Starting phenix.real_space_refine on Sat Jul 4 12:11:20 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/7lxn_23572/07_2026/7lxn_23572.cif Found real_map, /net/cci-nas-00/data/ceres_data/7lxn_23572/07_2026/7lxn_23572.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.85 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/7lxn_23572/07_2026/7lxn_23572.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7lxn_23572/07_2026/7lxn_23572.cif" restraint_files = "/net/cci-nas-00/data/ceres_data/7lxn_23572/07_2026/7lxn_23572.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/7lxn_23572/07_2026/7lxn_23572.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7lxn_23572/07_2026/7lxn_23572.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7lxn_23572/07_2026/7lxn_23572.map" } resolution = 3.85 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.002 sd= 0.105 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 114 5.16 5 C 12987 2.51 5 N 3351 2.21 5 O 4368 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 53 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 20820 Number of models: 1 Model: "" Number of chains: 60 Chain: "A" Number of atoms: 3450 Number of conformers: 1 Conformer: "" Number of residues, atoms: 434, 3450 Classifications: {'peptide': 434} Link IDs: {'PTRANS': 22, 'TRANS': 411} Chain breaks: 3 Chain: "B" Number of atoms: 950 Number of conformers: 1 Conformer: "" Number of residues, atoms: 118, 950 Classifications: {'peptide': 118} Link IDs: {'PTRANS': 1, 'TRANS': 116} Chain breaks: 1 Chain: "H" Number of atoms: 1041 Number of conformers: 1 Conformer: "" Number of residues, atoms: 131, 1041 Classifications: {'peptide': 131} Link IDs: {'PTRANS': 5, 'TRANS': 125} Chain: "L" Number of atoms: 823 Number of conformers: 1 Conformer: "" Number of residues, atoms: 108, 823 Classifications: {'peptide': 108} Link IDs: {'PTRANS': 8, 'TRANS': 99} Chain: "C" Number of atoms: 3450 Number of conformers: 1 Conformer: "" Number of residues, atoms: 434, 3450 Classifications: {'peptide': 434} Link IDs: {'PTRANS': 22, 'TRANS': 411} Chain breaks: 3 Chain: "D" Number of atoms: 950 Number of conformers: 1 Conformer: "" Number of residues, atoms: 118, 950 Classifications: {'peptide': 118} Link IDs: {'PTRANS': 1, 'TRANS': 116} Chain breaks: 1 Chain: "I" Number of atoms: 1041 Number of conformers: 1 Conformer: "" Number of residues, atoms: 131, 1041 Classifications: {'peptide': 131} Link IDs: {'PTRANS': 5, 'TRANS': 125} Chain: "M" Number of atoms: 823 Number of conformers: 1 Conformer: "" Number of residues, atoms: 108, 823 Classifications: {'peptide': 108} Link IDs: {'PTRANS': 8, 'TRANS': 99} Chain: "E" Number of atoms: 3450 Number of conformers: 1 Conformer: "" Number of residues, atoms: 434, 3450 Classifications: {'peptide': 434} Link IDs: {'PTRANS': 22, 'TRANS': 411} Chain breaks: 3 Chain: "F" Number of atoms: 950 Number of conformers: 1 Conformer: "" Number of residues, atoms: 118, 950 Classifications: {'peptide': 118} Link IDs: {'PTRANS': 1, 'TRANS': 116} Chain breaks: 1 Chain: "J" Number of atoms: 1041 Number of conformers: 1 Conformer: "" Number of residues, atoms: 131, 1041 Classifications: {'peptide': 131} Link IDs: {'PTRANS': 5, 'TRANS': 125} Chain: "N" Number of atoms: 823 Number of conformers: 1 Conformer: "" Number of residues, atoms: 108, 823 Classifications: {'peptide': 108} Link IDs: {'PTRANS': 8, 'TRANS': 99} Chain: "G" Number of atoms: 94 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 94 Unusual residues: {'BMA': 1, 'MAN': 5, 'NAG': 2} Classifications: {'undetermined': 8} Link IDs: {None: 7} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen chiralities: 8 Chain: "K" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "O" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "P" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "Q" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen 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 chiralities: 2 Chain: "S" 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 chiralities: 7 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 chiralities: 2 Chain: "U" 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 chiralities: 4 Chain: "V" Number of atoms: 105 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 105 Unusual residues: {'BMA': 1, 'MAN': 6, 'NAG': 2} Classifications: {'undetermined': 9} Link IDs: {None: 8} Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 18 Unresolved non-hydrogen chiralities: 9 Chain: "W" 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 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 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 chiralities: 2 Chain: "Z" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "a" Number of atoms: 94 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 94 Unusual residues: {'BMA': 1, 'MAN': 5, 'NAG': 2} Classifications: {'undetermined': 8} Link IDs: {None: 7} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen chiralities: 8 Chain: "b" 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 chiralities: 2 Chain: "c" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "d" 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 chiralities: 2 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 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 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 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 chiralities: 2 Chain: "i" 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 chiralities: 4 Chain: "j" Number of atoms: 105 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 105 Unusual residues: {'BMA': 1, 'MAN': 6, 'NAG': 2} Classifications: {'undetermined': 9} Link IDs: {None: 8} Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 18 Unresolved non-hydrogen chiralities: 9 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 chiralities: 3 Chain: "l" 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 chiralities: 3 Chain: "m" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "n" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "o" Number of atoms: 94 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 94 Unusual residues: {'BMA': 1, 'MAN': 5, 'NAG': 2} Classifications: {'undetermined': 8} Link IDs: {None: 7} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen chiralities: 8 Chain: "p" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "q" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen 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 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 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 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 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 chiralities: 2 Chain: "w" 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 chiralities: 4 Chain: "x" Number of atoms: 105 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 105 Unusual residues: {'BMA': 1, 'MAN': 6, 'NAG': 2} Classifications: {'undetermined': 9} Link IDs: {None: 8} Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 18 Unresolved non-hydrogen chiralities: 9 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 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 chiralities: 3 Chain: "0" 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 chiralities: 2 Chain: "1" 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 chiralities: 2 Chain: "A" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "B" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen chiralities: 1 Chain: "C" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "D" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen chiralities: 1 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 chiralities: 2 Chain: "F" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen chiralities: 1 Time building chain proxies: 4.38, per 1000 atoms: 0.21 Number of scatterers: 20820 At special positions: 0 Unit cell: (146.718, 155.952, 148.77, 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 114 16.00 O 4368 8.00 N 3351 7.00 C 12987 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=2.27 Simple disulfide: pdb=" SG CYS A 119 " - pdb=" SG CYS A 205 " distance=2.02 Simple disulfide: pdb=" SG CYS A 126 " - pdb=" SG CYS A 196 " distance=2.04 Simple disulfide: pdb=" SG CYS A 131 " - pdb=" SG CYS A 157 " distance=2.02 Simple disulfide: pdb=" SG CYS A 218 " - pdb=" SG CYS A 247 " distance=2.12 Simple disulfide: pdb=" SG CYS A 228 " - pdb=" SG CYS A 239 " distance=2.04 Simple disulfide: pdb=" SG CYS A 296 " - pdb=" SG CYS A 331 " distance=2.04 Simple disulfide: pdb=" SG CYS A 378 " - pdb=" SG CYS A 445 " distance=2.01 Simple disulfide: pdb=" SG CYS A 385 " - pdb=" SG CYS A 418 " distance=2.02 Simple disulfide: pdb=" SG CYS A 501 " - pdb=" SG CYS B 605 " distance=2.04 Simple disulfide: pdb=" SG CYS B 598 " - pdb=" SG CYS B 604 " distance=2.03 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 92 " distance=2.09 Simple disulfide: pdb=" SG CYS L 23 " - pdb=" SG CYS L 88 " distance=2.03 Simple disulfide: pdb=" SG CYS C 54 " - pdb=" SG CYS C 74 " distance=2.27 Simple disulfide: pdb=" SG CYS C 119 " - pdb=" SG CYS C 205 " distance=2.02 Simple disulfide: pdb=" SG CYS C 126 " - pdb=" SG CYS C 196 " distance=2.04 Simple disulfide: pdb=" SG CYS C 131 " - pdb=" SG CYS C 157 " distance=2.03 Simple disulfide: pdb=" SG CYS C 218 " - pdb=" SG CYS C 247 " distance=2.13 Simple disulfide: pdb=" SG CYS C 228 " - pdb=" SG CYS C 239 " distance=2.04 Simple disulfide: pdb=" SG CYS C 296 " - pdb=" SG CYS C 331 " distance=2.03 Simple disulfide: pdb=" SG CYS C 378 " - pdb=" SG CYS C 445 " distance=2.01 Simple disulfide: pdb=" SG CYS C 385 " - pdb=" SG CYS C 418 " distance=2.03 Simple disulfide: pdb=" SG CYS C 501 " - pdb=" SG CYS D 605 " distance=2.05 Simple disulfide: pdb=" SG CYS D 598 " - pdb=" SG CYS D 604 " distance=2.03 Simple disulfide: pdb=" SG CYS I 22 " - pdb=" SG CYS I 92 " distance=2.04 Simple disulfide: pdb=" SG CYS M 23 " - pdb=" SG CYS M 88 " distance=2.02 Simple disulfide: pdb=" SG CYS E 54 " - pdb=" SG CYS E 74 " distance=2.27 Simple disulfide: pdb=" SG CYS E 119 " - pdb=" SG CYS E 205 " distance=2.02 Simple disulfide: pdb=" SG CYS E 126 " - pdb=" SG CYS E 196 " distance=2.04 Simple disulfide: pdb=" SG CYS E 131 " - pdb=" SG CYS E 157 " distance=2.03 Simple disulfide: pdb=" SG CYS E 218 " - pdb=" SG CYS E 247 " distance=2.12 Simple disulfide: pdb=" SG CYS E 228 " - pdb=" SG CYS E 239 " distance=2.04 Simple disulfide: pdb=" SG CYS E 296 " - pdb=" SG CYS E 331 " distance=2.04 Simple disulfide: pdb=" SG CYS E 378 " - pdb=" SG CYS E 445 " distance=2.01 Simple disulfide: pdb=" SG CYS E 385 " - pdb=" SG CYS E 418 " distance=2.02 Simple disulfide: pdb=" SG CYS E 501 " - pdb=" SG CYS F 605 " distance=2.06 Simple disulfide: pdb=" SG CYS F 598 " - pdb=" SG CYS F 604 " distance=2.03 Simple disulfide: pdb=" SG CYS J 22 " - pdb=" SG CYS J 92 " distance=2.04 Simple disulfide: pdb=" SG CYS N 23 " - pdb=" SG CYS N 88 " distance=2.02 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 G 7 " - " MAN G 8 " " MAN S 4 " - " MAN S 5 " " MAN V 4 " - " MAN V 5 " " MAN V 5 " - " MAN V 6 " " MAN a 7 " - " MAN a 8 " " MAN g 4 " - " MAN g 5 " " MAN j 4 " - " MAN j 5 " " MAN j 5 " - " MAN j 6 " " MAN o 7 " - " MAN o 8 " " MAN u 4 " - " MAN u 5 " " MAN x 4 " - " MAN x 5 " " MAN x 5 " - " MAN x 6 " ALPHA1-3 " BMA G 3 " - " MAN G 7 " " MAN G 4 " - " MAN G 5 " " BMA S 3 " - " MAN S 4 " " BMA V 3 " - " MAN V 4 " " MAN V 7 " - " MAN V 8 " " BMA a 3 " - " MAN a 7 " " MAN a 4 " - " MAN a 5 " " BMA g 3 " - " MAN g 4 " " BMA j 3 " - " MAN j 4 " " MAN j 7 " - " MAN j 8 " " BMA o 3 " - " MAN o 7 " " MAN o 4 " - " MAN o 5 " " BMA u 3 " - " MAN u 4 " " BMA x 3 " - " MAN x 4 " " MAN x 7 " - " MAN x 8 " ALPHA1-6 " BMA G 3 " - " MAN G 4 " " MAN G 5 " - " MAN G 6 " " BMA S 3 " - " MAN S 6 " " MAN S 6 " - " MAN S 7 " " BMA U 3 " - " MAN U 4 " " BMA V 3 " - " MAN V 7 " " MAN V 7 " - " MAN V 9 " " BMA a 3 " - " MAN a 4 " " MAN a 5 " - " MAN a 6 " " BMA g 3 " - " MAN g 6 " " MAN g 6 " - " MAN g 7 " " BMA i 3 " - " MAN i 4 " " BMA j 3 " - " MAN j 7 " " MAN j 7 " - " MAN j 9 " " BMA o 3 " - " MAN o 4 " " MAN o 5 " - " MAN o 6 " " BMA u 3 " - " MAN u 6 " " MAN u 6 " - " MAN u 7 " " BMA w 3 " - " MAN w 4 " " BMA x 3 " - " MAN x 7 " " MAN x 7 " - " MAN x 9 " BETA1-4 " NAG 0 1 " - " NAG 0 2 " " NAG 1 1 " - " NAG 1 2 " " NAG G 1 " - " NAG G 2 " " NAG G 2 " - " BMA G 3 " " NAG K 1 " - " NAG K 2 " " NAG O 1 " - " NAG O 2 " " NAG P 1 " - " NAG P 2 " " NAG Q 1 " - " NAG Q 2 " " NAG R 1 " - " NAG R 2 " " NAG S 1 " - " NAG S 2 " " NAG S 2 " - " BMA S 3 " " NAG T 1 " - " NAG T 2 " " NAG U 1 " - " NAG U 2 " " NAG U 2 " - " BMA U 3 " " NAG V 1 " - " NAG V 2 " " NAG V 2 " - " BMA V 3 " " NAG W 1 " - " NAG W 2 " " NAG W 2 " - " BMA W 3 " " NAG X 1 " - " NAG X 2 " " NAG X 2 " - " BMA X 3 " " NAG Y 1 " - " NAG Y 2 " " NAG Z 1 " - " NAG Z 2 " " NAG a 1 " - " NAG a 2 " " NAG a 2 " - " BMA a 3 " " NAG b 1 " - " NAG b 2 " " NAG c 1 " - " NAG c 2 " " NAG d 1 " - " NAG d 2 " " 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 " - " BMA j 3 " " NAG k 1 " - " NAG k 2 " " NAG k 2 " - " BMA k 3 " " NAG l 1 " - " NAG l 2 " " NAG l 2 " - " BMA l 3 " " NAG m 1 " - " NAG m 2 " " NAG n 1 " - " NAG n 2 " " NAG o 1 " - " NAG o 2 " " NAG o 2 " - " BMA o 3 " " NAG p 1 " - " NAG p 2 " " NAG q 1 " - " NAG q 2 " " NAG r 1 " - " NAG r 2 " " NAG s 1 " - " NAG s 2 " " NAG t 1 " - " NAG t 2 " " NAG u 1 " - " NAG u 2 " " NAG u 2 " - " BMA u 3 " " NAG v 1 " - " NAG v 2 " " NAG w 1 " - " NAG w 2 " " NAG w 2 " - " BMA w 3 " " NAG x 1 " - " NAG x 2 " " NAG x 2 " - " BMA x 3 " " NAG y 1 " - " NAG y 2 " " NAG y 2 " - " BMA y 3 " " NAG z 1 " - " NAG z 2 " " NAG z 2 " - " BMA z 3 " NAG-ASN " NAG 0 1 " - " ASN E 197 " " NAG 1 1 " - " ASN E 276 " " NAG A 601 " - " ASN A 289 " " NAG A 602 " - " ASN A 392 " " NAG B 701 " - " ASN B 611 " " NAG C 601 " - " ASN C 289 " " NAG C 602 " - " ASN C 392 " " NAG D 701 " - " ASN D 611 " " NAG E 601 " - " ASN E 289 " " NAG E 602 " - " ASN E 392 " " NAG F 701 " - " ASN F 611 " " NAG G 1 " - " ASN A 138 " " NAG K 1 " - " ASN A 88 " " NAG O 1 " - " ASN A 130 " " NAG P 1 " - " ASN A 160 " " NAG Q 1 " - " ASN A 234 " " NAG R 1 " - " ASN A 241 " " NAG S 1 " - " ASN A 262 " " NAG T 1 " - " ASN A 295 " " NAG U 1 " - " ASN A 301 " " NAG V 1 " - " ASN A 332 " " NAG W 1 " - " ASN A 386 " " NAG X 1 " - " ASN A 448 " " NAG Y 1 " - " ASN A 197 " " NAG Z 1 " - " ASN A 276 " " NAG a 1 " - " ASN C 138 " " NAG b 1 " - " ASN C 88 " " NAG c 1 " - " ASN C 130 " " NAG d 1 " - " ASN C 160 " " NAG e 1 " - " ASN C 234 " " NAG f 1 " - " ASN C 241 " " NAG g 1 " - " ASN C 262 " " NAG h 1 " - " ASN C 295 " " NAG i 1 " - " ASN C 301 " " NAG j 1 " - " ASN C 332 " " NAG k 1 " - " ASN C 386 " " NAG l 1 " - " ASN C 448 " " NAG m 1 " - " ASN C 197 " " NAG n 1 " - " ASN C 276 " " NAG o 1 " - " ASN E 138 " " NAG p 1 " - " ASN E 88 " " NAG q 1 " - " ASN E 130 " " NAG r 1 " - " ASN E 160 " " NAG s 1 " - " ASN E 234 " " NAG t 1 " - " ASN E 241 " " NAG u 1 " - " ASN E 262 " " NAG v 1 " - " ASN E 295 " " NAG w 1 " - " ASN E 301 " " NAG x 1 " - " ASN E 332 " " NAG y 1 " - " ASN E 386 " " NAG z 1 " - " ASN E 448 " Time building additional restraints: 2.10 Conformation dependent library (CDL) restraints added in 684.1 milliseconds 4650 Ramachandran restraints generated. 2325 Oldfield, 0 Emsley, 2325 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4446 Finding SS restraints... Secondary structure from input PDB file: 54 helices and 44 sheets defined 22.0% alpha, 35.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.70 Creating SS restraints... Processing helix chain 'A' and resid 99 through 117 Processing helix chain 'A' and resid 122 through 126 Processing helix chain 'A' and resid 335 through 354 removed outlier: 3.791A pdb=" N GLU A 351 " --> pdb=" O LYS A 347 " (cutoff:3.500A) removed outlier: 4.178A pdb=" N HIS A 352 " --> pdb=" O LYS A 348 " (cutoff:3.500A) Processing helix chain 'A' and resid 368 through 373 Processing helix chain 'A' and resid 425 through 429 removed outlier: 3.710A pdb=" N GLN A 428 " --> pdb=" O ASN A 425 " (cutoff:3.500A) Processing helix chain 'A' and resid 475 through 484 removed outlier: 3.908A pdb=" N TRP A 479 " --> pdb=" O MET A 475 " (cutoff:3.500A) removed outlier: 4.369A pdb=" N GLU A 482 " --> pdb=" O ASN A 478 " (cutoff:3.500A) Processing helix chain 'B' and resid 531 through 535 Processing helix chain 'B' and resid 536 through 543 Processing helix chain 'B' and resid 569 through 596 Processing helix chain 'B' and resid 618 through 623 Processing helix chain 'B' and resid 627 through 636 Processing helix chain 'B' and resid 638 through 660 removed outlier: 3.792A pdb=" N ASN B 651 " --> pdb=" O GLU B 647 " (cutoff:3.500A) removed outlier: 4.403A pdb=" N GLU B 654 " --> pdb=" O GLN B 650 " (cutoff:3.500A) Processing helix chain 'H' and resid 28 through 32 removed outlier: 4.160A pdb=" N ASN H 32 " --> pdb=" O VAL H 29 " (cutoff:3.500A) Processing helix chain 'H' and resid 52 through 56 removed outlier: 3.790A pdb=" N GLY H 55 " --> pdb=" O HIS H 52 " (cutoff:3.500A) Processing helix chain 'H' and resid 63 through 65 No H-bonds generated for 'chain 'H' and resid 63 through 65' Processing helix chain 'H' and resid 83 through 87 Processing helix chain 'H' and resid 100D through 100H Processing helix chain 'L' and resid 79 through 83 Processing helix chain 'C' and resid 98 through 117 removed outlier: 4.172A pdb=" N GLU C 102 " --> pdb=" O ASN C 98 " (cutoff:3.500A) Processing helix chain 'C' and resid 122 through 126 Processing helix chain 'C' and resid 335 through 354 removed outlier: 3.873A pdb=" N GLU C 351 " --> pdb=" O LYS C 347 " (cutoff:3.500A) removed outlier: 4.213A pdb=" N HIS C 352 " --> pdb=" O LYS C 348 " (cutoff:3.500A) Processing helix chain 'C' and resid 368 through 373 Processing helix chain 'C' and resid 425 through 429 removed outlier: 3.700A pdb=" N GLN C 428 " --> pdb=" O ASN C 425 " (cutoff:3.500A) Processing helix chain 'C' and resid 475 through 484 removed outlier: 3.772A pdb=" N TRP C 479 " --> pdb=" O MET C 475 " (cutoff:3.500A) removed outlier: 4.363A pdb=" N GLU C 482 " --> pdb=" O ASN C 478 " (cutoff:3.500A) Processing helix chain 'D' and resid 531 through 535 Processing helix chain 'D' and resid 536 through 543 Processing helix chain 'D' and resid 569 through 596 Processing helix chain 'D' and resid 618 through 623 Processing helix chain 'D' and resid 627 through 636 removed outlier: 3.508A pdb=" N GLU D 634 " --> pdb=" O GLU D 630 " (cutoff:3.500A) Processing helix chain 'D' and resid 638 through 660 removed outlier: 3.512A pdb=" N SER D 649 " --> pdb=" O LEU D 645 " (cutoff:3.500A) removed outlier: 3.835A pdb=" N ASN D 651 " --> pdb=" O GLU D 647 " (cutoff:3.500A) removed outlier: 4.306A pdb=" N GLU D 654 " --> pdb=" O GLN D 650 " (cutoff:3.500A) Processing helix chain 'I' and resid 28 through 32 removed outlier: 4.127A pdb=" N ASN I 32 " --> pdb=" O VAL I 29 " (cutoff:3.500A) Processing helix chain 'I' and resid 52 through 56 removed outlier: 3.810A pdb=" N GLY I 55 " --> pdb=" O HIS I 52 " (cutoff:3.500A) Processing helix chain 'I' and resid 63 through 65 No H-bonds generated for 'chain 'I' and resid 63 through 65' Processing helix chain 'I' and resid 83 through 87 Processing helix chain 'I' and resid 100D through 100H Processing helix chain 'M' and resid 79 through 83 Processing helix chain 'E' and resid 98 through 117 removed outlier: 4.306A pdb=" N GLU E 102 " --> pdb=" O ASN E 98 " (cutoff:3.500A) Processing helix chain 'E' and resid 122 through 126 Processing helix chain 'E' and resid 335 through 354 removed outlier: 3.788A pdb=" N GLU E 351 " --> pdb=" O LYS E 347 " (cutoff:3.500A) removed outlier: 4.173A pdb=" N HIS E 352 " --> pdb=" O LYS E 348 " (cutoff:3.500A) Processing helix chain 'E' and resid 368 through 373 Processing helix chain 'E' and resid 425 through 429 removed outlier: 3.980A pdb=" N GLN E 428 " --> pdb=" O ASN E 425 " (cutoff:3.500A) Processing helix chain 'E' and resid 475 through 484 removed outlier: 3.901A pdb=" N TRP E 479 " --> pdb=" O MET E 475 " (cutoff:3.500A) removed outlier: 4.449A pdb=" N GLU E 482 " --> pdb=" O ASN E 478 " (cutoff:3.500A) Processing helix chain 'F' and resid 531 through 535 Processing helix chain 'F' and resid 536 through 543 Processing helix chain 'F' and resid 569 through 596 Processing helix chain 'F' and resid 618 through 623 Processing helix chain 'F' and resid 627 through 636 Processing helix chain 'F' and resid 638 through 660 removed outlier: 4.567A pdb=" N SER F 644 " --> pdb=" O ASP F 640 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N SER F 649 " --> pdb=" O LEU F 645 " (cutoff:3.500A) removed outlier: 4.023A pdb=" N ASN F 651 " --> pdb=" O GLU F 647 " (cutoff:3.500A) removed outlier: 4.375A pdb=" N GLU F 654 " --> pdb=" O GLN F 650 " (cutoff:3.500A) Processing helix chain 'J' and resid 28 through 32 removed outlier: 3.978A pdb=" N ASN J 32 " --> pdb=" O VAL J 29 " (cutoff:3.500A) Processing helix chain 'J' and resid 52 through 56 removed outlier: 3.875A pdb=" N GLY J 55 " --> pdb=" O HIS J 52 " (cutoff:3.500A) Processing helix chain 'J' and resid 63 through 65 No H-bonds generated for 'chain 'J' and resid 63 through 65' Processing helix chain 'J' and resid 83 through 87 Processing helix chain 'J' and resid 100D through 100H Processing helix chain 'N' and resid 79 through 83 Processing sheet with id=AA1, first strand: chain 'A' and resid 494 through 499 removed outlier: 4.349A pdb=" N VAL A 36 " --> pdb=" O THR B 606 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 45 through 47 removed outlier: 4.016A pdb=" N ILE A 225 " --> pdb=" O VAL A 245 " (cutoff:3.500A) removed outlier: 4.590A pdb=" N VAL A 242 " --> pdb=" O LEU A 86 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 75 through 76 removed outlier: 4.002A pdb=" N VAL A 75 " --> pdb=" O CYS A 54 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 91 through 94 Processing sheet with id=AA5, first strand: chain 'A' and resid 130 through 133 Processing sheet with id=AA6, first strand: chain 'A' and resid 181 through 183 Processing sheet with id=AA7, first strand: chain 'A' and resid 201 through 203 removed outlier: 6.721A pdb=" N THR A 202 " --> pdb=" O TYR A 435 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 259 through 261 removed outlier: 6.556A pdb=" N LEU A 260 " --> pdb=" O THR A 450 " (cutoff:3.500A) removed outlier: 5.575A pdb=" N GLY A 441 " --> pdb=" O ASN A 300 " (cutoff:3.500A) removed outlier: 5.840A pdb=" N ASN A 300 " --> pdb=" O GLY A 441 " (cutoff:3.500A) removed outlier: 6.472A pdb=" N GLY A 451 " --> pdb=" O GLU A 290 " (cutoff:3.500A) removed outlier: 10.229A pdb=" N GLU A 290 " --> pdb=" O GLY A 451 " (cutoff:3.500A) removed outlier: 11.768A pdb=" N LEU A 453 " --> pdb=" O LEU A 288 " (cutoff:3.500A) removed outlier: 11.764A pdb=" N LEU A 288 " --> pdb=" O LEU A 453 " (cutoff:3.500A) removed outlier: 10.949A pdb=" N THR A 455 " --> pdb=" O VAL A 286 " (cutoff:3.500A) removed outlier: 10.702A pdb=" N VAL A 286 " --> pdb=" O THR A 455 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 284 through 302 current: chain 'A' and resid 357 through 361 Processing sheet with id=AA9, first strand: chain 'A' and resid 271 through 273 removed outlier: 10.702A pdb=" N VAL A 286 " --> pdb=" O THR A 455 " (cutoff:3.500A) removed outlier: 10.949A pdb=" N THR A 455 " --> pdb=" O VAL A 286 " (cutoff:3.500A) removed outlier: 11.764A pdb=" N LEU A 288 " --> pdb=" O LEU A 453 " (cutoff:3.500A) removed outlier: 11.768A pdb=" N LEU A 453 " --> pdb=" O LEU A 288 " (cutoff:3.500A) removed outlier: 10.229A pdb=" N GLU A 290 " --> pdb=" O GLY A 451 " (cutoff:3.500A) removed outlier: 6.472A pdb=" N GLY A 451 " --> pdb=" O GLU A 290 " (cutoff:3.500A) removed outlier: 5.840A pdb=" N ASN A 300 " --> pdb=" O GLY A 441 " (cutoff:3.500A) removed outlier: 5.575A pdb=" N GLY A 441 " --> pdb=" O ASN A 300 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 441 through 456 current: chain 'A' and resid 413 through 420 Processing sheet with id=AB1, first strand: chain 'A' and resid 304 through 312 removed outlier: 6.162A pdb=" N GLN A 315 " --> pdb=" O ILE A 309 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'H' and resid 3 through 7 Processing sheet with id=AB3, first strand: chain 'H' and resid 11 through 12 removed outlier: 3.727A pdb=" N TYR H 33 " --> pdb=" O THR H 95 " (cutoff:3.500A) removed outlier: 6.681A pdb=" N TRP H 34 " --> pdb=" O TYR H 50 " (cutoff:3.500A) removed outlier: 4.487A pdb=" N TYR H 50 " --> pdb=" O TRP H 34 " (cutoff:3.500A) removed outlier: 6.791A pdb=" N TRP H 36 " --> pdb=" O ILE H 48 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'H' and resid 11 through 12 removed outlier: 7.155A pdb=" N CYS H 92 " --> pdb=" O TRP H 101 " (cutoff:3.500A) removed outlier: 4.764A pdb=" N TRP H 101 " --> pdb=" O CYS H 92 " (cutoff:3.500A) removed outlier: 6.403A pdb=" N THR H 94 " --> pdb=" O ASP H 100Q" (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'L' and resid 8 through 13 removed outlier: 6.394A pdb=" N THR L 8 " --> pdb=" O THR L 103 " (cutoff:3.500A) removed outlier: 7.316A pdb=" N ILE L 105 " --> pdb=" O THR L 8 " (cutoff:3.500A) removed outlier: 6.488A pdb=" N VAL L 11 " --> pdb=" O ILE L 105 " (cutoff:3.500A) removed outlier: 6.647A pdb=" N TRP L 35 " --> pdb=" O ILE L 47 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'L' and resid 19 through 23 Processing sheet with id=AB7, first strand: chain 'C' and resid 494 through 499 removed outlier: 4.284A pdb=" N VAL C 36 " --> pdb=" O THR D 606 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'C' and resid 45 through 47 removed outlier: 4.000A pdb=" N ILE C 225 " --> pdb=" O VAL C 245 " (cutoff:3.500A) removed outlier: 4.584A pdb=" N VAL C 242 " --> pdb=" O LEU C 86 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'C' and resid 53 through 55 Processing sheet with id=AC1, first strand: chain 'C' and resid 91 through 94 Processing sheet with id=AC2, first strand: chain 'C' and resid 130 through 133 Processing sheet with id=AC3, first strand: chain 'C' and resid 181 through 183 Processing sheet with id=AC4, first strand: chain 'C' and resid 201 through 203 removed outlier: 6.686A pdb=" N THR C 202 " --> pdb=" O TYR C 435 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'C' and resid 259 through 261 removed outlier: 6.549A pdb=" N LEU C 260 " --> pdb=" O THR C 450 " (cutoff:3.500A) removed outlier: 10.415A pdb=" N LYS C 442 " --> pdb=" O CYS C 296 " (cutoff:3.500A) removed outlier: 11.273A pdb=" N CYS C 296 " --> pdb=" O LYS C 442 " (cutoff:3.500A) removed outlier: 10.024A pdb=" N ARG C 444 " --> pdb=" O ILE C 294 " (cutoff:3.500A) removed outlier: 11.252A pdb=" N ILE C 294 " --> pdb=" O ARG C 444 " (cutoff:3.500A) removed outlier: 9.718A pdb=" N THR C 446 " --> pdb=" O VAL C 292 " (cutoff:3.500A) removed outlier: 10.658A pdb=" N VAL C 292 " --> pdb=" O THR C 446 " (cutoff:3.500A) removed outlier: 9.551A pdb=" N ASN C 448 " --> pdb=" O GLU C 290 " (cutoff:3.500A) removed outlier: 10.115A pdb=" N GLU C 290 " --> pdb=" O ASN C 448 " (cutoff:3.500A) removed outlier: 6.951A pdb=" N THR C 450 " --> pdb=" O LEU C 288 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'C' and resid 284 through 302 current: chain 'C' and resid 357 through 361 Processing sheet with id=AC6, first strand: chain 'C' and resid 271 through 273 removed outlier: 6.951A pdb=" N THR C 450 " --> pdb=" O LEU C 288 " (cutoff:3.500A) removed outlier: 10.115A pdb=" N GLU C 290 " --> pdb=" O ASN C 448 " (cutoff:3.500A) removed outlier: 9.551A pdb=" N ASN C 448 " --> pdb=" O GLU C 290 " (cutoff:3.500A) removed outlier: 10.658A pdb=" N VAL C 292 " --> pdb=" O THR C 446 " (cutoff:3.500A) removed outlier: 9.718A pdb=" N THR C 446 " --> pdb=" O VAL C 292 " (cutoff:3.500A) removed outlier: 11.252A pdb=" N ILE C 294 " --> pdb=" O ARG C 444 " (cutoff:3.500A) removed outlier: 10.024A pdb=" N ARG C 444 " --> pdb=" O ILE C 294 " (cutoff:3.500A) removed outlier: 11.273A pdb=" N CYS C 296 " --> pdb=" O LYS C 442 " (cutoff:3.500A) removed outlier: 10.415A pdb=" N LYS C 442 " --> pdb=" O CYS C 296 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'C' and resid 441 through 456 current: chain 'C' and resid 413 through 420 Processing sheet with id=AC7, first strand: chain 'C' and resid 304 through 312 removed outlier: 6.146A pdb=" N GLN C 315 " --> pdb=" O ILE C 309 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'I' and resid 3 through 7 Processing sheet with id=AC9, first strand: chain 'I' and resid 11 through 12 removed outlier: 3.824A pdb=" N TYR I 33 " --> pdb=" O THR I 95 " (cutoff:3.500A) removed outlier: 6.651A pdb=" N TRP I 34 " --> pdb=" O TYR I 50 " (cutoff:3.500A) removed outlier: 4.544A pdb=" N TYR I 50 " --> pdb=" O TRP I 34 " (cutoff:3.500A) removed outlier: 6.769A pdb=" N TRP I 36 " --> pdb=" O ILE I 48 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'I' and resid 11 through 12 removed outlier: 6.658A pdb=" N LYS I 96 " --> pdb=" O MET I 100P" (cutoff:3.500A) removed outlier: 5.159A pdb=" N MET I 100P" --> pdb=" O LYS I 96 " (cutoff:3.500A) removed outlier: 7.097A pdb=" N GLY I 98 " --> pdb=" O PHE I 100N" (cutoff:3.500A) removed outlier: 5.390A pdb=" N PHE I 100N" --> pdb=" O GLY I 98 " (cutoff:3.500A) removed outlier: 6.388A pdb=" N ARG I 100 " --> pdb=" O THR I 100L" (cutoff:3.500A) removed outlier: 5.581A pdb=" N THR I 100L" --> pdb=" O ARG I 100 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'M' and resid 8 through 13 removed outlier: 6.460A pdb=" N THR M 8 " --> pdb=" O THR M 103 " (cutoff:3.500A) removed outlier: 7.386A pdb=" N ILE M 105 " --> pdb=" O THR M 8 " (cutoff:3.500A) removed outlier: 6.489A pdb=" N VAL M 11 " --> pdb=" O ILE M 105 " (cutoff:3.500A) removed outlier: 5.586A pdb=" N GLU M 100 " --> pdb=" O CYS M 88 " (cutoff:3.500A) removed outlier: 5.247A pdb=" N CYS M 88 " --> pdb=" O GLU M 100 " (cutoff:3.500A) removed outlier: 6.675A pdb=" N TRP M 35 " --> pdb=" O ILE M 47 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'M' and resid 19 through 23 Processing sheet with id=AD4, first strand: chain 'E' and resid 494 through 499 removed outlier: 4.364A pdb=" N VAL E 36 " --> pdb=" O THR F 606 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'E' and resid 45 through 47 removed outlier: 4.002A pdb=" N ILE E 225 " --> pdb=" O VAL E 245 " (cutoff:3.500A) removed outlier: 4.610A pdb=" N VAL E 242 " --> pdb=" O LEU E 86 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'E' and resid 75 through 76 removed outlier: 3.982A pdb=" N VAL E 75 " --> pdb=" O CYS E 54 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'E' and resid 91 through 94 removed outlier: 3.651A pdb=" N GLU E 91 " --> pdb=" O CYS E 239 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'E' and resid 169 through 177 Processing sheet with id=AD9, first strand: chain 'E' and resid 202 through 203 removed outlier: 6.667A pdb=" N THR E 202 " --> pdb=" O TYR E 435 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'E' and resid 259 through 261 removed outlier: 6.547A pdb=" N LEU E 260 " --> pdb=" O THR E 450 " (cutoff:3.500A) removed outlier: 5.579A pdb=" N GLY E 441 " --> pdb=" O ASN E 300 " (cutoff:3.500A) removed outlier: 5.846A pdb=" N ASN E 300 " --> pdb=" O GLY E 441 " (cutoff:3.500A) removed outlier: 6.475A pdb=" N GLY E 451 " --> pdb=" O GLU E 290 " (cutoff:3.500A) removed outlier: 10.226A pdb=" N GLU E 290 " --> pdb=" O GLY E 451 " (cutoff:3.500A) removed outlier: 11.754A pdb=" N LEU E 453 " --> pdb=" O LEU E 288 " (cutoff:3.500A) removed outlier: 11.753A pdb=" N LEU E 288 " --> pdb=" O LEU E 453 " (cutoff:3.500A) removed outlier: 10.940A pdb=" N THR E 455 " --> pdb=" O VAL E 286 " (cutoff:3.500A) removed outlier: 10.697A pdb=" N VAL E 286 " --> pdb=" O THR E 455 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'E' and resid 284 through 302 current: chain 'E' and resid 357 through 361 Processing sheet with id=AE2, first strand: chain 'E' and resid 271 through 273 removed outlier: 10.697A pdb=" N VAL E 286 " --> pdb=" O THR E 455 " (cutoff:3.500A) removed outlier: 10.940A pdb=" N THR E 455 " --> pdb=" O VAL E 286 " (cutoff:3.500A) removed outlier: 11.753A pdb=" N LEU E 288 " --> pdb=" O LEU E 453 " (cutoff:3.500A) removed outlier: 11.754A pdb=" N LEU E 453 " --> pdb=" O LEU E 288 " (cutoff:3.500A) removed outlier: 10.226A pdb=" N GLU E 290 " --> pdb=" O GLY E 451 " (cutoff:3.500A) removed outlier: 6.475A pdb=" N GLY E 451 " --> pdb=" O GLU E 290 " (cutoff:3.500A) removed outlier: 5.846A pdb=" N ASN E 300 " --> pdb=" O GLY E 441 " (cutoff:3.500A) removed outlier: 5.579A pdb=" N GLY E 441 " --> pdb=" O ASN E 300 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'E' and resid 441 through 456 current: chain 'E' and resid 413 through 420 Processing sheet with id=AE3, first strand: chain 'E' and resid 304 through 312 removed outlier: 6.121A pdb=" N GLN E 315 " --> pdb=" O ILE E 309 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'J' and resid 3 through 7 Processing sheet with id=AE5, first strand: chain 'J' and resid 11 through 12 removed outlier: 3.746A pdb=" N TYR J 33 " --> pdb=" O THR J 95 " (cutoff:3.500A) removed outlier: 6.648A pdb=" N TRP J 34 " --> pdb=" O TYR J 50 " (cutoff:3.500A) removed outlier: 4.486A pdb=" N TYR J 50 " --> pdb=" O TRP J 34 " (cutoff:3.500A) removed outlier: 6.665A pdb=" N TRP J 36 " --> pdb=" O ILE J 48 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'J' and resid 11 through 12 removed outlier: 7.190A pdb=" N CYS J 92 " --> pdb=" O TRP J 101 " (cutoff:3.500A) removed outlier: 4.746A pdb=" N TRP J 101 " --> pdb=" O CYS J 92 " (cutoff:3.500A) removed outlier: 6.403A pdb=" N THR J 94 " --> pdb=" O ASP J 100Q" (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'N' and resid 8 through 13 removed outlier: 6.390A pdb=" N THR N 8 " --> pdb=" O THR N 103 " (cutoff:3.500A) removed outlier: 7.378A pdb=" N ILE N 105 " --> pdb=" O THR N 8 " (cutoff:3.500A) removed outlier: 6.328A pdb=" N VAL N 11 " --> pdb=" O ILE N 105 " (cutoff:3.500A) removed outlier: 6.657A pdb=" N TRP N 35 " --> pdb=" O ILE N 47 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'N' and resid 19 through 23 738 hydrogen bonds defined for protein. 1890 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 3.54 Time building geometry restraints manager: 2.68 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.32: 5147 1.32 - 1.46: 6949 1.46 - 1.60: 8990 1.60 - 1.74: 16 1.74 - 1.88: 132 Bond restraints: 21234 Sorted by residual: bond pdb=" CB HIS J 97 " pdb=" CG HIS J 97 " ideal model delta sigma weight residual 1.497 1.409 0.088 1.40e-02 5.10e+03 3.91e+01 bond pdb=" CB THR E 37 " pdb=" OG1 THR E 37 " ideal model delta sigma weight residual 1.433 1.336 0.097 1.60e-02 3.91e+03 3.70e+01 bond pdb=" CB THR C 37 " pdb=" OG1 THR C 37 " ideal model delta sigma weight residual 1.433 1.336 0.097 1.60e-02 3.91e+03 3.64e+01 bond pdb=" CB HIS I 97 " pdb=" CG HIS I 97 " ideal model delta sigma weight residual 1.497 1.413 0.084 1.40e-02 5.10e+03 3.61e+01 bond pdb=" CB HIS H 97 " pdb=" CG HIS H 97 " ideal model delta sigma weight residual 1.497 1.413 0.084 1.40e-02 5.10e+03 3.60e+01 ... (remaining 21229 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.27: 23991 2.27 - 4.54: 4092 4.54 - 6.80: 672 6.80 - 9.07: 90 9.07 - 11.34: 21 Bond angle restraints: 28866 Sorted by residual: angle pdb=" C VAL B 608 " pdb=" N PRO B 609 " pdb=" CA PRO B 609 " ideal model delta sigma weight residual 120.03 128.04 -8.01 9.90e-01 1.02e+00 6.55e+01 angle pdb=" N CYS E 73 " pdb=" CA CYS E 73 " pdb=" C CYS E 73 " ideal model delta sigma weight residual 114.56 104.56 10.00 1.27e+00 6.20e-01 6.20e+01 angle pdb=" C ARG C 298 " pdb=" N PRO C 299 " pdb=" CA PRO C 299 " ideal model delta sigma weight residual 119.56 127.11 -7.55 1.01e+00 9.80e-01 5.59e+01 angle pdb=" C VAL F 608 " pdb=" N PRO F 609 " pdb=" CA PRO F 609 " ideal model delta sigma weight residual 120.31 127.61 -7.30 9.80e-01 1.04e+00 5.55e+01 angle pdb=" C ARG E 298 " pdb=" N PRO E 299 " pdb=" CA PRO E 299 " ideal model delta sigma weight residual 119.56 127.05 -7.49 1.01e+00 9.80e-01 5.51e+01 ... (remaining 28861 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.65: 11134 17.65 - 35.30: 280 35.30 - 52.95: 92 52.95 - 70.60: 41 70.60 - 88.25: 12 Dihedral angle restraints: 11559 sinusoidal: 4683 harmonic: 6876 Sorted by residual: dihedral pdb=" CB CYS E 54 " pdb=" SG CYS E 54 " pdb=" SG CYS E 74 " pdb=" CB CYS E 74 " ideal model delta sinusoidal sigma weight residual -86.00 -2.51 -83.49 1 1.00e+01 1.00e-02 8.51e+01 dihedral pdb=" CB CYS A 54 " pdb=" SG CYS A 54 " pdb=" SG CYS A 74 " pdb=" CB CYS A 74 " ideal model delta sinusoidal sigma weight residual 93.00 29.45 63.55 1 1.00e+01 1.00e-02 5.32e+01 dihedral pdb=" CB CYS C 54 " pdb=" SG CYS C 54 " pdb=" SG CYS C 74 " pdb=" CB CYS C 74 " ideal model delta sinusoidal sigma weight residual 93.00 29.50 63.50 1 1.00e+01 1.00e-02 5.32e+01 ... (remaining 11556 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.108: 2556 0.108 - 0.216: 964 0.216 - 0.324: 168 0.324 - 0.431: 20 0.431 - 0.539: 15 Chirality restraints: 3723 Sorted by residual: chirality pdb=" C1 MAN o 7 " pdb=" O3 BMA o 3 " pdb=" C2 MAN o 7 " pdb=" O5 MAN o 7 " both_signs ideal model delta sigma weight residual False 2.40 2.11 0.29 2.00e-02 2.50e+03 2.09e+02 chirality pdb=" C1 MAN G 7 " pdb=" O3 BMA G 3 " pdb=" C2 MAN G 7 " pdb=" O5 MAN G 7 " both_signs ideal model delta sigma weight residual False 2.40 2.14 0.26 2.00e-02 2.50e+03 1.66e+02 chirality pdb=" C1 MAN a 7 " pdb=" O3 BMA a 3 " pdb=" C2 MAN a 7 " pdb=" O5 MAN a 7 " both_signs ideal model delta sigma weight residual False 2.40 2.15 0.25 2.00e-02 2.50e+03 1.62e+02 ... (remaining 3720 not shown) Planarity restraints: 3480 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB ASN C 138 " 0.126 2.00e-02 2.50e+03 1.30e-01 2.12e+02 pdb=" CG ASN C 138 " -0.053 2.00e-02 2.50e+03 pdb=" OD1 ASN C 138 " -0.023 2.00e-02 2.50e+03 pdb=" ND2 ASN C 138 " -0.205 2.00e-02 2.50e+03 pdb=" C1 NAG a 1 " 0.155 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN E 138 " 0.121 2.00e-02 2.50e+03 1.21e-01 1.84e+02 pdb=" CG ASN E 138 " -0.052 2.00e-02 2.50e+03 pdb=" OD1 ASN E 138 " -0.030 2.00e-02 2.50e+03 pdb=" ND2 ASN E 138 " -0.184 2.00e-02 2.50e+03 pdb=" C1 NAG o 1 " 0.146 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN A 138 " 0.118 2.00e-02 2.50e+03 1.18e-01 1.75e+02 pdb=" CG ASN A 138 " -0.050 2.00e-02 2.50e+03 pdb=" OD1 ASN A 138 " -0.030 2.00e-02 2.50e+03 pdb=" ND2 ASN A 138 " -0.180 2.00e-02 2.50e+03 pdb=" C1 NAG G 1 " 0.142 2.00e-02 2.50e+03 ... (remaining 3477 not shown) Histogram of nonbonded interaction distances: 2.26 - 2.79: 4975 2.79 - 3.31: 18639 3.31 - 3.84: 35363 3.84 - 4.37: 41379 4.37 - 4.90: 66457 Nonbonded interactions: 166813 Sorted by model distance: nonbonded pdb=" O4 NAG m 2 " pdb=" O6 NAG m 2 " model vdw 2.257 3.040 nonbonded pdb=" O4 NAG Y 2 " pdb=" O6 NAG Y 2 " model vdw 2.258 3.040 nonbonded pdb=" O4 NAG 0 2 " pdb=" O6 NAG 0 2 " model vdw 2.259 3.040 nonbonded pdb=" O4 NAG B 701 " pdb=" O6 NAG B 701 " model vdw 2.262 3.040 nonbonded pdb=" O4 MAN S 7 " pdb=" O6 MAN S 7 " model vdw 2.272 3.040 ... (remaining 166808 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: 0.01 Found NCS groups: ncs_group { reference = chain '0' selection = chain '1' selection = chain 'K' selection = chain 'O' selection = chain 'P' selection = chain 'Q' selection = chain 'R' selection = chain 'T' selection = chain 'Y' selection = chain 'Z' selection = chain 'b' selection = chain 'c' selection = chain 'd' selection = chain 'e' selection = chain 'f' selection = chain 'h' selection = chain 'm' selection = chain 'n' selection = chain 'p' selection = chain 'q' selection = chain 'r' selection = chain 's' selection = chain 't' selection = chain 'v' } ncs_group { reference = chain 'A' selection = chain 'C' selection = chain 'E' } ncs_group { reference = chain 'B' selection = chain 'D' selection = chain 'F' } ncs_group { reference = (chain 'G' and resid 5 through 8) selection = (chain 'S' and resid 4 through 7) selection = (chain 'V' and resid 6 through 9) selection = (chain 'a' and resid 5 through 8) selection = (chain 'g' and resid 4 through 7) selection = (chain 'j' and resid 6 through 9) selection = (chain 'o' and resid 5 through 8) selection = (chain 'u' and resid 4 through 7) selection = (chain 'x' and resid 6 through 9) } ncs_group { reference = chain 'H' selection = chain 'I' selection = chain 'J' } ncs_group { reference = chain 'L' selection = chain 'M' selection = chain 'N' } ncs_group { reference = chain 'U' selection = chain 'i' selection = chain 'w' } ncs_group { reference = chain 'W' selection = chain 'X' selection = chain 'k' selection = chain 'l' selection = chain 'y' selection = chain 'z' } 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: 0.990 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.380 Check model and map are aligned: 0.060 Set scattering table: 0.030 Process input model: 17.830 Find NCS groups from input model: 0.410 Set up NCS constraints: 0.090 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:0.920 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 20.720 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8004 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 : 0.021 0.243 21432 Z= 1.135 Angle : 1.841 13.183 29421 Z= 1.120 Chirality : 0.112 0.539 3723 Planarity : 0.009 0.059 3429 Dihedral : 10.205 88.246 6996 Min Nonbonded Distance : 2.257 Molprobity Statistics. All-atom Clashscore : 1.91 Ramachandran Plot: Outliers : 0.13 % Allowed : 1.29 % Favored : 98.58 % Rotamer: Outliers : 0.52 % Allowed : 0.43 % Favored : 99.05 % Cbeta Deviations : 0.13 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.84 (0.17), residues: 2325 helix: -0.69 (0.23), residues: 420 sheet: 1.20 (0.19), residues: 624 loop : 0.85 (0.17), residues: 1281 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG E 327 TYR 0.076 0.009 TYR C 40 PHE 0.037 0.007 PHE M 67C TRP 0.058 0.010 TRP E 112 HIS 0.011 0.002 HIS E 216 Details of bonding type rmsd/Z covalent geometry : bond 0.02047 / 1.09 (21234) covalent geometry : angle 1.79442 / 1.12 (28866) SS BOND : bond 0.07179 / 5.07 ( 39) SS BOND : angle 2.76578 / 1.77 ( 78) hydrogen bonds : bond 0.16176 / 10.96 ( 702) hydrogen bonds : angle 7.50471 / 5.24 ( 1890) link_ALPHA1-2 : bond 0.06239 / 3.83 ( 12) link_ALPHA1-2 : angle 4.17493 / 2.70 ( 36) link_ALPHA1-3 : bond 0.05750 / 3.73 ( 15) link_ALPHA1-3 : angle 5.03185 / 3.21 ( 45) link_ALPHA1-6 : bond 0.06055 / 3.81 ( 21) link_ALPHA1-6 : angle 3.63329 / 2.58 ( 63) link_BETA1-4 : bond 0.05800 / 3.89 ( 60) link_BETA1-4 : angle 3.81358 / 2.89 ( 180) link_NAG-ASN : bond 0.07728 / 4.96 ( 51) link_NAG-ASN : angle 2.54064 / 1.80 ( 153) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4650 Ramachandran restraints generated. 2325 Oldfield, 0 Emsley, 2325 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4650 Ramachandran restraints generated. 2325 Oldfield, 0 Emsley, 2325 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 556 residues out of total 2106 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 545 time to evaluate : 0.710 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 69 TRP cc_start: 0.8750 (m-90) cc_final: 0.8457 (m-90) REVERT: A 100 MET cc_start: 0.7993 (mtp) cc_final: 0.7715 (mtm) REVERT: B 584 GLU cc_start: 0.8881 (mt-10) cc_final: 0.8407 (mt-10) REVERT: B 648 GLU cc_start: 0.8877 (tt0) cc_final: 0.8658 (tm-30) REVERT: H 100 MET cc_start: 0.8863 (mpp) cc_final: 0.8634 (mpp) REVERT: L 36 TYR cc_start: 0.8021 (m-80) cc_final: 0.7351 (m-80) REVERT: C 104 MET cc_start: 0.8807 (ttm) cc_final: 0.8472 (ttm) REVERT: C 202 THR cc_start: 0.9607 (m) cc_final: 0.9143 (p) REVERT: C 217 TYR cc_start: 0.8096 (m-80) cc_final: 0.7741 (m-10) REVERT: C 475 MET cc_start: 0.8339 (mmm) cc_final: 0.8032 (mmm) REVERT: D 624 ASP cc_start: 0.8440 (t70) cc_final: 0.8212 (m-30) REVERT: D 629 MET cc_start: 0.8300 (mmm) cc_final: 0.8053 (mmm) REVERT: D 648 GLU cc_start: 0.9042 (tt0) cc_final: 0.8718 (tm-30) REVERT: I 100 MET cc_start: 0.8871 (mpp) cc_final: 0.8650 (mpp) REVERT: M 21 ILE cc_start: 0.9167 (mt) cc_final: 0.8964 (mt) REVERT: E 104 MET cc_start: 0.8883 (ttm) cc_final: 0.8392 (ttm) REVERT: E 112 TRP cc_start: 0.8586 (m100) cc_final: 0.7987 (m100) REVERT: E 195 ASN cc_start: 0.8622 (m-40) cc_final: 0.8409 (t0) REVERT: E 283 THR cc_start: 0.8606 (m) cc_final: 0.8315 (p) REVERT: E 326 ILE cc_start: 0.9034 (mt) cc_final: 0.8817 (tt) REVERT: E 434 MET cc_start: 0.9124 (ttp) cc_final: 0.8594 (ttp) REVERT: F 584 GLU cc_start: 0.9012 (mt-10) cc_final: 0.8593 (mt-10) REVERT: F 648 GLU cc_start: 0.8811 (tt0) cc_final: 0.8091 (tm-30) outliers start: 11 outliers final: 9 residues processed: 556 average time/residue: 0.1478 time to fit residues: 123.5369 Evaluate side-chains 278 residues out of total 2106 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 269 time to evaluate : 0.700 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 197 ASN Chi-restraints excluded: chain A residue 234 ASN Chi-restraints excluded: chain A residue 289 ASN Chi-restraints excluded: chain C residue 197 ASN Chi-restraints excluded: chain C residue 234 ASN Chi-restraints excluded: chain C residue 289 ASN Chi-restraints excluded: chain E residue 197 ASN Chi-restraints excluded: chain E residue 234 ASN Chi-restraints excluded: chain E residue 289 ASN Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 231 random chunks: chunk 216 optimal weight: 7.9990 chunk 98 optimal weight: 4.9990 chunk 194 optimal weight: 5.9990 chunk 227 optimal weight: 6.9990 chunk 107 optimal weight: 7.9990 chunk 10 optimal weight: 4.9990 chunk 66 optimal weight: 5.9990 chunk 130 optimal weight: 6.9990 chunk 124 optimal weight: 0.9990 chunk 103 optimal weight: 5.9990 chunk 200 optimal weight: 3.9990 overall best weight: 4.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 72 HIS A 362 ASN B 607 ASN B 650 GLN C 362 ASN ** D 591 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 650 GLN I 39 GLN I 68 HIS E 195 ASN E 229 ASN E 362 ASN F 591 GLN F 625 ASN J 68 HIS N 52 ASN N 95CASN Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3795 r_free = 0.3795 target = 0.099686 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3411 r_free = 0.3411 target = 0.077960 restraints weight = 63168.712| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3463 r_free = 0.3463 target = 0.080807 restraints weight = 34361.734| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3496 r_free = 0.3496 target = 0.082612 restraints weight = 24579.305| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 39)----------------| | r_work = 0.3516 r_free = 0.3516 target = 0.083704 restraints weight = 20226.745| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3527 r_free = 0.3527 target = 0.084312 restraints weight = 18024.744| |-----------------------------------------------------------------------------| r_work (final): 0.3529 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7830 moved from start: 0.3090 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.046 21432 Z= 0.244 Angle : 0.927 14.310 29421 Z= 0.436 Chirality : 0.054 0.389 3723 Planarity : 0.005 0.044 3429 Dihedral : 6.013 40.874 2556 Min Nonbonded Distance : 2.337 Molprobity Statistics. All-atom Clashscore : 8.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.63 % Favored : 98.37 % Rotamer: Outliers : 2.99 % Allowed : 8.21 % Favored : 88.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.67 (0.17), residues: 2325 helix: 0.42 (0.26), residues: 405 sheet: 0.86 (0.19), residues: 615 loop : 0.38 (0.17), residues: 1305 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG B 542 TYR 0.020 0.002 TYR J 33 PHE 0.028 0.002 PHE C 233 TRP 0.021 0.002 TRP E 112 HIS 0.009 0.002 HIS A 330 Details of bonding type rmsd/Z covalent geometry : bond 0.00539 / 0.24 (21234) covalent geometry : angle 0.86885 / 0.42 (28866) SS BOND : bond 0.00572 / 0.37 ( 39) SS BOND : angle 1.18628 / 0.80 ( 78) hydrogen bonds : bond 0.05676 / 3.86 ( 702) hydrogen bonds : angle 6.00746 / 4.23 ( 1890) link_ALPHA1-2 : bond 0.00818 / 0.51 ( 12) link_ALPHA1-2 : angle 2.24249 / 1.41 ( 36) link_ALPHA1-3 : bond 0.01241 / 0.82 ( 15) link_ALPHA1-3 : angle 1.93306 / 1.22 ( 45) link_ALPHA1-6 : bond 0.00528 / 0.31 ( 21) link_ALPHA1-6 : angle 1.86317 / 1.30 ( 63) link_BETA1-4 : bond 0.00627 / 0.42 ( 60) link_BETA1-4 : angle 2.61828 / 1.93 ( 180) link_NAG-ASN : bond 0.00614 / 0.38 ( 51) link_NAG-ASN : angle 3.23163 / 2.22 ( 153) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4650 Ramachandran restraints generated. 2325 Oldfield, 0 Emsley, 2325 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4650 Ramachandran restraints generated. 2325 Oldfield, 0 Emsley, 2325 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 382 residues out of total 2106 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 319 time to evaluate : 0.693 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 69 TRP cc_start: 0.8608 (m-90) cc_final: 0.8275 (m-90) REVERT: A 91 GLU cc_start: 0.7556 (mp0) cc_final: 0.7308 (mp0) REVERT: A 201 ILE cc_start: 0.9225 (OUTLIER) cc_final: 0.8960 (tt) REVERT: A 475 MET cc_start: 0.8218 (mmm) cc_final: 0.6312 (tpp) REVERT: A 479 TRP cc_start: 0.8233 (m-90) cc_final: 0.7795 (m-90) REVERT: B 581 LEU cc_start: 0.9482 (tp) cc_final: 0.9184 (tp) REVERT: B 623 TRP cc_start: 0.7254 (m100) cc_final: 0.6954 (m-10) REVERT: B 648 GLU cc_start: 0.8719 (tt0) cc_final: 0.8488 (tm-30) REVERT: H 16 GLU cc_start: 0.7430 (mt-10) cc_final: 0.7095 (tt0) REVERT: H 100 MET cc_start: 0.8792 (mpp) cc_final: 0.8585 (mmt) REVERT: L 28 LEU cc_start: 0.8459 (OUTLIER) cc_final: 0.8191 (mm) REVERT: L 36 TYR cc_start: 0.8432 (m-80) cc_final: 0.8230 (m-80) REVERT: L 78 VAL cc_start: 0.9299 (t) cc_final: 0.8943 (m) REVERT: L 95 ASN cc_start: 0.8629 (m-40) cc_final: 0.8377 (m-40) REVERT: C 104 MET cc_start: 0.8371 (ttm) cc_final: 0.8132 (ttm) REVERT: C 202 THR cc_start: 0.9564 (m) cc_final: 0.9282 (p) REVERT: C 260 LEU cc_start: 0.8705 (OUTLIER) cc_final: 0.8445 (mm) REVERT: C 475 MET cc_start: 0.8206 (mmm) cc_final: 0.7702 (mmm) REVERT: D 545 LEU cc_start: 0.6694 (OUTLIER) cc_final: 0.6441 (mm) REVERT: D 577 GLN cc_start: 0.8877 (tm-30) cc_final: 0.8652 (tm-30) REVERT: D 581 LEU cc_start: 0.9385 (tt) cc_final: 0.9181 (tp) REVERT: D 584 GLU cc_start: 0.8652 (mt-10) cc_final: 0.8289 (mt-10) REVERT: D 626 MET cc_start: 0.7848 (tpp) cc_final: 0.7442 (tpp) REVERT: D 630 GLU cc_start: 0.8481 (mm-30) cc_final: 0.8060 (mm-30) REVERT: D 648 GLU cc_start: 0.8897 (tt0) cc_final: 0.8647 (tm-30) REVERT: I 16 GLU cc_start: 0.7273 (mt-10) cc_final: 0.7071 (tt0) REVERT: I 22 CYS cc_start: 0.1350 (t) cc_final: 0.1127 (t) REVERT: M 36 TYR cc_start: 0.8555 (m-80) cc_final: 0.8256 (m-80) REVERT: M 50 ASN cc_start: 0.8931 (t0) cc_final: 0.8659 (t0) REVERT: M 95 ASN cc_start: 0.8457 (m-40) cc_final: 0.8190 (m-40) REVERT: E 159 PHE cc_start: 0.8360 (OUTLIER) cc_final: 0.8019 (m-80) REVERT: E 283 THR cc_start: 0.8510 (m) cc_final: 0.8121 (p) REVERT: E 475 MET cc_start: 0.8046 (tpp) cc_final: 0.7474 (tpp) REVERT: F 545 LEU cc_start: 0.6534 (OUTLIER) cc_final: 0.6327 (mm) REVERT: F 574 LYS cc_start: 0.8978 (mptt) cc_final: 0.8568 (tptt) REVERT: F 584 GLU cc_start: 0.8737 (mt-10) cc_final: 0.8499 (mt-10) REVERT: F 648 GLU cc_start: 0.8501 (tt0) cc_final: 0.8238 (tm-30) REVERT: J 16 GLU cc_start: 0.7247 (mt-10) cc_final: 0.7001 (tt0) REVERT: J 73 LYS cc_start: 0.8585 (OUTLIER) cc_final: 0.8143 (mtpp) REVERT: J 100 MET cc_start: 0.8822 (mpp) cc_final: 0.8523 (mmt) REVERT: N 79 GLU cc_start: 0.8187 (mp0) cc_final: 0.7951 (mp0) REVERT: N 103 THR cc_start: 0.8133 (m) cc_final: 0.7689 (m) outliers start: 63 outliers final: 35 residues processed: 362 average time/residue: 0.1384 time to fit residues: 78.2499 Evaluate side-chains 281 residues out of total 2106 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 239 time to evaluate : 0.765 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 95 MET Chi-restraints excluded: chain A residue 197 ASN Chi-restraints excluded: chain A residue 201 ILE Chi-restraints excluded: chain A residue 234 ASN Chi-restraints excluded: chain A residue 289 ASN Chi-restraints excluded: chain A residue 322 ILE Chi-restraints excluded: chain A residue 326 ILE Chi-restraints excluded: chain A residue 345 VAL Chi-restraints excluded: chain A residue 373 THR Chi-restraints excluded: chain A residue 491 ILE Chi-restraints excluded: chain B residue 539 VAL Chi-restraints excluded: chain B residue 603 ILE Chi-restraints excluded: chain H residue 89 ILE Chi-restraints excluded: chain H residue 92 CYS Chi-restraints excluded: chain L residue 28 LEU Chi-restraints excluded: chain C residue 197 ASN Chi-restraints excluded: chain C residue 234 ASN Chi-restraints excluded: chain C residue 260 LEU Chi-restraints excluded: chain C residue 289 ASN Chi-restraints excluded: chain C residue 373 THR Chi-restraints excluded: chain C residue 434 MET Chi-restraints excluded: chain D residue 545 LEU Chi-restraints excluded: chain I residue 21 THR Chi-restraints excluded: chain I residue 28 LEU Chi-restraints excluded: chain I residue 92 CYS Chi-restraints excluded: chain E residue 95 MET Chi-restraints excluded: chain E residue 108 ILE Chi-restraints excluded: chain E residue 159 PHE Chi-restraints excluded: chain E residue 197 ASN Chi-restraints excluded: chain E residue 234 ASN Chi-restraints excluded: chain E residue 260 LEU Chi-restraints excluded: chain E residue 289 ASN Chi-restraints excluded: chain E residue 322 ILE Chi-restraints excluded: chain E residue 373 THR Chi-restraints excluded: chain F residue 545 LEU Chi-restraints excluded: chain F residue 593 LEU Chi-restraints excluded: chain J residue 20 LEU Chi-restraints excluded: chain J residue 68 HIS Chi-restraints excluded: chain J residue 73 LYS Chi-restraints excluded: chain J residue 89 ILE Chi-restraints excluded: chain J residue 92 CYS Chi-restraints excluded: chain N residue 106 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 231 random chunks: chunk 199 optimal weight: 9.9990 chunk 128 optimal weight: 3.9990 chunk 1 optimal weight: 5.9990 chunk 92 optimal weight: 3.9990 chunk 58 optimal weight: 5.9990 chunk 68 optimal weight: 7.9990 chunk 141 optimal weight: 6.9990 chunk 157 optimal weight: 8.9990 chunk 47 optimal weight: 6.9990 chunk 70 optimal weight: 3.9990 chunk 9 optimal weight: 4.9990 overall best weight: 4.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 94 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 3 HIS H 97 HIS L 52 ASN C 72 HIS ** D 591 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 3 HIS M 52 ASN E 72 HIS F 625 ASN J 68 HIS Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3756 r_free = 0.3756 target = 0.096737 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3393 r_free = 0.3393 target = 0.076560 restraints weight = 63366.378| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3412 r_free = 0.3412 target = 0.078304 restraints weight = 37964.393| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3413 r_free = 0.3413 target = 0.078465 restraints weight = 28597.605| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3436 r_free = 0.3436 target = 0.079816 restraints weight = 26195.447| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3436 r_free = 0.3436 target = 0.079854 restraints weight = 22516.197| |-----------------------------------------------------------------------------| r_work (final): 0.3424 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7961 moved from start: 0.3724 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.064 21432 Z= 0.243 Angle : 0.832 11.305 29421 Z= 0.395 Chirality : 0.051 0.468 3723 Planarity : 0.005 0.137 3429 Dihedral : 5.863 41.136 2556 Min Nonbonded Distance : 2.295 Molprobity Statistics. All-atom Clashscore : 9.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.75 % Favored : 97.25 % Rotamer: Outliers : 3.51 % Allowed : 10.92 % Favored : 85.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.42 (0.17), residues: 2325 helix: 0.26 (0.26), residues: 405 sheet: 0.74 (0.19), residues: 663 loop : 0.14 (0.17), residues: 1257 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG F 542 TYR 0.022 0.002 TYR J 33 PHE 0.017 0.002 PHE C 233 TRP 0.021 0.002 TRP A 427 HIS 0.012 0.002 HIS J 68 Details of bonding type rmsd/Z covalent geometry : bond 0.00544 / 0.24 (21234) covalent geometry : angle 0.77856 / 0.38 (28866) SS BOND : bond 0.00631 / 0.41 ( 39) SS BOND : angle 1.12950 / 0.74 ( 78) hydrogen bonds : bond 0.05110 / 3.51 ( 702) hydrogen bonds : angle 5.68199 / 4.00 ( 1890) link_ALPHA1-2 : bond 0.00842 / 0.52 ( 12) link_ALPHA1-2 : angle 2.57865 / 1.64 ( 36) link_ALPHA1-3 : bond 0.01040 / 0.66 ( 15) link_ALPHA1-3 : angle 2.08022 / 1.34 ( 45) link_ALPHA1-6 : bond 0.00494 / 0.30 ( 21) link_ALPHA1-6 : angle 1.67806 / 1.16 ( 63) link_BETA1-4 : bond 0.00703 / 0.46 ( 60) link_BETA1-4 : angle 2.31358 / 1.72 ( 180) link_NAG-ASN : bond 0.00593 / 0.39 ( 51) link_NAG-ASN : angle 2.79999 / 1.94 ( 153) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4650 Ramachandran restraints generated. 2325 Oldfield, 0 Emsley, 2325 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4650 Ramachandran restraints generated. 2325 Oldfield, 0 Emsley, 2325 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 312 residues out of total 2106 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 74 poor density : 238 time to evaluate : 0.806 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 69 TRP cc_start: 0.8698 (m-90) cc_final: 0.8390 (m-90) REVERT: A 202 THR cc_start: 0.9589 (m) cc_final: 0.9194 (p) REVERT: A 475 MET cc_start: 0.8257 (mmm) cc_final: 0.7499 (tpp) REVERT: A 479 TRP cc_start: 0.8299 (m-90) cc_final: 0.8062 (m-90) REVERT: B 575 GLN cc_start: 0.8981 (tp40) cc_final: 0.8627 (tp40) REVERT: B 577 GLN cc_start: 0.8720 (tm-30) cc_final: 0.8519 (tm-30) REVERT: B 584 GLU cc_start: 0.8445 (mt-10) cc_final: 0.7832 (mp0) REVERT: B 623 TRP cc_start: 0.7168 (m-10) cc_final: 0.6823 (m-10) REVERT: B 629 MET cc_start: 0.8972 (mmm) cc_final: 0.8686 (mmm) REVERT: B 642 ILE cc_start: 0.9514 (mt) cc_final: 0.9282 (mm) REVERT: B 643 TYR cc_start: 0.8911 (m-10) cc_final: 0.8698 (m-10) REVERT: H 100 MET cc_start: 0.8782 (mpp) cc_final: 0.8461 (mmt) REVERT: C 104 MET cc_start: 0.8676 (ttm) cc_final: 0.8467 (ttm) REVERT: C 475 MET cc_start: 0.8129 (mmm) cc_final: 0.7894 (mmm) REVERT: D 577 GLN cc_start: 0.8944 (tm-30) cc_final: 0.8625 (tm-30) REVERT: D 584 GLU cc_start: 0.8609 (mt-10) cc_final: 0.8360 (mt-10) REVERT: D 648 GLU cc_start: 0.8845 (tt0) cc_final: 0.8607 (tm-30) REVERT: I 16 GLU cc_start: 0.7195 (mt-10) cc_final: 0.6957 (tt0) REVERT: M 36 TYR cc_start: 0.8580 (m-80) cc_final: 0.8373 (m-80) REVERT: M 83 GLU cc_start: 0.7841 (tm-30) cc_final: 0.7633 (tm-30) REVERT: E 159 PHE cc_start: 0.8309 (OUTLIER) cc_final: 0.8047 (m-80) REVERT: E 260 LEU cc_start: 0.8767 (OUTLIER) cc_final: 0.8481 (mm) REVERT: E 475 MET cc_start: 0.8236 (tpp) cc_final: 0.7853 (tpp) REVERT: J 16 GLU cc_start: 0.7510 (mt-10) cc_final: 0.7260 (tt0) REVERT: N 79 GLU cc_start: 0.8317 (mp0) cc_final: 0.8031 (mp0) outliers start: 74 outliers final: 56 residues processed: 287 average time/residue: 0.1366 time to fit residues: 61.4969 Evaluate side-chains 266 residues out of total 2106 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 208 time to evaluate : 0.536 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 95 MET Chi-restraints excluded: chain A residue 120 VAL Chi-restraints excluded: chain A residue 197 ASN Chi-restraints excluded: chain A residue 199 SER Chi-restraints excluded: chain A residue 234 ASN Chi-restraints excluded: chain A residue 289 ASN Chi-restraints excluded: chain A residue 322 ILE Chi-restraints excluded: chain A residue 326 ILE Chi-restraints excluded: chain A residue 345 VAL Chi-restraints excluded: chain A residue 373 THR Chi-restraints excluded: chain A residue 426 MET Chi-restraints excluded: chain A residue 491 ILE Chi-restraints excluded: chain B residue 536 THR Chi-restraints excluded: chain B residue 539 VAL Chi-restraints excluded: chain B residue 603 ILE Chi-restraints excluded: chain H residue 3 HIS Chi-restraints excluded: chain H residue 92 CYS Chi-restraints excluded: chain H residue 97 HIS Chi-restraints excluded: chain C residue 120 VAL Chi-restraints excluded: chain C residue 197 ASN Chi-restraints excluded: chain C residue 199 SER Chi-restraints excluded: chain C residue 234 ASN Chi-restraints excluded: chain C residue 244 THR Chi-restraints excluded: chain C residue 289 ASN Chi-restraints excluded: chain C residue 345 VAL Chi-restraints excluded: chain C residue 373 THR Chi-restraints excluded: chain C residue 491 ILE Chi-restraints excluded: chain D residue 530 MET Chi-restraints excluded: chain D residue 536 THR Chi-restraints excluded: chain D residue 545 LEU Chi-restraints excluded: chain D residue 644 SER Chi-restraints excluded: chain I residue 3 HIS Chi-restraints excluded: chain I residue 21 THR Chi-restraints excluded: chain I residue 92 CYS Chi-restraints excluded: chain I residue 105 THR Chi-restraints excluded: chain M residue 104 LEU Chi-restraints excluded: chain E residue 95 MET Chi-restraints excluded: chain E residue 108 ILE Chi-restraints excluded: chain E residue 120 VAL Chi-restraints excluded: chain E residue 159 PHE Chi-restraints excluded: chain E residue 197 ASN Chi-restraints excluded: chain E residue 199 SER Chi-restraints excluded: chain E residue 234 ASN Chi-restraints excluded: chain E residue 260 LEU Chi-restraints excluded: chain E residue 289 ASN Chi-restraints excluded: chain E residue 322 ILE Chi-restraints excluded: chain E residue 326 ILE Chi-restraints excluded: chain E residue 345 VAL Chi-restraints excluded: chain E residue 373 THR Chi-restraints excluded: chain E residue 491 ILE Chi-restraints excluded: chain F residue 530 MET Chi-restraints excluded: chain F residue 593 LEU Chi-restraints excluded: chain F residue 606 THR Chi-restraints excluded: chain J residue 77 LEU Chi-restraints excluded: chain J residue 89 ILE Chi-restraints excluded: chain J residue 92 CYS Chi-restraints excluded: chain J residue 105 THR Chi-restraints excluded: chain N residue 106 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 231 random chunks: chunk 50 optimal weight: 0.4980 chunk 218 optimal weight: 4.9990 chunk 64 optimal weight: 0.7980 chunk 165 optimal weight: 6.9990 chunk 2 optimal weight: 10.0000 chunk 141 optimal weight: 5.9990 chunk 76 optimal weight: 6.9990 chunk 187 optimal weight: 2.9990 chunk 211 optimal weight: 9.9990 chunk 140 optimal weight: 6.9990 chunk 14 optimal weight: 3.9990 overall best weight: 2.6586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 94 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 650 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 651 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 97 HIS D 591 GLN I 3 HIS E 425 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3802 r_free = 0.3802 target = 0.098623 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 27)----------------| | r_work = 0.3452 r_free = 0.3452 target = 0.078646 restraints weight = 63321.263| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3462 r_free = 0.3462 target = 0.080244 restraints weight = 39171.959| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3475 r_free = 0.3475 target = 0.081159 restraints weight = 29720.970| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3481 r_free = 0.3481 target = 0.081526 restraints weight = 25517.406| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3494 r_free = 0.3494 target = 0.082387 restraints weight = 23643.632| |-----------------------------------------------------------------------------| r_work (final): 0.3481 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7941 moved from start: 0.4010 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.074 21432 Z= 0.169 Angle : 0.750 10.376 29421 Z= 0.350 Chirality : 0.048 0.411 3723 Planarity : 0.004 0.046 3429 Dihedral : 5.698 44.460 2556 Min Nonbonded Distance : 2.336 Molprobity Statistics. All-atom Clashscore : 8.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.28 % Favored : 97.72 % Rotamer: Outliers : 2.85 % Allowed : 11.92 % Favored : 85.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.50 (0.17), residues: 2325 helix: 0.60 (0.27), residues: 393 sheet: 0.75 (0.19), residues: 672 loop : 0.12 (0.17), residues: 1260 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG M 20 TYR 0.034 0.002 TYR F 643 PHE 0.020 0.001 PHE N 62 TRP 0.015 0.001 TRP B 631 HIS 0.009 0.001 HIS H 97 Details of bonding type rmsd/Z covalent geometry : bond 0.00375 / 0.17 (21234) covalent geometry : angle 0.70067 / 0.34 (28866) SS BOND : bond 0.00612 / 0.34 ( 39) SS BOND : angle 0.99440 / 0.64 ( 78) hydrogen bonds : bond 0.04505 / 3.08 ( 702) hydrogen bonds : angle 5.43250 / 3.84 ( 1890) link_ALPHA1-2 : bond 0.00750 / 0.47 ( 12) link_ALPHA1-2 : angle 2.42263 / 1.53 ( 36) link_ALPHA1-3 : bond 0.00973 / 0.62 ( 15) link_ALPHA1-3 : angle 1.89150 / 1.25 ( 45) link_ALPHA1-6 : bond 0.00481 / 0.30 ( 21) link_ALPHA1-6 : angle 1.65146 / 1.13 ( 63) link_BETA1-4 : bond 0.00656 / 0.44 ( 60) link_BETA1-4 : angle 2.15267 / 1.61 ( 180) link_NAG-ASN : bond 0.00499 / 0.33 ( 51) link_NAG-ASN : angle 2.47224 / 1.74 ( 153) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4650 Ramachandran restraints generated. 2325 Oldfield, 0 Emsley, 2325 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4650 Ramachandran restraints generated. 2325 Oldfield, 0 Emsley, 2325 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 290 residues out of total 2106 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 230 time to evaluate : 0.788 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 69 TRP cc_start: 0.8678 (m-90) cc_final: 0.8300 (m-90) REVERT: A 475 MET cc_start: 0.8176 (mmm) cc_final: 0.6690 (tpp) REVERT: A 479 TRP cc_start: 0.8309 (m-90) cc_final: 0.7825 (m-90) REVERT: B 575 GLN cc_start: 0.9006 (tp40) cc_final: 0.8777 (tp40) REVERT: B 577 GLN cc_start: 0.8655 (tm-30) cc_final: 0.8435 (tm-30) REVERT: B 584 GLU cc_start: 0.8389 (OUTLIER) cc_final: 0.8135 (mt-10) REVERT: B 623 TRP cc_start: 0.7145 (m-10) cc_final: 0.6820 (m-10) REVERT: B 642 ILE cc_start: 0.9511 (mt) cc_final: 0.9276 (mm) REVERT: B 643 TYR cc_start: 0.8912 (m-10) cc_final: 0.8694 (m-10) REVERT: L 83 GLU cc_start: 0.7915 (tm-30) cc_final: 0.7698 (pp20) REVERT: C 104 MET cc_start: 0.8741 (ttm) cc_final: 0.8444 (ttm) REVERT: D 577 GLN cc_start: 0.8906 (tm-30) cc_final: 0.8547 (tm-30) REVERT: D 584 GLU cc_start: 0.8592 (mt-10) cc_final: 0.8337 (mt-10) REVERT: D 630 GLU cc_start: 0.8328 (mm-30) cc_final: 0.7851 (mm-30) REVERT: I 16 GLU cc_start: 0.7152 (mt-10) cc_final: 0.6919 (tt0) REVERT: I 105 THR cc_start: 0.8073 (OUTLIER) cc_final: 0.7789 (p) REVERT: M 83 GLU cc_start: 0.7981 (tm-30) cc_final: 0.7700 (pp20) REVERT: E 159 PHE cc_start: 0.8230 (OUTLIER) cc_final: 0.7944 (m-10) REVERT: E 260 LEU cc_start: 0.8903 (OUTLIER) cc_final: 0.8681 (mm) REVERT: F 584 GLU cc_start: 0.8536 (mt-10) cc_final: 0.7835 (mp0) REVERT: F 629 MET cc_start: 0.9067 (mmm) cc_final: 0.8730 (mmt) REVERT: J 16 GLU cc_start: 0.7467 (mt-10) cc_final: 0.7218 (tt0) REVERT: N 79 GLU cc_start: 0.8473 (mp0) cc_final: 0.8186 (mp0) REVERT: N 83 GLU cc_start: 0.8086 (tm-30) cc_final: 0.7849 (pp20) outliers start: 60 outliers final: 44 residues processed: 272 average time/residue: 0.1376 time to fit residues: 58.4015 Evaluate side-chains 247 residues out of total 2106 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 199 time to evaluate : 0.680 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 95 MET Chi-restraints excluded: chain A residue 120 VAL Chi-restraints excluded: chain A residue 197 ASN Chi-restraints excluded: chain A residue 234 ASN Chi-restraints excluded: chain A residue 274 SER Chi-restraints excluded: chain A residue 289 ASN Chi-restraints excluded: chain A residue 326 ILE Chi-restraints excluded: chain A residue 345 VAL Chi-restraints excluded: chain A residue 373 THR Chi-restraints excluded: chain A residue 491 ILE Chi-restraints excluded: chain B residue 539 VAL Chi-restraints excluded: chain B residue 584 GLU Chi-restraints excluded: chain B residue 603 ILE Chi-restraints excluded: chain H residue 31 ASP Chi-restraints excluded: chain H residue 92 CYS Chi-restraints excluded: chain C residue 120 VAL Chi-restraints excluded: chain C residue 197 ASN Chi-restraints excluded: chain C residue 202 THR Chi-restraints excluded: chain C residue 234 ASN Chi-restraints excluded: chain C residue 244 THR Chi-restraints excluded: chain C residue 289 ASN Chi-restraints excluded: chain C residue 373 THR Chi-restraints excluded: chain C residue 491 ILE Chi-restraints excluded: chain D residue 545 LEU Chi-restraints excluded: chain I residue 3 HIS Chi-restraints excluded: chain I residue 21 THR Chi-restraints excluded: chain I residue 28 LEU Chi-restraints excluded: chain I residue 92 CYS Chi-restraints excluded: chain I residue 105 THR Chi-restraints excluded: chain M residue 104 LEU Chi-restraints excluded: chain E residue 95 MET Chi-restraints excluded: chain E residue 120 VAL Chi-restraints excluded: chain E residue 159 PHE Chi-restraints excluded: chain E residue 197 ASN Chi-restraints excluded: chain E residue 234 ASN Chi-restraints excluded: chain E residue 260 LEU Chi-restraints excluded: chain E residue 289 ASN Chi-restraints excluded: chain E residue 345 VAL Chi-restraints excluded: chain E residue 373 THR Chi-restraints excluded: chain E residue 449 ILE Chi-restraints excluded: chain E residue 491 ILE Chi-restraints excluded: chain F residue 587 LEU Chi-restraints excluded: chain F residue 593 LEU Chi-restraints excluded: chain F residue 606 THR Chi-restraints excluded: chain J residue 28 LEU Chi-restraints excluded: chain J residue 77 LEU Chi-restraints excluded: chain J residue 92 CYS Chi-restraints excluded: chain J residue 105 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 231 random chunks: chunk 60 optimal weight: 0.4980 chunk 142 optimal weight: 0.9990 chunk 143 optimal weight: 6.9990 chunk 64 optimal weight: 3.9990 chunk 30 optimal weight: 10.0000 chunk 184 optimal weight: 9.9990 chunk 71 optimal weight: 0.9990 chunk 29 optimal weight: 3.9990 chunk 91 optimal weight: 9.9990 chunk 195 optimal weight: 10.0000 chunk 72 optimal weight: 0.0010 overall best weight: 1.2992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 607 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 651 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 3 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3832 r_free = 0.3832 target = 0.102417 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3452 r_free = 0.3452 target = 0.080775 restraints weight = 63389.126| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3506 r_free = 0.3506 target = 0.083669 restraints weight = 34651.377| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3538 r_free = 0.3538 target = 0.085468 restraints weight = 24836.191| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3557 r_free = 0.3557 target = 0.086563 restraints weight = 20472.864| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.3570 r_free = 0.3570 target = 0.087263 restraints weight = 18233.532| |-----------------------------------------------------------------------------| r_work (final): 0.3535 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7890 moved from start: 0.4238 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 21432 Z= 0.131 Angle : 0.712 10.537 29421 Z= 0.329 Chirality : 0.047 0.334 3723 Planarity : 0.004 0.073 3429 Dihedral : 5.498 45.702 2556 Min Nonbonded Distance : 2.367 Molprobity Statistics. All-atom Clashscore : 7.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.98 % Favored : 98.02 % Rotamer: Outliers : 2.33 % Allowed : 12.77 % Favored : 84.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.54 (0.17), residues: 2325 helix: 0.87 (0.28), residues: 372 sheet: 0.88 (0.20), residues: 636 loop : 0.02 (0.17), residues: 1317 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG M 20 TYR 0.048 0.001 TYR F 643 PHE 0.012 0.001 PHE C 233 TRP 0.015 0.001 TRP B 631 HIS 0.009 0.001 HIS I 3 Details of bonding type rmsd/Z covalent geometry : bond 0.00281 / 0.13 (21234) covalent geometry : angle 0.66717 / 0.32 (28866) SS BOND : bond 0.00372 / 0.23 ( 39) SS BOND : angle 0.98176 / 0.67 ( 78) hydrogen bonds : bond 0.04093 / 2.78 ( 702) hydrogen bonds : angle 5.24783 / 3.72 ( 1890) link_ALPHA1-2 : bond 0.00728 / 0.45 ( 12) link_ALPHA1-2 : angle 2.35180 / 1.48 ( 36) link_ALPHA1-3 : bond 0.01032 / 0.66 ( 15) link_ALPHA1-3 : angle 1.86140 / 1.25 ( 45) link_ALPHA1-6 : bond 0.00529 / 0.33 ( 21) link_ALPHA1-6 : angle 1.58731 / 1.07 ( 63) link_BETA1-4 : bond 0.00655 / 0.44 ( 60) link_BETA1-4 : angle 2.01819 / 1.52 ( 180) link_NAG-ASN : bond 0.00393 / 0.25 ( 51) link_NAG-ASN : angle 2.21529 / 1.57 ( 153) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4650 Ramachandran restraints generated. 2325 Oldfield, 0 Emsley, 2325 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4650 Ramachandran restraints generated. 2325 Oldfield, 0 Emsley, 2325 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 274 residues out of total 2106 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 225 time to evaluate : 0.794 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 69 TRP cc_start: 0.8606 (m-90) cc_final: 0.8272 (m-90) REVERT: A 475 MET cc_start: 0.8054 (mmm) cc_final: 0.6373 (tpp) REVERT: A 479 TRP cc_start: 0.8242 (m-90) cc_final: 0.7718 (m-90) REVERT: B 577 GLN cc_start: 0.8639 (tm-30) cc_final: 0.8393 (tm-30) REVERT: B 584 GLU cc_start: 0.8429 (OUTLIER) cc_final: 0.7864 (mt-10) REVERT: B 619 GLN cc_start: 0.7961 (tm-30) cc_final: 0.7714 (tm-30) REVERT: B 623 TRP cc_start: 0.7095 (m-10) cc_final: 0.6711 (m-10) REVERT: B 642 ILE cc_start: 0.9492 (mt) cc_final: 0.9247 (mm) REVERT: H 100 MET cc_start: 0.8623 (mpp) cc_final: 0.8362 (mpp) REVERT: C 479 TRP cc_start: 0.8277 (m-90) cc_final: 0.7924 (m-90) REVERT: D 577 GLN cc_start: 0.8834 (tm-30) cc_final: 0.8455 (tm-30) REVERT: D 584 GLU cc_start: 0.8636 (mt-10) cc_final: 0.8370 (mt-10) REVERT: D 586 TYR cc_start: 0.9033 (t80) cc_final: 0.8673 (t80) REVERT: D 589 ASP cc_start: 0.8737 (m-30) cc_final: 0.8523 (m-30) REVERT: I 105 THR cc_start: 0.7904 (OUTLIER) cc_final: 0.7640 (p) REVERT: M 83 GLU cc_start: 0.7901 (tm-30) cc_final: 0.7686 (pp20) REVERT: M 100 GLU cc_start: 0.6546 (mm-30) cc_final: 0.6333 (mp0) REVERT: E 260 LEU cc_start: 0.8871 (OUTLIER) cc_final: 0.8617 (mm) REVERT: F 530 MET cc_start: 0.6159 (OUTLIER) cc_final: 0.5873 (mtm) REVERT: F 584 GLU cc_start: 0.8444 (mt-10) cc_final: 0.7909 (mt-10) REVERT: F 626 MET cc_start: 0.7805 (tpp) cc_final: 0.7382 (tpp) REVERT: N 79 GLU cc_start: 0.8635 (mp0) cc_final: 0.8375 (mp0) outliers start: 49 outliers final: 34 residues processed: 260 average time/residue: 0.1312 time to fit residues: 53.8692 Evaluate side-chains 237 residues out of total 2106 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 199 time to evaluate : 0.699 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 95 MET Chi-restraints excluded: chain A residue 120 VAL Chi-restraints excluded: chain A residue 197 ASN Chi-restraints excluded: chain A residue 234 ASN Chi-restraints excluded: chain A residue 289 ASN Chi-restraints excluded: chain A residue 326 ILE Chi-restraints excluded: chain A residue 491 ILE Chi-restraints excluded: chain B residue 539 VAL Chi-restraints excluded: chain B residue 584 GLU Chi-restraints excluded: chain B residue 603 ILE Chi-restraints excluded: chain H residue 31 ASP Chi-restraints excluded: chain H residue 63 LEU Chi-restraints excluded: chain L residue 85 ASP Chi-restraints excluded: chain C residue 119 CYS Chi-restraints excluded: chain C residue 120 VAL Chi-restraints excluded: chain C residue 197 ASN Chi-restraints excluded: chain C residue 202 THR Chi-restraints excluded: chain C residue 244 THR Chi-restraints excluded: chain C residue 289 ASN Chi-restraints excluded: chain I residue 3 HIS Chi-restraints excluded: chain I residue 21 THR Chi-restraints excluded: chain I residue 22 CYS Chi-restraints excluded: chain I residue 28 LEU Chi-restraints excluded: chain I residue 105 THR Chi-restraints excluded: chain M residue 104 LEU Chi-restraints excluded: chain E residue 95 MET Chi-restraints excluded: chain E residue 108 ILE Chi-restraints excluded: chain E residue 120 VAL Chi-restraints excluded: chain E residue 234 ASN Chi-restraints excluded: chain E residue 260 LEU Chi-restraints excluded: chain E residue 289 ASN Chi-restraints excluded: chain E residue 449 ILE Chi-restraints excluded: chain F residue 530 MET Chi-restraints excluded: chain F residue 593 LEU Chi-restraints excluded: chain F residue 606 THR Chi-restraints excluded: chain J residue 77 LEU Chi-restraints excluded: chain J residue 92 CYS Chi-restraints excluded: chain J residue 105 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 231 random chunks: chunk 96 optimal weight: 10.0000 chunk 176 optimal weight: 8.9990 chunk 6 optimal weight: 20.0000 chunk 179 optimal weight: 6.9990 chunk 92 optimal weight: 10.0000 chunk 152 optimal weight: 7.9990 chunk 121 optimal weight: 5.9990 chunk 83 optimal weight: 9.9990 chunk 218 optimal weight: 5.9990 chunk 145 optimal weight: 6.9990 chunk 17 optimal weight: 7.9990 overall best weight: 6.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 94 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 287 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 362 ASN B 591 GLN H 3 HIS C 362 ASN ** D 591 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 362 ASN J 5 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3745 r_free = 0.3745 target = 0.097581 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3346 r_free = 0.3346 target = 0.075571 restraints weight = 64720.934| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.3398 r_free = 0.3398 target = 0.078234 restraints weight = 36499.993| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3429 r_free = 0.3429 target = 0.079900 restraints weight = 26562.857| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3448 r_free = 0.3448 target = 0.080895 restraints weight = 22100.478| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3458 r_free = 0.3458 target = 0.081466 restraints weight = 19874.681| |-----------------------------------------------------------------------------| r_work (final): 0.3424 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8053 moved from start: 0.4663 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.055 21432 Z= 0.309 Angle : 0.882 10.299 29421 Z= 0.412 Chirality : 0.051 0.458 3723 Planarity : 0.005 0.068 3429 Dihedral : 5.855 41.190 2552 Min Nonbonded Distance : 2.276 Molprobity Statistics. All-atom Clashscore : 12.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.22 % Favored : 95.78 % Rotamer: Outliers : 3.89 % Allowed : 11.59 % Favored : 84.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.14 (0.17), residues: 2325 helix: 0.45 (0.27), residues: 390 sheet: 0.74 (0.20), residues: 606 loop : -0.27 (0.17), residues: 1329 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG F 542 TYR 0.040 0.003 TYR F 643 PHE 0.023 0.003 PHE N 98 TRP 0.021 0.002 TRP M 91 HIS 0.021 0.002 HIS I 3 Details of bonding type rmsd/Z covalent geometry : bond 0.00702 / 0.31 (21234) covalent geometry : angle 0.83364 / 0.40 (28866) SS BOND : bond 0.00850 / 0.51 ( 39) SS BOND : angle 1.28548 / 0.81 ( 78) hydrogen bonds : bond 0.04904 / 3.36 ( 702) hydrogen bonds : angle 5.67319 / 4.01 ( 1890) link_ALPHA1-2 : bond 0.00447 / 0.27 ( 12) link_ALPHA1-2 : angle 2.75594 / 1.73 ( 36) link_ALPHA1-3 : bond 0.00796 / 0.50 ( 15) link_ALPHA1-3 : angle 2.31564 / 1.51 ( 45) link_ALPHA1-6 : bond 0.00312 / 0.20 ( 21) link_ALPHA1-6 : angle 1.93804 / 1.34 ( 63) link_BETA1-4 : bond 0.00639 / 0.43 ( 60) link_BETA1-4 : angle 2.26457 / 1.66 ( 180) link_NAG-ASN : bond 0.00761 / 0.50 ( 51) link_NAG-ASN : angle 2.57464 / 1.78 ( 153) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4650 Ramachandran restraints generated. 2325 Oldfield, 0 Emsley, 2325 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4650 Ramachandran restraints generated. 2325 Oldfield, 0 Emsley, 2325 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 270 residues out of total 2106 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 82 poor density : 188 time to evaluate : 0.709 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 69 TRP cc_start: 0.8755 (m-90) cc_final: 0.8423 (m-10) REVERT: A 475 MET cc_start: 0.8230 (mmm) cc_final: 0.7485 (tpp) REVERT: A 479 TRP cc_start: 0.8373 (m-90) cc_final: 0.8089 (m-90) REVERT: B 575 GLN cc_start: 0.9011 (tp40) cc_final: 0.8766 (tp40) REVERT: B 577 GLN cc_start: 0.8761 (tm-30) cc_final: 0.8511 (tm-30) REVERT: B 584 GLU cc_start: 0.8430 (OUTLIER) cc_final: 0.8179 (mt-10) REVERT: B 619 GLN cc_start: 0.8116 (tm-30) cc_final: 0.7864 (tm-30) REVERT: H 100 MET cc_start: 0.8748 (mpp) cc_final: 0.8427 (mmt) REVERT: L 28 LEU cc_start: 0.8865 (OUTLIER) cc_final: 0.8466 (mm) REVERT: C 104 MET cc_start: 0.9063 (ttm) cc_final: 0.8342 (ttm) REVERT: C 159 PHE cc_start: 0.8434 (m-10) cc_final: 0.8216 (m-80) REVERT: C 475 MET cc_start: 0.8232 (mmm) cc_final: 0.7677 (tmm) REVERT: D 577 GLN cc_start: 0.8926 (tm-30) cc_final: 0.8565 (tm-30) REVERT: D 584 GLU cc_start: 0.8552 (mt-10) cc_final: 0.8278 (mt-10) REVERT: M 83 GLU cc_start: 0.7953 (tm-30) cc_final: 0.7520 (pp20) REVERT: E 260 LEU cc_start: 0.8936 (OUTLIER) cc_final: 0.8676 (mm) REVERT: F 584 GLU cc_start: 0.8423 (mt-10) cc_final: 0.7930 (mt-10) REVERT: F 629 MET cc_start: 0.9143 (mmm) cc_final: 0.8502 (mmm) REVERT: N 79 GLU cc_start: 0.8645 (mp0) cc_final: 0.8326 (mp0) outliers start: 82 outliers final: 58 residues processed: 248 average time/residue: 0.1425 time to fit residues: 56.1193 Evaluate side-chains 238 residues out of total 2106 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 177 time to evaluate : 0.747 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 95 MET Chi-restraints excluded: chain A residue 115 SER Chi-restraints excluded: chain A residue 119 CYS Chi-restraints excluded: chain A residue 120 VAL Chi-restraints excluded: chain A residue 197 ASN Chi-restraints excluded: chain A residue 234 ASN Chi-restraints excluded: chain A residue 274 SER Chi-restraints excluded: chain A residue 289 ASN Chi-restraints excluded: chain A residue 322 ILE Chi-restraints excluded: chain A residue 326 ILE Chi-restraints excluded: chain A residue 345 VAL Chi-restraints excluded: chain A residue 373 THR Chi-restraints excluded: chain A residue 426 MET Chi-restraints excluded: chain A residue 491 ILE Chi-restraints excluded: chain B residue 536 THR Chi-restraints excluded: chain B residue 584 GLU Chi-restraints excluded: chain B residue 603 ILE Chi-restraints excluded: chain H residue 3 HIS Chi-restraints excluded: chain H residue 97 HIS Chi-restraints excluded: chain H residue 105 THR Chi-restraints excluded: chain L residue 28 LEU Chi-restraints excluded: chain C residue 95 MET Chi-restraints excluded: chain C residue 119 CYS Chi-restraints excluded: chain C residue 120 VAL Chi-restraints excluded: chain C residue 197 ASN Chi-restraints excluded: chain C residue 202 THR Chi-restraints excluded: chain C residue 244 THR Chi-restraints excluded: chain C residue 289 ASN Chi-restraints excluded: chain C residue 345 VAL Chi-restraints excluded: chain C residue 373 THR Chi-restraints excluded: chain C residue 491 ILE Chi-restraints excluded: chain D residue 536 THR Chi-restraints excluded: chain D residue 545 LEU Chi-restraints excluded: chain D residue 644 SER Chi-restraints excluded: chain I residue 21 THR Chi-restraints excluded: chain I residue 28 LEU Chi-restraints excluded: chain I residue 37 ILE Chi-restraints excluded: chain I residue 97 HIS Chi-restraints excluded: chain I residue 105 THR Chi-restraints excluded: chain M residue 104 LEU Chi-restraints excluded: chain E residue 95 MET Chi-restraints excluded: chain E residue 108 ILE Chi-restraints excluded: chain E residue 115 SER Chi-restraints excluded: chain E residue 120 VAL Chi-restraints excluded: chain E residue 197 ASN Chi-restraints excluded: chain E residue 215 ILE Chi-restraints excluded: chain E residue 234 ASN Chi-restraints excluded: chain E residue 260 LEU Chi-restraints excluded: chain E residue 289 ASN Chi-restraints excluded: chain E residue 326 ILE Chi-restraints excluded: chain E residue 345 VAL Chi-restraints excluded: chain E residue 373 THR Chi-restraints excluded: chain E residue 491 ILE Chi-restraints excluded: chain F residue 593 LEU Chi-restraints excluded: chain F residue 606 THR Chi-restraints excluded: chain F residue 639 THR Chi-restraints excluded: chain F residue 642 ILE Chi-restraints excluded: chain J residue 20 LEU Chi-restraints excluded: chain J residue 77 LEU Chi-restraints excluded: chain J residue 89 ILE Chi-restraints excluded: chain J residue 105 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 231 random chunks: chunk 106 optimal weight: 0.9980 chunk 182 optimal weight: 4.9990 chunk 195 optimal weight: 8.9990 chunk 172 optimal weight: 5.9990 chunk 59 optimal weight: 3.9990 chunk 62 optimal weight: 20.0000 chunk 13 optimal weight: 6.9990 chunk 219 optimal weight: 0.9980 chunk 176 optimal weight: 6.9990 chunk 49 optimal weight: 3.9990 chunk 101 optimal weight: 5.9990 overall best weight: 2.9986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 362 ASN ** B 591 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 3 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 362 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3774 r_free = 0.3774 target = 0.097004 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3419 r_free = 0.3419 target = 0.077248 restraints weight = 63093.099| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 24)----------------| | r_work = 0.3428 r_free = 0.3428 target = 0.078635 restraints weight = 40026.114| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3436 r_free = 0.3436 target = 0.079287 restraints weight = 32651.956| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3443 r_free = 0.3443 target = 0.079644 restraints weight = 28944.419| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3455 r_free = 0.3455 target = 0.080373 restraints weight = 26345.549| |-----------------------------------------------------------------------------| r_work (final): 0.3442 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8029 moved from start: 0.4785 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.074 21432 Z= 0.174 Angle : 0.772 13.041 29421 Z= 0.359 Chirality : 0.048 0.393 3723 Planarity : 0.004 0.053 3429 Dihedral : 5.693 40.598 2552 Min Nonbonded Distance : 2.309 Molprobity Statistics. All-atom Clashscore : 9.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.88 % Favored : 97.12 % Rotamer: Outliers : 2.85 % Allowed : 12.35 % Favored : 84.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.17 (0.17), residues: 2325 helix: 0.49 (0.27), residues: 390 sheet: 0.47 (0.19), residues: 663 loop : -0.11 (0.17), residues: 1272 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG I 99 TYR 0.031 0.002 TYR F 643 PHE 0.015 0.001 PHE C 233 TRP 0.013 0.001 TRP B 631 HIS 0.023 0.002 HIS H 3 Details of bonding type rmsd/Z covalent geometry : bond 0.00392 / 0.17 (21234) covalent geometry : angle 0.72459 / 0.35 (28866) SS BOND : bond 0.00632 / 0.39 ( 39) SS BOND : angle 1.73638 / 1.30 ( 78) hydrogen bonds : bond 0.04218 / 2.88 ( 702) hydrogen bonds : angle 5.41783 / 3.83 ( 1890) link_ALPHA1-2 : bond 0.00486 / 0.30 ( 12) link_ALPHA1-2 : angle 2.55153 / 1.60 ( 36) link_ALPHA1-3 : bond 0.00848 / 0.53 ( 15) link_ALPHA1-3 : angle 1.88782 / 1.28 ( 45) link_ALPHA1-6 : bond 0.00422 / 0.27 ( 21) link_ALPHA1-6 : angle 1.70002 / 1.15 ( 63) link_BETA1-4 : bond 0.00631 / 0.43 ( 60) link_BETA1-4 : angle 2.03538 / 1.51 ( 180) link_NAG-ASN : bond 0.00587 / 0.41 ( 51) link_NAG-ASN : angle 2.29130 / 1.60 ( 153) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4650 Ramachandran restraints generated. 2325 Oldfield, 0 Emsley, 2325 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4650 Ramachandran restraints generated. 2325 Oldfield, 0 Emsley, 2325 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 251 residues out of total 2106 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 191 time to evaluate : 0.836 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 69 TRP cc_start: 0.8792 (m-90) cc_final: 0.8420 (m-10) REVERT: A 475 MET cc_start: 0.8122 (mmm) cc_final: 0.6790 (tpp) REVERT: A 479 TRP cc_start: 0.8304 (m-90) cc_final: 0.7871 (m-90) REVERT: B 577 GLN cc_start: 0.8696 (tm-30) cc_final: 0.8432 (tm-30) REVERT: B 584 GLU cc_start: 0.8389 (OUTLIER) cc_final: 0.7842 (mt-10) REVERT: B 619 GLN cc_start: 0.8245 (tm-30) cc_final: 0.7905 (tm-30) REVERT: H 100 MET cc_start: 0.8670 (mpp) cc_final: 0.8305 (mmt) REVERT: C 91 GLU cc_start: 0.7092 (mp0) cc_final: 0.6621 (mp0) REVERT: C 104 MET cc_start: 0.8972 (ttm) cc_final: 0.8155 (ttm) REVERT: C 475 MET cc_start: 0.8160 (mmm) cc_final: 0.7686 (tmm) REVERT: D 577 GLN cc_start: 0.8860 (tm-30) cc_final: 0.8464 (tm-30) REVERT: D 584 GLU cc_start: 0.8500 (mt-10) cc_final: 0.8279 (mt-10) REVERT: D 630 GLU cc_start: 0.8547 (mm-30) cc_final: 0.8299 (mm-30) REVERT: M 83 GLU cc_start: 0.8043 (tm-30) cc_final: 0.7636 (pp20) REVERT: E 260 LEU cc_start: 0.8893 (OUTLIER) cc_final: 0.8618 (mm) REVERT: F 584 GLU cc_start: 0.8363 (mt-10) cc_final: 0.7923 (mt-10) REVERT: F 629 MET cc_start: 0.9076 (mmm) cc_final: 0.8768 (mmt) REVERT: N 79 GLU cc_start: 0.8639 (mp0) cc_final: 0.8387 (mp0) outliers start: 60 outliers final: 52 residues processed: 235 average time/residue: 0.1342 time to fit residues: 50.0036 Evaluate side-chains 229 residues out of total 2106 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 175 time to evaluate : 0.564 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 95 MET Chi-restraints excluded: chain A residue 115 SER Chi-restraints excluded: chain A residue 120 VAL Chi-restraints excluded: chain A residue 197 ASN Chi-restraints excluded: chain A residue 234 ASN Chi-restraints excluded: chain A residue 274 SER Chi-restraints excluded: chain A residue 289 ASN Chi-restraints excluded: chain A residue 326 ILE Chi-restraints excluded: chain A residue 345 VAL Chi-restraints excluded: chain A residue 373 THR Chi-restraints excluded: chain A residue 426 MET Chi-restraints excluded: chain A residue 491 ILE Chi-restraints excluded: chain B residue 536 THR Chi-restraints excluded: chain B residue 539 VAL Chi-restraints excluded: chain B residue 584 GLU Chi-restraints excluded: chain B residue 603 ILE Chi-restraints excluded: chain B residue 641 ILE Chi-restraints excluded: chain H residue 97 HIS Chi-restraints excluded: chain H residue 105 THR Chi-restraints excluded: chain C residue 95 MET Chi-restraints excluded: chain C residue 100 MET Chi-restraints excluded: chain C residue 119 CYS Chi-restraints excluded: chain C residue 120 VAL Chi-restraints excluded: chain C residue 197 ASN Chi-restraints excluded: chain C residue 202 THR Chi-restraints excluded: chain C residue 234 ASN Chi-restraints excluded: chain C residue 244 THR Chi-restraints excluded: chain C residue 289 ASN Chi-restraints excluded: chain C residue 373 THR Chi-restraints excluded: chain C residue 491 ILE Chi-restraints excluded: chain D residue 545 LEU Chi-restraints excluded: chain D residue 598 CYS Chi-restraints excluded: chain I residue 21 THR Chi-restraints excluded: chain I residue 28 LEU Chi-restraints excluded: chain I residue 97 HIS Chi-restraints excluded: chain I residue 105 THR Chi-restraints excluded: chain M residue 104 LEU Chi-restraints excluded: chain E residue 95 MET Chi-restraints excluded: chain E residue 108 ILE Chi-restraints excluded: chain E residue 115 SER Chi-restraints excluded: chain E residue 120 VAL Chi-restraints excluded: chain E residue 234 ASN Chi-restraints excluded: chain E residue 260 LEU Chi-restraints excluded: chain E residue 289 ASN Chi-restraints excluded: chain E residue 326 ILE Chi-restraints excluded: chain E residue 373 THR Chi-restraints excluded: chain E residue 491 ILE Chi-restraints excluded: chain F residue 537 LEU Chi-restraints excluded: chain F residue 587 LEU Chi-restraints excluded: chain F residue 593 LEU Chi-restraints excluded: chain F residue 606 THR Chi-restraints excluded: chain F residue 642 ILE Chi-restraints excluded: chain J residue 20 LEU Chi-restraints excluded: chain J residue 105 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 231 random chunks: chunk 109 optimal weight: 0.9980 chunk 26 optimal weight: 9.9990 chunk 24 optimal weight: 10.0000 chunk 219 optimal weight: 4.9990 chunk 216 optimal weight: 20.0000 chunk 86 optimal weight: 7.9990 chunk 80 optimal weight: 9.9990 chunk 23 optimal weight: 4.9990 chunk 15 optimal weight: 6.9990 chunk 143 optimal weight: 10.0000 chunk 126 optimal weight: 5.9990 overall best weight: 4.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 94 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 287 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 591 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 607 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 3 HIS H 32 ASN ** D 591 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 656 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3749 r_free = 0.3749 target = 0.095507 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3388 r_free = 0.3388 target = 0.075716 restraints weight = 63284.881| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3402 r_free = 0.3402 target = 0.077156 restraints weight = 40911.649| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3402 r_free = 0.3402 target = 0.077271 restraints weight = 33279.500| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3430 r_free = 0.3430 target = 0.079038 restraints weight = 29717.971| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3431 r_free = 0.3431 target = 0.079091 restraints weight = 24563.990| |-----------------------------------------------------------------------------| r_work (final): 0.3419 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8065 moved from start: 0.5013 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.075 21432 Z= 0.237 Angle : 0.813 12.000 29421 Z= 0.379 Chirality : 0.049 0.403 3723 Planarity : 0.005 0.054 3429 Dihedral : 5.788 38.859 2552 Min Nonbonded Distance : 2.297 Molprobity Statistics. All-atom Clashscore : 10.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.26 % Favored : 95.74 % Rotamer: Outliers : 3.37 % Allowed : 12.63 % Favored : 84.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.02 (0.17), residues: 2325 helix: 0.44 (0.27), residues: 390 sheet: 0.38 (0.20), residues: 663 loop : -0.24 (0.17), residues: 1272 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG H 99 TYR 0.027 0.002 TYR D 586 PHE 0.013 0.002 PHE N 98 TRP 0.015 0.002 TRP M 91 HIS 0.007 0.001 HIS H 52 Details of bonding type rmsd/Z covalent geometry : bond 0.00542 / 0.24 (21234) covalent geometry : angle 0.76558 / 0.37 (28866) SS BOND : bond 0.00718 / 0.45 ( 39) SS BOND : angle 1.73163 / 1.28 ( 78) hydrogen bonds : bond 0.04366 / 2.98 ( 702) hydrogen bonds : angle 5.42246 / 3.83 ( 1890) link_ALPHA1-2 : bond 0.00383 / 0.23 ( 12) link_ALPHA1-2 : angle 2.64925 / 1.66 ( 36) link_ALPHA1-3 : bond 0.00731 / 0.45 ( 15) link_ALPHA1-3 : angle 2.06214 / 1.36 ( 45) link_ALPHA1-6 : bond 0.00337 / 0.23 ( 21) link_ALPHA1-6 : angle 1.81493 / 1.24 ( 63) link_BETA1-4 : bond 0.00624 / 0.42 ( 60) link_BETA1-4 : angle 2.06340 / 1.51 ( 180) link_NAG-ASN : bond 0.00630 / 0.42 ( 51) link_NAG-ASN : angle 2.36651 / 1.64 ( 153) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4650 Ramachandran restraints generated. 2325 Oldfield, 0 Emsley, 2325 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4650 Ramachandran restraints generated. 2325 Oldfield, 0 Emsley, 2325 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 251 residues out of total 2106 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 71 poor density : 180 time to evaluate : 0.776 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 475 MET cc_start: 0.8037 (mmm) cc_final: 0.7108 (tpp) REVERT: A 479 TRP cc_start: 0.8330 (m-90) cc_final: 0.7998 (m-90) REVERT: B 577 GLN cc_start: 0.8673 (tm-30) cc_final: 0.8362 (tm-30) REVERT: B 584 GLU cc_start: 0.8367 (OUTLIER) cc_final: 0.7830 (mt-10) REVERT: B 619 GLN cc_start: 0.8308 (tm-30) cc_final: 0.7946 (tm-30) REVERT: H 100 MET cc_start: 0.8683 (mpp) cc_final: 0.8329 (mpp) REVERT: L 28 LEU cc_start: 0.8807 (OUTLIER) cc_final: 0.8450 (mm) REVERT: C 91 GLU cc_start: 0.7215 (mp0) cc_final: 0.6900 (mp0) REVERT: C 95 MET cc_start: 0.7132 (OUTLIER) cc_final: 0.6866 (ptp) REVERT: C 104 MET cc_start: 0.9044 (ttm) cc_final: 0.8339 (ttm) REVERT: C 475 MET cc_start: 0.8253 (mmm) cc_final: 0.7846 (tmm) REVERT: D 577 GLN cc_start: 0.8881 (tm-30) cc_final: 0.8522 (tm-30) REVERT: D 584 GLU cc_start: 0.8512 (mt-10) cc_final: 0.8289 (mt-10) REVERT: D 586 TYR cc_start: 0.9116 (t80) cc_final: 0.8914 (t80) REVERT: D 630 GLU cc_start: 0.8614 (mm-30) cc_final: 0.8412 (mm-30) REVERT: M 83 GLU cc_start: 0.7972 (tm-30) cc_final: 0.7600 (pp20) REVERT: E 260 LEU cc_start: 0.8977 (OUTLIER) cc_final: 0.8760 (mm) REVERT: F 574 LYS cc_start: 0.8985 (mptt) cc_final: 0.8621 (tptt) REVERT: F 584 GLU cc_start: 0.8402 (mt-10) cc_final: 0.8006 (mt-10) REVERT: F 629 MET cc_start: 0.9147 (mmm) cc_final: 0.8650 (mmm) REVERT: N 79 GLU cc_start: 0.8583 (mp0) cc_final: 0.8336 (mp0) REVERT: N 83 GLU cc_start: 0.8162 (pp20) cc_final: 0.7636 (pp20) outliers start: 71 outliers final: 55 residues processed: 234 average time/residue: 0.1283 time to fit residues: 47.9371 Evaluate side-chains 232 residues out of total 2106 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 173 time to evaluate : 0.734 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 95 MET Chi-restraints excluded: chain A residue 115 SER Chi-restraints excluded: chain A residue 119 CYS Chi-restraints excluded: chain A residue 120 VAL Chi-restraints excluded: chain A residue 197 ASN Chi-restraints excluded: chain A residue 234 ASN Chi-restraints excluded: chain A residue 274 SER Chi-restraints excluded: chain A residue 289 ASN Chi-restraints excluded: chain A residue 322 ILE Chi-restraints excluded: chain A residue 326 ILE Chi-restraints excluded: chain A residue 345 VAL Chi-restraints excluded: chain A residue 373 THR Chi-restraints excluded: chain A residue 426 MET Chi-restraints excluded: chain A residue 491 ILE Chi-restraints excluded: chain B residue 536 THR Chi-restraints excluded: chain B residue 584 GLU Chi-restraints excluded: chain B residue 598 CYS Chi-restraints excluded: chain B residue 603 ILE Chi-restraints excluded: chain H residue 97 HIS Chi-restraints excluded: chain H residue 105 THR Chi-restraints excluded: chain L residue 28 LEU Chi-restraints excluded: chain C residue 95 MET Chi-restraints excluded: chain C residue 100 MET Chi-restraints excluded: chain C residue 119 CYS Chi-restraints excluded: chain C residue 120 VAL Chi-restraints excluded: chain C residue 197 ASN Chi-restraints excluded: chain C residue 202 THR Chi-restraints excluded: chain C residue 234 ASN Chi-restraints excluded: chain C residue 244 THR Chi-restraints excluded: chain C residue 289 ASN Chi-restraints excluded: chain C residue 345 VAL Chi-restraints excluded: chain C residue 373 THR Chi-restraints excluded: chain C residue 491 ILE Chi-restraints excluded: chain D residue 534 SER Chi-restraints excluded: chain D residue 536 THR Chi-restraints excluded: chain D residue 598 CYS Chi-restraints excluded: chain D residue 644 SER Chi-restraints excluded: chain I residue 21 THR Chi-restraints excluded: chain I residue 28 LEU Chi-restraints excluded: chain I residue 105 THR Chi-restraints excluded: chain M residue 51 ASN Chi-restraints excluded: chain M residue 104 LEU Chi-restraints excluded: chain E residue 95 MET Chi-restraints excluded: chain E residue 108 ILE Chi-restraints excluded: chain E residue 115 SER Chi-restraints excluded: chain E residue 120 VAL Chi-restraints excluded: chain E residue 234 ASN Chi-restraints excluded: chain E residue 260 LEU Chi-restraints excluded: chain E residue 289 ASN Chi-restraints excluded: chain E residue 326 ILE Chi-restraints excluded: chain E residue 345 VAL Chi-restraints excluded: chain E residue 373 THR Chi-restraints excluded: chain E residue 491 ILE Chi-restraints excluded: chain F residue 587 LEU Chi-restraints excluded: chain F residue 593 LEU Chi-restraints excluded: chain F residue 606 THR Chi-restraints excluded: chain F residue 642 ILE Chi-restraints excluded: chain J residue 89 ILE Chi-restraints excluded: chain J residue 105 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 231 random chunks: chunk 18 optimal weight: 3.9990 chunk 213 optimal weight: 0.9980 chunk 113 optimal weight: 0.0980 chunk 150 optimal weight: 1.9990 chunk 216 optimal weight: 20.0000 chunk 139 optimal weight: 20.0000 chunk 78 optimal weight: 4.9990 chunk 24 optimal weight: 9.9990 chunk 181 optimal weight: 10.0000 chunk 94 optimal weight: 0.9980 chunk 67 optimal weight: 4.9990 overall best weight: 1.6184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 607 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 362 ASN F 656 ASN J 58 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3778 r_free = 0.3778 target = 0.098807 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3412 r_free = 0.3412 target = 0.077689 restraints weight = 64256.577| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3450 r_free = 0.3450 target = 0.079875 restraints weight = 35839.626| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3473 r_free = 0.3473 target = 0.081430 restraints weight = 25778.924| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3482 r_free = 0.3482 target = 0.081818 restraints weight = 24642.817| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3480 r_free = 0.3480 target = 0.081748 restraints weight = 21246.674| |-----------------------------------------------------------------------------| r_work (final): 0.3469 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8004 moved from start: 0.5097 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.058 21432 Z= 0.136 Angle : 0.730 11.024 29421 Z= 0.340 Chirality : 0.046 0.315 3723 Planarity : 0.004 0.054 3429 Dihedral : 5.546 39.940 2552 Min Nonbonded Distance : 2.338 Molprobity Statistics. All-atom Clashscore : 9.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.49 % Favored : 97.51 % Rotamer: Outliers : 2.37 % Allowed : 13.91 % Favored : 83.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.23 (0.17), residues: 2325 helix: 0.65 (0.28), residues: 387 sheet: 0.36 (0.19), residues: 669 loop : -0.02 (0.18), residues: 1269 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG N 20 TYR 0.033 0.002 TYR B 643 PHE 0.015 0.001 PHE C 233 TRP 0.017 0.001 TRP E 479 HIS 0.006 0.001 HIS H 52 Details of bonding type rmsd/Z covalent geometry : bond 0.00303 / 0.13 (21234) covalent geometry : angle 0.68813 / 0.33 (28866) SS BOND : bond 0.00491 / 0.30 ( 39) SS BOND : angle 1.47951 / 1.09 ( 78) hydrogen bonds : bond 0.03887 / 2.65 ( 702) hydrogen bonds : angle 5.13279 / 3.63 ( 1890) link_ALPHA1-2 : bond 0.00510 / 0.32 ( 12) link_ALPHA1-2 : angle 2.46218 / 1.55 ( 36) link_ALPHA1-3 : bond 0.00866 / 0.54 ( 15) link_ALPHA1-3 : angle 1.73469 / 1.19 ( 45) link_ALPHA1-6 : bond 0.00500 / 0.32 ( 21) link_ALPHA1-6 : angle 1.62981 / 1.10 ( 63) link_BETA1-4 : bond 0.00629 / 0.43 ( 60) link_BETA1-4 : angle 1.88131 / 1.40 ( 180) link_NAG-ASN : bond 0.00384 / 0.26 ( 51) link_NAG-ASN : angle 2.07973 / 1.46 ( 153) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4650 Ramachandran restraints generated. 2325 Oldfield, 0 Emsley, 2325 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4650 Ramachandran restraints generated. 2325 Oldfield, 0 Emsley, 2325 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 236 residues out of total 2106 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 186 time to evaluate : 0.514 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 69 TRP cc_start: 0.8835 (m-90) cc_final: 0.8390 (m-10) REVERT: A 475 MET cc_start: 0.7970 (mmm) cc_final: 0.6632 (tpp) REVERT: A 479 TRP cc_start: 0.8246 (m-90) cc_final: 0.7792 (m-90) REVERT: B 577 GLN cc_start: 0.8630 (tm-30) cc_final: 0.8289 (tm-30) REVERT: B 584 GLU cc_start: 0.8432 (OUTLIER) cc_final: 0.7623 (mp0) REVERT: B 619 GLN cc_start: 0.8325 (tm-30) cc_final: 0.7957 (tm-30) REVERT: H 100 MET cc_start: 0.8620 (mpp) cc_final: 0.8381 (mpp) REVERT: L 20 ARG cc_start: 0.8078 (mmm-85) cc_final: 0.7721 (mmm-85) REVERT: C 91 GLU cc_start: 0.7249 (mp0) cc_final: 0.6795 (mp0) REVERT: C 95 MET cc_start: 0.7094 (OUTLIER) cc_final: 0.6833 (ptp) REVERT: C 104 MET cc_start: 0.8936 (ttm) cc_final: 0.8309 (ttm) REVERT: C 475 MET cc_start: 0.8139 (mmm) cc_final: 0.6695 (tpp) REVERT: C 479 TRP cc_start: 0.8233 (m-90) cc_final: 0.7820 (m-90) REVERT: D 577 GLN cc_start: 0.8832 (tm-30) cc_final: 0.8472 (tm-30) REVERT: D 584 GLU cc_start: 0.8516 (mt-10) cc_final: 0.8267 (mt-10) REVERT: D 586 TYR cc_start: 0.9051 (t80) cc_final: 0.8850 (t80) REVERT: D 626 MET cc_start: 0.7876 (tpp) cc_final: 0.7554 (tpp) REVERT: D 630 GLU cc_start: 0.8645 (mm-30) cc_final: 0.7799 (tp30) REVERT: M 83 GLU cc_start: 0.8052 (tm-30) cc_final: 0.7770 (pp20) REVERT: E 260 LEU cc_start: 0.8865 (OUTLIER) cc_final: 0.8581 (mm) REVERT: F 584 GLU cc_start: 0.8422 (mt-10) cc_final: 0.7991 (mt-10) REVERT: N 79 GLU cc_start: 0.8497 (mp0) cc_final: 0.8213 (mp0) REVERT: N 83 GLU cc_start: 0.8222 (pp20) cc_final: 0.7746 (pp20) outliers start: 50 outliers final: 38 residues processed: 222 average time/residue: 0.1335 time to fit residues: 46.9118 Evaluate side-chains 219 residues out of total 2106 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 178 time to evaluate : 0.672 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 95 MET Chi-restraints excluded: chain A residue 119 CYS Chi-restraints excluded: chain A residue 120 VAL Chi-restraints excluded: chain A residue 197 ASN Chi-restraints excluded: chain A residue 234 ASN Chi-restraints excluded: chain A residue 274 SER Chi-restraints excluded: chain A residue 289 ASN Chi-restraints excluded: chain A residue 326 ILE Chi-restraints excluded: chain A residue 373 THR Chi-restraints excluded: chain B residue 536 THR Chi-restraints excluded: chain B residue 584 GLU Chi-restraints excluded: chain B residue 598 CYS Chi-restraints excluded: chain B residue 641 ILE Chi-restraints excluded: chain H residue 105 THR Chi-restraints excluded: chain C residue 95 MET Chi-restraints excluded: chain C residue 100 MET Chi-restraints excluded: chain C residue 119 CYS Chi-restraints excluded: chain C residue 120 VAL Chi-restraints excluded: chain C residue 197 ASN Chi-restraints excluded: chain C residue 202 THR Chi-restraints excluded: chain C residue 234 ASN Chi-restraints excluded: chain C residue 244 THR Chi-restraints excluded: chain C residue 289 ASN Chi-restraints excluded: chain D residue 534 SER Chi-restraints excluded: chain D residue 598 CYS Chi-restraints excluded: chain D residue 644 SER Chi-restraints excluded: chain I residue 21 THR Chi-restraints excluded: chain I residue 105 THR Chi-restraints excluded: chain M residue 104 LEU Chi-restraints excluded: chain E residue 95 MET Chi-restraints excluded: chain E residue 234 ASN Chi-restraints excluded: chain E residue 260 LEU Chi-restraints excluded: chain E residue 289 ASN Chi-restraints excluded: chain E residue 326 ILE Chi-restraints excluded: chain E residue 373 THR Chi-restraints excluded: chain F residue 587 LEU Chi-restraints excluded: chain F residue 593 LEU Chi-restraints excluded: chain F residue 606 THR Chi-restraints excluded: chain F residue 642 ILE Chi-restraints excluded: chain J residue 92 CYS Chi-restraints excluded: chain J residue 105 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 231 random chunks: chunk 141 optimal weight: 9.9990 chunk 215 optimal weight: 9.9990 chunk 206 optimal weight: 7.9990 chunk 62 optimal weight: 5.9990 chunk 228 optimal weight: 9.9990 chunk 115 optimal weight: 10.0000 chunk 147 optimal weight: 3.9990 chunk 177 optimal weight: 3.9990 chunk 48 optimal weight: 5.9990 chunk 117 optimal weight: 9.9990 chunk 145 optimal weight: 0.9990 overall best weight: 4.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 287 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 656 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3746 r_free = 0.3746 target = 0.097023 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3359 r_free = 0.3359 target = 0.074968 restraints weight = 64853.911| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3412 r_free = 0.3412 target = 0.077665 restraints weight = 36714.521| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3444 r_free = 0.3444 target = 0.079338 restraints weight = 26782.835| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.3463 r_free = 0.3463 target = 0.080360 restraints weight = 22317.208| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3472 r_free = 0.3472 target = 0.080924 restraints weight = 20031.148| |-----------------------------------------------------------------------------| r_work (final): 0.3457 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8023 moved from start: 0.5204 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.060 21432 Z= 0.210 Angle : 0.773 11.145 29421 Z= 0.360 Chirality : 0.048 0.351 3723 Planarity : 0.004 0.053 3429 Dihedral : 5.630 38.878 2552 Min Nonbonded Distance : 2.313 Molprobity Statistics. All-atom Clashscore : 10.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.87 % Favored : 96.13 % Rotamer: Outliers : 2.23 % Allowed : 14.34 % Favored : 83.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.15 (0.17), residues: 2325 helix: 0.72 (0.28), residues: 372 sheet: 0.34 (0.20), residues: 663 loop : -0.12 (0.18), residues: 1290 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG J 99 TYR 0.029 0.002 TYR F 643 PHE 0.012 0.002 PHE N 98 TRP 0.014 0.002 TRP E 479 HIS 0.007 0.001 HIS H 52 Details of bonding type rmsd/Z covalent geometry : bond 0.00482 / 0.21 (21234) covalent geometry : angle 0.72842 / 0.35 (28866) SS BOND : bond 0.00630 / 0.39 ( 39) SS BOND : angle 1.52093 / 1.11 ( 78) hydrogen bonds : bond 0.04106 / 2.79 ( 702) hydrogen bonds : angle 5.25951 / 3.72 ( 1890) link_ALPHA1-2 : bond 0.00362 / 0.22 ( 12) link_ALPHA1-2 : angle 2.53097 / 1.59 ( 36) link_ALPHA1-3 : bond 0.00657 / 0.41 ( 15) link_ALPHA1-3 : angle 1.92780 / 1.27 ( 45) link_ALPHA1-6 : bond 0.00353 / 0.24 ( 21) link_ALPHA1-6 : angle 1.78159 / 1.22 ( 63) link_BETA1-4 : bond 0.00609 / 0.41 ( 60) link_BETA1-4 : angle 1.98497 / 1.45 ( 180) link_NAG-ASN : bond 0.00536 / 0.36 ( 51) link_NAG-ASN : angle 2.23115 / 1.55 ( 153) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4650 Ramachandran restraints generated. 2325 Oldfield, 0 Emsley, 2325 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4650 Ramachandran restraints generated. 2325 Oldfield, 0 Emsley, 2325 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 226 residues out of total 2106 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 179 time to evaluate : 0.776 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 69 TRP cc_start: 0.8801 (m-90) cc_final: 0.8385 (m-10) REVERT: A 475 MET cc_start: 0.7992 (mmm) cc_final: 0.6669 (tpp) REVERT: A 479 TRP cc_start: 0.8335 (m-90) cc_final: 0.7843 (m-90) REVERT: B 577 GLN cc_start: 0.8672 (tm-30) cc_final: 0.8327 (tm-30) REVERT: B 584 GLU cc_start: 0.8438 (OUTLIER) cc_final: 0.7618 (mp0) REVERT: B 619 GLN cc_start: 0.8349 (tm-30) cc_final: 0.8042 (tm-30) REVERT: H 100 MET cc_start: 0.8673 (mpp) cc_final: 0.8320 (mpp) REVERT: L 20 ARG cc_start: 0.8112 (mmm-85) cc_final: 0.7763 (mmm-85) REVERT: C 91 GLU cc_start: 0.7209 (mp0) cc_final: 0.6724 (mp0) REVERT: C 104 MET cc_start: 0.9017 (ttm) cc_final: 0.8275 (ttm) REVERT: C 475 MET cc_start: 0.8231 (mmm) cc_final: 0.7831 (tmm) REVERT: D 577 GLN cc_start: 0.8898 (tm-30) cc_final: 0.8516 (tm-30) REVERT: D 584 GLU cc_start: 0.8552 (mt-10) cc_final: 0.8284 (mt-10) REVERT: D 626 MET cc_start: 0.8022 (tpp) cc_final: 0.7615 (tpp) REVERT: D 630 GLU cc_start: 0.8562 (mm-30) cc_final: 0.7715 (tp30) REVERT: M 83 GLU cc_start: 0.7975 (tm-30) cc_final: 0.7708 (pp20) REVERT: E 260 LEU cc_start: 0.8906 (OUTLIER) cc_final: 0.8678 (mm) REVERT: F 574 LYS cc_start: 0.8946 (mptt) cc_final: 0.8553 (tptt) REVERT: F 584 GLU cc_start: 0.8458 (mt-10) cc_final: 0.8003 (mt-10) REVERT: N 79 GLU cc_start: 0.8605 (mp0) cc_final: 0.8335 (mp0) REVERT: N 83 GLU cc_start: 0.8121 (pp20) cc_final: 0.7622 (pp20) outliers start: 47 outliers final: 42 residues processed: 214 average time/residue: 0.1330 time to fit residues: 45.3735 Evaluate side-chains 213 residues out of total 2106 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 169 time to evaluate : 0.703 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 95 MET Chi-restraints excluded: chain A residue 119 CYS Chi-restraints excluded: chain A residue 120 VAL Chi-restraints excluded: chain A residue 197 ASN Chi-restraints excluded: chain A residue 234 ASN Chi-restraints excluded: chain A residue 274 SER Chi-restraints excluded: chain A residue 289 ASN Chi-restraints excluded: chain A residue 326 ILE Chi-restraints excluded: chain A residue 373 THR Chi-restraints excluded: chain B residue 536 THR Chi-restraints excluded: chain B residue 584 GLU Chi-restraints excluded: chain B residue 598 CYS Chi-restraints excluded: chain B residue 641 ILE Chi-restraints excluded: chain H residue 31 ASP Chi-restraints excluded: chain H residue 105 THR Chi-restraints excluded: chain C residue 100 MET Chi-restraints excluded: chain C residue 119 CYS Chi-restraints excluded: chain C residue 120 VAL Chi-restraints excluded: chain C residue 197 ASN Chi-restraints excluded: chain C residue 202 THR Chi-restraints excluded: chain C residue 234 ASN Chi-restraints excluded: chain C residue 244 THR Chi-restraints excluded: chain C residue 289 ASN Chi-restraints excluded: chain C residue 373 THR Chi-restraints excluded: chain D residue 534 SER Chi-restraints excluded: chain D residue 644 SER Chi-restraints excluded: chain I residue 21 THR Chi-restraints excluded: chain I residue 105 THR Chi-restraints excluded: chain M residue 104 LEU Chi-restraints excluded: chain E residue 95 MET Chi-restraints excluded: chain E residue 115 SER Chi-restraints excluded: chain E residue 234 ASN Chi-restraints excluded: chain E residue 260 LEU Chi-restraints excluded: chain E residue 289 ASN Chi-restraints excluded: chain E residue 326 ILE Chi-restraints excluded: chain E residue 345 VAL Chi-restraints excluded: chain E residue 373 THR Chi-restraints excluded: chain F residue 530 MET Chi-restraints excluded: chain F residue 587 LEU Chi-restraints excluded: chain F residue 593 LEU Chi-restraints excluded: chain F residue 606 THR Chi-restraints excluded: chain F residue 642 ILE Chi-restraints excluded: chain J residue 20 LEU Chi-restraints excluded: chain J residue 105 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 231 random chunks: chunk 176 optimal weight: 20.0000 chunk 230 optimal weight: 4.9990 chunk 107 optimal weight: 4.9990 chunk 44 optimal weight: 3.9990 chunk 228 optimal weight: 5.9990 chunk 60 optimal weight: 6.9990 chunk 124 optimal weight: 10.0000 chunk 18 optimal weight: 0.6980 chunk 67 optimal weight: 20.0000 chunk 111 optimal weight: 8.9990 chunk 218 optimal weight: 6.9990 overall best weight: 4.1388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... I 5 GLN F 656 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3767 r_free = 0.3767 target = 0.098734 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3380 r_free = 0.3380 target = 0.077140 restraints weight = 64752.151| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3432 r_free = 0.3432 target = 0.079826 restraints weight = 36208.486| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3463 r_free = 0.3463 target = 0.081485 restraints weight = 26246.767| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 46)----------------| | r_work = 0.3482 r_free = 0.3482 target = 0.082506 restraints weight = 21836.347| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3493 r_free = 0.3493 target = 0.083114 restraints weight = 19557.676| |-----------------------------------------------------------------------------| r_work (final): 0.3456 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8027 moved from start: 0.5329 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.060 21432 Z= 0.206 Angle : 0.774 10.877 29421 Z= 0.361 Chirality : 0.047 0.359 3723 Planarity : 0.004 0.054 3429 Dihedral : 5.661 38.204 2552 Min Nonbonded Distance : 2.297 Molprobity Statistics. All-atom Clashscore : 10.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.53 % Favored : 96.47 % Rotamer: Outliers : 2.71 % Allowed : 13.82 % Favored : 83.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.07 (0.17), residues: 2325 helix: 0.64 (0.28), residues: 372 sheet: 0.26 (0.20), residues: 663 loop : -0.15 (0.18), residues: 1290 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG I 99 TYR 0.035 0.002 TYR B 643 PHE 0.012 0.002 PHE C 233 TRP 0.025 0.002 TRP E 69 HIS 0.007 0.001 HIS H 52 Details of bonding type rmsd/Z covalent geometry : bond 0.00474 / 0.21 (21234) covalent geometry : angle 0.73083 / 0.35 (28866) SS BOND : bond 0.00620 / 0.38 ( 39) SS BOND : angle 1.51583 / 1.10 ( 78) hydrogen bonds : bond 0.04137 / 2.80 ( 702) hydrogen bonds : angle 5.26912 / 3.73 ( 1890) link_ALPHA1-2 : bond 0.00363 / 0.22 ( 12) link_ALPHA1-2 : angle 2.52725 / 1.58 ( 36) link_ALPHA1-3 : bond 0.00650 / 0.40 ( 15) link_ALPHA1-3 : angle 1.87823 / 1.23 ( 45) link_ALPHA1-6 : bond 0.00378 / 0.25 ( 21) link_ALPHA1-6 : angle 1.75055 / 1.19 ( 63) link_BETA1-4 : bond 0.00606 / 0.41 ( 60) link_BETA1-4 : angle 1.95288 / 1.43 ( 180) link_NAG-ASN : bond 0.00508 / 0.34 ( 51) link_NAG-ASN : angle 2.20366 / 1.54 ( 153) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2914.28 seconds wall clock time: 51 minutes 39.26 seconds (3099.26 seconds total)