 1.520 1.576 -0.056 3.00e-02 1.11e+03 3.49e+00 bond pdb=" C VAL A 12 " pdb=" N ARG A 13 " ideal model delta sigma weight residual 1.327 1.380 -0.053 2.86e-02 1.22e+03 3.39e+00 bond pdb=" N SER d 410 " pdb=" CA SER d 410 " ideal model delta sigma weight residual 1.458 1.492 -0.034 1.90e-02 2.77e+03 3.17e+00 bond pdb=" N SER b 410 " pdb=" CA SER b 410 " ideal model delta sigma weight residual 1.458 1.492 -0.034 1.90e-02 2.77e+03 3.14e+00 bond pdb=" N GLN A 1 " pdb=" CA GLN A 1 " ideal model delta sigma weight residual 1.458 1.491 -0.033 1.90e-02 2.77e+03 3.07e+00 ... (remaining 17615 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.45: 23236 2.45 - 4.90: 602 4.90 - 7.35: 61 7.35 - 9.80: 8 9.80 - 12.25: 2 Bond angle restraints: 23909 Sorted by residual: angle pdb=" CB LYS B 108 " pdb=" CG LYS B 108 " pdb=" CD LYS B 108 " ideal model delta sigma weight residual 111.30 123.55 -12.25 2.30e+00 1.89e-01 2.84e+01 angle pdb=" N VAL d 464 " pdb=" CA VAL d 464 " pdb=" C VAL d 464 " ideal model delta sigma weight residual 112.29 107.82 4.47 9.40e-01 1.13e+00 2.27e+01 angle pdb=" N VAL f 289 " pdb=" CA VAL f 289 " pdb=" C VAL f 289 " ideal model delta sigma weight residual 111.81 107.84 3.97 8.60e-01 1.35e+00 2.13e+01 angle pdb=" CB GLU c 659 " pdb=" CG GLU c 659 " pdb=" CD GLU c 659 " ideal model delta sigma weight residual 112.60 119.71 -7.11 1.70e+00 3.46e-01 1.75e+01 angle pdb=" CA ASN f 339 " pdb=" CB ASN f 339 " pdb=" CG ASN f 339 " ideal model delta sigma weight residual 112.60 116.75 -4.15 1.00e+00 1.00e+00 1.72e+01 ... (remaining 23904 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.93: 11317 17.93 - 35.85: 651 35.85 - 53.78: 207 53.78 - 71.70: 53 71.70 - 89.63: 18 Dihedral angle restraints: 12246 sinusoidal: 6583 harmonic: 5663 Sorted by residual: dihedral pdb=" CB CYS b 126 " pdb=" SG CYS b 126 " pdb=" SG CYS b 196 " pdb=" CB CYS b 196 " ideal model delta sinusoidal sigma weight residual 93.00 160.49 -67.49 1 1.00e+01 1.00e-02 5.92e+01 dihedral pdb=" CB CYS f 126 " pdb=" SG CYS f 126 " pdb=" SG CYS f 196 " pdb=" CB CYS f 196 " ideal model delta sinusoidal sigma weight residual 93.00 158.00 -65.00 1 1.00e+01 1.00e-02 5.54e+01 dihedral pdb=" CB CYS d 126 " pdb=" SG CYS d 126 " pdb=" SG CYS d 196 " pdb=" CB CYS d 196 " ideal model delta sinusoidal sigma weight residual 93.00 146.31 -53.31 1 1.00e+01 1.00e-02 3.86e+01 ... (remaining 12243 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.092: 2804 0.092 - 0.183: 226 0.183 - 0.275: 3 0.275 - 0.366: 1 0.366 - 0.458: 3 Chirality restraints: 3037 Sorted by residual: chirality pdb=" C1 NAG f 603 " pdb=" ND2 ASN f 339 " pdb=" C2 NAG f 603 " pdb=" O5 NAG f 603 " both_signs ideal model delta sigma weight residual False -2.40 -1.94 -0.46 2.00e-01 2.50e+01 5.25e+00 chirality pdb=" C1 NAG f 601 " pdb=" ND2 ASN f 88 " pdb=" C2 NAG f 601 " pdb=" O5 NAG f 601 " both_signs ideal model delta sigma weight residual False -2.40 -1.99 -0.41 2.00e-01 2.50e+01 4.28e+00 chirality pdb=" C1 NAG b 601 " pdb=" ND2 ASN b 88 " pdb=" C2 NAG b 601 " pdb=" O5 NAG b 601 " both_signs ideal model delta sigma weight residual False -2.40 -1.99 -0.41 2.00e-01 2.50e+01 4.15e+00 ... (remaining 3034 not shown) Planarity restraints: 2929 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CG GLU g 659 " 0.012 2.00e-02 2.50e+03 2.41e-02 5.81e+00 pdb=" CD GLU g 659 " -0.042 2.00e-02 2.50e+03 pdb=" OE1 GLU g 659 " 0.015 2.00e-02 2.50e+03 pdb=" OE2 GLU g 659 " 0.015 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASP b 167 " -0.011 2.00e-02 2.50e+03 2.31e-02 5.32e+00 pdb=" CG ASP b 167 " 0.040 2.00e-02 2.50e+03 pdb=" OD1 ASP b 167 " -0.014 2.00e-02 2.50e+03 pdb=" OD2 ASP b 167 " -0.014 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN b 88 " -0.022 2.00e-02 2.50e+03 2.03e-02 5.16e+00 pdb=" CG ASN b 88 " 0.027 2.00e-02 2.50e+03 pdb=" OD1 ASN b 88 " -0.003 2.00e-02 2.50e+03 pdb=" ND2 ASN b 88 " 0.020 2.00e-02 2.50e+03 pdb=" C1 NAG b 601 " -0.021 2.00e-02 2.50e+03 ... (remaining 2926 not shown) Histogram of nonbonded interaction distances: 1.94 - 2.53: 59 2.53 - 3.12: 13493 3.12 - 3.71: 24517 3.71 - 4.31: 35107 4.31 - 4.90: 59066 Nonbonded interactions: 132242 Sorted by model distance: nonbonded pdb=" OG SER B 26 " pdb=" OE1 GLN B 27 " model vdw 1.935 3.040 nonbonded pdb=" O6 NAG q 1 " pdb=" O5 NAG q 2 " model vdw 2.079 3.040 nonbonded pdb=" O2 BMA S 3 " pdb=" O6 BMA S 3 " model vdw 2.108 3.040 nonbonded pdb=" O TRP f 401 " pdb=" O3 NAG f 603 " model vdw 2.248 3.040 nonbonded pdb=" OG SER c 612 " pdb=" OD1 ASN c 616 " model vdw 2.269 3.040 ... (remaining 132237 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 'C' selection = chain 'F' selection = chain 'G' selection = chain 'H' selection = chain 'I' selection = chain 'K' selection = chain 'L' selection = chain 'M' selection = chain 'N' selection = chain 'O' selection = chain 'R' selection = chain 'T' selection = chain 'U' selection = chain 'V' selection = chain 'W' selection = chain 'X' selection = chain 'Y' selection = chain 'Z' selection = chain 'a' selection = chain 'h' selection = chain 'j' selection = chain 'm' selection = chain 'o' selection = chain 'p' selection = chain 'q' selection = chain 'r' selection = chain 's' selection = chain 't' selection = chain 'u' } ncs_group { reference = chain 'D' selection = chain 'J' selection = chain 'P' selection = chain 'k' } ncs_group { reference = chain 'E' selection = chain 'Q' selection = chain 'l' selection = chain 'n' } ncs_group { reference = (chain 'b' and resid 33 through 606) selection = chain 'd' selection = (chain 'f' and resid 33 through 606) } ncs_group { reference = chain 'c' selection = chain 'e' selection = chain 'g' } 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: 4.670 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.380 Check model and map are aligned: 0.060 Set scattering table: 0.040 Process input model: 16.110 Find NCS groups from input model: 0.680 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:1.090 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 23.120 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8185 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 : 0.004 0.061 17781 Z= 0.184 Angle : 1.005 12.721 24354 Z= 0.510 Chirality : 0.049 0.458 3037 Planarity : 0.005 0.084 2864 Dihedral : 12.722 89.630 8476 Min Nonbonded Distance : 1.935 Molprobity Statistics. All-atom Clashscore : 2.76 Ramachandran Plot: Outliers : 0.05 % Allowed : 4.53 % Favored : 95.42 % Rotamer: Outliers : 0.12 % Allowed : 8.29 % Favored : 91.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.41 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.59 (0.18), residues: 1922 helix: -0.68 (0.27), residues: 375 sheet: -0.97 (0.22), residues: 517 loop : -1.18 (0.18), residues: 1030 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG c 588 TYR 0.030 0.001 TYR g 638 PHE 0.029 0.001 PHE B 76 TRP 0.029 0.002 TRP A 37 HIS 0.017 0.001 HIS A 104 Details of bonding type rmsd/Z covalent geometry : bond 0.00388 / 0.18 (17620) covalent geometry : angle 0.91539 / 0.49 (23909) SS BOND : bond 0.00310 / 0.20 ( 38) SS BOND : angle 1.56148 / 0.94 ( 76) hydrogen bonds : bond 0.23905 / 16.52 ( 547) hydrogen bonds : angle 8.59302 / 5.74 ( 1533) link_ALPHA1-3 : bond 0.01678 / 0.76 ( 6) link_ALPHA1-3 : angle 2.25970 / 1.33 ( 18) link_ALPHA1-6 : bond 0.01427 / 0.67 ( 5) link_ALPHA1-6 : angle 2.10960 / 1.23 ( 15) link_BETA1-4 : bond 0.00757 / 0.56 ( 47) link_BETA1-4 : angle 3.90672 / 2.38 ( 141) link_NAG-ASN : bond 0.00841 / 0.32 ( 65) link_NAG-ASN : angle 3.27387 / 2.28 ( 195) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3844 Ramachandran restraints generated. 1922 Oldfield, 0 Emsley, 1922 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3844 Ramachandran restraints generated. 1922 Oldfield, 0 Emsley, 1922 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 202 residues out of total 1736 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 200 time to evaluate : 0.696 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: A 68 ARG cc_start: 0.8232 (mtp-110) cc_final: 0.7801 (mtp-110) REVERT: A 74 ASP cc_start: 0.8586 (p0) cc_final: 0.8145 (p0) REVERT: B 11 LEU cc_start: 0.8882 (tp) cc_final: 0.8651 (tt) REVERT: B 40 TRP cc_start: 0.8687 (m100) cc_final: 0.8029 (m100) REVERT: B 65 ASP cc_start: 0.9649 (p0) cc_final: 0.9378 (t0) REVERT: B 67 PHE cc_start: 0.8583 (m-80) cc_final: 0.8067 (m-80) REVERT: B 84 GLU cc_start: 0.6790 (mp0) cc_final: 0.6121 (mp0) REVERT: c 568 LEU cc_start: 0.7966 (tt) cc_final: 0.7488 (mm) REVERT: c 588 ARG cc_start: 0.8889 (ttp80) cc_final: 0.8377 (ttm-80) REVERT: e 519 ARG cc_start: 0.7719 (mmp80) cc_final: 0.7253 (tpp-160) REVERT: e 536 THR cc_start: 0.8778 (p) cc_final: 0.8355 (t) REVERT: e 607 ASN cc_start: 0.9271 (m110) cc_final: 0.8825 (p0) REVERT: e 638 TYR cc_start: 0.9072 (m-80) cc_final: 0.8739 (m-80) REVERT: f 161 MET cc_start: 0.8422 (tpp) cc_final: 0.7855 (tpp) REVERT: g 588 ARG cc_start: 0.8895 (ttm110) cc_final: 0.7948 (tmm-80) REVERT: g 589 ASP cc_start: 0.8389 (m-30) cc_final: 0.8014 (m-30) REVERT: g 601 LYS cc_start: 0.8508 (mttm) cc_final: 0.8086 (mtpp) REVERT: g 621 GLU cc_start: 0.8982 (pt0) cc_final: 0.7713 (tm-30) REVERT: g 634 GLU cc_start: 0.8360 (mt-10) cc_final: 0.8051 (mm-30) outliers start: 2 outliers final: 1 residues processed: 201 average time/residue: 0.1656 time to fit residues: 47.6178 Evaluate side-chains 148 residues out of total 1736 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 147 time to evaluate : 0.678 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain f residue 339 ASN Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 98 optimal weight: 3.9990 chunk 107 optimal weight: 3.9990 chunk 10 optimal weight: 3.9990 chunk 66 optimal weight: 0.6980 chunk 130 optimal weight: 7.9990 chunk 124 optimal weight: 5.9990 chunk 103 optimal weight: 5.9990 chunk 77 optimal weight: 1.9990 chunk 122 optimal weight: 4.9990 chunk 91 optimal weight: 7.9990 chunk 149 optimal weight: 5.9990 overall best weight: 2.9388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 1 GLN c 624 ASN e 607 ASN e 624 ASN f 330 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3704 r_free = 0.3704 target = 0.088152 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3211 r_free = 0.3211 target = 0.063050 restraints weight = 47109.504| |-----------------------------------------------------------------------------| r_work (start): 0.3172 rms_B_bonded: 4.41 r_work: 0.2991 rms_B_bonded: 4.55 restraints_weight: 0.5000 r_work (final): 0.2991 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8756 moved from start: 0.1546 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.055 17781 Z= 0.258 Angle : 0.858 16.626 24354 Z= 0.391 Chirality : 0.049 0.374 3037 Planarity : 0.005 0.045 2864 Dihedral : 9.164 71.797 4756 Min Nonbonded Distance : 2.473 Molprobity Statistics. All-atom Clashscore : 2.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.49 % Favored : 96.51 % Rotamer: Outliers : 1.21 % Allowed : 9.74 % Favored : 89.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.41 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.03 (0.19), residues: 1922 helix: -0.22 (0.26), residues: 387 sheet: -0.57 (0.21), residues: 530 loop : -0.85 (0.19), residues: 1005 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG d 46 TYR 0.020 0.002 TYR B 54 PHE 0.019 0.002 PHE B 76 TRP 0.015 0.002 TRP c 631 HIS 0.009 0.001 HIS A 104 Details of bonding type rmsd/Z covalent geometry : bond 0.00603 / 0.26 (17620) covalent geometry : angle 0.77690 / 0.37 (23909) SS BOND : bond 0.00330 / 0.22 ( 38) SS BOND : angle 1.16103 / 0.71 ( 76) hydrogen bonds : bond 0.05716 / 3.91 ( 547) hydrogen bonds : angle 6.11476 / 4.08 ( 1533) link_ALPHA1-3 : bond 0.00822 / 0.39 ( 6) link_ALPHA1-3 : angle 2.37699 / 1.36 ( 18) link_ALPHA1-6 : bond 0.00767 / 0.35 ( 5) link_ALPHA1-6 : angle 1.74468 / 1.12 ( 15) link_BETA1-4 : bond 0.00628 / 0.47 ( 47) link_BETA1-4 : angle 3.52334 / 2.14 ( 141) link_NAG-ASN : bond 0.00398 / 0.26 ( 65) link_NAG-ASN : angle 2.77932 / 2.01 ( 195) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3844 Ramachandran restraints generated. 1922 Oldfield, 0 Emsley, 1922 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3844 Ramachandran restraints generated. 1922 Oldfield, 0 Emsley, 1922 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 179 residues out of total 1736 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 158 time to evaluate : 0.597 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: A 39 ARG cc_start: 0.8731 (ptt180) cc_final: 0.8340 (ptm-80) REVERT: A 68 ARG cc_start: 0.8573 (mtp-110) cc_final: 0.8096 (mtp-110) REVERT: A 74 ASP cc_start: 0.8721 (p0) cc_final: 0.7723 (p0) REVERT: A 79 GLN cc_start: 0.9121 (pt0) cc_final: 0.8845 (pp30) REVERT: B 11 LEU cc_start: 0.9043 (tp) cc_final: 0.8721 (tt) REVERT: B 47 GLN cc_start: 0.8563 (tt0) cc_final: 0.8340 (tp40) REVERT: B 60 ASP cc_start: 0.8603 (t0) cc_final: 0.8399 (t0) REVERT: b 164 GLU cc_start: 0.8621 (OUTLIER) cc_final: 0.8146 (mt-10) REVERT: c 631 TRP cc_start: 0.8111 (t-100) cc_final: 0.7504 (t-100) REVERT: c 659 GLU cc_start: 0.8025 (tm-30) cc_final: 0.7784 (tp30) REVERT: e 536 THR cc_start: 0.9165 (p) cc_final: 0.8726 (t) REVERT: e 638 TYR cc_start: 0.9238 (m-80) cc_final: 0.9004 (m-80) REVERT: e 647 GLU cc_start: 0.8527 (mt-10) cc_final: 0.8169 (mt-10) REVERT: f 161 MET cc_start: 0.8857 (tpp) cc_final: 0.8268 (tpp) REVERT: g 588 ARG cc_start: 0.9148 (ttm110) cc_final: 0.8447 (tmm-80) REVERT: g 601 LYS cc_start: 0.8960 (mttm) cc_final: 0.8689 (mtpp) REVERT: g 621 GLU cc_start: 0.8804 (pt0) cc_final: 0.7876 (tm-30) REVERT: g 644 ARG cc_start: 0.9258 (ptp-170) cc_final: 0.8868 (ptt-90) REVERT: g 657 GLU cc_start: 0.7344 (mm-30) cc_final: 0.6881 (tm-30) outliers start: 21 outliers final: 16 residues processed: 173 average time/residue: 0.1552 time to fit residues: 38.3996 Evaluate side-chains 155 residues out of total 1736 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 138 time to evaluate : 0.641 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 77 LYS Chi-restraints excluded: chain A residue 82 LEU Chi-restraints excluded: chain A residue 100 ASP Chi-restraints excluded: chain B residue 74 THR Chi-restraints excluded: chain B residue 101 LEU Chi-restraints excluded: chain b residue 126 CYS Chi-restraints excluded: chain b residue 164 GLU Chi-restraints excluded: chain c residue 641 LEU Chi-restraints excluded: chain d residue 125 LEU Chi-restraints excluded: chain e residue 580 VAL Chi-restraints excluded: chain e residue 581 LEU Chi-restraints excluded: chain f residue 36 VAL Chi-restraints excluded: chain f residue 244 THR Chi-restraints excluded: chain f residue 286 VAL Chi-restraints excluded: chain f residue 339 ASN Chi-restraints excluded: chain f residue 375 SER Chi-restraints excluded: chain g residue 538 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 46 optimal weight: 1.9990 chunk 21 optimal weight: 30.0000 chunk 162 optimal weight: 0.8980 chunk 15 optimal weight: 10.0000 chunk 33 optimal weight: 4.9990 chunk 153 optimal weight: 6.9990 chunk 36 optimal weight: 3.9990 chunk 74 optimal weight: 4.9990 chunk 58 optimal weight: 5.9990 chunk 139 optimal weight: 0.7980 chunk 47 optimal weight: 0.9990 overall best weight: 1.7386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... b 330 HIS b 422 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3715 r_free = 0.3715 target = 0.088673 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3225 r_free = 0.3225 target = 0.063664 restraints weight = 47289.607| |-----------------------------------------------------------------------------| r_work (start): 0.3185 rms_B_bonded: 4.42 r_work: 0.3012 rms_B_bonded: 4.51 restraints_weight: 0.5000 r_work (final): 0.3012 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8742 moved from start: 0.1882 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 17781 Z= 0.174 Angle : 0.745 16.142 24354 Z= 0.336 Chirality : 0.046 0.346 3037 Planarity : 0.004 0.041 2864 Dihedral : 8.678 65.765 4756 Min Nonbonded Distance : 2.477 Molprobity Statistics. All-atom Clashscore : 3.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.17 % Favored : 96.83 % Rotamer: Outliers : 1.61 % Allowed : 10.14 % Favored : 88.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.41 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.82 (0.19), residues: 1922 helix: -0.14 (0.27), residues: 402 sheet: -0.21 (0.22), residues: 507 loop : -0.82 (0.19), residues: 1013 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG b 46 TYR 0.017 0.001 TYR B 54 PHE 0.019 0.002 PHE B 76 TRP 0.012 0.001 TRP d 338 HIS 0.007 0.001 HIS A 104 Details of bonding type rmsd/Z covalent geometry : bond 0.00398 / 0.17 (17620) covalent geometry : angle 0.66847 / 0.32 (23909) SS BOND : bond 0.00238 / 0.16 ( 38) SS BOND : angle 0.83643 / 0.50 ( 76) hydrogen bonds : bond 0.04799 / 3.27 ( 547) hydrogen bonds : angle 5.50467 / 3.67 ( 1533) link_ALPHA1-3 : bond 0.00943 / 0.45 ( 6) link_ALPHA1-3 : angle 2.13510 / 1.19 ( 18) link_ALPHA1-6 : bond 0.00805 / 0.37 ( 5) link_ALPHA1-6 : angle 1.66510 / 1.04 ( 15) link_BETA1-4 : bond 0.00697 / 0.54 ( 47) link_BETA1-4 : angle 3.20500 / 1.95 ( 141) link_NAG-ASN : bond 0.00365 / 0.26 ( 65) link_NAG-ASN : angle 2.49400 / 1.78 ( 195) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3844 Ramachandran restraints generated. 1922 Oldfield, 0 Emsley, 1922 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3844 Ramachandran restraints generated. 1922 Oldfield, 0 Emsley, 1922 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 178 residues out of total 1736 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 150 time to evaluate : 0.723 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: A 39 ARG cc_start: 0.8810 (ptt180) cc_final: 0.8355 (ptm-80) REVERT: A 74 ASP cc_start: 0.8676 (p0) cc_final: 0.7476 (p0) REVERT: A 79 GLN cc_start: 0.9150 (pt0) cc_final: 0.8808 (pp30) REVERT: B 47 GLN cc_start: 0.8573 (tt0) cc_final: 0.8343 (tp40) REVERT: B 60 ASP cc_start: 0.8574 (t0) cc_final: 0.8297 (t0) REVERT: B 67 PHE cc_start: 0.8637 (m-80) cc_final: 0.8163 (m-80) REVERT: b 164 GLU cc_start: 0.8604 (OUTLIER) cc_final: 0.8189 (mt-10) REVERT: c 657 GLU cc_start: 0.8659 (tp30) cc_final: 0.8094 (tt0) REVERT: d 164 GLU cc_start: 0.8629 (OUTLIER) cc_final: 0.8417 (mm-30) REVERT: e 536 THR cc_start: 0.9235 (p) cc_final: 0.8857 (t) REVERT: e 631 TRP cc_start: 0.9009 (t-100) cc_final: 0.8701 (t-100) REVERT: e 647 GLU cc_start: 0.8609 (mt-10) cc_final: 0.8209 (mt-10) REVERT: f 161 MET cc_start: 0.8828 (tpp) cc_final: 0.8211 (tpp) REVERT: f 375 SER cc_start: 0.9200 (OUTLIER) cc_final: 0.8714 (p) REVERT: g 588 ARG cc_start: 0.9132 (ttm110) cc_final: 0.8412 (tmm-80) REVERT: g 589 ASP cc_start: 0.8866 (m-30) cc_final: 0.8480 (m-30) REVERT: g 601 LYS cc_start: 0.8961 (mttm) cc_final: 0.8696 (mtpp) REVERT: g 621 GLU cc_start: 0.8785 (pt0) cc_final: 0.7843 (tm-30) outliers start: 28 outliers final: 11 residues processed: 170 average time/residue: 0.1420 time to fit residues: 35.4187 Evaluate side-chains 150 residues out of total 1736 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 136 time to evaluate : 0.636 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 77 LYS Chi-restraints excluded: chain A residue 100 ASP Chi-restraints excluded: chain b residue 38 VAL Chi-restraints excluded: chain b residue 126 CYS Chi-restraints excluded: chain b residue 164 GLU Chi-restraints excluded: chain b residue 320 MET Chi-restraints excluded: chain d residue 125 LEU Chi-restraints excluded: chain d residue 164 GLU Chi-restraints excluded: chain d residue 165 LEU Chi-restraints excluded: chain e residue 581 LEU Chi-restraints excluded: chain f residue 36 VAL Chi-restraints excluded: chain f residue 38 VAL Chi-restraints excluded: chain f residue 286 VAL Chi-restraints excluded: chain f residue 375 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 72 optimal weight: 1.9990 chunk 156 optimal weight: 4.9990 chunk 150 optimal weight: 2.9990 chunk 188 optimal weight: 8.9990 chunk 157 optimal weight: 4.9990 chunk 73 optimal weight: 4.9990 chunk 64 optimal weight: 9.9990 chunk 112 optimal weight: 0.9980 chunk 86 optimal weight: 4.9990 chunk 95 optimal weight: 1.9990 chunk 59 optimal weight: 8.9990 overall best weight: 2.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** d 72 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3688 r_free = 0.3688 target = 0.087161 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3186 r_free = 0.3186 target = 0.061921 restraints weight = 47411.798| |-----------------------------------------------------------------------------| r_work (start): 0.3166 rms_B_bonded: 4.41 r_work: 0.2995 rms_B_bonded: 4.47 restraints_weight: 0.5000 r_work (final): 0.2995 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8795 moved from start: 0.2212 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.054 17781 Z= 0.235 Angle : 0.784 16.885 24354 Z= 0.353 Chirality : 0.047 0.400 3037 Planarity : 0.004 0.044 2864 Dihedral : 8.551 64.195 4754 Min Nonbonded Distance : 2.460 Molprobity Statistics. All-atom Clashscore : 3.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.69 % Favored : 96.31 % Rotamer: Outliers : 2.25 % Allowed : 10.66 % Favored : 87.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.41 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.78 (0.19), residues: 1922 helix: -0.08 (0.27), residues: 402 sheet: -0.19 (0.22), residues: 496 loop : -0.80 (0.19), residues: 1024 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG g 644 TYR 0.016 0.001 TYR A 61 PHE 0.021 0.002 PHE B 76 TRP 0.012 0.001 TRP f 112 HIS 0.010 0.001 HIS A 104 Details of bonding type rmsd/Z covalent geometry : bond 0.00546 / 0.23 (17620) covalent geometry : angle 0.70357 / 0.33 (23909) SS BOND : bond 0.00285 / 0.19 ( 38) SS BOND : angle 0.85658 / 0.52 ( 76) hydrogen bonds : bond 0.04545 / 3.10 ( 547) hydrogen bonds : angle 5.39317 / 3.57 ( 1533) link_ALPHA1-3 : bond 0.00850 / 0.41 ( 6) link_ALPHA1-3 : angle 2.25443 / 1.27 ( 18) link_ALPHA1-6 : bond 0.00866 / 0.40 ( 5) link_ALPHA1-6 : angle 1.79322 / 1.13 ( 15) link_BETA1-4 : bond 0.00641 / 0.49 ( 47) link_BETA1-4 : angle 3.14727 / 1.92 ( 141) link_NAG-ASN : bond 0.00463 / 0.33 ( 65) link_NAG-ASN : angle 2.82092 / 2.06 ( 195) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3844 Ramachandran restraints generated. 1922 Oldfield, 0 Emsley, 1922 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3844 Ramachandran restraints generated. 1922 Oldfield, 0 Emsley, 1922 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 181 residues out of total 1736 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 142 time to evaluate : 0.705 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 16 GLU cc_start: 0.9162 (pt0) cc_final: 0.8751 (pm20) REVERT: A 39 ARG cc_start: 0.8868 (ptt180) cc_final: 0.8392 (ptm-80) REVERT: A 74 ASP cc_start: 0.8668 (p0) cc_final: 0.7462 (p0) REVERT: A 79 GLN cc_start: 0.9112 (pt0) cc_final: 0.8769 (pp30) REVERT: B 47 GLN cc_start: 0.8823 (tt0) cc_final: 0.8517 (tp40) REVERT: B 60 ASP cc_start: 0.8578 (t0) cc_final: 0.8296 (t0) REVERT: b 164 GLU cc_start: 0.8638 (OUTLIER) cc_final: 0.8154 (mt-10) REVERT: c 657 GLU cc_start: 0.8657 (tp30) cc_final: 0.8067 (tt0) REVERT: d 161 MET cc_start: 0.9065 (mmm) cc_final: 0.8741 (mmm) REVERT: d 164 GLU cc_start: 0.8679 (OUTLIER) cc_final: 0.8397 (mm-30) REVERT: d 270 ILE cc_start: 0.9465 (OUTLIER) cc_final: 0.9245 (mp) REVERT: e 536 THR cc_start: 0.9251 (p) cc_final: 0.8851 (t) REVERT: e 647 GLU cc_start: 0.8603 (mt-10) cc_final: 0.8329 (mt-10) REVERT: e 659 GLU cc_start: 0.7473 (tt0) cc_final: 0.7018 (tt0) REVERT: f 161 MET cc_start: 0.8885 (tpp) cc_final: 0.8234 (tpp) REVERT: g 588 ARG cc_start: 0.9135 (ttm110) cc_final: 0.8463 (tmm-80) REVERT: g 601 LYS cc_start: 0.8994 (mttm) cc_final: 0.8646 (mtpp) REVERT: g 621 GLU cc_start: 0.8772 (pt0) cc_final: 0.7852 (tm-30) outliers start: 39 outliers final: 28 residues processed: 171 average time/residue: 0.1364 time to fit residues: 34.7003 Evaluate side-chains 165 residues out of total 1736 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 134 time to evaluate : 0.665 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 77 LYS Chi-restraints excluded: chain A residue 82 LEU Chi-restraints excluded: chain A residue 100 ASP Chi-restraints excluded: chain B residue 80 ILE Chi-restraints excluded: chain B residue 101 LEU Chi-restraints excluded: chain b residue 38 VAL Chi-restraints excluded: chain b residue 120 VAL Chi-restraints excluded: chain b residue 126 CYS Chi-restraints excluded: chain b residue 164 GLU Chi-restraints excluded: chain b residue 265 LEU Chi-restraints excluded: chain b residue 320 MET Chi-restraints excluded: chain b residue 445 CYS Chi-restraints excluded: chain c residue 530 MET Chi-restraints excluded: chain d residue 125 LEU Chi-restraints excluded: chain d residue 164 GLU Chi-restraints excluded: chain d residue 165 LEU Chi-restraints excluded: chain d residue 270 ILE Chi-restraints excluded: chain e residue 580 VAL Chi-restraints excluded: chain e residue 581 LEU Chi-restraints excluded: chain f residue 36 VAL Chi-restraints excluded: chain f residue 38 VAL Chi-restraints excluded: chain f residue 68 VAL Chi-restraints excluded: chain f residue 244 THR Chi-restraints excluded: chain f residue 254 VAL Chi-restraints excluded: chain f residue 286 VAL Chi-restraints excluded: chain f residue 323 ILE Chi-restraints excluded: chain f residue 375 SER Chi-restraints excluded: chain f residue 445 CYS Chi-restraints excluded: chain f residue 494 LEU Chi-restraints excluded: chain g residue 538 THR Chi-restraints excluded: chain g residue 599 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 173 optimal weight: 0.5980 chunk 5 optimal weight: 5.9990 chunk 60 optimal weight: 1.9990 chunk 158 optimal weight: 2.9990 chunk 151 optimal weight: 4.9990 chunk 85 optimal weight: 6.9990 chunk 46 optimal weight: 1.9990 chunk 29 optimal weight: 7.9990 chunk 57 optimal weight: 0.9980 chunk 88 optimal weight: 1.9990 chunk 143 optimal weight: 0.9980 overall best weight: 1.3184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** d 72 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3712 r_free = 0.3712 target = 0.088418 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3219 r_free = 0.3219 target = 0.063335 restraints weight = 46785.882| |-----------------------------------------------------------------------------| r_work (start): 0.3198 rms_B_bonded: 4.41 r_work: 0.3025 rms_B_bonded: 4.49 restraints_weight: 0.5000 r_work (final): 0.3025 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8767 moved from start: 0.2322 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 17781 Z= 0.143 Angle : 0.714 15.915 24354 Z= 0.319 Chirality : 0.048 0.697 3037 Planarity : 0.003 0.041 2864 Dihedral : 8.167 60.643 4754 Min Nonbonded Distance : 2.470 Molprobity Statistics. All-atom Clashscore : 3.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.33 % Favored : 96.67 % Rotamer: Outliers : 2.19 % Allowed : 11.23 % Favored : 86.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.41 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.66 (0.19), residues: 1922 helix: 0.13 (0.27), residues: 420 sheet: -0.08 (0.23), residues: 497 loop : -0.82 (0.19), residues: 1005 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG g 644 TYR 0.014 0.001 TYR B 54 PHE 0.015 0.001 PHE B 76 TRP 0.011 0.001 TRP c 631 HIS 0.010 0.001 HIS A 104 Details of bonding type rmsd/Z covalent geometry : bond 0.00324 / 0.14 (17620) covalent geometry : angle 0.63943 / 0.30 (23909) SS BOND : bond 0.00200 / 0.13 ( 38) SS BOND : angle 0.70404 / 0.43 ( 76) hydrogen bonds : bond 0.04138 / 2.79 ( 547) hydrogen bonds : angle 5.17955 / 3.44 ( 1533) link_ALPHA1-3 : bond 0.00950 / 0.45 ( 6) link_ALPHA1-3 : angle 2.06112 / 1.16 ( 18) link_ALPHA1-6 : bond 0.00857 / 0.39 ( 5) link_ALPHA1-6 : angle 1.67562 / 1.04 ( 15) link_BETA1-4 : bond 0.00660 / 0.51 ( 47) link_BETA1-4 : angle 3.00315 / 1.83 ( 141) link_NAG-ASN : bond 0.00318 / 0.22 ( 65) link_NAG-ASN : angle 2.48253 / 1.77 ( 195) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3844 Ramachandran restraints generated. 1922 Oldfield, 0 Emsley, 1922 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3844 Ramachandran restraints generated. 1922 Oldfield, 0 Emsley, 1922 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 185 residues out of total 1736 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 147 time to evaluate : 0.651 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 16 GLU cc_start: 0.9252 (OUTLIER) cc_final: 0.8841 (pm20) REVERT: A 39 ARG cc_start: 0.8868 (ptt180) cc_final: 0.8407 (ptm-80) REVERT: A 71 ILE cc_start: 0.9102 (OUTLIER) cc_final: 0.8767 (mm) REVERT: A 74 ASP cc_start: 0.8676 (p0) cc_final: 0.7601 (p0) REVERT: A 79 GLN cc_start: 0.9108 (pt0) cc_final: 0.8791 (pp30) REVERT: B 47 GLN cc_start: 0.8848 (tt0) cc_final: 0.8553 (tp40) REVERT: B 60 ASP cc_start: 0.8560 (t0) cc_final: 0.8305 (t0) REVERT: B 66 ARG cc_start: 0.8129 (ptp90) cc_final: 0.7822 (ptp90) REVERT: b 164 GLU cc_start: 0.8566 (OUTLIER) cc_final: 0.8193 (mt-10) REVERT: c 657 GLU cc_start: 0.8652 (tp30) cc_final: 0.8082 (tt0) REVERT: d 164 GLU cc_start: 0.8579 (OUTLIER) cc_final: 0.8294 (mm-30) REVERT: e 536 THR cc_start: 0.9215 (p) cc_final: 0.8830 (t) REVERT: e 647 GLU cc_start: 0.8599 (mt-10) cc_final: 0.8142 (mt-10) REVERT: f 161 MET cc_start: 0.8813 (tpp) cc_final: 0.8238 (tpp) REVERT: f 375 SER cc_start: 0.9233 (OUTLIER) cc_final: 0.9018 (p) REVERT: g 588 ARG cc_start: 0.9107 (ttm110) cc_final: 0.8431 (tmm-80) REVERT: g 601 LYS cc_start: 0.8967 (mttm) cc_final: 0.8646 (mtpp) REVERT: g 621 GLU cc_start: 0.8753 (pt0) cc_final: 0.7860 (tm-30) outliers start: 38 outliers final: 22 residues processed: 174 average time/residue: 0.1529 time to fit residues: 39.2609 Evaluate side-chains 162 residues out of total 1736 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 135 time to evaluate : 0.656 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 16 GLU Chi-restraints excluded: chain A residue 71 ILE Chi-restraints excluded: chain A residue 77 LYS Chi-restraints excluded: chain A residue 82 LEU Chi-restraints excluded: chain A residue 100 ASP Chi-restraints excluded: chain B residue 80 ILE Chi-restraints excluded: chain B residue 101 LEU Chi-restraints excluded: chain b residue 38 VAL Chi-restraints excluded: chain b residue 126 CYS Chi-restraints excluded: chain b residue 164 GLU Chi-restraints excluded: chain b residue 445 CYS Chi-restraints excluded: chain b residue 488 VAL Chi-restraints excluded: chain c residue 530 MET Chi-restraints excluded: chain c residue 641 LEU Chi-restraints excluded: chain d residue 38 VAL Chi-restraints excluded: chain d residue 125 LEU Chi-restraints excluded: chain d residue 164 GLU Chi-restraints excluded: chain d residue 165 LEU Chi-restraints excluded: chain e residue 580 VAL Chi-restraints excluded: chain e residue 635 ILE Chi-restraints excluded: chain f residue 36 VAL Chi-restraints excluded: chain f residue 38 VAL Chi-restraints excluded: chain f residue 286 VAL Chi-restraints excluded: chain f residue 323 ILE Chi-restraints excluded: chain f residue 375 SER Chi-restraints excluded: chain f residue 445 CYS Chi-restraints excluded: chain g residue 599 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 106 optimal weight: 3.9990 chunk 16 optimal weight: 9.9990 chunk 34 optimal weight: 5.9990 chunk 116 optimal weight: 0.8980 chunk 45 optimal weight: 4.9990 chunk 55 optimal weight: 2.9990 chunk 49 optimal weight: 0.9990 chunk 65 optimal weight: 3.9990 chunk 173 optimal weight: 5.9990 chunk 101 optimal weight: 2.9990 chunk 72 optimal weight: 0.9990 overall best weight: 1.7788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** d 72 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3706 r_free = 0.3706 target = 0.087957 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3212 r_free = 0.3212 target = 0.062867 restraints weight = 46892.093| |-----------------------------------------------------------------------------| r_work (start): 0.3199 rms_B_bonded: 4.39 r_work: 0.3038 rms_B_bonded: 4.39 restraints_weight: 0.5000 r_work (final): 0.3038 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8762 moved from start: 0.2489 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 17781 Z= 0.173 Angle : 0.707 15.964 24354 Z= 0.318 Chirality : 0.046 0.388 3037 Planarity : 0.003 0.045 2864 Dihedral : 8.062 58.927 4754 Min Nonbonded Distance : 2.462 Molprobity Statistics. All-atom Clashscore : 3.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.64 % Favored : 96.36 % Rotamer: Outliers : 2.36 % Allowed : 11.52 % Favored : 86.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.41 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.59 (0.19), residues: 1922 helix: 0.19 (0.27), residues: 420 sheet: -0.06 (0.23), residues: 497 loop : -0.76 (0.19), residues: 1005 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 83 TYR 0.012 0.001 TYR B 54 PHE 0.016 0.002 PHE B 76 TRP 0.013 0.001 TRP c 631 HIS 0.016 0.001 HIS A 104 Details of bonding type rmsd/Z covalent geometry : bond 0.00401 / 0.17 (17620) covalent geometry : angle 0.63609 / 0.30 (23909) SS BOND : bond 0.00234 / 0.16 ( 38) SS BOND : angle 0.75249 / 0.46 ( 76) hydrogen bonds : bond 0.03973 / 2.69 ( 547) hydrogen bonds : angle 5.12430 / 3.41 ( 1533) link_ALPHA1-3 : bond 0.00890 / 0.43 ( 6) link_ALPHA1-3 : angle 2.02606 / 1.15 ( 18) link_ALPHA1-6 : bond 0.00838 / 0.38 ( 5) link_ALPHA1-6 : angle 1.62049 / 1.00 ( 15) link_BETA1-4 : bond 0.00663 / 0.51 ( 47) link_BETA1-4 : angle 2.95047 / 1.80 ( 141) link_NAG-ASN : bond 0.00349 / 0.25 ( 65) link_NAG-ASN : angle 2.38998 / 1.70 ( 195) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3844 Ramachandran restraints generated. 1922 Oldfield, 0 Emsley, 1922 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3844 Ramachandran restraints generated. 1922 Oldfield, 0 Emsley, 1922 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 186 residues out of total 1736 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 145 time to evaluate : 0.560 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 16 GLU cc_start: 0.9270 (OUTLIER) cc_final: 0.8869 (pm20) REVERT: A 39 ARG cc_start: 0.8908 (ptt180) cc_final: 0.8303 (ptm-80) REVERT: A 71 ILE cc_start: 0.9083 (OUTLIER) cc_final: 0.8758 (mm) REVERT: A 74 ASP cc_start: 0.8641 (p0) cc_final: 0.7505 (p0) REVERT: A 79 GLN cc_start: 0.9092 (pt0) cc_final: 0.8755 (pp30) REVERT: B 47 GLN cc_start: 0.8832 (tt0) cc_final: 0.8523 (tp40) REVERT: B 50 ARG cc_start: 0.8499 (mtp-110) cc_final: 0.8136 (mtp-110) REVERT: B 60 ASP cc_start: 0.8499 (t0) cc_final: 0.8267 (t0) REVERT: B 66 ARG cc_start: 0.8334 (ptp90) cc_final: 0.7977 (ptp90) REVERT: b 164 GLU cc_start: 0.8632 (OUTLIER) cc_final: 0.8194 (mt-10) REVERT: c 641 LEU cc_start: 0.9081 (OUTLIER) cc_final: 0.8820 (mm) REVERT: d 164 GLU cc_start: 0.8585 (OUTLIER) cc_final: 0.8270 (mm-30) REVERT: d 270 ILE cc_start: 0.9433 (OUTLIER) cc_final: 0.9222 (mp) REVERT: e 536 THR cc_start: 0.9211 (p) cc_final: 0.8833 (t) REVERT: e 647 GLU cc_start: 0.8600 (mt-10) cc_final: 0.8266 (mt-10) REVERT: f 125 LEU cc_start: 0.9524 (OUTLIER) cc_final: 0.9260 (tt) REVERT: f 161 MET cc_start: 0.8855 (tpp) cc_final: 0.8246 (tpp) REVERT: g 588 ARG cc_start: 0.9100 (ttm110) cc_final: 0.8434 (tmm-80) REVERT: g 601 LYS cc_start: 0.8958 (mttm) cc_final: 0.8634 (mtpp) REVERT: g 621 GLU cc_start: 0.8768 (pt0) cc_final: 0.7911 (tm-30) outliers start: 41 outliers final: 28 residues processed: 174 average time/residue: 0.1551 time to fit residues: 39.5630 Evaluate side-chains 171 residues out of total 1736 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 136 time to evaluate : 0.664 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 16 GLU Chi-restraints excluded: chain A residue 71 ILE Chi-restraints excluded: chain A residue 82 LEU Chi-restraints excluded: chain A residue 100 ASP Chi-restraints excluded: chain B residue 11 LEU Chi-restraints excluded: chain B residue 80 ILE Chi-restraints excluded: chain B residue 101 LEU Chi-restraints excluded: chain b residue 38 VAL Chi-restraints excluded: chain b residue 120 VAL Chi-restraints excluded: chain b residue 126 CYS Chi-restraints excluded: chain b residue 164 GLU Chi-restraints excluded: chain b residue 265 LEU Chi-restraints excluded: chain b residue 320 MET Chi-restraints excluded: chain b residue 445 CYS Chi-restraints excluded: chain b residue 488 VAL Chi-restraints excluded: chain c residue 530 MET Chi-restraints excluded: chain c residue 641 LEU Chi-restraints excluded: chain d residue 38 VAL Chi-restraints excluded: chain d residue 125 LEU Chi-restraints excluded: chain d residue 164 GLU Chi-restraints excluded: chain d residue 270 ILE Chi-restraints excluded: chain e residue 580 VAL Chi-restraints excluded: chain e residue 635 ILE Chi-restraints excluded: chain f residue 36 VAL Chi-restraints excluded: chain f residue 38 VAL Chi-restraints excluded: chain f residue 68 VAL Chi-restraints excluded: chain f residue 125 LEU Chi-restraints excluded: chain f residue 126 CYS Chi-restraints excluded: chain f residue 213 ILE Chi-restraints excluded: chain f residue 254 VAL Chi-restraints excluded: chain f residue 286 VAL Chi-restraints excluded: chain f residue 323 ILE Chi-restraints excluded: chain f residue 375 SER Chi-restraints excluded: chain f residue 445 CYS Chi-restraints excluded: chain g residue 599 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 66 optimal weight: 2.9990 chunk 33 optimal weight: 4.9990 chunk 145 optimal weight: 0.8980 chunk 56 optimal weight: 3.9990 chunk 58 optimal weight: 0.9990 chunk 39 optimal weight: 0.9990 chunk 23 optimal weight: 4.9990 chunk 130 optimal weight: 0.7980 chunk 94 optimal weight: 2.9990 chunk 90 optimal weight: 0.7980 chunk 92 optimal weight: 0.9990 overall best weight: 0.8984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 104 HIS ** d 72 HIS ** 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 = 0.3732 r_free = 0.3732 target = 0.089210 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3250 r_free = 0.3250 target = 0.064453 restraints weight = 46462.576| |-----------------------------------------------------------------------------| r_work (start): 0.3218 rms_B_bonded: 4.35 r_work: 0.3051 rms_B_bonded: 4.42 restraints_weight: 0.5000 r_work (final): 0.3051 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8755 moved from start: 0.2600 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.056 17781 Z= 0.120 Angle : 0.679 15.664 24354 Z= 0.304 Chirality : 0.045 0.308 3037 Planarity : 0.003 0.043 2864 Dihedral : 7.821 57.554 4754 Min Nonbonded Distance : 2.472 Molprobity Statistics. All-atom Clashscore : 4.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.97 % Favored : 97.03 % Rotamer: Outliers : 2.02 % Allowed : 12.44 % Favored : 85.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.41 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.52 (0.19), residues: 1922 helix: 0.14 (0.27), residues: 438 sheet: -0.01 (0.23), residues: 497 loop : -0.67 (0.19), residues: 987 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 83 TYR 0.012 0.001 TYR A 61 PHE 0.015 0.001 PHE B 76 TRP 0.013 0.001 TRP e 631 HIS 0.009 0.001 HIS A 104 Details of bonding type rmsd/Z covalent geometry : bond 0.00272 / 0.12 (17620) covalent geometry : angle 0.61095 / 0.29 (23909) SS BOND : bond 0.00173 / 0.11 ( 38) SS BOND : angle 0.66076 / 0.41 ( 76) hydrogen bonds : bond 0.03681 / 2.49 ( 547) hydrogen bonds : angle 4.99108 / 3.33 ( 1533) link_ALPHA1-3 : bond 0.00954 / 0.46 ( 6) link_ALPHA1-3 : angle 1.89545 / 1.07 ( 18) link_ALPHA1-6 : bond 0.00856 / 0.39 ( 5) link_ALPHA1-6 : angle 1.53750 / 0.93 ( 15) link_BETA1-4 : bond 0.00688 / 0.52 ( 47) link_BETA1-4 : angle 2.86275 / 1.75 ( 141) link_NAG-ASN : bond 0.00300 / 0.21 ( 65) link_NAG-ASN : angle 2.26462 / 1.62 ( 195) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3844 Ramachandran restraints generated. 1922 Oldfield, 0 Emsley, 1922 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3844 Ramachandran restraints generated. 1922 Oldfield, 0 Emsley, 1922 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 180 residues out of total 1736 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 145 time to evaluate : 0.666 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 16 GLU cc_start: 0.9266 (OUTLIER) cc_final: 0.8838 (pm20) REVERT: A 39 ARG cc_start: 0.8920 (ptt180) cc_final: 0.8369 (ptm-80) REVERT: A 71 ILE cc_start: 0.9037 (OUTLIER) cc_final: 0.8713 (mm) REVERT: A 74 ASP cc_start: 0.8627 (p0) cc_final: 0.7410 (p0) REVERT: A 79 GLN cc_start: 0.9062 (pt0) cc_final: 0.8724 (pp30) REVERT: A 83 ARG cc_start: 0.9275 (mtp-110) cc_final: 0.9045 (mtp-110) REVERT: B 47 GLN cc_start: 0.8876 (tt0) cc_final: 0.8532 (tp40) REVERT: B 66 ARG cc_start: 0.8321 (ptp90) cc_final: 0.7653 (ptp90) REVERT: B 82 ARG cc_start: 0.8874 (ttp80) cc_final: 0.8451 (ttp80) REVERT: b 164 GLU cc_start: 0.8559 (OUTLIER) cc_final: 0.8282 (mt-10) REVERT: c 641 LEU cc_start: 0.9034 (OUTLIER) cc_final: 0.8644 (pp) REVERT: c 657 GLU cc_start: 0.8588 (tp30) cc_final: 0.7950 (tt0) REVERT: d 161 MET cc_start: 0.8891 (mmm) cc_final: 0.8659 (mmm) REVERT: d 164 GLU cc_start: 0.8495 (OUTLIER) cc_final: 0.8213 (mm-30) REVERT: d 270 ILE cc_start: 0.9428 (OUTLIER) cc_final: 0.9196 (mp) REVERT: e 536 THR cc_start: 0.9176 (p) cc_final: 0.8808 (t) REVERT: e 647 GLU cc_start: 0.8529 (mt-10) cc_final: 0.8195 (mt-10) REVERT: f 161 MET cc_start: 0.8787 (tpp) cc_final: 0.8282 (tpp) REVERT: g 588 ARG cc_start: 0.9048 (ttm110) cc_final: 0.8468 (tmm-80) REVERT: g 601 LYS cc_start: 0.8935 (mttm) cc_final: 0.8651 (mtpp) REVERT: g 621 GLU cc_start: 0.8662 (pt0) cc_final: 0.7855 (tm-30) outliers start: 35 outliers final: 20 residues processed: 170 average time/residue: 0.1415 time to fit residues: 35.7385 Evaluate side-chains 163 residues out of total 1736 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 137 time to evaluate : 0.609 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 16 GLU Chi-restraints excluded: chain A residue 71 ILE Chi-restraints excluded: chain A residue 82 LEU Chi-restraints excluded: chain A residue 100 ASP Chi-restraints excluded: chain B residue 11 LEU Chi-restraints excluded: chain B residue 80 ILE Chi-restraints excluded: chain B residue 101 LEU Chi-restraints excluded: chain b residue 38 VAL Chi-restraints excluded: chain b residue 164 GLU Chi-restraints excluded: chain b residue 265 LEU Chi-restraints excluded: chain b residue 445 CYS Chi-restraints excluded: chain c residue 530 MET Chi-restraints excluded: chain c residue 641 LEU Chi-restraints excluded: chain d residue 38 VAL Chi-restraints excluded: chain d residue 125 LEU Chi-restraints excluded: chain d residue 164 GLU Chi-restraints excluded: chain d residue 270 ILE Chi-restraints excluded: chain e residue 635 ILE Chi-restraints excluded: chain f residue 38 VAL Chi-restraints excluded: chain f residue 120 VAL Chi-restraints excluded: chain f residue 213 ILE Chi-restraints excluded: chain f residue 254 VAL Chi-restraints excluded: chain f residue 286 VAL Chi-restraints excluded: chain f residue 323 ILE Chi-restraints excluded: chain f residue 445 CYS Chi-restraints excluded: chain g residue 599 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 87 optimal weight: 2.9990 chunk 41 optimal weight: 0.5980 chunk 163 optimal weight: 0.7980 chunk 115 optimal weight: 5.9990 chunk 106 optimal weight: 3.9990 chunk 162 optimal weight: 1.9990 chunk 84 optimal weight: 2.9990 chunk 33 optimal weight: 2.9990 chunk 114 optimal weight: 2.9990 chunk 152 optimal weight: 6.9990 chunk 80 optimal weight: 0.0980 overall best weight: 1.2984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... c 624 ASN ** d 72 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** f 374 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3724 r_free = 0.3724 target = 0.088765 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3241 r_free = 0.3241 target = 0.064015 restraints weight = 46365.608| |-----------------------------------------------------------------------------| r_work (start): 0.3220 rms_B_bonded: 4.34 r_work: 0.3061 rms_B_bonded: 4.37 restraints_weight: 0.5000 r_work (final): 0.3061 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8740 moved from start: 0.2702 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 17781 Z= 0.142 Angle : 0.684 15.684 24354 Z= 0.309 Chirality : 0.045 0.301 3037 Planarity : 0.003 0.045 2864 Dihedral : 7.746 57.538 4754 Min Nonbonded Distance : 2.363 Molprobity Statistics. All-atom Clashscore : 4.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.33 % Favored : 96.67 % Rotamer: Outliers : 2.19 % Allowed : 11.87 % Favored : 85.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.41 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.50 (0.19), residues: 1922 helix: 0.12 (0.27), residues: 438 sheet: -0.04 (0.23), residues: 494 loop : -0.60 (0.19), residues: 990 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 83 TYR 0.012 0.001 TYR A 61 PHE 0.015 0.001 PHE B 76 TRP 0.010 0.001 TRP c 631 HIS 0.005 0.001 HIS f 374 Details of bonding type rmsd/Z covalent geometry : bond 0.00327 / 0.14 (17620) covalent geometry : angle 0.61735 / 0.29 (23909) SS BOND : bond 0.00188 / 0.12 ( 38) SS BOND : angle 0.86651 / 0.53 ( 76) hydrogen bonds : bond 0.03655 / 2.47 ( 547) hydrogen bonds : angle 4.96926 / 3.32 ( 1533) link_ALPHA1-3 : bond 0.00900 / 0.43 ( 6) link_ALPHA1-3 : angle 1.90948 / 1.09 ( 18) link_ALPHA1-6 : bond 0.00850 / 0.39 ( 5) link_ALPHA1-6 : angle 1.52365 / 0.91 ( 15) link_BETA1-4 : bond 0.00690 / 0.53 ( 47) link_BETA1-4 : angle 2.84218 / 1.74 ( 141) link_NAG-ASN : bond 0.00319 / 0.22 ( 65) link_NAG-ASN : angle 2.24662 / 1.61 ( 195) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3844 Ramachandran restraints generated. 1922 Oldfield, 0 Emsley, 1922 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3844 Ramachandran restraints generated. 1922 Oldfield, 0 Emsley, 1922 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 179 residues out of total 1736 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 141 time to evaluate : 0.621 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 16 GLU cc_start: 0.9290 (OUTLIER) cc_final: 0.8857 (pm20) REVERT: A 39 ARG cc_start: 0.8904 (ptt180) cc_final: 0.8317 (ptm-80) REVERT: A 68 ARG cc_start: 0.8836 (mtp-110) cc_final: 0.8532 (mtm110) REVERT: A 71 ILE cc_start: 0.9033 (OUTLIER) cc_final: 0.8722 (mm) REVERT: A 74 ASP cc_start: 0.8634 (p0) cc_final: 0.8318 (p0) REVERT: A 83 ARG cc_start: 0.9295 (mtp-110) cc_final: 0.9065 (mtp-110) REVERT: B 47 GLN cc_start: 0.8870 (tt0) cc_final: 0.8512 (tp40) REVERT: B 66 ARG cc_start: 0.8459 (ptp90) cc_final: 0.7916 (ptp90) REVERT: b 164 GLU cc_start: 0.8600 (OUTLIER) cc_final: 0.8347 (mt-10) REVERT: c 641 LEU cc_start: 0.9045 (OUTLIER) cc_final: 0.8640 (pp) REVERT: c 657 GLU cc_start: 0.8569 (tp30) cc_final: 0.7924 (tt0) REVERT: d 161 MET cc_start: 0.8931 (mmm) cc_final: 0.8721 (mmm) REVERT: d 164 GLU cc_start: 0.8509 (OUTLIER) cc_final: 0.8200 (mm-30) REVERT: d 270 ILE cc_start: 0.9393 (OUTLIER) cc_final: 0.9185 (mp) REVERT: e 530 MET cc_start: 0.8372 (mmt) cc_final: 0.7855 (mmt) REVERT: e 536 THR cc_start: 0.9179 (p) cc_final: 0.8805 (t) REVERT: e 647 GLU cc_start: 0.8578 (mt-10) cc_final: 0.8221 (mt-10) REVERT: f 125 LEU cc_start: 0.9511 (OUTLIER) cc_final: 0.9271 (tt) REVERT: f 161 MET cc_start: 0.8826 (tpp) cc_final: 0.8274 (tpp) REVERT: g 588 ARG cc_start: 0.9002 (ttm110) cc_final: 0.8466 (tmm-80) REVERT: g 601 LYS cc_start: 0.8930 (mttm) cc_final: 0.8611 (mtpp) REVERT: g 621 GLU cc_start: 0.8742 (pt0) cc_final: 0.7905 (tm-30) REVERT: g 644 ARG cc_start: 0.9205 (ptp-170) cc_final: 0.8966 (ptt-90) outliers start: 38 outliers final: 28 residues processed: 167 average time/residue: 0.1488 time to fit residues: 37.0287 Evaluate side-chains 171 residues out of total 1736 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 136 time to evaluate : 0.629 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 11 LEU Chi-restraints excluded: chain A residue 16 GLU Chi-restraints excluded: chain A residue 71 ILE Chi-restraints excluded: chain A residue 82 LEU Chi-restraints excluded: chain A residue 100 ASP Chi-restraints excluded: chain B residue 5 THR Chi-restraints excluded: chain B residue 80 ILE Chi-restraints excluded: chain B residue 101 LEU Chi-restraints excluded: chain b residue 38 VAL Chi-restraints excluded: chain b residue 126 CYS Chi-restraints excluded: chain b residue 164 GLU Chi-restraints excluded: chain b residue 265 LEU Chi-restraints excluded: chain b residue 320 MET Chi-restraints excluded: chain b residue 445 CYS Chi-restraints excluded: chain b residue 488 VAL Chi-restraints excluded: chain c residue 530 MET Chi-restraints excluded: chain c residue 641 LEU Chi-restraints excluded: chain d residue 38 VAL Chi-restraints excluded: chain d residue 125 LEU Chi-restraints excluded: chain d residue 164 GLU Chi-restraints excluded: chain d residue 165 LEU Chi-restraints excluded: chain d residue 270 ILE Chi-restraints excluded: chain e residue 635 ILE Chi-restraints excluded: chain f residue 36 VAL Chi-restraints excluded: chain f residue 38 VAL Chi-restraints excluded: chain f residue 120 VAL Chi-restraints excluded: chain f residue 125 LEU Chi-restraints excluded: chain f residue 126 CYS Chi-restraints excluded: chain f residue 213 ILE Chi-restraints excluded: chain f residue 254 VAL Chi-restraints excluded: chain f residue 286 VAL Chi-restraints excluded: chain f residue 323 ILE Chi-restraints excluded: chain f residue 445 CYS Chi-restraints excluded: chain g residue 538 THR Chi-restraints excluded: chain g residue 599 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 148 optimal weight: 0.9990 chunk 34 optimal weight: 2.9990 chunk 186 optimal weight: 5.9990 chunk 178 optimal weight: 3.9990 chunk 81 optimal weight: 3.9990 chunk 25 optimal weight: 2.9990 chunk 71 optimal weight: 0.9980 chunk 26 optimal weight: 0.0870 chunk 95 optimal weight: 0.0980 chunk 150 optimal weight: 0.9980 chunk 123 optimal weight: 2.9990 overall best weight: 0.6360 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 79 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3734 r_free = 0.3734 target = 0.089648 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3258 r_free = 0.3258 target = 0.065003 restraints weight = 47101.663| |-----------------------------------------------------------------------------| r_work (start): 0.3226 rms_B_bonded: 4.41 r_work: 0.3055 rms_B_bonded: 4.49 restraints_weight: 0.5000 r_work (final): 0.3055 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8719 moved from start: 0.2804 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.041 17781 Z= 0.107 Angle : 0.656 15.443 24354 Z= 0.296 Chirality : 0.045 0.288 3037 Planarity : 0.003 0.042 2864 Dihedral : 7.510 57.796 4754 Min Nonbonded Distance : 2.410 Molprobity Statistics. All-atom Clashscore : 4.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.07 % Favored : 96.93 % Rotamer: Outliers : 1.84 % Allowed : 12.90 % Favored : 85.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.41 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.35 (0.19), residues: 1922 helix: 0.45 (0.28), residues: 420 sheet: -0.14 (0.23), residues: 512 loop : -0.49 (0.20), residues: 990 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 83 TYR 0.013 0.001 TYR A 61 PHE 0.011 0.001 PHE B 76 TRP 0.016 0.001 TRP g 631 HIS 0.003 0.001 HIS A 104 Details of bonding type rmsd/Z covalent geometry : bond 0.00235 / 0.10 (17620) covalent geometry : angle 0.59227 / 0.28 (23909) SS BOND : bond 0.00159 / 0.09 ( 38) SS BOND : angle 0.73048 / 0.45 ( 76) hydrogen bonds : bond 0.03345 / 2.27 ( 547) hydrogen bonds : angle 4.83940 / 3.25 ( 1533) link_ALPHA1-3 : bond 0.00950 / 0.45 ( 6) link_ALPHA1-3 : angle 1.81157 / 1.03 ( 18) link_ALPHA1-6 : bond 0.00861 / 0.39 ( 5) link_ALPHA1-6 : angle 1.49531 / 0.89 ( 15) link_BETA1-4 : bond 0.00691 / 0.52 ( 47) link_BETA1-4 : angle 2.75375 / 1.69 ( 141) link_NAG-ASN : bond 0.00310 / 0.21 ( 65) link_NAG-ASN : angle 2.14644 / 1.55 ( 195) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3844 Ramachandran restraints generated. 1922 Oldfield, 0 Emsley, 1922 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3844 Ramachandran restraints generated. 1922 Oldfield, 0 Emsley, 1922 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 184 residues out of total 1736 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 152 time to evaluate : 1.022 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: A 16 GLU cc_start: 0.9271 (OUTLIER) cc_final: 0.8828 (pm20) REVERT: A 39 ARG cc_start: 0.8917 (ptt180) cc_final: 0.8365 (ptm-80) REVERT: A 53 ASP cc_start: 0.8166 (t0) cc_final: 0.7946 (t0) REVERT: A 68 ARG cc_start: 0.8826 (mtp-110) cc_final: 0.8529 (mtm110) REVERT: A 71 ILE cc_start: 0.8984 (OUTLIER) cc_final: 0.8679 (mm) REVERT: A 74 ASP cc_start: 0.8609 (p0) cc_final: 0.7360 (p0) REVERT: A 79 GLN cc_start: 0.8807 (pt0) cc_final: 0.8471 (pp30) REVERT: B 47 GLN cc_start: 0.8904 (tt0) cc_final: 0.8515 (tp40) REVERT: B 66 ARG cc_start: 0.8402 (ptp90) cc_final: 0.7890 (ptp90) REVERT: b 434 MET cc_start: 0.8077 (ttm) cc_final: 0.7393 (ttm) REVERT: c 641 LEU cc_start: 0.9029 (OUTLIER) cc_final: 0.8795 (mm) REVERT: c 657 GLU cc_start: 0.8590 (tp30) cc_final: 0.7947 (tt0) REVERT: d 161 MET cc_start: 0.8933 (mmm) cc_final: 0.8698 (mmm) REVERT: d 164 GLU cc_start: 0.8498 (OUTLIER) cc_final: 0.8202 (mm-30) REVERT: d 270 ILE cc_start: 0.9375 (OUTLIER) cc_final: 0.9169 (mp) REVERT: e 530 MET cc_start: 0.8364 (mmt) cc_final: 0.8105 (mmt) REVERT: e 536 THR cc_start: 0.9125 (p) cc_final: 0.8750 (t) REVERT: e 647 GLU cc_start: 0.8544 (mt-10) cc_final: 0.8170 (mt-10) REVERT: f 161 MET cc_start: 0.8799 (tpp) cc_final: 0.8338 (tpp) REVERT: g 588 ARG cc_start: 0.8967 (ttm110) cc_final: 0.8461 (tmm-80) REVERT: g 621 GLU cc_start: 0.8676 (pt0) cc_final: 0.7880 (tm-30) REVERT: g 644 ARG cc_start: 0.9202 (ptp-170) cc_final: 0.8986 (ptt-90) outliers start: 32 outliers final: 25 residues processed: 175 average time/residue: 0.1471 time to fit residues: 38.1899 Evaluate side-chains 171 residues out of total 1736 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 141 time to evaluate : 0.648 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 16 GLU Chi-restraints excluded: chain A residue 71 ILE Chi-restraints excluded: chain A residue 82 LEU Chi-restraints excluded: chain A residue 100 ASP Chi-restraints excluded: chain B residue 80 ILE Chi-restraints excluded: chain b residue 38 VAL Chi-restraints excluded: chain b residue 120 VAL Chi-restraints excluded: chain b residue 126 CYS Chi-restraints excluded: chain b residue 265 LEU Chi-restraints excluded: chain b residue 320 MET Chi-restraints excluded: chain b residue 445 CYS Chi-restraints excluded: chain b residue 488 VAL Chi-restraints excluded: chain c residue 530 MET Chi-restraints excluded: chain c residue 641 LEU Chi-restraints excluded: chain d residue 38 VAL Chi-restraints excluded: chain d residue 125 LEU Chi-restraints excluded: chain d residue 164 GLU Chi-restraints excluded: chain d residue 270 ILE Chi-restraints excluded: chain e residue 635 ILE Chi-restraints excluded: chain f residue 36 VAL Chi-restraints excluded: chain f residue 38 VAL Chi-restraints excluded: chain f residue 120 VAL Chi-restraints excluded: chain f residue 126 CYS Chi-restraints excluded: chain f residue 213 ILE Chi-restraints excluded: chain f residue 254 VAL Chi-restraints excluded: chain f residue 286 VAL Chi-restraints excluded: chain f residue 323 ILE Chi-restraints excluded: chain f residue 445 CYS Chi-restraints excluded: chain g residue 538 THR Chi-restraints excluded: chain g residue 599 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 139 optimal weight: 9.9990 chunk 176 optimal weight: 4.9990 chunk 14 optimal weight: 7.9990 chunk 81 optimal weight: 3.9990 chunk 137 optimal weight: 0.6980 chunk 77 optimal weight: 6.9990 chunk 121 optimal weight: 2.9990 chunk 113 optimal weight: 3.9990 chunk 103 optimal weight: 0.6980 chunk 6 optimal weight: 7.9990 chunk 88 optimal weight: 1.9990 overall best weight: 2.0786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 5 GLN A 104 HIS B 39 ASN ** d 72 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** d 330 HIS f 33 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3611 r_free = 0.3611 target = 0.085535 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3104 r_free = 0.3104 target = 0.060595 restraints weight = 47970.772| |-----------------------------------------------------------------------------| r_work (start): 0.3077 rms_B_bonded: 4.42 r_work: 0.2898 rms_B_bonded: 4.57 restraints_weight: 0.5000 r_work (final): 0.2898 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8672 moved from start: 0.2891 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 17781 Z= 0.191 Angle : 0.704 15.737 24354 Z= 0.322 Chirality : 0.045 0.290 3037 Planarity : 0.004 0.044 2864 Dihedral : 7.667 58.822 4754 Min Nonbonded Distance : 2.417 Molprobity Statistics. All-atom Clashscore : 4.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.85 % Favored : 96.15 % Rotamer: Outliers : 1.90 % Allowed : 13.31 % Favored : 84.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.41 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.43 (0.19), residues: 1922 helix: 0.53 (0.28), residues: 402 sheet: -0.11 (0.23), residues: 500 loop : -0.65 (0.19), residues: 1020 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A 83 TYR 0.028 0.001 TYR B 54 PHE 0.016 0.002 PHE b 382 TRP 0.009 0.001 TRP g 631 HIS 0.024 0.001 HIS A 104 Details of bonding type rmsd/Z covalent geometry : bond 0.00446 / 0.19 (17620) covalent geometry : angle 0.64116 / 0.31 (23909) SS BOND : bond 0.00217 / 0.14 ( 38) SS BOND : angle 0.82068 / 0.51 ( 76) hydrogen bonds : bond 0.03721 / 2.53 ( 547) hydrogen bonds : angle 4.95082 / 3.31 ( 1533) link_ALPHA1-3 : bond 0.00770 / 0.36 ( 6) link_ALPHA1-3 : angle 1.96704 / 1.12 ( 18) link_ALPHA1-6 : bond 0.00833 / 0.38 ( 5) link_ALPHA1-6 : angle 1.51110 / 0.91 ( 15) link_BETA1-4 : bond 0.00649 / 0.50 ( 47) link_BETA1-4 : angle 2.79785 / 1.72 ( 141) link_NAG-ASN : bond 0.00368 / 0.26 ( 65) link_NAG-ASN : angle 2.25459 / 1.62 ( 195) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3844 Ramachandran restraints generated. 1922 Oldfield, 0 Emsley, 1922 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3844 Ramachandran restraints generated. 1922 Oldfield, 0 Emsley, 1922 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 165 residues out of total 1736 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 132 time to evaluate : 0.674 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: A 16 GLU cc_start: 0.9322 (OUTLIER) cc_final: 0.8909 (pm20) REVERT: A 39 ARG cc_start: 0.8859 (ptt180) cc_final: 0.8311 (ptm-80) REVERT: A 68 ARG cc_start: 0.8841 (mtp-110) cc_final: 0.8546 (mtp-110) REVERT: A 71 ILE cc_start: 0.9014 (OUTLIER) cc_final: 0.8731 (mm) REVERT: A 74 ASP cc_start: 0.8569 (p0) cc_final: 0.8274 (p0) REVERT: B 47 GLN cc_start: 0.8825 (tt0) cc_final: 0.8444 (tp40) REVERT: B 66 ARG cc_start: 0.8388 (ptp90) cc_final: 0.7493 (ptp90) REVERT: B 82 ARG cc_start: 0.8841 (ttp80) cc_final: 0.8339 (ttp80) REVERT: c 641 LEU cc_start: 0.9106 (OUTLIER) cc_final: 0.8865 (mm) REVERT: c 657 GLU cc_start: 0.8480 (tp30) cc_final: 0.7718 (tt0) REVERT: d 164 GLU cc_start: 0.8564 (OUTLIER) cc_final: 0.8192 (mm-30) REVERT: e 530 MET cc_start: 0.8417 (mmt) cc_final: 0.8053 (mmt) REVERT: e 536 THR cc_start: 0.9146 (p) cc_final: 0.8753 (t) REVERT: e 647 GLU cc_start: 0.8604 (mt-10) cc_final: 0.8213 (mt-10) REVERT: e 659 GLU cc_start: 0.7373 (tt0) cc_final: 0.7087 (tt0) REVERT: f 161 MET cc_start: 0.8891 (tpp) cc_final: 0.8251 (tpp) REVERT: g 588 ARG cc_start: 0.9024 (ttm110) cc_final: 0.8374 (tmm-80) REVERT: g 621 GLU cc_start: 0.8972 (pt0) cc_final: 0.8005 (tm-30) REVERT: g 644 ARG cc_start: 0.9389 (ptp-170) cc_final: 0.9106 (ptt-90) outliers start: 33 outliers final: 25 residues processed: 156 average time/residue: 0.1519 time to fit residues: 35.3082 Evaluate side-chains 159 residues out of total 1736 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 130 time to evaluate : 0.852 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 16 GLU Chi-restraints excluded: chain A residue 71 ILE Chi-restraints excluded: chain A residue 82 LEU Chi-restraints excluded: chain A residue 100 ASP Chi-restraints excluded: chain B residue 80 ILE Chi-restraints excluded: chain b residue 38 VAL Chi-restraints excluded: chain b residue 120 VAL Chi-restraints excluded: chain b residue 126 CYS Chi-restraints excluded: chain b residue 265 LEU Chi-restraints excluded: chain b residue 445 CYS Chi-restraints excluded: chain b residue 488 VAL Chi-restraints excluded: chain c residue 530 MET Chi-restraints excluded: chain c residue 641 LEU Chi-restraints excluded: chain d residue 38 VAL Chi-restraints excluded: chain d residue 125 LEU Chi-restraints excluded: chain d residue 164 GLU Chi-restraints excluded: chain e residue 535 ILE Chi-restraints excluded: chain e residue 635 ILE Chi-restraints excluded: chain f residue 33 ASN Chi-restraints excluded: chain f residue 36 VAL Chi-restraints excluded: chain f residue 38 VAL Chi-restraints excluded: chain f residue 120 VAL Chi-restraints excluded: chain f residue 125 LEU Chi-restraints excluded: chain f residue 126 CYS Chi-restraints excluded: chain f residue 213 ILE Chi-restraints excluded: chain f residue 254 VAL Chi-restraints excluded: chain f residue 286 VAL Chi-restraints excluded: chain f residue 445 CYS Chi-restraints excluded: chain g residue 538 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 90 optimal weight: 0.9980 chunk 27 optimal weight: 2.9990 chunk 109 optimal weight: 2.9990 chunk 126 optimal weight: 5.9990 chunk 165 optimal weight: 0.9990 chunk 186 optimal weight: 5.9990 chunk 64 optimal weight: 0.0970 chunk 52 optimal weight: 3.9990 chunk 180 optimal weight: 3.9990 chunk 33 optimal weight: 4.9990 chunk 62 optimal weight: 4.9990 overall best weight: 1.6184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** d 72 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** f 33 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3613 r_free = 0.3613 target = 0.085655 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3103 r_free = 0.3103 target = 0.060664 restraints weight = 48280.419| |-----------------------------------------------------------------------------| r_work (start): 0.3087 rms_B_bonded: 4.36 r_work: 0.2909 rms_B_bonded: 4.52 restraints_weight: 0.5000 r_work (final): 0.2909 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8717 moved from start: 0.2893 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.135 17781 Z= 0.208 Angle : 0.860 59.199 24354 Z= 0.441 Chirality : 0.047 0.668 3037 Planarity : 0.004 0.043 2864 Dihedral : 7.667 58.826 4754 Min Nonbonded Distance : 1.932 Molprobity Statistics. All-atom Clashscore : 5.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.80 % Favored : 96.20 % Rotamer: Outliers : 2.02 % Allowed : 12.96 % Favored : 85.02 % Cbeta Deviations : 0.05 % Peptide Plane: Cis-proline : 2.41 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.44 (0.19), residues: 1922 helix: 0.52 (0.28), residues: 402 sheet: -0.12 (0.23), residues: 500 loop : -0.65 (0.19), residues: 1020 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 83 TYR 0.025 0.001 TYR B 54 PHE 0.015 0.002 PHE b 382 TRP 0.009 0.001 TRP g 631 HIS 0.017 0.001 HIS A 104 Details of bonding type rmsd/Z covalent geometry : bond 0.00481 / 0.21 (17620) covalent geometry : angle 0.81187 / 0.43 (23909) SS BOND : bond 0.00222 / 0.14 ( 38) SS BOND : angle 0.80595 / 0.50 ( 76) hydrogen bonds : bond 0.03704 / 2.51 ( 547) hydrogen bonds : angle 4.95845 / 3.32 ( 1533) link_ALPHA1-3 : bond 0.00786 / 0.38 ( 6) link_ALPHA1-3 : angle 1.95944 / 1.12 ( 18) link_ALPHA1-6 : bond 0.00826 / 0.38 ( 5) link_ALPHA1-6 : angle 1.51135 / 0.91 ( 15) link_BETA1-4 : bond 0.00637 / 0.49 ( 47) link_BETA1-4 : angle 2.79768 / 1.72 ( 141) link_NAG-ASN : bond 0.00360 / 0.25 ( 65) link_NAG-ASN : angle 2.25391 / 1.62 ( 195) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4184.18 seconds wall clock time: 72 minutes 41.26 seconds (4361.26 seconds total)