Starting phenix.real_space_refine on Wed Jun 18 09:15:39 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8dy6_27776/06_2025/8dy6_27776.cif Found real_map, /net/cci-nas-00/data/ceres_data/8dy6_27776/06_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_27776/06_2025/8dy6_27776.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8dy6_27776/06_2025/8dy6_27776.map" model { file = "/net/cci-nas-00/data/ceres_data/8dy6_27776/06_2025/8dy6_27776.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8dy6_27776/06_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-5710/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: 12.61, per 1000 atoms: 0.61 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: 6.63 Conformation dependent library (CDL) restraints added in 2.7 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: 2.60 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: 6.40 Time building geometry restraints manager: 7.53 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: 2.200 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: 0.790 Check model and map are aligned: 0.150 Set scattering table: 0.180 Process input model: 47.550 Find NCS groups from input model: 1.300 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: 0.010 Load rotamer database and sin/cos tables:2.830 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 55.180 ------------------------------------------------------------------------------- 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 : 2.505 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: 0.2898 time to fit residues: 25.1671 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 : 2.274 ------------------------------------------------------------------------------- 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 = 43)----------------| | r_work = 0.2528 r_free = 0.2528 target = 0.018816 restraints weight = 326110.163| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.2562 r_free = 0.2562 target = 0.019340 restraints weight = 197355.834| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.2584 r_free = 0.2584 target = 0.019689 restraints weight = 145080.723| |-----------------------------------------------------------------------------| 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 0.01044 ( 7) link_ALPHA1-3 : angle 2.29857 ( 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 : 2.364 Fit side-chains revert: symmetry clash REVERT: B 530 MET cc_start: 0.8177 (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: 0.2971 time to fit residues: 24.9696 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 : 2.273 ------------------------------------------------------------------------------- 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: 7.9990 chunk 215 optimal weight: 3.9990 chunk 84 optimal weight: 10.0000 chunk 1 optimal weight: 7.9990 chunk 38 optimal weight: 2.9990 overall best weight: 5.5990 ------------------------------------------------------------------------------- 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 J 577 GLN L 39 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2851 r_free = 0.2851 target = 0.023835 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2495 r_free = 0.2495 target = 0.018346 restraints weight = 327069.804| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.2528 r_free = 0.2528 target = 0.018852 restraints weight = 199837.445| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.2550 r_free = 0.2550 target = 0.019188 restraints weight = 147693.051| |-----------------------------------------------------------------------------| r_work (final): 0.2538 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8737 moved from start: 0.1379 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.044 21367 Z= 0.233 Angle : 0.704 8.876 29301 Z= 0.328 Chirality : 0.045 0.278 3619 Planarity : 0.004 0.040 3492 Dihedral : 11.669 82.663 5328 Min Nonbonded Distance : 2.386 Molprobity Statistics. All-atom Clashscore : 7.69 Ramachandran Plot: Outliers : 0.08 % Allowed : 4.02 % Favored : 95.90 % Rotamer: Outliers : 0.00 % Allowed : 3.02 % Favored : 96.98 % 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: -0.30 (0.18), residues: 2415 helix: 1.09 (0.28), residues: 399 sheet: -0.13 (0.20), residues: 657 loop : -0.58 (0.18), residues: 1359 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP G 36 HIS 0.005 0.001 HIS H 41 PHE 0.017 0.002 PHE I 382 TYR 0.045 0.002 TYR L 51 ARG 0.003 0.000 ARG A 503 Details of bonding type rmsd link_NAG-ASN : bond 0.00601 ( 46) link_NAG-ASN : angle 2.47197 ( 138) link_ALPHA1-6 : bond 0.00332 ( 6) link_ALPHA1-6 : angle 1.99615 ( 18) link_BETA1-4 : bond 0.00543 ( 65) link_BETA1-4 : angle 2.10307 ( 195) link_ALPHA1-2 : bond 0.00544 ( 6) link_ALPHA1-2 : angle 2.30609 ( 18) link_ALPHA1-3 : bond 0.00887 ( 7) link_ALPHA1-3 : angle 2.24193 ( 21) hydrogen bonds : bond 0.04140 ( 517) hydrogen bonds : angle 5.21625 ( 1416) SS BOND : bond 0.00356 ( 39) SS BOND : angle 0.77473 ( 78) covalent geometry : bond 0.00498 (21198) covalent geometry : angle 0.65862 (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 : 2.240 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 104 MET cc_start: 0.9232 (tmm) cc_final: 0.8850 (tmm) REVERT: K 70 MET cc_start: 0.8157 (mtm) cc_final: 0.7781 (mtp) outliers start: 0 outliers final: 0 residues processed: 45 average time/residue: 0.3023 time to fit residues: 24.8656 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 : 2.566 ------------------------------------------------------------------------------- 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: 8.9990 chunk 82 optimal weight: 7.9990 chunk 42 optimal weight: 20.0000 chunk 227 optimal weight: 7.9990 chunk 36 optimal weight: 20.0000 chunk 130 optimal weight: 7.9990 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: 4.9990 overall best weight: 6.9990 ------------------------------------------------------------------------------- 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 ** I 350 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2840 r_free = 0.2840 target = 0.023679 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2481 r_free = 0.2481 target = 0.018155 restraints weight = 333642.722| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.2514 r_free = 0.2514 target = 0.018651 restraints weight = 205099.706| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.2535 r_free = 0.2535 target = 0.018976 restraints weight = 152871.466| |-----------------------------------------------------------------------------| r_work (final): 0.2523 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8763 moved from start: 0.1852 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.068 21367 Z= 0.278 Angle : 0.735 9.093 29301 Z= 0.346 Chirality : 0.046 0.272 3619 Planarity : 0.004 0.039 3492 Dihedral : 10.607 84.329 5328 Min Nonbonded Distance : 2.364 Molprobity Statistics. All-atom Clashscore : 9.58 Ramachandran Plot: Outliers : 0.04 % Allowed : 5.05 % Favored : 94.91 % Rotamer: Outliers : 0.05 % Allowed : 3.39 % Favored : 96.56 % 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: -0.50 (0.18), residues: 2415 helix: 0.99 (0.28), residues: 402 sheet: -0.54 (0.19), residues: 681 loop : -0.56 (0.18), residues: 1332 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.039 0.002 TRP J 614 HIS 0.005 0.002 HIS G 32 PHE 0.021 0.002 PHE I 382 TYR 0.036 0.002 TYR L 51 ARG 0.003 0.000 ARG A 503 Details of bonding type rmsd link_NAG-ASN : bond 0.00672 ( 46) link_NAG-ASN : angle 2.48336 ( 138) link_ALPHA1-6 : bond 0.00461 ( 6) link_ALPHA1-6 : angle 2.14128 ( 18) link_BETA1-4 : bond 0.00550 ( 65) link_BETA1-4 : angle 2.06075 ( 195) link_ALPHA1-2 : bond 0.00769 ( 6) link_ALPHA1-2 : angle 2.31134 ( 18) link_ALPHA1-3 : bond 0.00880 ( 7) link_ALPHA1-3 : angle 2.39777 ( 21) hydrogen bonds : bond 0.04326 ( 517) hydrogen bonds : angle 5.38681 ( 1416) SS BOND : bond 0.00312 ( 39) SS BOND : angle 0.75876 ( 78) covalent geometry : bond 0.00592 (21198) covalent geometry : angle 0.69196 (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 : 2.489 Fit side-chains REVERT: I 104 MET cc_start: 0.9313 (tmm) cc_final: 0.8743 (tmm) REVERT: I 434 MET cc_start: 0.8833 (mmm) cc_final: 0.8473 (ttm) REVERT: K 70 MET cc_start: 0.7997 (mtm) cc_final: 0.7689 (mtp) outliers start: 1 outliers final: 0 residues processed: 46 average time/residue: 0.3056 time to fit residues: 25.7285 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 : 2.479 ------------------------------------------------------------------------------- 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: 6.9990 chunk 155 optimal weight: 9.9990 chunk 128 optimal weight: 10.0000 chunk 7 optimal weight: 0.9980 chunk 135 optimal weight: 5.9990 chunk 133 optimal weight: 8.9990 chunk 20 optimal weight: 7.9990 chunk 56 optimal weight: 8.9990 chunk 233 optimal weight: 20.0000 chunk 199 optimal weight: 6.9990 overall best weight: 5.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 103 GLN ** I 350 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2846 r_free = 0.2846 target = 0.023800 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.2489 r_free = 0.2489 target = 0.018285 restraints weight = 330993.123| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.2521 r_free = 0.2521 target = 0.018786 restraints weight = 204723.401| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.2542 r_free = 0.2542 target = 0.019108 restraints weight = 152524.935| |-----------------------------------------------------------------------------| r_work (final): 0.2530 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8751 moved from start: 0.1969 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.044 21367 Z= 0.235 Angle : 0.695 9.814 29301 Z= 0.326 Chirality : 0.045 0.269 3619 Planarity : 0.004 0.035 3492 Dihedral : 10.235 85.656 5328 Min Nonbonded Distance : 2.367 Molprobity Statistics. All-atom Clashscore : 9.11 Ramachandran Plot: Outliers : 0.04 % Allowed : 4.89 % Favored : 95.07 % Rotamer: Outliers : 0.00 % Allowed : 1.46 % Favored : 98.54 % 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: -0.47 (0.18), residues: 2415 helix: 1.11 (0.28), residues: 402 sheet: -0.59 (0.20), residues: 672 loop : -0.53 (0.18), residues: 1341 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP J 614 HIS 0.004 0.001 HIS C 32 PHE 0.016 0.002 PHE I 382 TYR 0.028 0.002 TYR L 51 ARG 0.003 0.000 ARG I 503 Details of bonding type rmsd link_NAG-ASN : bond 0.00577 ( 46) link_NAG-ASN : angle 2.50991 ( 138) link_ALPHA1-6 : bond 0.00510 ( 6) link_ALPHA1-6 : angle 2.06472 ( 18) link_BETA1-4 : bond 0.00519 ( 65) link_BETA1-4 : angle 1.89003 ( 195) link_ALPHA1-2 : bond 0.00655 ( 6) link_ALPHA1-2 : angle 2.23299 ( 18) link_ALPHA1-3 : bond 0.00942 ( 7) link_ALPHA1-3 : angle 2.20985 ( 21) hydrogen bonds : bond 0.04171 ( 517) hydrogen bonds : angle 5.29088 ( 1416) SS BOND : bond 0.00306 ( 39) SS BOND : angle 0.78808 ( 78) covalent geometry : bond 0.00503 (21198) covalent geometry : angle 0.65257 (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 45 residues out of total 2121 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 45 time to evaluate : 2.454 Fit side-chains revert: symmetry clash REVERT: I 104 MET cc_start: 0.9251 (tmm) cc_final: 0.8633 (tmm) REVERT: K 70 MET cc_start: 0.8301 (mtm) cc_final: 0.7444 (mtm) outliers start: 0 outliers final: 0 residues processed: 45 average time/residue: 0.3034 time to fit residues: 25.0365 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 : 2.383 ------------------------------------------------------------------------------- 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: 2.9990 chunk 148 optimal weight: 10.0000 chunk 25 optimal weight: 6.9990 chunk 91 optimal weight: 5.9990 chunk 234 optimal weight: 9.9990 chunk 137 optimal weight: 4.9990 chunk 45 optimal weight: 9.9990 chunk 10 optimal weight: 0.0870 chunk 174 optimal weight: 0.0040 chunk 1 optimal weight: 20.0000 chunk 212 optimal weight: 10.0000 overall best weight: 2.8176 ------------------------------------------------------------------------------- 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 = 0.2866 r_free = 0.2866 target = 0.024092 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2512 r_free = 0.2512 target = 0.018579 restraints weight = 323591.707| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.2546 r_free = 0.2546 target = 0.019098 restraints weight = 198167.408| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.2567 r_free = 0.2567 target = 0.019432 restraints weight = 146992.002| |-----------------------------------------------------------------------------| r_work (final): 0.2555 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8714 moved from start: 0.1955 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= 0.134 Angle : 0.602 9.524 29301 Z= 0.283 Chirality : 0.044 0.277 3619 Planarity : 0.003 0.034 3492 Dihedral : 9.365 86.746 5328 Min Nonbonded Distance : 2.392 Molprobity Statistics. All-atom Clashscore : 7.02 Ramachandran Plot: Outliers : 0.04 % Allowed : 3.77 % Favored : 96.19 % Rotamer: Outliers : 0.00 % Allowed : 1.27 % Favored : 98.73 % 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: -0.19 (0.18), residues: 2415 helix: 1.45 (0.28), residues: 399 sheet: -0.44 (0.20), residues: 669 loop : -0.37 (0.18), residues: 1347 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP E 112 HIS 0.002 0.001 HIS I 105 PHE 0.011 0.001 PHE I 382 TYR 0.025 0.001 TYR E 217 ARG 0.005 0.000 ARG E 503 Details of bonding type rmsd link_NAG-ASN : bond 0.00331 ( 46) link_NAG-ASN : angle 2.25077 ( 138) link_ALPHA1-6 : bond 0.00742 ( 6) link_ALPHA1-6 : angle 1.59553 ( 18) link_BETA1-4 : bond 0.00465 ( 65) link_BETA1-4 : angle 1.68309 ( 195) link_ALPHA1-2 : bond 0.00378 ( 6) link_ALPHA1-2 : angle 1.99073 ( 18) link_ALPHA1-3 : bond 0.01128 ( 7) link_ALPHA1-3 : angle 1.84377 ( 21) hydrogen bonds : bond 0.03652 ( 517) hydrogen bonds : angle 5.00665 ( 1416) SS BOND : bond 0.00248 ( 39) SS BOND : angle 0.65438 ( 78) covalent geometry : bond 0.00286 (21198) covalent geometry : angle 0.56312 (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 47 residues out of total 2121 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 47 time to evaluate : 2.548 Fit side-chains revert: symmetry clash REVERT: A 104 MET cc_start: 0.9390 (tmm) cc_final: 0.8551 (tmm) REVERT: C 48 MET cc_start: 0.9044 (pmm) cc_final: 0.8727 (pmm) REVERT: I 104 MET cc_start: 0.9208 (tmm) cc_final: 0.8531 (tmm) REVERT: J 626 MET cc_start: 0.8199 (tpt) cc_final: 0.7317 (tpp) REVERT: K 70 MET cc_start: 0.8051 (mtm) cc_final: 0.7642 (mtp) outliers start: 0 outliers final: 0 residues processed: 47 average time/residue: 0.3342 time to fit residues: 27.7062 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 : 2.534 ------------------------------------------------------------------------------- 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: 6.9990 chunk 166 optimal weight: 9.9990 chunk 49 optimal weight: 7.9990 chunk 235 optimal weight: 7.9990 chunk 160 optimal weight: 4.9990 chunk 117 optimal weight: 4.9990 chunk 217 optimal weight: 5.9990 chunk 4 optimal weight: 9.9990 chunk 202 optimal weight: 7.9990 chunk 119 optimal weight: 9.9990 chunk 100 optimal weight: 20.0000 overall best weight: 6.1990 ------------------------------------------------------------------------------- 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** I 350 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2846 r_free = 0.2846 target = 0.023799 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2490 r_free = 0.2490 target = 0.018309 restraints weight = 330019.816| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.2522 r_free = 0.2522 target = 0.018808 restraints weight = 203466.550| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.2544 r_free = 0.2544 target = 0.019137 restraints weight = 151616.621| |-----------------------------------------------------------------------------| r_work (final): 0.2531 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8751 moved from start: 0.2160 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.043 21367 Z= 0.249 Angle : 0.703 9.591 29301 Z= 0.330 Chirality : 0.045 0.256 3619 Planarity : 0.004 0.032 3492 Dihedral : 9.364 88.050 5328 Min Nonbonded Distance : 2.367 Molprobity Statistics. All-atom Clashscore : 10.34 Ramachandran Plot: Outliers : 0.04 % Allowed : 5.05 % Favored : 94.91 % Rotamer: Outliers : 0.05 % Allowed : 0.99 % Favored : 98.96 % 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: -0.38 (0.18), residues: 2415 helix: 1.29 (0.28), residues: 402 sheet: -0.60 (0.20), residues: 672 loop : -0.47 (0.18), residues: 1341 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.002 TRP B 614 HIS 0.004 0.001 HIS C 32 PHE 0.016 0.002 PHE I 382 TYR 0.048 0.002 TYR L 51 ARG 0.004 0.000 ARG G 57 Details of bonding type rmsd link_NAG-ASN : bond 0.00631 ( 46) link_NAG-ASN : angle 2.49263 ( 138) link_ALPHA1-6 : bond 0.00663 ( 6) link_ALPHA1-6 : angle 1.67791 ( 18) link_BETA1-4 : bond 0.00527 ( 65) link_BETA1-4 : angle 1.86723 ( 195) link_ALPHA1-2 : bond 0.00743 ( 6) link_ALPHA1-2 : angle 2.22375 ( 18) link_ALPHA1-3 : bond 0.00937 ( 7) link_ALPHA1-3 : angle 2.10129 ( 21) hydrogen bonds : bond 0.04067 ( 517) hydrogen bonds : angle 5.25069 ( 1416) SS BOND : bond 0.00315 ( 39) SS BOND : angle 0.75033 ( 78) covalent geometry : bond 0.00533 (21198) covalent geometry : angle 0.66273 (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 47 residues out of total 2121 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 46 time to evaluate : 2.358 Fit side-chains revert: symmetry clash REVERT: I 350 GLN cc_start: 0.9228 (OUTLIER) cc_final: 0.8582 (tm-30) REVERT: K 70 MET cc_start: 0.7986 (mtm) cc_final: 0.7576 (mtp) outliers start: 1 outliers final: 0 residues processed: 47 average time/residue: 0.3304 time to fit residues: 27.0510 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 : 2.483 ------------------------------------------------------------------------------- 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: 4.9990 chunk 210 optimal weight: 9.9990 chunk 214 optimal weight: 9.9990 chunk 94 optimal weight: 9.9990 chunk 146 optimal weight: 8.9990 chunk 11 optimal weight: 20.0000 chunk 80 optimal weight: 10.0000 chunk 124 optimal weight: 5.9990 chunk 89 optimal weight: 3.9990 chunk 19 optimal weight: 0.7980 chunk 46 optimal weight: 5.9990 overall best weight: 4.3588 ------------------------------------------------------------------------------- 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 = 0.2856 r_free = 0.2856 target = 0.023941 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.2500 r_free = 0.2500 target = 0.018429 restraints weight = 327700.101| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.2533 r_free = 0.2533 target = 0.018939 restraints weight = 200950.358| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 23)----------------| | r_work = 0.2554 r_free = 0.2554 target = 0.019270 restraints weight = 149537.992| |-----------------------------------------------------------------------------| r_work (final): 0.2542 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8735 moved from start: 0.2185 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= 0.183 Angle : 0.634 9.262 29301 Z= 0.299 Chirality : 0.044 0.267 3619 Planarity : 0.003 0.034 3492 Dihedral : 9.003 89.460 5328 Min Nonbonded Distance : 2.382 Molprobity Statistics. All-atom Clashscore : 8.87 Ramachandran Plot: Outliers : 0.04 % Allowed : 4.47 % Favored : 95.49 % Rotamer: Outliers : 0.00 % Allowed : 0.66 % Favored : 99.34 % 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: -0.30 (0.18), residues: 2415 helix: 1.47 (0.28), residues: 402 sheet: -0.55 (0.20), residues: 663 loop : -0.46 (0.18), residues: 1350 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP B 614 HIS 0.004 0.001 HIS I 352 PHE 0.013 0.001 PHE I 382 TYR 0.042 0.002 TYR L 51 ARG 0.007 0.000 ARG G 38 Details of bonding type rmsd link_NAG-ASN : bond 0.00419 ( 46) link_NAG-ASN : angle 2.28578 ( 138) link_ALPHA1-6 : bond 0.00748 ( 6) link_ALPHA1-6 : angle 1.39878 ( 18) link_BETA1-4 : bond 0.00494 ( 65) link_BETA1-4 : angle 1.70247 ( 195) link_ALPHA1-2 : bond 0.00566 ( 6) link_ALPHA1-2 : angle 2.07675 ( 18) link_ALPHA1-3 : bond 0.01042 ( 7) link_ALPHA1-3 : angle 1.84858 ( 21) hydrogen bonds : bond 0.03789 ( 517) hydrogen bonds : angle 5.09677 ( 1416) SS BOND : bond 0.00274 ( 39) SS BOND : angle 0.64760 ( 78) covalent geometry : bond 0.00393 (21198) covalent geometry : angle 0.59727 (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 46 residues out of total 2121 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 46 time to evaluate : 2.503 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 48 MET cc_start: 0.9054 (pmm) cc_final: 0.8778 (pmm) REVERT: K 70 MET cc_start: 0.7947 (mtm) cc_final: 0.7576 (mtp) outliers start: 0 outliers final: 0 residues processed: 46 average time/residue: 0.3127 time to fit residues: 25.6008 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 : 2.484 ------------------------------------------------------------------------------- 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: 30.0000 chunk 56 optimal weight: 7.9990 chunk 49 optimal weight: 6.9990 chunk 157 optimal weight: 30.0000 chunk 103 optimal weight: 0.0070 chunk 53 optimal weight: 20.0000 chunk 201 optimal weight: 9.9990 chunk 137 optimal weight: 3.9990 chunk 132 optimal weight: 9.9990 chunk 91 optimal weight: 3.9990 chunk 111 optimal weight: 9.9990 overall best weight: 4.6006 ------------------------------------------------------------------------------- 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 = 0.2855 r_free = 0.2855 target = 0.023918 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.2498 r_free = 0.2498 target = 0.018404 restraints weight = 329173.016| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.2531 r_free = 0.2531 target = 0.018914 restraints weight = 202045.779| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.2553 r_free = 0.2553 target = 0.019244 restraints weight = 150087.227| |-----------------------------------------------------------------------------| r_work (final): 0.2540 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8739 moved from start: 0.2255 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= 0.193 Angle : 0.646 9.184 29301 Z= 0.305 Chirality : 0.044 0.267 3619 Planarity : 0.003 0.032 3492 Dihedral : 8.881 88.640 5328 Min Nonbonded Distance : 2.382 Molprobity Statistics. All-atom Clashscore : 9.16 Ramachandran Plot: Outliers : 0.04 % Allowed : 4.68 % Favored : 95.28 % Rotamer: Outliers : 0.00 % Allowed : 0.42 % Favored : 99.58 % 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: -0.34 (0.18), residues: 2415 helix: 1.50 (0.28), residues: 402 sheet: -0.68 (0.20), residues: 675 loop : -0.44 (0.18), residues: 1338 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP B 614 HIS 0.008 0.001 HIS A 66 PHE 0.013 0.001 PHE A 382 TYR 0.038 0.002 TYR L 51 ARG 0.003 0.000 ARG I 503 Details of bonding type rmsd link_NAG-ASN : bond 0.00479 ( 46) link_NAG-ASN : angle 2.32644 ( 138) link_ALPHA1-6 : bond 0.00703 ( 6) link_ALPHA1-6 : angle 1.36207 ( 18) link_BETA1-4 : bond 0.00499 ( 65) link_BETA1-4 : angle 1.73622 ( 195) link_ALPHA1-2 : bond 0.00606 ( 6) link_ALPHA1-2 : angle 2.10427 ( 18) link_ALPHA1-3 : bond 0.00979 ( 7) link_ALPHA1-3 : angle 1.85579 ( 21) hydrogen bonds : bond 0.03820 ( 517) hydrogen bonds : angle 5.06464 ( 1416) SS BOND : bond 0.00270 ( 39) SS BOND : angle 0.64275 ( 78) covalent geometry : bond 0.00415 (21198) covalent geometry : angle 0.60879 (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 : 2.228 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 104 MET cc_start: 0.8810 (tmm) cc_final: 0.8333 (tmm) REVERT: I 104 MET cc_start: 0.8999 (tmm) cc_final: 0.8655 (tmm) REVERT: K 70 MET cc_start: 0.7940 (mtm) cc_final: 0.7552 (mtp) outliers start: 0 outliers final: 0 residues processed: 46 average time/residue: 0.3179 time to fit residues: 25.7867 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 : 2.219 ------------------------------------------------------------------------------- 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: 4.9990 chunk 120 optimal weight: 5.9990 chunk 190 optimal weight: 20.0000 chunk 222 optimal weight: 8.9990 chunk 57 optimal weight: 8.9990 chunk 164 optimal weight: 1.9990 chunk 192 optimal weight: 3.9990 chunk 9 optimal weight: 7.9990 chunk 135 optimal weight: 0.0970 chunk 78 optimal weight: 0.5980 chunk 130 optimal weight: 3.9990 overall best weight: 2.1384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 39 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2872 r_free = 0.2872 target = 0.024198 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2517 r_free = 0.2517 target = 0.018660 restraints weight = 324049.608| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.2551 r_free = 0.2551 target = 0.019179 restraints weight = 198030.629| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.2573 r_free = 0.2573 target = 0.019518 restraints weight = 146868.168| |-----------------------------------------------------------------------------| r_work (final): 0.2560 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8708 moved from start: 0.2218 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 21367 Z= 0.118 Angle : 0.586 8.861 29301 Z= 0.276 Chirality : 0.043 0.274 3619 Planarity : 0.003 0.034 3492 Dihedral : 8.437 89.918 5328 Min Nonbonded Distance : 2.411 Molprobity Statistics. All-atom Clashscore : 7.05 Ramachandran Plot: Outliers : 0.04 % Allowed : 3.93 % Favored : 96.02 % Rotamer: Outliers : 0.00 % Allowed : 0.38 % Favored : 99.62 % 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: -0.17 (0.18), residues: 2415 helix: 1.68 (0.28), residues: 402 sheet: -0.60 (0.19), residues: 693 loop : -0.32 (0.18), residues: 1320 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP F 631 HIS 0.002 0.001 HIS A 374 PHE 0.009 0.001 PHE A 382 TYR 0.034 0.001 TYR L 51 ARG 0.003 0.000 ARG E 500 Details of bonding type rmsd link_NAG-ASN : bond 0.00307 ( 46) link_NAG-ASN : angle 2.11814 ( 138) link_ALPHA1-6 : bond 0.00778 ( 6) link_ALPHA1-6 : angle 1.26781 ( 18) link_BETA1-4 : bond 0.00474 ( 65) link_BETA1-4 : angle 1.58106 ( 195) link_ALPHA1-2 : bond 0.00389 ( 6) link_ALPHA1-2 : angle 1.90684 ( 18) link_ALPHA1-3 : bond 0.01093 ( 7) link_ALPHA1-3 : angle 1.71808 ( 21) hydrogen bonds : bond 0.03394 ( 517) hydrogen bonds : angle 4.82512 ( 1416) SS BOND : bond 0.00221 ( 39) SS BOND : angle 0.59513 ( 78) covalent geometry : bond 0.00254 (21198) covalent geometry : angle 0.55166 (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 : 2.357 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 104 MET cc_start: 0.8712 (tmm) cc_final: 0.8234 (tmm) REVERT: A 434 MET cc_start: 0.9066 (ttm) cc_final: 0.8678 (ttp) REVERT: I 104 MET cc_start: 0.8901 (tmm) cc_final: 0.8590 (tmm) REVERT: K 70 MET cc_start: 0.8265 (mtm) cc_final: 0.7503 (mtp) outliers start: 0 outliers final: 0 residues processed: 46 average time/residue: 0.3197 time to fit residues: 25.8899 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 : 2.189 ------------------------------------------------------------------------------- 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: 0.9990 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: 4.9990 chunk 194 optimal weight: 8.9990 chunk 39 optimal weight: 0.9990 chunk 148 optimal weight: 7.9990 chunk 51 optimal weight: 0.0170 overall best weight: 2.4026 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 39 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2873 r_free = 0.2873 target = 0.024185 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2518 r_free = 0.2518 target = 0.018651 restraints weight = 323135.679| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.2552 r_free = 0.2552 target = 0.019170 restraints weight = 197531.687| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.2574 r_free = 0.2574 target = 0.019515 restraints weight = 146334.822| |-----------------------------------------------------------------------------| r_work (final): 0.2562 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8706 moved from start: 0.2245 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= 0.123 Angle : 0.578 8.865 29301 Z= 0.273 Chirality : 0.043 0.273 3619 Planarity : 0.003 0.032 3492 Dihedral : 8.208 86.448 5328 Min Nonbonded Distance : 2.409 Molprobity Statistics. All-atom Clashscore : 7.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.06 % Favored : 95.94 % Rotamer: Outliers : 0.00 % Allowed : 0.24 % Favored : 99.76 % 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: 1.72 (0.28), residues: 402 sheet: -0.55 (0.19), residues: 726 loop : -0.29 (0.18), residues: 1287 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 614 HIS 0.003 0.001 HIS A 66 PHE 0.009 0.001 PHE A 382 TYR 0.034 0.001 TYR L 51 ARG 0.002 0.000 ARG A 503 Details of bonding type rmsd link_NAG-ASN : bond 0.00322 ( 46) link_NAG-ASN : angle 2.12897 ( 138) link_ALPHA1-6 : bond 0.00735 ( 6) link_ALPHA1-6 : angle 1.24967 ( 18) link_BETA1-4 : bond 0.00472 ( 65) link_BETA1-4 : angle 1.60775 ( 195) link_ALPHA1-2 : bond 0.00424 ( 6) link_ALPHA1-2 : angle 1.93484 ( 18) link_ALPHA1-3 : bond 0.01018 ( 7) link_ALPHA1-3 : angle 1.69089 ( 21) hydrogen bonds : bond 0.03328 ( 517) hydrogen bonds : angle 4.74029 ( 1416) SS BOND : bond 0.00223 ( 39) SS BOND : angle 0.56817 ( 78) covalent geometry : bond 0.00265 (21198) covalent geometry : angle 0.54212 (28833) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5026.07 seconds wall clock time: 89 minutes 38.67 seconds (5378.67 seconds total)