Starting phenix.real_space_refine on Fri Feb 6 00:48:43 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9oog_70663/02_2026/9oog_70663.cif Found real_map, /net/cci-nas-00/data/ceres_data/9oog_70663/02_2026/9oog_70663.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9oog_70663/02_2026/9oog_70663.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9oog_70663/02_2026/9oog_70663.map" model { file = "/net/cci-nas-00/data/ceres_data/9oog_70663/02_2026/9oog_70663.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9oog_70663/02_2026/9oog_70663.cif" } resolution = 3.1 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.015 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 126 5.16 5 C 13129 2.51 5 N 3425 2.21 5 O 4338 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 17 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 21018 Number of models: 1 Model: "" Number of chains: 56 Chain: "H" Number of atoms: 1024 Number of conformers: 1 Conformer: "" Number of residues, atoms: 132, 1024 Classifications: {'peptide': 132} Link IDs: {'PTRANS': 3, 'TRANS': 128} Chain: "L" Number of atoms: 809 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 809 Classifications: {'peptide': 107} Link IDs: {'PCIS': 1, 'PTRANS': 5, 'TRANS': 100} Chain: "b" Number of atoms: 3523 Number of conformers: 1 Conformer: "" Number of residues, atoms: 445, 3523 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: "I" Number of atoms: 1024 Number of conformers: 1 Conformer: "" Number of residues, atoms: 132, 1024 Classifications: {'peptide': 132} Link IDs: {'PTRANS': 3, 'TRANS': 128} Chain: "M" Number of atoms: 809 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 809 Classifications: {'peptide': 107} Link IDs: {'PCIS': 1, 'PTRANS': 5, 'TRANS': 100} Chain: "d" Number of atoms: 3523 Number of conformers: 1 Conformer: "" Number of residues, atoms: 445, 3523 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: "J" Number of atoms: 1024 Number of conformers: 1 Conformer: "" Number of residues, atoms: 132, 1024 Classifications: {'peptide': 132} Link IDs: {'PTRANS': 3, 'TRANS': 128} Chain: "N" Number of atoms: 809 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 809 Classifications: {'peptide': 107} Link IDs: {'PCIS': 1, 'PTRANS': 5, 'TRANS': 100} Chain: "f" Number of atoms: 3523 Number of conformers: 1 Conformer: "" Number of residues, atoms: 445, 3523 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: "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: "B" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "C" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Chain: "D" Number of atoms: 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: "E" Number of atoms: 72 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 72 Unusual residues: {'BMA': 1, 'MAN': 3, 'NAG': 2} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 18 Unresolved non-hydrogen chiralities: 6 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: "K" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "O" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "P" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "Q" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "R" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "S" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "T" Number of atoms: 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: "U" 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: "V" 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: "W" Number of atoms: 72 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 72 Unusual residues: {'BMA': 1, 'MAN': 3, 'NAG': 2} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 18 Unresolved non-hydrogen chiralities: 6 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: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "j" Number of atoms: 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: 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: "o" 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: "p" 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: "q" Number of atoms: 72 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 72 Unusual residues: {'BMA': 1, 'MAN': 3, 'NAG': 2} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 18 Unresolved non-hydrogen chiralities: 6 Chain: "r" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "s" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "t" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "u" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "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: "b" Number of atoms: 112 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 112 Unusual residues: {'NAG': 8} Classifications: {'undetermined': 8} Link IDs: {None: 7} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen dihedrals: 24 Unresolved non-hydrogen chiralities: 8 Chain: "c" Number of atoms: 42 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 42 Unusual residues: {'NAG': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "d" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 84 Unusual residues: {'NAG': 6} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 18 Unresolved non-hydrogen chiralities: 6 Chain: "e" Number of atoms: 42 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 42 Unusual residues: {'NAG': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "f" Number of atoms: 112 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 112 Unusual residues: {'NAG': 8} Classifications: {'undetermined': 8} Link IDs: {None: 7} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen dihedrals: 24 Unresolved non-hydrogen chiralities: 8 Chain: "g" Number of atoms: 42 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 42 Unusual residues: {'NAG': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Time building chain proxies: 5.49, per 1000 atoms: 0.26 Number of scatterers: 21018 At special positions: 0 Unit cell: (133.65, 134.475, 160.05, 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 126 16.00 O 4338 8.00 N 3425 7.00 C 13129 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=42, symmetry=0 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 92 " distance=2.03 Simple disulfide: pdb=" SG CYS L 23 " - pdb=" SG CYS L 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=2.04 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=2.06 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 I 22 " - pdb=" SG CYS I 92 " distance=2.03 Simple disulfide: pdb=" SG CYS M 23 " - pdb=" SG CYS M 88 " distance=2.03 Simple disulfide: pdb=" SG CYS d 54 " - pdb=" SG CYS d 74 " distance=2.04 Simple disulfide: pdb=" SG CYS d 119 " - pdb=" SG CYS d 205 " distance=2.03 Simple disulfide: pdb=" SG CYS d 126 " - pdb=" SG CYS d 196 " distance=2.03 Simple disulfide: pdb=" SG CYS d 131 " - pdb=" SG CYS d 157 " distance=2.03 Simple disulfide: pdb=" SG CYS d 201 " - pdb=" SG CYS d 433 " distance=2.03 Simple disulfide: pdb=" SG CYS d 218 " - pdb=" SG CYS d 247 " distance=2.03 Simple disulfide: pdb=" SG CYS d 228 " - pdb=" SG CYS d 239 " distance=2.03 Simple disulfide: pdb=" SG CYS d 296 " - pdb=" SG CYS d 331 " distance=2.03 Simple disulfide: pdb=" SG CYS d 378 " - pdb=" SG CYS d 445 " distance=2.03 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 J 22 " - pdb=" SG CYS J 92 " distance=2.03 Simple disulfide: pdb=" SG CYS N 23 " - pdb=" SG CYS N 88 " distance=2.03 Simple disulfide: pdb=" SG CYS f 54 " - pdb=" SG CYS f 74 " distance=2.04 Simple disulfide: pdb=" SG CYS f 119 " - pdb=" SG CYS f 205 " distance=2.03 Simple disulfide: pdb=" SG CYS f 126 " - pdb=" SG CYS f 196 " distance=2.03 Simple disulfide: pdb=" SG CYS f 131 " - pdb=" SG CYS f 157 " distance=2.03 Simple disulfide: pdb=" SG CYS f 201 " - pdb=" SG CYS f 433 " distance=2.03 Simple disulfide: pdb=" SG CYS f 218 " - pdb=" SG CYS f 247 " distance=2.03 Simple disulfide: pdb=" SG CYS f 228 " - pdb=" SG CYS f 239 " distance=2.03 Simple disulfide: pdb=" SG CYS f 296 " - pdb=" SG CYS f 331 " distance=2.03 Simple disulfide: pdb=" SG CYS f 378 " - pdb=" SG CYS f 445 " distance=2.03 Simple disulfide: pdb=" SG CYS f 385 " - pdb=" SG CYS f 418 " distance=2.03 Simple disulfide: pdb=" SG CYS f 501 " - pdb=" SG CYS g 605 " distance=2.03 Simple disulfide: pdb=" SG CYS g 598 " - pdb=" SG CYS g 604 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied ALPHA1-2 " MAN E 4 " - " MAN E 5 " " MAN W 4 " - " MAN W 5 " " MAN q 4 " - " MAN q 5 " ALPHA1-3 " BMA C 3 " - " MAN C 4 " " BMA E 3 " - " MAN E 4 " " BMA U 3 " - " MAN U 4 " " BMA W 3 " - " MAN W 4 " " BMA o 3 " - " MAN o 4 " " BMA q 3 " - " MAN q 4 " ALPHA1-6 " BMA C 3 " - " MAN C 5 " " BMA D 3 " - " MAN D 4 " " MAN D 4 " - " MAN D 5 " " BMA E 3 " - " MAN E 6 " " BMA U 3 " - " MAN U 5 " " BMA V 3 " - " MAN V 4 " " MAN V 4 " - " MAN V 5 " " BMA W 3 " - " MAN W 6 " " BMA o 3 " - " MAN o 5 " " BMA p 3 " - " MAN p 4 " " MAN p 4 " - " MAN p 5 " " BMA q 3 " - " MAN q 6 " BETA1-4 " NAG A 1 " - " NAG A 2 " " NAG B 1 " - " NAG B 2 " " NAG B 2 " - " BMA B 3 " " NAG C 1 " - " NAG C 2 " " NAG C 2 " - " BMA C 3 " " NAG D 1 " - " NAG D 2 " " NAG D 2 " - " BMA D 3 " " NAG E 1 " - " NAG E 2 " " NAG E 2 " - " BMA E 3 " " NAG F 1 " - " NAG F 2 " " NAG G 1 " - " NAG G 2 " " NAG K 1 " - " NAG K 2 " " NAG K 2 " - " BMA K 3 " " NAG O 1 " - " NAG O 2 " " NAG P 1 " - " NAG P 2 " " NAG Q 1 " - " NAG Q 2 " " NAG R 1 " - " NAG R 2 " " NAG S 1 " - " NAG S 2 " " NAG T 1 " - " NAG T 2 " " NAG T 2 " - " BMA T 3 " " NAG U 1 " - " NAG U 2 " " NAG U 2 " - " BMA U 3 " " NAG V 1 " - " NAG V 2 " " NAG V 2 " - " BMA V 3 " " NAG W 1 " - " NAG W 2 " " NAG W 2 " - " BMA W 3 " " 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 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 n 2 " - " BMA n 3 " " NAG o 1 " - " NAG o 2 " " NAG o 2 " - " BMA o 3 " " 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 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-ASN " NAG A 1 " - " ASN b 392 " " NAG B 1 " - " ASN b 332 " " NAG C 1 " - " ASN b 262 " " NAG D 1 " - " ASN b 156 " " NAG E 1 " - " ASN b 160 " " NAG F 1 " - " ASN b 197 " " NAG G 1 " - " ASN b 234 " " NAG K 1 " - " ASN b 241 " " NAG O 1 " - " ASN b 276 " " NAG P 1 " - " ASN b 301 " " NAG Q 1 " - " ASN b 448 " " NAG R 1 " - " ASN b 465 " " NAG S 1 " - " ASN d 392 " " NAG T 1 " - " ASN d 332 " " NAG U 1 " - " ASN d 262 " " NAG V 1 " - " ASN d 156 " " NAG W 1 " - " ASN d 160 " " NAG X 1 " - " ASN d 197 " " NAG Y 1 " - " ASN d 234 " " NAG Z 1 " - " ASN d 241 " " NAG a 1 " - " ASN d 276 " " NAG b 601 " - " ASN b 88 " " NAG b 602 " - " ASN b 133 " " NAG b 603 " - " ASN b 339 " " NAG b 604 " - " ASN b 355 " " NAG b 605 " - " ASN b 269 " " NAG b 606 " - " ASN b 363 " " NAG b 607 " - " ASN b 386 " " NAG b 608 " - " ASN b 398 " " 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 605 " - " ASN d 339 " " NAG d 606 " - " ASN d 398 " " 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 606 " - " ASN f 398 " " NAG f 607 " - " ASN f 386 " " NAG f 608 " - " ASN f 363 " " NAG g 701 " - " ASN g 611 " " NAG g 702 " - " ASN g 637 " " NAG g 703 " - " ASN g 625 " " NAG h 1 " - " ASN d 301 " " NAG k 1 " - " ASN d 448 " " NAG l 1 " - " ASN d 465 " " NAG m 1 " - " ASN f 392 " " NAG n 1 " - " ASN f 332 " " NAG o 1 " - " ASN f 262 " " NAG p 1 " - " ASN f 156 " " NAG q 1 " - " ASN f 160 " " NAG r 1 " - " ASN f 197 " " NAG s 1 " - " ASN f 234 " " NAG t 1 " - " ASN f 241 " " NAG u 1 " - " ASN f 276 " " NAG v 1 " - " ASN f 301 " " NAG w 1 " - " ASN f 448 " " NAG x 1 " - " ASN f 465 " Time building additional restraints: 2.22 Conformation dependent library (CDL) restraints added in 1.2 seconds 4770 Ramachandran restraints generated. 2385 Oldfield, 0 Emsley, 2385 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4500 Finding SS restraints... Secondary structure from input PDB file: 50 helices and 48 sheets defined 20.6% alpha, 33.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.68 Creating SS restraints... Processing helix chain 'H' and resid 28 through 32 removed outlier: 3.850A pdb=" N TYR H 32 " --> pdb=" O PHE H 29 " (cutoff:3.500A) Processing helix chain 'H' and resid 83 through 87 Processing helix chain 'L' and resid 79 through 83 removed outlier: 4.047A pdb=" N PHE L 83 " --> pdb=" O PRO L 80 " (cutoff:3.500A) Processing helix chain 'b' and resid 70 through 74 Processing helix chain 'b' and resid 99 through 117 Processing helix chain 'b' and resid 122 through 126 removed outlier: 3.799A pdb=" N LEU b 125 " --> pdb=" O LEU b 122 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N CYS b 126 " --> pdb=" O THR b 123 " (cutoff:3.500A) No H-bonds generated for 'chain 'b' and resid 122 through 126' Processing helix chain 'b' and resid 334 through 351 removed outlier: 3.649A pdb=" N THR b 341 " --> pdb=" O ARG b 337 " (cutoff:3.500A) Processing helix chain 'b' and resid 368 through 373 Processing helix chain 'b' and resid 387 through 390 Processing helix chain 'b' and resid 475 through 484 removed outlier: 4.061A pdb=" N TRP b 479 " --> pdb=" O MET b 475 " (cutoff:3.500A) removed outlier: 4.038A pdb=" N GLU b 482 " --> pdb=" O ASN b 478 " (cutoff:3.500A) Processing helix chain 'c' and resid 523 through 527 removed outlier: 3.703A pdb=" N ALA c 526 " --> pdb=" O LEU c 523 " (cutoff:3.500A) removed outlier: 4.572A pdb=" N GLY c 527 " --> pdb=" O GLY c 524 " (cutoff:3.500A) No H-bonds generated for 'chain 'c' and resid 523 through 527' Processing helix chain 'c' and resid 529 through 534 Processing helix chain 'c' and resid 536 through 543 removed outlier: 3.771A pdb=" N GLN c 540 " --> pdb=" O THR c 536 " (cutoff:3.500A) removed outlier: 3.900A pdb=" N GLN c 543 " --> pdb=" O VAL c 539 " (cutoff:3.500A) Processing helix chain 'c' and resid 569 through 596 removed outlier: 3.813A pdb=" N LEU c 592 " --> pdb=" O ARG c 588 " (cutoff:3.500A) Processing helix chain 'c' and resid 618 through 625 removed outlier: 3.708A pdb=" N TRP c 623 " --> pdb=" O LEU c 619 " (cutoff:3.500A) Processing helix chain 'c' and resid 627 through 636 removed outlier: 3.765A pdb=" N LYS c 633 " --> pdb=" O LEU c 629 " (cutoff:3.500A) removed outlier: 3.932A pdb=" N GLU c 634 " --> pdb=" O GLN c 630 " (cutoff:3.500A) Processing helix chain 'c' and resid 638 through 658 removed outlier: 3.613A pdb=" N GLU c 647 " --> pdb=" O TYR c 643 " (cutoff:3.500A) removed outlier: 3.910A pdb=" N GLU c 648 " --> pdb=" O ARG c 644 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N SER c 649 " --> pdb=" O LEU c 645 " (cutoff:3.500A) removed outlier: 3.856A pdb=" N GLN c 653 " --> pdb=" O SER c 649 " (cutoff:3.500A) Processing helix chain 'I' and resid 28 through 32 removed outlier: 3.855A pdb=" N TYR I 32 " --> pdb=" O PHE I 29 " (cutoff:3.500A) Processing helix chain 'I' and resid 83 through 87 Processing helix chain 'M' and resid 79 through 83 removed outlier: 4.015A pdb=" N PHE M 83 " --> pdb=" O PRO M 80 " (cutoff:3.500A) Processing helix chain 'd' and resid 70 through 74 Processing helix chain 'd' and resid 99 through 117 Processing helix chain 'd' and resid 122 through 126 removed outlier: 3.561A pdb=" N LEU d 125 " --> pdb=" O LEU d 122 " (cutoff:3.500A) removed outlier: 3.644A 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 removed outlier: 3.607A pdb=" N THR d 341 " --> pdb=" O ARG d 337 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N LEU d 342 " --> pdb=" O TRP d 338 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N GLN d 343 " --> pdb=" O ASN d 339 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N THR d 351 " --> pdb=" O GLU d 347 " (cutoff:3.500A) Processing helix chain 'd' and resid 368 through 373 Processing helix chain 'd' and resid 475 through 484 removed outlier: 4.008A pdb=" N TRP d 479 " --> pdb=" O MET d 475 " (cutoff:3.500A) removed outlier: 4.055A pdb=" N GLU d 482 " --> pdb=" O ASN d 478 " (cutoff:3.500A) Processing helix chain 'e' and resid 523 through 527 removed outlier: 3.712A pdb=" N ALA e 526 " --> pdb=" O LEU e 523 " (cutoff:3.500A) removed outlier: 4.558A pdb=" N GLY e 527 " --> pdb=" O GLY e 524 " (cutoff:3.500A) No H-bonds generated for 'chain 'e' and resid 523 through 527' Processing helix chain 'e' and resid 529 through 534 Processing helix chain 'e' and resid 536 through 543 removed outlier: 3.722A pdb=" N GLN e 540 " --> pdb=" O THR e 536 " (cutoff:3.500A) removed outlier: 3.856A pdb=" N GLN e 543 " --> pdb=" O VAL e 539 " (cutoff:3.500A) Processing helix chain 'e' and resid 544 through 546 No H-bonds generated for 'chain 'e' and resid 544 through 546' Processing helix chain 'e' and resid 569 through 596 removed outlier: 3.855A pdb=" N LEU e 592 " --> pdb=" O ARG e 588 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N LEU e 593 " --> pdb=" O ASP e 589 " (cutoff:3.500A) Processing helix chain 'e' and resid 619 through 625 Processing helix chain 'e' and resid 627 through 658 removed outlier: 3.766A pdb=" N LYS e 633 " --> pdb=" O LEU e 629 " (cutoff:3.500A) removed outlier: 3.917A pdb=" N GLU e 634 " --> pdb=" O GLN e 630 " (cutoff:3.500A) removed outlier: 5.283A pdb=" N ASN e 637 " --> pdb=" O LYS e 633 " (cutoff:3.500A) removed outlier: 5.066A pdb=" N TYR e 638 " --> pdb=" O GLU e 634 " (cutoff:3.500A) removed outlier: 4.607A pdb=" N GLN e 640 " --> pdb=" O GLY e 636 " (cutoff:3.500A) removed outlier: 5.270A pdb=" N LEU e 641 " --> pdb=" O ASN e 637 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N GLU e 648 " --> pdb=" O ARG e 644 " (cutoff:3.500A) removed outlier: 3.776A pdb=" N GLN e 653 " --> pdb=" O SER e 649 " (cutoff:3.500A) Processing helix chain 'J' and resid 28 through 32 removed outlier: 3.871A pdb=" N TYR J 32 " --> pdb=" O PHE J 29 " (cutoff:3.500A) Processing helix chain 'J' and resid 83 through 87 Processing helix chain 'N' and resid 79 through 83 removed outlier: 3.557A pdb=" N PHE N 83 " --> pdb=" O PRO N 80 " (cutoff:3.500A) Processing helix chain 'f' and resid 70 through 74 Processing helix chain 'f' and resid 98 through 117 removed outlier: 4.331A pdb=" N GLU f 102 " --> pdb=" O ASN f 98 " (cutoff:3.500A) Processing helix chain 'f' and resid 334 through 351 removed outlier: 3.623A 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 475 through 484 removed outlier: 3.993A pdb=" N TRP f 479 " --> pdb=" O MET f 475 " (cutoff:3.500A) removed outlier: 4.076A pdb=" N GLU f 482 " --> pdb=" O ASN f 478 " (cutoff:3.500A) Processing helix chain 'g' and resid 523 through 527 removed outlier: 3.661A pdb=" N ALA g 526 " --> pdb=" O LEU g 523 " (cutoff:3.500A) removed outlier: 4.539A pdb=" N GLY g 527 " --> pdb=" O GLY g 524 " (cutoff:3.500A) No H-bonds generated for 'chain 'g' and resid 523 through 527' Processing helix chain 'g' and resid 529 through 534 Processing helix chain 'g' and resid 536 through 543 removed outlier: 3.774A pdb=" N GLN g 540 " --> pdb=" O THR g 536 " (cutoff:3.500A) removed outlier: 3.819A pdb=" N GLN g 543 " --> pdb=" O VAL g 539 " (cutoff:3.500A) Processing helix chain 'g' and resid 544 through 546 No H-bonds generated for 'chain 'g' and resid 544 through 546' Processing helix chain 'g' and resid 569 through 596 removed outlier: 3.931A pdb=" N LEU g 592 " --> pdb=" O ARG g 588 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N LEU g 593 " --> pdb=" O ASP g 589 " (cutoff:3.500A) Processing helix chain 'g' and resid 620 through 625 Processing helix chain 'g' and resid 627 through 636 removed outlier: 3.844A pdb=" N LYS g 633 " --> pdb=" O LEU g 629 " (cutoff:3.500A) removed outlier: 3.868A pdb=" N GLU g 634 " --> pdb=" O GLN g 630 " (cutoff:3.500A) Processing helix chain 'g' and resid 638 through 658 Processing sheet with id=AA1, first strand: chain 'H' and resid 3 through 7 Processing sheet with id=AA2, first strand: chain 'H' and resid 11 through 12 removed outlier: 6.951A pdb=" N MET H 34 " --> pdb=" O SER H 50 " (cutoff:3.500A) removed outlier: 4.538A pdb=" N SER H 50 " --> pdb=" O MET H 34 " (cutoff:3.500A) removed outlier: 6.698A pdb=" N TRP H 36 " --> pdb=" O ILE H 48 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'H' and resid 11 through 12 removed outlier: 3.693A pdb=" N TYR H 102 " --> pdb=" O LYS H 94 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'H' and resid 100A through 100C Processing sheet with id=AA5, first strand: chain 'L' and resid 4 through 7 removed outlier: 4.015A pdb=" N ASP L 70 " --> pdb=" O SER L 67 " (cutoff:3.500A) removed outlier: 3.686A pdb=" N SER L 63 " --> pdb=" O THR L 74 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'L' and resid 10 through 13 Processing sheet with id=AA7, first strand: chain 'L' and resid 45 through 48 removed outlier: 5.418A pdb=" N SER L 46 " --> pdb=" O GLN L 37 " (cutoff:3.500A) removed outlier: 6.238A pdb=" N GLN L 37 " --> pdb=" O SER L 46 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'b' and resid 494 through 499 removed outlier: 5.557A pdb=" N VAL c 608 " --> pdb=" O VAL b 36 " (cutoff:3.500A) removed outlier: 8.067A pdb=" N VAL b 38 " --> pdb=" O THR c 606 " (cutoff:3.500A) removed outlier: 7.678A pdb=" N THR c 606 " --> pdb=" O VAL b 38 " (cutoff:3.500A) removed outlier: 8.084A pdb=" N TYR b 40 " --> pdb=" O CYS c 604 " (cutoff:3.500A) removed outlier: 8.685A pdb=" N CYS c 604 " --> pdb=" O TYR b 40 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'b' and resid 45 through 47 removed outlier: 4.671A pdb=" N VAL b 242 " --> pdb=" O LEU b 86 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'b' and resid 55 through 56 Processing sheet with id=AB2, first strand: chain 'b' and resid 66 through 67 removed outlier: 6.996A pdb=" N HIS b 66 " --> pdb=" O SER b 209 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB2 Processing sheet with id=AB3, first strand: chain 'b' and resid 91 through 94 Processing sheet with id=AB4, first strand: chain 'b' and resid 181 through 183 Processing sheet with id=AB5, first strand: chain 'b' and resid 202 through 203 removed outlier: 6.370A pdb=" N THR b 202 " --> pdb=" O TYR b 435 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'b' and resid 259 through 261 removed outlier: 3.512A pdb=" N GLY b 451 " --> pdb=" O LEU b 260 " (cutoff:3.500A) removed outlier: 9.997A pdb=" N LYS b 444 " --> pdb=" O ILE b 294 " (cutoff:3.500A) removed outlier: 11.187A pdb=" N ILE b 294 " --> pdb=" O LYS b 444 " (cutoff:3.500A) removed outlier: 9.678A pdb=" N GLU b 446 " --> pdb=" O VAL b 292 " (cutoff:3.500A) removed outlier: 10.226A pdb=" N VAL b 292 " --> pdb=" O GLU b 446 " (cutoff:3.500A) removed outlier: 9.202A pdb=" N ASN b 448 " --> pdb=" O GLN b 290 " (cutoff:3.500A) removed outlier: 9.752A pdb=" N GLN b 290 " --> pdb=" O ASN b 448 " (cutoff:3.500A) removed outlier: 6.316A pdb=" N THR b 450 " --> pdb=" O LEU b 288 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N HIS b 330 " --> pdb=" O ILE b 297 " (cutoff:3.500A) removed outlier: 4.363A pdb=" N ALA b 329 " --> pdb=" O CYS b 418 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N LYS b 421 " --> pdb=" O PHE b 382 " (cutoff:3.500A) removed outlier: 4.593A pdb=" N PHE b 382 " --> pdb=" O LYS b 421 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N PHE b 376 " --> pdb=" O PHE b 383 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'b' and resid 271 through 273 removed outlier: 6.316A pdb=" N THR b 450 " --> pdb=" O LEU b 288 " (cutoff:3.500A) removed outlier: 9.752A pdb=" N GLN b 290 " --> pdb=" O ASN b 448 " (cutoff:3.500A) removed outlier: 9.202A pdb=" N ASN b 448 " --> pdb=" O GLN b 290 " (cutoff:3.500A) removed outlier: 10.226A pdb=" N VAL b 292 " --> pdb=" O GLU b 446 " (cutoff:3.500A) removed outlier: 9.678A pdb=" N GLU b 446 " --> pdb=" O VAL b 292 " (cutoff:3.500A) removed outlier: 11.187A pdb=" N ILE b 294 " --> pdb=" O LYS b 444 " (cutoff:3.500A) removed outlier: 9.997A pdb=" N LYS b 444 " --> pdb=" O ILE b 294 " (cutoff:3.500A) removed outlier: 6.590A pdb=" N THR b 357 " --> pdb=" O GLU b 466 " (cutoff:3.500A) removed outlier: 7.792A pdb=" N PHE b 468 " --> pdb=" O THR b 357 " (cutoff:3.500A) removed outlier: 6.623A pdb=" N ILE b 359 " --> pdb=" O PHE b 468 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'b' and resid 301 through 312 removed outlier: 7.176A pdb=" N ASN b 301 " --> pdb=" O ILE b 323 " (cutoff:3.500A) removed outlier: 4.932A pdb=" N ILE b 323 " --> pdb=" O ASN b 301 " (cutoff:3.500A) removed outlier: 4.070A pdb=" N THR b 303 " --> pdb=" O GLY b 321 " (cutoff:3.500A) removed outlier: 7.262A pdb=" N GLN b 315 " --> pdb=" O ILE b 309 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'I' and resid 3 through 7 Processing sheet with id=AC1, first strand: chain 'I' and resid 11 through 12 removed outlier: 6.358A pdb=" N ARG I 38 " --> pdb=" O TRP I 47 " (cutoff:3.500A) removed outlier: 5.556A pdb=" N TRP I 47 " --> pdb=" O ARG I 38 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'I' and resid 11 through 12 removed outlier: 3.839A pdb=" N TYR I 102 " --> pdb=" O LYS I 94 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'I' and resid 100A through 100C Processing sheet with id=AC4, first strand: chain 'M' and resid 4 through 7 removed outlier: 4.206A pdb=" N ASP M 70 " --> pdb=" O SER M 67 " (cutoff:3.500A) removed outlier: 3.794A pdb=" N SER M 63 " --> pdb=" O THR M 74 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'M' and resid 10 through 13 removed outlier: 6.652A pdb=" N TRP M 35 " --> pdb=" O LEU M 47 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'd' and resid 494 through 499 removed outlier: 5.575A pdb=" N VAL e 608 " --> pdb=" O VAL d 36 " (cutoff:3.500A) removed outlier: 8.110A pdb=" N VAL d 38 " --> pdb=" O THR e 606 " (cutoff:3.500A) removed outlier: 7.702A pdb=" N THR e 606 " --> pdb=" O VAL d 38 " (cutoff:3.500A) removed outlier: 8.046A pdb=" N TYR d 40 " --> pdb=" O CYS e 604 " (cutoff:3.500A) removed outlier: 8.649A pdb=" N CYS e 604 " --> pdb=" O TYR d 40 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'd' and resid 45 through 47 Processing sheet with id=AC8, first strand: chain 'd' and resid 75 through 76 removed outlier: 3.818A pdb=" N VAL d 75 " --> pdb=" O CYS d 54 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'd' and resid 66 through 67 removed outlier: 7.047A pdb=" N HIS d 66 " --> pdb=" O SER d 209 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC9 Processing sheet with id=AD1, first strand: chain 'd' and resid 91 through 94 Processing sheet with id=AD2, first strand: chain 'd' and resid 181 through 183 Processing sheet with id=AD3, first strand: chain 'd' and resid 202 through 203 removed outlier: 6.296A pdb=" N THR d 202 " --> pdb=" O TYR d 435 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'd' and resid 259 through 261 removed outlier: 3.600A pdb=" N GLY d 451 " --> pdb=" O LEU d 260 " (cutoff:3.500A) removed outlier: 9.966A pdb=" N LYS d 444 " --> pdb=" O ILE d 294 " (cutoff:3.500A) removed outlier: 11.277A pdb=" N ILE d 294 " --> pdb=" O LYS d 444 " (cutoff:3.500A) removed outlier: 9.698A pdb=" N GLU d 446 " --> pdb=" O VAL d 292 " (cutoff:3.500A) removed outlier: 10.488A pdb=" N VAL d 292 " --> pdb=" O GLU d 446 " (cutoff:3.500A) removed outlier: 9.169A pdb=" N ASN d 448 " --> pdb=" O GLN d 290 " (cutoff:3.500A) removed outlier: 9.772A pdb=" N GLN d 290 " --> pdb=" O ASN d 448 " (cutoff:3.500A) removed outlier: 6.330A pdb=" N THR d 450 " --> pdb=" O LEU d 288 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N HIS d 330 " --> pdb=" O ILE d 297 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N LYS d 421 " --> pdb=" O PHE d 382 " (cutoff:3.500A) removed outlier: 4.527A pdb=" N PHE d 382 " --> pdb=" O LYS d 421 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'd' and resid 271 through 273 removed outlier: 6.330A pdb=" N THR d 450 " --> pdb=" O LEU d 288 " (cutoff:3.500A) removed outlier: 9.772A pdb=" N GLN d 290 " --> pdb=" O ASN d 448 " (cutoff:3.500A) removed outlier: 9.169A pdb=" N ASN d 448 " --> pdb=" O GLN d 290 " (cutoff:3.500A) removed outlier: 10.488A pdb=" N VAL d 292 " --> pdb=" O GLU d 446 " (cutoff:3.500A) removed outlier: 9.698A pdb=" N GLU d 446 " --> pdb=" O VAL d 292 " (cutoff:3.500A) removed outlier: 11.277A pdb=" N ILE d 294 " --> pdb=" O LYS d 444 " (cutoff:3.500A) removed outlier: 9.966A pdb=" N LYS d 444 " --> pdb=" O ILE d 294 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'd' and resid 301 through 312 removed outlier: 6.982A pdb=" N ASN d 301 " --> pdb=" O ILE d 323 " (cutoff:3.500A) removed outlier: 4.953A pdb=" N ILE d 323 " --> pdb=" O ASN d 301 " (cutoff:3.500A) removed outlier: 4.384A pdb=" N THR d 303 " --> pdb=" O GLY d 321 " (cutoff:3.500A) removed outlier: 7.264A pdb=" N GLN d 315 " --> pdb=" O ILE d 309 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'J' and resid 3 through 7 Processing sheet with id=AD8, first strand: chain 'J' and resid 11 through 12 removed outlier: 6.874A pdb=" N MET J 34 " --> pdb=" O SER J 50 " (cutoff:3.500A) removed outlier: 4.461A pdb=" N SER J 50 " --> pdb=" O MET J 34 " (cutoff:3.500A) removed outlier: 6.645A pdb=" N TRP J 36 " --> pdb=" O ILE J 48 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'J' and resid 11 through 12 removed outlier: 3.860A pdb=" N TYR J 102 " --> pdb=" O LYS J 94 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'J' and resid 100A through 100C Processing sheet with id=AE2, first strand: chain 'N' and resid 4 through 7 removed outlier: 3.646A pdb=" N VAL N 19 " --> pdb=" O ILE N 75 " (cutoff:3.500A) removed outlier: 4.067A pdb=" N ASP N 70 " --> pdb=" O SER N 67 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'N' and resid 10 through 13 removed outlier: 3.504A pdb=" N LEU N 11 " --> pdb=" O GLU N 103 " (cutoff:3.500A) removed outlier: 6.634A pdb=" N TRP N 35 " --> pdb=" O LEU N 47 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'f' and resid 494 through 499 removed outlier: 5.549A pdb=" N VAL g 608 " --> pdb=" O VAL f 36 " (cutoff:3.500A) removed outlier: 7.978A pdb=" N VAL f 38 " --> pdb=" O THR g 606 " (cutoff:3.500A) removed outlier: 7.651A pdb=" N THR g 606 " --> pdb=" O VAL f 38 " (cutoff:3.500A) removed outlier: 8.073A pdb=" N TYR f 40 " --> pdb=" O CYS g 604 " (cutoff:3.500A) removed outlier: 8.695A pdb=" N CYS g 604 " --> pdb=" O TYR f 40 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'f' and resid 45 through 47 Processing sheet with id=AE6, first strand: chain 'f' and resid 75 through 76 removed outlier: 3.852A pdb=" N VAL f 75 " --> pdb=" O CYS f 54 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'f' and resid 91 through 94 Processing sheet with id=AE8, first strand: chain 'f' and resid 181 through 183 Processing sheet with id=AE9, first strand: chain 'f' and resid 202 through 203 removed outlier: 6.293A pdb=" N THR f 202 " --> pdb=" O TYR f 435 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'f' and resid 259 through 261 removed outlier: 3.587A pdb=" N GLY f 451 " --> pdb=" O LEU f 260 " (cutoff:3.500A) removed outlier: 10.054A pdb=" N LYS f 444 " --> pdb=" O ILE f 294 " (cutoff:3.500A) removed outlier: 11.349A pdb=" N ILE f 294 " --> pdb=" O LYS f 444 " (cutoff:3.500A) removed outlier: 9.725A pdb=" N GLU f 446 " --> pdb=" O VAL f 292 " (cutoff:3.500A) removed outlier: 10.544A pdb=" N VAL f 292 " --> pdb=" O GLU f 446 " (cutoff:3.500A) removed outlier: 9.054A pdb=" N ASN f 448 " --> pdb=" O GLN f 290 " (cutoff:3.500A) removed outlier: 9.778A pdb=" N GLN f 290 " --> pdb=" O ASN f 448 " (cutoff:3.500A) removed outlier: 6.289A pdb=" N THR f 450 " --> pdb=" O LEU f 288 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N HIS f 330 " --> pdb=" O ILE f 297 " (cutoff:3.500A) removed outlier: 4.400A pdb=" N ALA f 329 " --> pdb=" O CYS f 418 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N LYS f 421 " --> pdb=" O PHE f 382 " (cutoff:3.500A) removed outlier: 4.613A pdb=" N PHE f 382 " --> pdb=" O LYS f 421 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'f' and resid 271 through 273 removed outlier: 6.289A pdb=" N THR f 450 " --> pdb=" O LEU f 288 " (cutoff:3.500A) removed outlier: 9.778A pdb=" N GLN f 290 " --> pdb=" O ASN f 448 " (cutoff:3.500A) removed outlier: 9.054A pdb=" N ASN f 448 " --> pdb=" O GLN f 290 " (cutoff:3.500A) removed outlier: 10.544A pdb=" N VAL f 292 " --> pdb=" O GLU f 446 " (cutoff:3.500A) removed outlier: 9.725A pdb=" N GLU f 446 " --> pdb=" O VAL f 292 " (cutoff:3.500A) removed outlier: 11.349A pdb=" N ILE f 294 " --> pdb=" O LYS f 444 " (cutoff:3.500A) removed outlier: 10.054A pdb=" N LYS f 444 " --> pdb=" O ILE f 294 " (cutoff:3.500A) removed outlier: 6.359A pdb=" N THR f 357 " --> pdb=" O GLU f 466 " (cutoff:3.500A) removed outlier: 7.717A pdb=" N PHE f 468 " --> pdb=" O THR f 357 " (cutoff:3.500A) removed outlier: 6.462A pdb=" N ILE f 359 " --> pdb=" O PHE f 468 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'f' and resid 301 through 312 removed outlier: 6.955A pdb=" N ASN f 301 " --> pdb=" O ILE f 323 " (cutoff:3.500A) removed outlier: 4.909A pdb=" N ILE f 323 " --> pdb=" O ASN f 301 " (cutoff:3.500A) removed outlier: 4.822A pdb=" N THR f 303 " --> pdb=" O GLY f 321 " (cutoff:3.500A) removed outlier: 7.261A pdb=" N GLN f 315 " --> pdb=" O ILE f 309 " (cutoff:3.500A) 724 hydrogen bonds defined for protein. 1914 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 4.55 Time building geometry restraints manager: 2.85 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 5236 1.33 - 1.46: 6007 1.46 - 1.59: 10021 1.59 - 1.71: 0 1.71 - 1.84: 168 Bond restraints: 21432 Sorted by residual: bond pdb=" N ASP M 82 " pdb=" CA ASP M 82 " ideal model delta sigma weight residual 1.456 1.498 -0.042 1.18e-02 7.18e+03 1.26e+01 bond pdb=" C1 BMA D 3 " pdb=" O5 BMA D 3 " ideal model delta sigma weight residual 1.410 1.472 -0.062 2.00e-02 2.50e+03 9.53e+00 bond pdb=" C1 BMA D 3 " pdb=" C2 BMA D 3 " ideal model delta sigma weight residual 1.519 1.580 -0.061 2.00e-02 2.50e+03 9.27e+00 bond pdb=" C GLY d 321 " pdb=" O GLY d 321 " ideal model delta sigma weight residual 1.234 1.263 -0.029 9.80e-03 1.04e+04 8.93e+00 bond pdb=" N ILE b 323A" pdb=" CA ILE b 323A" ideal model delta sigma weight residual 1.459 1.493 -0.034 1.20e-02 6.94e+03 8.24e+00 ... (remaining 21427 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.21: 28059 2.21 - 4.42: 880 4.42 - 6.63: 100 6.63 - 8.85: 13 8.85 - 11.06: 5 Bond angle restraints: 29057 Sorted by residual: angle pdb=" N LEU M 78 " pdb=" CA LEU M 78 " pdb=" CB LEU M 78 " ideal model delta sigma weight residual 109.48 100.55 8.93 1.55e+00 4.16e-01 3.32e+01 angle pdb=" N ASN d 339 " pdb=" CA ASN d 339 " pdb=" C ASN d 339 " ideal model delta sigma weight residual 113.18 106.21 6.97 1.21e+00 6.83e-01 3.31e+01 angle pdb=" CA ASP M 82 " pdb=" CB ASP M 82 " pdb=" CG ASP M 82 " ideal model delta sigma weight residual 112.60 117.54 -4.94 1.00e+00 1.00e+00 2.44e+01 angle pdb=" CA CYS b 126 " pdb=" C CYS b 126 " pdb=" O CYS b 126 " ideal model delta sigma weight residual 121.66 116.14 5.52 1.17e+00 7.31e-01 2.22e+01 angle pdb=" C ASP N 82 " pdb=" CA ASP N 82 " pdb=" CB ASP N 82 " ideal model delta sigma weight residual 110.01 101.64 8.37 1.80e+00 3.09e-01 2.16e+01 ... (remaining 29052 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.42: 13372 17.42 - 34.84: 892 34.84 - 52.26: 264 52.26 - 69.68: 88 69.68 - 87.11: 25 Dihedral angle restraints: 14641 sinusoidal: 7639 harmonic: 7002 Sorted by residual: dihedral pdb=" CB CYS b 126 " pdb=" SG CYS b 126 " pdb=" SG CYS b 196 " pdb=" CB CYS b 196 " ideal model delta sinusoidal sigma weight residual 93.00 154.84 -61.84 1 1.00e+01 1.00e-02 5.07e+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 93.00 151.03 -58.03 1 1.00e+01 1.00e-02 4.52e+01 dihedral pdb=" CB CYS f 126 " pdb=" SG CYS f 126 " pdb=" SG CYS f 196 " pdb=" CB CYS f 196 " ideal model delta sinusoidal sigma weight residual 93.00 150.34 -57.34 1 1.00e+01 1.00e-02 4.42e+01 ... (remaining 14638 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.141: 3556 0.141 - 0.283: 60 0.283 - 0.424: 0 0.424 - 0.565: 4 0.565 - 0.706: 2 Chirality restraints: 3622 Sorted by residual: chirality pdb=" C1 NAG x 2 " pdb=" O4 NAG x 1 " pdb=" C2 NAG x 2 " pdb=" O5 NAG x 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.23 -0.17 2.00e-02 2.50e+03 7.20e+01 chirality pdb=" C1 NAG b 608 " pdb=" ND2 ASN b 398 " pdb=" C2 NAG b 608 " pdb=" O5 NAG b 608 " both_signs ideal model delta sigma weight residual False -2.40 -1.69 -0.71 2.00e-01 2.50e+01 1.25e+01 chirality pdb=" C1 NAG d 606 " pdb=" ND2 ASN d 398 " pdb=" C2 NAG d 606 " pdb=" O5 NAG d 606 " both_signs ideal model delta sigma weight residual False -2.40 -1.79 -0.61 2.00e-01 2.50e+01 9.43e+00 ... (remaining 3619 not shown) Planarity restraints: 3564 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C2 NAG d 605 " -0.143 2.00e-02 2.50e+03 1.18e-01 1.75e+02 pdb=" C7 NAG d 605 " 0.035 2.00e-02 2.50e+03 pdb=" C8 NAG d 605 " -0.105 2.00e-02 2.50e+03 pdb=" N2 NAG d 605 " 0.192 2.00e-02 2.50e+03 pdb=" O7 NAG d 605 " 0.020 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG x 1 " -0.099 2.00e-02 2.50e+03 8.09e-02 8.18e+01 pdb=" C7 NAG x 1 " 0.029 2.00e-02 2.50e+03 pdb=" C8 NAG x 1 " -0.075 2.00e-02 2.50e+03 pdb=" N2 NAG x 1 " 0.128 2.00e-02 2.50e+03 pdb=" O7 NAG x 1 " 0.017 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG d 606 " 0.097 2.00e-02 2.50e+03 8.07e-02 8.14e+01 pdb=" C7 NAG d 606 " -0.024 2.00e-02 2.50e+03 pdb=" C8 NAG d 606 " 0.072 2.00e-02 2.50e+03 pdb=" N2 NAG d 606 " -0.132 2.00e-02 2.50e+03 pdb=" O7 NAG d 606 " -0.013 2.00e-02 2.50e+03 ... (remaining 3561 not shown) Histogram of nonbonded interaction distances: 2.22 - 2.76: 2667 2.76 - 3.29: 20650 3.29 - 3.83: 32741 3.83 - 4.36: 40000 4.36 - 4.90: 69860 Nonbonded interactions: 165918 Sorted by model distance: nonbonded pdb=" O TRP f 401 " pdb=" O3 NAG f 603 " model vdw 2.220 3.040 nonbonded pdb=" OG1 THR I 87 " pdb=" OG1 THR I 110 " model vdw 2.233 3.040 nonbonded pdb=" O TRP b 401 " pdb=" O3 NAG b 603 " model vdw 2.242 3.040 nonbonded pdb=" O6 NAG i 1 " pdb=" O6 NAG i 2 " model vdw 2.248 3.040 nonbonded pdb=" O CYS N 88 " pdb=" N GLY N 99 " model vdw 2.282 3.120 ... (remaining 165913 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'F' selection = chain 'G' selection = chain 'O' selection = chain 'P' selection = chain 'Q' selection = chain 'R' selection = chain 'S' selection = chain 'X' selection = chain 'Y' selection = chain 'Z' selection = chain 'a' selection = chain 'h' selection = chain 'i' selection = chain 'j' selection = chain 'k' selection = chain 'l' selection = chain 'm' selection = chain 'r' selection = chain 's' selection = chain 't' selection = chain 'u' selection = chain 'v' selection = chain 'w' selection = chain 'x' } ncs_group { reference = chain 'B' selection = chain 'K' selection = chain 'T' selection = chain 'n' } ncs_group { reference = chain 'C' selection = chain 'D' selection = chain 'U' selection = chain 'V' selection = chain 'o' selection = chain 'p' } ncs_group { reference = chain 'E' selection = chain 'W' selection = chain 'q' } ncs_group { reference = chain 'H' selection = chain 'I' selection = chain 'J' } ncs_group { reference = chain 'L' selection = chain 'M' selection = chain 'N' } ncs_group { reference = (chain 'b' and resid 33 through 606) selection = chain 'd' selection = (chain 'f' and resid 33 through 606) } ncs_group { reference = chain 'c' selection = chain 'e' selection = chain 'g' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.96 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: 5.670 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.370 Check model and map are aligned: 0.060 Set scattering table: 0.060 Process input model: 22.330 Find NCS groups from input model: 0.600 Set up NCS constraints: 0.100 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.140 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 31.350 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8369 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 : 0.005 0.062 21613 Z= 0.254 Angle : 0.971 11.989 29558 Z= 0.523 Chirality : 0.054 0.706 3622 Planarity : 0.005 0.118 3497 Dihedral : 13.170 87.106 10015 Min Nonbonded Distance : 2.220 Molprobity Statistics. All-atom Clashscore : 2.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.15 % Favored : 95.85 % Rotamer: Outliers : 0.00 % Allowed : 8.96 % Favored : 91.04 % Cbeta Deviations : 0.09 % Peptide Plane: Cis-proline : 3.12 % 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: -1.27 (0.17), residues: 2385 helix: -0.41 (0.27), residues: 387 sheet: -0.59 (0.20), residues: 597 loop : -1.06 (0.16), residues: 1401 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG f 456 TYR 0.041 0.002 TYR H 100N PHE 0.017 0.001 PHE J 100C TRP 0.026 0.002 TRP d 338 HIS 0.005 0.001 HIS g 564 Details of bonding type rmsd covalent geometry : bond 0.00455 (21432) covalent geometry : angle 0.89721 (29057) SS BOND : bond 0.00612 ( 42) SS BOND : angle 1.60895 ( 84) hydrogen bonds : bond 0.23620 ( 694) hydrogen bonds : angle 9.02081 ( 1914) link_ALPHA1-2 : bond 0.01056 ( 3) link_ALPHA1-2 : angle 1.93346 ( 9) link_ALPHA1-3 : bond 0.01741 ( 6) link_ALPHA1-3 : angle 1.33326 ( 18) link_ALPHA1-6 : bond 0.01560 ( 12) link_ALPHA1-6 : angle 2.25185 ( 36) link_BETA1-4 : bond 0.01297 ( 51) link_BETA1-4 : angle 3.74019 ( 153) link_NAG-ASN : bond 0.00500 ( 67) link_NAG-ASN : angle 3.06253 ( 201) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4770 Ramachandran restraints generated. 2385 Oldfield, 0 Emsley, 2385 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4770 Ramachandran restraints generated. 2385 Oldfield, 0 Emsley, 2385 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 297 residues out of total 2121 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 297 time to evaluate : 0.788 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 75 LYS cc_start: 0.9537 (mtmm) cc_final: 0.9143 (mtmm) REVERT: L 19 VAL cc_start: 0.7706 (m) cc_final: 0.7372 (m) REVERT: b 268 LYS cc_start: 0.8724 (mmmt) cc_final: 0.8393 (ptmt) REVERT: c 654 GLU cc_start: 0.8320 (mm-30) cc_final: 0.7591 (mm-30) REVERT: I 102 TYR cc_start: 0.8102 (m-80) cc_final: 0.7708 (m-80) REVERT: M 79 GLN cc_start: 0.8411 (mm110) cc_final: 0.7448 (mm-40) REVERT: d 268 LYS cc_start: 0.8758 (mmmt) cc_final: 0.8444 (ptmt) REVERT: e 621 GLU cc_start: 0.8408 (pt0) cc_final: 0.8173 (pt0) REVERT: e 632 ASP cc_start: 0.8817 (t70) cc_final: 0.8597 (t0) REVERT: e 654 GLU cc_start: 0.8559 (mm-30) cc_final: 0.7575 (mm-30) REVERT: N 4 MET cc_start: 0.8428 (mmm) cc_final: 0.8124 (mmm) REVERT: N 17 ASP cc_start: 0.7992 (t0) cc_final: 0.7655 (t0) REVERT: N 79 GLN cc_start: 0.8665 (mm-40) cc_final: 0.8394 (mm-40) REVERT: N 89 GLN cc_start: 0.8012 (tt0) cc_final: 0.7810 (tt0) REVERT: f 268 LYS cc_start: 0.8780 (mmmt) cc_final: 0.8479 (ptmm) outliers start: 0 outliers final: 0 residues processed: 297 average time/residue: 0.1803 time to fit residues: 78.7261 Evaluate side-chains 203 residues out of total 2121 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 203 time to evaluate : 0.758 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 237 random chunks: chunk 216 optimal weight: 7.9990 chunk 98 optimal weight: 9.9990 chunk 194 optimal weight: 7.9990 chunk 227 optimal weight: 0.0970 chunk 107 optimal weight: 0.6980 chunk 10 optimal weight: 5.9990 chunk 66 optimal weight: 1.9990 chunk 130 optimal weight: 4.9990 chunk 124 optimal weight: 9.9990 chunk 103 optimal weight: 5.9990 chunk 235 optimal weight: 5.9990 overall best weight: 2.7584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: e 624 ASN ** N 24 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** g 651 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3529 r_free = 0.3529 target = 0.072375 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3128 r_free = 0.3128 target = 0.054349 restraints weight = 66632.605| |-----------------------------------------------------------------------------| r_work (start): 0.3120 rms_B_bonded: 4.01 r_work: 0.2973 rms_B_bonded: 4.10 restraints_weight: 0.5000 r_work (final): 0.2973 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2982 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2982 r_free = 0.2982 target_work(ls_wunit_k1) = 0.049 | | occupancies: max = 1.00 min = 0.96 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2982 r_free = 0.2982 target_work(ls_wunit_k1) = 0.049 | | occupancies: max = 1.00 min = 1.00 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2982 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8578 moved from start: 0.1512 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.049 21613 Z= 0.219 Angle : 0.772 16.543 29558 Z= 0.360 Chirality : 0.048 0.301 3622 Planarity : 0.004 0.044 3497 Dihedral : 8.724 63.103 5506 Min Nonbonded Distance : 2.461 Molprobity Statistics. All-atom Clashscore : 3.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.81 % Favored : 97.19 % Rotamer: Outliers : 1.74 % Allowed : 11.41 % Favored : 86.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % 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: -1.09 (0.17), residues: 2385 helix: -0.45 (0.26), residues: 426 sheet: -0.58 (0.20), residues: 615 loop : -0.82 (0.16), residues: 1344 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG L 61 TYR 0.023 0.002 TYR M 49 PHE 0.014 0.002 PHE J 100C TRP 0.021 0.002 TRP g 631 HIS 0.002 0.001 HIS f 66 Details of bonding type rmsd covalent geometry : bond 0.00507 (21432) covalent geometry : angle 0.69693 (29057) SS BOND : bond 0.00516 ( 42) SS BOND : angle 1.31882 ( 84) hydrogen bonds : bond 0.05264 ( 694) hydrogen bonds : angle 6.17950 ( 1914) link_ALPHA1-2 : bond 0.00608 ( 3) link_ALPHA1-2 : angle 1.55008 ( 9) link_ALPHA1-3 : bond 0.00876 ( 6) link_ALPHA1-3 : angle 1.75944 ( 18) link_ALPHA1-6 : bond 0.00811 ( 12) link_ALPHA1-6 : angle 1.68697 ( 36) link_BETA1-4 : bond 0.00596 ( 51) link_BETA1-4 : angle 3.26072 ( 153) link_NAG-ASN : bond 0.00399 ( 67) link_NAG-ASN : angle 2.77988 ( 201) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4770 Ramachandran restraints generated. 2385 Oldfield, 0 Emsley, 2385 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4770 Ramachandran restraints generated. 2385 Oldfield, 0 Emsley, 2385 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 229 residues out of total 2121 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 192 time to evaluate : 0.778 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 75 LYS cc_start: 0.9642 (mtmm) cc_final: 0.9403 (mtmm) REVERT: H 83 ARG cc_start: 0.8302 (mpp80) cc_final: 0.8035 (mpp80) REVERT: H 100 LEU cc_start: 0.9122 (OUTLIER) cc_final: 0.8900 (mp) REVERT: L 17 ASP cc_start: 0.7955 (t0) cc_final: 0.7704 (t0) REVERT: L 24 GLN cc_start: 0.8869 (mt0) cc_final: 0.8359 (tp40) REVERT: L 103 GLU cc_start: 0.7561 (tm-30) cc_final: 0.7264 (tm-30) REVERT: c 654 GLU cc_start: 0.8303 (mm-30) cc_final: 0.7755 (mm-30) REVERT: I 83 ARG cc_start: 0.8331 (mpp80) cc_final: 0.8050 (mpp80) REVERT: M 3 GLN cc_start: 0.8640 (pm20) cc_final: 0.8306 (pm20) REVERT: M 79 GLN cc_start: 0.7926 (mm110) cc_final: 0.7468 (mp10) REVERT: M 103 GLU cc_start: 0.7679 (tm-30) cc_final: 0.7438 (tm-30) REVERT: e 632 ASP cc_start: 0.8900 (t70) cc_final: 0.8669 (t0) REVERT: e 654 GLU cc_start: 0.8416 (mm-30) cc_final: 0.7993 (mm-30) REVERT: N 17 ASP cc_start: 0.8235 (t0) cc_final: 0.7931 (t0) outliers start: 37 outliers final: 21 residues processed: 219 average time/residue: 0.1655 time to fit residues: 54.5746 Evaluate side-chains 187 residues out of total 2121 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 165 time to evaluate : 0.671 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 11 LEU Chi-restraints excluded: chain H residue 13 THR Chi-restraints excluded: chain H residue 37 VAL Chi-restraints excluded: chain H residue 100 LEU Chi-restraints excluded: chain b residue 125 LEU Chi-restraints excluded: chain b residue 286 VAL Chi-restraints excluded: chain I residue 4 LEU Chi-restraints excluded: chain I residue 11 LEU Chi-restraints excluded: chain I residue 13 THR Chi-restraints excluded: chain I residue 37 VAL Chi-restraints excluded: chain M residue 58 VAL Chi-restraints excluded: chain M residue 69 THR Chi-restraints excluded: chain d residue 125 LEU Chi-restraints excluded: chain d residue 286 VAL Chi-restraints excluded: chain J residue 11 LEU Chi-restraints excluded: chain J residue 13 THR Chi-restraints excluded: chain J residue 37 VAL Chi-restraints excluded: chain N residue 88 CYS Chi-restraints excluded: chain f residue 125 LEU Chi-restraints excluded: chain f residue 286 VAL Chi-restraints excluded: chain g residue 535 ILE Chi-restraints excluded: chain g residue 546 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 237 random chunks: chunk 29 optimal weight: 5.9990 chunk 110 optimal weight: 0.9980 chunk 120 optimal weight: 5.9990 chunk 169 optimal weight: 0.5980 chunk 99 optimal weight: 10.0000 chunk 179 optimal weight: 0.6980 chunk 220 optimal weight: 6.9990 chunk 148 optimal weight: 0.5980 chunk 106 optimal weight: 2.9990 chunk 74 optimal weight: 5.9990 chunk 66 optimal weight: 0.0270 overall best weight: 0.5838 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: I 39 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3648 r_free = 0.3648 target = 0.076262 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3276 r_free = 0.3276 target = 0.059056 restraints weight = 66031.146| |-----------------------------------------------------------------------------| r_work (start): 0.3180 rms_B_bonded: 4.05 r_work: 0.3032 rms_B_bonded: 4.28 restraints_weight: 0.5000 r_work (final): 0.3032 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8426 moved from start: 0.1738 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 21613 Z= 0.110 Angle : 0.663 16.622 29558 Z= 0.304 Chirality : 0.045 0.282 3622 Planarity : 0.003 0.040 3497 Dihedral : 8.001 57.029 5506 Min Nonbonded Distance : 2.460 Molprobity Statistics. All-atom Clashscore : 3.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.56 % Favored : 97.44 % Rotamer: Outliers : 1.51 % Allowed : 11.46 % Favored : 87.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % 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: -0.79 (0.17), residues: 2385 helix: -0.26 (0.26), residues: 426 sheet: -0.38 (0.20), residues: 612 loop : -0.61 (0.16), residues: 1347 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG L 61 TYR 0.020 0.001 TYR L 49 PHE 0.008 0.001 PHE I 100C TRP 0.014 0.001 TRP g 631 HIS 0.002 0.000 HIS f 374 Details of bonding type rmsd covalent geometry : bond 0.00226 (21432) covalent geometry : angle 0.59189 (29057) SS BOND : bond 0.00248 ( 42) SS BOND : angle 0.83476 ( 84) hydrogen bonds : bond 0.04124 ( 694) hydrogen bonds : angle 5.54110 ( 1914) link_ALPHA1-2 : bond 0.00724 ( 3) link_ALPHA1-2 : angle 1.63045 ( 9) link_ALPHA1-3 : bond 0.01161 ( 6) link_ALPHA1-3 : angle 1.32787 ( 18) link_ALPHA1-6 : bond 0.01037 ( 12) link_ALPHA1-6 : angle 1.59634 ( 36) link_BETA1-4 : bond 0.00665 ( 51) link_BETA1-4 : angle 2.94471 ( 153) link_NAG-ASN : bond 0.00335 ( 67) link_NAG-ASN : angle 2.54106 ( 201) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4770 Ramachandran restraints generated. 2385 Oldfield, 0 Emsley, 2385 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4770 Ramachandran restraints generated. 2385 Oldfield, 0 Emsley, 2385 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 233 residues out of total 2121 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 201 time to evaluate : 0.805 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 75 LYS cc_start: 0.9625 (mtmm) cc_final: 0.9371 (mtmm) REVERT: H 82 MET cc_start: 0.8709 (mtm) cc_final: 0.8471 (mtm) REVERT: H 83 ARG cc_start: 0.8182 (mpp80) cc_final: 0.7926 (mpp80) REVERT: H 100 LEU cc_start: 0.9143 (OUTLIER) cc_final: 0.8922 (mp) REVERT: L 24 GLN cc_start: 0.8788 (mt0) cc_final: 0.8187 (tp40) REVERT: L 69 THR cc_start: 0.9203 (m) cc_final: 0.8847 (m) REVERT: L 103 GLU cc_start: 0.7376 (tm-30) cc_final: 0.7113 (tm-30) REVERT: c 620 ASP cc_start: 0.9058 (t0) cc_final: 0.8631 (p0) REVERT: c 654 GLU cc_start: 0.8222 (mm-30) cc_final: 0.7722 (mm-30) REVERT: I 72 ASP cc_start: 0.8038 (t0) cc_final: 0.7357 (t0) REVERT: I 75 LYS cc_start: 0.9637 (mtpp) cc_final: 0.9248 (mtmm) REVERT: I 83 ARG cc_start: 0.8192 (mpp80) cc_final: 0.7905 (mpp80) REVERT: M 92 ASP cc_start: 0.7506 (OUTLIER) cc_final: 0.6988 (m-30) REVERT: M 103 GLU cc_start: 0.7417 (tm-30) cc_final: 0.7088 (tm-30) REVERT: e 632 ASP cc_start: 0.8817 (t70) cc_final: 0.8606 (t0) REVERT: e 654 GLU cc_start: 0.8301 (mm-30) cc_final: 0.7856 (mm-30) REVERT: N 17 ASP cc_start: 0.8213 (t0) cc_final: 0.7933 (t0) REVERT: N 33 LEU cc_start: 0.9249 (OUTLIER) cc_final: 0.8991 (tp) REVERT: N 103 GLU cc_start: 0.7415 (tm-30) cc_final: 0.7013 (tm-30) REVERT: g 621 GLU cc_start: 0.8689 (pt0) cc_final: 0.8295 (pp20) outliers start: 32 outliers final: 13 residues processed: 229 average time/residue: 0.1636 time to fit residues: 56.6325 Evaluate side-chains 193 residues out of total 2121 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 177 time to evaluate : 0.791 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 11 LEU Chi-restraints excluded: chain H residue 100 LEU Chi-restraints excluded: chain L residue 73 LEU Chi-restraints excluded: chain b residue 286 VAL Chi-restraints excluded: chain M residue 58 VAL Chi-restraints excluded: chain M residue 92 ASP Chi-restraints excluded: chain d residue 125 LEU Chi-restraints excluded: chain d residue 286 VAL Chi-restraints excluded: chain d residue 452 LEU Chi-restraints excluded: chain J residue 11 LEU Chi-restraints excluded: chain J residue 43 LYS Chi-restraints excluded: chain N residue 33 LEU Chi-restraints excluded: chain f residue 50 THR Chi-restraints excluded: chain f residue 125 LEU Chi-restraints excluded: chain f residue 286 VAL Chi-restraints excluded: chain g residue 535 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 237 random chunks: chunk 65 optimal weight: 0.7980 chunk 127 optimal weight: 1.9990 chunk 13 optimal weight: 0.9990 chunk 80 optimal weight: 1.9990 chunk 72 optimal weight: 0.6980 chunk 74 optimal weight: 9.9990 chunk 213 optimal weight: 0.6980 chunk 48 optimal weight: 5.9990 chunk 133 optimal weight: 10.0000 chunk 226 optimal weight: 3.9990 chunk 132 optimal weight: 9.9990 overall best weight: 1.0384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: b 330 HIS d 330 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3640 r_free = 0.3640 target = 0.075929 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3265 r_free = 0.3265 target = 0.058650 restraints weight = 66440.038| |-----------------------------------------------------------------------------| r_work (start): 0.3156 rms_B_bonded: 4.05 r_work: 0.3006 rms_B_bonded: 4.29 restraints_weight: 0.5000 r_work (final): 0.3006 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8439 moved from start: 0.1968 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 21613 Z= 0.120 Angle : 0.650 16.436 29558 Z= 0.297 Chirality : 0.045 0.277 3622 Planarity : 0.003 0.054 3497 Dihedral : 7.743 59.702 5506 Min Nonbonded Distance : 2.450 Molprobity Statistics. All-atom Clashscore : 3.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.39 % Favored : 97.61 % Rotamer: Outliers : 1.89 % Allowed : 11.69 % Favored : 86.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % 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: -0.72 (0.17), residues: 2385 helix: -0.14 (0.26), residues: 426 sheet: -0.25 (0.21), residues: 570 loop : -0.62 (0.16), residues: 1389 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG L 61 TYR 0.038 0.001 TYR L 49 PHE 0.010 0.001 PHE I 100C TRP 0.010 0.001 TRP e 631 HIS 0.003 0.001 HIS f 374 Details of bonding type rmsd covalent geometry : bond 0.00266 (21432) covalent geometry : angle 0.57948 (29057) SS BOND : bond 0.00235 ( 42) SS BOND : angle 0.94721 ( 84) hydrogen bonds : bond 0.03730 ( 694) hydrogen bonds : angle 5.28125 ( 1914) link_ALPHA1-2 : bond 0.00649 ( 3) link_ALPHA1-2 : angle 1.61199 ( 9) link_ALPHA1-3 : bond 0.01065 ( 6) link_ALPHA1-3 : angle 1.47641 ( 18) link_ALPHA1-6 : bond 0.00977 ( 12) link_ALPHA1-6 : angle 1.58916 ( 36) link_BETA1-4 : bond 0.00626 ( 51) link_BETA1-4 : angle 2.84130 ( 153) link_NAG-ASN : bond 0.00316 ( 67) link_NAG-ASN : angle 2.49573 ( 201) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4770 Ramachandran restraints generated. 2385 Oldfield, 0 Emsley, 2385 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4770 Ramachandran restraints generated. 2385 Oldfield, 0 Emsley, 2385 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 235 residues out of total 2121 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 195 time to evaluate : 0.734 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 75 LYS cc_start: 0.9626 (mtmm) cc_final: 0.9371 (mtmm) REVERT: H 83 ARG cc_start: 0.8198 (mpp80) cc_final: 0.7939 (mpp80) REVERT: L 24 GLN cc_start: 0.8821 (mt0) cc_final: 0.8203 (tp40) REVERT: L 69 THR cc_start: 0.9178 (m) cc_final: 0.8812 (m) REVERT: L 79 GLN cc_start: 0.7956 (mm110) cc_final: 0.7700 (mm110) REVERT: L 103 GLU cc_start: 0.7375 (tm-30) cc_final: 0.7156 (tm-30) REVERT: c 654 GLU cc_start: 0.8220 (mm-30) cc_final: 0.7817 (mm-30) REVERT: I 72 ASP cc_start: 0.8140 (t0) cc_final: 0.7510 (t0) REVERT: I 75 LYS cc_start: 0.9638 (OUTLIER) cc_final: 0.9232 (mtmm) REVERT: I 83 ARG cc_start: 0.8256 (mpp80) cc_final: 0.7969 (mpp80) REVERT: I 100 LYS cc_start: 0.8456 (mmmt) cc_final: 0.8064 (mppt) REVERT: I 102 TYR cc_start: 0.8223 (m-80) cc_final: 0.7992 (m-80) REVERT: M 55 GLU cc_start: 0.8327 (tt0) cc_final: 0.7984 (tt0) REVERT: M 92 ASP cc_start: 0.7945 (OUTLIER) cc_final: 0.7110 (m-30) REVERT: M 103 GLU cc_start: 0.7401 (tm-30) cc_final: 0.7024 (tm-30) REVERT: N 17 ASP cc_start: 0.8216 (t0) cc_final: 0.7910 (t0) REVERT: N 79 GLN cc_start: 0.8039 (mm-40) cc_final: 0.7798 (mp10) REVERT: N 103 GLU cc_start: 0.7514 (tm-30) cc_final: 0.7183 (tm-30) REVERT: g 536 THR cc_start: 0.9154 (p) cc_final: 0.8923 (t) REVERT: g 621 GLU cc_start: 0.8756 (pt0) cc_final: 0.8384 (pp20) outliers start: 40 outliers final: 20 residues processed: 223 average time/residue: 0.1541 time to fit residues: 52.4034 Evaluate side-chains 196 residues out of total 2121 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 174 time to evaluate : 0.750 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 11 LEU Chi-restraints excluded: chain H residue 13 THR Chi-restraints excluded: chain H residue 37 VAL Chi-restraints excluded: chain L residue 58 VAL Chi-restraints excluded: chain L residue 73 LEU Chi-restraints excluded: chain b residue 286 VAL Chi-restraints excluded: chain I residue 4 LEU Chi-restraints excluded: chain I residue 13 THR Chi-restraints excluded: chain I residue 75 LYS Chi-restraints excluded: chain M residue 58 VAL Chi-restraints excluded: chain M residue 92 ASP Chi-restraints excluded: chain d residue 125 LEU Chi-restraints excluded: chain d residue 286 VAL Chi-restraints excluded: chain d residue 452 LEU Chi-restraints excluded: chain d residue 488 VAL Chi-restraints excluded: chain J residue 11 LEU Chi-restraints excluded: chain J residue 13 THR Chi-restraints excluded: chain J residue 37 VAL Chi-restraints excluded: chain J residue 100 LEU Chi-restraints excluded: chain f residue 50 THR Chi-restraints excluded: chain f residue 286 VAL Chi-restraints excluded: chain g residue 535 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 237 random chunks: chunk 152 optimal weight: 4.9990 chunk 14 optimal weight: 9.9990 chunk 151 optimal weight: 0.6980 chunk 198 optimal weight: 0.1980 chunk 124 optimal weight: 0.9990 chunk 59 optimal weight: 7.9990 chunk 21 optimal weight: 0.9990 chunk 95 optimal weight: 7.9990 chunk 221 optimal weight: 9.9990 chunk 75 optimal weight: 0.6980 chunk 139 optimal weight: 0.0060 overall best weight: 0.5198 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** N 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3655 r_free = 0.3655 target = 0.076589 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3284 r_free = 0.3284 target = 0.059390 restraints weight = 65680.145| |-----------------------------------------------------------------------------| r_work (start): 0.3186 rms_B_bonded: 4.05 r_work: 0.3039 rms_B_bonded: 4.28 restraints_weight: 0.5000 r_work (final): 0.3039 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8419 moved from start: 0.2130 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 21613 Z= 0.101 Angle : 0.628 16.258 29558 Z= 0.287 Chirality : 0.045 0.284 3622 Planarity : 0.003 0.041 3497 Dihedral : 7.435 56.445 5506 Min Nonbonded Distance : 2.445 Molprobity Statistics. All-atom Clashscore : 3.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.43 % Favored : 97.57 % Rotamer: Outliers : 1.79 % Allowed : 12.07 % Favored : 86.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % 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: -0.51 (0.17), residues: 2385 helix: 0.04 (0.27), residues: 420 sheet: -0.15 (0.20), residues: 612 loop : -0.47 (0.16), residues: 1353 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG L 61 TYR 0.029 0.001 TYR L 49 PHE 0.014 0.001 PHE M 71 TRP 0.015 0.001 TRP g 631 HIS 0.002 0.000 HIS f 374 Details of bonding type rmsd covalent geometry : bond 0.00211 (21432) covalent geometry : angle 0.56180 (29057) SS BOND : bond 0.00242 ( 42) SS BOND : angle 0.77397 ( 84) hydrogen bonds : bond 0.03455 ( 694) hydrogen bonds : angle 5.12524 ( 1914) link_ALPHA1-2 : bond 0.00688 ( 3) link_ALPHA1-2 : angle 1.62262 ( 9) link_ALPHA1-3 : bond 0.01108 ( 6) link_ALPHA1-3 : angle 1.33070 ( 18) link_ALPHA1-6 : bond 0.01058 ( 12) link_ALPHA1-6 : angle 1.55904 ( 36) link_BETA1-4 : bond 0.00641 ( 51) link_BETA1-4 : angle 2.74791 ( 153) link_NAG-ASN : bond 0.00326 ( 67) link_NAG-ASN : angle 2.39495 ( 201) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4770 Ramachandran restraints generated. 2385 Oldfield, 0 Emsley, 2385 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4770 Ramachandran restraints generated. 2385 Oldfield, 0 Emsley, 2385 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 235 residues out of total 2121 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 197 time to evaluate : 0.849 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 75 LYS cc_start: 0.9625 (mtmm) cc_final: 0.9362 (mtmm) REVERT: H 83 ARG cc_start: 0.8198 (mpp80) cc_final: 0.7935 (mpp80) REVERT: L 81 GLU cc_start: 0.8651 (pm20) cc_final: 0.8303 (pm20) REVERT: c 620 ASP cc_start: 0.8996 (t0) cc_final: 0.8597 (p0) REVERT: c 654 GLU cc_start: 0.8211 (mm-30) cc_final: 0.7808 (mm-30) REVERT: I 72 ASP cc_start: 0.8130 (t0) cc_final: 0.7608 (t0) REVERT: I 75 LYS cc_start: 0.9639 (OUTLIER) cc_final: 0.9218 (mtmm) REVERT: I 83 ARG cc_start: 0.8217 (mpp80) cc_final: 0.7928 (mpp80) REVERT: I 100 LYS cc_start: 0.8428 (mmmt) cc_final: 0.8094 (mppt) REVERT: M 55 GLU cc_start: 0.8180 (tt0) cc_final: 0.7843 (tt0) REVERT: M 92 ASP cc_start: 0.7921 (OUTLIER) cc_final: 0.7113 (m-30) REVERT: M 103 GLU cc_start: 0.7397 (tm-30) cc_final: 0.6928 (tm-30) REVERT: N 17 ASP cc_start: 0.8201 (t0) cc_final: 0.7901 (t0) REVERT: g 536 THR cc_start: 0.9127 (p) cc_final: 0.8913 (t) REVERT: g 621 GLU cc_start: 0.8727 (pt0) cc_final: 0.8367 (pp20) REVERT: g 639 THR cc_start: 0.8308 (m) cc_final: 0.8055 (m) outliers start: 38 outliers final: 22 residues processed: 225 average time/residue: 0.1560 time to fit residues: 54.1812 Evaluate side-chains 202 residues out of total 2121 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 178 time to evaluate : 0.663 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 11 LEU Chi-restraints excluded: chain H residue 13 THR Chi-restraints excluded: chain H residue 37 VAL Chi-restraints excluded: chain H residue 107 VAL Chi-restraints excluded: chain L residue 55 GLU Chi-restraints excluded: chain L residue 58 VAL Chi-restraints excluded: chain L residue 73 LEU Chi-restraints excluded: chain b residue 259 LEU Chi-restraints excluded: chain b residue 286 VAL Chi-restraints excluded: chain b residue 488 VAL Chi-restraints excluded: chain I residue 13 THR Chi-restraints excluded: chain I residue 75 LYS Chi-restraints excluded: chain M residue 58 VAL Chi-restraints excluded: chain M residue 92 ASP Chi-restraints excluded: chain d residue 125 LEU Chi-restraints excluded: chain d residue 286 VAL Chi-restraints excluded: chain d residue 452 LEU Chi-restraints excluded: chain d residue 488 VAL Chi-restraints excluded: chain J residue 11 LEU Chi-restraints excluded: chain J residue 13 THR Chi-restraints excluded: chain J residue 43 LYS Chi-restraints excluded: chain f residue 50 THR Chi-restraints excluded: chain f residue 286 VAL Chi-restraints excluded: chain g residue 535 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 237 random chunks: chunk 169 optimal weight: 3.9990 chunk 153 optimal weight: 9.9990 chunk 116 optimal weight: 1.9990 chunk 176 optimal weight: 7.9990 chunk 223 optimal weight: 3.9990 chunk 69 optimal weight: 0.9980 chunk 45 optimal weight: 8.9990 chunk 189 optimal weight: 8.9990 chunk 48 optimal weight: 7.9990 chunk 154 optimal weight: 10.0000 chunk 140 optimal weight: 0.0030 overall best weight: 2.1996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L 24 GLN ** c 540 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** f 72 HIS f 330 HIS ** g 540 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 = 0.3611 r_free = 0.3611 target = 0.074626 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3228 r_free = 0.3228 target = 0.057292 restraints weight = 65802.207| |-----------------------------------------------------------------------------| r_work (start): 0.3117 rms_B_bonded: 4.03 r_work: 0.2966 rms_B_bonded: 4.23 restraints_weight: 0.5000 r_work (final): 0.2966 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8477 moved from start: 0.2298 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 21613 Z= 0.185 Angle : 0.675 16.122 29558 Z= 0.313 Chirality : 0.046 0.280 3622 Planarity : 0.003 0.043 3497 Dihedral : 7.485 58.570 5506 Min Nonbonded Distance : 2.434 Molprobity Statistics. All-atom Clashscore : 4.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.89 % Favored : 97.11 % Rotamer: Outliers : 1.93 % Allowed : 12.59 % Favored : 85.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % 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: -0.64 (0.17), residues: 2385 helix: -0.02 (0.27), residues: 420 sheet: -0.20 (0.20), residues: 594 loop : -0.59 (0.16), residues: 1371 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG L 61 TYR 0.030 0.001 TYR N 49 PHE 0.013 0.001 PHE I 100C TRP 0.010 0.001 TRP d 338 HIS 0.003 0.001 HIS f 374 Details of bonding type rmsd covalent geometry : bond 0.00430 (21432) covalent geometry : angle 0.61174 (29057) SS BOND : bond 0.00282 ( 42) SS BOND : angle 0.94098 ( 84) hydrogen bonds : bond 0.03775 ( 694) hydrogen bonds : angle 5.19133 ( 1914) link_ALPHA1-2 : bond 0.00623 ( 3) link_ALPHA1-2 : angle 1.51436 ( 9) link_ALPHA1-3 : bond 0.00925 ( 6) link_ALPHA1-3 : angle 1.42932 ( 18) link_ALPHA1-6 : bond 0.00898 ( 12) link_ALPHA1-6 : angle 1.58686 ( 36) link_BETA1-4 : bond 0.00588 ( 51) link_BETA1-4 : angle 2.72908 ( 153) link_NAG-ASN : bond 0.00351 ( 67) link_NAG-ASN : angle 2.49512 ( 201) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4770 Ramachandran restraints generated. 2385 Oldfield, 0 Emsley, 2385 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4770 Ramachandran restraints generated. 2385 Oldfield, 0 Emsley, 2385 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 224 residues out of total 2121 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 183 time to evaluate : 0.598 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 75 LYS cc_start: 0.9626 (mtmm) cc_final: 0.9274 (mtmm) REVERT: H 83 ARG cc_start: 0.8244 (mpp80) cc_final: 0.7972 (mpp80) REVERT: L 81 GLU cc_start: 0.8571 (pm20) cc_final: 0.8273 (pm20) REVERT: I 72 ASP cc_start: 0.8211 (t0) cc_final: 0.7551 (t0) REVERT: I 75 LYS cc_start: 0.9653 (OUTLIER) cc_final: 0.9187 (mtmm) REVERT: I 83 ARG cc_start: 0.8254 (mpp80) cc_final: 0.7954 (mpp80) REVERT: I 100 LYS cc_start: 0.8690 (mmmt) cc_final: 0.8293 (mppt) REVERT: I 105 GLN cc_start: 0.8286 (mm110) cc_final: 0.7960 (tp-100) REVERT: M 55 GLU cc_start: 0.8130 (tt0) cc_final: 0.7832 (tt0) REVERT: M 92 ASP cc_start: 0.8062 (OUTLIER) cc_final: 0.7284 (m-30) REVERT: M 103 GLU cc_start: 0.7518 (tm-30) cc_final: 0.6996 (tm-30) REVERT: e 601 LYS cc_start: 0.8877 (mttm) cc_final: 0.8372 (mtmt) REVERT: e 648 GLU cc_start: 0.8749 (OUTLIER) cc_final: 0.8368 (pm20) REVERT: J 100 LEU cc_start: 0.9229 (OUTLIER) cc_final: 0.9021 (mp) REVERT: N 17 ASP cc_start: 0.8172 (t0) cc_final: 0.7872 (t0) REVERT: g 536 THR cc_start: 0.9148 (p) cc_final: 0.8913 (t) REVERT: g 621 GLU cc_start: 0.8846 (pt0) cc_final: 0.8467 (pp20) outliers start: 41 outliers final: 25 residues processed: 215 average time/residue: 0.1641 time to fit residues: 53.5721 Evaluate side-chains 197 residues out of total 2121 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 168 time to evaluate : 0.753 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 11 LEU Chi-restraints excluded: chain H residue 13 THR Chi-restraints excluded: chain H residue 37 VAL Chi-restraints excluded: chain H residue 107 VAL Chi-restraints excluded: chain H residue 111 VAL Chi-restraints excluded: chain L residue 55 GLU Chi-restraints excluded: chain L residue 58 VAL Chi-restraints excluded: chain L residue 73 LEU Chi-restraints excluded: chain b residue 120 VAL Chi-restraints excluded: chain b residue 286 VAL Chi-restraints excluded: chain b residue 488 VAL Chi-restraints excluded: chain I residue 13 THR Chi-restraints excluded: chain I residue 75 LYS Chi-restraints excluded: chain I residue 107 VAL Chi-restraints excluded: chain M residue 58 VAL Chi-restraints excluded: chain M residue 92 ASP 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 d residue 488 VAL Chi-restraints excluded: chain e residue 648 GLU Chi-restraints excluded: chain J residue 11 LEU Chi-restraints excluded: chain J residue 13 THR Chi-restraints excluded: chain J residue 37 VAL Chi-restraints excluded: chain J residue 100 LEU Chi-restraints excluded: chain N residue 104 VAL Chi-restraints excluded: chain f residue 125 LEU Chi-restraints excluded: chain f residue 286 VAL Chi-restraints excluded: chain g residue 535 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 237 random chunks: chunk 158 optimal weight: 10.0000 chunk 201 optimal weight: 2.9990 chunk 93 optimal weight: 9.9990 chunk 75 optimal weight: 0.7980 chunk 13 optimal weight: 7.9990 chunk 150 optimal weight: 0.9980 chunk 231 optimal weight: 0.9990 chunk 61 optimal weight: 0.0670 chunk 198 optimal weight: 0.8980 chunk 133 optimal weight: 10.0000 chunk 94 optimal weight: 7.9990 overall best weight: 0.7520 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L 24 GLN ** c 540 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3641 r_free = 0.3641 target = 0.075999 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3267 r_free = 0.3267 target = 0.058803 restraints weight = 65810.886| |-----------------------------------------------------------------------------| r_work (start): 0.3175 rms_B_bonded: 4.05 r_work: 0.3032 rms_B_bonded: 4.23 restraints_weight: 0.5000 r_work (final): 0.3032 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8434 moved from start: 0.2420 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.039 21613 Z= 0.106 Angle : 0.619 16.155 29558 Z= 0.286 Chirality : 0.044 0.286 3622 Planarity : 0.003 0.045 3497 Dihedral : 7.208 59.605 5506 Min Nonbonded Distance : 2.438 Molprobity Statistics. All-atom Clashscore : 3.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.31 % Favored : 97.69 % Rotamer: Outliers : 2.07 % Allowed : 12.78 % Favored : 85.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.44 (0.17), residues: 2385 helix: 0.03 (0.27), residues: 429 sheet: -0.14 (0.20), residues: 642 loop : -0.39 (0.17), residues: 1314 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG L 61 TYR 0.029 0.001 TYR L 49 PHE 0.010 0.001 PHE I 100C TRP 0.011 0.001 TRP J 47 HIS 0.003 0.000 HIS b 374 Details of bonding type rmsd covalent geometry : bond 0.00230 (21432) covalent geometry : angle 0.55655 (29057) SS BOND : bond 0.00225 ( 42) SS BOND : angle 0.73958 ( 84) hydrogen bonds : bond 0.03369 ( 694) hydrogen bonds : angle 4.99802 ( 1914) link_ALPHA1-2 : bond 0.00714 ( 3) link_ALPHA1-2 : angle 1.62415 ( 9) link_ALPHA1-3 : bond 0.01044 ( 6) link_ALPHA1-3 : angle 1.22305 ( 18) link_ALPHA1-6 : bond 0.00992 ( 12) link_ALPHA1-6 : angle 1.43062 ( 36) link_BETA1-4 : bond 0.00637 ( 51) link_BETA1-4 : angle 2.64400 ( 153) link_NAG-ASN : bond 0.00324 ( 67) link_NAG-ASN : angle 2.33456 ( 201) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4770 Ramachandran restraints generated. 2385 Oldfield, 0 Emsley, 2385 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4770 Ramachandran restraints generated. 2385 Oldfield, 0 Emsley, 2385 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 235 residues out of total 2121 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 191 time to evaluate : 0.787 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 75 LYS cc_start: 0.9621 (mtmm) cc_final: 0.9265 (mtmm) REVERT: H 83 ARG cc_start: 0.8221 (mpp80) cc_final: 0.7953 (mpp80) REVERT: L 24 GLN cc_start: 0.8730 (tt0) cc_final: 0.8268 (mm110) REVERT: L 49 TYR cc_start: 0.8096 (p90) cc_final: 0.7816 (p90) REVERT: L 79 GLN cc_start: 0.8133 (mm110) cc_final: 0.7793 (mp10) REVERT: L 81 GLU cc_start: 0.8548 (pm20) cc_final: 0.8267 (pm20) REVERT: c 620 ASP cc_start: 0.8975 (t0) cc_final: 0.8589 (p0) REVERT: c 621 GLU cc_start: 0.8859 (pt0) cc_final: 0.8643 (pp20) REVERT: I 72 ASP cc_start: 0.8185 (t0) cc_final: 0.7677 (t0) REVERT: I 75 LYS cc_start: 0.9644 (OUTLIER) cc_final: 0.9219 (mtmm) REVERT: I 83 ARG cc_start: 0.8210 (mpp80) cc_final: 0.7912 (mpp80) REVERT: I 100 LYS cc_start: 0.8668 (mmmt) cc_final: 0.8292 (mppt) REVERT: M 92 ASP cc_start: 0.8046 (OUTLIER) cc_final: 0.7216 (m-30) REVERT: M 103 GLU cc_start: 0.7462 (tm-30) cc_final: 0.7124 (tm-30) REVERT: e 601 LYS cc_start: 0.8839 (mttm) cc_final: 0.8530 (mtmt) REVERT: e 644 ARG cc_start: 0.8868 (mmp80) cc_final: 0.8474 (mmp80) REVERT: e 648 GLU cc_start: 0.8695 (OUTLIER) cc_final: 0.8199 (pm20) REVERT: N 17 ASP cc_start: 0.8208 (t0) cc_final: 0.7962 (t0) REVERT: g 536 THR cc_start: 0.9146 (p) cc_final: 0.8914 (t) REVERT: g 621 GLU cc_start: 0.8817 (pt0) cc_final: 0.8471 (pp20) outliers start: 44 outliers final: 29 residues processed: 224 average time/residue: 0.1674 time to fit residues: 56.3002 Evaluate side-chains 207 residues out of total 2121 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 175 time to evaluate : 0.849 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 11 LEU Chi-restraints excluded: chain H residue 13 THR Chi-restraints excluded: chain H residue 37 VAL Chi-restraints excluded: chain H residue 43 LYS Chi-restraints excluded: chain H residue 107 VAL Chi-restraints excluded: chain L residue 58 VAL Chi-restraints excluded: chain L residue 73 LEU Chi-restraints excluded: chain b residue 120 VAL Chi-restraints excluded: chain b residue 259 LEU Chi-restraints excluded: chain b residue 286 VAL Chi-restraints excluded: chain b residue 445 CYS Chi-restraints excluded: chain b residue 488 VAL Chi-restraints excluded: chain I residue 13 THR Chi-restraints excluded: chain I residue 75 LYS Chi-restraints excluded: chain I residue 107 VAL Chi-restraints excluded: chain M residue 58 VAL Chi-restraints excluded: chain M residue 92 ASP Chi-restraints excluded: chain d residue 120 VAL Chi-restraints excluded: chain d residue 125 LEU Chi-restraints excluded: chain d residue 242 VAL Chi-restraints excluded: chain d residue 286 VAL Chi-restraints excluded: chain d residue 488 VAL Chi-restraints excluded: chain e residue 648 GLU Chi-restraints excluded: chain J residue 11 LEU Chi-restraints excluded: chain J residue 13 THR Chi-restraints excluded: chain J residue 37 VAL Chi-restraints excluded: chain J residue 43 LYS Chi-restraints excluded: chain J residue 107 VAL Chi-restraints excluded: chain J residue 111 VAL Chi-restraints excluded: chain N residue 104 VAL Chi-restraints excluded: chain f residue 286 VAL Chi-restraints excluded: chain g residue 535 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 237 random chunks: chunk 196 optimal weight: 7.9990 chunk 136 optimal weight: 7.9990 chunk 27 optimal weight: 1.9990 chunk 8 optimal weight: 9.9990 chunk 227 optimal weight: 4.9990 chunk 125 optimal weight: 0.0770 chunk 46 optimal weight: 0.6980 chunk 18 optimal weight: 3.9990 chunk 51 optimal weight: 3.9990 chunk 175 optimal weight: 5.9990 chunk 98 optimal weight: 10.0000 overall best weight: 2.1544 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** c 540 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 100 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** d 72 HIS ** N 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 540 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3610 r_free = 0.3610 target = 0.074538 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3231 r_free = 0.3231 target = 0.057335 restraints weight = 65883.330| |-----------------------------------------------------------------------------| r_work (start): 0.3143 rms_B_bonded: 4.01 r_work: 0.2997 rms_B_bonded: 4.19 restraints_weight: 0.5000 r_work (final): 0.2997 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8480 moved from start: 0.2516 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 21613 Z= 0.181 Angle : 0.656 16.006 29558 Z= 0.305 Chirality : 0.045 0.283 3622 Planarity : 0.003 0.043 3497 Dihedral : 7.274 59.909 5506 Min Nonbonded Distance : 2.429 Molprobity Statistics. All-atom Clashscore : 4.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.10 % Favored : 96.90 % Rotamer: Outliers : 1.65 % Allowed : 13.44 % Favored : 84.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % 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: -0.45 (0.17), residues: 2385 helix: 0.13 (0.27), residues: 420 sheet: -0.14 (0.20), residues: 669 loop : -0.43 (0.17), residues: 1296 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG e 519 TYR 0.027 0.001 TYR N 49 PHE 0.012 0.001 PHE I 100C TRP 0.010 0.001 TRP f 96 HIS 0.003 0.001 HIS f 374 Details of bonding type rmsd covalent geometry : bond 0.00424 (21432) covalent geometry : angle 0.59463 (29057) SS BOND : bond 0.00290 ( 42) SS BOND : angle 0.85302 ( 84) hydrogen bonds : bond 0.03643 ( 694) hydrogen bonds : angle 5.05914 ( 1914) link_ALPHA1-2 : bond 0.00630 ( 3) link_ALPHA1-2 : angle 1.50230 ( 9) link_ALPHA1-3 : bond 0.00879 ( 6) link_ALPHA1-3 : angle 1.32747 ( 18) link_ALPHA1-6 : bond 0.00891 ( 12) link_ALPHA1-6 : angle 1.44934 ( 36) link_BETA1-4 : bond 0.00584 ( 51) link_BETA1-4 : angle 2.62550 ( 153) link_NAG-ASN : bond 0.00340 ( 67) link_NAG-ASN : angle 2.43417 ( 201) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4770 Ramachandran restraints generated. 2385 Oldfield, 0 Emsley, 2385 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4770 Ramachandran restraints generated. 2385 Oldfield, 0 Emsley, 2385 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 218 residues out of total 2121 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 183 time to evaluate : 0.634 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 83 ARG cc_start: 0.8204 (mpp80) cc_final: 0.7925 (mpp80) REVERT: L 24 GLN cc_start: 0.8746 (tt0) cc_final: 0.8297 (mm110) REVERT: L 79 GLN cc_start: 0.8083 (mm110) cc_final: 0.7757 (mp10) REVERT: L 81 GLU cc_start: 0.8550 (pm20) cc_final: 0.8274 (pm20) REVERT: I 72 ASP cc_start: 0.8196 (t0) cc_final: 0.7663 (t0) REVERT: I 75 LYS cc_start: 0.9650 (OUTLIER) cc_final: 0.9186 (mtmm) REVERT: I 83 ARG cc_start: 0.8240 (mpp80) cc_final: 0.7935 (mpp80) REVERT: I 100 LYS cc_start: 0.8759 (mmmt) cc_final: 0.8392 (mppt) REVERT: I 105 GLN cc_start: 0.8315 (mm110) cc_final: 0.7980 (tp-100) REVERT: M 92 ASP cc_start: 0.8161 (OUTLIER) cc_final: 0.7369 (m-30) REVERT: e 601 LYS cc_start: 0.8834 (mttm) cc_final: 0.8513 (mtmt) REVERT: e 644 ARG cc_start: 0.8908 (mmp80) cc_final: 0.8554 (mmp80) REVERT: e 648 GLU cc_start: 0.8731 (OUTLIER) cc_final: 0.8329 (pm20) REVERT: N 4 MET cc_start: 0.8500 (mmm) cc_final: 0.8293 (mtp) REVERT: N 17 ASP cc_start: 0.8171 (t0) cc_final: 0.7900 (t0) REVERT: g 536 THR cc_start: 0.9149 (p) cc_final: 0.8915 (t) REVERT: g 601 LYS cc_start: 0.8841 (mttm) cc_final: 0.8354 (mtmt) outliers start: 35 outliers final: 28 residues processed: 211 average time/residue: 0.1519 time to fit residues: 48.4247 Evaluate side-chains 211 residues out of total 2121 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 180 time to evaluate : 0.673 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 11 LEU Chi-restraints excluded: chain H residue 13 THR Chi-restraints excluded: chain H residue 37 VAL Chi-restraints excluded: chain H residue 107 VAL Chi-restraints excluded: chain H residue 111 VAL Chi-restraints excluded: chain L residue 58 VAL Chi-restraints excluded: chain L residue 73 LEU Chi-restraints excluded: chain b residue 120 VAL Chi-restraints excluded: chain b residue 213 ILE Chi-restraints excluded: chain b residue 286 VAL Chi-restraints excluded: chain b residue 488 VAL Chi-restraints excluded: chain I residue 13 THR Chi-restraints excluded: chain I residue 75 LYS Chi-restraints excluded: chain I residue 107 VAL Chi-restraints excluded: chain M residue 58 VAL Chi-restraints excluded: chain M residue 92 ASP 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 d residue 488 VAL Chi-restraints excluded: chain e residue 648 GLU Chi-restraints excluded: chain J residue 11 LEU Chi-restraints excluded: chain J residue 13 THR Chi-restraints excluded: chain J residue 37 VAL Chi-restraints excluded: chain J residue 107 VAL Chi-restraints excluded: chain J residue 111 VAL Chi-restraints excluded: chain N residue 104 VAL Chi-restraints excluded: chain f residue 120 VAL Chi-restraints excluded: chain f residue 125 LEU Chi-restraints excluded: chain f residue 286 VAL Chi-restraints excluded: chain g residue 535 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 237 random chunks: chunk 109 optimal weight: 0.9990 chunk 203 optimal weight: 8.9990 chunk 157 optimal weight: 1.9990 chunk 63 optimal weight: 10.0000 chunk 57 optimal weight: 6.9990 chunk 97 optimal weight: 10.0000 chunk 150 optimal weight: 0.9980 chunk 223 optimal weight: 0.9980 chunk 11 optimal weight: 2.9990 chunk 19 optimal weight: 0.9990 chunk 185 optimal weight: 1.9990 overall best weight: 1.1986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: b 72 HIS ** c 540 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 100 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 540 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3627 r_free = 0.3627 target = 0.075271 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3252 r_free = 0.3252 target = 0.058130 restraints weight = 65622.661| |-----------------------------------------------------------------------------| r_work (start): 0.3167 rms_B_bonded: 4.03 r_work: 0.3018 rms_B_bonded: 4.22 restraints_weight: 0.5000 r_work (final): 0.3018 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8458 moved from start: 0.2598 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 21613 Z= 0.124 Angle : 0.624 16.049 29558 Z= 0.291 Chirality : 0.044 0.286 3622 Planarity : 0.003 0.043 3497 Dihedral : 7.096 57.015 5506 Min Nonbonded Distance : 2.439 Molprobity Statistics. All-atom Clashscore : 4.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.85 % Favored : 97.15 % Rotamer: Outliers : 1.65 % Allowed : 13.44 % Favored : 84.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.35 (0.17), residues: 2385 helix: 0.08 (0.27), residues: 429 sheet: -0.04 (0.20), residues: 645 loop : -0.35 (0.17), residues: 1311 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG c 644 TYR 0.033 0.001 TYR L 49 PHE 0.011 0.001 PHE I 100C TRP 0.010 0.001 TRP J 47 HIS 0.003 0.001 HIS d 374 Details of bonding type rmsd covalent geometry : bond 0.00280 (21432) covalent geometry : angle 0.56409 (29057) SS BOND : bond 0.00257 ( 42) SS BOND : angle 0.75181 ( 84) hydrogen bonds : bond 0.03432 ( 694) hydrogen bonds : angle 4.98667 ( 1914) link_ALPHA1-2 : bond 0.00688 ( 3) link_ALPHA1-2 : angle 1.57260 ( 9) link_ALPHA1-3 : bond 0.00927 ( 6) link_ALPHA1-3 : angle 1.19766 ( 18) link_ALPHA1-6 : bond 0.00962 ( 12) link_ALPHA1-6 : angle 1.38633 ( 36) link_BETA1-4 : bond 0.00606 ( 51) link_BETA1-4 : angle 2.57099 ( 153) link_NAG-ASN : bond 0.00303 ( 67) link_NAG-ASN : angle 2.34289 ( 201) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4770 Ramachandran restraints generated. 2385 Oldfield, 0 Emsley, 2385 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4770 Ramachandran restraints generated. 2385 Oldfield, 0 Emsley, 2385 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 226 residues out of total 2121 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 191 time to evaluate : 0.743 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 83 ARG cc_start: 0.8179 (mpp80) cc_final: 0.7900 (mpp80) REVERT: L 24 GLN cc_start: 0.8705 (tt0) cc_final: 0.8268 (mm110) REVERT: L 81 GLU cc_start: 0.8523 (pm20) cc_final: 0.8246 (pm20) REVERT: c 620 ASP cc_start: 0.8972 (t0) cc_final: 0.8628 (p0) REVERT: I 72 ASP cc_start: 0.8184 (t0) cc_final: 0.7670 (t0) REVERT: I 75 LYS cc_start: 0.9651 (OUTLIER) cc_final: 0.9201 (mtmm) REVERT: I 83 ARG cc_start: 0.8189 (mpp80) cc_final: 0.7882 (mpp80) REVERT: I 97 GLU cc_start: 0.8630 (tt0) cc_final: 0.8387 (tt0) REVERT: I 100 LYS cc_start: 0.8776 (mmmt) cc_final: 0.8472 (mppt) REVERT: I 105 GLN cc_start: 0.8368 (mm110) cc_final: 0.8018 (tp-100) REVERT: M 24 GLN cc_start: 0.8511 (tt0) cc_final: 0.7901 (tp40) REVERT: M 92 ASP cc_start: 0.8197 (OUTLIER) cc_final: 0.7864 (m-30) REVERT: e 601 LYS cc_start: 0.8852 (mttm) cc_final: 0.8527 (mtmt) REVERT: e 644 ARG cc_start: 0.8873 (mmp80) cc_final: 0.8500 (mmp80) REVERT: e 648 GLU cc_start: 0.8741 (OUTLIER) cc_final: 0.8270 (pm20) REVERT: N 17 ASP cc_start: 0.8183 (t0) cc_final: 0.7929 (t0) REVERT: g 536 THR cc_start: 0.9144 (p) cc_final: 0.8926 (t) REVERT: g 601 LYS cc_start: 0.8813 (mttm) cc_final: 0.8304 (mtmt) outliers start: 35 outliers final: 27 residues processed: 218 average time/residue: 0.1618 time to fit residues: 52.8071 Evaluate side-chains 213 residues out of total 2121 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 183 time to evaluate : 0.705 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 11 LEU Chi-restraints excluded: chain H residue 13 THR Chi-restraints excluded: chain H residue 37 VAL Chi-restraints excluded: chain H residue 107 VAL Chi-restraints excluded: chain L residue 58 VAL Chi-restraints excluded: chain L residue 73 LEU Chi-restraints excluded: chain b residue 120 VAL Chi-restraints excluded: chain b residue 259 LEU Chi-restraints excluded: chain b residue 286 VAL Chi-restraints excluded: chain b residue 488 VAL Chi-restraints excluded: chain I residue 13 THR Chi-restraints excluded: chain I residue 75 LYS Chi-restraints excluded: chain I residue 107 VAL Chi-restraints excluded: chain M residue 58 VAL Chi-restraints excluded: chain M residue 92 ASP 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 d residue 488 VAL Chi-restraints excluded: chain e residue 622 ILE Chi-restraints excluded: chain e residue 648 GLU Chi-restraints excluded: chain J residue 11 LEU Chi-restraints excluded: chain J residue 13 THR Chi-restraints excluded: chain J residue 37 VAL Chi-restraints excluded: chain J residue 107 VAL Chi-restraints excluded: chain J residue 111 VAL Chi-restraints excluded: chain N residue 104 VAL Chi-restraints excluded: chain f residue 120 VAL Chi-restraints excluded: chain f residue 286 VAL Chi-restraints excluded: chain g residue 535 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 237 random chunks: chunk 209 optimal weight: 1.9990 chunk 99 optimal weight: 9.9990 chunk 104 optimal weight: 6.9990 chunk 98 optimal weight: 5.9990 chunk 7 optimal weight: 1.9990 chunk 112 optimal weight: 0.9980 chunk 27 optimal weight: 0.7980 chunk 148 optimal weight: 1.9990 chunk 147 optimal weight: 0.9990 chunk 22 optimal weight: 0.9990 chunk 170 optimal weight: 2.9990 overall best weight: 1.1586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** c 540 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 100 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 540 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3628 r_free = 0.3628 target = 0.075374 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3253 r_free = 0.3253 target = 0.058225 restraints weight = 65759.015| |-----------------------------------------------------------------------------| r_work (start): 0.3159 rms_B_bonded: 4.02 r_work: 0.3010 rms_B_bonded: 4.22 restraints_weight: 0.5000 r_work (final): 0.3010 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8454 moved from start: 0.2653 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 21613 Z= 0.124 Angle : 0.624 15.947 29558 Z= 0.291 Chirality : 0.044 0.285 3622 Planarity : 0.003 0.042 3497 Dihedral : 7.005 56.775 5506 Min Nonbonded Distance : 2.433 Molprobity Statistics. All-atom Clashscore : 4.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.94 % Favored : 97.06 % Rotamer: Outliers : 1.51 % Allowed : 13.53 % Favored : 84.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % 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: -0.34 (0.17), residues: 2385 helix: 0.11 (0.27), residues: 429 sheet: -0.04 (0.20), residues: 645 loop : -0.33 (0.17), residues: 1311 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG g 519 TYR 0.033 0.001 TYR L 49 PHE 0.010 0.001 PHE I 100C TRP 0.010 0.001 TRP J 47 HIS 0.003 0.001 HIS d 374 Details of bonding type rmsd covalent geometry : bond 0.00283 (21432) covalent geometry : angle 0.56402 (29057) SS BOND : bond 0.00255 ( 42) SS BOND : angle 0.89833 ( 84) hydrogen bonds : bond 0.03388 ( 694) hydrogen bonds : angle 4.95170 ( 1914) link_ALPHA1-2 : bond 0.00661 ( 3) link_ALPHA1-2 : angle 1.55817 ( 9) link_ALPHA1-3 : bond 0.00862 ( 6) link_ALPHA1-3 : angle 1.22240 ( 18) link_ALPHA1-6 : bond 0.00929 ( 12) link_ALPHA1-6 : angle 1.40138 ( 36) link_BETA1-4 : bond 0.00600 ( 51) link_BETA1-4 : angle 2.52866 ( 153) link_NAG-ASN : bond 0.00309 ( 67) link_NAG-ASN : angle 2.33574 ( 201) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4770 Ramachandran restraints generated. 2385 Oldfield, 0 Emsley, 2385 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4770 Ramachandran restraints generated. 2385 Oldfield, 0 Emsley, 2385 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 218 residues out of total 2121 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 186 time to evaluate : 0.825 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: H 75 LYS cc_start: 0.9629 (mtmm) cc_final: 0.9356 (mtmm) REVERT: H 83 ARG cc_start: 0.8208 (mpp80) cc_final: 0.7933 (mpp80) REVERT: L 24 GLN cc_start: 0.8674 (tt0) cc_final: 0.8226 (mm110) REVERT: L 49 TYR cc_start: 0.8175 (p90) cc_final: 0.7869 (p90) REVERT: L 79 GLN cc_start: 0.7834 (mm110) cc_final: 0.7411 (mp10) REVERT: L 81 GLU cc_start: 0.8506 (pm20) cc_final: 0.8238 (pm20) REVERT: c 620 ASP cc_start: 0.9008 (t0) cc_final: 0.8730 (p0) REVERT: I 72 ASP cc_start: 0.8182 (t0) cc_final: 0.7649 (t0) REVERT: I 75 LYS cc_start: 0.9643 (OUTLIER) cc_final: 0.9194 (mtmm) REVERT: I 83 ARG cc_start: 0.8168 (mpp80) cc_final: 0.7858 (mpp80) REVERT: I 97 GLU cc_start: 0.8617 (tt0) cc_final: 0.8366 (tt0) REVERT: I 100 LYS cc_start: 0.8777 (mmmt) cc_final: 0.8493 (mppt) REVERT: I 105 GLN cc_start: 0.8359 (mm110) cc_final: 0.8003 (tp-100) REVERT: M 24 GLN cc_start: 0.8538 (tt0) cc_final: 0.8035 (tp40) REVERT: M 92 ASP cc_start: 0.8251 (OUTLIER) cc_final: 0.7933 (m-30) REVERT: e 601 LYS cc_start: 0.8852 (mttm) cc_final: 0.8536 (mtmt) REVERT: e 644 ARG cc_start: 0.8880 (mmp80) cc_final: 0.8510 (mmp80) REVERT: e 648 GLU cc_start: 0.8738 (OUTLIER) cc_final: 0.8274 (pm20) REVERT: J 83 ARG cc_start: 0.8229 (mpp80) cc_final: 0.7959 (mpp80) REVERT: N 17 ASP cc_start: 0.8202 (t0) cc_final: 0.7948 (t0) REVERT: g 536 THR cc_start: 0.9149 (p) cc_final: 0.8934 (t) REVERT: g 601 LYS cc_start: 0.8802 (mttm) cc_final: 0.8303 (mtmt) REVERT: g 621 GLU cc_start: 0.8904 (pt0) cc_final: 0.8557 (pp20) outliers start: 32 outliers final: 29 residues processed: 212 average time/residue: 0.1761 time to fit residues: 55.4491 Evaluate side-chains 213 residues out of total 2121 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 181 time to evaluate : 0.810 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 11 LEU Chi-restraints excluded: chain H residue 13 THR Chi-restraints excluded: chain H residue 37 VAL Chi-restraints excluded: chain H residue 107 VAL Chi-restraints excluded: chain L residue 58 VAL Chi-restraints excluded: chain L residue 73 LEU Chi-restraints excluded: chain b residue 120 VAL Chi-restraints excluded: chain b residue 259 LEU Chi-restraints excluded: chain b residue 286 VAL Chi-restraints excluded: chain b residue 488 VAL Chi-restraints excluded: chain I residue 13 THR Chi-restraints excluded: chain I residue 75 LYS Chi-restraints excluded: chain I residue 107 VAL Chi-restraints excluded: chain M residue 58 VAL Chi-restraints excluded: chain M residue 75 ILE Chi-restraints excluded: chain M residue 92 ASP Chi-restraints excluded: chain d residue 120 VAL Chi-restraints excluded: chain d residue 125 LEU Chi-restraints excluded: chain d residue 242 VAL Chi-restraints excluded: chain d residue 286 VAL Chi-restraints excluded: chain d residue 488 VAL Chi-restraints excluded: chain e residue 622 ILE Chi-restraints excluded: chain e residue 648 GLU Chi-restraints excluded: chain J residue 11 LEU Chi-restraints excluded: chain J residue 13 THR Chi-restraints excluded: chain J residue 37 VAL Chi-restraints excluded: chain J residue 107 VAL Chi-restraints excluded: chain J residue 111 VAL Chi-restraints excluded: chain N residue 104 VAL Chi-restraints excluded: chain f residue 120 VAL Chi-restraints excluded: chain f residue 286 VAL Chi-restraints excluded: chain g residue 535 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 237 random chunks: chunk 83 optimal weight: 7.9990 chunk 117 optimal weight: 2.9990 chunk 104 optimal weight: 7.9990 chunk 23 optimal weight: 6.9990 chunk 127 optimal weight: 0.9990 chunk 199 optimal weight: 2.9990 chunk 88 optimal weight: 6.9990 chunk 191 optimal weight: 0.9980 chunk 63 optimal weight: 10.0000 chunk 141 optimal weight: 6.9990 chunk 158 optimal weight: 10.0000 overall best weight: 2.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** c 540 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 90 GLN ** M 100 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 90 GLN ** g 540 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3586 r_free = 0.3586 target = 0.073473 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3199 r_free = 0.3199 target = 0.056160 restraints weight = 66233.520| |-----------------------------------------------------------------------------| r_work (start): 0.3104 rms_B_bonded: 4.02 r_work: 0.2954 rms_B_bonded: 4.18 restraints_weight: 0.5000 r_work (final): 0.2954 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8512 moved from start: 0.2779 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.057 21613 Z= 0.240 Angle : 0.703 15.884 29558 Z= 0.332 Chirality : 0.047 0.287 3622 Planarity : 0.004 0.041 3497 Dihedral : 7.359 59.944 5506 Min Nonbonded Distance : 2.427 Molprobity Statistics. All-atom Clashscore : 5.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.94 % Favored : 96.06 % Rotamer: Outliers : 1.84 % Allowed : 13.58 % Favored : 84.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % 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: -0.58 (0.17), residues: 2385 helix: 0.07 (0.27), residues: 420 sheet: -0.23 (0.20), residues: 642 loop : -0.53 (0.17), residues: 1323 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG g 519 TYR 0.033 0.002 TYR L 49 PHE 0.013 0.002 PHE H 100C TRP 0.010 0.002 TRP d 338 HIS 0.004 0.001 HIS f 374 Details of bonding type rmsd covalent geometry : bond 0.00559 (21432) covalent geometry : angle 0.64478 (29057) SS BOND : bond 0.00328 ( 42) SS BOND : angle 1.11145 ( 84) hydrogen bonds : bond 0.03933 ( 694) hydrogen bonds : angle 5.17711 ( 1914) link_ALPHA1-2 : bond 0.00580 ( 3) link_ALPHA1-2 : angle 1.46380 ( 9) link_ALPHA1-3 : bond 0.00709 ( 6) link_ALPHA1-3 : angle 1.34112 ( 18) link_ALPHA1-6 : bond 0.00836 ( 12) link_ALPHA1-6 : angle 1.50969 ( 36) link_BETA1-4 : bond 0.00536 ( 51) link_BETA1-4 : angle 2.57353 ( 153) link_NAG-ASN : bond 0.00422 ( 67) link_NAG-ASN : angle 2.51037 ( 201) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4537.54 seconds wall clock time: 79 minutes 15.90 seconds (4755.90 seconds total)