Starting phenix.real_space_refine on Fri Feb 6 01:06:29 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9oom_70666/02_2026/9oom_70666.cif Found real_map, /net/cci-nas-00/data/ceres_data/9oom_70666/02_2026/9oom_70666.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.5 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9oom_70666/02_2026/9oom_70666.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9oom_70666/02_2026/9oom_70666.map" model { file = "/net/cci-nas-00/data/ceres_data/9oom_70666/02_2026/9oom_70666.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9oom_70666/02_2026/9oom_70666.cif" } resolution = 3.5 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.014 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 13152 2.51 5 N 3429 2.21 5 O 4352 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 9 residue(s): 0.02s 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: 21059 Number of models: 1 Model: "" Number of chains: 57 Chain: "H" Number of atoms: 1019 Number of conformers: 1 Conformer: "" Number of residues, atoms: 132, 1019 Classifications: {'peptide': 132} Link IDs: {'PTRANS': 3, 'TRANS': 128} Chain: "L" Number of atoms: 810 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 810 Classifications: {'peptide': 107} Link IDs: {'PCIS': 1, 'PTRANS': 6, 'TRANS': 99} Chain: "b" Number of atoms: 3525 Number of conformers: 1 Conformer: "" Number of residues, atoms: 445, 3525 Classifications: {'peptide': 445} Link IDs: {'PTRANS': 22, 'TRANS': 422} Chain breaks: 3 Chain: "c" Number of atoms: 1026 Number of conformers: 1 Conformer: "" Number of residues, atoms: 127, 1026 Classifications: {'peptide': 127} Link IDs: {'PTRANS': 1, 'TRANS': 125} Chain breaks: 1 Chain: "d" Number of atoms: 3525 Number of conformers: 1 Conformer: "" Number of residues, atoms: 445, 3525 Classifications: {'peptide': 445} Link IDs: {'PTRANS': 22, 'TRANS': 422} Chain breaks: 3 Chain: "e" Number of atoms: 1026 Number of conformers: 1 Conformer: "" Number of residues, atoms: 127, 1026 Classifications: {'peptide': 127} Link IDs: {'PTRANS': 1, 'TRANS': 125} Chain breaks: 1 Chain: "f" Number of atoms: 3525 Number of conformers: 1 Conformer: "" Number of residues, atoms: 445, 3525 Classifications: {'peptide': 445} Link IDs: {'PTRANS': 22, 'TRANS': 422} Chain breaks: 3 Chain: "g" Number of atoms: 1026 Number of conformers: 1 Conformer: "" Number of residues, atoms: 127, 1026 Classifications: {'peptide': 127} Link IDs: {'PTRANS': 1, 'TRANS': 125} Chain breaks: 1 Chain: "I" Number of atoms: 1019 Number of conformers: 1 Conformer: "" Number of residues, atoms: 132, 1019 Classifications: {'peptide': 132} Link IDs: {'PTRANS': 3, 'TRANS': 128} Chain: "M" Number of atoms: 810 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 810 Classifications: {'peptide': 107} Link IDs: {'PCIS': 1, 'PTRANS': 6, 'TRANS': 99} Chain: "J" Number of atoms: 1019 Number of conformers: 1 Conformer: "" Number of residues, atoms: 132, 1019 Classifications: {'peptide': 132} Link IDs: {'PTRANS': 3, 'TRANS': 128} Chain: "N" Number of atoms: 810 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 810 Classifications: {'peptide': 107} Link IDs: {'PCIS': 1, 'PTRANS': 6, 'TRANS': 99} 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: 94 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 94 Unusual residues: {'BMA': 1, 'MAN': 5, 'NAG': 2} Classifications: {'undetermined': 8} Link IDs: {None: 7} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen dihedrals: 24 Unresolved non-hydrogen chiralities: 8 Chain: "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: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "O" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "P" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "Q" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "R" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "S" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "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: 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: "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: 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: "X" 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: "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: 94 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 94 Unusual residues: {'BMA': 1, 'MAN': 5, 'NAG': 2} Classifications: {'undetermined': 8} Link IDs: {None: 7} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen dihedrals: 24 Unresolved non-hydrogen chiralities: 8 Chain: "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: "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: "b" Number of atoms: 98 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 98 Unusual residues: {'NAG': 7} Classifications: {'undetermined': 7} Link IDs: {None: 6} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 21 Unresolved non-hydrogen chiralities: 7 Chain: "c" Number of atoms: 42 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 42 Unusual residues: {'NAG': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "d" Number of atoms: 98 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 98 Unusual residues: {'NAG': 7} Classifications: {'undetermined': 7} Link IDs: {None: 6} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 21 Unresolved non-hydrogen chiralities: 7 Chain: "e" Number of atoms: 42 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 42 Unusual residues: {'NAG': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "f" Number of atoms: 98 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 98 Unusual residues: {'NAG': 7} Classifications: {'undetermined': 7} Link IDs: {None: 6} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 21 Unresolved non-hydrogen chiralities: 7 Chain: "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: 5.36, per 1000 atoms: 0.25 Number of scatterers: 21059 At special positions: 0 Unit cell: (132.8, 132.8, 160.19, 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 4352 8.00 N 3429 7.00 C 13152 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=2.04 Simple disulfide: pdb=" SG CYS b 54 " - pdb=" SG CYS b 74 " distance=2.04 Simple disulfide: pdb=" SG CYS b 119 " - pdb=" SG CYS b 205 " distance=2.03 Simple disulfide: pdb=" SG CYS b 126 " - pdb=" SG CYS b 196 " distance=2.03 Simple disulfide: pdb=" SG CYS b 131 " - pdb=" SG CYS b 157 " distance=2.03 Simple disulfide: pdb=" SG CYS b 201 " - pdb=" SG CYS b 433 " distance=2.03 Simple disulfide: pdb=" SG CYS b 218 " - pdb=" SG CYS b 247 " distance=2.03 Simple disulfide: pdb=" SG CYS b 228 " - pdb=" SG CYS b 239 " distance=2.03 Simple disulfide: pdb=" SG CYS b 296 " - pdb=" SG CYS b 331 " distance=2.03 Simple disulfide: pdb=" SG CYS b 378 " - pdb=" SG CYS b 445 " distance=2.04 Simple disulfide: pdb=" SG CYS b 385 " - pdb=" SG CYS b 418 " distance=2.03 Simple disulfide: pdb=" SG CYS b 501 " - pdb=" SG CYS c 605 " distance=2.03 Simple disulfide: pdb=" SG CYS c 598 " - pdb=" SG CYS c 604 " distance=2.03 Simple disulfide: pdb=" SG CYS d 54 " - pdb=" SG CYS d 74 " distance=2.04 Simple disulfide: pdb=" SG CYS d 119 " - pdb=" SG CYS d 205 " distance=2.03 Simple disulfide: pdb=" SG CYS d 126 " - pdb=" SG CYS d 196 " distance=2.03 Simple disulfide: pdb=" SG CYS d 131 " - pdb=" SG CYS d 157 " distance=2.03 Simple disulfide: pdb=" SG CYS d 201 " - pdb=" SG CYS d 433 " distance=2.03 Simple disulfide: pdb=" SG CYS d 218 " - pdb=" SG CYS d 247 " distance=2.03 Simple disulfide: pdb=" SG CYS d 228 " - pdb=" SG CYS d 239 " distance=2.03 Simple disulfide: pdb=" SG CYS d 296 " - pdb=" SG CYS d 331 " distance=2.03 Simple disulfide: pdb=" SG CYS d 378 " - pdb=" SG CYS d 445 " distance=2.04 Simple disulfide: pdb=" SG CYS d 385 " - pdb=" SG CYS d 418 " distance=2.03 Simple disulfide: pdb=" SG CYS d 501 " - pdb=" SG CYS e 605 " distance=2.03 Simple disulfide: pdb=" SG CYS e 598 " - pdb=" SG CYS e 604 " distance=2.03 Simple disulfide: pdb=" SG CYS f 54 " - pdb=" SG CYS f 74 " distance=2.04 Simple disulfide: pdb=" SG CYS f 119 " - pdb=" SG CYS f 205 " distance=2.03 Simple disulfide: pdb=" SG CYS f 126 " - pdb=" SG CYS f 196 " distance=2.03 Simple disulfide: pdb=" SG CYS f 131 " - pdb=" SG CYS f 157 " distance=2.03 Simple disulfide: pdb=" SG CYS f 201 " - pdb=" SG CYS f 433 " distance=2.03 Simple disulfide: pdb=" SG CYS f 218 " - pdb=" SG CYS f 247 " distance=2.03 Simple disulfide: pdb=" SG CYS f 228 " - pdb=" SG CYS f 239 " distance=2.03 Simple disulfide: pdb=" SG CYS f 296 " - pdb=" SG CYS f 331 " distance=2.03 Simple disulfide: pdb=" SG CYS f 378 " - pdb=" SG CYS f 445 " distance=2.04 Simple disulfide: pdb=" SG CYS f 385 " - pdb=" SG CYS f 418 " distance=2.03 Simple disulfide: pdb=" SG CYS f 501 " - pdb=" SG CYS g 605 " distance=2.03 Simple disulfide: pdb=" SG CYS g 598 " - pdb=" SG CYS g 604 " distance=2.03 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=2.04 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=2.04 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 X 4 " - " MAN X 5 " " MAN q 4 " - " MAN q 5 " ALPHA1-3 " BMA C 3 " - " MAN C 4 " " MAN D 4 " - " MAN D 5 " " BMA E 3 " - " MAN E 4 " " MAN E 6 " - " MAN E 7 " " BMA V 3 " - " MAN V 4 " " BMA X 3 " - " MAN X 4 " " BMA o 3 " - " MAN o 4 " " BMA q 3 " - " MAN q 4 " " MAN q 6 " - " MAN q 7 " ALPHA1-6 " BMA C 3 " - " MAN C 5 " " BMA D 3 " - " MAN D 4 " " BMA E 3 " - " MAN E 6 " " MAN E 6 " - " MAN E 8 " " BMA V 3 " - " MAN V 5 " " BMA W 3 " - " MAN W 4 " " MAN W 4 " - " MAN W 5 " " BMA X 3 " - " MAN X 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 " " MAN q 6 " - " MAN q 8 " 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 O 1 " - " NAG O 2 " " NAG P 1 " - " NAG P 2 " " NAG Q 1 " - " NAG Q 2 " " NAG R 1 " - " NAG R 2 " " NAG S 1 " - " NAG S 2 " " NAG T 1 " - " NAG T 2 " " NAG U 1 " - " NAG U 2 " " NAG 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 X 2 " - " BMA X 3 " " 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 y 1 " - " NAG y 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 b 386 " " NAG T 1 " - " ASN d 392 " " NAG U 1 " - " ASN d 332 " " NAG V 1 " - " ASN d 262 " " NAG W 1 " - " ASN d 156 " " NAG X 1 " - " ASN d 160 " " NAG Y 1 " - " ASN d 197 " " NAG Z 1 " - " ASN d 234 " " NAG a 1 " - " ASN d 241 " " 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 398 " " NAG b 607 " - " ASN b 363 " " NAG c 701 " - " ASN c 611 " " NAG c 702 " - " ASN c 637 " " NAG c 703 " - " ASN c 625 " " NAG d 601 " - " ASN d 88 " " NAG d 602 " - " ASN d 133 " " NAG d 603 " - " ASN d 339 " " NAG d 604 " - " ASN d 355 " " NAG d 605 " - " ASN d 269 " " NAG d 606 " - " ASN d 398 " " NAG d 607 " - " ASN d 386 " " NAG e 701 " - " ASN e 611 " " NAG e 702 " - " ASN e 637 " " NAG e 703 " - " ASN e 625 " " NAG f 601 " - " ASN f 88 " " NAG f 602 " - " ASN f 133 " " NAG f 603 " - " ASN f 339 " " NAG f 604 " - " ASN f 355 " " NAG f 605 " - " ASN f 269 " " NAG f 606 " - " ASN f 398 " " NAG f 607 " - " ASN f 386 " " NAG g 701 " - " ASN g 611 " " NAG g 702 " - " ASN g 637 " " NAG g 703 " - " ASN g 625 " " NAG h 1 " - " ASN d 276 " " NAG i 1 " - " ASN d 301 " " NAG j 1 " - " ASN d 448 " " NAG k 1 " - " ASN d 465 " " NAG l 1 " - " ASN d 363 " " 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 " " NAG y 1 " - " ASN f 363 " Time building additional restraints: 2.38 Conformation dependent library (CDL) restraints added in 926.0 milliseconds 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: 4494 Finding SS restraints... Secondary structure from input PDB file: 42 helices and 48 sheets defined 19.2% alpha, 32.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.98 Creating SS restraints... Processing helix chain 'H' and resid 28 through 32 removed outlier: 3.811A pdb=" N TYR H 32 " --> pdb=" O PHE H 29 " (cutoff:3.500A) Processing helix chain 'H' and resid 61 through 64 removed outlier: 3.697A pdb=" N MET H 64 " --> pdb=" O ASP H 61 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 61 through 64' Processing helix chain 'b' and resid 70 through 74 removed outlier: 3.526A pdb=" N ALA b 73 " --> pdb=" O ALA b 70 " (cutoff:3.500A) Processing helix chain 'b' and resid 99 through 115 Processing helix chain 'b' and resid 195 through 198 Processing helix chain 'b' and resid 334 through 351 removed outlier: 3.804A pdb=" N LYS b 340 " --> pdb=" O SER b 336 " (cutoff:3.500A) removed outlier: 3.789A pdb=" N THR b 341 " --> pdb=" O ARG b 337 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N GLN b 343 " --> pdb=" O ASN b 339 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N THR b 351 " --> pdb=" O GLU b 347 " (cutoff:3.500A) Processing helix chain 'b' and resid 368 through 373 Processing helix chain 'b' and resid 475 through 484 removed outlier: 4.056A pdb=" N TRP b 479 " --> pdb=" O MET b 475 " (cutoff:3.500A) removed outlier: 4.133A pdb=" N GLU b 482 " --> pdb=" O ASN b 478 " (cutoff:3.500A) Processing helix chain 'c' and resid 529 through 534 Processing helix chain 'c' and resid 536 through 543 removed outlier: 3.878A pdb=" N GLN c 540 " --> pdb=" O THR c 536 " (cutoff:3.500A) Processing helix chain 'c' and resid 544 through 546 No H-bonds generated for 'chain 'c' and resid 544 through 546' Processing helix chain 'c' and resid 569 through 596 removed outlier: 4.204A pdb=" N LEU c 592 " --> pdb=" O ARG c 588 " (cutoff:3.500A) removed outlier: 4.007A pdb=" N LEU c 593 " --> pdb=" O ASP c 589 " (cutoff:3.500A) Processing helix chain 'c' and resid 618 through 625 removed outlier: 3.655A pdb=" N ILE c 622 " --> pdb=" O SER c 618 " (cutoff:3.500A) removed outlier: 3.890A pdb=" N TRP c 623 " --> pdb=" O LEU c 619 " (cutoff:3.500A) Processing helix chain 'c' and resid 627 through 658 removed outlier: 3.728A pdb=" N LYS c 633 " --> pdb=" O LEU c 629 " (cutoff:3.500A) removed outlier: 4.264A pdb=" N GLU c 634 " --> pdb=" O GLN c 630 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N GLY c 636 " --> pdb=" O ASP c 632 " (cutoff:3.500A) removed outlier: 6.524A pdb=" N ASN c 637 " --> pdb=" O LYS c 633 " (cutoff:3.500A) removed outlier: 5.382A pdb=" N TYR c 638 " --> pdb=" O GLU c 634 " (cutoff:3.500A) removed outlier: 4.684A pdb=" N GLN c 640 " --> pdb=" O GLY c 636 " (cutoff:3.500A) removed outlier: 5.493A pdb=" N LEU c 641 " --> pdb=" O ASN c 637 " (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 195 through 198 Processing helix chain 'd' and resid 334 through 351 removed outlier: 3.646A pdb=" N THR d 341 " --> pdb=" O ARG d 337 " (cutoff:3.500A) removed outlier: 3.575A 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: 4.147A pdb=" N TRP d 479 " --> pdb=" O MET d 475 " (cutoff:3.500A) removed outlier: 4.076A pdb=" N GLU d 482 " --> pdb=" O ASN d 478 " (cutoff:3.500A) Processing helix chain 'e' and resid 529 through 534 Processing helix chain 'e' and resid 536 through 543 removed outlier: 3.886A pdb=" N GLN e 540 " --> pdb=" O THR e 536 " (cutoff:3.500A) Processing helix chain 'e' and resid 544 through 546 No H-bonds generated for 'chain 'e' and resid 544 through 546' Processing helix chain 'e' and resid 569 through 596 removed outlier: 4.150A pdb=" N LEU e 592 " --> pdb=" O ARG e 588 " (cutoff:3.500A) removed outlier: 4.030A pdb=" N LEU e 593 " --> pdb=" O ASP e 589 " (cutoff:3.500A) Processing helix chain 'e' and resid 618 through 625 removed outlier: 3.636A pdb=" N ILE e 622 " --> pdb=" O SER e 618 " (cutoff:3.500A) Processing helix chain 'e' and resid 627 through 658 removed outlier: 3.621A pdb=" N LYS e 633 " --> pdb=" O LEU e 629 " (cutoff:3.500A) removed outlier: 4.034A pdb=" N GLU e 634 " --> pdb=" O GLN e 630 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N ILE e 635 " --> pdb=" O TRP e 631 " (cutoff:3.500A) removed outlier: 6.430A pdb=" N ASN e 637 " --> pdb=" O LYS e 633 " (cutoff:3.500A) removed outlier: 5.558A pdb=" N TYR e 638 " --> pdb=" O GLU e 634 " (cutoff:3.500A) removed outlier: 4.602A pdb=" N GLN e 640 " --> pdb=" O GLY e 636 " (cutoff:3.500A) removed outlier: 5.257A pdb=" N LEU e 641 " --> pdb=" O ASN e 637 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N GLU e 648 " --> pdb=" O ARG e 644 " (cutoff:3.500A) Processing helix chain 'f' and resid 70 through 74 removed outlier: 3.500A pdb=" N ALA f 73 " --> pdb=" O ALA f 70 " (cutoff:3.500A) Processing helix chain 'f' and resid 99 through 117 Processing helix chain 'f' and resid 195 through 198 Processing helix chain 'f' and resid 334 through 351 removed outlier: 3.772A pdb=" N THR f 341 " --> pdb=" O ARG f 337 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N THR f 351 " --> pdb=" O GLU f 347 " (cutoff:3.500A) Processing helix chain 'f' and resid 368 through 373 Processing helix chain 'f' and resid 475 through 484 removed outlier: 4.098A pdb=" N TRP f 479 " --> pdb=" O MET f 475 " (cutoff:3.500A) removed outlier: 4.168A pdb=" N GLU f 482 " --> pdb=" O ASN f 478 " (cutoff:3.500A) Processing helix chain 'g' and resid 529 through 534 removed outlier: 3.602A pdb=" N SER g 534 " --> pdb=" O MET g 530 " (cutoff:3.500A) Processing helix chain 'g' and resid 536 through 543 removed outlier: 3.882A pdb=" N GLN g 540 " --> pdb=" O THR g 536 " (cutoff:3.500A) removed outlier: 3.531A 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: 4.188A pdb=" N LEU g 592 " --> pdb=" O ARG g 588 " (cutoff:3.500A) removed outlier: 3.936A pdb=" N LEU g 593 " --> pdb=" O ASP g 589 " (cutoff:3.500A) Processing helix chain 'g' and resid 618 through 625 removed outlier: 3.634A pdb=" N ILE g 622 " --> pdb=" O SER g 618 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N TRP g 623 " --> pdb=" O LEU g 619 " (cutoff:3.500A) Processing helix chain 'g' and resid 627 through 658 removed outlier: 3.581A pdb=" N LYS g 633 " --> pdb=" O LEU g 629 " (cutoff:3.500A) removed outlier: 4.123A pdb=" N GLU g 634 " --> pdb=" O GLN g 630 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N ILE g 635 " --> pdb=" O TRP g 631 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N GLY g 636 " --> pdb=" O ASP g 632 " (cutoff:3.500A) removed outlier: 6.426A pdb=" N ASN g 637 " --> pdb=" O LYS g 633 " (cutoff:3.500A) removed outlier: 5.502A pdb=" N TYR g 638 " --> pdb=" O GLU g 634 " (cutoff:3.500A) removed outlier: 4.673A pdb=" N GLN g 640 " --> pdb=" O GLY g 636 " (cutoff:3.500A) removed outlier: 5.350A pdb=" N LEU g 641 " --> pdb=" O ASN g 637 " (cutoff:3.500A) Processing helix chain 'I' and resid 28 through 32 removed outlier: 3.811A pdb=" N TYR I 32 " --> pdb=" O PHE I 29 " (cutoff:3.500A) Processing helix chain 'I' and resid 61 through 64 removed outlier: 3.697A pdb=" N MET I 64 " --> pdb=" O ASP I 61 " (cutoff:3.500A) No H-bonds generated for 'chain 'I' and resid 61 through 64' Processing helix chain 'J' and resid 28 through 32 removed outlier: 3.811A pdb=" N TYR J 32 " --> pdb=" O PHE J 29 " (cutoff:3.500A) Processing helix chain 'J' and resid 61 through 64 removed outlier: 3.698A pdb=" N MET J 64 " --> pdb=" O ASP J 61 " (cutoff:3.500A) No H-bonds generated for 'chain 'J' and resid 61 through 64' 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: 3.776A pdb=" N GLN H 39 " --> pdb=" O VAL H 89 " (cutoff:3.500A) removed outlier: 7.036A pdb=" N MET H 34 " --> pdb=" O GLY H 50 " (cutoff:3.500A) removed outlier: 4.627A pdb=" N GLY H 50 " --> pdb=" O MET H 34 " (cutoff:3.500A) removed outlier: 6.611A 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: 3.683A 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 Processing sheet with id=AA6, first strand: chain 'L' and resid 10 through 13 removed outlier: 3.592A pdb=" N GLU L 105 " --> pdb=" O LEU L 11 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'L' and resid 45 through 48 removed outlier: 6.659A pdb=" N TRP L 35 " --> pdb=" O LEU L 47 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'b' and resid 495 through 499 removed outlier: 5.432A pdb=" N VAL c 608 " --> pdb=" O VAL b 36 " (cutoff:3.500A) removed outlier: 8.075A pdb=" N VAL b 38 " --> pdb=" O THR c 606 " (cutoff:3.500A) removed outlier: 7.485A pdb=" N THR c 606 " --> pdb=" O VAL b 38 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'b' and resid 45 through 47 Processing sheet with id=AB1, first strand: chain 'b' and resid 75 through 76 Processing sheet with id=AB2, first strand: chain 'b' and resid 66 through 67 removed outlier: 7.077A 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 removed outlier: 3.529A pdb=" N GLU b 91 " --> pdb=" O CYS b 239 " (cutoff:3.500A) 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: 6.644A pdb=" N THR b 202 " --> pdb=" O TYR b 435 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'b' and resid 260 through 261 removed outlier: 3.579A pdb=" N GLY b 451 " --> pdb=" O LEU b 260 " (cutoff:3.500A) removed outlier: 10.272A pdb=" N LYS b 444 " --> pdb=" O ILE b 294 " (cutoff:3.500A) removed outlier: 11.624A pdb=" N ILE b 294 " --> pdb=" O LYS b 444 " (cutoff:3.500A) removed outlier: 9.816A pdb=" N GLU b 446 " --> pdb=" O VAL b 292 " (cutoff:3.500A) removed outlier: 10.665A pdb=" N VAL b 292 " --> pdb=" O GLU b 446 " (cutoff:3.500A) removed outlier: 9.009A pdb=" N ASN b 448 " --> pdb=" O GLN b 290 " (cutoff:3.500A) removed outlier: 9.719A pdb=" N GLN b 290 " --> pdb=" O ASN b 448 " (cutoff:3.500A) removed outlier: 6.646A pdb=" N THR b 450 " --> pdb=" O LEU b 288 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N HIS b 330 " --> pdb=" O ILE b 297 " (cutoff:3.500A) removed outlier: 3.552A 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: 6.646A pdb=" N THR b 450 " --> pdb=" O LEU b 288 " (cutoff:3.500A) removed outlier: 9.719A pdb=" N GLN b 290 " --> pdb=" O ASN b 448 " (cutoff:3.500A) removed outlier: 9.009A pdb=" N ASN b 448 " --> pdb=" O GLN b 290 " (cutoff:3.500A) removed outlier: 10.665A pdb=" N VAL b 292 " --> pdb=" O GLU b 446 " (cutoff:3.500A) removed outlier: 9.816A pdb=" N GLU b 446 " --> pdb=" O VAL b 292 " (cutoff:3.500A) removed outlier: 11.624A pdb=" N ILE b 294 " --> pdb=" O LYS b 444 " (cutoff:3.500A) removed outlier: 10.272A pdb=" N LYS b 444 " --> pdb=" O ILE b 294 " (cutoff:3.500A) removed outlier: 6.485A pdb=" N THR b 357 " --> pdb=" O GLU b 466 " (cutoff:3.500A) removed outlier: 7.738A pdb=" N PHE b 468 " --> pdb=" O THR b 357 " (cutoff:3.500A) removed outlier: 6.662A 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: 7.223A pdb=" N ASN b 301 " --> pdb=" O ILE b 323 " (cutoff:3.500A) removed outlier: 4.570A pdb=" N ILE b 323 " --> pdb=" O ASN b 301 " (cutoff:3.500A) removed outlier: 6.460A pdb=" N THR b 303 " --> pdb=" O GLY b 321 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N LYS b 305 " --> pdb=" O ALA b 319 " (cutoff:3.500A) removed outlier: 7.170A pdb=" N GLN b 315 " --> pdb=" O ILE b 309 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'd' and resid 495 through 499 removed outlier: 5.417A pdb=" N VAL e 608 " --> pdb=" O VAL d 36 " (cutoff:3.500A) removed outlier: 8.016A pdb=" N VAL d 38 " --> pdb=" O THR e 606 " (cutoff:3.500A) removed outlier: 7.500A pdb=" N THR e 606 " --> pdb=" O VAL d 38 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'd' and resid 45 through 47 Processing sheet with id=AC2, first strand: chain 'd' and resid 75 through 76 removed outlier: 3.580A pdb=" N VAL d 75 " --> pdb=" O CYS d 54 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'd' and resid 91 through 94 Processing sheet with id=AC4, first strand: chain 'd' and resid 181 through 182 Processing sheet with id=AC5, first strand: chain 'd' and resid 202 through 203 removed outlier: 6.503A pdb=" N THR d 202 " --> pdb=" O TYR d 435 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'd' and resid 259 through 261 removed outlier: 3.645A pdb=" N GLY d 451 " --> pdb=" O LEU d 260 " (cutoff:3.500A) removed outlier: 10.163A pdb=" N LYS d 444 " --> pdb=" O ILE d 294 " (cutoff:3.500A) removed outlier: 11.551A pdb=" N ILE d 294 " --> pdb=" O LYS d 444 " (cutoff:3.500A) removed outlier: 9.740A pdb=" N GLU d 446 " --> pdb=" O VAL d 292 " (cutoff:3.500A) removed outlier: 10.622A pdb=" N VAL d 292 " --> pdb=" O GLU d 446 " (cutoff:3.500A) removed outlier: 9.354A pdb=" N ASN d 448 " --> pdb=" O GLN d 290 " (cutoff:3.500A) removed outlier: 9.941A pdb=" N GLN d 290 " --> pdb=" O ASN d 448 " (cutoff:3.500A) removed outlier: 6.676A pdb=" N THR d 450 " --> pdb=" O LEU d 288 " (cutoff:3.500A) removed outlier: 3.750A pdb=" N HIS d 330 " --> pdb=" O ILE d 297 " (cutoff:3.500A) removed outlier: 3.813A pdb=" N LYS d 421 " --> pdb=" O PHE d 382 " (cutoff:3.500A) removed outlier: 4.701A pdb=" N PHE d 382 " --> pdb=" O LYS d 421 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N PHE d 376 " --> pdb=" O PHE d 383 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'd' and resid 271 through 273 removed outlier: 6.676A pdb=" N THR d 450 " --> pdb=" O LEU d 288 " (cutoff:3.500A) removed outlier: 9.941A pdb=" N GLN d 290 " --> pdb=" O ASN d 448 " (cutoff:3.500A) removed outlier: 9.354A pdb=" N ASN d 448 " --> pdb=" O GLN d 290 " (cutoff:3.500A) removed outlier: 10.622A pdb=" N VAL d 292 " --> pdb=" O GLU d 446 " (cutoff:3.500A) removed outlier: 9.740A pdb=" N GLU d 446 " --> pdb=" O VAL d 292 " (cutoff:3.500A) removed outlier: 11.551A pdb=" N ILE d 294 " --> pdb=" O LYS d 444 " (cutoff:3.500A) removed outlier: 10.163A pdb=" N LYS d 444 " --> pdb=" O ILE d 294 " (cutoff:3.500A) removed outlier: 6.521A pdb=" N THR d 357 " --> pdb=" O GLU d 466 " (cutoff:3.500A) removed outlier: 7.730A pdb=" N PHE d 468 " --> pdb=" O THR d 357 " (cutoff:3.500A) removed outlier: 6.682A pdb=" N ILE d 359 " --> pdb=" O PHE d 468 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'd' and resid 301 through 312 removed outlier: 7.195A pdb=" N ASN d 301 " --> pdb=" O ILE d 323 " (cutoff:3.500A) removed outlier: 4.644A pdb=" N ILE d 323 " --> pdb=" O ASN d 301 " (cutoff:3.500A) removed outlier: 6.517A pdb=" N THR d 303 " --> pdb=" O GLY d 321 " (cutoff:3.500A) removed outlier: 7.188A pdb=" N GLN d 315 " --> pdb=" O ILE d 309 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'f' and resid 495 through 499 removed outlier: 5.591A pdb=" N VAL g 608 " --> pdb=" O VAL f 36 " (cutoff:3.500A) removed outlier: 8.136A pdb=" N VAL f 38 " --> pdb=" O THR g 606 " (cutoff:3.500A) removed outlier: 7.703A pdb=" N THR g 606 " --> pdb=" O VAL f 38 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'f' and resid 45 through 47 Processing sheet with id=AD2, first strand: chain 'f' and resid 75 through 76 Processing sheet with id=AD3, first strand: chain 'f' and resid 91 through 94 Processing sheet with id=AD4, first strand: chain 'f' and resid 130 through 133 Processing sheet with id=AD5, first strand: chain 'f' and resid 181 through 183 Processing sheet with id=AD6, first strand: chain 'f' and resid 202 through 203 removed outlier: 6.328A pdb=" N THR f 202 " --> pdb=" O TYR f 435 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'f' and resid 260 through 261 removed outlier: 3.594A pdb=" N GLY f 451 " --> pdb=" O LEU f 260 " (cutoff:3.500A) removed outlier: 10.280A pdb=" N LYS f 444 " --> pdb=" O ILE f 294 " (cutoff:3.500A) removed outlier: 11.624A pdb=" N ILE f 294 " --> pdb=" O LYS f 444 " (cutoff:3.500A) removed outlier: 9.831A pdb=" N GLU f 446 " --> pdb=" O VAL f 292 " (cutoff:3.500A) removed outlier: 10.731A pdb=" N VAL f 292 " --> pdb=" O GLU f 446 " (cutoff:3.500A) removed outlier: 9.061A pdb=" N ASN f 448 " --> pdb=" O GLN f 290 " (cutoff:3.500A) removed outlier: 9.832A pdb=" N GLN f 290 " --> pdb=" O ASN f 448 " (cutoff:3.500A) removed outlier: 6.682A pdb=" N THR f 450 " --> pdb=" O LEU f 288 " (cutoff:3.500A) removed outlier: 3.770A pdb=" N HIS f 330 " --> pdb=" O ILE f 297 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'f' and resid 271 through 273 removed outlier: 6.682A pdb=" N THR f 450 " --> pdb=" O LEU f 288 " (cutoff:3.500A) removed outlier: 9.832A pdb=" N GLN f 290 " --> pdb=" O ASN f 448 " (cutoff:3.500A) removed outlier: 9.061A pdb=" N ASN f 448 " --> pdb=" O GLN f 290 " (cutoff:3.500A) removed outlier: 10.731A pdb=" N VAL f 292 " --> pdb=" O GLU f 446 " (cutoff:3.500A) removed outlier: 9.831A pdb=" N GLU f 446 " --> pdb=" O VAL f 292 " (cutoff:3.500A) removed outlier: 11.624A pdb=" N ILE f 294 " --> pdb=" O LYS f 444 " (cutoff:3.500A) removed outlier: 10.280A pdb=" N LYS f 444 " --> pdb=" O ILE f 294 " (cutoff:3.500A) removed outlier: 6.387A pdb=" N THR f 357 " --> pdb=" O GLU f 466 " (cutoff:3.500A) removed outlier: 7.664A pdb=" N PHE f 468 " --> pdb=" O THR f 357 " (cutoff:3.500A) removed outlier: 6.533A pdb=" N ILE f 359 " --> pdb=" O PHE f 468 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'f' and resid 304 through 312 removed outlier: 3.565A pdb=" N LYS f 305 " --> pdb=" O ALA f 319 " (cutoff:3.500A) removed outlier: 7.207A pdb=" N GLN f 315 " --> pdb=" O ILE f 309 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'I' and resid 3 through 7 Processing sheet with id=AE2, first strand: chain 'I' and resid 11 through 12 removed outlier: 4.569A pdb=" N GLN I 39 " --> pdb=" O VAL I 89 " (cutoff:3.500A) removed outlier: 7.035A pdb=" N MET I 34 " --> pdb=" O GLY I 50 " (cutoff:3.500A) removed outlier: 4.627A pdb=" N GLY I 50 " --> pdb=" O MET I 34 " (cutoff:3.500A) removed outlier: 6.611A pdb=" N TRP I 36 " --> pdb=" O ILE I 48 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'I' and resid 11 through 12 removed outlier: 3.683A pdb=" N TYR I 102 " --> pdb=" O LYS I 94 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'M' and resid 4 through 7 Processing sheet with id=AE5, first strand: chain 'M' and resid 10 through 13 removed outlier: 3.591A pdb=" N GLU M 105 " --> pdb=" O LEU M 11 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'M' and resid 45 through 48 removed outlier: 6.659A pdb=" N TRP M 35 " --> pdb=" O LEU M 47 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'J' and resid 3 through 7 Processing sheet with id=AE8, first strand: chain 'J' and resid 11 through 12 removed outlier: 4.476A pdb=" N GLN J 39 " --> pdb=" O VAL J 89 " (cutoff:3.500A) removed outlier: 7.035A pdb=" N MET J 34 " --> pdb=" O GLY J 50 " (cutoff:3.500A) removed outlier: 4.627A pdb=" N GLY J 50 " --> pdb=" O MET J 34 " (cutoff:3.500A) removed outlier: 6.612A pdb=" N TRP J 36 " --> pdb=" O ILE J 48 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'J' and resid 11 through 12 removed outlier: 3.682A pdb=" N TYR J 102 " --> pdb=" O LYS J 94 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'N' and resid 4 through 7 Processing sheet with id=AF2, first strand: chain 'N' and resid 10 through 13 removed outlier: 3.591A pdb=" N GLU N 105 " --> pdb=" O LEU N 11 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'N' and resid 45 through 48 removed outlier: 6.659A pdb=" N TRP N 35 " --> pdb=" O LEU N 47 " (cutoff:3.500A) 700 hydrogen bonds defined for protein. 1815 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: 4.41 Time building geometry restraints manager: 2.99 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.34: 6020 1.34 - 1.46: 4469 1.46 - 1.58: 10813 1.58 - 1.70: 0 1.70 - 1.82: 168 Bond restraints: 21470 Sorted by residual: bond pdb=" N PRO N 80 " pdb=" CA PRO N 80 " ideal model delta sigma weight residual 1.474 1.447 0.027 7.40e-03 1.83e+04 1.33e+01 bond pdb=" CA SER M 14 " pdb=" CB SER M 14 " ideal model delta sigma weight residual 1.539 1.489 0.050 1.36e-02 5.41e+03 1.33e+01 bond pdb=" CA SER L 14 " pdb=" CB SER L 14 " ideal model delta sigma weight residual 1.539 1.490 0.049 1.36e-02 5.41e+03 1.32e+01 bond pdb=" CA SER N 14 " pdb=" CB SER N 14 " ideal model delta sigma weight residual 1.539 1.490 0.049 1.36e-02 5.41e+03 1.31e+01 bond pdb=" N PRO M 80 " pdb=" CA PRO M 80 " ideal model delta sigma weight residual 1.474 1.448 0.026 7.40e-03 1.83e+04 1.25e+01 ... (remaining 21465 not shown) Histogram of bond angle deviations from ideal: 0.00 - 4.49: 28918 4.49 - 8.98: 180 8.98 - 13.47: 7 13.47 - 17.96: 0 17.96 - 22.45: 1 Bond angle restraints: 29106 Sorted by residual: angle pdb=" C ASN d 339 " pdb=" CA ASN d 339 " pdb=" CB ASN d 339 " ideal model delta sigma weight residual 110.81 88.36 22.45 1.60e+00 3.91e-01 1.97e+02 angle pdb=" C TYR I 90 " pdb=" CA TYR I 90 " pdb=" CB TYR I 90 " ideal model delta sigma weight residual 109.80 117.13 -7.33 1.23e+00 6.61e-01 3.55e+01 angle pdb=" C TYR J 90 " pdb=" CA TYR J 90 " pdb=" CB TYR J 90 " ideal model delta sigma weight residual 109.80 116.85 -7.05 1.23e+00 6.61e-01 3.28e+01 angle pdb=" C ASN b 195 " pdb=" CA ASN b 195 " pdb=" CB ASN b 195 " ideal model delta sigma weight residual 110.11 99.86 10.25 1.90e+00 2.77e-01 2.91e+01 angle pdb=" C ASN f 195 " pdb=" CA ASN f 195 " pdb=" CB ASN f 195 " ideal model delta sigma weight residual 110.17 99.20 10.97 2.04e+00 2.40e-01 2.89e+01 ... (remaining 29101 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 21.38: 13757 21.38 - 42.75: 672 42.75 - 64.13: 176 64.13 - 85.50: 89 85.50 - 106.88: 37 Dihedral angle restraints: 14731 sinusoidal: 7735 harmonic: 6996 Sorted by residual: dihedral pdb=" C ASN d 339 " pdb=" N ASN d 339 " pdb=" CA ASN d 339 " pdb=" CB ASN d 339 " ideal model delta harmonic sigma weight residual -122.60 -96.00 -26.60 0 2.50e+00 1.60e-01 1.13e+02 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 93.00 145.19 -52.19 1 1.00e+01 1.00e-02 3.71e+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 93.00 144.93 -51.93 1 1.00e+01 1.00e-02 3.68e+01 ... (remaining 14728 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.233: 3591 0.233 - 0.465: 43 0.465 - 0.698: 5 0.698 - 0.930: 1 0.930 - 1.163: 1 Chirality restraints: 3641 Sorted by residual: chirality pdb=" C1 NAG l 2 " pdb=" O4 NAG l 1 " pdb=" C2 NAG l 2 " pdb=" O5 NAG l 2 " both_signs ideal model delta sigma weight residual False -2.40 -1.24 -1.16 2.00e-02 2.50e+03 3.38e+03 chirality pdb=" C1 MAN p 4 " pdb=" O6 BMA p 3 " pdb=" C2 MAN p 4 " pdb=" O5 MAN p 4 " both_signs ideal model delta sigma weight residual False 2.40 1.68 0.72 2.00e-02 2.50e+03 1.31e+03 chirality pdb=" C1 NAG V 2 " pdb=" O4 NAG V 1 " pdb=" C2 NAG V 2 " pdb=" O5 NAG V 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.00 -0.40 2.00e-02 2.50e+03 4.06e+02 ... (remaining 3638 not shown) Planarity restraints: 3567 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C2 NAG f 607 " -0.290 2.00e-02 2.50e+03 2.51e-01 7.88e+02 pdb=" C7 NAG f 607 " 0.063 2.00e-02 2.50e+03 pdb=" C8 NAG f 607 " -0.011 2.00e-02 2.50e+03 pdb=" N2 NAG f 607 " 0.434 2.00e-02 2.50e+03 pdb=" O7 NAG f 607 " -0.197 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG k 1 " -0.287 2.00e-02 2.50e+03 2.40e-01 7.17e+02 pdb=" C7 NAG k 1 " 0.082 2.00e-02 2.50e+03 pdb=" C8 NAG k 1 " -0.190 2.00e-02 2.50e+03 pdb=" N2 NAG k 1 " 0.402 2.00e-02 2.50e+03 pdb=" O7 NAG k 1 " -0.007 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG G 1 " -0.238 2.00e-02 2.50e+03 1.96e-01 4.82e+02 pdb=" C7 NAG G 1 " 0.067 2.00e-02 2.50e+03 pdb=" C8 NAG G 1 " -0.168 2.00e-02 2.50e+03 pdb=" N2 NAG G 1 " 0.322 2.00e-02 2.50e+03 pdb=" O7 NAG G 1 " 0.017 2.00e-02 2.50e+03 ... (remaining 3564 not shown) Histogram of nonbonded interaction distances: 2.23 - 2.76: 3140 2.76 - 3.30: 20888 3.30 - 3.83: 33048 3.83 - 4.37: 38917 4.37 - 4.90: 67996 Nonbonded interactions: 163989 Sorted by model distance: nonbonded pdb=" OD2 ASP f 457 " pdb=" OG1 THR f 467 " model vdw 2.227 3.040 nonbonded pdb=" O3 NAG X 2 " pdb=" O5 BMA X 3 " model vdw 2.266 3.040 nonbonded pdb=" OD2 ASP d 457 " pdb=" OG1 THR d 467 " model vdw 2.301 3.040 nonbonded pdb=" O LYS g 655 " pdb=" NZ LYS g 655 " model vdw 2.306 3.120 nonbonded pdb=" OG SER b 256 " pdb=" O LEU b 259 " model vdw 2.307 3.040 ... (remaining 163984 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 'K' selection = chain 'O' selection = chain 'P' selection = chain 'Q' selection = chain 'R' selection = chain 'S' selection = chain 'T' 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' selection = chain 'y' } ncs_group { reference = chain 'B' selection = chain 'U' selection = chain 'n' } ncs_group { reference = chain 'C' selection = chain 'D' selection = chain 'V' selection = chain 'W' selection = chain 'o' selection = chain 'p' } ncs_group { reference = chain 'E' 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' selection = chain 'd' selection = chain 'f' } ncs_group { reference = chain 'c' selection = chain 'e' selection = chain 'g' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 3.770 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: 0.410 Check model and map are aligned: 0.070 Set scattering table: 0.060 Process input model: 21.480 Find NCS groups from input model: 0.570 Set up NCS constraints: 0.080 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.370 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 27.830 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8130 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 : 0.007 0.053 21657 Z= 0.376 Angle : 1.136 22.452 29625 Z= 0.591 Chirality : 0.070 1.163 3641 Planarity : 0.012 0.251 3498 Dihedral : 15.106 106.881 10111 Min Nonbonded Distance : 2.227 Molprobity Statistics. All-atom Clashscore : 4.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.28 % Favored : 94.72 % Rotamer: Outliers : 0.09 % Allowed : 10.36 % Favored : 89.55 % Cbeta Deviations : 0.27 % Peptide Plane: Cis-proline : 3.03 % 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: 0.00 (0.27), residues: 375 sheet: -0.92 (0.21), residues: 603 loop : -1.02 (0.16), residues: 1407 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG H 105 TYR 0.017 0.001 TYR N 91 PHE 0.016 0.002 PHE M 71 TRP 0.011 0.001 TRP b 338 HIS 0.002 0.001 HIS c 564 Details of bonding type rmsd covalent geometry : bond 0.00615 (21470) covalent geometry : angle 0.98735 (29106) SS BOND : bond 0.00451 ( 42) SS BOND : angle 2.00977 ( 84) hydrogen bonds : bond 0.25238 ( 670) hydrogen bonds : angle 8.95658 ( 1815) link_ALPHA1-2 : bond 0.03796 ( 3) link_ALPHA1-2 : angle 5.51892 ( 9) link_ALPHA1-3 : bond 0.04372 ( 9) link_ALPHA1-3 : angle 4.43592 ( 27) link_ALPHA1-6 : bond 0.03554 ( 13) link_ALPHA1-6 : angle 4.18966 ( 39) link_BETA1-4 : bond 0.03843 ( 51) link_BETA1-4 : angle 6.08606 ( 153) link_NAG-ASN : bond 0.00684 ( 69) link_NAG-ASN : angle 3.37652 ( 207) *********************** 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 2124 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 295 time to evaluate : 0.855 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 67 PHE cc_start: 0.8653 (m-10) cc_final: 0.8377 (m-80) REVERT: H 72 ASP cc_start: 0.8112 (t70) cc_final: 0.7900 (t0) REVERT: H 81 GLN cc_start: 0.9066 (tp40) cc_final: 0.8017 (tm-30) REVERT: H 91 TYR cc_start: 0.8427 (m-80) cc_final: 0.8061 (m-10) REVERT: L 49 TYR cc_start: 0.8386 (p90) cc_final: 0.7912 (p90) REVERT: c 542 ARG cc_start: 0.8855 (ttm110) cc_final: 0.8191 (ttp80) REVERT: c 584 GLU cc_start: 0.8894 (mt-10) cc_final: 0.8466 (mt-10) REVERT: c 624 ASN cc_start: 0.9172 (m-40) cc_final: 0.8647 (m110) REVERT: c 643 TYR cc_start: 0.9351 (m-10) cc_final: 0.9057 (m-10) REVERT: c 647 GLU cc_start: 0.8700 (mt-10) cc_final: 0.8472 (mt-10) REVERT: c 656 ASN cc_start: 0.9350 (m-40) cc_final: 0.9054 (m110) REVERT: e 584 GLU cc_start: 0.8763 (mt-10) cc_final: 0.8252 (mt-10) REVERT: e 601 LYS cc_start: 0.8608 (mtpp) cc_final: 0.7967 (mtmm) REVERT: e 603 ILE cc_start: 0.8721 (mt) cc_final: 0.8512 (mt) REVERT: e 644 ARG cc_start: 0.8519 (mmp80) cc_final: 0.8256 (mmp80) REVERT: e 647 GLU cc_start: 0.8577 (mt-10) cc_final: 0.7576 (mp0) REVERT: e 656 ASN cc_start: 0.9374 (m-40) cc_final: 0.9132 (m110) REVERT: g 535 ILE cc_start: 0.9614 (mt) cc_final: 0.9405 (mp) REVERT: g 542 ARG cc_start: 0.8886 (ttm170) cc_final: 0.8562 (ttp80) REVERT: g 588 ARG cc_start: 0.8377 (ttm170) cc_final: 0.8129 (ttp80) REVERT: g 601 LYS cc_start: 0.8477 (mtpp) cc_final: 0.8112 (mtmm) REVERT: g 633 LYS cc_start: 0.9067 (mttp) cc_final: 0.8772 (mtmm) REVERT: g 654 GLU cc_start: 0.8959 (tp30) cc_final: 0.8667 (mm-30) REVERT: g 655 LYS cc_start: 0.8955 (tptp) cc_final: 0.8168 (tptp) REVERT: g 656 ASN cc_start: 0.9369 (m-40) cc_final: 0.9169 (m110) REVERT: g 659 GLU cc_start: 0.7969 (tt0) cc_final: 0.7472 (tm-30) REVERT: I 67 PHE cc_start: 0.8684 (m-10) cc_final: 0.8482 (m-80) REVERT: I 72 ASP cc_start: 0.8378 (t70) cc_final: 0.8025 (t0) REVERT: I 81 GLN cc_start: 0.9025 (tp40) cc_final: 0.7923 (tm-30) REVERT: J 59 TYR cc_start: 0.8290 (m-80) cc_final: 0.8069 (m-80) REVERT: J 81 GLN cc_start: 0.9054 (tp40) cc_final: 0.7942 (tm-30) outliers start: 2 outliers final: 2 residues processed: 297 average time/residue: 0.1961 time to fit residues: 84.1120 Evaluate side-chains 216 residues out of total 2124 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 214 time to evaluate : 0.830 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain b residue 445 CYS Chi-restraints excluded: chain f residue 445 CYS Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 237 random chunks: chunk 216 optimal weight: 2.9990 chunk 98 optimal weight: 6.9990 chunk 194 optimal weight: 5.9990 chunk 227 optimal weight: 8.9990 chunk 107 optimal weight: 3.9990 chunk 10 optimal weight: 5.9990 chunk 66 optimal weight: 7.9990 chunk 130 optimal weight: 3.9990 chunk 124 optimal weight: 2.9990 chunk 103 optimal weight: 3.9990 chunk 235 optimal weight: 5.9990 overall best weight: 3.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 35 ASN H 39 GLN L 38 GLN d 185 ASN I 35 ASN I 39 GLN J 35 ASN ** J 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3415 r_free = 0.3415 target = 0.063924 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2985 r_free = 0.2985 target = 0.047398 restraints weight = 78236.958| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3042 r_free = 0.3042 target = 0.049417 restraints weight = 38640.767| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3079 r_free = 0.3079 target = 0.050742 restraints weight = 26095.640| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3102 r_free = 0.3102 target = 0.051560 restraints weight = 20691.327| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3116 r_free = 0.3116 target = 0.052065 restraints weight = 17984.396| |-----------------------------------------------------------------------------| r_work (final): 0.3090 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8528 moved from start: 0.1755 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.076 21657 Z= 0.263 Angle : 0.845 17.539 29625 Z= 0.384 Chirality : 0.048 0.274 3641 Planarity : 0.005 0.045 3498 Dihedral : 10.580 78.936 5586 Min Nonbonded Distance : 2.501 Molprobity Statistics. All-atom Clashscore : 4.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.48 % Favored : 96.52 % Rotamer: Outliers : 1.88 % Allowed : 11.63 % Favored : 86.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % 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: -1.14 (0.16), residues: 2385 helix: 0.01 (0.25), residues: 429 sheet: -0.71 (0.20), residues: 594 loop : -0.99 (0.16), residues: 1362 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG H 105 TYR 0.020 0.002 TYR e 643 PHE 0.017 0.002 PHE M 62 TRP 0.011 0.001 TRP c 631 HIS 0.003 0.001 HIS f 216 Details of bonding type rmsd covalent geometry : bond 0.00600 (21470) covalent geometry : angle 0.76206 (29106) SS BOND : bond 0.00390 ( 42) SS BOND : angle 1.15762 ( 84) hydrogen bonds : bond 0.05099 ( 670) hydrogen bonds : angle 6.14649 ( 1815) link_ALPHA1-2 : bond 0.00664 ( 3) link_ALPHA1-2 : angle 2.69157 ( 9) link_ALPHA1-3 : bond 0.00455 ( 9) link_ALPHA1-3 : angle 2.36152 ( 27) link_ALPHA1-6 : bond 0.01254 ( 13) link_ALPHA1-6 : angle 2.29480 ( 39) link_BETA1-4 : bond 0.00749 ( 51) link_BETA1-4 : angle 3.60702 ( 153) link_NAG-ASN : bond 0.00442 ( 69) link_NAG-ASN : angle 2.86750 ( 207) *********************** 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 259 residues out of total 2124 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 219 time to evaluate : 0.799 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 81 GLN cc_start: 0.8638 (tp40) cc_final: 0.7735 (tm-30) REVERT: L 49 TYR cc_start: 0.8821 (p90) cc_final: 0.8355 (p90) REVERT: c 584 GLU cc_start: 0.8726 (mt-10) cc_final: 0.8262 (mt-10) REVERT: c 633 LYS cc_start: 0.9171 (mttm) cc_final: 0.8828 (mtmm) REVERT: c 644 ARG cc_start: 0.8653 (mmp80) cc_final: 0.8123 (mmp80) REVERT: c 647 GLU cc_start: 0.8517 (mt-10) cc_final: 0.8125 (mt-10) REVERT: c 654 GLU cc_start: 0.8736 (mm-30) cc_final: 0.8400 (mm-30) REVERT: c 655 LYS cc_start: 0.8901 (tptp) cc_final: 0.8534 (tppp) REVERT: c 656 ASN cc_start: 0.9405 (m-40) cc_final: 0.9067 (m110) REVERT: e 584 GLU cc_start: 0.8631 (mt-10) cc_final: 0.8027 (mt-10) REVERT: e 624 ASN cc_start: 0.9351 (m-40) cc_final: 0.9049 (m-40) REVERT: e 633 LYS cc_start: 0.9121 (mttp) cc_final: 0.8829 (mtmm) REVERT: e 643 TYR cc_start: 0.9393 (m-10) cc_final: 0.9024 (m-10) REVERT: e 644 ARG cc_start: 0.8613 (mmp80) cc_final: 0.8314 (mmp80) REVERT: e 647 GLU cc_start: 0.8675 (mt-10) cc_final: 0.7555 (mp0) REVERT: e 654 GLU cc_start: 0.8960 (tp30) cc_final: 0.8709 (tp30) REVERT: e 656 ASN cc_start: 0.9324 (m-40) cc_final: 0.9103 (m110) REVERT: e 659 GLU cc_start: 0.7224 (tm-30) cc_final: 0.6963 (tm-30) REVERT: g 633 LYS cc_start: 0.9062 (mttp) cc_final: 0.8785 (mtmm) REVERT: g 654 GLU cc_start: 0.8940 (tp30) cc_final: 0.8665 (mm-30) REVERT: g 655 LYS cc_start: 0.9117 (tptp) cc_final: 0.8452 (tptp) REVERT: g 659 GLU cc_start: 0.8326 (tt0) cc_final: 0.7736 (tm-30) REVERT: I 81 GLN cc_start: 0.8759 (tp40) cc_final: 0.7698 (tm-30) REVERT: M 81 GLU cc_start: 0.8908 (mm-30) cc_final: 0.8573 (mp0) REVERT: J 81 GLN cc_start: 0.8718 (tp40) cc_final: 0.7742 (tm-30) REVERT: N 27 GLN cc_start: 0.8158 (OUTLIER) cc_final: 0.7862 (mm-40) REVERT: N 81 GLU cc_start: 0.9254 (OUTLIER) cc_final: 0.8350 (tm-30) outliers start: 40 outliers final: 16 residues processed: 246 average time/residue: 0.1813 time to fit residues: 65.2026 Evaluate side-chains 205 residues out of total 2124 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 187 time to evaluate : 0.830 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 11 LEU Chi-restraints excluded: chain L residue 38 GLN Chi-restraints excluded: chain b residue 274 SER Chi-restraints excluded: chain d residue 38 VAL Chi-restraints excluded: chain d residue 125 LEU Chi-restraints excluded: chain d residue 445 CYS Chi-restraints excluded: chain d residue 491 ILE Chi-restraints excluded: chain f residue 51 THR Chi-restraints excluded: chain f residue 125 LEU Chi-restraints excluded: chain f residue 491 ILE Chi-restraints excluded: chain I residue 11 LEU Chi-restraints excluded: chain I residue 69 ILE Chi-restraints excluded: chain M residue 27 GLN Chi-restraints excluded: chain M residue 75 ILE Chi-restraints excluded: chain J residue 11 LEU Chi-restraints excluded: chain N residue 27 GLN Chi-restraints excluded: chain N residue 79 GLN Chi-restraints excluded: chain N residue 81 GLU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 237 random chunks: chunk 66 optimal weight: 4.9990 chunk 177 optimal weight: 1.9990 chunk 65 optimal weight: 0.8980 chunk 5 optimal weight: 3.9990 chunk 18 optimal weight: 9.9990 chunk 200 optimal weight: 5.9990 chunk 93 optimal weight: 1.9990 chunk 14 optimal weight: 6.9990 chunk 126 optimal weight: 8.9990 chunk 96 optimal weight: 2.9990 chunk 198 optimal weight: 6.9990 overall best weight: 2.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 39 GLN L 38 GLN d 258 GLN J 39 GLN N 38 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3375 r_free = 0.3375 target = 0.062903 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2933 r_free = 0.2933 target = 0.046037 restraints weight = 78360.974| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.2990 r_free = 0.2990 target = 0.048047 restraints weight = 38893.277| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3027 r_free = 0.3027 target = 0.049367 restraints weight = 26384.153| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 40)----------------| | r_work = 0.3050 r_free = 0.3050 target = 0.050179 restraints weight = 20996.934| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3064 r_free = 0.3064 target = 0.050682 restraints weight = 18314.904| |-----------------------------------------------------------------------------| r_work (final): 0.3076 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8535 moved from start: 0.2122 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 21657 Z= 0.183 Angle : 0.734 17.625 29625 Z= 0.332 Chirality : 0.046 0.277 3641 Planarity : 0.004 0.045 3498 Dihedral : 9.619 70.407 5584 Min Nonbonded Distance : 2.496 Molprobity Statistics. All-atom Clashscore : 5.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.82 % Favored : 96.18 % Rotamer: Outliers : 2.31 % Allowed : 10.73 % Favored : 86.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % 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: -0.84 (0.17), residues: 2385 helix: 0.62 (0.28), residues: 393 sheet: -0.50 (0.20), residues: 618 loop : -0.92 (0.16), residues: 1374 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG I 105 TYR 0.014 0.001 TYR M 91 PHE 0.015 0.002 PHE N 62 TRP 0.010 0.001 TRP c 631 HIS 0.002 0.001 HIS f 374 Details of bonding type rmsd covalent geometry : bond 0.00416 (21470) covalent geometry : angle 0.65439 (29106) SS BOND : bond 0.00286 ( 42) SS BOND : angle 0.90957 ( 84) hydrogen bonds : bond 0.04381 ( 670) hydrogen bonds : angle 5.62831 ( 1815) link_ALPHA1-2 : bond 0.00679 ( 3) link_ALPHA1-2 : angle 2.61616 ( 9) link_ALPHA1-3 : bond 0.00685 ( 9) link_ALPHA1-3 : angle 1.95859 ( 27) link_ALPHA1-6 : bond 0.00861 ( 13) link_ALPHA1-6 : angle 2.27706 ( 39) link_BETA1-4 : bond 0.00741 ( 51) link_BETA1-4 : angle 3.25982 ( 153) link_NAG-ASN : bond 0.00320 ( 69) link_NAG-ASN : angle 2.62129 ( 207) *********************** 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 259 residues out of total 2124 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 210 time to evaluate : 0.851 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 81 GLN cc_start: 0.8630 (tp40) cc_final: 0.7678 (tm-30) REVERT: L 18 LYS cc_start: 0.8670 (ttmm) cc_final: 0.8076 (tptt) REVERT: L 27 GLN cc_start: 0.8286 (mp10) cc_final: 0.7967 (mm-40) REVERT: L 49 TYR cc_start: 0.8855 (p90) cc_final: 0.8446 (p90) REVERT: L 81 GLU cc_start: 0.8848 (mm-30) cc_final: 0.8392 (tm-30) REVERT: c 584 GLU cc_start: 0.8712 (mt-10) cc_final: 0.8264 (mt-10) REVERT: c 632 ASP cc_start: 0.8820 (t70) cc_final: 0.8616 (t0) REVERT: c 633 LYS cc_start: 0.9166 (mttm) cc_final: 0.8789 (mtmm) REVERT: c 644 ARG cc_start: 0.8720 (mmp80) cc_final: 0.8502 (mmp80) REVERT: c 647 GLU cc_start: 0.8566 (mt-10) cc_final: 0.8348 (mt-10) REVERT: c 654 GLU cc_start: 0.8711 (mm-30) cc_final: 0.8505 (mm-30) REVERT: c 655 LYS cc_start: 0.8894 (tptp) cc_final: 0.8596 (tppp) REVERT: c 658 LYS cc_start: 0.8546 (mttt) cc_final: 0.8187 (mttt) REVERT: c 659 GLU cc_start: 0.7714 (tm-30) cc_final: 0.7464 (tm-30) REVERT: e 584 GLU cc_start: 0.8631 (mt-10) cc_final: 0.8124 (mt-10) REVERT: e 624 ASN cc_start: 0.9414 (m-40) cc_final: 0.9076 (m-40) REVERT: e 633 LYS cc_start: 0.9098 (mttp) cc_final: 0.8764 (mtmm) REVERT: e 643 TYR cc_start: 0.9344 (m-10) cc_final: 0.8920 (m-80) REVERT: e 644 ARG cc_start: 0.8594 (mmp80) cc_final: 0.8355 (mmp80) REVERT: e 647 GLU cc_start: 0.8688 (mt-10) cc_final: 0.7521 (mp0) REVERT: e 654 GLU cc_start: 0.8971 (tp30) cc_final: 0.8521 (tp30) REVERT: e 656 ASN cc_start: 0.9235 (m-40) cc_final: 0.8982 (m110) REVERT: g 633 LYS cc_start: 0.9081 (mttp) cc_final: 0.8786 (mtmm) REVERT: g 647 GLU cc_start: 0.8704 (mt-10) cc_final: 0.8411 (mt-10) REVERT: g 654 GLU cc_start: 0.8922 (OUTLIER) cc_final: 0.8718 (tt0) REVERT: g 655 LYS cc_start: 0.9117 (tptp) cc_final: 0.8399 (tptp) REVERT: g 659 GLU cc_start: 0.8383 (tt0) cc_final: 0.7769 (tm-30) REVERT: I 81 GLN cc_start: 0.8713 (tp40) cc_final: 0.7670 (tm-30) REVERT: I 83 ARG cc_start: 0.8349 (mpp80) cc_final: 0.7981 (mpp80) REVERT: M 4 MET cc_start: 0.8885 (mmp) cc_final: 0.8651 (mmm) REVERT: M 18 LYS cc_start: 0.8560 (ttmm) cc_final: 0.8049 (tptt) REVERT: M 81 GLU cc_start: 0.9020 (mm-30) cc_final: 0.8327 (tm-30) REVERT: J 81 GLN cc_start: 0.8686 (tp40) cc_final: 0.7631 (tm-30) REVERT: N 27 GLN cc_start: 0.8236 (OUTLIER) cc_final: 0.7926 (mm-40) REVERT: N 36 TYR cc_start: 0.8573 (m-80) cc_final: 0.8187 (m-80) REVERT: N 37 GLN cc_start: 0.8208 (OUTLIER) cc_final: 0.7610 (tm-30) REVERT: N 79 GLN cc_start: 0.7871 (tt0) cc_final: 0.6045 (tt0) REVERT: N 81 GLU cc_start: 0.9340 (OUTLIER) cc_final: 0.8412 (tm-30) outliers start: 49 outliers final: 19 residues processed: 249 average time/residue: 0.1741 time to fit residues: 64.8781 Evaluate side-chains 199 residues out of total 2124 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 176 time to evaluate : 0.848 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain b residue 38 VAL Chi-restraints excluded: chain b residue 274 SER Chi-restraints excluded: chain b residue 320 MET Chi-restraints excluded: chain b residue 445 CYS Chi-restraints excluded: chain d residue 38 VAL Chi-restraints excluded: chain d residue 125 LEU Chi-restraints excluded: chain d residue 445 CYS Chi-restraints excluded: chain d residue 488 VAL Chi-restraints excluded: chain d residue 491 ILE Chi-restraints excluded: chain f residue 38 VAL Chi-restraints excluded: chain f residue 51 THR Chi-restraints excluded: chain f residue 125 LEU Chi-restraints excluded: chain f residue 286 VAL Chi-restraints excluded: chain f residue 445 CYS Chi-restraints excluded: chain f residue 488 VAL Chi-restraints excluded: chain f residue 491 ILE Chi-restraints excluded: chain g residue 654 GLU Chi-restraints excluded: chain I residue 69 ILE Chi-restraints excluded: chain M residue 19 VAL Chi-restraints excluded: chain N residue 27 GLN Chi-restraints excluded: chain N residue 37 GLN Chi-restraints excluded: chain N residue 38 GLN Chi-restraints excluded: chain N residue 81 GLU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 237 random chunks: chunk 169 optimal weight: 5.9990 chunk 157 optimal weight: 2.9990 chunk 146 optimal weight: 2.9990 chunk 54 optimal weight: 3.9990 chunk 113 optimal weight: 4.9990 chunk 85 optimal weight: 0.4980 chunk 77 optimal weight: 5.9990 chunk 46 optimal weight: 6.9990 chunk 35 optimal weight: 2.9990 chunk 103 optimal weight: 3.9990 chunk 216 optimal weight: 8.9990 overall best weight: 2.6988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: b 478 ASN c 651 ASN d 478 ASN f 478 ASN J 39 GLN N 38 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3403 r_free = 0.3403 target = 0.063379 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.2968 r_free = 0.2968 target = 0.046799 restraints weight = 78292.976| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3025 r_free = 0.3025 target = 0.048790 restraints weight = 39468.315| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.3062 r_free = 0.3062 target = 0.050079 restraints weight = 26905.176| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3084 r_free = 0.3084 target = 0.050878 restraints weight = 21483.848| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3098 r_free = 0.3098 target = 0.051375 restraints weight = 18762.005| |-----------------------------------------------------------------------------| r_work (final): 0.3074 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8555 moved from start: 0.2444 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.043 21657 Z= 0.202 Angle : 0.729 17.288 29625 Z= 0.329 Chirality : 0.045 0.275 3641 Planarity : 0.004 0.045 3498 Dihedral : 9.060 61.595 5584 Min Nonbonded Distance : 2.491 Molprobity Statistics. All-atom Clashscore : 6.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.86 % Favored : 96.14 % Rotamer: Outliers : 1.98 % Allowed : 12.34 % Favored : 85.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % 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: -0.76 (0.17), residues: 2385 helix: 0.69 (0.27), residues: 390 sheet: -0.41 (0.20), residues: 606 loop : -0.87 (0.16), residues: 1389 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG H 105 TYR 0.014 0.001 TYR N 91 PHE 0.013 0.002 PHE L 71 TRP 0.009 0.001 TRP c 631 HIS 0.003 0.001 HIS d 374 Details of bonding type rmsd covalent geometry : bond 0.00464 (21470) covalent geometry : angle 0.65474 (29106) SS BOND : bond 0.00492 ( 42) SS BOND : angle 0.95250 ( 84) hydrogen bonds : bond 0.03987 ( 670) hydrogen bonds : angle 5.47581 ( 1815) link_ALPHA1-2 : bond 0.00640 ( 3) link_ALPHA1-2 : angle 2.40687 ( 9) link_ALPHA1-3 : bond 0.00679 ( 9) link_ALPHA1-3 : angle 2.10124 ( 27) link_ALPHA1-6 : bond 0.00915 ( 13) link_ALPHA1-6 : angle 2.23550 ( 39) link_BETA1-4 : bond 0.00674 ( 51) link_BETA1-4 : angle 3.09262 ( 153) link_NAG-ASN : bond 0.00357 ( 69) link_NAG-ASN : angle 2.57036 ( 207) *********************** 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 233 residues out of total 2124 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 191 time to evaluate : 0.808 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 81 GLN cc_start: 0.8649 (tp40) cc_final: 0.7681 (tm-30) REVERT: L 18 LYS cc_start: 0.8657 (ttmm) cc_final: 0.8076 (tptt) REVERT: L 27 GLN cc_start: 0.8307 (mp10) cc_final: 0.7995 (mm-40) REVERT: L 81 GLU cc_start: 0.8908 (mm-30) cc_final: 0.8427 (tm-30) REVERT: c 584 GLU cc_start: 0.8670 (mt-10) cc_final: 0.8254 (mt-10) REVERT: c 632 ASP cc_start: 0.8805 (t70) cc_final: 0.8599 (t0) REVERT: c 633 LYS cc_start: 0.9135 (mttm) cc_final: 0.8878 (mmtt) REVERT: c 644 ARG cc_start: 0.8695 (mmp80) cc_final: 0.8131 (mmp80) REVERT: c 647 GLU cc_start: 0.8563 (mt-10) cc_final: 0.7744 (mt-10) REVERT: c 654 GLU cc_start: 0.8794 (mm-30) cc_final: 0.8439 (mm-30) REVERT: c 655 LYS cc_start: 0.8907 (tptp) cc_final: 0.8665 (tppp) REVERT: c 658 LYS cc_start: 0.8452 (mttt) cc_final: 0.7927 (mttp) REVERT: c 659 GLU cc_start: 0.7821 (tm-30) cc_final: 0.7490 (tm-30) REVERT: e 584 GLU cc_start: 0.8626 (mt-10) cc_final: 0.8126 (mt-10) REVERT: e 624 ASN cc_start: 0.9393 (m-40) cc_final: 0.9101 (m-40) REVERT: e 643 TYR cc_start: 0.9349 (m-10) cc_final: 0.8948 (m-80) REVERT: e 647 GLU cc_start: 0.8694 (mt-10) cc_final: 0.7662 (mp0) REVERT: e 654 GLU cc_start: 0.8908 (tp30) cc_final: 0.8561 (tp30) REVERT: g 520 ARG cc_start: 0.8935 (OUTLIER) cc_final: 0.7998 (mpp80) REVERT: g 633 LYS cc_start: 0.9045 (mttp) cc_final: 0.8768 (mtmm) REVERT: g 647 GLU cc_start: 0.8659 (mt-10) cc_final: 0.8425 (mt-10) REVERT: g 655 LYS cc_start: 0.9125 (tptp) cc_final: 0.8445 (tppp) REVERT: g 659 GLU cc_start: 0.8394 (tt0) cc_final: 0.7859 (tm-30) REVERT: I 81 GLN cc_start: 0.8724 (tp40) cc_final: 0.7674 (tm-30) REVERT: M 18 LYS cc_start: 0.8568 (ttmm) cc_final: 0.8046 (tptt) REVERT: M 27 GLN cc_start: 0.8363 (OUTLIER) cc_final: 0.7972 (mp10) REVERT: M 37 GLN cc_start: 0.8572 (OUTLIER) cc_final: 0.7890 (tm-30) REVERT: M 81 GLU cc_start: 0.9038 (mm-30) cc_final: 0.8334 (tm-30) REVERT: M 103 GLU cc_start: 0.7429 (tm-30) cc_final: 0.7056 (tm-30) REVERT: J 81 GLN cc_start: 0.8686 (tp40) cc_final: 0.7637 (tm-30) REVERT: N 18 LYS cc_start: 0.8620 (ttmm) cc_final: 0.8055 (tptt) REVERT: N 27 GLN cc_start: 0.8261 (mp10) cc_final: 0.7934 (mm-40) REVERT: N 36 TYR cc_start: 0.8714 (m-80) cc_final: 0.8299 (m-80) REVERT: N 79 GLN cc_start: 0.8001 (tt0) cc_final: 0.7786 (tt0) REVERT: N 81 GLU cc_start: 0.9332 (mm-30) cc_final: 0.9040 (mp0) outliers start: 42 outliers final: 23 residues processed: 223 average time/residue: 0.1926 time to fit residues: 62.7631 Evaluate side-chains 199 residues out of total 2124 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 173 time to evaluate : 0.896 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 11 LEU Chi-restraints excluded: chain b residue 38 VAL Chi-restraints excluded: chain b residue 274 SER Chi-restraints excluded: chain b residue 320 MET Chi-restraints excluded: chain b residue 445 CYS Chi-restraints excluded: chain d residue 38 VAL Chi-restraints excluded: chain d residue 125 LEU Chi-restraints excluded: chain d residue 194 ILE Chi-restraints excluded: chain d residue 434 MET Chi-restraints excluded: chain d residue 445 CYS Chi-restraints excluded: chain d residue 488 VAL Chi-restraints excluded: chain d residue 491 ILE Chi-restraints excluded: chain f residue 38 VAL Chi-restraints excluded: chain f residue 100 MET Chi-restraints excluded: chain f residue 125 LEU Chi-restraints excluded: chain f residue 286 VAL Chi-restraints excluded: chain f residue 445 CYS Chi-restraints excluded: chain f residue 488 VAL Chi-restraints excluded: chain f residue 491 ILE Chi-restraints excluded: chain g residue 520 ARG Chi-restraints excluded: chain I residue 11 LEU Chi-restraints excluded: chain I residue 69 ILE Chi-restraints excluded: chain M residue 27 GLN Chi-restraints excluded: chain M residue 37 GLN Chi-restraints excluded: chain J residue 11 LEU Chi-restraints excluded: chain N residue 38 GLN Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 237 random chunks: chunk 22 optimal weight: 7.9990 chunk 183 optimal weight: 4.9990 chunk 91 optimal weight: 4.9990 chunk 202 optimal weight: 4.9990 chunk 211 optimal weight: 10.0000 chunk 222 optimal weight: 10.0000 chunk 38 optimal weight: 4.9990 chunk 92 optimal weight: 0.3980 chunk 36 optimal weight: 0.9980 chunk 146 optimal weight: 1.9990 chunk 134 optimal weight: 5.9990 overall best weight: 2.6786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: c 543 GLN N 38 GLN N 90 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3369 r_free = 0.3369 target = 0.062430 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2920 r_free = 0.2920 target = 0.045532 restraints weight = 78560.666| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.2978 r_free = 0.2978 target = 0.047499 restraints weight = 39900.401| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3014 r_free = 0.3014 target = 0.048762 restraints weight = 27448.461| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 39)----------------| | r_work = 0.3037 r_free = 0.3037 target = 0.049562 restraints weight = 22079.877| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.3050 r_free = 0.3050 target = 0.050039 restraints weight = 19338.816| |-----------------------------------------------------------------------------| r_work (final): 0.3043 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8570 moved from start: 0.2678 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.043 21657 Z= 0.200 Angle : 0.716 17.119 29625 Z= 0.324 Chirality : 0.045 0.276 3641 Planarity : 0.004 0.044 3498 Dihedral : 8.747 59.899 5584 Min Nonbonded Distance : 2.488 Molprobity Statistics. All-atom Clashscore : 6.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.90 % Favored : 96.10 % Rotamer: Outliers : 2.35 % Allowed : 12.57 % Favored : 85.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % 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: -0.74 (0.17), residues: 2385 helix: 0.56 (0.27), residues: 408 sheet: -0.36 (0.20), residues: 603 loop : -0.84 (0.16), residues: 1374 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG J 105 TYR 0.014 0.001 TYR N 91 PHE 0.013 0.002 PHE N 71 TRP 0.008 0.001 TRP e 628 HIS 0.003 0.001 HIS f 374 Details of bonding type rmsd covalent geometry : bond 0.00459 (21470) covalent geometry : angle 0.64574 (29106) SS BOND : bond 0.00356 ( 42) SS BOND : angle 0.94561 ( 84) hydrogen bonds : bond 0.03863 ( 670) hydrogen bonds : angle 5.37829 ( 1815) link_ALPHA1-2 : bond 0.00637 ( 3) link_ALPHA1-2 : angle 2.36759 ( 9) link_ALPHA1-3 : bond 0.00715 ( 9) link_ALPHA1-3 : angle 2.04661 ( 27) link_ALPHA1-6 : bond 0.00848 ( 13) link_ALPHA1-6 : angle 1.87162 ( 39) link_BETA1-4 : bond 0.00668 ( 51) link_BETA1-4 : angle 2.98373 ( 153) link_NAG-ASN : bond 0.00347 ( 69) link_NAG-ASN : angle 2.52411 ( 207) *********************** 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 231 residues out of total 2124 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 181 time to evaluate : 0.833 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 81 GLN cc_start: 0.8680 (tp40) cc_final: 0.7659 (tm-30) REVERT: L 18 LYS cc_start: 0.8652 (ttmm) cc_final: 0.8063 (tptt) REVERT: L 27 GLN cc_start: 0.8348 (mp10) cc_final: 0.8032 (mm-40) REVERT: L 81 GLU cc_start: 0.8960 (mm-30) cc_final: 0.8700 (mp0) REVERT: c 584 GLU cc_start: 0.8676 (mt-10) cc_final: 0.8242 (mt-10) REVERT: c 632 ASP cc_start: 0.8804 (t70) cc_final: 0.8596 (t0) REVERT: c 633 LYS cc_start: 0.9126 (mttm) cc_final: 0.8863 (mmtt) REVERT: c 644 ARG cc_start: 0.8706 (mmp80) cc_final: 0.8173 (mmp80) REVERT: c 647 GLU cc_start: 0.8608 (mt-10) cc_final: 0.7807 (mt-10) REVERT: c 654 GLU cc_start: 0.8857 (mm-30) cc_final: 0.8424 (mm-30) REVERT: c 655 LYS cc_start: 0.8953 (tptp) cc_final: 0.8722 (tppp) REVERT: c 658 LYS cc_start: 0.8489 (mttp) cc_final: 0.7907 (mttt) REVERT: c 659 GLU cc_start: 0.7878 (tm-30) cc_final: 0.7496 (tm-30) REVERT: e 584 GLU cc_start: 0.8651 (mt-10) cc_final: 0.8158 (mt-10) REVERT: e 624 ASN cc_start: 0.9428 (m-40) cc_final: 0.9126 (m110) REVERT: e 644 ARG cc_start: 0.8833 (mmp80) cc_final: 0.8258 (mmp-170) REVERT: e 647 GLU cc_start: 0.8720 (mt-10) cc_final: 0.6740 (mt-10) REVERT: e 654 GLU cc_start: 0.8962 (tp30) cc_final: 0.8352 (tp30) REVERT: e 658 LYS cc_start: 0.8358 (mttt) cc_final: 0.7733 (mttp) REVERT: g 520 ARG cc_start: 0.8947 (OUTLIER) cc_final: 0.8008 (mpp80) REVERT: g 633 LYS cc_start: 0.9075 (mttp) cc_final: 0.8779 (mtmm) REVERT: g 644 ARG cc_start: 0.8829 (mmp80) cc_final: 0.8389 (mmp80) REVERT: g 655 LYS cc_start: 0.9148 (tptp) cc_final: 0.8537 (tptp) REVERT: g 659 GLU cc_start: 0.8434 (tt0) cc_final: 0.7816 (tm-30) REVERT: I 81 GLN cc_start: 0.8713 (tp40) cc_final: 0.7655 (tm-30) REVERT: M 18 LYS cc_start: 0.8560 (ttmm) cc_final: 0.8004 (tptt) REVERT: M 27 GLN cc_start: 0.8367 (mp10) cc_final: 0.7932 (mp10) REVERT: M 37 GLN cc_start: 0.8590 (OUTLIER) cc_final: 0.7818 (tm-30) REVERT: M 81 GLU cc_start: 0.9080 (mm-30) cc_final: 0.8561 (mp0) REVERT: M 103 GLU cc_start: 0.7397 (tm-30) cc_final: 0.7030 (tm-30) REVERT: J 81 GLN cc_start: 0.8693 (tp40) cc_final: 0.7641 (tm-30) REVERT: N 4 MET cc_start: 0.8912 (mmp) cc_final: 0.8703 (mmm) REVERT: N 18 LYS cc_start: 0.8618 (ttmm) cc_final: 0.8040 (tptt) REVERT: N 27 GLN cc_start: 0.8299 (mp10) cc_final: 0.7965 (mm-40) REVERT: N 37 GLN cc_start: 0.8571 (OUTLIER) cc_final: 0.7875 (tm-30) REVERT: N 79 GLN cc_start: 0.8047 (tt0) cc_final: 0.7826 (tt0) REVERT: N 81 GLU cc_start: 0.9369 (mm-30) cc_final: 0.9055 (mp0) outliers start: 50 outliers final: 29 residues processed: 222 average time/residue: 0.1895 time to fit residues: 61.6154 Evaluate side-chains 198 residues out of total 2124 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 166 time to evaluate : 0.843 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 11 LEU Chi-restraints excluded: chain L residue 97 SER Chi-restraints excluded: chain b residue 38 VAL Chi-restraints excluded: chain b residue 125 LEU Chi-restraints excluded: chain b residue 274 SER Chi-restraints excluded: chain b residue 320 MET Chi-restraints excluded: chain b residue 445 CYS Chi-restraints excluded: chain b residue 494 LEU Chi-restraints excluded: chain d residue 38 VAL Chi-restraints excluded: chain d residue 125 LEU Chi-restraints excluded: chain d residue 126 CYS Chi-restraints excluded: chain d residue 194 ILE Chi-restraints excluded: chain d residue 434 MET Chi-restraints excluded: chain d residue 445 CYS Chi-restraints excluded: chain d residue 488 VAL Chi-restraints excluded: chain d residue 491 ILE Chi-restraints excluded: chain f residue 38 VAL Chi-restraints excluded: chain f residue 100 MET Chi-restraints excluded: chain f residue 125 LEU Chi-restraints excluded: chain f residue 194 ILE Chi-restraints excluded: chain f residue 286 VAL Chi-restraints excluded: chain f residue 445 CYS Chi-restraints excluded: chain f residue 488 VAL Chi-restraints excluded: chain f residue 491 ILE Chi-restraints excluded: chain g residue 520 ARG Chi-restraints excluded: chain I residue 11 LEU Chi-restraints excluded: chain I residue 69 ILE Chi-restraints excluded: chain M residue 37 GLN Chi-restraints excluded: chain J residue 11 LEU Chi-restraints excluded: chain N residue 37 GLN Chi-restraints excluded: chain N residue 38 GLN Chi-restraints excluded: chain N residue 75 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 237 random chunks: chunk 7 optimal weight: 0.9990 chunk 175 optimal weight: 9.9990 chunk 97 optimal weight: 8.9990 chunk 229 optimal weight: 9.9990 chunk 131 optimal weight: 0.0670 chunk 121 optimal weight: 2.9990 chunk 217 optimal weight: 7.9990 chunk 116 optimal weight: 0.8980 chunk 119 optimal weight: 10.0000 chunk 58 optimal weight: 9.9990 chunk 35 optimal weight: 2.9990 overall best weight: 1.5924 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: g 640 GLN M 38 GLN N 38 GLN N 90 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3397 r_free = 0.3397 target = 0.063356 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2971 r_free = 0.2971 target = 0.046904 restraints weight = 76853.916| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3027 r_free = 0.3027 target = 0.048892 restraints weight = 37602.813| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3063 r_free = 0.3063 target = 0.050188 restraints weight = 25276.955| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.3086 r_free = 0.3086 target = 0.051008 restraints weight = 19994.769| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3100 r_free = 0.3100 target = 0.051511 restraints weight = 17339.825| |-----------------------------------------------------------------------------| r_work (final): 0.3076 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8532 moved from start: 0.2760 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 21657 Z= 0.142 Angle : 0.678 16.896 29625 Z= 0.306 Chirality : 0.045 0.269 3641 Planarity : 0.003 0.045 3498 Dihedral : 8.372 59.541 5584 Min Nonbonded Distance : 2.487 Molprobity Statistics. All-atom Clashscore : 6.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.56 % Favored : 96.44 % Rotamer: Outliers : 1.65 % Allowed : 13.51 % Favored : 84.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % 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: -0.67 (0.17), residues: 2385 helix: 0.65 (0.28), residues: 408 sheet: -0.33 (0.21), residues: 576 loop : -0.80 (0.16), residues: 1401 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG I 105 TYR 0.014 0.001 TYR N 91 PHE 0.010 0.001 PHE f 317 TRP 0.008 0.001 TRP I 47 HIS 0.003 0.000 HIS d 374 Details of bonding type rmsd covalent geometry : bond 0.00324 (21470) covalent geometry : angle 0.60878 (29106) SS BOND : bond 0.00302 ( 42) SS BOND : angle 0.84154 ( 84) hydrogen bonds : bond 0.03608 ( 670) hydrogen bonds : angle 5.24324 ( 1815) link_ALPHA1-2 : bond 0.00665 ( 3) link_ALPHA1-2 : angle 2.29489 ( 9) link_ALPHA1-3 : bond 0.00821 ( 9) link_ALPHA1-3 : angle 1.92511 ( 27) link_ALPHA1-6 : bond 0.00945 ( 13) link_ALPHA1-6 : angle 1.67820 ( 39) link_BETA1-4 : bond 0.00680 ( 51) link_BETA1-4 : angle 2.89539 ( 153) link_NAG-ASN : bond 0.00327 ( 69) link_NAG-ASN : angle 2.43791 ( 207) *********************** 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 229 residues out of total 2124 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 194 time to evaluate : 0.819 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 68 ILE cc_start: 0.9648 (mm) cc_final: 0.9177 (tt) REVERT: H 81 GLN cc_start: 0.8711 (tp40) cc_final: 0.7637 (tm-30) REVERT: L 18 LYS cc_start: 0.8664 (ttmm) cc_final: 0.8049 (tptt) REVERT: L 81 GLU cc_start: 0.8959 (mm-30) cc_final: 0.8534 (mp0) REVERT: b 161 MET cc_start: 0.8375 (tpp) cc_final: 0.7656 (tpp) REVERT: c 584 GLU cc_start: 0.8699 (mt-10) cc_final: 0.8266 (mt-10) REVERT: c 632 ASP cc_start: 0.8808 (t70) cc_final: 0.8604 (t0) REVERT: c 633 LYS cc_start: 0.9083 (mttm) cc_final: 0.8805 (mmtt) REVERT: c 644 ARG cc_start: 0.8696 (mmp80) cc_final: 0.8136 (mmp80) REVERT: c 647 GLU cc_start: 0.8615 (mt-10) cc_final: 0.7799 (mt-10) REVERT: c 654 GLU cc_start: 0.8840 (mm-30) cc_final: 0.8612 (mm-30) REVERT: c 655 LYS cc_start: 0.8986 (tptp) cc_final: 0.8747 (tppp) REVERT: c 658 LYS cc_start: 0.8435 (mttp) cc_final: 0.8054 (mttp) REVERT: c 659 GLU cc_start: 0.7889 (tm-30) cc_final: 0.7495 (tm-30) REVERT: d 95 MET cc_start: 0.8878 (ptm) cc_final: 0.8598 (ppp) REVERT: e 584 GLU cc_start: 0.8658 (mt-10) cc_final: 0.8142 (mt-10) REVERT: e 624 ASN cc_start: 0.9444 (m-40) cc_final: 0.9133 (m110) REVERT: e 644 ARG cc_start: 0.8789 (mmp80) cc_final: 0.8325 (mmp80) REVERT: e 647 GLU cc_start: 0.8812 (mt-10) cc_final: 0.7911 (mt-10) REVERT: e 654 GLU cc_start: 0.8952 (tp30) cc_final: 0.8534 (tp30) REVERT: e 658 LYS cc_start: 0.8361 (mttt) cc_final: 0.7819 (mttp) REVERT: g 520 ARG cc_start: 0.8936 (OUTLIER) cc_final: 0.8012 (mpp80) REVERT: g 542 ARG cc_start: 0.8890 (ttm110) cc_final: 0.8551 (ttp80) REVERT: g 633 LYS cc_start: 0.9074 (mttp) cc_final: 0.8821 (mmtt) REVERT: g 655 LYS cc_start: 0.9170 (tptp) cc_final: 0.8567 (tppp) REVERT: g 659 GLU cc_start: 0.8395 (tt0) cc_final: 0.7857 (tm-30) REVERT: I 81 GLN cc_start: 0.8711 (tp40) cc_final: 0.7651 (tm-30) REVERT: I 100 LYS cc_start: 0.8911 (mmmt) cc_final: 0.8560 (mmmt) REVERT: M 18 LYS cc_start: 0.8551 (ttmm) cc_final: 0.7983 (tptt) REVERT: M 27 GLN cc_start: 0.8388 (mp10) cc_final: 0.7915 (mp10) REVERT: M 37 GLN cc_start: 0.8618 (OUTLIER) cc_final: 0.7884 (tm-30) REVERT: M 81 GLU cc_start: 0.9078 (mm-30) cc_final: 0.8683 (mp0) REVERT: M 92 ASN cc_start: 0.9129 (t0) cc_final: 0.8708 (m-40) REVERT: M 103 GLU cc_start: 0.7385 (tm-30) cc_final: 0.6996 (tm-30) REVERT: J 81 GLN cc_start: 0.8639 (tp40) cc_final: 0.7584 (tm-30) REVERT: N 18 LYS cc_start: 0.8648 (ttmm) cc_final: 0.8068 (tptt) REVERT: N 37 GLN cc_start: 0.8603 (OUTLIER) cc_final: 0.7922 (tm-30) REVERT: N 55 GLU cc_start: 0.8942 (tp30) cc_final: 0.8716 (tp30) REVERT: N 81 GLU cc_start: 0.9363 (mm-30) cc_final: 0.9070 (mp0) REVERT: N 92 ASN cc_start: 0.9135 (t0) cc_final: 0.8890 (m-40) outliers start: 35 outliers final: 18 residues processed: 220 average time/residue: 0.1866 time to fit residues: 59.9139 Evaluate side-chains 195 residues out of total 2124 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 174 time to evaluate : 0.770 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 11 LEU Chi-restraints excluded: chain b residue 38 VAL Chi-restraints excluded: chain b residue 125 LEU Chi-restraints excluded: chain b residue 274 SER Chi-restraints excluded: chain b residue 445 CYS Chi-restraints excluded: chain d residue 125 LEU Chi-restraints excluded: chain d residue 434 MET Chi-restraints excluded: chain d residue 445 CYS Chi-restraints excluded: chain d residue 488 VAL Chi-restraints excluded: chain d residue 491 ILE Chi-restraints excluded: chain f residue 125 LEU Chi-restraints excluded: chain f residue 194 ILE Chi-restraints excluded: chain f residue 286 VAL Chi-restraints excluded: chain f residue 445 CYS Chi-restraints excluded: chain f residue 491 ILE Chi-restraints excluded: chain g residue 520 ARG Chi-restraints excluded: chain I residue 69 ILE Chi-restraints excluded: chain M residue 37 GLN Chi-restraints excluded: chain M residue 60 SER Chi-restraints excluded: chain N residue 37 GLN Chi-restraints excluded: chain N residue 75 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 237 random chunks: chunk 183 optimal weight: 0.7980 chunk 12 optimal weight: 5.9990 chunk 211 optimal weight: 20.0000 chunk 87 optimal weight: 2.9990 chunk 129 optimal weight: 0.6980 chunk 41 optimal weight: 0.4980 chunk 150 optimal weight: 6.9990 chunk 92 optimal weight: 0.8980 chunk 30 optimal weight: 2.9990 chunk 189 optimal weight: 2.9990 chunk 186 optimal weight: 10.0000 overall best weight: 1.1782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3404 r_free = 0.3404 target = 0.063629 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2968 r_free = 0.2968 target = 0.046948 restraints weight = 77599.003| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3026 r_free = 0.3026 target = 0.048971 restraints weight = 38410.662| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3064 r_free = 0.3064 target = 0.050299 restraints weight = 26011.130| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.3086 r_free = 0.3086 target = 0.051116 restraints weight = 20644.292| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3100 r_free = 0.3100 target = 0.051612 restraints weight = 17943.130| |-----------------------------------------------------------------------------| r_work (final): 0.3101 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8520 moved from start: 0.2885 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 21657 Z= 0.124 Angle : 0.663 16.582 29625 Z= 0.301 Chirality : 0.044 0.270 3641 Planarity : 0.003 0.044 3498 Dihedral : 7.985 59.284 5584 Min Nonbonded Distance : 2.482 Molprobity Statistics. All-atom Clashscore : 5.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.69 % Favored : 96.31 % Rotamer: Outliers : 1.41 % Allowed : 14.45 % Favored : 84.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % 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: -0.55 (0.17), residues: 2385 helix: 0.72 (0.28), residues: 408 sheet: -0.19 (0.21), residues: 576 loop : -0.75 (0.16), residues: 1401 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG J 105 TYR 0.014 0.001 TYR M 91 PHE 0.008 0.001 PHE H 100C TRP 0.008 0.001 TRP I 47 HIS 0.002 0.000 HIS d 374 Details of bonding type rmsd covalent geometry : bond 0.00281 (21470) covalent geometry : angle 0.59804 (29106) SS BOND : bond 0.00280 ( 42) SS BOND : angle 0.76202 ( 84) hydrogen bonds : bond 0.03373 ( 670) hydrogen bonds : angle 5.12345 ( 1815) link_ALPHA1-2 : bond 0.00670 ( 3) link_ALPHA1-2 : angle 2.20386 ( 9) link_ALPHA1-3 : bond 0.00874 ( 9) link_ALPHA1-3 : angle 1.81664 ( 27) link_ALPHA1-6 : bond 0.00995 ( 13) link_ALPHA1-6 : angle 1.50829 ( 39) link_BETA1-4 : bond 0.00684 ( 51) link_BETA1-4 : angle 2.80840 ( 153) link_NAG-ASN : bond 0.00327 ( 69) link_NAG-ASN : angle 2.35853 ( 207) *********************** 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 2124 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 205 time to evaluate : 0.803 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: L 18 LYS cc_start: 0.8653 (ttmm) cc_final: 0.8044 (tptt) REVERT: L 81 GLU cc_start: 0.8892 (mm-30) cc_final: 0.8543 (mp0) REVERT: b 161 MET cc_start: 0.8357 (tpp) cc_final: 0.7636 (tpp) REVERT: c 530 MET cc_start: 0.8277 (mtt) cc_final: 0.7784 (mtt) REVERT: c 584 GLU cc_start: 0.8694 (mt-10) cc_final: 0.8278 (mt-10) REVERT: c 632 ASP cc_start: 0.8795 (t70) cc_final: 0.8533 (t0) REVERT: c 633 LYS cc_start: 0.9083 (mttm) cc_final: 0.8800 (mmtt) REVERT: c 644 ARG cc_start: 0.8691 (mmp80) cc_final: 0.7859 (mmp80) REVERT: c 647 GLU cc_start: 0.8602 (mt-10) cc_final: 0.7560 (mt-10) REVERT: c 655 LYS cc_start: 0.8976 (tptp) cc_final: 0.8747 (tppp) REVERT: c 658 LYS cc_start: 0.8424 (mttp) cc_final: 0.8043 (mttp) REVERT: c 659 GLU cc_start: 0.7901 (tm-30) cc_final: 0.7511 (tm-30) REVERT: d 95 MET cc_start: 0.8895 (ptm) cc_final: 0.8596 (ppp) REVERT: e 584 GLU cc_start: 0.8668 (mt-10) cc_final: 0.8329 (mt-10) REVERT: e 624 ASN cc_start: 0.9459 (m-40) cc_final: 0.9126 (m110) REVERT: e 644 ARG cc_start: 0.8773 (mmp80) cc_final: 0.8403 (mmp80) REVERT: e 654 GLU cc_start: 0.8936 (tp30) cc_final: 0.8512 (tp30) REVERT: e 658 LYS cc_start: 0.8320 (mttt) cc_final: 0.7776 (mttp) REVERT: g 520 ARG cc_start: 0.8937 (OUTLIER) cc_final: 0.8019 (mpp80) REVERT: g 542 ARG cc_start: 0.8884 (ttm110) cc_final: 0.8593 (ttp80) REVERT: g 633 LYS cc_start: 0.9063 (mttp) cc_final: 0.8832 (mmtt) REVERT: g 647 GLU cc_start: 0.8787 (mt-10) cc_final: 0.8302 (mt-10) REVERT: g 655 LYS cc_start: 0.9189 (tptp) cc_final: 0.8672 (tptp) REVERT: g 659 GLU cc_start: 0.8352 (tt0) cc_final: 0.7766 (tm-30) REVERT: I 81 GLN cc_start: 0.8724 (tp40) cc_final: 0.7506 (tm-30) REVERT: I 100 LYS cc_start: 0.8890 (mmmt) cc_final: 0.8565 (mmmt) REVERT: M 18 LYS cc_start: 0.8536 (ttmm) cc_final: 0.7930 (tptt) REVERT: M 27 GLN cc_start: 0.8388 (mp10) cc_final: 0.7867 (mp10) REVERT: M 37 GLN cc_start: 0.8556 (OUTLIER) cc_final: 0.7898 (tm-30) REVERT: M 81 GLU cc_start: 0.9094 (mm-30) cc_final: 0.8728 (mp0) REVERT: M 92 ASN cc_start: 0.9102 (t0) cc_final: 0.8418 (m-40) REVERT: M 103 GLU cc_start: 0.7370 (tm-30) cc_final: 0.6941 (tm-30) REVERT: J 81 GLN cc_start: 0.8661 (tp40) cc_final: 0.7588 (tm-30) REVERT: N 18 LYS cc_start: 0.8660 (ttmm) cc_final: 0.8068 (tptt) REVERT: N 27 GLN cc_start: 0.8365 (mp10) cc_final: 0.8091 (mp10) REVERT: N 36 TYR cc_start: 0.8796 (m-80) cc_final: 0.8361 (m-80) REVERT: N 37 GLN cc_start: 0.8634 (OUTLIER) cc_final: 0.7977 (tm-30) REVERT: N 55 GLU cc_start: 0.8928 (tp30) cc_final: 0.8688 (tp30) REVERT: N 79 GLN cc_start: 0.7966 (tt0) cc_final: 0.7756 (tt0) REVERT: N 81 GLU cc_start: 0.9377 (mm-30) cc_final: 0.9015 (mp0) REVERT: N 92 ASN cc_start: 0.9149 (t0) cc_final: 0.8901 (m-40) outliers start: 30 outliers final: 17 residues processed: 227 average time/residue: 0.1946 time to fit residues: 64.0139 Evaluate side-chains 200 residues out of total 2124 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 180 time to evaluate : 0.805 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain b residue 38 VAL Chi-restraints excluded: chain b residue 244 THR Chi-restraints excluded: chain b residue 445 CYS Chi-restraints excluded: chain d residue 38 VAL Chi-restraints excluded: chain d residue 125 LEU Chi-restraints excluded: chain d residue 445 CYS Chi-restraints excluded: chain d residue 488 VAL Chi-restraints excluded: chain d residue 491 ILE Chi-restraints excluded: chain e residue 567 LYS Chi-restraints excluded: chain f residue 38 VAL Chi-restraints excluded: chain f residue 286 VAL Chi-restraints excluded: chain f residue 445 CYS Chi-restraints excluded: chain f residue 488 VAL Chi-restraints excluded: chain f residue 491 ILE Chi-restraints excluded: chain g residue 520 ARG Chi-restraints excluded: chain I residue 69 ILE Chi-restraints excluded: chain M residue 37 GLN Chi-restraints excluded: chain M residue 60 SER Chi-restraints excluded: chain N residue 37 GLN Chi-restraints excluded: chain N residue 75 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 237 random chunks: chunk 208 optimal weight: 5.9990 chunk 198 optimal weight: 8.9990 chunk 171 optimal weight: 0.7980 chunk 62 optimal weight: 4.9990 chunk 179 optimal weight: 0.9990 chunk 26 optimal weight: 4.9990 chunk 165 optimal weight: 0.8980 chunk 24 optimal weight: 4.9990 chunk 102 optimal weight: 8.9990 chunk 221 optimal weight: 8.9990 chunk 155 optimal weight: 5.9990 overall best weight: 2.5386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 81 GLN b 258 GLN f 258 GLN N 90 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3383 r_free = 0.3383 target = 0.062761 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2943 r_free = 0.2943 target = 0.046057 restraints weight = 77872.910| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3001 r_free = 0.3001 target = 0.048041 restraints weight = 38508.916| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3038 r_free = 0.3038 target = 0.049350 restraints weight = 26072.167| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3061 r_free = 0.3061 target = 0.050143 restraints weight = 20710.615| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3074 r_free = 0.3074 target = 0.050637 restraints weight = 18040.414| |-----------------------------------------------------------------------------| r_work (final): 0.3054 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8558 moved from start: 0.3039 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 21657 Z= 0.191 Angle : 0.692 16.456 29625 Z= 0.316 Chirality : 0.044 0.273 3641 Planarity : 0.004 0.046 3498 Dihedral : 7.929 59.987 5584 Min Nonbonded Distance : 2.478 Molprobity Statistics. All-atom Clashscore : 6.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.11 % Favored : 95.89 % Rotamer: Outliers : 1.93 % Allowed : 14.69 % Favored : 83.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.52 (0.17), residues: 2385 helix: 0.76 (0.28), residues: 408 sheet: -0.22 (0.20), residues: 636 loop : -0.71 (0.17), residues: 1341 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG H 105 TYR 0.017 0.001 TYR L 91 PHE 0.012 0.001 PHE f 317 TRP 0.009 0.001 TRP L 32 HIS 0.003 0.001 HIS f 374 Details of bonding type rmsd covalent geometry : bond 0.00440 (21470) covalent geometry : angle 0.62928 (29106) SS BOND : bond 0.00307 ( 42) SS BOND : angle 0.90064 ( 84) hydrogen bonds : bond 0.03562 ( 670) hydrogen bonds : angle 5.12992 ( 1815) link_ALPHA1-2 : bond 0.00561 ( 3) link_ALPHA1-2 : angle 2.12385 ( 9) link_ALPHA1-3 : bond 0.00700 ( 9) link_ALPHA1-3 : angle 1.90375 ( 27) link_ALPHA1-6 : bond 0.00906 ( 13) link_ALPHA1-6 : angle 1.51799 ( 39) link_BETA1-4 : bond 0.00640 ( 51) link_BETA1-4 : angle 2.76703 ( 153) link_NAG-ASN : bond 0.00353 ( 69) link_NAG-ASN : angle 2.40501 ( 207) *********************** 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 222 residues out of total 2124 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 181 time to evaluate : 0.830 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 3 GLN cc_start: 0.8294 (tp-100) cc_final: 0.8061 (tp-100) REVERT: L 18 LYS cc_start: 0.8633 (ttmm) cc_final: 0.8009 (tptt) REVERT: L 81 GLU cc_start: 0.8963 (mm-30) cc_final: 0.8643 (mp0) REVERT: c 584 GLU cc_start: 0.8720 (mt-10) cc_final: 0.8293 (mt-10) REVERT: c 632 ASP cc_start: 0.8903 (t70) cc_final: 0.8675 (t0) REVERT: c 633 LYS cc_start: 0.9106 (mttm) cc_final: 0.8756 (mtmm) REVERT: c 644 ARG cc_start: 0.8697 (mmp80) cc_final: 0.8038 (mmp80) REVERT: c 647 GLU cc_start: 0.8570 (mt-10) cc_final: 0.7404 (mt-10) REVERT: c 654 GLU cc_start: 0.8937 (mm-30) cc_final: 0.8612 (mm-30) REVERT: c 655 LYS cc_start: 0.8994 (tptp) cc_final: 0.8748 (tppp) REVERT: c 658 LYS cc_start: 0.8456 (mttp) cc_final: 0.8038 (mttp) REVERT: c 659 GLU cc_start: 0.7950 (tm-30) cc_final: 0.7563 (tm-30) REVERT: e 584 GLU cc_start: 0.8680 (mt-10) cc_final: 0.8160 (mt-10) REVERT: e 624 ASN cc_start: 0.9464 (m-40) cc_final: 0.9152 (m110) REVERT: e 644 ARG cc_start: 0.8762 (mmp80) cc_final: 0.8413 (mmp80) REVERT: e 654 GLU cc_start: 0.8928 (tp30) cc_final: 0.8359 (tp30) REVERT: e 658 LYS cc_start: 0.8391 (mttt) cc_final: 0.7749 (mttp) REVERT: g 520 ARG cc_start: 0.8960 (OUTLIER) cc_final: 0.8031 (mpp80) REVERT: g 633 LYS cc_start: 0.9082 (mttp) cc_final: 0.8861 (mmtt) REVERT: g 647 GLU cc_start: 0.8810 (mt-10) cc_final: 0.8504 (mt-10) REVERT: g 655 LYS cc_start: 0.9123 (tptp) cc_final: 0.8582 (tptp) REVERT: g 659 GLU cc_start: 0.8375 (tt0) cc_final: 0.7755 (tm-30) REVERT: I 75 LYS cc_start: 0.9523 (mtpp) cc_final: 0.9299 (mtmm) REVERT: I 81 GLN cc_start: 0.8562 (tp40) cc_final: 0.7612 (tm-30) REVERT: I 83 ARG cc_start: 0.8244 (mpp80) cc_final: 0.7699 (mpp80) REVERT: I 100 LYS cc_start: 0.8933 (mmmt) cc_final: 0.8671 (mmmt) REVERT: M 18 LYS cc_start: 0.8548 (ttmm) cc_final: 0.7984 (tptt) REVERT: M 27 GLN cc_start: 0.8413 (mp10) cc_final: 0.7882 (mp10) REVERT: M 37 GLN cc_start: 0.8566 (OUTLIER) cc_final: 0.7954 (tm-30) REVERT: M 55 GLU cc_start: 0.8686 (tp30) cc_final: 0.8357 (tp30) REVERT: M 81 GLU cc_start: 0.9071 (mm-30) cc_final: 0.8634 (mp0) REVERT: M 92 ASN cc_start: 0.9115 (t0) cc_final: 0.8816 (m-40) REVERT: M 103 GLU cc_start: 0.7374 (tm-30) cc_final: 0.6956 (tm-30) REVERT: J 81 GLN cc_start: 0.8655 (tp40) cc_final: 0.7530 (tm-30) REVERT: N 18 LYS cc_start: 0.8667 (ttmm) cc_final: 0.8074 (tptt) REVERT: N 36 TYR cc_start: 0.8853 (m-80) cc_final: 0.8406 (m-80) REVERT: N 37 GLN cc_start: 0.8659 (OUTLIER) cc_final: 0.8019 (tm-30) REVERT: N 55 GLU cc_start: 0.8923 (tp30) cc_final: 0.8659 (tp30) REVERT: N 79 GLN cc_start: 0.7986 (tt0) cc_final: 0.7767 (tt0) REVERT: N 81 GLU cc_start: 0.9367 (mm-30) cc_final: 0.9001 (mp0) outliers start: 41 outliers final: 27 residues processed: 216 average time/residue: 0.1770 time to fit residues: 56.3675 Evaluate side-chains 203 residues out of total 2124 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 173 time to evaluate : 0.592 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 11 LEU Chi-restraints excluded: chain H residue 81 GLN Chi-restraints excluded: chain L residue 97 SER Chi-restraints excluded: chain b residue 38 VAL Chi-restraints excluded: chain b residue 125 LEU Chi-restraints excluded: chain b residue 245 VAL Chi-restraints excluded: chain b residue 320 MET Chi-restraints excluded: chain b residue 445 CYS Chi-restraints excluded: chain d residue 38 VAL Chi-restraints excluded: chain d residue 125 LEU Chi-restraints excluded: chain d residue 445 CYS Chi-restraints excluded: chain d residue 488 VAL Chi-restraints excluded: chain d residue 491 ILE Chi-restraints excluded: chain e residue 567 LYS Chi-restraints excluded: chain f residue 38 VAL Chi-restraints excluded: chain f residue 125 LEU Chi-restraints excluded: chain f residue 194 ILE Chi-restraints excluded: chain f residue 245 VAL Chi-restraints excluded: chain f residue 286 VAL Chi-restraints excluded: chain f residue 445 CYS Chi-restraints excluded: chain f residue 488 VAL Chi-restraints excluded: chain f residue 491 ILE Chi-restraints excluded: chain g residue 520 ARG Chi-restraints excluded: chain I residue 11 LEU Chi-restraints excluded: chain I residue 69 ILE Chi-restraints excluded: chain M residue 37 GLN Chi-restraints excluded: chain M residue 60 SER Chi-restraints excluded: chain J residue 11 LEU Chi-restraints excluded: chain N residue 37 GLN Chi-restraints excluded: chain N residue 75 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 237 random chunks: chunk 215 optimal weight: 30.0000 chunk 201 optimal weight: 4.9990 chunk 229 optimal weight: 8.9990 chunk 163 optimal weight: 3.9990 chunk 191 optimal weight: 10.0000 chunk 177 optimal weight: 3.9990 chunk 148 optimal weight: 7.9990 chunk 42 optimal weight: 4.9990 chunk 43 optimal weight: 4.9990 chunk 27 optimal weight: 0.9980 chunk 179 optimal weight: 7.9990 overall best weight: 3.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 81 GLN L 90 GLN f 330 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3340 r_free = 0.3340 target = 0.061505 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2868 r_free = 0.2868 target = 0.044166 restraints weight = 81284.010| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 45)----------------| | r_work = 0.2925 r_free = 0.2925 target = 0.046064 restraints weight = 43568.853| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.2961 r_free = 0.2961 target = 0.047295 restraints weight = 30970.479| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.2983 r_free = 0.2983 target = 0.048049 restraints weight = 25370.472| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 21)----------------| | r_work = 0.2994 r_free = 0.2994 target = 0.048475 restraints weight = 22513.248| |-----------------------------------------------------------------------------| r_work (final): 0.2994 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8621 moved from start: 0.3189 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.050 21657 Z= 0.269 Angle : 0.749 16.571 29625 Z= 0.344 Chirality : 0.045 0.291 3641 Planarity : 0.004 0.047 3498 Dihedral : 8.018 59.936 5584 Min Nonbonded Distance : 2.475 Molprobity Statistics. All-atom Clashscore : 7.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.44 % Favored : 95.56 % Rotamer: Outliers : 1.84 % Allowed : 15.16 % Favored : 83.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % 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: -0.62 (0.17), residues: 2385 helix: 0.59 (0.27), residues: 411 sheet: -0.24 (0.20), residues: 627 loop : -0.77 (0.17), residues: 1347 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG I 105 TYR 0.015 0.001 TYR M 91 PHE 0.027 0.002 PHE b 468 TRP 0.022 0.001 TRP L 32 HIS 0.003 0.001 HIS f 374 Details of bonding type rmsd covalent geometry : bond 0.00617 (21470) covalent geometry : angle 0.68995 (29106) SS BOND : bond 0.00366 ( 42) SS BOND : angle 1.02339 ( 84) hydrogen bonds : bond 0.03804 ( 670) hydrogen bonds : angle 5.24005 ( 1815) link_ALPHA1-2 : bond 0.00478 ( 3) link_ALPHA1-2 : angle 2.10972 ( 9) link_ALPHA1-3 : bond 0.00563 ( 9) link_ALPHA1-3 : angle 1.95269 ( 27) link_ALPHA1-6 : bond 0.00829 ( 13) link_ALPHA1-6 : angle 1.54386 ( 39) link_BETA1-4 : bond 0.00628 ( 51) link_BETA1-4 : angle 2.75740 ( 153) link_NAG-ASN : bond 0.00413 ( 69) link_NAG-ASN : angle 2.47336 ( 207) *********************** 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 212 residues out of total 2124 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 173 time to evaluate : 0.796 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: L 18 LYS cc_start: 0.8639 (ttmm) cc_final: 0.8012 (tptt) REVERT: L 90 GLN cc_start: 0.9096 (OUTLIER) cc_final: 0.8511 (pp30) REVERT: b 161 MET cc_start: 0.8270 (tpp) cc_final: 0.7623 (tpp) REVERT: c 584 GLU cc_start: 0.8597 (mt-10) cc_final: 0.8244 (mt-10) REVERT: c 632 ASP cc_start: 0.8871 (t70) cc_final: 0.8653 (t0) REVERT: c 633 LYS cc_start: 0.9065 (mttm) cc_final: 0.8740 (mtmm) REVERT: c 644 ARG cc_start: 0.8678 (mmp80) cc_final: 0.8053 (mmp80) REVERT: c 647 GLU cc_start: 0.8541 (mt-10) cc_final: 0.7335 (mt-10) REVERT: c 654 GLU cc_start: 0.8990 (mm-30) cc_final: 0.8662 (mm-30) REVERT: c 655 LYS cc_start: 0.9037 (tptp) cc_final: 0.8786 (tppp) REVERT: c 658 LYS cc_start: 0.8505 (mttp) cc_final: 0.8084 (mttp) REVERT: c 659 GLU cc_start: 0.7974 (tm-30) cc_final: 0.7590 (tm-30) REVERT: e 584 GLU cc_start: 0.8602 (mt-10) cc_final: 0.8144 (mt-10) REVERT: e 644 ARG cc_start: 0.8722 (mmp80) cc_final: 0.8364 (mmp80) REVERT: e 654 GLU cc_start: 0.8956 (tp30) cc_final: 0.8565 (tp30) REVERT: e 658 LYS cc_start: 0.8462 (mttt) cc_final: 0.7967 (mttt) REVERT: g 520 ARG cc_start: 0.8987 (OUTLIER) cc_final: 0.8052 (mpp80) REVERT: g 633 LYS cc_start: 0.9055 (mttp) cc_final: 0.8783 (mtmm) REVERT: g 647 GLU cc_start: 0.8823 (mt-10) cc_final: 0.8583 (mt-10) REVERT: g 655 LYS cc_start: 0.9126 (tptp) cc_final: 0.8556 (tptp) REVERT: g 659 GLU cc_start: 0.8432 (tt0) cc_final: 0.7793 (tm-30) REVERT: I 81 GLN cc_start: 0.8580 (tp40) cc_final: 0.7519 (tm-30) REVERT: I 83 ARG cc_start: 0.8247 (mpp80) cc_final: 0.7736 (mpp80) REVERT: M 18 LYS cc_start: 0.8561 (ttmm) cc_final: 0.7986 (tptp) REVERT: M 27 GLN cc_start: 0.8433 (mp10) cc_final: 0.7920 (mp10) REVERT: M 37 GLN cc_start: 0.8627 (OUTLIER) cc_final: 0.7998 (tm-30) REVERT: M 55 GLU cc_start: 0.8711 (tp30) cc_final: 0.8403 (tp30) REVERT: M 81 GLU cc_start: 0.9106 (mm-30) cc_final: 0.8683 (mp0) REVERT: M 103 GLU cc_start: 0.7430 (tm-30) cc_final: 0.7008 (tm-30) REVERT: J 81 GLN cc_start: 0.8648 (tp40) cc_final: 0.7484 (tm-30) REVERT: N 18 LYS cc_start: 0.8666 (ttmm) cc_final: 0.8066 (tptt) REVERT: N 37 GLN cc_start: 0.8664 (OUTLIER) cc_final: 0.8039 (tm-30) REVERT: N 55 GLU cc_start: 0.8933 (tp30) cc_final: 0.8689 (tp30) REVERT: N 79 GLN cc_start: 0.8064 (tt0) cc_final: 0.7844 (tt0) REVERT: N 81 GLU cc_start: 0.9369 (mm-30) cc_final: 0.8992 (mp0) REVERT: N 92 ASN cc_start: 0.9074 (m-40) cc_final: 0.8754 (m-40) outliers start: 39 outliers final: 33 residues processed: 203 average time/residue: 0.1867 time to fit residues: 54.9384 Evaluate side-chains 204 residues out of total 2124 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 167 time to evaluate : 0.812 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 11 LEU Chi-restraints excluded: chain H residue 82 MET Chi-restraints excluded: chain L residue 90 GLN Chi-restraints excluded: chain L residue 97 SER Chi-restraints excluded: chain b residue 38 VAL Chi-restraints excluded: chain b residue 125 LEU Chi-restraints excluded: chain b residue 245 VAL Chi-restraints excluded: chain b residue 274 SER Chi-restraints excluded: chain b residue 320 MET Chi-restraints excluded: chain b residue 445 CYS Chi-restraints excluded: chain d residue 38 VAL Chi-restraints excluded: chain d residue 125 LEU Chi-restraints excluded: chain d residue 126 CYS Chi-restraints excluded: chain d residue 434 MET Chi-restraints excluded: chain d residue 445 CYS Chi-restraints excluded: chain d residue 488 VAL Chi-restraints excluded: chain d residue 491 ILE Chi-restraints excluded: chain e residue 567 LYS Chi-restraints excluded: chain f residue 38 VAL Chi-restraints excluded: chain f residue 51 THR Chi-restraints excluded: chain f residue 100 MET Chi-restraints excluded: chain f residue 125 LEU Chi-restraints excluded: chain f residue 194 ILE Chi-restraints excluded: chain f residue 245 VAL Chi-restraints excluded: chain f residue 286 VAL Chi-restraints excluded: chain f residue 445 CYS Chi-restraints excluded: chain f residue 488 VAL Chi-restraints excluded: chain f residue 491 ILE Chi-restraints excluded: chain g residue 520 ARG Chi-restraints excluded: chain I residue 11 LEU Chi-restraints excluded: chain I residue 68 ILE Chi-restraints excluded: chain I residue 69 ILE Chi-restraints excluded: chain M residue 37 GLN Chi-restraints excluded: chain M residue 60 SER Chi-restraints excluded: chain J residue 11 LEU Chi-restraints excluded: chain N residue 37 GLN Chi-restraints excluded: chain N residue 75 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 237 random chunks: chunk 15 optimal weight: 7.9990 chunk 89 optimal weight: 5.9990 chunk 80 optimal weight: 0.6980 chunk 228 optimal weight: 0.0770 chunk 213 optimal weight: 5.9990 chunk 19 optimal weight: 5.9990 chunk 95 optimal weight: 3.9990 chunk 203 optimal weight: 7.9990 chunk 215 optimal weight: 0.6980 chunk 152 optimal weight: 20.0000 chunk 45 optimal weight: 0.9990 overall best weight: 1.2942 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** L 92 ASN ** 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 = 0.3371 r_free = 0.3371 target = 0.062726 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2913 r_free = 0.2913 target = 0.045571 restraints weight = 80347.517| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.2972 r_free = 0.2972 target = 0.047565 restraints weight = 41674.474| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3009 r_free = 0.3009 target = 0.048867 restraints weight = 28939.778| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 40)----------------| | r_work = 0.3032 r_free = 0.3032 target = 0.049664 restraints weight = 23353.771| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 21)----------------| | r_work = 0.3043 r_free = 0.3043 target = 0.050085 restraints weight = 20523.236| |-----------------------------------------------------------------------------| r_work (final): 0.3043 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8563 moved from start: 0.3200 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 21657 Z= 0.135 Angle : 0.684 16.345 29625 Z= 0.313 Chirality : 0.044 0.271 3641 Planarity : 0.003 0.044 3498 Dihedral : 7.776 59.815 5584 Min Nonbonded Distance : 2.483 Molprobity Statistics. All-atom Clashscore : 6.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.82 % Favored : 96.18 % Rotamer: Outliers : 1.22 % Allowed : 15.63 % Favored : 83.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.50 (0.17), residues: 2385 helix: 0.76 (0.28), residues: 402 sheet: -0.05 (0.21), residues: 576 loop : -0.76 (0.16), residues: 1407 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG I 105 TYR 0.018 0.001 TYR N 91 PHE 0.020 0.001 PHE b 468 TRP 0.008 0.001 TRP J 47 HIS 0.002 0.000 HIS f 374 Details of bonding type rmsd covalent geometry : bond 0.00308 (21470) covalent geometry : angle 0.62416 (29106) SS BOND : bond 0.00267 ( 42) SS BOND : angle 0.79888 ( 84) hydrogen bonds : bond 0.03445 ( 670) hydrogen bonds : angle 5.08451 ( 1815) link_ALPHA1-2 : bond 0.00600 ( 3) link_ALPHA1-2 : angle 2.19201 ( 9) link_ALPHA1-3 : bond 0.00767 ( 9) link_ALPHA1-3 : angle 1.66191 ( 27) link_ALPHA1-6 : bond 0.00947 ( 13) link_ALPHA1-6 : angle 1.41954 ( 39) link_BETA1-4 : bond 0.00673 ( 51) link_BETA1-4 : angle 2.71637 ( 153) link_NAG-ASN : bond 0.00327 ( 69) link_NAG-ASN : angle 2.34439 ( 207) ********************** 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 209 residues out of total 2124 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 183 time to evaluate : 0.787 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: L 18 LYS cc_start: 0.8630 (ttmm) cc_final: 0.7995 (tptt) REVERT: L 81 GLU cc_start: 0.9056 (mm-30) cc_final: 0.8628 (mp0) REVERT: c 530 MET cc_start: 0.8361 (mtt) cc_final: 0.7842 (mtt) REVERT: c 584 GLU cc_start: 0.8659 (mt-10) cc_final: 0.8281 (mt-10) REVERT: c 632 ASP cc_start: 0.8861 (t70) cc_final: 0.8623 (t0) REVERT: c 633 LYS cc_start: 0.9034 (mttm) cc_final: 0.8744 (mmtt) REVERT: c 644 ARG cc_start: 0.8684 (mmp80) cc_final: 0.8036 (mmp80) REVERT: c 647 GLU cc_start: 0.8597 (mt-10) cc_final: 0.7389 (mt-10) REVERT: c 654 GLU cc_start: 0.8990 (mm-30) cc_final: 0.8649 (mm-30) REVERT: c 655 LYS cc_start: 0.9025 (tptp) cc_final: 0.8764 (tppp) REVERT: c 658 LYS cc_start: 0.8485 (mttp) cc_final: 0.8056 (mttp) REVERT: c 659 GLU cc_start: 0.7933 (tm-30) cc_final: 0.7544 (tm-30) REVERT: e 584 GLU cc_start: 0.8629 (mt-10) cc_final: 0.8291 (mt-10) REVERT: e 644 ARG cc_start: 0.8738 (mmp80) cc_final: 0.8377 (mmp80) REVERT: e 654 GLU cc_start: 0.8951 (tp30) cc_final: 0.8432 (tp30) REVERT: e 658 LYS cc_start: 0.8438 (mttt) cc_final: 0.7855 (mttp) REVERT: g 520 ARG cc_start: 0.8986 (OUTLIER) cc_final: 0.8063 (mpp80) REVERT: g 633 LYS cc_start: 0.9034 (mttp) cc_final: 0.8818 (mmtt) REVERT: g 647 GLU cc_start: 0.8871 (mt-10) cc_final: 0.8552 (mt-10) REVERT: g 655 LYS cc_start: 0.9109 (tptp) cc_final: 0.8615 (tptp) REVERT: g 659 GLU cc_start: 0.8375 (tt0) cc_final: 0.7767 (tm-30) REVERT: I 81 GLN cc_start: 0.8535 (tp40) cc_final: 0.7495 (tm-30) REVERT: I 83 ARG cc_start: 0.8290 (mpp80) cc_final: 0.7775 (mpp80) REVERT: M 27 GLN cc_start: 0.8425 (mp10) cc_final: 0.7892 (mp10) REVERT: M 37 GLN cc_start: 0.8569 (OUTLIER) cc_final: 0.7963 (tm-30) REVERT: M 55 GLU cc_start: 0.8604 (tp30) cc_final: 0.8306 (tp30) REVERT: M 81 GLU cc_start: 0.9111 (mm-30) cc_final: 0.8726 (mp0) REVERT: M 103 GLU cc_start: 0.7406 (tm-30) cc_final: 0.6962 (tm-30) REVERT: J 75 LYS cc_start: 0.9556 (mtpp) cc_final: 0.9323 (mtmm) REVERT: N 18 LYS cc_start: 0.8687 (ttmm) cc_final: 0.8066 (tptt) REVERT: N 36 TYR cc_start: 0.8812 (m-80) cc_final: 0.8353 (m-80) REVERT: N 37 GLN cc_start: 0.8636 (OUTLIER) cc_final: 0.8034 (tm-30) REVERT: N 55 GLU cc_start: 0.8888 (tp30) cc_final: 0.8633 (tp30) REVERT: N 79 GLN cc_start: 0.7964 (tt0) cc_final: 0.7754 (tt0) REVERT: N 81 GLU cc_start: 0.9378 (mm-30) cc_final: 0.9006 (mp0) REVERT: N 92 ASN cc_start: 0.8994 (m-40) cc_final: 0.8397 (m110) outliers start: 26 outliers final: 20 residues processed: 202 average time/residue: 0.1876 time to fit residues: 55.1799 Evaluate side-chains 199 residues out of total 2124 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 176 time to evaluate : 0.727 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain b residue 38 VAL Chi-restraints excluded: chain b residue 125 LEU Chi-restraints excluded: chain b residue 245 VAL Chi-restraints excluded: chain b residue 445 CYS Chi-restraints excluded: chain d residue 38 VAL Chi-restraints excluded: chain d residue 125 LEU Chi-restraints excluded: chain d residue 434 MET Chi-restraints excluded: chain d residue 445 CYS Chi-restraints excluded: chain d residue 488 VAL Chi-restraints excluded: chain d residue 491 ILE Chi-restraints excluded: chain e residue 567 LYS Chi-restraints excluded: chain f residue 38 VAL Chi-restraints excluded: chain f residue 245 VAL Chi-restraints excluded: chain f residue 286 VAL Chi-restraints excluded: chain f residue 445 CYS Chi-restraints excluded: chain f residue 488 VAL Chi-restraints excluded: chain f residue 491 ILE Chi-restraints excluded: chain g residue 520 ARG Chi-restraints excluded: chain I residue 69 ILE Chi-restraints excluded: chain M residue 37 GLN Chi-restraints excluded: chain M residue 60 SER Chi-restraints excluded: chain N residue 37 GLN Chi-restraints excluded: chain N residue 75 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 237 random chunks: chunk 155 optimal weight: 0.9980 chunk 116 optimal weight: 3.9990 chunk 15 optimal weight: 8.9990 chunk 220 optimal weight: 8.9990 chunk 141 optimal weight: 3.9990 chunk 109 optimal weight: 0.9990 chunk 162 optimal weight: 4.9990 chunk 2 optimal weight: 8.9990 chunk 99 optimal weight: 4.9990 chunk 47 optimal weight: 0.8980 chunk 77 optimal weight: 4.9990 overall best weight: 2.1786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: J 81 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3372 r_free = 0.3372 target = 0.062491 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2920 r_free = 0.2920 target = 0.045528 restraints weight = 78652.783| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.2978 r_free = 0.2978 target = 0.047496 restraints weight = 40311.092| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3015 r_free = 0.3015 target = 0.048783 restraints weight = 27804.663| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.3038 r_free = 0.3038 target = 0.049566 restraints weight = 22322.840| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3051 r_free = 0.3051 target = 0.050049 restraints weight = 19574.864| |-----------------------------------------------------------------------------| r_work (final): 0.3051 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8566 moved from start: 0.3273 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 21657 Z= 0.172 Angle : 0.693 16.251 29625 Z= 0.318 Chirality : 0.044 0.275 3641 Planarity : 0.003 0.046 3498 Dihedral : 7.750 59.628 5584 Min Nonbonded Distance : 2.478 Molprobity Statistics. All-atom Clashscore : 6.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.32 % Favored : 95.68 % Rotamer: Outliers : 1.41 % Allowed : 15.73 % Favored : 82.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % 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: -0.48 (0.17), residues: 2385 helix: 0.74 (0.27), residues: 408 sheet: -0.12 (0.20), residues: 636 loop : -0.71 (0.17), residues: 1341 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG I 105 TYR 0.018 0.001 TYR L 49 PHE 0.019 0.001 PHE b 468 TRP 0.014 0.001 TRP M 32 HIS 0.002 0.000 HIS f 374 Details of bonding type rmsd covalent geometry : bond 0.00399 (21470) covalent geometry : angle 0.63413 (29106) SS BOND : bond 0.00284 ( 42) SS BOND : angle 0.90728 ( 84) hydrogen bonds : bond 0.03483 ( 670) hydrogen bonds : angle 5.07788 ( 1815) link_ALPHA1-2 : bond 0.00552 ( 3) link_ALPHA1-2 : angle 2.10019 ( 9) link_ALPHA1-3 : bond 0.00636 ( 9) link_ALPHA1-3 : angle 1.71825 ( 27) link_ALPHA1-6 : bond 0.00865 ( 13) link_ALPHA1-6 : angle 1.45391 ( 39) link_BETA1-4 : bond 0.00635 ( 51) link_BETA1-4 : angle 2.67529 ( 153) link_NAG-ASN : bond 0.00346 ( 69) link_NAG-ASN : angle 2.36131 ( 207) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3401.14 seconds wall clock time: 60 minutes 6.52 seconds (3606.52 seconds total)