Starting phenix.real_space_refine on Sat Jul 4 02:59:31 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9zrz_74656/07_2026/9zrz_74656.cif Found real_map, /net/cci-nas-00/data/ceres_data/9zrz_74656/07_2026/9zrz_74656.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9zrz_74656/07_2026/9zrz_74656.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9zrz_74656/07_2026/9zrz_74656.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9zrz_74656/07_2026/9zrz_74656.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9zrz_74656/07_2026/9zrz_74656.map" } resolution = 2.9 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.015 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 109 5.16 5 C 10717 2.51 5 N 2837 2.21 5 O 3541 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 19 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: 17204 Number of models: 1 Model: "" Number of chains: 51 Chain: "A" Number of atoms: 1036 Number of conformers: 1 Conformer: "" Number of residues, atoms: 134, 1036 Classifications: {'peptide': 134} Link IDs: {'PTRANS': 2, 'TRANS': 131} 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: 822 Number of conformers: 1 Conformer: "" Number of residues, atoms: 109, 822 Classifications: {'peptide': 109} Link IDs: {'PCIS': 2, 'PTRANS': 4, 'TRANS': 102} 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: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "J" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "K" Number of atoms: 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: 94 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 94 Unusual residues: {'BMA': 1, 'MAN': 5, 'NAG': 2} Classifications: {'undetermined': 8} Link IDs: {None: 7} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen dihedrals: 24 Unresolved non-hydrogen chiralities: 8 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: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "j" Number of atoms: 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: "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: 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: "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: 98 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 98 Unusual residues: {'NAG': 7} Classifications: {'undetermined': 7} Link IDs: {None: 6} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 21 Unresolved non-hydrogen chiralities: 7 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: 4.10, per 1000 atoms: 0.24 Number of scatterers: 17204 At special positions: 0 Unit cell: (133.63, 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 109 16.00 O 3541 8.00 N 2837 7.00 C 10717 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 98 " distance=2.04 Simple disulfide: pdb=" SG CYS B 23 " - pdb=" SG CYS B 88 " distance=2.03 Simple disulfide: pdb=" SG CYS b 54 " - pdb=" SG CYS b 74 " distance=2.04 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=2.03 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=2.03 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=2.02 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 ALPHA1-2 " MAN S 4 " - " MAN S 5 " ALPHA1-3 " BMA E 3 " - " MAN E 4 " " BMA Q 3 " - " MAN Q 4 " " BMA S 3 " - " MAN S 4 " " MAN S 6 " - " MAN S 7 " " BMA j 3 " - " MAN j 4 " ALPHA1-6 " BMA E 3 " - " MAN E 5 " " BMA Q 3 " - " MAN Q 5 " " BMA S 3 " - " MAN S 6 " " MAN S 6 " - " MAN S 8 " " BMA j 3 " - " MAN j 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 I 2 " - " BMA I 3 " " NAG J 1 " - " NAG J 2 " " 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 i 1 " - " NAG i 2 " " NAG i 2 " - " BMA i 3 " " NAG j 1 " - " NAG j 2 " " NAG j 2 " - " BMA j 3 " " NAG k 1 " - " NAG k 2 " " NAG l 1 " - " NAG l 2 " " NAG m 1 " - " NAG m 2 " " NAG n 1 " - " NAG n 2 " " 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-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 197 " " NAG H 1 " - " ASN b 234 " " NAG I 1 " - " ASN b 241 " " NAG J 1 " - " ASN b 276 " " NAG K 1 " - " ASN b 301 " " NAG L 1 " - " ASN b 448 " " NAG M 1 " - " ASN b 465 " " NAG N 1 " - " ASN b 386 " " 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 448 " " NAG Z 1 " - " ASN d 465 " " NAG a 1 " - " ASN d 363 " " NAG b 601 " - " ASN b 88 " " NAG b 602 " - " ASN b 133 " " NAG b 603 " - " ASN b 160 " " NAG b 604 " - " ASN b 339 " " NAG b 605 " - " ASN b 355 " " NAG b 606 " - " ASN b 269 " " NAG b 608 " - " ASN b 363 " " 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 d 607 " - " ASN d 386 " " 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 363 " " NAG f 608 " - " ASN f 386 " " NAG g 701 " - " ASN g 611 " " NAG g 702 " - " ASN g 637 " " NAG g 703 " - " ASN g 625 " " NAG h 1 " - " ASN f 392 " " NAG i 1 " - " ASN f 332 " " NAG j 1 " - " ASN f 262 " " NAG k 1 " - " ASN f 156 " " NAG l 1 " - " ASN f 160 " " NAG m 1 " - " ASN f 197 " " NAG n 1 " - " ASN f 234 " " NAG o 1 " - " ASN f 241 " " NAG p 1 " - " ASN f 276 " " NAG q 1 " - " ASN f 301 " " NAG r 1 " - " ASN f 448 " " NAG s 1 " - " ASN f 465 " Time building additional restraints: 2.01 Conformation dependent library (CDL) restraints added in 743.5 milliseconds 3832 Ramachandran restraints generated. 1916 Oldfield, 0 Emsley, 1916 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3640 Finding SS restraints... Secondary structure from input PDB file: 44 helices and 35 sheets defined 23.4% alpha, 32.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.47 Creating SS restraints... Processing helix chain 'A' and resid 28 through 30 No H-bonds generated for 'chain 'A' and resid 28 through 30' Processing helix chain 'A' and resid 53 through 57 Processing helix chain 'A' and resid 89 through 93 Processing helix chain 'B' and resid 79 through 83 Processing helix chain 'b' and resid 99 through 117 removed outlier: 3.541A pdb=" N THR b 106 " --> pdb=" O GLU b 102 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N LEU b 116 " --> pdb=" O TRP b 112 " (cutoff:3.500A) Processing helix chain 'b' and resid 122 through 126 Processing helix chain 'b' and resid 334 through 351 removed outlier: 3.516A pdb=" N LYS b 340 " --> pdb=" O SER b 336 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N THR b 341 " --> pdb=" O ARG b 337 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N LEU b 342 " --> pdb=" O TRP b 338 " (cutoff:3.500A) Processing helix chain 'b' and resid 368 through 373 Processing helix chain 'b' and resid 387 through 390 removed outlier: 3.524A pdb=" N LEU b 390 " --> pdb=" O THR b 387 " (cutoff:3.500A) No H-bonds generated for 'chain 'b' and resid 387 through 390' Processing helix chain 'b' and resid 475 through 484 removed outlier: 3.974A pdb=" N TRP b 479 " --> pdb=" O MET b 475 " (cutoff:3.500A) removed outlier: 4.025A pdb=" N GLU b 482 " --> pdb=" O ASN b 478 " (cutoff:3.500A) Processing helix chain 'c' and resid 529 through 534 Processing helix chain 'c' and resid 536 through 543 removed outlier: 4.021A pdb=" N GLN c 540 " --> pdb=" O THR c 536 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N GLN c 543 " --> pdb=" O VAL c 539 " (cutoff:3.500A) Processing helix chain 'c' and resid 569 through 596 removed outlier: 3.552A pdb=" N ASP c 589 " --> pdb=" O ARG c 585 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N LEU c 592 " --> pdb=" O ARG c 588 " (cutoff:3.500A) Processing helix chain 'c' and resid 611 through 615 Processing helix chain 'c' and resid 618 through 625 removed outlier: 3.673A pdb=" N ILE c 622 " --> pdb=" O SER c 618 " (cutoff:3.500A) Processing helix chain 'c' and resid 627 through 636 removed outlier: 3.908A pdb=" N LYS c 633 " --> pdb=" O LEU c 629 " (cutoff:3.500A) removed outlier: 4.075A pdb=" N GLU c 634 " --> pdb=" O GLN c 630 " (cutoff:3.500A) Processing helix chain 'c' and resid 638 through 658 Processing helix chain 'd' and resid 70 through 74 Processing helix chain 'd' and resid 99 through 115 removed outlier: 3.543A pdb=" N THR d 106 " --> pdb=" O GLU d 102 " (cutoff:3.500A) Processing helix chain 'd' and resid 122 through 126 removed outlier: 3.593A pdb=" N LEU d 125 " --> pdb=" O LEU d 122 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N CYS d 126 " --> pdb=" O THR d 123 " (cutoff:3.500A) No H-bonds generated for 'chain 'd' and resid 122 through 126' Processing helix chain 'd' and resid 334 through 351 Processing helix chain 'd' and resid 368 through 373 Processing helix chain 'd' and resid 387 through 390 removed outlier: 3.511A pdb=" N LEU d 390 " --> pdb=" O THR d 387 " (cutoff:3.500A) No H-bonds generated for 'chain 'd' and resid 387 through 390' Processing helix chain 'd' and resid 475 through 481 removed outlier: 3.935A 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: 3.827A pdb=" N GLN e 540 " --> pdb=" O THR e 536 " (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: 3.579A pdb=" N LEU e 592 " --> pdb=" O ARG e 588 " (cutoff:3.500A) Processing helix chain 'e' and resid 618 through 625 removed outlier: 3.901A pdb=" N ILE e 622 " --> pdb=" O SER e 618 " (cutoff:3.500A) Processing helix chain 'e' and resid 628 through 636 removed outlier: 4.165A pdb=" N LYS e 633 " --> pdb=" O LEU e 629 " (cutoff:3.500A) removed outlier: 4.901A pdb=" N GLU e 634 " --> pdb=" O GLN e 630 " (cutoff:3.500A) Processing helix chain 'e' and resid 638 through 658 removed outlier: 3.570A pdb=" N ARG e 644 " --> pdb=" O GLN e 640 " (cutoff:3.500A) removed outlier: 3.982A pdb=" N GLU e 647 " --> pdb=" O TYR e 643 " (cutoff:3.500A) removed outlier: 4.364A pdb=" N GLU e 648 " --> pdb=" O ARG e 644 " (cutoff:3.500A) Processing helix chain 'f' and resid 98 through 117 removed outlier: 4.260A pdb=" N GLU f 102 " --> pdb=" O ASN f 98 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N LEU f 116 " --> pdb=" O TRP f 112 " (cutoff:3.500A) Processing helix chain 'f' and resid 122 through 126 Processing helix chain 'f' and resid 334 through 351 removed outlier: 3.530A pdb=" N THR f 341 " --> pdb=" O ARG f 337 " (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 474 through 484 removed outlier: 4.135A pdb=" N ASN f 478 " --> pdb=" O ASP f 474 " (cutoff:3.500A) removed outlier: 3.754A pdb=" N TRP f 479 " --> pdb=" O MET f 475 " (cutoff:3.500A) removed outlier: 3.980A pdb=" N GLU f 482 " --> pdb=" O ASN f 478 " (cutoff:3.500A) Processing helix chain 'g' and resid 529 through 534 Processing helix chain 'g' and resid 536 through 543 removed outlier: 3.928A pdb=" N GLN g 540 " --> pdb=" O THR g 536 " (cutoff:3.500A) removed outlier: 3.794A pdb=" N GLN g 543 " --> pdb=" O VAL g 539 " (cutoff:3.500A) Processing helix chain 'g' and resid 569 through 596 removed outlier: 3.506A pdb=" N ASP g 589 " --> pdb=" O ARG g 585 " (cutoff:3.500A) removed outlier: 4.054A pdb=" N LEU g 592 " --> pdb=" O ARG g 588 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N LEU g 593 " --> pdb=" O ASP g 589 " (cutoff:3.500A) Processing helix chain 'g' and resid 618 through 625 removed outlier: 3.728A pdb=" N TRP g 623 " --> pdb=" O LEU g 619 " (cutoff:3.500A) Processing helix chain 'g' and resid 627 through 636 removed outlier: 4.296A pdb=" N LYS g 633 " --> pdb=" O LEU g 629 " (cutoff:3.500A) removed outlier: 4.609A pdb=" N GLU g 634 " --> pdb=" O GLN g 630 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N ILE g 635 " --> pdb=" O TRP g 631 " (cutoff:3.500A) Processing helix chain 'g' and resid 638 through 658 Processing sheet with id=AA1, first strand: chain 'A' and resid 3 through 7 removed outlier: 3.654A pdb=" N THR A 80 " --> pdb=" O GLU A 75 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 10 through 12 removed outlier: 6.386A pdb=" N GLY A 10 " --> pdb=" O THR A 131 " (cutoff:3.500A) removed outlier: 4.292A pdb=" N GLY A 33 " --> pdb=" O GLY A 101 " (cutoff:3.500A) removed outlier: 6.657A pdb=" N ILE A 34 " --> pdb=" O ARG A 50 " (cutoff:3.500A) removed outlier: 4.385A pdb=" N ARG A 50 " --> pdb=" O ILE A 34 " (cutoff:3.500A) removed outlier: 6.773A pdb=" N TRP A 36 " --> pdb=" O ILE A 48 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 107 through 108 removed outlier: 3.555A pdb=" N TYR A 114 " --> pdb=" O TYR A 107 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 4 through 7 removed outlier: 3.702A pdb=" N ASP B 70 " --> pdb=" O SER B 67 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 10 through 13 removed outlier: 6.669A pdb=" N VAL B 33 " --> pdb=" O HIS B 49 " (cutoff:3.500A) removed outlier: 4.718A pdb=" N HIS B 49 " --> pdb=" O VAL B 33 " (cutoff:3.500A) removed outlier: 6.754A pdb=" N TRP B 35 " --> pdb=" O LEU B 47 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 10 through 13 removed outlier: 3.765A pdb=" N THR B 97 " --> pdb=" O GLN B 90 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'b' and resid 494 through 499 removed outlier: 5.457A pdb=" N VAL c 608 " --> pdb=" O VAL b 36 " (cutoff:3.500A) removed outlier: 8.231A pdb=" N VAL b 38 " --> pdb=" O THR c 606 " (cutoff:3.500A) removed outlier: 7.753A pdb=" N THR c 606 " --> pdb=" O VAL b 38 " (cutoff:3.500A) removed outlier: 7.993A pdb=" N TYR b 40 " --> pdb=" O CYS c 604 " (cutoff:3.500A) removed outlier: 8.547A pdb=" N CYS c 604 " --> pdb=" O TYR b 40 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'b' and resid 45 through 47 Processing sheet with id=AA9, first strand: chain 'b' and resid 53 through 55 Processing sheet with id=AB1, first strand: chain 'b' and resid 66 through 67 removed outlier: 7.078A 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: 6.288A 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: 3.672A pdb=" N GLY b 451 " --> pdb=" O LEU b 260 " (cutoff:3.500A) removed outlier: 10.131A pdb=" N LYS b 444 " --> pdb=" O ILE b 294 " (cutoff:3.500A) removed outlier: 11.471A pdb=" N ILE b 294 " --> pdb=" O LYS b 444 " (cutoff:3.500A) removed outlier: 9.828A pdb=" N GLU b 446 " --> pdb=" O VAL b 292 " (cutoff:3.500A) removed outlier: 10.760A pdb=" N VAL b 292 " --> pdb=" O GLU b 446 " (cutoff:3.500A) removed outlier: 9.301A pdb=" N ASN b 448 " --> pdb=" O GLN b 290 " (cutoff:3.500A) removed outlier: 10.156A pdb=" N GLN b 290 " --> pdb=" O ASN b 448 " (cutoff:3.500A) removed outlier: 6.718A pdb=" N THR b 450 " --> pdb=" O LEU b 288 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N HIS b 330 " --> pdb=" O ILE b 297 " (cutoff:3.500A) removed outlier: 3.862A pdb=" N LYS b 421 " --> pdb=" O PHE b 382 " (cutoff:3.500A) removed outlier: 4.719A 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: 6.718A pdb=" N THR b 450 " --> pdb=" O LEU b 288 " (cutoff:3.500A) removed outlier: 10.156A pdb=" N GLN b 290 " --> pdb=" O ASN b 448 " (cutoff:3.500A) removed outlier: 9.301A pdb=" N ASN b 448 " --> pdb=" O GLN b 290 " (cutoff:3.500A) removed outlier: 10.760A pdb=" N VAL b 292 " --> pdb=" O GLU b 446 " (cutoff:3.500A) removed outlier: 9.828A pdb=" N GLU b 446 " --> pdb=" O VAL b 292 " (cutoff:3.500A) removed outlier: 11.471A pdb=" N ILE b 294 " --> pdb=" O LYS b 444 " (cutoff:3.500A) removed outlier: 10.131A pdb=" N LYS b 444 " --> pdb=" O ILE b 294 " (cutoff:3.500A) removed outlier: 6.854A pdb=" N THR b 357 " --> pdb=" O GLU b 466 " (cutoff:3.500A) removed outlier: 7.983A pdb=" N PHE b 468 " --> pdb=" O THR b 357 " (cutoff:3.500A) removed outlier: 6.850A 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: 7.358A pdb=" N ASN b 301 " --> pdb=" O ILE b 323 " (cutoff:3.500A) removed outlier: 5.194A pdb=" N ILE b 323 " --> pdb=" O ASN b 301 " (cutoff:3.500A) removed outlier: 4.662A pdb=" N THR b 303 " --> pdb=" O GLY b 321 " (cutoff:3.500A) removed outlier: 7.160A 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: 4.724A pdb=" N VAL d 36 " --> pdb=" O THR e 606 " (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 91 through 94 Processing sheet with id=AC2, first strand: chain 'd' and resid 130 through 132 Processing sheet with id=AC3, first strand: chain 'd' and resid 181 through 183 Processing sheet with id=AC4, first strand: chain 'd' and resid 202 through 203 removed outlier: 6.297A pdb=" N THR d 202 " --> pdb=" O TYR d 435 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'd' and resid 259 through 261 removed outlier: 3.566A pdb=" N GLY d 451 " --> pdb=" O LEU d 260 " (cutoff:3.500A) removed outlier: 10.073A pdb=" N LYS d 444 " --> pdb=" O ILE d 294 " (cutoff:3.500A) removed outlier: 11.440A pdb=" N ILE d 294 " --> pdb=" O LYS d 444 " (cutoff:3.500A) removed outlier: 9.715A pdb=" N GLU d 446 " --> pdb=" O VAL d 292 " (cutoff:3.500A) removed outlier: 10.715A pdb=" N VAL d 292 " --> pdb=" O GLU d 446 " (cutoff:3.500A) removed outlier: 9.206A pdb=" N ASN d 448 " --> pdb=" O GLN d 290 " (cutoff:3.500A) removed outlier: 10.090A pdb=" N GLN d 290 " --> pdb=" O ASN d 448 " (cutoff:3.500A) removed outlier: 6.723A pdb=" N THR d 450 " --> pdb=" O LEU d 288 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N HIS d 330 " --> pdb=" O ILE d 297 " (cutoff:3.500A) removed outlier: 4.360A pdb=" N ALA d 329 " --> pdb=" O CYS d 418 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N LYS d 421 " --> pdb=" O PHE d 382 " (cutoff:3.500A) removed outlier: 4.694A pdb=" N PHE d 382 " --> pdb=" O LYS d 421 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'd' and resid 271 through 273 removed outlier: 6.723A pdb=" N THR d 450 " --> pdb=" O LEU d 288 " (cutoff:3.500A) removed outlier: 10.090A pdb=" N GLN d 290 " --> pdb=" O ASN d 448 " (cutoff:3.500A) removed outlier: 9.206A pdb=" N ASN d 448 " --> pdb=" O GLN d 290 " (cutoff:3.500A) removed outlier: 10.715A pdb=" N VAL d 292 " --> pdb=" O GLU d 446 " (cutoff:3.500A) removed outlier: 9.715A pdb=" N GLU d 446 " --> pdb=" O VAL d 292 " (cutoff:3.500A) removed outlier: 11.440A pdb=" N ILE d 294 " --> pdb=" O LYS d 444 " (cutoff:3.500A) removed outlier: 10.073A pdb=" N LYS d 444 " --> pdb=" O ILE d 294 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'd' and resid 301 through 312 removed outlier: 6.993A pdb=" N ASN d 301 " --> pdb=" O ILE d 323 " (cutoff:3.500A) removed outlier: 5.014A pdb=" N ILE d 323 " --> pdb=" O ASN d 301 " (cutoff:3.500A) removed outlier: 4.928A pdb=" N THR d 303 " --> pdb=" O GLY d 321 " (cutoff:3.500A) removed outlier: 7.135A pdb=" N GLN d 315 " --> pdb=" O ILE d 309 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'f' and resid 494 through 499 removed outlier: 5.429A pdb=" N VAL g 608 " --> pdb=" O VAL f 36 " (cutoff:3.500A) removed outlier: 8.109A pdb=" N VAL f 38 " --> pdb=" O THR g 606 " (cutoff:3.500A) removed outlier: 7.596A pdb=" N THR g 606 " --> pdb=" O VAL f 38 " (cutoff:3.500A) removed outlier: 8.086A pdb=" N TYR f 40 " --> pdb=" O CYS g 604 " (cutoff:3.500A) removed outlier: 8.681A pdb=" N CYS g 604 " --> pdb=" O TYR f 40 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'f' and resid 45 through 47 Processing sheet with id=AD1, first strand: chain 'f' and resid 53 through 55 Processing sheet with id=AD2, first strand: chain 'f' and resid 66 through 67 removed outlier: 6.975A pdb=" N HIS f 66 " --> pdb=" O SER f 209 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD2 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: 6.415A 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: 3.504A pdb=" N GLY f 451 " --> pdb=" O LEU f 260 " (cutoff:3.500A) removed outlier: 10.117A pdb=" N LYS f 444 " --> pdb=" O ILE f 294 " (cutoff:3.500A) removed outlier: 11.464A pdb=" N ILE f 294 " --> pdb=" O LYS f 444 " (cutoff:3.500A) removed outlier: 9.712A pdb=" N GLU f 446 " --> pdb=" O VAL f 292 " (cutoff:3.500A) removed outlier: 10.693A pdb=" N VAL f 292 " --> pdb=" O GLU f 446 " (cutoff:3.500A) removed outlier: 9.124A pdb=" N ASN f 448 " --> pdb=" O GLN f 290 " (cutoff:3.500A) removed outlier: 9.986A pdb=" N GLN f 290 " --> pdb=" O ASN f 448 " (cutoff:3.500A) removed outlier: 6.402A pdb=" N THR f 450 " --> pdb=" O LEU f 288 " (cutoff:3.500A) removed outlier: 4.268A pdb=" N ALA f 329 " --> pdb=" O CYS f 418 " (cutoff:3.500A) removed outlier: 3.768A pdb=" N LYS f 421 " --> pdb=" O PHE f 382 " (cutoff:3.500A) removed outlier: 4.657A 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: 6.402A pdb=" N THR f 450 " --> pdb=" O LEU f 288 " (cutoff:3.500A) removed outlier: 9.986A pdb=" N GLN f 290 " --> pdb=" O ASN f 448 " (cutoff:3.500A) removed outlier: 9.124A pdb=" N ASN f 448 " --> pdb=" O GLN f 290 " (cutoff:3.500A) removed outlier: 10.693A pdb=" N VAL f 292 " --> pdb=" O GLU f 446 " (cutoff:3.500A) removed outlier: 9.712A pdb=" N GLU f 446 " --> pdb=" O VAL f 292 " (cutoff:3.500A) removed outlier: 11.464A pdb=" N ILE f 294 " --> pdb=" O LYS f 444 " (cutoff:3.500A) removed outlier: 10.117A pdb=" N LYS f 444 " --> pdb=" O ILE f 294 " (cutoff:3.500A) removed outlier: 6.389A pdb=" N THR f 357 " --> pdb=" O GLU f 466 " (cutoff:3.500A) removed outlier: 7.766A pdb=" N PHE f 468 " --> pdb=" O THR f 357 " (cutoff:3.500A) removed outlier: 6.714A pdb=" N ILE f 359 " --> pdb=" O PHE f 468 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'f' and resid 301 through 312 removed outlier: 6.934A pdb=" N ASN f 301 " --> pdb=" O ILE f 323 " (cutoff:3.500A) removed outlier: 4.965A pdb=" N ILE f 323 " --> pdb=" O ASN f 301 " (cutoff:3.500A) removed outlier: 4.742A pdb=" N THR f 303 " --> pdb=" O GLY f 321 " (cutoff:3.500A) removed outlier: 7.158A pdb=" N GLN f 315 " --> pdb=" O ILE f 309 " (cutoff:3.500A) 582 hydrogen bonds defined for protein. 1563 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 3.24 Time building geometry restraints manager: 2.45 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: 5204 1.34 - 1.46: 4354 1.46 - 1.58: 7826 1.58 - 1.70: 1 1.70 - 1.82: 140 Bond restraints: 17525 Sorted by residual: bond pdb=" CA SER f 189 " pdb=" CB SER f 189 " ideal model delta sigma weight residual 1.535 1.495 0.040 1.37e-02 5.33e+03 8.59e+00 bond pdb=" N CYS f 385 " pdb=" CA CYS f 385 " ideal model delta sigma weight residual 1.454 1.488 -0.034 1.17e-02 7.31e+03 8.33e+00 bond pdb=" N ASN f 363 " pdb=" CA ASN f 363 " ideal model delta sigma weight residual 1.453 1.488 -0.035 1.31e-02 5.83e+03 7.09e+00 bond pdb=" N VAL f 182 " pdb=" CA VAL f 182 " ideal model delta sigma weight residual 1.461 1.493 -0.032 1.23e-02 6.61e+03 6.81e+00 bond pdb=" N ASN b 363 " pdb=" CA ASN b 363 " ideal model delta sigma weight residual 1.454 1.488 -0.035 1.34e-02 5.57e+03 6.73e+00 ... (remaining 17520 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.24: 22929 2.24 - 4.48: 729 4.48 - 6.72: 87 6.72 - 8.96: 16 8.96 - 11.21: 6 Bond angle restraints: 23767 Sorted by residual: angle pdb=" N VAL d 464 " pdb=" CA VAL d 464 " pdb=" C VAL d 464 " ideal model delta sigma weight residual 111.91 107.28 4.63 8.90e-01 1.26e+00 2.71e+01 angle pdb=" CA LYS d 207 " pdb=" CB LYS d 207 " pdb=" CG LYS d 207 " ideal model delta sigma weight residual 114.10 124.39 -10.29 2.00e+00 2.50e-01 2.65e+01 angle pdb=" N ASN d 425 " pdb=" CA ASN d 425 " pdb=" C ASN d 425 " ideal model delta sigma weight residual 108.02 100.61 7.41 1.75e+00 3.27e-01 1.79e+01 angle pdb=" CA GLN A 3 " pdb=" CB GLN A 3 " pdb=" CG GLN A 3 " ideal model delta sigma weight residual 114.10 122.48 -8.38 2.00e+00 2.50e-01 1.76e+01 angle pdb=" N ASN b 425 " pdb=" CA ASN b 425 " pdb=" C ASN b 425 " ideal model delta sigma weight residual 109.07 102.72 6.35 1.61e+00 3.86e-01 1.55e+01 ... (remaining 23762 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 18.08: 11135 18.08 - 36.15: 706 36.15 - 54.23: 222 54.23 - 72.30: 60 72.30 - 90.38: 25 Dihedral angle restraints: 12148 sinusoidal: 6503 harmonic: 5645 Sorted by residual: 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 93.00 151.99 -58.99 1 1.00e+01 1.00e-02 4.65e+01 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 93.00 151.76 -58.76 1 1.00e+01 1.00e-02 4.62e+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 93.00 150.43 -57.43 1 1.00e+01 1.00e-02 4.43e+01 ... (remaining 12145 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.081: 2685 0.081 - 0.163: 307 0.163 - 0.244: 8 0.244 - 0.326: 2 0.326 - 0.407: 3 Chirality restraints: 3005 Sorted by residual: 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 4.14e+00 chirality pdb=" C1 NAG d 601 " pdb=" ND2 ASN d 88 " pdb=" C2 NAG d 601 " pdb=" O5 NAG d 601 " both_signs ideal model delta sigma weight residual False -2.40 -2.01 -0.39 2.00e-01 2.50e+01 3.77e+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 -2.04 -0.36 2.00e-01 2.50e+01 3.19e+00 ... (remaining 3002 not shown) Planarity restraints: 2922 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C2 NAG b 608 " 0.230 2.00e-02 2.50e+03 1.99e-01 4.94e+02 pdb=" C7 NAG b 608 " -0.041 2.00e-02 2.50e+03 pdb=" C8 NAG b 608 " -0.019 2.00e-02 2.50e+03 pdb=" N2 NAG b 608 " -0.338 2.00e-02 2.50e+03 pdb=" O7 NAG b 608 " 0.168 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG N 1 " 0.113 2.00e-02 2.50e+03 9.38e-02 1.10e+02 pdb=" C7 NAG N 1 " -0.027 2.00e-02 2.50e+03 pdb=" C8 NAG N 1 " 0.084 2.00e-02 2.50e+03 pdb=" N2 NAG N 1 " -0.152 2.00e-02 2.50e+03 pdb=" O7 NAG N 1 " -0.018 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG f 608 " 0.086 2.00e-02 2.50e+03 7.12e-02 6.33e+01 pdb=" C7 NAG f 608 " -0.022 2.00e-02 2.50e+03 pdb=" C8 NAG f 608 " 0.064 2.00e-02 2.50e+03 pdb=" N2 NAG f 608 " -0.115 2.00e-02 2.50e+03 pdb=" O7 NAG f 608 " -0.013 2.00e-02 2.50e+03 ... (remaining 2919 not shown) Histogram of nonbonded interaction distances: 2.20 - 2.74: 1296 2.74 - 3.28: 17329 3.28 - 3.82: 26466 3.82 - 4.36: 32574 4.36 - 4.90: 56459 Nonbonded interactions: 134124 Sorted by model distance: nonbonded pdb=" O TRP b 401 " pdb=" O3 NAG b 604 " model vdw 2.197 3.040 nonbonded pdb=" O THR c 536 " pdb=" OG1 THR c 536 " model vdw 2.204 3.040 nonbonded pdb=" O THR A 116 " pdb=" OG1 THR A 116 " model vdw 2.270 3.040 nonbonded pdb=" N GLU e 634 " pdb=" OE1 GLU e 634 " model vdw 2.277 3.120 nonbonded pdb=" O VAL f 36 " pdb=" OG1 THR g 606 " model vdw 2.282 3.040 ... (remaining 134119 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 'J' 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 'k' selection = chain 'l' selection = chain 'm' selection = chain 'n' selection = chain 'o' selection = chain 'p' selection = chain 'q' selection = chain 'r' selection = chain 's' } ncs_group { reference = chain 'D' selection = chain 'I' selection = chain 'P' selection = chain 'i' } ncs_group { reference = chain 'E' selection = chain 'Q' selection = chain 'j' } ncs_group { reference = (chain 'b' and resid 33 through 607) selection = chain 'd' selection = (chain 'f' and resid 33 through 607) } 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: 3.880 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.380 Check model and map are aligned: 0.050 Set scattering table: 0.040 Process input model: 17.240 Find NCS groups from input model: 0.460 Set up NCS constraints: 0.090 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:7.910 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 30.070 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8308 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 0.053 17684 Z= 0.214 Angle : 1.037 13.375 24206 Z= 0.527 Chirality : 0.050 0.407 3005 Planarity : 0.007 0.199 2857 Dihedral : 13.409 90.376 8394 Min Nonbonded Distance : 2.197 Molprobity Statistics. All-atom Clashscore : 2.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.65 % Favored : 95.35 % Rotamer: Outliers : 0.35 % Allowed : 10.91 % Favored : 88.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.60 % 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: -1.24 (0.18), residues: 1916 helix: -0.68 (0.26), residues: 393 sheet: -0.60 (0.23), residues: 473 loop : -0.91 (0.18), residues: 1050 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG e 588 TYR 0.022 0.002 TYR e 643 PHE 0.027 0.002 PHE B 98 TRP 0.126 0.003 TRP g 631 HIS 0.005 0.001 HIS f 72 Details of bonding type rmsd/Z covalent geometry : bond 0.00430 / 0.21 (17525) covalent geometry : angle 0.93497 / 0.51 (23767) SS BOND : bond 0.00337 / 0.23 ( 38) SS BOND : angle 1.61061 / 1.08 ( 76) hydrogen bonds : bond 0.23796 / 16.15 ( 562) hydrogen bonds : angle 8.80407 / 5.97 ( 1563) link_ALPHA1-2 : bond 0.01131 / 0.60 ( 1) link_ALPHA1-2 : angle 3.30266 / 1.78 ( 3) link_ALPHA1-3 : bond 0.01729 / 1.02 ( 5) link_ALPHA1-3 : angle 2.16809 / 1.23 ( 15) link_ALPHA1-6 : bond 0.01751 / 0.99 ( 5) link_ALPHA1-6 : angle 2.63514 / 1.51 ( 15) link_BETA1-4 : bond 0.01019 / 0.54 ( 45) link_BETA1-4 : angle 3.90650 / 2.61 ( 135) link_NAG-ASN : bond 0.00471 / 0.28 ( 65) link_NAG-ASN : angle 3.77224 / 2.59 ( 195) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3832 Ramachandran restraints generated. 1916 Oldfield, 0 Emsley, 1916 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3832 Ramachandran restraints generated. 1916 Oldfield, 0 Emsley, 1916 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 289 residues out of total 1723 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 283 time to evaluate : 0.700 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 18 LEU cc_start: 0.8003 (tt) cc_final: 0.7559 (tm) REVERT: A 69 ARG cc_start: 0.8198 (mtm180) cc_final: 0.7633 (ptt90) REVERT: B 34 ASN cc_start: 0.6903 (m-40) cc_final: 0.6488 (t0) REVERT: B 37 GLN cc_start: 0.7590 (tt0) cc_final: 0.7352 (tp40) REVERT: b 35 TRP cc_start: 0.8679 (m100) cc_final: 0.8189 (m100) REVERT: b 46 ARG cc_start: 0.8419 (mtp85) cc_final: 0.7971 (mtm-85) REVERT: b 207 LYS cc_start: 0.8773 (mmmm) cc_final: 0.8059 (tmtm) REVERT: c 520 ARG cc_start: 0.8482 (mtt90) cc_final: 0.8269 (mpt-90) REVERT: c 616 ASN cc_start: 0.9001 (m-40) cc_final: 0.8488 (p0) REVERT: c 617 LYS cc_start: 0.8870 (mtpp) cc_final: 0.8617 (mtpt) REVERT: c 635 ILE cc_start: 0.8656 (mm) cc_final: 0.8254 (mp) REVERT: d 46 ARG cc_start: 0.8487 (ttm170) cc_final: 0.8165 (ttm-80) REVERT: e 536 THR cc_start: 0.8639 (p) cc_final: 0.8233 (t) REVERT: e 584 GLU cc_start: 0.8905 (mt-10) cc_final: 0.8383 (mt-10) REVERT: e 588 ARG cc_start: 0.8676 (ttp80) cc_final: 0.8269 (ttm170) REVERT: e 635 ILE cc_start: 0.8522 (mm) cc_final: 0.8219 (mp) REVERT: e 638 TYR cc_start: 0.8185 (m-80) cc_final: 0.7734 (m-80) REVERT: e 648 GLU cc_start: 0.7930 (tp30) cc_final: 0.7726 (pm20) REVERT: f 238 LEU cc_start: 0.9243 (mp) cc_final: 0.9033 (mm) REVERT: f 368 ASP cc_start: 0.7839 (m-30) cc_final: 0.7574 (p0) REVERT: g 520 ARG cc_start: 0.8056 (tpp80) cc_final: 0.7208 (mmt90) REVERT: g 601 LYS cc_start: 0.9037 (mttm) cc_final: 0.8770 (mtmt) outliers start: 6 outliers final: 1 residues processed: 286 average time/residue: 0.6700 time to fit residues: 211.3699 Evaluate side-chains 180 residues out of total 1723 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 179 time to evaluate : 0.590 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain d residue 38 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 191 random chunks: chunk 98 optimal weight: 1.9990 chunk 107 optimal weight: 5.9990 chunk 10 optimal weight: 3.9990 chunk 66 optimal weight: 2.9990 chunk 130 optimal weight: 9.9990 chunk 124 optimal weight: 2.9990 chunk 103 optimal weight: 5.9990 chunk 77 optimal weight: 0.9990 chunk 122 optimal weight: 0.7980 chunk 91 optimal weight: 3.9990 chunk 149 optimal weight: 0.7980 overall best weight: 1.5186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 3 GLN B 37 GLN B 53 ASN ** B 100 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** c 543 GLN ** d 185 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** f 185 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3790 r_free = 0.3790 target = 0.101332 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3285 r_free = 0.3285 target = 0.072190 restraints weight = 40377.715| |-----------------------------------------------------------------------------| r_work (start): 0.3253 rms_B_bonded: 3.85 r_work: 0.3103 rms_B_bonded: 4.04 restraints_weight: 0.5000 r_work (final): 0.3103 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8692 moved from start: 0.1855 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.056 17684 Z= 0.184 Angle : 0.834 17.261 24206 Z= 0.374 Chirality : 0.049 0.301 3005 Planarity : 0.005 0.041 2857 Dihedral : 9.377 85.046 4694 Min Nonbonded Distance : 2.454 Molprobity Statistics. All-atom Clashscore : 4.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.87 % Favored : 97.13 % Rotamer: Outliers : 2.55 % Allowed : 13.17 % Favored : 84.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.60 % 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: -0.80 (0.19), residues: 1916 helix: -0.11 (0.25), residues: 411 sheet: -0.43 (0.22), residues: 519 loop : -0.68 (0.19), residues: 986 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG e 519 TYR 0.018 0.001 TYR B 91 PHE 0.022 0.002 PHE b 176 TRP 0.037 0.002 TRP g 631 HIS 0.007 0.001 HIS f 72 Details of bonding type rmsd/Z covalent geometry : bond 0.00425 / 0.18 (17525) covalent geometry : angle 0.73416 / 0.35 (23767) SS BOND : bond 0.00273 / 0.19 ( 38) SS BOND : angle 1.11134 / 0.78 ( 76) hydrogen bonds : bond 0.05710 / 3.93 ( 562) hydrogen bonds : angle 6.11279 / 4.07 ( 1563) link_ALPHA1-2 : bond 0.00492 / 0.26 ( 1) link_ALPHA1-2 : angle 2.62633 / 1.39 ( 3) link_ALPHA1-3 : bond 0.00987 / 0.55 ( 5) link_ALPHA1-3 : angle 1.94567 / 1.10 ( 15) link_ALPHA1-6 : bond 0.01189 / 0.61 ( 5) link_ALPHA1-6 : angle 1.79039 / 1.02 ( 15) link_BETA1-4 : bond 0.00634 / 0.45 ( 45) link_BETA1-4 : angle 3.25697 / 2.21 ( 135) link_NAG-ASN : bond 0.00467 / 0.31 ( 65) link_NAG-ASN : angle 3.47763 / 2.46 ( 195) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3832 Ramachandran restraints generated. 1916 Oldfield, 0 Emsley, 1916 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3832 Ramachandran restraints generated. 1916 Oldfield, 0 Emsley, 1916 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 238 residues out of total 1723 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 194 time to evaluate : 0.662 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 59 GLU cc_start: 0.8089 (tm-30) cc_final: 0.7632 (tm-30) REVERT: A 69 ARG cc_start: 0.8274 (mtm180) cc_final: 0.7067 (ptm-80) REVERT: A 70 PHE cc_start: 0.6991 (m-80) cc_final: 0.6463 (m-80) REVERT: A 75 GLU cc_start: 0.8624 (mt-10) cc_final: 0.8181 (tt0) REVERT: A 78 ARG cc_start: 0.9170 (ptp-170) cc_final: 0.8369 (ptp90) REVERT: A 85 MET cc_start: 0.8947 (mpp) cc_final: 0.8590 (mpp) REVERT: A 92 ASP cc_start: 0.5770 (m-30) cc_final: 0.5314 (m-30) REVERT: B 11 LEU cc_start: 0.6829 (pp) cc_final: 0.6349 (pt) REVERT: B 27 GLN cc_start: 0.7325 (pt0) cc_final: 0.6820 (pt0) REVERT: B 61 ARG cc_start: 0.8326 (ptt-90) cc_final: 0.7321 (ttm170) REVERT: B 90 GLN cc_start: 0.8941 (pp30) cc_final: 0.8549 (pp30) REVERT: B 91 TYR cc_start: 0.7491 (p90) cc_final: 0.7234 (p90) REVERT: b 35 TRP cc_start: 0.8757 (m100) cc_final: 0.8200 (m100) REVERT: b 46 ARG cc_start: 0.8805 (mtp85) cc_final: 0.8554 (ptp-110) REVERT: b 173 TYR cc_start: 0.8138 (p90) cc_final: 0.7892 (p90) REVERT: b 207 LYS cc_start: 0.8792 (mmmm) cc_final: 0.7997 (tptt) REVERT: c 601 LYS cc_start: 0.8876 (mttm) cc_final: 0.8420 (mtpp) REVERT: c 616 ASN cc_start: 0.8919 (m-40) cc_final: 0.8446 (p0) REVERT: c 617 LYS cc_start: 0.8759 (mtpp) cc_final: 0.8433 (mtmt) REVERT: c 626 MET cc_start: 0.7064 (ttp) cc_final: 0.6723 (ttm) REVERT: e 536 THR cc_start: 0.8884 (p) cc_final: 0.8603 (t) REVERT: e 584 GLU cc_start: 0.8851 (mt-10) cc_final: 0.8469 (mt-10) REVERT: e 588 ARG cc_start: 0.8818 (ttp80) cc_final: 0.8410 (ttm170) REVERT: g 601 LYS cc_start: 0.9153 (mttm) cc_final: 0.8900 (mtmt) outliers start: 44 outliers final: 12 residues processed: 225 average time/residue: 0.6478 time to fit residues: 161.5152 Evaluate side-chains 174 residues out of total 1723 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 162 time to evaluate : 0.664 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 28 THR Chi-restraints excluded: chain A residue 113 ASP Chi-restraints excluded: chain b residue 38 VAL Chi-restraints excluded: chain b residue 286 VAL Chi-restraints excluded: chain d residue 38 VAL Chi-restraints excluded: chain d residue 286 VAL Chi-restraints excluded: chain e residue 546 SER Chi-restraints excluded: chain e residue 606 THR Chi-restraints excluded: chain e residue 633 LYS Chi-restraints excluded: chain f residue 38 VAL Chi-restraints excluded: chain f residue 286 VAL Chi-restraints excluded: chain g residue 573 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 191 random chunks: chunk 27 optimal weight: 0.0370 chunk 23 optimal weight: 4.9990 chunk 164 optimal weight: 2.9990 chunk 137 optimal weight: 5.9990 chunk 41 optimal weight: 1.9990 chunk 29 optimal weight: 2.9990 chunk 91 optimal weight: 0.6980 chunk 62 optimal weight: 0.5980 chunk 144 optimal weight: 2.9990 chunk 160 optimal weight: 0.8980 chunk 78 optimal weight: 0.8980 overall best weight: 0.6258 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 126 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 3 GLN B 100 GLN ** d 188 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** d 330 HIS f 185 ASN f 195 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3803 r_free = 0.3803 target = 0.102043 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3305 r_free = 0.3305 target = 0.073014 restraints weight = 40393.350| |-----------------------------------------------------------------------------| r_work (start): 0.3272 rms_B_bonded: 3.86 r_work: 0.3124 rms_B_bonded: 4.05 restraints_weight: 0.5000 r_work (final): 0.3124 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8675 moved from start: 0.2186 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 17684 Z= 0.129 Angle : 0.756 17.502 24206 Z= 0.337 Chirality : 0.046 0.257 3005 Planarity : 0.004 0.041 2857 Dihedral : 8.910 81.954 4694 Min Nonbonded Distance : 2.507 Molprobity Statistics. All-atom Clashscore : 4.34 Ramachandran Plot: Outliers : 0.05 % Allowed : 3.03 % Favored : 96.92 % Rotamer: Outliers : 2.21 % Allowed : 13.35 % Favored : 84.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.60 % 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: -0.39 (0.19), residues: 1916 helix: 0.49 (0.27), residues: 369 sheet: -0.00 (0.24), residues: 468 loop : -0.59 (0.19), residues: 1079 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG B 24 TYR 0.019 0.001 TYR e 638 PHE 0.010 0.001 PHE B 98 TRP 0.025 0.001 TRP g 631 HIS 0.005 0.001 HIS f 72 Details of bonding type rmsd/Z covalent geometry : bond 0.00278 / 0.13 (17525) covalent geometry : angle 0.66551 / 0.32 (23767) SS BOND : bond 0.00215 / 0.15 ( 38) SS BOND : angle 0.85265 / 0.59 ( 76) hydrogen bonds : bond 0.04779 / 3.30 ( 562) hydrogen bonds : angle 5.60372 / 3.75 ( 1563) link_ALPHA1-2 : bond 0.00618 / 0.33 ( 1) link_ALPHA1-2 : angle 2.25907 / 1.19 ( 3) link_ALPHA1-3 : bond 0.01117 / 0.63 ( 5) link_ALPHA1-3 : angle 1.77572 / 0.97 ( 15) link_ALPHA1-6 : bond 0.01244 / 0.66 ( 5) link_ALPHA1-6 : angle 1.72092 / 0.98 ( 15) link_BETA1-4 : bond 0.00633 / 0.46 ( 45) link_BETA1-4 : angle 3.00017 / 2.05 ( 135) link_NAG-ASN : bond 0.00403 / 0.29 ( 65) link_NAG-ASN : angle 3.13534 / 2.25 ( 195) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3832 Ramachandran restraints generated. 1916 Oldfield, 0 Emsley, 1916 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3832 Ramachandran restraints generated. 1916 Oldfield, 0 Emsley, 1916 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 217 residues out of total 1723 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 179 time to evaluate : 0.622 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 38 ARG cc_start: 0.7939 (ptt180) cc_final: 0.7372 (ttp-170) REVERT: A 59 GLU cc_start: 0.8163 (tm-30) cc_final: 0.7634 (tm-30) REVERT: A 75 GLU cc_start: 0.8585 (mt-10) cc_final: 0.8296 (mt-10) REVERT: A 78 ARG cc_start: 0.9150 (ptp-170) cc_final: 0.8795 (ptp90) REVERT: A 85 MET cc_start: 0.8771 (mpp) cc_final: 0.8366 (mpp) REVERT: B 11 LEU cc_start: 0.6755 (OUTLIER) cc_final: 0.6548 (pt) REVERT: B 27 GLN cc_start: 0.7233 (pt0) cc_final: 0.6926 (pt0) REVERT: B 47 LEU cc_start: 0.9441 (pt) cc_final: 0.9234 (pt) REVERT: B 61 ARG cc_start: 0.8259 (ptt-90) cc_final: 0.7771 (tmm-80) REVERT: B 90 GLN cc_start: 0.8878 (pp30) cc_final: 0.8337 (pp30) REVERT: B 91 TYR cc_start: 0.7673 (p90) cc_final: 0.7428 (p90) REVERT: b 35 TRP cc_start: 0.8716 (m100) cc_final: 0.8405 (m100) REVERT: b 46 ARG cc_start: 0.8830 (mtp85) cc_final: 0.8615 (ptp-110) REVERT: b 173 TYR cc_start: 0.8139 (p90) cc_final: 0.7824 (p90) REVERT: b 207 LYS cc_start: 0.8780 (mmmm) cc_final: 0.8080 (tmtm) REVERT: c 601 LYS cc_start: 0.8892 (mttm) cc_final: 0.8407 (mtpp) REVERT: c 616 ASN cc_start: 0.8922 (m-40) cc_final: 0.8442 (p0) REVERT: c 626 MET cc_start: 0.7186 (ttp) cc_final: 0.6850 (ttm) REVERT: d 207 LYS cc_start: 0.7892 (tppt) cc_final: 0.7570 (tppt) REVERT: e 536 THR cc_start: 0.8846 (p) cc_final: 0.8577 (t) REVERT: e 588 ARG cc_start: 0.8828 (ttp80) cc_final: 0.8384 (ttm170) REVERT: e 617 LYS cc_start: 0.8123 (mttt) cc_final: 0.7756 (tttt) REVERT: g 601 LYS cc_start: 0.9118 (mttm) cc_final: 0.8891 (mtmt) outliers start: 38 outliers final: 12 residues processed: 204 average time/residue: 0.6414 time to fit residues: 145.0013 Evaluate side-chains 176 residues out of total 1723 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 163 time to evaluate : 0.669 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 113 ASP Chi-restraints excluded: chain B residue 11 LEU Chi-restraints excluded: chain B residue 97 THR Chi-restraints excluded: chain b residue 38 VAL Chi-restraints excluded: chain b residue 125 LEU Chi-restraints excluded: chain b residue 286 VAL Chi-restraints excluded: chain d residue 38 VAL Chi-restraints excluded: chain d residue 125 LEU Chi-restraints excluded: chain d residue 286 VAL Chi-restraints excluded: chain e residue 546 SER Chi-restraints excluded: chain e residue 606 THR Chi-restraints excluded: chain f residue 38 VAL Chi-restraints excluded: chain g residue 638 TYR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 191 random chunks: chunk 25 optimal weight: 0.3980 chunk 89 optimal weight: 3.9990 chunk 82 optimal weight: 3.9990 chunk 87 optimal weight: 0.6980 chunk 156 optimal weight: 2.9990 chunk 168 optimal weight: 3.9990 chunk 110 optimal weight: 4.9990 chunk 162 optimal weight: 4.9990 chunk 36 optimal weight: 0.8980 chunk 86 optimal weight: 0.8980 chunk 24 optimal weight: 0.0270 overall best weight: 0.5838 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 126 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** b 72 HIS c 577 GLN ** d 188 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** f 195 ASN f 328 GLN ** g 577 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** g 652 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3806 r_free = 0.3806 target = 0.102155 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3310 r_free = 0.3310 target = 0.073337 restraints weight = 40130.043| |-----------------------------------------------------------------------------| r_work (start): 0.3278 rms_B_bonded: 3.83 r_work: 0.3129 rms_B_bonded: 4.03 restraints_weight: 0.5000 r_work (final): 0.3129 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8661 moved from start: 0.2426 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 17684 Z= 0.119 Angle : 0.713 17.357 24206 Z= 0.317 Chirality : 0.045 0.245 3005 Planarity : 0.003 0.035 2857 Dihedral : 8.655 78.907 4694 Min Nonbonded Distance : 2.531 Molprobity Statistics. All-atom Clashscore : 4.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.82 % Favored : 97.18 % Rotamer: Outliers : 2.15 % Allowed : 14.45 % Favored : 83.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.60 % 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: -0.37 (0.19), residues: 1916 helix: 0.67 (0.28), residues: 369 sheet: -0.21 (0.23), residues: 512 loop : -0.53 (0.19), residues: 1035 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG e 519 TYR 0.023 0.001 TYR f 173 PHE 0.014 0.001 PHE B 98 TRP 0.017 0.001 TRP g 631 HIS 0.005 0.001 HIS f 72 Details of bonding type rmsd/Z covalent geometry : bond 0.00260 / 0.12 (17525) covalent geometry : angle 0.62765 / 0.30 (23767) SS BOND : bond 0.00193 / 0.13 ( 38) SS BOND : angle 0.75485 / 0.52 ( 76) hydrogen bonds : bond 0.04162 / 2.86 ( 562) hydrogen bonds : angle 5.32989 / 3.58 ( 1563) link_ALPHA1-2 : bond 0.00536 / 0.28 ( 1) link_ALPHA1-2 : angle 2.14195 / 1.13 ( 3) link_ALPHA1-3 : bond 0.01085 / 0.61 ( 5) link_ALPHA1-3 : angle 1.81880 / 1.00 ( 15) link_ALPHA1-6 : bond 0.01441 / 0.76 ( 5) link_ALPHA1-6 : angle 1.69857 / 0.99 ( 15) link_BETA1-4 : bond 0.00620 / 0.45 ( 45) link_BETA1-4 : angle 2.86237 / 1.96 ( 135) link_NAG-ASN : bond 0.00354 / 0.26 ( 65) link_NAG-ASN : angle 2.94160 / 2.12 ( 195) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3832 Ramachandran restraints generated. 1916 Oldfield, 0 Emsley, 1916 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3832 Ramachandran restraints generated. 1916 Oldfield, 0 Emsley, 1916 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 215 residues out of total 1723 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 178 time to evaluate : 0.657 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 38 ARG cc_start: 0.7925 (ptt180) cc_final: 0.7354 (ttp-170) REVERT: A 59 GLU cc_start: 0.8213 (tm-30) cc_final: 0.7756 (tm-30) REVERT: A 75 GLU cc_start: 0.8583 (mt-10) cc_final: 0.8046 (tt0) REVERT: A 78 ARG cc_start: 0.9129 (ptp-170) cc_final: 0.8363 (ptp90) REVERT: A 85 MET cc_start: 0.8739 (mpp) cc_final: 0.8397 (mpp) REVERT: A 92 ASP cc_start: 0.5477 (m-30) cc_final: 0.5213 (m-30) REVERT: B 61 ARG cc_start: 0.8292 (ptt-90) cc_final: 0.7814 (tmm-80) REVERT: B 90 GLN cc_start: 0.8778 (pp30) cc_final: 0.8213 (pp30) REVERT: B 91 TYR cc_start: 0.7904 (p90) cc_final: 0.7586 (p90) REVERT: b 35 TRP cc_start: 0.8752 (m100) cc_final: 0.8529 (m100) REVERT: b 46 ARG cc_start: 0.8796 (mtp85) cc_final: 0.8593 (ptp-110) REVERT: b 207 LYS cc_start: 0.8777 (mmmm) cc_final: 0.8019 (tmtm) REVERT: c 519 ARG cc_start: 0.7346 (ttp80) cc_final: 0.7094 (ppp80) REVERT: c 601 LYS cc_start: 0.8883 (mttm) cc_final: 0.8404 (mtpp) REVERT: c 616 ASN cc_start: 0.8899 (m-40) cc_final: 0.8451 (p0) REVERT: d 207 LYS cc_start: 0.7936 (tppt) cc_final: 0.7706 (tptt) REVERT: e 536 THR cc_start: 0.8859 (p) cc_final: 0.8574 (t) REVERT: e 588 ARG cc_start: 0.8867 (ttp80) cc_final: 0.8397 (ttm170) REVERT: e 654 GLU cc_start: 0.8072 (OUTLIER) cc_final: 0.7853 (tp30) REVERT: e 657 GLU cc_start: 0.6554 (tp30) cc_final: 0.6347 (tt0) REVERT: g 601 LYS cc_start: 0.9139 (mttm) cc_final: 0.8902 (mtmt) outliers start: 37 outliers final: 14 residues processed: 202 average time/residue: 0.5859 time to fit residues: 131.5202 Evaluate side-chains 178 residues out of total 1723 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 163 time to evaluate : 0.719 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 28 THR Chi-restraints excluded: chain A residue 113 ASP Chi-restraints excluded: chain B residue 97 THR Chi-restraints excluded: chain b residue 38 VAL Chi-restraints excluded: chain b residue 190 GLU Chi-restraints excluded: chain b residue 286 VAL Chi-restraints excluded: chain c residue 638 TYR Chi-restraints excluded: chain d residue 38 VAL Chi-restraints excluded: chain d residue 125 LEU Chi-restraints excluded: chain d residue 286 VAL Chi-restraints excluded: chain e residue 654 GLU Chi-restraints excluded: chain f residue 38 VAL Chi-restraints excluded: chain f residue 426 MET Chi-restraints excluded: chain g residue 599 SER Chi-restraints excluded: chain g residue 638 TYR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 191 random chunks: chunk 35 optimal weight: 4.9990 chunk 96 optimal weight: 0.0170 chunk 21 optimal weight: 5.9990 chunk 149 optimal weight: 0.9980 chunk 116 optimal weight: 5.9990 chunk 134 optimal weight: 10.0000 chunk 187 optimal weight: 9.9990 chunk 150 optimal weight: 0.7980 chunk 108 optimal weight: 4.9990 chunk 60 optimal weight: 5.9990 chunk 58 optimal weight: 5.9990 overall best weight: 2.3622 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 126 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 92 ASN b 72 HIS ** d 185 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 188 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** f 195 ASN f 330 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3749 r_free = 0.3749 target = 0.098876 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3222 r_free = 0.3222 target = 0.069176 restraints weight = 40013.600| |-----------------------------------------------------------------------------| r_work (start): 0.3195 rms_B_bonded: 3.86 r_work: 0.3046 rms_B_bonded: 3.99 restraints_weight: 0.5000 r_work (final): 0.3046 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8746 moved from start: 0.2748 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.059 17684 Z= 0.238 Angle : 0.790 17.885 24206 Z= 0.358 Chirality : 0.048 0.268 3005 Planarity : 0.004 0.041 2857 Dihedral : 8.757 75.775 4694 Min Nonbonded Distance : 2.509 Molprobity Statistics. All-atom Clashscore : 5.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.29 % Favored : 96.71 % Rotamer: Outliers : 2.84 % Allowed : 15.03 % Favored : 82.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.60 % 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: -0.57 (0.19), residues: 1916 helix: 0.30 (0.27), residues: 387 sheet: -0.16 (0.23), residues: 486 loop : -0.69 (0.19), residues: 1043 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG e 519 TYR 0.022 0.002 TYR e 638 PHE 0.015 0.002 PHE f 383 TRP 0.013 0.002 TRP d 96 HIS 0.005 0.001 HIS f 72 Details of bonding type rmsd/Z covalent geometry : bond 0.00575 / 0.24 (17525) covalent geometry : angle 0.71067 / 0.34 (23767) SS BOND : bond 0.00418 / 0.27 ( 38) SS BOND : angle 1.07864 / 0.74 ( 76) hydrogen bonds : bond 0.04689 / 3.23 ( 562) hydrogen bonds : angle 5.49596 / 3.70 ( 1563) link_ALPHA1-2 : bond 0.00484 / 0.25 ( 1) link_ALPHA1-2 : angle 1.89620 / 1.00 ( 3) link_ALPHA1-3 : bond 0.00914 / 0.50 ( 5) link_ALPHA1-3 : angle 1.85092 / 1.05 ( 15) link_ALPHA1-6 : bond 0.01238 / 0.63 ( 5) link_ALPHA1-6 : angle 1.77062 / 1.08 ( 15) link_BETA1-4 : bond 0.00572 / 0.42 ( 45) link_BETA1-4 : angle 2.87206 / 1.97 ( 135) link_NAG-ASN : bond 0.00371 / 0.27 ( 65) link_NAG-ASN : angle 3.02755 / 2.17 ( 195) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3832 Ramachandran restraints generated. 1916 Oldfield, 0 Emsley, 1916 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3832 Ramachandran restraints generated. 1916 Oldfield, 0 Emsley, 1916 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 221 residues out of total 1723 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 172 time to evaluate : 0.695 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 50 ARG cc_start: 0.7937 (OUTLIER) cc_final: 0.7437 (ptt-90) REVERT: A 59 GLU cc_start: 0.8361 (tm-30) cc_final: 0.7918 (tm-30) REVERT: A 75 GLU cc_start: 0.8511 (mt-10) cc_final: 0.8169 (mt-10) REVERT: A 78 ARG cc_start: 0.9128 (ptp-170) cc_final: 0.8841 (ptp90) REVERT: A 85 MET cc_start: 0.8829 (mpp) cc_final: 0.8516 (mpp) REVERT: B 27 GLN cc_start: 0.7628 (pt0) cc_final: 0.7389 (pm20) REVERT: B 47 LEU cc_start: 0.9502 (OUTLIER) cc_final: 0.8528 (pt) REVERT: B 61 ARG cc_start: 0.8280 (ptt-90) cc_final: 0.7837 (tmm-80) REVERT: B 90 GLN cc_start: 0.8803 (pp30) cc_final: 0.8256 (pp30) REVERT: b 46 ARG cc_start: 0.8802 (mtp85) cc_final: 0.8571 (ptp-110) REVERT: b 164 GLU cc_start: 0.8620 (OUTLIER) cc_final: 0.8336 (mp0) REVERT: b 207 LYS cc_start: 0.8843 (mmmm) cc_final: 0.8155 (tmtm) REVERT: c 601 LYS cc_start: 0.8875 (mttm) cc_final: 0.8338 (mtpp) REVERT: c 616 ASN cc_start: 0.8911 (m-40) cc_final: 0.8422 (p0) REVERT: d 207 LYS cc_start: 0.8015 (tppt) cc_final: 0.7740 (tptt) REVERT: e 536 THR cc_start: 0.8939 (p) cc_final: 0.8659 (t) REVERT: e 588 ARG cc_start: 0.8909 (ttp80) cc_final: 0.8512 (ttm170) REVERT: g 601 LYS cc_start: 0.9166 (mttm) cc_final: 0.8908 (mtmt) outliers start: 49 outliers final: 23 residues processed: 206 average time/residue: 0.6557 time to fit residues: 149.1678 Evaluate side-chains 181 residues out of total 1723 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 155 time to evaluate : 0.654 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 28 THR Chi-restraints excluded: chain A residue 37 VAL Chi-restraints excluded: chain A residue 50 ARG Chi-restraints excluded: chain A residue 113 ASP Chi-restraints excluded: chain B residue 47 LEU Chi-restraints excluded: chain B residue 94 ASP Chi-restraints excluded: chain B residue 97 THR Chi-restraints excluded: chain b residue 38 VAL Chi-restraints excluded: chain b residue 68 VAL Chi-restraints excluded: chain b residue 164 GLU Chi-restraints excluded: chain b residue 190 GLU Chi-restraints excluded: chain b residue 195 ASN Chi-restraints excluded: chain b residue 286 VAL Chi-restraints excluded: chain b residue 485 LYS Chi-restraints excluded: chain c residue 638 TYR Chi-restraints excluded: chain d residue 36 VAL Chi-restraints excluded: chain d residue 38 VAL Chi-restraints excluded: chain d residue 125 LEU Chi-restraints excluded: chain d residue 286 VAL Chi-restraints excluded: chain e residue 538 THR Chi-restraints excluded: chain f residue 38 VAL Chi-restraints excluded: chain f residue 120 VAL Chi-restraints excluded: chain f residue 426 MET Chi-restraints excluded: chain g residue 599 SER Chi-restraints excluded: chain g residue 634 GLU Chi-restraints excluded: chain g residue 638 TYR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 191 random chunks: chunk 59 optimal weight: 0.3980 chunk 49 optimal weight: 0.7980 chunk 44 optimal weight: 2.9990 chunk 69 optimal weight: 0.0570 chunk 11 optimal weight: 5.9990 chunk 43 optimal weight: 0.6980 chunk 74 optimal weight: 0.9990 chunk 185 optimal weight: 0.9980 chunk 127 optimal weight: 3.9990 chunk 45 optimal weight: 0.4980 chunk 61 optimal weight: 0.9980 overall best weight: 0.4898 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 126 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 92 ASN b 72 HIS ** d 185 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** f 195 ASN ** g 577 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3786 r_free = 0.3786 target = 0.101069 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3277 r_free = 0.3277 target = 0.071788 restraints weight = 39683.927| |-----------------------------------------------------------------------------| r_work (start): 0.3253 rms_B_bonded: 3.84 r_work: 0.3105 rms_B_bonded: 4.00 restraints_weight: 0.5000 r_work (final): 0.3105 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8683 moved from start: 0.2873 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 17684 Z= 0.118 Angle : 0.722 17.708 24206 Z= 0.323 Chirality : 0.045 0.264 3005 Planarity : 0.003 0.045 2857 Dihedral : 8.419 71.465 4694 Min Nonbonded Distance : 2.393 Molprobity Statistics. All-atom Clashscore : 5.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.87 % Favored : 97.13 % Rotamer: Outliers : 2.32 % Allowed : 16.08 % Favored : 81.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.60 % 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: -0.29 (0.19), residues: 1916 helix: 1.04 (0.28), residues: 357 sheet: -0.14 (0.23), residues: 500 loop : -0.60 (0.19), residues: 1059 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG e 519 TYR 0.015 0.001 TYR A 96 PHE 0.008 0.001 PHE f 383 TRP 0.013 0.001 TRP f 338 HIS 0.004 0.001 HIS f 72 Details of bonding type rmsd/Z covalent geometry : bond 0.00255 / 0.12 (17525) covalent geometry : angle 0.64384 / 0.30 (23767) SS BOND : bond 0.00289 / 0.21 ( 38) SS BOND : angle 1.08504 / 0.70 ( 76) hydrogen bonds : bond 0.03950 / 2.71 ( 562) hydrogen bonds : angle 5.23302 / 3.52 ( 1563) link_ALPHA1-2 : bond 0.00586 / 0.31 ( 1) link_ALPHA1-2 : angle 1.89447 / 1.00 ( 3) link_ALPHA1-3 : bond 0.01067 / 0.60 ( 5) link_ALPHA1-3 : angle 1.68041 / 0.91 ( 15) link_ALPHA1-6 : bond 0.01439 / 0.76 ( 5) link_ALPHA1-6 : angle 1.57111 / 0.94 ( 15) link_BETA1-4 : bond 0.00615 / 0.45 ( 45) link_BETA1-4 : angle 2.71990 / 1.87 ( 135) link_NAG-ASN : bond 0.00324 / 0.24 ( 65) link_NAG-ASN : angle 2.86799 / 2.07 ( 195) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3832 Ramachandran restraints generated. 1916 Oldfield, 0 Emsley, 1916 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3832 Ramachandran restraints generated. 1916 Oldfield, 0 Emsley, 1916 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 213 residues out of total 1723 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 173 time to evaluate : 0.540 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 59 GLU cc_start: 0.8342 (tm-30) cc_final: 0.7781 (tm-30) REVERT: A 75 GLU cc_start: 0.8504 (mt-10) cc_final: 0.8219 (mt-10) REVERT: A 78 ARG cc_start: 0.9136 (ptp-170) cc_final: 0.8861 (ptp90) REVERT: A 85 MET cc_start: 0.8738 (mpp) cc_final: 0.8500 (mpp) REVERT: B 61 ARG cc_start: 0.8348 (ptt-90) cc_final: 0.7924 (tmm-80) REVERT: B 90 GLN cc_start: 0.8634 (pp30) cc_final: 0.8384 (pp30) REVERT: B 94 ASP cc_start: 0.8919 (OUTLIER) cc_final: 0.8599 (m-30) REVERT: b 46 ARG cc_start: 0.8792 (mtp85) cc_final: 0.8573 (ptp-110) REVERT: b 173 TYR cc_start: 0.7997 (p90) cc_final: 0.7712 (p90) REVERT: b 207 LYS cc_start: 0.8826 (mmmm) cc_final: 0.8093 (tmtm) REVERT: c 601 LYS cc_start: 0.8862 (mttm) cc_final: 0.8324 (mtpp) REVERT: c 616 ASN cc_start: 0.8873 (m-40) cc_final: 0.8367 (p0) REVERT: d 207 LYS cc_start: 0.8026 (tppt) cc_final: 0.7757 (tptt) REVERT: e 536 THR cc_start: 0.8875 (p) cc_final: 0.8597 (t) REVERT: e 588 ARG cc_start: 0.8915 (ttp80) cc_final: 0.8530 (ttm170) REVERT: f 51 THR cc_start: 0.9237 (OUTLIER) cc_final: 0.8869 (p) REVERT: g 535 ILE cc_start: 0.8879 (mp) cc_final: 0.8673 (tp) REVERT: g 601 LYS cc_start: 0.9167 (mttm) cc_final: 0.8916 (mtmt) outliers start: 40 outliers final: 22 residues processed: 202 average time/residue: 0.6194 time to fit residues: 139.2140 Evaluate side-chains 184 residues out of total 1723 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 160 time to evaluate : 0.525 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 28 THR Chi-restraints excluded: chain A residue 37 VAL Chi-restraints excluded: chain A residue 70 PHE Chi-restraints excluded: chain A residue 113 ASP Chi-restraints excluded: chain B residue 94 ASP Chi-restraints excluded: chain b residue 38 VAL Chi-restraints excluded: chain b residue 181 ILE Chi-restraints excluded: chain b residue 190 GLU Chi-restraints excluded: chain b residue 195 ASN Chi-restraints excluded: chain b residue 286 VAL Chi-restraints excluded: chain b residue 445 CYS Chi-restraints excluded: chain c residue 568 LEU Chi-restraints excluded: chain c residue 635 ILE Chi-restraints excluded: chain c residue 638 TYR Chi-restraints excluded: chain c residue 644 ARG Chi-restraints excluded: chain d residue 36 VAL Chi-restraints excluded: chain d residue 38 VAL Chi-restraints excluded: chain d residue 125 LEU Chi-restraints excluded: chain d residue 286 VAL Chi-restraints excluded: chain e residue 544 LEU Chi-restraints excluded: chain f residue 38 VAL Chi-restraints excluded: chain f residue 51 THR Chi-restraints excluded: chain g residue 599 SER Chi-restraints excluded: chain g residue 638 TYR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 191 random chunks: chunk 63 optimal weight: 1.9990 chunk 113 optimal weight: 1.9990 chunk 36 optimal weight: 0.0060 chunk 163 optimal weight: 2.9990 chunk 118 optimal weight: 0.9990 chunk 81 optimal weight: 0.9980 chunk 39 optimal weight: 0.9990 chunk 80 optimal weight: 0.7980 chunk 33 optimal weight: 5.9990 chunk 183 optimal weight: 5.9990 chunk 44 optimal weight: 1.9990 overall best weight: 0.7600 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 126 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** b 72 HIS b 330 HIS f 195 ASN g 563 GLN ** g 577 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3787 r_free = 0.3787 target = 0.101088 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3279 r_free = 0.3279 target = 0.071779 restraints weight = 39910.458| |-----------------------------------------------------------------------------| r_work (start): 0.3249 rms_B_bonded: 3.88 r_work: 0.3100 rms_B_bonded: 4.05 restraints_weight: 0.5000 r_work (final): 0.3100 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8722 moved from start: 0.3001 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 17684 Z= 0.124 Angle : 0.717 17.358 24206 Z= 0.321 Chirality : 0.045 0.276 3005 Planarity : 0.003 0.056 2857 Dihedral : 8.110 64.678 4694 Min Nonbonded Distance : 2.502 Molprobity Statistics. All-atom Clashscore : 5.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.87 % Favored : 97.13 % Rotamer: Outliers : 1.80 % Allowed : 16.60 % Favored : 81.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.60 % 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: -0.14 (0.19), residues: 1916 helix: 1.22 (0.29), residues: 351 sheet: -0.13 (0.22), residues: 527 loop : -0.47 (0.19), residues: 1038 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.000 ARG c 519 TYR 0.032 0.001 TYR e 638 PHE 0.027 0.001 PHE B 98 TRP 0.009 0.001 TRP f 338 HIS 0.004 0.001 HIS f 72 Details of bonding type rmsd/Z covalent geometry : bond 0.00280 / 0.12 (17525) covalent geometry : angle 0.64276 / 0.30 (23767) SS BOND : bond 0.00209 / 0.14 ( 38) SS BOND : angle 0.94703 / 0.62 ( 76) hydrogen bonds : bond 0.03752 / 2.58 ( 562) hydrogen bonds : angle 5.12159 / 3.45 ( 1563) link_ALPHA1-2 : bond 0.00492 / 0.26 ( 1) link_ALPHA1-2 : angle 1.81349 / 0.95 ( 3) link_ALPHA1-3 : bond 0.01051 / 0.58 ( 5) link_ALPHA1-3 : angle 1.75299 / 0.95 ( 15) link_ALPHA1-6 : bond 0.01475 / 0.78 ( 5) link_ALPHA1-6 : angle 1.62336 / 0.99 ( 15) link_BETA1-4 : bond 0.00612 / 0.45 ( 45) link_BETA1-4 : angle 2.66424 / 1.84 ( 135) link_NAG-ASN : bond 0.00309 / 0.23 ( 65) link_NAG-ASN : angle 2.78353 / 2.02 ( 195) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3832 Ramachandran restraints generated. 1916 Oldfield, 0 Emsley, 1916 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3832 Ramachandran restraints generated. 1916 Oldfield, 0 Emsley, 1916 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 202 residues out of total 1723 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 171 time to evaluate : 0.517 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 20 LEU cc_start: 0.8741 (mp) cc_final: 0.8310 (mp) REVERT: A 59 GLU cc_start: 0.8357 (tm-30) cc_final: 0.7866 (tm-30) REVERT: A 75 GLU cc_start: 0.8442 (mt-10) cc_final: 0.8144 (mt-10) REVERT: A 78 ARG cc_start: 0.9132 (ptp-170) cc_final: 0.8867 (ptp90) REVERT: A 85 MET cc_start: 0.8814 (mpp) cc_final: 0.8546 (mpp) REVERT: B 4 MET cc_start: 0.7610 (ppp) cc_final: 0.7217 (ppp) REVERT: B 61 ARG cc_start: 0.8358 (ptt-90) cc_final: 0.7995 (tmm-80) REVERT: B 90 GLN cc_start: 0.8571 (pp30) cc_final: 0.8320 (pp30) REVERT: B 94 ASP cc_start: 0.8785 (m-30) cc_final: 0.8500 (m-30) REVERT: B 105 GLU cc_start: 0.7581 (mp0) cc_final: 0.7354 (tt0) REVERT: b 46 ARG cc_start: 0.8801 (mtp85) cc_final: 0.8600 (ptp-110) REVERT: b 173 TYR cc_start: 0.8016 (p90) cc_final: 0.7745 (p90) REVERT: b 186 GLU cc_start: 0.7563 (tp30) cc_final: 0.6974 (tm-30) REVERT: b 207 LYS cc_start: 0.8800 (mmmm) cc_final: 0.8121 (tmtm) REVERT: c 520 ARG cc_start: 0.8150 (mpt-90) cc_final: 0.7892 (mpt-90) REVERT: c 601 LYS cc_start: 0.8884 (mttm) cc_final: 0.8401 (mtpp) REVERT: c 616 ASN cc_start: 0.8830 (m-40) cc_final: 0.8329 (p0) REVERT: d 207 LYS cc_start: 0.8065 (tppt) cc_final: 0.7806 (tptt) REVERT: e 536 THR cc_start: 0.8889 (p) cc_final: 0.8612 (t) REVERT: e 588 ARG cc_start: 0.8955 (ttp80) cc_final: 0.8590 (ttm170) REVERT: g 601 LYS cc_start: 0.9168 (mttm) cc_final: 0.8967 (mtmt) outliers start: 31 outliers final: 24 residues processed: 190 average time/residue: 0.5828 time to fit residues: 122.9622 Evaluate side-chains 182 residues out of total 1723 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 158 time to evaluate : 0.407 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 28 THR Chi-restraints excluded: chain A residue 37 VAL Chi-restraints excluded: chain A residue 70 PHE Chi-restraints excluded: chain A residue 113 ASP Chi-restraints excluded: chain B residue 33 VAL Chi-restraints excluded: chain b residue 38 VAL Chi-restraints excluded: chain b residue 161 MET Chi-restraints excluded: chain b residue 190 GLU Chi-restraints excluded: chain b residue 195 ASN Chi-restraints excluded: chain b residue 286 VAL Chi-restraints excluded: chain b residue 445 CYS Chi-restraints excluded: chain c residue 568 LEU Chi-restraints excluded: chain c residue 635 ILE Chi-restraints excluded: chain c residue 638 TYR Chi-restraints excluded: chain c residue 644 ARG Chi-restraints excluded: chain d residue 36 VAL Chi-restraints excluded: chain d residue 38 VAL Chi-restraints excluded: chain d residue 125 LEU Chi-restraints excluded: chain d residue 286 VAL Chi-restraints excluded: chain e residue 538 THR Chi-restraints excluded: chain e residue 544 LEU Chi-restraints excluded: chain f residue 38 VAL Chi-restraints excluded: chain g residue 599 SER Chi-restraints excluded: chain g residue 638 TYR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 191 random chunks: chunk 10 optimal weight: 5.9990 chunk 126 optimal weight: 7.9990 chunk 141 optimal weight: 4.9990 chunk 85 optimal weight: 3.9990 chunk 146 optimal weight: 1.9990 chunk 120 optimal weight: 2.9990 chunk 167 optimal weight: 0.9980 chunk 86 optimal weight: 1.9990 chunk 110 optimal weight: 0.9980 chunk 6 optimal weight: 7.9990 chunk 41 optimal weight: 5.9990 overall best weight: 1.7986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** b 72 HIS ** d 188 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** f 195 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3759 r_free = 0.3759 target = 0.099375 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3236 r_free = 0.3236 target = 0.069821 restraints weight = 40084.521| |-----------------------------------------------------------------------------| r_work (start): 0.3209 rms_B_bonded: 3.85 r_work: 0.3059 rms_B_bonded: 4.00 restraints_weight: 0.5000 r_work (final): 0.3059 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8730 moved from start: 0.3141 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.051 17684 Z= 0.192 Angle : 0.760 17.707 24206 Z= 0.342 Chirality : 0.046 0.289 3005 Planarity : 0.003 0.032 2857 Dihedral : 8.139 59.853 4694 Min Nonbonded Distance : 2.459 Molprobity Statistics. All-atom Clashscore : 5.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.24 % Favored : 96.76 % Rotamer: Outliers : 1.80 % Allowed : 16.60 % Favored : 81.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.60 % 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: -0.22 (0.19), residues: 1916 helix: 1.12 (0.29), residues: 351 sheet: -0.12 (0.23), residues: 501 loop : -0.54 (0.19), residues: 1064 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.001 ARG c 519 TYR 0.022 0.001 TYR A 96 PHE 0.013 0.001 PHE f 383 TRP 0.009 0.001 TRP e 631 HIS 0.004 0.001 HIS f 85 Details of bonding type rmsd/Z covalent geometry : bond 0.00459 / 0.19 (17525) covalent geometry : angle 0.68828 / 0.33 (23767) SS BOND : bond 0.00292 / 0.21 ( 38) SS BOND : angle 1.04270 / 0.69 ( 76) hydrogen bonds : bond 0.04175 / 2.87 ( 562) hydrogen bonds : angle 5.20419 / 3.49 ( 1563) link_ALPHA1-2 : bond 0.00514 / 0.27 ( 1) link_ALPHA1-2 : angle 1.64270 / 0.86 ( 3) link_ALPHA1-3 : bond 0.00932 / 0.51 ( 5) link_ALPHA1-3 : angle 1.70896 / 0.95 ( 15) link_ALPHA1-6 : bond 0.01359 / 0.70 ( 5) link_ALPHA1-6 : angle 1.72192 / 1.08 ( 15) link_BETA1-4 : bond 0.00577 / 0.43 ( 45) link_BETA1-4 : angle 2.66974 / 1.84 ( 135) link_NAG-ASN : bond 0.00323 / 0.24 ( 65) link_NAG-ASN : angle 2.85967 / 2.06 ( 195) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3832 Ramachandran restraints generated. 1916 Oldfield, 0 Emsley, 1916 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3832 Ramachandran restraints generated. 1916 Oldfield, 0 Emsley, 1916 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 201 residues out of total 1723 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 170 time to evaluate : 0.637 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 50 ARG cc_start: 0.7753 (OUTLIER) cc_final: 0.7457 (ptt180) REVERT: A 59 GLU cc_start: 0.8435 (tm-30) cc_final: 0.7917 (tm-30) REVERT: A 75 GLU cc_start: 0.8455 (mt-10) cc_final: 0.8052 (mt-10) REVERT: A 78 ARG cc_start: 0.9112 (ptp-170) cc_final: 0.8727 (ptp90) REVERT: B 62 PHE cc_start: 0.7935 (m-80) cc_final: 0.7496 (m-80) REVERT: B 105 GLU cc_start: 0.7559 (mp0) cc_final: 0.7356 (tt0) REVERT: b 46 ARG cc_start: 0.8811 (mtp85) cc_final: 0.8585 (ptp-110) REVERT: b 164 GLU cc_start: 0.8563 (OUTLIER) cc_final: 0.8225 (mp0) REVERT: b 173 TYR cc_start: 0.8003 (p90) cc_final: 0.7740 (p90) REVERT: b 207 LYS cc_start: 0.8853 (mmmm) cc_final: 0.8164 (tmtm) REVERT: b 268 LYS cc_start: 0.8852 (mmtp) cc_final: 0.8598 (mptt) REVERT: c 520 ARG cc_start: 0.8093 (mpt-90) cc_final: 0.7810 (mpt-90) REVERT: c 601 LYS cc_start: 0.8883 (mttm) cc_final: 0.8343 (mtpp) REVERT: c 616 ASN cc_start: 0.8891 (m-40) cc_final: 0.8380 (p0) REVERT: d 207 LYS cc_start: 0.8050 (tppt) cc_final: 0.7782 (tptt) REVERT: e 536 THR cc_start: 0.8921 (p) cc_final: 0.8680 (t) REVERT: e 588 ARG cc_start: 0.8975 (ttp80) cc_final: 0.8603 (ttm170) REVERT: g 543 GLN cc_start: 0.8556 (mp10) cc_final: 0.8349 (mp10) REVERT: g 601 LYS cc_start: 0.9206 (mttm) cc_final: 0.8964 (mtmt) REVERT: g 617 LYS cc_start: 0.9192 (mmmm) cc_final: 0.8935 (mmmt) REVERT: g 626 MET cc_start: 0.7124 (ttm) cc_final: 0.6715 (ttm) outliers start: 31 outliers final: 24 residues processed: 192 average time/residue: 0.6206 time to fit residues: 132.6302 Evaluate side-chains 182 residues out of total 1723 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 156 time to evaluate : 0.674 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 28 THR Chi-restraints excluded: chain A residue 37 VAL Chi-restraints excluded: chain A residue 50 ARG Chi-restraints excluded: chain A residue 113 ASP Chi-restraints excluded: chain B residue 33 VAL Chi-restraints excluded: chain b residue 38 VAL Chi-restraints excluded: chain b residue 125 LEU Chi-restraints excluded: chain b residue 161 MET Chi-restraints excluded: chain b residue 164 GLU Chi-restraints excluded: chain b residue 190 GLU Chi-restraints excluded: chain b residue 195 ASN Chi-restraints excluded: chain b residue 286 VAL Chi-restraints excluded: chain c residue 568 LEU Chi-restraints excluded: chain c residue 635 ILE Chi-restraints excluded: chain c residue 638 TYR Chi-restraints excluded: chain c residue 644 ARG Chi-restraints excluded: chain d residue 36 VAL Chi-restraints excluded: chain d residue 38 VAL Chi-restraints excluded: chain d residue 125 LEU Chi-restraints excluded: chain d residue 286 VAL Chi-restraints excluded: chain e residue 538 THR Chi-restraints excluded: chain e residue 544 LEU Chi-restraints excluded: chain f residue 38 VAL Chi-restraints excluded: chain f residue 426 MET Chi-restraints excluded: chain g residue 599 SER Chi-restraints excluded: chain g residue 638 TYR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 191 random chunks: chunk 124 optimal weight: 0.0870 chunk 75 optimal weight: 10.0000 chunk 58 optimal weight: 5.9990 chunk 7 optimal weight: 7.9990 chunk 154 optimal weight: 5.9990 chunk 20 optimal weight: 5.9990 chunk 4 optimal weight: 9.9990 chunk 82 optimal weight: 2.9990 chunk 134 optimal weight: 1.9990 chunk 74 optimal weight: 1.9990 chunk 56 optimal weight: 0.9990 overall best weight: 1.6166 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** b 72 HIS ** d 188 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** f 195 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3760 r_free = 0.3760 target = 0.099398 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3246 r_free = 0.3246 target = 0.070147 restraints weight = 40168.892| |-----------------------------------------------------------------------------| r_work (start): 0.3214 rms_B_bonded: 3.84 r_work: 0.3064 rms_B_bonded: 4.01 restraints_weight: 0.5000 r_work (final): 0.3064 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8757 moved from start: 0.3220 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 17684 Z= 0.178 Angle : 0.769 17.932 24206 Z= 0.349 Chirality : 0.046 0.278 3005 Planarity : 0.003 0.033 2857 Dihedral : 8.097 59.655 4694 Min Nonbonded Distance : 2.419 Molprobity Statistics. All-atom Clashscore : 5.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.13 % Favored : 96.87 % Rotamer: Outliers : 2.15 % Allowed : 16.37 % Favored : 81.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.60 % 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: -0.33 (0.19), residues: 1916 helix: 0.76 (0.28), residues: 372 sheet: 0.01 (0.23), residues: 478 loop : -0.64 (0.19), residues: 1066 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG g 520 TYR 0.030 0.001 TYR e 638 PHE 0.036 0.001 PHE B 98 TRP 0.009 0.001 TRP g 631 HIS 0.004 0.001 HIS f 72 Details of bonding type rmsd/Z covalent geometry : bond 0.00425 / 0.18 (17525) covalent geometry : angle 0.69849 / 0.33 (23767) SS BOND : bond 0.00270 / 0.19 ( 38) SS BOND : angle 1.01304 / 0.68 ( 76) hydrogen bonds : bond 0.04228 / 2.90 ( 562) hydrogen bonds : angle 5.21210 / 3.49 ( 1563) link_ALPHA1-2 : bond 0.00500 / 0.26 ( 1) link_ALPHA1-2 : angle 1.60331 / 0.83 ( 3) link_ALPHA1-3 : bond 0.00926 / 0.50 ( 5) link_ALPHA1-3 : angle 1.63314 / 0.89 ( 15) link_ALPHA1-6 : bond 0.01362 / 0.71 ( 5) link_ALPHA1-6 : angle 1.74663 / 1.09 ( 15) link_BETA1-4 : bond 0.00586 / 0.43 ( 45) link_BETA1-4 : angle 2.63832 / 1.82 ( 135) link_NAG-ASN : bond 0.00297 / 0.22 ( 65) link_NAG-ASN : angle 2.87691 / 2.07 ( 195) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3832 Ramachandran restraints generated. 1916 Oldfield, 0 Emsley, 1916 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3832 Ramachandran restraints generated. 1916 Oldfield, 0 Emsley, 1916 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 197 residues out of total 1723 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 160 time to evaluate : 0.704 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 50 ARG cc_start: 0.7747 (OUTLIER) cc_final: 0.7487 (ptt180) REVERT: A 59 GLU cc_start: 0.8479 (tm-30) cc_final: 0.8001 (tm-30) REVERT: A 75 GLU cc_start: 0.8454 (mt-10) cc_final: 0.7659 (tt0) REVERT: A 78 ARG cc_start: 0.9105 (ptp-170) cc_final: 0.8425 (ptp90) REVERT: B 98 PHE cc_start: 0.8158 (m-80) cc_final: 0.7589 (m-10) REVERT: B 105 GLU cc_start: 0.7643 (mp0) cc_final: 0.7442 (tt0) REVERT: b 46 ARG cc_start: 0.8832 (mtp85) cc_final: 0.8615 (ptp-110) REVERT: b 164 GLU cc_start: 0.8529 (OUTLIER) cc_final: 0.8228 (mp0) REVERT: b 173 TYR cc_start: 0.8004 (p90) cc_final: 0.7762 (p90) REVERT: b 207 LYS cc_start: 0.8877 (mmmm) cc_final: 0.8228 (tmtm) REVERT: c 601 LYS cc_start: 0.8900 (mttm) cc_final: 0.8375 (mtpp) REVERT: c 616 ASN cc_start: 0.8832 (m-40) cc_final: 0.8333 (p0) REVERT: d 207 LYS cc_start: 0.8034 (tppt) cc_final: 0.7797 (tptt) REVERT: e 536 THR cc_start: 0.8919 (p) cc_final: 0.8681 (t) REVERT: e 588 ARG cc_start: 0.8998 (ttp80) cc_final: 0.8648 (ttm170) REVERT: e 638 TYR cc_start: 0.7823 (m-80) cc_final: 0.7491 (m-80) REVERT: g 601 LYS cc_start: 0.9217 (mttm) cc_final: 0.8998 (mtmt) REVERT: g 617 LYS cc_start: 0.9217 (mmmm) cc_final: 0.8965 (mmmt) REVERT: g 626 MET cc_start: 0.7156 (ttm) cc_final: 0.6806 (ttm) outliers start: 37 outliers final: 26 residues processed: 188 average time/residue: 0.6164 time to fit residues: 129.3989 Evaluate side-chains 182 residues out of total 1723 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 154 time to evaluate : 0.643 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 28 THR Chi-restraints excluded: chain A residue 37 VAL Chi-restraints excluded: chain A residue 50 ARG Chi-restraints excluded: chain A residue 113 ASP Chi-restraints excluded: chain B residue 33 VAL Chi-restraints excluded: chain b residue 38 VAL Chi-restraints excluded: chain b residue 125 LEU Chi-restraints excluded: chain b residue 161 MET Chi-restraints excluded: chain b residue 164 GLU Chi-restraints excluded: chain b residue 190 GLU Chi-restraints excluded: chain b residue 195 ASN Chi-restraints excluded: chain b residue 286 VAL Chi-restraints excluded: chain b residue 445 CYS Chi-restraints excluded: chain c residue 568 LEU Chi-restraints excluded: chain c residue 635 ILE Chi-restraints excluded: chain c residue 638 TYR Chi-restraints excluded: chain d residue 36 VAL Chi-restraints excluded: chain d residue 38 VAL Chi-restraints excluded: chain d residue 120 VAL Chi-restraints excluded: chain d residue 125 LEU Chi-restraints excluded: chain d residue 286 VAL Chi-restraints excluded: chain e residue 538 THR Chi-restraints excluded: chain e residue 544 LEU Chi-restraints excluded: chain f residue 38 VAL Chi-restraints excluded: chain f residue 120 VAL Chi-restraints excluded: chain f residue 426 MET Chi-restraints excluded: chain g residue 599 SER Chi-restraints excluded: chain g residue 634 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 191 random chunks: chunk 26 optimal weight: 2.9990 chunk 34 optimal weight: 3.9990 chunk 184 optimal weight: 2.9990 chunk 174 optimal weight: 0.9980 chunk 87 optimal weight: 0.8980 chunk 68 optimal weight: 4.9990 chunk 37 optimal weight: 2.9990 chunk 28 optimal weight: 0.8980 chunk 59 optimal weight: 0.9990 chunk 121 optimal weight: 3.9990 chunk 6 optimal weight: 5.9990 overall best weight: 1.3584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 126 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** b 72 HIS ** d 188 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** f 195 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3764 r_free = 0.3764 target = 0.099670 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3243 r_free = 0.3243 target = 0.070227 restraints weight = 39867.102| |-----------------------------------------------------------------------------| r_work (start): 0.3218 rms_B_bonded: 3.83 r_work: 0.3072 rms_B_bonded: 3.96 restraints_weight: 0.5000 r_work (final): 0.3072 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8718 moved from start: 0.3302 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 17684 Z= 0.162 Angle : 0.767 17.803 24206 Z= 0.346 Chirality : 0.046 0.286 3005 Planarity : 0.003 0.039 2857 Dihedral : 8.114 64.250 4694 Min Nonbonded Distance : 2.404 Molprobity Statistics. All-atom Clashscore : 5.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.18 % Favored : 96.82 % Rotamer: Outliers : 1.74 % Allowed : 16.95 % Favored : 81.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.60 % 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: -0.28 (0.19), residues: 1916 helix: 0.80 (0.28), residues: 372 sheet: 0.04 (0.23), residues: 492 loop : -0.61 (0.19), residues: 1052 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.000 ARG c 519 TYR 0.027 0.001 TYR e 638 PHE 0.036 0.001 PHE B 98 TRP 0.011 0.001 TRP e 631 HIS 0.004 0.001 HIS f 72 Details of bonding type rmsd/Z covalent geometry : bond 0.00381 / 0.16 (17525) covalent geometry : angle 0.68979 / 0.33 (23767) SS BOND : bond 0.00254 / 0.17 ( 38) SS BOND : angle 0.94169 / 0.63 ( 76) hydrogen bonds : bond 0.04119 / 2.84 ( 562) hydrogen bonds : angle 5.20941 / 3.49 ( 1563) link_ALPHA1-2 : bond 0.00574 / 0.30 ( 1) link_ALPHA1-2 : angle 1.58495 / 0.83 ( 3) link_ALPHA1-3 : bond 0.00917 / 0.50 ( 5) link_ALPHA1-3 : angle 1.58707 / 0.86 ( 15) link_ALPHA1-6 : bond 0.01332 / 0.70 ( 5) link_ALPHA1-6 : angle 1.76606 / 1.09 ( 15) link_BETA1-4 : bond 0.00598 / 0.44 ( 45) link_BETA1-4 : angle 2.61004 / 1.81 ( 135) link_NAG-ASN : bond 0.00339 / 0.25 ( 65) link_NAG-ASN : angle 3.09630 / 2.21 ( 195) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3832 Ramachandran restraints generated. 1916 Oldfield, 0 Emsley, 1916 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3832 Ramachandran restraints generated. 1916 Oldfield, 0 Emsley, 1916 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 187 residues out of total 1723 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 157 time to evaluate : 0.656 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 50 ARG cc_start: 0.7665 (OUTLIER) cc_final: 0.7451 (ptt180) REVERT: A 59 GLU cc_start: 0.8466 (tm-30) cc_final: 0.7964 (tm-30) REVERT: A 75 GLU cc_start: 0.8481 (mt-10) cc_final: 0.7690 (tt0) REVERT: A 78 ARG cc_start: 0.9108 (ptp-170) cc_final: 0.8435 (ptp90) REVERT: b 46 ARG cc_start: 0.8827 (mtp85) cc_final: 0.8592 (ptp-110) REVERT: b 164 GLU cc_start: 0.8531 (OUTLIER) cc_final: 0.8175 (mp0) REVERT: b 186 GLU cc_start: 0.7648 (tp30) cc_final: 0.6689 (tm-30) REVERT: b 207 LYS cc_start: 0.8912 (mmmm) cc_final: 0.8214 (tmtm) REVERT: b 268 LYS cc_start: 0.8883 (mmtp) cc_final: 0.8583 (mptt) REVERT: b 434 MET cc_start: 0.8742 (ttt) cc_final: 0.8436 (ttt) REVERT: c 601 LYS cc_start: 0.8889 (mttm) cc_final: 0.8328 (mtpp) REVERT: c 616 ASN cc_start: 0.8875 (m-40) cc_final: 0.8387 (p0) REVERT: d 207 LYS cc_start: 0.8048 (tppt) cc_final: 0.7800 (tptt) REVERT: e 536 THR cc_start: 0.8898 (p) cc_final: 0.8660 (t) REVERT: e 588 ARG cc_start: 0.8994 (ttp80) cc_final: 0.8629 (ttm170) REVERT: g 601 LYS cc_start: 0.9193 (mttm) cc_final: 0.8958 (mtmt) REVERT: g 617 LYS cc_start: 0.9191 (mmmm) cc_final: 0.8932 (mmmt) REVERT: g 626 MET cc_start: 0.7098 (ttm) cc_final: 0.6767 (ttm) outliers start: 30 outliers final: 26 residues processed: 179 average time/residue: 0.6166 time to fit residues: 123.5919 Evaluate side-chains 182 residues out of total 1723 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 154 time to evaluate : 0.656 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 28 THR Chi-restraints excluded: chain A residue 37 VAL Chi-restraints excluded: chain A residue 50 ARG Chi-restraints excluded: chain A residue 113 ASP Chi-restraints excluded: chain B residue 33 VAL Chi-restraints excluded: chain b residue 38 VAL Chi-restraints excluded: chain b residue 125 LEU Chi-restraints excluded: chain b residue 161 MET Chi-restraints excluded: chain b residue 164 GLU Chi-restraints excluded: chain b residue 190 GLU Chi-restraints excluded: chain b residue 195 ASN Chi-restraints excluded: chain b residue 286 VAL Chi-restraints excluded: chain b residue 445 CYS Chi-restraints excluded: chain c residue 568 LEU Chi-restraints excluded: chain c residue 635 ILE Chi-restraints excluded: chain c residue 638 TYR Chi-restraints excluded: chain c residue 644 ARG Chi-restraints excluded: chain d residue 36 VAL Chi-restraints excluded: chain d residue 38 VAL Chi-restraints excluded: chain d residue 120 VAL Chi-restraints excluded: chain d residue 125 LEU Chi-restraints excluded: chain d residue 286 VAL Chi-restraints excluded: chain e residue 538 THR Chi-restraints excluded: chain e residue 544 LEU Chi-restraints excluded: chain f residue 38 VAL Chi-restraints excluded: chain f residue 120 VAL Chi-restraints excluded: chain f residue 426 MET Chi-restraints excluded: chain g residue 599 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 191 random chunks: chunk 28 optimal weight: 0.9980 chunk 115 optimal weight: 2.9990 chunk 102 optimal weight: 3.9990 chunk 89 optimal weight: 4.9990 chunk 53 optimal weight: 3.9990 chunk 31 optimal weight: 0.8980 chunk 70 optimal weight: 8.9990 chunk 175 optimal weight: 7.9990 chunk 84 optimal weight: 6.9990 chunk 75 optimal weight: 9.9990 chunk 30 optimal weight: 0.9990 overall best weight: 1.9786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** b 72 HIS ** d 188 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** d 195 ASN f 195 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3744 r_free = 0.3744 target = 0.099390 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3222 r_free = 0.3222 target = 0.069932 restraints weight = 39885.481| |-----------------------------------------------------------------------------| r_work (start): 0.3205 rms_B_bonded: 3.83 r_work: 0.3057 rms_B_bonded: 3.95 restraints_weight: 0.5000 r_work (final): 0.3057 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8717 moved from start: 0.3401 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.055 17684 Z= 0.208 Angle : 0.784 18.057 24206 Z= 0.357 Chirality : 0.046 0.293 3005 Planarity : 0.004 0.036 2857 Dihedral : 8.232 80.044 4694 Min Nonbonded Distance : 2.395 Molprobity Statistics. All-atom Clashscore : 6.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.60 % Favored : 96.40 % Rotamer: Outliers : 1.74 % Allowed : 17.30 % Favored : 80.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.60 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.36 (0.19), residues: 1916 helix: 0.75 (0.28), residues: 372 sheet: 0.02 (0.23), residues: 492 loop : -0.68 (0.19), residues: 1052 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.000 ARG c 519 TYR 0.019 0.001 TYR c 643 PHE 0.043 0.002 PHE B 98 TRP 0.009 0.001 TRP g 631 HIS 0.005 0.001 HIS f 85 Details of bonding type rmsd/Z covalent geometry : bond 0.00497 / 0.21 (17525) covalent geometry : angle 0.70747 / 0.34 (23767) SS BOND : bond 0.00310 / 0.22 ( 38) SS BOND : angle 1.04390 / 0.70 ( 76) hydrogen bonds : bond 0.04354 / 2.97 ( 562) hydrogen bonds : angle 5.26352 / 3.52 ( 1563) link_ALPHA1-2 : bond 0.00472 / 0.25 ( 1) link_ALPHA1-2 : angle 1.56914 / 0.82 ( 3) link_ALPHA1-3 : bond 0.00833 / 0.44 ( 5) link_ALPHA1-3 : angle 1.59662 / 0.87 ( 15) link_ALPHA1-6 : bond 0.01222 / 0.63 ( 5) link_ALPHA1-6 : angle 1.82034 / 1.08 ( 15) link_BETA1-4 : bond 0.00587 / 0.43 ( 45) link_BETA1-4 : angle 2.62806 / 1.82 ( 135) link_NAG-ASN : bond 0.00354 / 0.26 ( 65) link_NAG-ASN : angle 3.10403 / 2.21 ( 195) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5494.24 seconds wall clock time: 94 minutes 46.51 seconds (5686.51 seconds total)