Starting phenix.real_space_refine on Wed May 21 06:06:52 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8dy6_27776/05_2025/8dy6_27776.cif Found real_map, /net/cci-nas-00/data/ceres_data/8dy6_27776/05_2025/8dy6_27776.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.32 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8dy6_27776/05_2025/8dy6_27776.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8dy6_27776/05_2025/8dy6_27776.map" model { file = "/net/cci-nas-00/data/ceres_data/8dy6_27776/05_2025/8dy6_27776.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8dy6_27776/05_2025/8dy6_27776.cif" } resolution = 4.32 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } 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= 0.006 sd= 0.128 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 132 5.16 5 C 12918 2.51 5 N 3363 2.21 5 O 4365 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 2 residue(s): 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/chem_data/mon_lib" Total number of atoms: 20778 Number of models: 1 Model: "" Number of chains: 54 Chain: "A" Number of atoms: 3604 Number of conformers: 1 Conformer: "" Number of residues, atoms: 461, 3604 Classifications: {'peptide': 461} Link IDs: {'PTRANS': 23, 'TRANS': 437} Chain: "B" Number of atoms: 972 Number of conformers: 1 Conformer: "" Number of residues, atoms: 122, 972 Classifications: {'peptide': 122} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 120} Chain breaks: 1 Chain: "C" Number of atoms: 999 Number of conformers: 1 Conformer: "" Number of residues, atoms: 126, 999 Classifications: {'peptide': 126} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 121} Chain: "D" Number of atoms: 777 Number of conformers: 1 Conformer: "" Number of residues, atoms: 106, 777 Classifications: {'peptide': 106} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 6, 'TRANS': 99} Chain: "E" Number of atoms: 3604 Number of conformers: 1 Conformer: "" Number of residues, atoms: 461, 3604 Classifications: {'peptide': 461} Link IDs: {'PTRANS': 23, 'TRANS': 437} Chain: "F" Number of atoms: 972 Number of conformers: 1 Conformer: "" Number of residues, atoms: 122, 972 Classifications: {'peptide': 122} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 120} Chain breaks: 1 Chain: "G" Number of atoms: 999 Number of conformers: 1 Conformer: "" Number of residues, atoms: 126, 999 Classifications: {'peptide': 126} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 121} Chain: "H" Number of atoms: 777 Number of conformers: 1 Conformer: "" Number of residues, atoms: 106, 777 Classifications: {'peptide': 106} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 6, 'TRANS': 99} Chain: "I" Number of atoms: 3604 Number of conformers: 1 Conformer: "" Number of residues, atoms: 461, 3604 Classifications: {'peptide': 461} Link IDs: {'PTRANS': 23, 'TRANS': 437} Chain: "J" Number of atoms: 972 Number of conformers: 1 Conformer: "" Number of residues, atoms: 122, 972 Classifications: {'peptide': 122} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 120} Chain breaks: 1 Chain: "K" Number of atoms: 999 Number of conformers: 1 Conformer: "" Number of residues, atoms: 126, 999 Classifications: {'peptide': 126} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 121} Chain: "L" Number of atoms: 777 Number of conformers: 1 Conformer: "" Number of residues, atoms: 106, 777 Classifications: {'peptide': 106} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 6, 'TRANS': 99} Chain: "M" 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: "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: 50 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 50 Unusual residues: {'BMA': 1, 'MAN': 1, 'NAG': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Chain: "P" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "Q" Number of atoms: 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: "R" 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: "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: 83 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 83 Unusual residues: {'BMA': 1, 'MAN': 4, 'NAG': 2} Classifications: {'undetermined': 7} Link IDs: {None: 6} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 21 Unresolved non-hydrogen chiralities: 7 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: 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: 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: "Y" 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: "Z" 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: "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: 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: "d" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "e" Number of atoms: 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: "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: 83 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 83 Unusual residues: {'BMA': 1, 'MAN': 4, 'NAG': 2} Classifications: {'undetermined': 7} Link IDs: {None: 6} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 21 Unresolved non-hydrogen chiralities: 7 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: 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: "j" 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: "k" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "l" Number of atoms: 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: 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: "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: 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: "p" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "q" Number of atoms: 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: 83 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 83 Unusual residues: {'BMA': 1, 'MAN': 4, 'NAG': 2} Classifications: {'undetermined': 7} Link IDs: {None: 6} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 21 Unresolved non-hydrogen chiralities: 7 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: 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: 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: "x" 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: "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: "A" 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: "E" Number of atoms: 56 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 56 Unusual residues: {'NAG': 4} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Chain: "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 Time building chain proxies: 12.78, per 1000 atoms: 0.62 Number of scatterers: 20778 At special positions: 0 Unit cell: (159.84, 156.6, 137.16, 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 132 16.00 O 4365 8.00 N 3363 7.00 C 12918 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=39, symmetry=0 Simple disulfide: pdb=" SG CYS A 54 " - pdb=" SG CYS A 74 " distance=2.03 Simple disulfide: pdb=" SG CYS A 119 " - pdb=" SG CYS A 205 " distance=2.03 Simple disulfide: pdb=" SG CYS A 126 " - pdb=" SG CYS A 196 " distance=2.03 Simple disulfide: pdb=" SG CYS A 131 " - pdb=" SG CYS A 155 " distance=2.03 Simple disulfide: pdb=" SG CYS A 201 " - pdb=" SG CYS A 433 " distance=2.02 Simple disulfide: pdb=" SG CYS A 218 " - pdb=" SG CYS A 247 " distance=2.03 Simple disulfide: pdb=" SG CYS A 228 " - pdb=" SG CYS A 239 " distance=2.03 Simple disulfide: pdb=" SG CYS A 296 " - pdb=" SG CYS A 331 " distance=2.02 Simple disulfide: pdb=" SG CYS A 378 " - pdb=" SG CYS A 445 " distance=2.03 Simple disulfide: pdb=" SG CYS A 385 " - pdb=" SG CYS A 418 " distance=2.03 Simple disulfide: pdb=" SG CYS B 598 " - pdb=" SG CYS B 604 " distance=2.03 Simple disulfide: pdb=" SG CYS C 22 " - pdb=" SG CYS C 96 " distance=2.04 Simple disulfide: pdb=" SG CYS D 22 " - pdb=" SG CYS D 90 " distance=2.02 Simple disulfide: pdb=" SG CYS E 54 " - pdb=" SG CYS E 74 " distance=2.03 Simple disulfide: pdb=" SG CYS E 119 " - pdb=" SG CYS E 205 " distance=2.03 Simple disulfide: pdb=" SG CYS E 126 " - pdb=" SG CYS E 196 " distance=2.03 Simple disulfide: pdb=" SG CYS E 131 " - pdb=" SG CYS E 155 " distance=2.03 Simple disulfide: pdb=" SG CYS E 201 " - pdb=" SG CYS E 433 " distance=2.03 Simple disulfide: pdb=" SG CYS E 218 " - pdb=" SG CYS E 247 " distance=2.03 Simple disulfide: pdb=" SG CYS E 228 " - pdb=" SG CYS E 239 " distance=2.03 Simple disulfide: pdb=" SG CYS E 296 " - pdb=" SG CYS E 331 " distance=2.03 Simple disulfide: pdb=" SG CYS E 378 " - pdb=" SG CYS E 445 " distance=2.03 Simple disulfide: pdb=" SG CYS E 385 " - pdb=" SG CYS E 418 " distance=2.03 Simple disulfide: pdb=" SG CYS F 598 " - pdb=" SG CYS F 604 " distance=2.03 Simple disulfide: pdb=" SG CYS G 22 " - pdb=" SG CYS G 96 " distance=2.04 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 90 " distance=2.03 Simple disulfide: pdb=" SG CYS I 54 " - pdb=" SG CYS I 74 " distance=2.03 Simple disulfide: pdb=" SG CYS I 119 " - pdb=" SG CYS I 205 " distance=2.03 Simple disulfide: pdb=" SG CYS I 126 " - pdb=" SG CYS I 196 " distance=2.03 Simple disulfide: pdb=" SG CYS I 131 " - pdb=" SG CYS I 155 " distance=2.03 Simple disulfide: pdb=" SG CYS I 201 " - pdb=" SG CYS I 433 " distance=2.03 Simple disulfide: pdb=" SG CYS I 218 " - pdb=" SG CYS I 247 " distance=2.03 Simple disulfide: pdb=" SG CYS I 228 " - pdb=" SG CYS I 239 " distance=2.03 Simple disulfide: pdb=" SG CYS I 296 " - pdb=" SG CYS I 331 " distance=2.02 Simple disulfide: pdb=" SG CYS I 378 " - pdb=" SG CYS I 445 " distance=2.04 Simple disulfide: pdb=" SG CYS I 385 " - pdb=" SG CYS I 418 " distance=2.03 Simple disulfide: pdb=" SG CYS J 598 " - pdb=" SG CYS J 604 " distance=2.03 Simple disulfide: pdb=" SG CYS K 22 " - pdb=" SG CYS K 96 " distance=2.04 Simple disulfide: pdb=" SG CYS L 22 " - pdb=" SG CYS L 90 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied ALPHA1-2 " MAN U 4 " - " MAN U 5 " " MAN U 5 " - " MAN U 6 " " MAN g 4 " - " MAN g 5 " " MAN g 5 " - " MAN g 6 " " MAN t 4 " - " MAN t 5 " " MAN t 5 " - " MAN t 6 " ALPHA1-3 " BMA O 3 " - " MAN O 4 " " BMA U 3 " - " MAN U 4 " " BMA W 3 " - " MAN W 4 " " BMA g 3 " - " MAN g 4 " " BMA i 3 " - " MAN i 4 " " BMA t 3 " - " MAN t 4 " " BMA v 3 " - " MAN v 4 " ALPHA1-6 " BMA U 3 " - " MAN U 7 " " BMA W 3 " - " MAN W 5 " " BMA g 3 " - " MAN g 7 " " BMA i 3 " - " MAN i 5 " " BMA t 3 " - " MAN t 7 " " BMA v 3 " - " MAN v 5 " BETA1-4 " NAG M 1 " - " NAG M 2 " " NAG M 2 " - " BMA M 3 " " 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 R 2 " - " BMA R 3 " " 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 W 1 " - " NAG W 2 " " NAG W 2 " - " BMA W 3 " " NAG X 1 " - " NAG X 2 " " NAG X 2 " - " NAG X 3 " " NAG Y 1 " - " NAG Y 2 " " NAG Y 2 " - " BMA Y 3 " " NAG Z 1 " - " NAG Z 2 " " NAG Z 2 " - " BMA Z 3 " " 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 f 1 " - " NAG f 2 " " NAG g 1 " - " NAG g 2 " " NAG g 2 " - " BMA g 3 " " NAG h 1 " - " NAG h 2 " " NAG i 1 " - " NAG i 2 " " NAG i 2 " - " BMA i 3 " " NAG j 1 " - " NAG j 2 " " NAG j 2 " - " NAG j 3 " " NAG k 1 " - " NAG k 2 " " NAG k 2 " - " BMA k 3 " " NAG l 1 " - " NAG l 2 " " NAG m 1 " - " NAG m 2 " " NAG m 2 " - " BMA m 3 " " 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 r 1 " - " NAG r 2 " " NAG s 1 " - " NAG s 2 " " NAG t 1 " - " NAG t 2 " " NAG t 2 " - " BMA t 3 " " NAG u 1 " - " NAG u 2 " " NAG v 1 " - " NAG v 2 " " NAG v 2 " - " BMA v 3 " " NAG w 1 " - " NAG w 2 " " NAG w 2 " - " NAG w 3 " " NAG x 1 " - " NAG x 2 " " NAG x 2 " - " BMA x 3 " " NAG y 1 " - " NAG y 2 " NAG-ASN " NAG A 701 " - " ASN A 355 " " NAG A 702 " - " ASN A 396 " " NAG A 703 " - " ASN A 234 " " NAG E 701 " - " ASN E 355 " " NAG E 702 " - " ASN E 234 " " NAG E 703 " - " ASN E 339 " " NAG E 704 " - " ASN E 396 " " NAG I 701 " - " ASN I 355 " " NAG I 702 " - " ASN I 234 " " NAG M 1 " - " ASN A 154 " " NAG N 1 " - " ASN E 154 " " NAG O 1 " - " ASN I 154 " " NAG P 1 " - " ASN E 442 " " NAG Q 1 " - " ASN E 301 " " NAG R 1 " - " ASN E 197 " " NAG S 1 " - " ASN E 392 " " NAG T 1 " - " ASN E 241 " " NAG U 1 " - " ASN E 332 " " NAG V 1 " - " ASN E 158 " " NAG W 1 " - " ASN E 262 " " NAG X 1 " - " ASN E 448 " " NAG Y 1 " - " ASN E 276 " " NAG Z 1 " - " ASN E 386 " " NAG a 1 " - " ASN E 362 " " NAG b 1 " - " ASN A 442 " " NAG c 1 " - " ASN A 301 " " NAG d 1 " - " ASN A 197 " " NAG e 1 " - " ASN A 392 " " NAG f 1 " - " ASN A 241 " " NAG g 1 " - " ASN A 332 " " NAG h 1 " - " ASN A 158 " " NAG j 1 " - " ASN A 448 " " NAG k 1 " - " ASN A 386 " " NAG l 1 " - " ASN A 362 " " NAG m 1 " - " ASN A 276 " " NAG n 1 " - " ASN A 339 " " NAG o 1 " - " ASN I 442 " " NAG p 1 " - " ASN I 301 " " NAG q 1 " - " ASN I 197 " " NAG r 1 " - " ASN I 392 " " NAG s 1 " - " ASN I 241 " " NAG t 1 " - " ASN I 332 " " NAG u 1 " - " ASN I 158 " " NAG w 1 " - " ASN I 448 " " NAG x 1 " - " ASN I 386 " " NAG y 1 " - " ASN I 362 " Time building additional restraints: 7.19 Conformation dependent library (CDL) restraints added in 2.6 seconds 4830 Ramachandran restraints generated. 2415 Oldfield, 0 Emsley, 2415 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4518 Finding SS restraints... Secondary structure from input PDB file: 49 helices and 33 sheets defined 19.8% alpha, 22.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.86 Creating SS restraints... Processing helix chain 'A' and resid 70 through 74 Processing helix chain 'A' and resid 98 through 117 removed outlier: 4.565A pdb=" N ASP A 102 " --> pdb=" O ASN A 98 " (cutoff:3.500A) Processing helix chain 'A' and resid 195 through 198 Processing helix chain 'A' and resid 335 through 351 Processing helix chain 'A' and resid 368 through 373 Processing helix chain 'A' and resid 403 through 407 Processing helix chain 'A' and resid 475 through 481 removed outlier: 3.686A pdb=" N TRP A 479 " --> pdb=" O MET A 475 " (cutoff:3.500A) removed outlier: 3.903A pdb=" N SER A 481 " --> pdb=" O ASP A 477 " (cutoff:3.500A) Processing helix chain 'B' and resid 529 through 534 Processing helix chain 'B' and resid 537 through 543 removed outlier: 4.246A pdb=" N ALA B 541 " --> pdb=" O LEU B 537 " (cutoff:3.500A) removed outlier: 3.817A pdb=" N ASN B 543 " --> pdb=" O VAL B 539 " (cutoff:3.500A) Processing helix chain 'B' and resid 570 through 597 removed outlier: 3.942A pdb=" N LYS B 574 " --> pdb=" O VAL B 570 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N ARG B 579 " --> pdb=" O GLN B 575 " (cutoff:3.500A) removed outlier: 3.921A pdb=" N ASP B 589 " --> pdb=" O ARG B 585 " (cutoff:3.500A) Processing helix chain 'B' and resid 618 through 624 Processing helix chain 'B' and resid 627 through 636 removed outlier: 3.865A pdb=" N LYS B 633 " --> pdb=" O LEU B 629 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N GLU B 634 " --> pdb=" O GLN B 630 " (cutoff:3.500A) Processing helix chain 'B' and resid 639 through 662 removed outlier: 4.037A pdb=" N TYR B 643 " --> pdb=" O THR B 639 " (cutoff:3.500A) removed outlier: 4.355A pdb=" N GLY B 644 " --> pdb=" O GLN B 640 " (cutoff:3.500A) Processing helix chain 'C' and resid 28 through 30 No H-bonds generated for 'chain 'C' and resid 28 through 30' Processing helix chain 'C' and resid 62 through 65 removed outlier: 3.790A pdb=" N GLN C 65 " --> pdb=" O GLN C 62 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 62 through 65' Processing helix chain 'C' and resid 87 through 91 removed outlier: 3.686A pdb=" N THR C 91 " --> pdb=" O SER C 88 " (cutoff:3.500A) Processing helix chain 'D' and resid 81 through 85 removed outlier: 3.689A pdb=" N ALA D 85 " --> pdb=" O ALA D 82 " (cutoff:3.500A) Processing helix chain 'E' and resid 70 through 74 Processing helix chain 'E' and resid 99 through 117 Processing helix chain 'E' and resid 195 through 198 Processing helix chain 'E' and resid 335 through 351 Processing helix chain 'E' and resid 368 through 373 Processing helix chain 'E' and resid 427 through 430 Processing helix chain 'E' and resid 475 through 481 removed outlier: 3.564A pdb=" N TRP E 479 " --> pdb=" O MET E 475 " (cutoff:3.500A) Processing helix chain 'F' and resid 529 through 543 removed outlier: 3.630A pdb=" N SER F 534 " --> pdb=" O MET F 530 " (cutoff:3.500A) removed outlier: 4.495A pdb=" N MET F 535 " --> pdb=" O GLY F 531 " (cutoff:3.500A) removed outlier: 3.893A pdb=" N THR F 536 " --> pdb=" O ALA F 532 " (cutoff:3.500A) removed outlier: 6.182A pdb=" N THR F 538 " --> pdb=" O SER F 534 " (cutoff:3.500A) removed outlier: 5.822A pdb=" N VAL F 539 " --> pdb=" O MET F 535 " (cutoff:3.500A) removed outlier: 3.836A pdb=" N GLN F 540 " --> pdb=" O THR F 536 " (cutoff:3.500A) Processing helix chain 'F' and resid 570 through 597 removed outlier: 4.135A pdb=" N ASP F 589 " --> pdb=" O ARG F 585 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N GLN F 590 " --> pdb=" O TYR F 586 " (cutoff:3.500A) Processing helix chain 'F' and resid 618 through 624 Processing helix chain 'F' and resid 627 through 635 Processing helix chain 'F' and resid 638 through 662 removed outlier: 4.126A pdb=" N ILE F 642 " --> pdb=" O TYR F 638 " (cutoff:3.500A) removed outlier: 3.947A pdb=" N TYR F 643 " --> pdb=" O THR F 639 " (cutoff:3.500A) removed outlier: 5.252A pdb=" N GLY F 644 " --> pdb=" O GLN F 640 " (cutoff:3.500A) Processing helix chain 'G' and resid 28 through 30 No H-bonds generated for 'chain 'G' and resid 28 through 30' Processing helix chain 'G' and resid 62 through 65 removed outlier: 3.830A pdb=" N GLN G 65 " --> pdb=" O GLN G 62 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 62 through 65' Processing helix chain 'G' and resid 87 through 91 removed outlier: 3.799A pdb=" N THR G 91 " --> pdb=" O SER G 88 " (cutoff:3.500A) Processing helix chain 'H' and resid 81 through 85 Processing helix chain 'I' and resid 70 through 74 removed outlier: 3.509A pdb=" N CYS I 74 " --> pdb=" O THR I 71 " (cutoff:3.500A) Processing helix chain 'I' and resid 98 through 117 removed outlier: 4.589A pdb=" N ASP I 102 " --> pdb=" O ASN I 98 " (cutoff:3.500A) Processing helix chain 'I' and resid 195 through 198 Processing helix chain 'I' and resid 335 through 351 removed outlier: 3.632A pdb=" N LYS I 351 " --> pdb=" O ILE I 347 " (cutoff:3.500A) Processing helix chain 'I' and resid 368 through 373 Processing helix chain 'I' and resid 475 through 480 Processing helix chain 'J' and resid 529 through 534 Processing helix chain 'J' and resid 537 through 542 removed outlier: 4.222A pdb=" N ALA J 541 " --> pdb=" O LEU J 537 " (cutoff:3.500A) Processing helix chain 'J' and resid 570 through 597 removed outlier: 4.292A pdb=" N ASP J 589 " --> pdb=" O ARG J 585 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N GLN J 590 " --> pdb=" O TYR J 586 " (cutoff:3.500A) Processing helix chain 'J' and resid 618 through 624 Processing helix chain 'J' and resid 627 through 635 removed outlier: 3.788A pdb=" N LYS J 633 " --> pdb=" O LEU J 629 " (cutoff:3.500A) removed outlier: 3.731A pdb=" N GLU J 634 " --> pdb=" O GLN J 630 " (cutoff:3.500A) Processing helix chain 'J' and resid 638 through 663 removed outlier: 3.608A pdb=" N GLY J 644 " --> pdb=" O GLN J 640 " (cutoff:3.500A) removed outlier: 4.186A pdb=" N LEU J 663 " --> pdb=" O ASP J 659 " (cutoff:3.500A) Processing helix chain 'K' and resid 28 through 30 No H-bonds generated for 'chain 'K' and resid 28 through 30' Processing helix chain 'K' and resid 62 through 65 removed outlier: 3.748A pdb=" N GLN K 65 " --> pdb=" O GLN K 62 " (cutoff:3.500A) No H-bonds generated for 'chain 'K' and resid 62 through 65' Processing helix chain 'K' and resid 87 through 91 removed outlier: 3.784A pdb=" N THR K 91 " --> pdb=" O SER K 88 " (cutoff:3.500A) Processing helix chain 'L' and resid 81 through 85 Processing sheet with id=AA1, first strand: chain 'A' and resid 36 through 40 Processing sheet with id=AA2, first strand: chain 'A' and resid 45 through 47 removed outlier: 3.549A pdb=" N ILE A 225 " --> pdb=" O VAL A 245 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N LEU A 84 " --> pdb=" O THR A 244 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 53 through 55 Processing sheet with id=AA4, first strand: chain 'A' and resid 91 through 94 removed outlier: 3.561A pdb=" N GLU A 91 " --> pdb=" O CYS A 239 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 167 through 175 Processing sheet with id=AA6, first strand: chain 'A' and resid 202 through 203 removed outlier: 6.789A pdb=" N THR A 202 " --> pdb=" O TYR A 435 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 259 through 261 WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 259 through 261 current: chain 'A' and resid 284 through 308 removed outlier: 6.855A pdb=" N ASN A 301 " --> pdb=" O ILE A 322 " (cutoff:3.500A) removed outlier: 4.725A pdb=" N ILE A 322 " --> pdb=" O ASN A 301 " (cutoff:3.500A) removed outlier: 7.038A pdb=" N THR A 303 " --> pdb=" O GLY A 321 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 316 through 323 current: chain 'A' and resid 381 through 385 WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 381 through 385 current: chain 'A' and resid 465 through 470 Processing sheet with id=AA8, first strand: chain 'C' and resid 3 through 6 removed outlier: 3.800A pdb=" N THR C 71 " --> pdb=" O TYR C 80 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'C' and resid 10 through 12 removed outlier: 6.488A pdb=" N GLU C 10 " --> pdb=" O THR C 124 " (cutoff:3.500A) removed outlier: 4.570A pdb=" N TYR C 33 " --> pdb=" O GLY C 99 " (cutoff:3.500A) removed outlier: 6.736A pdb=" N ILE C 34 " --> pdb=" O TRP C 50 " (cutoff:3.500A) removed outlier: 4.499A pdb=" N TRP C 50 " --> pdb=" O ILE C 34 " (cutoff:3.500A) removed outlier: 7.224A pdb=" N TRP C 36 " --> pdb=" O MET C 48 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'D' and resid 9 through 12 WARNING: can't find start of bonding for strands! previous: chain 'D' and resid 9 through 12 current: chain 'D' and resid 46 through 50 WARNING: can't find start of bonding for strands! previous: chain 'D' and resid 46 through 50 current: chain 'D' and resid 98 through 101 No H-bonds generated for sheet with id=AB1 Processing sheet with id=AB2, first strand: chain 'D' and resid 18 through 23 Processing sheet with id=AB3, first strand: chain 'E' and resid 494 through 498 removed outlier: 5.267A pdb=" N VAL F 608 " --> pdb=" O VAL E 36 " (cutoff:3.500A) removed outlier: 8.838A pdb=" N VAL E 38 " --> pdb=" O THR F 606 " (cutoff:3.500A) removed outlier: 7.707A pdb=" N THR F 606 " --> pdb=" O VAL E 38 " (cutoff:3.500A) removed outlier: 8.323A pdb=" N TYR E 40 " --> pdb=" O CYS F 604 " (cutoff:3.500A) removed outlier: 8.454A pdb=" N CYS F 604 " --> pdb=" O TYR E 40 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'E' and resid 45 through 47 removed outlier: 3.653A pdb=" N ILE E 225 " --> pdb=" O VAL E 245 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'E' and resid 75 through 76 removed outlier: 7.427A pdb=" N CYS E 54 " --> pdb=" O VAL E 75 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'E' and resid 91 through 94 removed outlier: 3.513A pdb=" N GLU E 91 " --> pdb=" O CYS E 239 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N PHE E 93 " --> pdb=" O GLY E 237 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N GLY E 237 " --> pdb=" O PHE E 93 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'E' and resid 167 through 175 Processing sheet with id=AB8, first strand: chain 'E' and resid 202 through 203 removed outlier: 6.764A pdb=" N THR E 202 " --> pdb=" O TYR E 435 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'E' and resid 259 through 261 WARNING: can't find start of bonding for strands! previous: chain 'E' and resid 259 through 261 current: chain 'E' and resid 284 through 308 removed outlier: 6.921A pdb=" N ASN E 301 " --> pdb=" O ILE E 322 " (cutoff:3.500A) removed outlier: 4.466A pdb=" N ILE E 322 " --> pdb=" O ASN E 301 " (cutoff:3.500A) removed outlier: 6.760A pdb=" N THR E 303 " --> pdb=" O GLY E 321 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'E' and resid 316 through 323 current: chain 'E' and resid 381 through 385 WARNING: can't find start of bonding for strands! previous: chain 'E' and resid 381 through 385 current: chain 'E' and resid 465 through 470 Processing sheet with id=AC1, first strand: chain 'G' and resid 3 through 6 Processing sheet with id=AC2, first strand: chain 'G' and resid 10 through 12 removed outlier: 6.389A pdb=" N GLU G 10 " --> pdb=" O THR G 124 " (cutoff:3.500A) removed outlier: 4.598A pdb=" N TYR G 33 " --> pdb=" O GLY G 99 " (cutoff:3.500A) removed outlier: 6.774A pdb=" N ILE G 34 " --> pdb=" O TRP G 50 " (cutoff:3.500A) removed outlier: 4.614A pdb=" N TRP G 50 " --> pdb=" O ILE G 34 " (cutoff:3.500A) removed outlier: 7.393A pdb=" N TRP G 36 " --> pdb=" O MET G 48 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'H' and resid 9 through 12 WARNING: can't find start of bonding for strands! previous: chain 'H' and resid 9 through 12 current: chain 'H' and resid 47 through 50 WARNING: can't find start of bonding for strands! previous: chain 'H' and resid 47 through 50 current: chain 'H' and resid 99 through 101 No H-bonds generated for sheet with id=AC3 Processing sheet with id=AC4, first strand: chain 'H' and resid 18 through 23 Processing sheet with id=AC5, first strand: chain 'I' and resid 494 through 498 removed outlier: 5.268A pdb=" N VAL J 608 " --> pdb=" O VAL I 36 " (cutoff:3.500A) removed outlier: 8.730A pdb=" N VAL I 38 " --> pdb=" O THR J 606 " (cutoff:3.500A) removed outlier: 7.689A pdb=" N THR J 606 " --> pdb=" O VAL I 38 " (cutoff:3.500A) removed outlier: 8.308A pdb=" N TYR I 40 " --> pdb=" O CYS J 604 " (cutoff:3.500A) removed outlier: 8.296A pdb=" N CYS J 604 " --> pdb=" O TYR I 40 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'I' and resid 45 through 47 removed outlier: 3.601A pdb=" N ILE I 225 " --> pdb=" O VAL I 245 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'I' and resid 53 through 55 Processing sheet with id=AC8, first strand: chain 'I' and resid 91 through 94 removed outlier: 3.519A pdb=" N GLU I 91 " --> pdb=" O CYS I 239 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'I' and resid 167 through 175 Processing sheet with id=AD1, first strand: chain 'I' and resid 201 through 203 removed outlier: 3.525A pdb=" N ILE I 424 " --> pdb=" O MET I 434 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'I' and resid 259 through 261 WARNING: can't find start of bonding for strands! previous: chain 'I' and resid 259 through 261 current: chain 'I' and resid 284 through 309 removed outlier: 6.909A pdb=" N ASN I 301 " --> pdb=" O ILE I 322 " (cutoff:3.500A) removed outlier: 4.577A pdb=" N ILE I 322 " --> pdb=" O ASN I 301 " (cutoff:3.500A) removed outlier: 6.839A pdb=" N THR I 303 " --> pdb=" O GLY I 321 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N GLN I 315 " --> pdb=" O ILE I 309 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'I' and resid 315 through 323 current: chain 'I' and resid 381 through 385 WARNING: can't find start of bonding for strands! previous: chain 'I' and resid 413 through 420 current: chain 'I' and resid 465 through 470 Processing sheet with id=AD3, first strand: chain 'K' and resid 3 through 6 Processing sheet with id=AD4, first strand: chain 'K' and resid 10 through 12 WARNING: can't find start of bonding for strands! previous: chain 'K' and resid 10 through 12 current: chain 'K' and resid 45 through 51 WARNING: can't find start of bonding for strands! previous: chain 'K' and resid 58 through 60 current: chain 'K' and resid 116 through 117 Processing sheet with id=AD5, first strand: chain 'L' and resid 9 through 12 WARNING: can't find start of bonding for strands! previous: chain 'L' and resid 9 through 12 current: chain 'L' and resid 46 through 50 WARNING: can't find start of bonding for strands! previous: chain 'L' and resid 46 through 50 current: chain 'L' and resid 98 through 101 No H-bonds generated for sheet with id=AD5 Processing sheet with id=AD6, first strand: chain 'L' and resid 18 through 23 517 hydrogen bonds defined for protein. 1416 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: 6.31 Time building geometry restraints manager: 8.04 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 6275 1.34 - 1.46: 5236 1.46 - 1.58: 9510 1.58 - 1.70: 0 1.70 - 1.82: 177 Bond restraints: 21198 Sorted by residual: bond pdb=" C3 BMA O 3 " pdb=" O3 BMA O 3 " ideal model delta sigma weight residual 1.406 1.481 -0.075 2.00e-02 2.50e+03 1.41e+01 bond pdb=" N ASN I 262 " pdb=" CA ASN I 262 " ideal model delta sigma weight residual 1.457 1.485 -0.028 1.29e-02 6.01e+03 4.72e+00 bond pdb=" C1 NAG m 2 " pdb=" O5 NAG m 2 " ideal model delta sigma weight residual 1.406 1.448 -0.042 2.00e-02 2.50e+03 4.49e+00 bond pdb=" C1 NAG e 2 " pdb=" O5 NAG e 2 " ideal model delta sigma weight residual 1.406 1.448 -0.042 2.00e-02 2.50e+03 4.34e+00 bond pdb=" C1 MAN U 4 " pdb=" O5 MAN U 4 " ideal model delta sigma weight residual 1.399 1.440 -0.041 2.00e-02 2.50e+03 4.22e+00 ... (remaining 21193 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.25: 27685 2.25 - 4.49: 972 4.49 - 6.74: 129 6.74 - 8.98: 42 8.98 - 11.23: 5 Bond angle restraints: 28833 Sorted by residual: angle pdb=" N ILE J 635 " pdb=" CA ILE J 635 " pdb=" C ILE J 635 " ideal model delta sigma weight residual 112.29 108.07 4.22 9.40e-01 1.13e+00 2.02e+01 angle pdb=" N ILE F 635 " pdb=" CA ILE F 635 " pdb=" C ILE F 635 " ideal model delta sigma weight residual 112.29 108.20 4.09 9.40e-01 1.13e+00 1.89e+01 angle pdb=" C TRP C 47 " pdb=" N MET C 48 " pdb=" CA MET C 48 " ideal model delta sigma weight residual 122.08 115.55 6.53 1.53e+00 4.27e-01 1.82e+01 angle pdb=" C LEU I 261 " pdb=" N ASN I 262 " pdb=" CA ASN I 262 " ideal model delta sigma weight residual 121.54 129.65 -8.11 1.91e+00 2.74e-01 1.80e+01 angle pdb=" C ASN E 276 " pdb=" N LEU E 277 " pdb=" CA LEU E 277 " ideal model delta sigma weight residual 121.54 129.22 -7.68 1.91e+00 2.74e-01 1.62e+01 ... (remaining 28828 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 22.16: 13167 22.16 - 44.31: 778 44.31 - 66.47: 147 66.47 - 88.63: 165 88.63 - 110.78: 92 Dihedral angle restraints: 14349 sinusoidal: 7293 harmonic: 7056 Sorted by residual: dihedral pdb=" CB CYS I 126 " pdb=" SG CYS I 126 " pdb=" SG CYS I 196 " pdb=" CB CYS I 196 " ideal model delta sinusoidal sigma weight residual 93.00 160.57 -67.57 1 1.00e+01 1.00e-02 5.94e+01 dihedral pdb=" CB CYS A 126 " pdb=" SG CYS A 126 " pdb=" SG CYS A 196 " pdb=" CB CYS A 196 " ideal model delta sinusoidal sigma weight residual 93.00 157.13 -64.13 1 1.00e+01 1.00e-02 5.41e+01 dihedral pdb=" CB CYS E 126 " pdb=" SG CYS E 126 " pdb=" SG CYS E 196 " pdb=" CB CYS E 196 " ideal model delta sinusoidal sigma weight residual 93.00 153.42 -60.42 1 1.00e+01 1.00e-02 4.86e+01 ... (remaining 14346 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.076: 2991 0.076 - 0.151: 551 0.151 - 0.227: 49 0.227 - 0.302: 22 0.302 - 0.378: 6 Chirality restraints: 3619 Sorted by residual: chirality pdb=" C1 NAG E 702 " pdb=" ND2 ASN E 234 " pdb=" C2 NAG E 702 " pdb=" O5 NAG E 702 " both_signs ideal model delta sigma weight residual False -2.40 -2.02 -0.38 2.00e-01 2.50e+01 3.56e+00 chirality pdb=" C1 NAG m 1 " pdb=" ND2 ASN A 276 " pdb=" C2 NAG m 1 " pdb=" O5 NAG m 1 " both_signs ideal model delta sigma weight residual False -2.40 -2.05 -0.35 2.00e-01 2.50e+01 3.14e+00 chirality pdb=" C5 BMA v 3 " pdb=" C4 BMA v 3 " pdb=" C6 BMA v 3 " pdb=" O5 BMA v 3 " both_signs ideal model delta sigma weight residual False -2.27 -2.61 0.34 2.00e-01 2.50e+01 2.85e+00 ... (remaining 3616 not shown) Planarity restraints: 3538 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA GLN F 653 " -0.014 2.00e-02 2.50e+03 2.88e-02 8.28e+00 pdb=" C GLN F 653 " 0.050 2.00e-02 2.50e+03 pdb=" O GLN F 653 " -0.019 2.00e-02 2.50e+03 pdb=" N GLU F 654 " -0.017 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LEU F 646 " 0.014 2.00e-02 2.50e+03 2.83e-02 7.99e+00 pdb=" C LEU F 646 " -0.049 2.00e-02 2.50e+03 pdb=" O LEU F 646 " 0.018 2.00e-02 2.50e+03 pdb=" N GLU F 647 " 0.016 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLN F 652 " -0.012 2.00e-02 2.50e+03 2.47e-02 6.09e+00 pdb=" C GLN F 652 " 0.043 2.00e-02 2.50e+03 pdb=" O GLN F 652 " -0.016 2.00e-02 2.50e+03 pdb=" N GLN F 653 " -0.014 2.00e-02 2.50e+03 ... (remaining 3535 not shown) Histogram of nonbonded interaction distances: 2.27 - 2.79: 5210 2.79 - 3.32: 19098 3.32 - 3.85: 35670 3.85 - 4.37: 39146 4.37 - 4.90: 67020 Nonbonded interactions: 166144 Sorted by model distance: nonbonded pdb=" O ALA D 94 " pdb=" OG1 THR D 98 " model vdw 2.266 3.040 nonbonded pdb=" O ILE I 358 " pdb=" OG1 THR I 394 " model vdw 2.272 3.040 nonbonded pdb=" O MET I 369 " pdb=" OG1 THR I 373 " model vdw 2.282 3.040 nonbonded pdb=" O MET E 369 " pdb=" OG1 THR E 373 " model vdw 2.282 3.040 nonbonded pdb=" O MET A 369 " pdb=" OG1 THR A 373 " model vdw 2.284 3.040 ... (remaining 166139 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' and (resid 33 through 505 or resid 701 through 702)) selection = (chain 'E' and (resid 33 through 505 or resid 701 through 702)) selection = chain 'I' } ncs_group { reference = chain 'B' selection = chain 'F' selection = chain 'J' } ncs_group { reference = chain 'C' selection = chain 'G' selection = chain 'K' } ncs_group { reference = chain 'D' selection = chain 'H' selection = chain 'L' } ncs_group { reference = (chain 'M' and resid 1 through 2) selection = (chain 'N' and resid 1 through 2) selection = (chain 'P' and resid 1 through 2) selection = (chain 'Q' and resid 1 through 2) selection = (chain 'R' and resid 1 through 2) selection = (chain 'X' and resid 1 through 2) selection = (chain 'Y' and resid 1 through 2) selection = (chain 'Z' and resid 1 through 2) selection = (chain 'b' and resid 1 through 2) selection = (chain 'c' and resid 1 through 2) selection = (chain 'd' and resid 1 through 2) selection = (chain 'j' and resid 1 through 2) selection = (chain 'k' and resid 1 through 2) selection = (chain 'm' and resid 1 through 2) selection = (chain 'n' and resid 1 through 2) selection = (chain 'o' and resid 1 through 2) selection = (chain 'p' and resid 1 through 2) selection = (chain 'w' and resid 1 through 2) selection = (chain 'x' and resid 1 through 2) } ncs_group { reference = chain 'S' selection = chain 'T' selection = chain 'V' selection = chain 'a' selection = chain 'e' selection = chain 'f' selection = chain 'h' selection = chain 'l' selection = chain 'q' selection = chain 'r' selection = chain 's' selection = chain 'u' selection = chain 'y' } ncs_group { reference = chain 'U' selection = chain 'g' selection = chain 't' } ncs_group { reference = chain 'W' selection = chain 'i' selection = chain 'v' } 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: 2.210 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.750 Check model and map are aligned: 0.160 Set scattering table: 0.210 Process input model: 48.750 Find NCS groups from input model: 1.260 Set up NCS constraints: 0.150 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.640 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 56.150 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8572 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 : 0.006 0.075 21367 Z= 0.312 Angle : 1.016 15.068 29301 Z= 0.492 Chirality : 0.061 0.378 3619 Planarity : 0.006 0.048 3492 Dihedral : 19.225 110.784 9714 Min Nonbonded Distance : 2.266 Molprobity Statistics. All-atom Clashscore : 4.49 Ramachandran Plot: Outliers : 0.17 % Allowed : 4.43 % Favored : 95.40 % Rotamer: Outliers : 0.00 % Allowed : 0.33 % Favored : 99.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.13 (0.16), residues: 2415 helix: -0.65 (0.24), residues: 408 sheet: -0.17 (0.20), residues: 636 loop : -1.04 (0.16), residues: 1371 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.032 0.003 TRP C 36 HIS 0.005 0.002 HIS K 35 PHE 0.016 0.002 PHE I 53 TYR 0.029 0.002 TYR A 217 ARG 0.005 0.001 ARG B 585 Details of bonding type rmsd link_NAG-ASN : bond 0.00695 ( 46) link_NAG-ASN : angle 3.38701 ( 138) link_ALPHA1-6 : bond 0.00099 ( 6) link_ALPHA1-6 : angle 1.85314 ( 18) link_BETA1-4 : bond 0.00760 ( 65) link_BETA1-4 : angle 2.30257 ( 195) link_ALPHA1-2 : bond 0.00574 ( 6) link_ALPHA1-2 : angle 2.95635 ( 18) link_ALPHA1-3 : bond 0.00581 ( 7) link_ALPHA1-3 : angle 2.34741 ( 21) hydrogen bonds : bond 0.14143 ( 517) hydrogen bonds : angle 6.28534 ( 1416) SS BOND : bond 0.00427 ( 39) SS BOND : angle 1.03704 ( 78) covalent geometry : bond 0.00640 (21198) covalent geometry : angle 0.97160 (28833) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4830 Ramachandran restraints generated. 2415 Oldfield, 0 Emsley, 2415 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4830 Ramachandran restraints generated. 2415 Oldfield, 0 Emsley, 2415 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 47 residues out of total 2121 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 47 time to evaluate : 2.264 Fit side-chains REVERT: C 81 MET cc_start: 0.8905 (mmp) cc_final: 0.8612 (mmp) REVERT: E 104 MET cc_start: 0.9262 (tpp) cc_final: 0.8634 (tpp) REVERT: G 70 MET cc_start: 0.8330 (mpp) cc_final: 0.7959 (mpp) REVERT: I 104 MET cc_start: 0.9067 (tmm) cc_final: 0.8795 (tmm) REVERT: K 70 MET cc_start: 0.7839 (mtm) cc_final: 0.7553 (mtp) outliers start: 0 outliers final: 0 residues processed: 47 average time/residue: 0.2939 time to fit residues: 25.0753 Evaluate side-chains 46 residues out of total 2121 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 46 time to evaluate : 2.463 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 202 optimal weight: 30.0000 chunk 181 optimal weight: 4.9990 chunk 100 optimal weight: 20.0000 chunk 62 optimal weight: 2.9990 chunk 122 optimal weight: 2.9990 chunk 97 optimal weight: 6.9990 chunk 188 optimal weight: 10.0000 chunk 72 optimal weight: 0.6980 chunk 114 optimal weight: 0.8980 chunk 140 optimal weight: 7.9990 chunk 217 optimal weight: 6.9990 overall best weight: 2.5186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 577 GLN B 651 ASN E 229 ASN E 428 GLN F 651 ASN H 39 GLN I 425 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2876 r_free = 0.2876 target = 0.024258 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.2528 r_free = 0.2528 target = 0.018817 restraints weight = 326110.147| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.2562 r_free = 0.2562 target = 0.019340 restraints weight = 197357.532| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.2584 r_free = 0.2584 target = 0.019689 restraints weight = 145071.909| |-----------------------------------------------------------------------------| r_work (final): 0.2573 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8687 moved from start: 0.0922 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 21367 Z= 0.133 Angle : 0.643 9.725 29301 Z= 0.296 Chirality : 0.045 0.291 3619 Planarity : 0.004 0.039 3492 Dihedral : 14.245 81.282 5328 Min Nonbonded Distance : 2.372 Molprobity Statistics. All-atom Clashscore : 5.38 Ramachandran Plot: Outliers : 0.12 % Allowed : 2.82 % Favored : 97.06 % Rotamer: Outliers : 0.00 % Allowed : 2.69 % Favored : 97.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.42 (0.17), residues: 2415 helix: 0.70 (0.27), residues: 396 sheet: -0.03 (0.20), residues: 630 loop : -0.65 (0.17), residues: 1389 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP G 36 HIS 0.003 0.001 HIS A 287 PHE 0.012 0.001 PHE K 60 TYR 0.019 0.001 TYR L 51 ARG 0.004 0.000 ARG A 192 Details of bonding type rmsd link_NAG-ASN : bond 0.00349 ( 46) link_NAG-ASN : angle 2.30719 ( 138) link_ALPHA1-6 : bond 0.00452 ( 6) link_ALPHA1-6 : angle 2.02740 ( 18) link_BETA1-4 : bond 0.00496 ( 65) link_BETA1-4 : angle 2.24533 ( 195) link_ALPHA1-2 : bond 0.00352 ( 6) link_ALPHA1-2 : angle 2.15870 ( 18) link_ALPHA1-3 : bond 0.01043 ( 7) link_ALPHA1-3 : angle 2.29855 ( 21) hydrogen bonds : bond 0.04063 ( 517) hydrogen bonds : angle 5.17186 ( 1416) SS BOND : bond 0.00241 ( 39) SS BOND : angle 0.66661 ( 78) covalent geometry : bond 0.00281 (21198) covalent geometry : angle 0.59164 (28833) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4830 Ramachandran restraints generated. 2415 Oldfield, 0 Emsley, 2415 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4830 Ramachandran restraints generated. 2415 Oldfield, 0 Emsley, 2415 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 46 residues out of total 2121 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 46 time to evaluate : 2.266 Fit side-chains revert: symmetry clash REVERT: B 530 MET cc_start: 0.8176 (mpp) cc_final: 0.7802 (ptp) REVERT: K 70 MET cc_start: 0.8141 (mtm) cc_final: 0.7874 (mtp) outliers start: 0 outliers final: 0 residues processed: 46 average time/residue: 0.2835 time to fit residues: 23.7223 Evaluate side-chains 46 residues out of total 2121 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 46 time to evaluate : 2.243 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 71 optimal weight: 30.0000 chunk 129 optimal weight: 6.9990 chunk 141 optimal weight: 20.0000 chunk 36 optimal weight: 20.0000 chunk 145 optimal weight: 8.9990 chunk 91 optimal weight: 5.9990 chunk 237 optimal weight: 9.9990 chunk 215 optimal weight: 0.4980 chunk 84 optimal weight: 8.9990 chunk 1 optimal weight: 9.9990 chunk 38 optimal weight: 0.8980 overall best weight: 4.6786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 105 HIS B 630 GLN D 39 GLN H 39 GLN L 39 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2858 r_free = 0.2858 target = 0.023962 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2504 r_free = 0.2504 target = 0.018471 restraints weight = 325827.886| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.2537 r_free = 0.2537 target = 0.018978 restraints weight = 198889.207| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.2559 r_free = 0.2559 target = 0.019320 restraints weight = 147277.028| |-----------------------------------------------------------------------------| r_work (final): 0.2547 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8725 moved from start: 0.1314 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 21367 Z= 0.199 Angle : 0.670 8.936 29301 Z= 0.313 Chirality : 0.045 0.282 3619 Planarity : 0.004 0.044 3492 Dihedral : 11.464 82.586 5328 Min Nonbonded Distance : 2.377 Molprobity Statistics. All-atom Clashscore : 6.71 Ramachandran Plot: Outliers : 0.08 % Allowed : 3.89 % Favored : 96.02 % Rotamer: Outliers : 0.00 % Allowed : 2.69 % Favored : 97.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.26 (0.18), residues: 2415 helix: 1.12 (0.28), residues: 399 sheet: -0.12 (0.20), residues: 663 loop : -0.54 (0.18), residues: 1353 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP G 36 HIS 0.004 0.001 HIS A 374 PHE 0.015 0.002 PHE I 382 TYR 0.023 0.002 TYR L 51 ARG 0.003 0.000 ARG J 585 Details of bonding type rmsd link_NAG-ASN : bond 0.00491 ( 46) link_NAG-ASN : angle 2.38712 ( 138) link_ALPHA1-6 : bond 0.00376 ( 6) link_ALPHA1-6 : angle 1.90715 ( 18) link_BETA1-4 : bond 0.00573 ( 65) link_BETA1-4 : angle 2.05607 ( 195) link_ALPHA1-2 : bond 0.00424 ( 6) link_ALPHA1-2 : angle 2.24131 ( 18) link_ALPHA1-3 : bond 0.00994 ( 7) link_ALPHA1-3 : angle 2.17848 ( 21) hydrogen bonds : bond 0.03993 ( 517) hydrogen bonds : angle 5.12255 ( 1416) SS BOND : bond 0.00291 ( 39) SS BOND : angle 0.75505 ( 78) covalent geometry : bond 0.00424 (21198) covalent geometry : angle 0.62490 (28833) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4830 Ramachandran restraints generated. 2415 Oldfield, 0 Emsley, 2415 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4830 Ramachandran restraints generated. 2415 Oldfield, 0 Emsley, 2415 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 45 residues out of total 2121 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 45 time to evaluate : 2.256 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 104 MET cc_start: 0.9192 (tmm) cc_final: 0.8720 (tmm) REVERT: I 104 MET cc_start: 0.9276 (tmm) cc_final: 0.8791 (tmm) REVERT: K 70 MET cc_start: 0.8111 (mtm) cc_final: 0.7789 (mtp) outliers start: 0 outliers final: 0 residues processed: 45 average time/residue: 0.2955 time to fit residues: 24.5192 Evaluate side-chains 45 residues out of total 2121 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 45 time to evaluate : 2.408 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 191 optimal weight: 10.0000 chunk 82 optimal weight: 7.9990 chunk 42 optimal weight: 20.0000 chunk 227 optimal weight: 20.0000 chunk 36 optimal weight: 3.9990 chunk 130 optimal weight: 9.9990 chunk 25 optimal weight: 9.9990 chunk 127 optimal weight: 20.0000 chunk 107 optimal weight: 5.9990 chunk 53 optimal weight: 20.0000 chunk 70 optimal weight: 0.7980 overall best weight: 5.7588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 103 GLN F 651 ASN J 577 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2852 r_free = 0.2852 target = 0.023853 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2494 r_free = 0.2494 target = 0.018323 restraints weight = 331928.863| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.2527 r_free = 0.2527 target = 0.018825 restraints weight = 203173.175| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.2549 r_free = 0.2549 target = 0.019159 restraints weight = 150843.647| |-----------------------------------------------------------------------------| r_work (final): 0.2537 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8743 moved from start: 0.1652 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.061 21367 Z= 0.231 Angle : 0.681 9.084 29301 Z= 0.319 Chirality : 0.045 0.277 3619 Planarity : 0.004 0.040 3492 Dihedral : 10.405 83.836 5328 Min Nonbonded Distance : 2.386 Molprobity Statistics. All-atom Clashscore : 8.43 Ramachandran Plot: Outliers : 0.04 % Allowed : 4.31 % Favored : 95.65 % Rotamer: Outliers : 0.05 % Allowed : 2.69 % Favored : 97.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.31 (0.18), residues: 2415 helix: 1.15 (0.28), residues: 402 sheet: -0.27 (0.20), residues: 657 loop : -0.53 (0.18), residues: 1356 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.002 TRP E 112 HIS 0.004 0.001 HIS G 32 PHE 0.018 0.002 PHE I 382 TYR 0.034 0.002 TYR L 51 ARG 0.003 0.000 ARG J 585 Details of bonding type rmsd link_NAG-ASN : bond 0.00556 ( 46) link_NAG-ASN : angle 2.35741 ( 138) link_ALPHA1-6 : bond 0.00487 ( 6) link_ALPHA1-6 : angle 2.10584 ( 18) link_BETA1-4 : bond 0.00520 ( 65) link_BETA1-4 : angle 2.02610 ( 195) link_ALPHA1-2 : bond 0.00611 ( 6) link_ALPHA1-2 : angle 2.20459 ( 18) link_ALPHA1-3 : bond 0.00882 ( 7) link_ALPHA1-3 : angle 2.28522 ( 21) hydrogen bonds : bond 0.04017 ( 517) hydrogen bonds : angle 5.18982 ( 1416) SS BOND : bond 0.00273 ( 39) SS BOND : angle 0.65550 ( 78) covalent geometry : bond 0.00495 (21198) covalent geometry : angle 0.63756 (28833) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4830 Ramachandran restraints generated. 2415 Oldfield, 0 Emsley, 2415 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4830 Ramachandran restraints generated. 2415 Oldfield, 0 Emsley, 2415 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 46 residues out of total 2121 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 45 time to evaluate : 2.710 Fit side-chains REVERT: A 100 MET cc_start: 0.9584 (mtt) cc_final: 0.9365 (mtt) REVERT: A 104 MET cc_start: 0.9312 (tmm) cc_final: 0.9086 (tmm) REVERT: I 434 MET cc_start: 0.8826 (mmm) cc_final: 0.8432 (ttm) REVERT: K 70 MET cc_start: 0.7992 (mtm) cc_final: 0.7639 (mtp) outliers start: 1 outliers final: 0 residues processed: 46 average time/residue: 0.2767 time to fit residues: 23.5470 Evaluate side-chains 45 residues out of total 2121 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 45 time to evaluate : 2.085 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 0 optimal weight: 10.0000 chunk 141 optimal weight: 5.9990 chunk 155 optimal weight: 20.0000 chunk 128 optimal weight: 10.0000 chunk 7 optimal weight: 0.9980 chunk 135 optimal weight: 9.9990 chunk 133 optimal weight: 5.9990 chunk 20 optimal weight: 5.9990 chunk 56 optimal weight: 9.9990 chunk 233 optimal weight: 20.0000 chunk 199 optimal weight: 0.3980 overall best weight: 3.8786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 103 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2865 r_free = 0.2865 target = 0.024079 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 26)----------------| | r_work = 0.2511 r_free = 0.2511 target = 0.018564 restraints weight = 326287.500| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.2545 r_free = 0.2545 target = 0.019083 restraints weight = 199962.845| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.2567 r_free = 0.2567 target = 0.019418 restraints weight = 148282.474| |-----------------------------------------------------------------------------| r_work (final): 0.2555 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8718 moved from start: 0.1765 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 21367 Z= 0.166 Angle : 0.625 11.057 29301 Z= 0.293 Chirality : 0.044 0.279 3619 Planarity : 0.003 0.034 3492 Dihedral : 9.809 85.015 5328 Min Nonbonded Distance : 2.390 Molprobity Statistics. All-atom Clashscore : 7.42 Ramachandran Plot: Outliers : 0.04 % Allowed : 4.02 % Favored : 95.94 % Rotamer: Outliers : 0.00 % Allowed : 1.74 % Favored : 98.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.26 (0.18), residues: 2415 helix: 1.32 (0.28), residues: 402 sheet: -0.42 (0.20), residues: 693 loop : -0.42 (0.18), residues: 1320 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP J 614 HIS 0.003 0.001 HIS E 105 PHE 0.014 0.001 PHE A 53 TYR 0.024 0.001 TYR L 51 ARG 0.003 0.000 ARG I 503 Details of bonding type rmsd link_NAG-ASN : bond 0.00415 ( 46) link_NAG-ASN : angle 2.34895 ( 138) link_ALPHA1-6 : bond 0.00607 ( 6) link_ALPHA1-6 : angle 1.91261 ( 18) link_BETA1-4 : bond 0.00473 ( 65) link_BETA1-4 : angle 1.77282 ( 195) link_ALPHA1-2 : bond 0.00419 ( 6) link_ALPHA1-2 : angle 2.07173 ( 18) link_ALPHA1-3 : bond 0.00995 ( 7) link_ALPHA1-3 : angle 2.01088 ( 21) hydrogen bonds : bond 0.03775 ( 517) hydrogen bonds : angle 4.99759 ( 1416) SS BOND : bond 0.00242 ( 39) SS BOND : angle 0.70755 ( 78) covalent geometry : bond 0.00355 (21198) covalent geometry : angle 0.58355 (28833) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4830 Ramachandran restraints generated. 2415 Oldfield, 0 Emsley, 2415 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4830 Ramachandran restraints generated. 2415 Oldfield, 0 Emsley, 2415 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 48 residues out of total 2121 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 48 time to evaluate : 2.332 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 100 MET cc_start: 0.9545 (mtt) cc_final: 0.9332 (mtt) REVERT: I 434 MET cc_start: 0.8838 (mmm) cc_final: 0.8364 (ttm) REVERT: K 70 MET cc_start: 0.8282 (mtm) cc_final: 0.7567 (mtp) outliers start: 0 outliers final: 0 residues processed: 48 average time/residue: 0.3136 time to fit residues: 26.3411 Evaluate side-chains 46 residues out of total 2121 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 46 time to evaluate : 2.407 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 176 optimal weight: 8.9990 chunk 148 optimal weight: 8.9990 chunk 25 optimal weight: 8.9990 chunk 91 optimal weight: 5.9990 chunk 234 optimal weight: 2.9990 chunk 137 optimal weight: 7.9990 chunk 45 optimal weight: 20.0000 chunk 10 optimal weight: 0.3980 chunk 174 optimal weight: 0.0060 chunk 1 optimal weight: 8.9990 chunk 212 optimal weight: 20.0000 overall best weight: 3.4802 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F 607 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 = 0.2868 r_free = 0.2868 target = 0.024109 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.2514 r_free = 0.2514 target = 0.018586 restraints weight = 323972.787| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.2547 r_free = 0.2547 target = 0.019101 restraints weight = 199019.921| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 23)----------------| | r_work = 0.2569 r_free = 0.2569 target = 0.019441 restraints weight = 147302.486| |-----------------------------------------------------------------------------| r_work (final): 0.2557 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8714 moved from start: 0.1855 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 21367 Z= 0.153 Angle : 0.611 9.895 29301 Z= 0.286 Chirality : 0.044 0.277 3619 Planarity : 0.003 0.034 3492 Dihedral : 9.338 86.125 5328 Min Nonbonded Distance : 2.396 Molprobity Statistics. All-atom Clashscore : 7.69 Ramachandran Plot: Outliers : 0.04 % Allowed : 4.06 % Favored : 95.90 % Rotamer: Outliers : 0.00 % Allowed : 0.94 % Favored : 99.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.15 (0.18), residues: 2415 helix: 1.44 (0.28), residues: 402 sheet: -0.35 (0.20), residues: 687 loop : -0.36 (0.18), residues: 1326 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP F 614 HIS 0.002 0.001 HIS C 32 PHE 0.011 0.001 PHE I 382 TYR 0.033 0.001 TYR L 51 ARG 0.003 0.000 ARG I 503 Details of bonding type rmsd link_NAG-ASN : bond 0.00389 ( 46) link_NAG-ASN : angle 2.29565 ( 138) link_ALPHA1-6 : bond 0.00719 ( 6) link_ALPHA1-6 : angle 1.69765 ( 18) link_BETA1-4 : bond 0.00481 ( 65) link_BETA1-4 : angle 1.73836 ( 195) link_ALPHA1-2 : bond 0.00395 ( 6) link_ALPHA1-2 : angle 2.04669 ( 18) link_ALPHA1-3 : bond 0.01064 ( 7) link_ALPHA1-3 : angle 1.95550 ( 21) hydrogen bonds : bond 0.03645 ( 517) hydrogen bonds : angle 4.93916 ( 1416) SS BOND : bond 0.00242 ( 39) SS BOND : angle 0.64664 ( 78) covalent geometry : bond 0.00329 (21198) covalent geometry : angle 0.57001 (28833) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4830 Ramachandran restraints generated. 2415 Oldfield, 0 Emsley, 2415 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4830 Ramachandran restraints generated. 2415 Oldfield, 0 Emsley, 2415 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 46 residues out of total 2121 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 46 time to evaluate : 2.144 Fit side-chains revert: symmetry clash REVERT: A 100 MET cc_start: 0.9552 (mtt) cc_final: 0.9328 (mtt) REVERT: K 70 MET cc_start: 0.8046 (mtm) cc_final: 0.7629 (mtp) outliers start: 0 outliers final: 0 residues processed: 46 average time/residue: 0.3131 time to fit residues: 25.2896 Evaluate side-chains 46 residues out of total 2121 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 46 time to evaluate : 2.428 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 192 optimal weight: 0.3980 chunk 166 optimal weight: 10.0000 chunk 49 optimal weight: 7.9990 chunk 235 optimal weight: 20.0000 chunk 160 optimal weight: 1.9990 chunk 117 optimal weight: 7.9990 chunk 217 optimal weight: 0.9980 chunk 4 optimal weight: 7.9990 chunk 202 optimal weight: 8.9990 chunk 119 optimal weight: 8.9990 chunk 100 optimal weight: 20.0000 overall best weight: 3.8786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F 607 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 = 0.2865 r_free = 0.2865 target = 0.024049 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2511 r_free = 0.2511 target = 0.018526 restraints weight = 324779.583| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.2544 r_free = 0.2544 target = 0.019040 restraints weight = 199733.680| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.2565 r_free = 0.2565 target = 0.019375 restraints weight = 148164.339| |-----------------------------------------------------------------------------| r_work (final): 0.2554 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8719 moved from start: 0.1945 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.029 21367 Z= 0.166 Angle : 0.617 9.704 29301 Z= 0.289 Chirality : 0.044 0.273 3619 Planarity : 0.003 0.033 3492 Dihedral : 8.978 87.094 5328 Min Nonbonded Distance : 2.391 Molprobity Statistics. All-atom Clashscore : 8.30 Ramachandran Plot: Outliers : 0.04 % Allowed : 4.31 % Favored : 95.65 % Rotamer: Outliers : 0.00 % Allowed : 0.61 % Favored : 99.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.15 (0.18), residues: 2415 helix: 1.54 (0.28), residues: 402 sheet: -0.42 (0.20), residues: 678 loop : -0.36 (0.18), residues: 1335 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP F 614 HIS 0.003 0.001 HIS C 32 PHE 0.011 0.001 PHE I 382 TYR 0.047 0.001 TYR L 51 ARG 0.003 0.000 ARG I 503 Details of bonding type rmsd link_NAG-ASN : bond 0.00404 ( 46) link_NAG-ASN : angle 2.28000 ( 138) link_ALPHA1-6 : bond 0.00774 ( 6) link_ALPHA1-6 : angle 1.48107 ( 18) link_BETA1-4 : bond 0.00486 ( 65) link_BETA1-4 : angle 1.72064 ( 195) link_ALPHA1-2 : bond 0.00493 ( 6) link_ALPHA1-2 : angle 2.06212 ( 18) link_ALPHA1-3 : bond 0.01047 ( 7) link_ALPHA1-3 : angle 1.91083 ( 21) hydrogen bonds : bond 0.03608 ( 517) hydrogen bonds : angle 4.94782 ( 1416) SS BOND : bond 0.00301 ( 39) SS BOND : angle 0.66660 ( 78) covalent geometry : bond 0.00356 (21198) covalent geometry : angle 0.57774 (28833) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4830 Ramachandran restraints generated. 2415 Oldfield, 0 Emsley, 2415 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4830 Ramachandran restraints generated. 2415 Oldfield, 0 Emsley, 2415 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 46 residues out of total 2121 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 46 time to evaluate : 2.191 Fit side-chains revert: symmetry clash REVERT: C 48 MET cc_start: 0.8974 (pmm) cc_final: 0.8416 (pmm) REVERT: I 104 MET cc_start: 0.9090 (tmm) cc_final: 0.8663 (tmm) REVERT: K 70 MET cc_start: 0.8043 (mtm) cc_final: 0.7630 (mtp) outliers start: 0 outliers final: 0 residues processed: 46 average time/residue: 0.3112 time to fit residues: 25.2023 Evaluate side-chains 46 residues out of total 2121 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 46 time to evaluate : 2.242 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 220 optimal weight: 10.0000 chunk 210 optimal weight: 9.9990 chunk 214 optimal weight: 8.9990 chunk 94 optimal weight: 7.9990 chunk 146 optimal weight: 7.9990 chunk 11 optimal weight: 20.0000 chunk 80 optimal weight: 10.0000 chunk 124 optimal weight: 0.8980 chunk 89 optimal weight: 5.9990 chunk 19 optimal weight: 0.9990 chunk 46 optimal weight: 7.9990 overall best weight: 4.7788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: I 350 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2857 r_free = 0.2857 target = 0.023953 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.2503 r_free = 0.2503 target = 0.018436 restraints weight = 327010.253| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.2535 r_free = 0.2535 target = 0.018936 restraints weight = 201059.348| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.2556 r_free = 0.2556 target = 0.019272 restraints weight = 149452.052| |-----------------------------------------------------------------------------| r_work (final): 0.2544 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8733 moved from start: 0.2072 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 21367 Z= 0.197 Angle : 0.642 9.487 29301 Z= 0.302 Chirality : 0.044 0.258 3619 Planarity : 0.003 0.033 3492 Dihedral : 8.853 88.522 5328 Min Nonbonded Distance : 2.382 Molprobity Statistics. All-atom Clashscore : 8.70 Ramachandran Plot: Outliers : 0.04 % Allowed : 4.64 % Favored : 95.32 % Rotamer: Outliers : 0.05 % Allowed : 0.57 % Favored : 99.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.22 (0.18), residues: 2415 helix: 1.51 (0.28), residues: 402 sheet: -0.46 (0.20), residues: 675 loop : -0.42 (0.18), residues: 1338 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP B 614 HIS 0.003 0.001 HIS C 32 PHE 0.013 0.001 PHE I 382 TYR 0.042 0.002 TYR L 51 ARG 0.003 0.000 ARG I 503 Details of bonding type rmsd link_NAG-ASN : bond 0.00488 ( 46) link_NAG-ASN : angle 2.31797 ( 138) link_ALPHA1-6 : bond 0.00747 ( 6) link_ALPHA1-6 : angle 1.39698 ( 18) link_BETA1-4 : bond 0.00496 ( 65) link_BETA1-4 : angle 1.74507 ( 195) link_ALPHA1-2 : bond 0.00604 ( 6) link_ALPHA1-2 : angle 2.12715 ( 18) link_ALPHA1-3 : bond 0.01013 ( 7) link_ALPHA1-3 : angle 1.91219 ( 21) hydrogen bonds : bond 0.03720 ( 517) hydrogen bonds : angle 4.99892 ( 1416) SS BOND : bond 0.00282 ( 39) SS BOND : angle 0.66496 ( 78) covalent geometry : bond 0.00422 (21198) covalent geometry : angle 0.60356 (28833) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4830 Ramachandran restraints generated. 2415 Oldfield, 0 Emsley, 2415 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4830 Ramachandran restraints generated. 2415 Oldfield, 0 Emsley, 2415 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 47 residues out of total 2121 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 46 time to evaluate : 2.165 Fit side-chains revert: symmetry clash REVERT: I 350 GLN cc_start: 0.9246 (OUTLIER) cc_final: 0.8628 (tm-30) REVERT: K 70 MET cc_start: 0.7932 (mtm) cc_final: 0.7559 (mtp) outliers start: 1 outliers final: 0 residues processed: 47 average time/residue: 0.3103 time to fit residues: 25.4983 Evaluate side-chains 47 residues out of total 2121 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 46 time to evaluate : 2.138 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 10 optimal weight: 40.0000 chunk 56 optimal weight: 7.9990 chunk 49 optimal weight: 6.9990 chunk 157 optimal weight: 30.0000 chunk 103 optimal weight: 9.9990 chunk 53 optimal weight: 20.0000 chunk 201 optimal weight: 0.0040 chunk 137 optimal weight: 3.9990 chunk 132 optimal weight: 8.9990 chunk 91 optimal weight: 5.9990 chunk 111 optimal weight: 0.7980 overall best weight: 3.5598 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: I 350 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2866 r_free = 0.2866 target = 0.024099 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2512 r_free = 0.2512 target = 0.018566 restraints weight = 324225.257| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.2545 r_free = 0.2545 target = 0.019082 restraints weight = 199151.611| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.2567 r_free = 0.2567 target = 0.019415 restraints weight = 147756.559| |-----------------------------------------------------------------------------| r_work (final): 0.2555 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8718 moved from start: 0.2107 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 21367 Z= 0.155 Angle : 0.608 9.232 29301 Z= 0.286 Chirality : 0.043 0.268 3619 Planarity : 0.003 0.034 3492 Dihedral : 8.595 89.743 5328 Min Nonbonded Distance : 2.389 Molprobity Statistics. All-atom Clashscore : 7.69 Ramachandran Plot: Outliers : 0.04 % Allowed : 4.10 % Favored : 95.86 % Rotamer: Outliers : 0.00 % Allowed : 0.47 % Favored : 99.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.16 (0.18), residues: 2415 helix: 1.62 (0.28), residues: 402 sheet: -0.42 (0.20), residues: 672 loop : -0.41 (0.18), residues: 1341 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP B 614 HIS 0.003 0.001 HIS I 352 PHE 0.011 0.001 PHE I 382 TYR 0.035 0.001 TYR L 51 ARG 0.002 0.000 ARG I 503 Details of bonding type rmsd link_NAG-ASN : bond 0.00367 ( 46) link_NAG-ASN : angle 2.19024 ( 138) link_ALPHA1-6 : bond 0.00754 ( 6) link_ALPHA1-6 : angle 1.28537 ( 18) link_BETA1-4 : bond 0.00484 ( 65) link_BETA1-4 : angle 1.65176 ( 195) link_ALPHA1-2 : bond 0.00503 ( 6) link_ALPHA1-2 : angle 2.02127 ( 18) link_ALPHA1-3 : bond 0.01045 ( 7) link_ALPHA1-3 : angle 1.78996 ( 21) hydrogen bonds : bond 0.03544 ( 517) hydrogen bonds : angle 4.91530 ( 1416) SS BOND : bond 0.00246 ( 39) SS BOND : angle 0.58772 ( 78) covalent geometry : bond 0.00333 (21198) covalent geometry : angle 0.57168 (28833) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4830 Ramachandran restraints generated. 2415 Oldfield, 0 Emsley, 2415 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4830 Ramachandran restraints generated. 2415 Oldfield, 0 Emsley, 2415 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 46 residues out of total 2121 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 46 time to evaluate : 2.400 Fit side-chains revert: symmetry clash REVERT: A 104 MET cc_start: 0.8955 (tmm) cc_final: 0.8451 (tmm) REVERT: I 104 MET cc_start: 0.9027 (tmm) cc_final: 0.8769 (tmm) REVERT: I 434 MET cc_start: 0.9230 (tpt) cc_final: 0.8951 (mmm) REVERT: K 70 MET cc_start: 0.7986 (mtm) cc_final: 0.7591 (mtp) outliers start: 0 outliers final: 0 residues processed: 46 average time/residue: 0.3312 time to fit residues: 26.9407 Evaluate side-chains 46 residues out of total 2121 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 46 time to evaluate : 2.388 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 21 optimal weight: 10.0000 chunk 120 optimal weight: 5.9990 chunk 190 optimal weight: 6.9990 chunk 222 optimal weight: 7.9990 chunk 57 optimal weight: 10.0000 chunk 164 optimal weight: 0.0970 chunk 192 optimal weight: 6.9990 chunk 9 optimal weight: 2.9990 chunk 135 optimal weight: 10.0000 chunk 78 optimal weight: 20.0000 chunk 130 optimal weight: 10.0000 overall best weight: 4.6186 ------------------------------------------------------------------------------- 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 = 0.2859 r_free = 0.2859 target = 0.023980 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2503 r_free = 0.2503 target = 0.018452 restraints weight = 326276.062| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.2536 r_free = 0.2536 target = 0.018958 restraints weight = 200904.162| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.2558 r_free = 0.2558 target = 0.019289 restraints weight = 149631.373| |-----------------------------------------------------------------------------| r_work (final): 0.2545 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8731 moved from start: 0.2180 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 21367 Z= 0.193 Angle : 0.637 9.151 29301 Z= 0.300 Chirality : 0.044 0.267 3619 Planarity : 0.003 0.033 3492 Dihedral : 8.611 89.087 5328 Min Nonbonded Distance : 2.384 Molprobity Statistics. All-atom Clashscore : 8.38 Ramachandran Plot: Outliers : 0.04 % Allowed : 4.55 % Favored : 95.40 % Rotamer: Outliers : 0.00 % Allowed : 0.14 % Favored : 99.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.21 (0.18), residues: 2415 helix: 1.53 (0.28), residues: 402 sheet: -0.50 (0.20), residues: 675 loop : -0.39 (0.18), residues: 1338 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP B 614 HIS 0.003 0.001 HIS G 32 PHE 0.012 0.001 PHE I 382 TYR 0.035 0.002 TYR L 51 ARG 0.007 0.000 ARG G 38 Details of bonding type rmsd link_NAG-ASN : bond 0.00457 ( 46) link_NAG-ASN : angle 2.27636 ( 138) link_ALPHA1-6 : bond 0.00698 ( 6) link_ALPHA1-6 : angle 1.31247 ( 18) link_BETA1-4 : bond 0.00493 ( 65) link_BETA1-4 : angle 1.70020 ( 195) link_ALPHA1-2 : bond 0.00590 ( 6) link_ALPHA1-2 : angle 2.07470 ( 18) link_ALPHA1-3 : bond 0.00965 ( 7) link_ALPHA1-3 : angle 1.82274 ( 21) hydrogen bonds : bond 0.03694 ( 517) hydrogen bonds : angle 4.98032 ( 1416) SS BOND : bond 0.00273 ( 39) SS BOND : angle 0.61420 ( 78) covalent geometry : bond 0.00417 (21198) covalent geometry : angle 0.60088 (28833) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4830 Ramachandran restraints generated. 2415 Oldfield, 0 Emsley, 2415 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4830 Ramachandran restraints generated. 2415 Oldfield, 0 Emsley, 2415 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 46 residues out of total 2121 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 46 time to evaluate : 2.438 Fit side-chains revert: symmetry clash REVERT: A 434 MET cc_start: 0.9036 (ttm) cc_final: 0.8813 (ttp) REVERT: I 104 MET cc_start: 0.9069 (tmm) cc_final: 0.8664 (tmm) REVERT: I 434 MET cc_start: 0.9197 (tpt) cc_final: 0.8942 (mmm) REVERT: K 70 MET cc_start: 0.7910 (mtm) cc_final: 0.7567 (mtp) outliers start: 0 outliers final: 0 residues processed: 46 average time/residue: 0.3227 time to fit residues: 25.9528 Evaluate side-chains 46 residues out of total 2121 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 46 time to evaluate : 2.417 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 73 optimal weight: 20.0000 chunk 211 optimal weight: 2.9990 chunk 78 optimal weight: 8.9990 chunk 13 optimal weight: 10.0000 chunk 239 optimal weight: 4.9990 chunk 138 optimal weight: 5.9990 chunk 27 optimal weight: 0.1980 chunk 194 optimal weight: 2.9990 chunk 39 optimal weight: 5.9990 chunk 148 optimal weight: 4.9990 chunk 51 optimal weight: 0.9990 overall best weight: 2.4388 ------------------------------------------------------------------------------- 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 = 0.2872 r_free = 0.2872 target = 0.024187 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2519 r_free = 0.2519 target = 0.018656 restraints weight = 324892.459| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.2552 r_free = 0.2552 target = 0.019173 restraints weight = 198429.664| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.2574 r_free = 0.2574 target = 0.019514 restraints weight = 147306.882| |-----------------------------------------------------------------------------| r_work (final): 0.2562 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8707 moved from start: 0.2171 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 21367 Z= 0.124 Angle : 0.582 8.898 29301 Z= 0.274 Chirality : 0.043 0.273 3619 Planarity : 0.003 0.033 3492 Dihedral : 8.305 88.379 5328 Min Nonbonded Distance : 2.399 Molprobity Statistics. All-atom Clashscore : 6.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.93 % Favored : 96.07 % Rotamer: Outliers : 0.00 % Allowed : 0.19 % Favored : 99.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.12 (0.18), residues: 2415 helix: 1.62 (0.28), residues: 402 sheet: -0.43 (0.19), residues: 708 loop : -0.34 (0.18), residues: 1305 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 628 HIS 0.002 0.001 HIS C 32 PHE 0.008 0.001 PHE A 382 TYR 0.031 0.001 TYR L 51 ARG 0.002 0.000 ARG C 38 Details of bonding type rmsd link_NAG-ASN : bond 0.00320 ( 46) link_NAG-ASN : angle 2.12710 ( 138) link_ALPHA1-6 : bond 0.00758 ( 6) link_ALPHA1-6 : angle 1.25029 ( 18) link_BETA1-4 : bond 0.00474 ( 65) link_BETA1-4 : angle 1.58773 ( 195) link_ALPHA1-2 : bond 0.00432 ( 6) link_ALPHA1-2 : angle 1.94390 ( 18) link_ALPHA1-3 : bond 0.01039 ( 7) link_ALPHA1-3 : angle 1.71426 ( 21) hydrogen bonds : bond 0.03375 ( 517) hydrogen bonds : angle 4.79139 ( 1416) SS BOND : bond 0.00229 ( 39) SS BOND : angle 0.56994 ( 78) covalent geometry : bond 0.00266 (21198) covalent geometry : angle 0.54743 (28833) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4619.87 seconds wall clock time: 83 minutes 27.23 seconds (5007.23 seconds total)