Starting phenix.real_space_refine on Sun Sep 13 03:49:28 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/6p65_20260/09_2026/6p65_20260.cif Found real_map, /net/cci-nas-00/data/ceres_data/6p65_20260/09_2026/6p65_20260.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.94 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/6p65_20260/09_2026/6p65_20260.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6p65_20260/09_2026/6p65_20260.map" model { file = "/net/cci-nas-00/data/ceres_data/6p65_20260/09_2026/6p65_20260.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6p65_20260/09_2026/6p65_20260.cif" restraint_files = "/net/cci-nas-00/data/ceres_data/6p65_20260/09_2026/6p65_20260.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/6p65_20260/09_2026/6p65_20260.cif" } resolution = 3.94 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.010 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 129 5.16 5 C 12705 2.51 5 N 3291 2.21 5 O 4194 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 78 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2.1-6174/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 20319 Number of models: 1 Model: "" Number of chains: 57 Chain: "A" Number of atoms: 4405 Number of conformers: 1 Conformer: "" Number of residues, atoms: 557, 4405 Classifications: {'peptide': 557} Link IDs: {'PTRANS': 25, 'TRANS': 531} Chain breaks: 6 Chain: "H" Number of atoms: 943 Number of conformers: 1 Conformer: "" Number of residues, atoms: 126, 943 Classifications: {'peptide': 126} Link IDs: {'PTRANS': 3, 'TRANS': 122} Chain: "L" Number of atoms: 820 Number of conformers: 1 Conformer: "" Number of residues, atoms: 110, 820 Classifications: {'peptide': 110} Link IDs: {'PCIS': 1, 'PTRANS': 4, 'TRANS': 104} Chain: "B" Number of atoms: 4405 Number of conformers: 1 Conformer: "" Number of residues, atoms: 557, 4405 Classifications: {'peptide': 557} Link IDs: {'PTRANS': 25, 'TRANS': 531} Chain breaks: 6 Chain: "C" Number of atoms: 943 Number of conformers: 1 Conformer: "" Number of residues, atoms: 126, 943 Classifications: {'peptide': 126} Link IDs: {'PTRANS': 3, 'TRANS': 122} Chain: "D" Number of atoms: 820 Number of conformers: 1 Conformer: "" Number of residues, atoms: 110, 820 Classifications: {'peptide': 110} Link IDs: {'PCIS': 1, 'PTRANS': 4, 'TRANS': 104} Chain: "E" Number of atoms: 4405 Number of conformers: 1 Conformer: "" Number of residues, atoms: 557, 4405 Classifications: {'peptide': 557} Link IDs: {'PTRANS': 25, 'TRANS': 531} Chain breaks: 6 Chain: "F" Number of atoms: 943 Number of conformers: 1 Conformer: "" Number of residues, atoms: 126, 943 Classifications: {'peptide': 126} Link IDs: {'PTRANS': 3, 'TRANS': 122} Chain: "G" Number of atoms: 820 Number of conformers: 1 Conformer: "" Number of residues, atoms: 110, 820 Classifications: {'peptide': 110} Link IDs: {'PCIS': 1, 'PTRANS': 4, 'TRANS': 104} Chain: "I" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen chiralities: 5 Chain: "J" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "K" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "M" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen 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: 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: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen chiralities: 5 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: 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: "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: 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: "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: 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: "X" Number of atoms: 38 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 38 Unusual residues: {'FUC': 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: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen chiralities: 5 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: 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: 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: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen chiralities: 5 Chain: "g" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "h" 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: "i" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "j" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "k" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "l" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "m" Number of atoms: 38 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 38 Unusual residues: {'FUC': 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: "n" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen chiralities: 5 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: 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: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen chiralities: 5 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: 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: 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: "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: "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: 38 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 38 Unusual residues: {'FUC': 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: "A" Number of atoms: 98 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 98 Unusual residues: {'NAG': 7} Classifications: {'undetermined': 7} Link IDs: {None: 6} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen chiralities: 7 Chain: "B" Number of atoms: 98 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 98 Unusual residues: {'NAG': 7} Classifications: {'undetermined': 7} Link IDs: {None: 6} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen chiralities: 7 Chain: "E" Number of atoms: 98 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 98 Unusual residues: {'NAG': 7} Classifications: {'undetermined': 7} Link IDs: {None: 6} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen chiralities: 7 Time building chain proxies: 5.00, per 1000 atoms: 0.25 Number of scatterers: 20319 At special positions: 0 Unit cell: (132.25, 136.85, 148.35, 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 129 16.00 O 4194 8.00 N 3291 7.00 C 12705 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=39, symmetry=0 Simple disulfide: pdb=" SG CYS A 54 " - pdb=" SG CYS A 74 " distance=2.03 Simple disulfide: pdb=" SG CYS A 119 " - pdb=" SG CYS A 205 " distance=2.03 Simple disulfide: pdb=" SG CYS A 126 " - pdb=" SG CYS A 196 " distance=2.05 Simple disulfide: pdb=" SG CYS A 131 " - pdb=" SG CYS A 157 " distance=2.03 Simple disulfide: pdb=" SG CYS A 201 " - pdb=" SG CYS A 433 " distance=2.13 Simple disulfide: pdb=" SG CYS A 218 " - pdb=" SG CYS A 247 " distance=2.03 Simple disulfide: pdb=" SG CYS A 228 " - pdb=" SG CYS A 239 " distance=2.03 Simple disulfide: pdb=" SG CYS A 296 " - pdb=" SG CYS A 331 " distance=2.03 Simple disulfide: pdb=" SG CYS A 378 " - pdb=" SG CYS A 445 " distance=2.03 Simple disulfide: pdb=" SG CYS A 385 " - pdb=" SG CYS A 418 " distance=2.03 Simple disulfide: pdb=" SG CYS A 598 " - pdb=" SG CYS A 604 " distance=2.04 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 92 " distance=2.03 Simple disulfide: pdb=" SG CYS L 23 " - pdb=" SG CYS L 88 " distance=2.06 Simple disulfide: pdb=" SG CYS B 54 " - pdb=" SG CYS B 74 " distance=2.03 Simple disulfide: pdb=" SG CYS B 119 " - pdb=" SG CYS B 205 " distance=2.03 Simple disulfide: pdb=" SG CYS B 126 " - pdb=" SG CYS B 196 " distance=2.05 Simple disulfide: pdb=" SG CYS B 131 " - pdb=" SG CYS B 157 " distance=2.03 Simple disulfide: pdb=" SG CYS B 201 " - pdb=" SG CYS B 433 " distance=2.13 Simple disulfide: pdb=" SG CYS B 218 " - pdb=" SG CYS B 247 " distance=2.03 Simple disulfide: pdb=" SG CYS B 228 " - pdb=" SG CYS B 239 " distance=2.03 Simple disulfide: pdb=" SG CYS B 296 " - pdb=" SG CYS B 331 " distance=2.03 Simple disulfide: pdb=" SG CYS B 378 " - pdb=" SG CYS B 445 " distance=2.03 Simple disulfide: pdb=" SG CYS B 385 " - pdb=" SG CYS B 418 " distance=2.02 Simple disulfide: pdb=" SG CYS B 598 " - pdb=" SG CYS B 604 " distance=2.04 Simple disulfide: pdb=" SG CYS C 22 " - pdb=" SG CYS C 92 " distance=2.03 Simple disulfide: pdb=" SG CYS D 23 " - pdb=" SG CYS D 88 " distance=2.06 Simple disulfide: pdb=" SG CYS E 54 " - pdb=" SG CYS E 74 " distance=2.03 Simple disulfide: pdb=" SG CYS E 119 " - pdb=" SG CYS E 205 " distance=2.03 Simple disulfide: pdb=" SG CYS E 126 " - pdb=" SG CYS E 196 " distance=2.05 Simple disulfide: pdb=" SG CYS E 131 " - pdb=" SG CYS E 157 " distance=2.03 Simple disulfide: pdb=" SG CYS E 201 " - pdb=" SG CYS E 433 " distance=2.13 Simple disulfide: pdb=" SG CYS E 218 " - pdb=" SG CYS E 247 " distance=2.03 Simple disulfide: pdb=" SG CYS E 228 " - pdb=" SG CYS E 239 " distance=2.03 Simple disulfide: pdb=" SG CYS E 296 " - pdb=" SG CYS E 331 " distance=2.03 Simple disulfide: pdb=" SG CYS E 378 " - pdb=" SG CYS E 445 " distance=2.03 Simple disulfide: pdb=" SG CYS E 385 " - pdb=" SG CYS E 418 " distance=2.02 Simple disulfide: pdb=" SG CYS E 598 " - pdb=" SG CYS E 604 " distance=2.04 Simple disulfide: pdb=" SG CYS F 22 " - pdb=" SG CYS F 92 " distance=2.03 Simple disulfide: pdb=" SG CYS G 23 " - pdb=" SG CYS G 88 " distance=2.06 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 ALPHA1-3 " BMA I 3 " - " MAN I 4 " " BMA Q 3 " - " MAN Q 4 " " BMA Y 3 " - " MAN Y 4 " " BMA f 3 " - " MAN f 4 " " BMA n 3 " - " MAN n 4 " " BMA u 3 " - " MAN u 4 " ALPHA1-6 " BMA I 3 " - " MAN I 5 " " BMA Q 3 " - " MAN Q 5 " " BMA Y 3 " - " MAN Y 5 " " BMA f 3 " - " MAN f 5 " " BMA n 3 " - " MAN n 5 " " BMA u 3 " - " MAN u 5 " BETA1-4 " NAG 0 1 " - " NAG 0 2 " " NAG 1 1 " - " NAG 1 2 " " NAG I 1 " - " NAG I 2 " " NAG I 2 " - " BMA I 3 " " NAG J 1 " - " NAG J 2 " " NAG K 1 " - " NAG K 2 " " NAG M 1 " - " NAG M 2 " " NAG N 1 " - " NAG N 2 " " NAG O 1 " - " NAG O 2 " " NAG P 1 " - " NAG P 2 " " NAG Q 1 " - " NAG Q 2 " " NAG Q 2 " - " BMA Q 3 " " NAG R 1 " - " NAG R 2 " " NAG S 1 " - " NAG S 2 " " NAG S 2 " - " BMA S 3 " " NAG T 1 " - " NAG T 2 " " NAG U 1 " - " NAG U 2 " " NAG V 1 " - " NAG V 2 " " NAG W 1 " - " NAG W 2 " " NAG X 1 " - " NAG X 2 " " NAG Y 1 " - " NAG Y 2 " " NAG Y 2 " - " BMA Y 3 " " NAG Z 1 " - " NAG Z 2 " " NAG a 1 " - " NAG a 2 " " 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 f 2 " - " BMA f 3 " " NAG g 1 " - " NAG g 2 " " NAG h 1 " - " NAG h 2 " " NAG h 2 " - " BMA h 3 " " NAG i 1 " - " NAG i 2 " " NAG j 1 " - " NAG j 2 " " NAG k 1 " - " NAG k 2 " " NAG l 1 " - " NAG l 2 " " NAG m 1 " - " NAG m 2 " " NAG n 1 " - " NAG n 2 " " NAG n 2 " - " BMA n 3 " " NAG o 1 " - " NAG o 2 " " NAG 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 y 1 " - " NAG y 2 " " NAG z 1 " - " NAG z 2 " BETA1-6 " NAG 1 1 " - " FUC 1 3 " ~> Even though FUC is an alpha isomer, a beta linkage is required... " NAG X 1 " - " FUC X 3 " " NAG m 1 " - " FUC m 3 " NAG-ASN " NAG 0 1 " - " ASN E 392 " " NAG 1 1 " - " ASN E 625 " " NAG A 710 " - " ASN A 187 " " NAG A 729 " - " ASN A 301 " " NAG A 738 " - " ASN A 398 " " NAG A 739 " - " ASN A 442 " " NAG A 740 " - " ASN A 448 " " NAG A 741 " - " ASN A 611 " " NAG A 745 " - " ASN A 637 " " NAG B 710 " - " ASN B 187 " " NAG B 729 " - " ASN B 301 " " NAG B 738 " - " ASN B 398 " " NAG B 739 " - " ASN B 442 " " NAG B 740 " - " ASN B 448 " " NAG B 741 " - " ASN B 611 " " NAG B 745 " - " ASN B 637 " " NAG E 710 " - " ASN E 187 " " NAG E 729 " - " ASN E 301 " " NAG E 738 " - " ASN E 398 " " NAG E 739 " - " ASN E 442 " " NAG E 740 " - " ASN E 448 " " NAG E 741 " - " ASN E 611 " " NAG E 745 " - " ASN E 637 " " NAG I 1 " - " ASN A 88 " " NAG J 1 " - " ASN A 156 " " NAG K 1 " - " ASN A 160 " " NAG M 1 " - " ASN A 197 " " NAG N 1 " - " ASN A 230 " " NAG O 1 " - " ASN A 234 " " NAG P 1 " - " ASN A 241 " " NAG Q 1 " - " ASN A 262 " " NAG R 1 " - " ASN A 276 " " NAG S 1 " - " ASN A 289 " " NAG T 1 " - " ASN A 332 " " NAG U 1 " - " ASN A 359 " " NAG V 1 " - " ASN A 386 " " NAG W 1 " - " ASN A 392 " " NAG X 1 " - " ASN A 625 " " NAG Y 1 " - " ASN B 88 " " NAG Z 1 " - " ASN B 156 " " NAG a 1 " - " ASN B 160 " " NAG b 1 " - " ASN B 197 " " NAG c 1 " - " ASN B 230 " " NAG d 1 " - " ASN B 234 " " NAG e 1 " - " ASN B 241 " " NAG f 1 " - " ASN B 262 " " NAG g 1 " - " ASN B 276 " " NAG h 1 " - " ASN B 289 " " NAG i 1 " - " ASN B 332 " " NAG j 1 " - " ASN B 359 " " NAG k 1 " - " ASN B 386 " " NAG l 1 " - " ASN B 392 " " NAG m 1 " - " ASN B 625 " " NAG n 1 " - " ASN E 88 " " NAG o 1 " - " ASN E 156 " " NAG p 1 " - " ASN E 160 " " NAG q 1 " - " ASN E 197 " " NAG r 1 " - " ASN E 230 " " NAG s 1 " - " ASN E 234 " " NAG t 1 " - " ASN E 241 " " NAG u 1 " - " ASN E 262 " " NAG v 1 " - " ASN E 276 " " NAG w 1 " - " ASN E 289 " " NAG x 1 " - " ASN E 332 " " NAG y 1 " - " ASN E 359 " " NAG z 1 " - " ASN E 386 " Time building additional restraints: 2.63 Conformation dependent library (CDL) restraints added in 902.7 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: 4374 Finding SS restraints... Secondary structure from input PDB file: 51 helices and 39 sheets defined 20.8% alpha, 35.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.72 Creating SS restraints... Processing helix chain 'A' and resid 98 through 117 removed outlier: 3.655A pdb=" N GLU A 102 " --> pdb=" O ASN A 98 " (cutoff:3.500A) removed outlier: 3.777A pdb=" N LEU A 116 " --> pdb=" O TRP A 112 " (cutoff:3.500A) Processing helix chain 'A' and resid 122 through 126 Processing helix chain 'A' and resid 335 through 353 Processing helix chain 'A' and resid 368 through 373 Processing helix chain 'A' and resid 427 through 429 No H-bonds generated for 'chain 'A' and resid 427 through 429' Processing helix chain 'A' and resid 476 through 484 removed outlier: 4.728A pdb=" N GLU A 482 " --> pdb=" O ASN A 478 " (cutoff:3.500A) Processing helix chain 'A' and resid 529 through 541 removed outlier: 3.867A pdb=" N THR A 538 " --> pdb=" O SER A 534 " (cutoff:3.500A) removed outlier: 4.601A pdb=" N VAL A 539 " --> pdb=" O ILE A 535 " (cutoff:3.500A) Processing helix chain 'A' and resid 542 through 548 Processing helix chain 'A' and resid 568 through 568 No H-bonds generated for 'chain 'A' and resid 568 through 568' Processing helix chain 'A' and resid 569 through 596 Processing helix chain 'A' and resid 618 through 624 Processing helix chain 'A' and resid 627 through 635 Processing helix chain 'A' and resid 638 through 649 Processing helix chain 'A' and resid 649 through 660 removed outlier: 4.575A pdb=" N GLN A 655 " --> pdb=" O ASN A 651 " (cutoff:3.500A) removed outlier: 4.571A pdb=" N LYS A 658 " --> pdb=" O GLU A 654 " (cutoff:3.500A) Processing helix chain 'A' and resid 661 through 663 No H-bonds generated for 'chain 'A' and resid 661 through 663' Processing helix chain 'H' and resid 59 through 64 Processing helix chain 'H' and resid 83 through 87 Processing helix chain 'B' and resid 98 through 117 removed outlier: 3.654A pdb=" N GLU B 102 " --> pdb=" O ASN B 98 " (cutoff:3.500A) removed outlier: 3.777A pdb=" N LEU B 116 " --> pdb=" O TRP B 112 " (cutoff:3.500A) Processing helix chain 'B' and resid 122 through 126 Processing helix chain 'B' and resid 335 through 353 Processing helix chain 'B' and resid 368 through 373 Processing helix chain 'B' and resid 427 through 429 No H-bonds generated for 'chain 'B' and resid 427 through 429' Processing helix chain 'B' and resid 476 through 484 removed outlier: 4.728A pdb=" N GLU B 482 " --> pdb=" O ASN B 478 " (cutoff:3.500A) Processing helix chain 'B' and resid 529 through 541 removed outlier: 3.868A pdb=" N THR B 538 " --> pdb=" O SER B 534 " (cutoff:3.500A) removed outlier: 4.600A pdb=" N VAL B 539 " --> pdb=" O ILE B 535 " (cutoff:3.500A) Processing helix chain 'B' and resid 542 through 548 Processing helix chain 'B' and resid 568 through 568 No H-bonds generated for 'chain 'B' and resid 568 through 568' Processing helix chain 'B' and resid 569 through 596 Processing helix chain 'B' and resid 618 through 624 Processing helix chain 'B' and resid 627 through 635 Processing helix chain 'B' and resid 638 through 649 Processing helix chain 'B' and resid 649 through 660 removed outlier: 4.575A pdb=" N GLN B 655 " --> pdb=" O ASN B 651 " (cutoff:3.500A) removed outlier: 4.571A pdb=" N LYS B 658 " --> pdb=" O GLU B 654 " (cutoff:3.500A) Processing helix chain 'B' and resid 661 through 663 No H-bonds generated for 'chain 'B' and resid 661 through 663' Processing helix chain 'C' and resid 59 through 64 Processing helix chain 'C' and resid 83 through 87 Processing helix chain 'E' and resid 98 through 117 removed outlier: 3.654A pdb=" N GLU E 102 " --> pdb=" O ASN E 98 " (cutoff:3.500A) removed outlier: 3.778A pdb=" N LEU E 116 " --> pdb=" O TRP E 112 " (cutoff:3.500A) Processing helix chain 'E' and resid 122 through 126 Processing helix chain 'E' and resid 335 through 353 Processing helix chain 'E' and resid 368 through 373 Processing helix chain 'E' and resid 427 through 429 No H-bonds generated for 'chain 'E' and resid 427 through 429' Processing helix chain 'E' and resid 476 through 484 removed outlier: 4.728A pdb=" N GLU E 482 " --> pdb=" O ASN E 478 " (cutoff:3.500A) Processing helix chain 'E' and resid 529 through 541 removed outlier: 3.867A pdb=" N THR E 538 " --> pdb=" O SER E 534 " (cutoff:3.500A) removed outlier: 4.601A pdb=" N VAL E 539 " --> pdb=" O ILE E 535 " (cutoff:3.500A) Processing helix chain 'E' and resid 542 through 548 Processing helix chain 'E' and resid 568 through 568 No H-bonds generated for 'chain 'E' and resid 568 through 568' Processing helix chain 'E' and resid 569 through 596 Processing helix chain 'E' and resid 618 through 624 Processing helix chain 'E' and resid 627 through 635 Processing helix chain 'E' and resid 638 through 649 Processing helix chain 'E' and resid 649 through 660 removed outlier: 4.575A pdb=" N GLN E 655 " --> pdb=" O ASN E 651 " (cutoff:3.500A) removed outlier: 4.571A pdb=" N LYS E 658 " --> pdb=" O GLU E 654 " (cutoff:3.500A) Processing helix chain 'E' and resid 661 through 663 No H-bonds generated for 'chain 'E' and resid 661 through 663' Processing helix chain 'F' and resid 59 through 64 Processing helix chain 'F' and resid 83 through 87 Processing sheet with id=AA1, first strand: chain 'A' and resid 494 through 499 removed outlier: 5.151A pdb=" N VAL A 608 " --> pdb=" O VAL A 36 " (cutoff:3.500A) removed outlier: 7.605A pdb=" N VAL A 38 " --> pdb=" O THR A 606 " (cutoff:3.500A) removed outlier: 7.243A pdb=" N THR A 606 " --> pdb=" O VAL A 38 " (cutoff:3.500A) removed outlier: 7.897A pdb=" N TYR A 40 " --> pdb=" O CYS A 604 " (cutoff:3.500A) removed outlier: 8.127A pdb=" N CYS A 604 " --> pdb=" O TYR A 40 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 45 through 47 removed outlier: 4.838A pdb=" N VAL A 242 " --> pdb=" O LEU A 86 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 53 through 55 Processing sheet with id=AA4, first strand: chain 'A' and resid 91 through 94 Processing sheet with id=AA5, first strand: chain 'A' and resid 169 through 177 Processing sheet with id=AA6, first strand: chain 'A' and resid 202 through 203 removed outlier: 6.572A pdb=" N THR A 202 " --> pdb=" O TYR A 435 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 259 through 261 removed outlier: 6.651A pdb=" N LEU A 260 " --> pdb=" O THR A 450 " (cutoff:3.500A) removed outlier: 10.303A pdb=" N THR A 444 " --> pdb=" O ILE A 294 " (cutoff:3.500A) removed outlier: 11.608A pdb=" N ILE A 294 " --> pdb=" O THR A 444 " (cutoff:3.500A) removed outlier: 9.863A pdb=" N LYS A 446 " --> pdb=" O VAL A 292 " (cutoff:3.500A) removed outlier: 10.636A pdb=" N VAL A 292 " --> pdb=" O LYS A 446 " (cutoff:3.500A) removed outlier: 9.192A pdb=" N ASN A 448 " --> pdb=" O GLU A 290 " (cutoff:3.500A) removed outlier: 9.790A pdb=" N GLU A 290 " --> pdb=" O ASN A 448 " (cutoff:3.500A) removed outlier: 6.896A pdb=" N THR A 450 " --> pdb=" O LEU A 288 " (cutoff:3.500A) removed outlier: 6.438A pdb=" N GLU A 293 " --> pdb=" O SER A 334 " (cutoff:3.500A) removed outlier: 4.124A pdb=" N ALA A 329 " --> pdb=" O CYS A 418 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 271 through 273 removed outlier: 6.896A pdb=" N THR A 450 " --> pdb=" O LEU A 288 " (cutoff:3.500A) removed outlier: 9.790A pdb=" N GLU A 290 " --> pdb=" O ASN A 448 " (cutoff:3.500A) removed outlier: 9.192A pdb=" N ASN A 448 " --> pdb=" O GLU A 290 " (cutoff:3.500A) removed outlier: 10.636A pdb=" N VAL A 292 " --> pdb=" O LYS A 446 " (cutoff:3.500A) removed outlier: 9.863A pdb=" N LYS A 446 " --> pdb=" O VAL A 292 " (cutoff:3.500A) removed outlier: 11.608A pdb=" N ILE A 294 " --> pdb=" O THR A 444 " (cutoff:3.500A) removed outlier: 10.303A pdb=" N THR A 444 " --> pdb=" O ILE A 294 " (cutoff:3.500A) removed outlier: 6.352A pdb=" N ILE A 357 " --> pdb=" O GLU A 466 " (cutoff:3.500A) removed outlier: 7.472A pdb=" N PHE A 468 " --> pdb=" O ILE A 357 " (cutoff:3.500A) removed outlier: 6.526A pdb=" N ASN A 359 " --> pdb=" O PHE A 468 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 303 through 312 removed outlier: 6.420A pdb=" N GLN A 315 " --> pdb=" O ILE A 309 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'H' and resid 3 through 7 Processing sheet with id=AB2, first strand: chain 'H' and resid 56 through 58 removed outlier: 6.616A pdb=" N TRP H 36 " --> pdb=" O ILE H 48 " (cutoff:3.500A) removed outlier: 4.332A pdb=" N CYS H 50 " --> pdb=" O MET H 35 " (cutoff:3.500A) removed outlier: 6.037A pdb=" N MET H 35 " --> pdb=" O CYS H 50 " (cutoff:3.500A) removed outlier: 7.553A pdb=" N ALA H 96 " --> pdb=" O PHE H 100J" (cutoff:3.500A) removed outlier: 5.634A pdb=" N PHE H 100J" --> pdb=" O ALA H 96 " (cutoff:3.500A) removed outlier: 8.107A pdb=" N THR H 98 " --> pdb=" O LYS H 100H" (cutoff:3.500A) removed outlier: 7.121A pdb=" N LYS H 100H" --> pdb=" O THR H 98 " (cutoff:3.500A) removed outlier: 5.714A pdb=" N GLY L 91 " --> pdb=" O LEU H 100G" (cutoff:3.500A) removed outlier: 9.227A pdb=" N HIS H 100I" --> pdb=" O LEU L 89 " (cutoff:3.500A) removed outlier: 11.166A pdb=" N LEU L 89 " --> pdb=" O HIS H 100I" (cutoff:3.500A) removed outlier: 13.391A pdb=" N ASN H 101 " --> pdb=" O TYR L 87 " (cutoff:3.500A) removed outlier: 15.550A pdb=" N TYR L 87 " --> pdb=" O ASN H 101 " (cutoff:3.500A) removed outlier: 15.427A pdb=" N TRP H 103 " --> pdb=" O THR L 85 " (cutoff:3.500A) removed outlier: 17.159A pdb=" N THR L 85 " --> pdb=" O TRP H 103 " (cutoff:3.500A) removed outlier: 6.544A pdb=" N LEU L 33 " --> pdb=" O TYR L 49 " (cutoff:3.500A) removed outlier: 5.053A pdb=" N TYR L 49 " --> pdb=" O LEU L 33 " (cutoff:3.500A) removed outlier: 6.409A pdb=" N TRP L 35 " --> pdb=" O LEU L 47 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'L' and resid 10 through 14 Processing sheet with id=AB4, first strand: chain 'L' and resid 4 through 7 Processing sheet with id=AB5, first strand: chain 'B' and resid 494 through 499 removed outlier: 5.151A pdb=" N VAL B 608 " --> pdb=" O VAL B 36 " (cutoff:3.500A) removed outlier: 7.605A pdb=" N VAL B 38 " --> pdb=" O THR B 606 " (cutoff:3.500A) removed outlier: 7.244A pdb=" N THR B 606 " --> pdb=" O VAL B 38 " (cutoff:3.500A) removed outlier: 7.897A pdb=" N TYR B 40 " --> pdb=" O CYS B 604 " (cutoff:3.500A) removed outlier: 8.127A pdb=" N CYS B 604 " --> pdb=" O TYR B 40 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'B' and resid 45 through 47 removed outlier: 4.838A pdb=" N VAL B 242 " --> pdb=" O LEU B 86 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'B' and resid 53 through 55 Processing sheet with id=AB8, first strand: chain 'B' and resid 91 through 94 Processing sheet with id=AB9, first strand: chain 'B' and resid 169 through 177 Processing sheet with id=AC1, first strand: chain 'B' and resid 202 through 203 removed outlier: 6.572A pdb=" N THR B 202 " --> pdb=" O TYR B 435 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'B' and resid 259 through 261 removed outlier: 6.651A pdb=" N LEU B 260 " --> pdb=" O THR B 450 " (cutoff:3.500A) removed outlier: 10.302A pdb=" N THR B 444 " --> pdb=" O ILE B 294 " (cutoff:3.500A) removed outlier: 11.609A pdb=" N ILE B 294 " --> pdb=" O THR B 444 " (cutoff:3.500A) removed outlier: 9.863A pdb=" N LYS B 446 " --> pdb=" O VAL B 292 " (cutoff:3.500A) removed outlier: 10.635A pdb=" N VAL B 292 " --> pdb=" O LYS B 446 " (cutoff:3.500A) removed outlier: 9.192A pdb=" N ASN B 448 " --> pdb=" O GLU B 290 " (cutoff:3.500A) removed outlier: 9.790A pdb=" N GLU B 290 " --> pdb=" O ASN B 448 " (cutoff:3.500A) removed outlier: 6.895A pdb=" N THR B 450 " --> pdb=" O LEU B 288 " (cutoff:3.500A) removed outlier: 6.438A pdb=" N GLU B 293 " --> pdb=" O SER B 334 " (cutoff:3.500A) removed outlier: 4.125A pdb=" N ALA B 329 " --> pdb=" O CYS B 418 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'B' and resid 271 through 273 removed outlier: 6.895A pdb=" N THR B 450 " --> pdb=" O LEU B 288 " (cutoff:3.500A) removed outlier: 9.790A pdb=" N GLU B 290 " --> pdb=" O ASN B 448 " (cutoff:3.500A) removed outlier: 9.192A pdb=" N ASN B 448 " --> pdb=" O GLU B 290 " (cutoff:3.500A) removed outlier: 10.635A pdb=" N VAL B 292 " --> pdb=" O LYS B 446 " (cutoff:3.500A) removed outlier: 9.863A pdb=" N LYS B 446 " --> pdb=" O VAL B 292 " (cutoff:3.500A) removed outlier: 11.609A pdb=" N ILE B 294 " --> pdb=" O THR B 444 " (cutoff:3.500A) removed outlier: 10.302A pdb=" N THR B 444 " --> pdb=" O ILE B 294 " (cutoff:3.500A) removed outlier: 6.352A pdb=" N ILE B 357 " --> pdb=" O GLU B 466 " (cutoff:3.500A) removed outlier: 7.472A pdb=" N PHE B 468 " --> pdb=" O ILE B 357 " (cutoff:3.500A) removed outlier: 6.526A pdb=" N ASN B 359 " --> pdb=" O PHE B 468 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'B' and resid 303 through 312 removed outlier: 6.420A pdb=" N GLN B 315 " --> pdb=" O ILE B 309 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'C' and resid 3 through 7 Processing sheet with id=AC6, first strand: chain 'C' and resid 56 through 58 removed outlier: 6.616A pdb=" N TRP C 36 " --> pdb=" O ILE C 48 " (cutoff:3.500A) removed outlier: 4.332A pdb=" N CYS C 50 " --> pdb=" O MET C 35 " (cutoff:3.500A) removed outlier: 6.037A pdb=" N MET C 35 " --> pdb=" O CYS C 50 " (cutoff:3.500A) removed outlier: 6.934A pdb=" N CYS C 92 " --> pdb=" O LEU C 102 " (cutoff:3.500A) removed outlier: 7.046A pdb=" N LEU C 102 " --> pdb=" O CYS C 92 " (cutoff:3.500A) removed outlier: 6.420A pdb=" N ARG C 94 " --> pdb=" O PHE C 100J" (cutoff:3.500A) removed outlier: 4.354A pdb=" N PHE C 100J" --> pdb=" O ARG C 94 " (cutoff:3.500A) removed outlier: 6.418A pdb=" N ALA C 96 " --> pdb=" O LYS C 100H" (cutoff:3.500A) removed outlier: 5.715A pdb=" N GLY D 91 " --> pdb=" O LEU C 100G" (cutoff:3.500A) removed outlier: 9.228A pdb=" N HIS C 100I" --> pdb=" O LEU D 89 " (cutoff:3.500A) removed outlier: 11.166A pdb=" N LEU D 89 " --> pdb=" O HIS C 100I" (cutoff:3.500A) removed outlier: 13.391A pdb=" N ASN C 101 " --> pdb=" O TYR D 87 " (cutoff:3.500A) removed outlier: 15.550A pdb=" N TYR D 87 " --> pdb=" O ASN C 101 " (cutoff:3.500A) removed outlier: 15.427A pdb=" N TRP C 103 " --> pdb=" O THR D 85 " (cutoff:3.500A) removed outlier: 17.159A pdb=" N THR D 85 " --> pdb=" O TRP C 103 " (cutoff:3.500A) removed outlier: 6.545A pdb=" N LEU D 33 " --> pdb=" O TYR D 49 " (cutoff:3.500A) removed outlier: 5.053A pdb=" N TYR D 49 " --> pdb=" O LEU D 33 " (cutoff:3.500A) removed outlier: 6.409A pdb=" N TRP D 35 " --> pdb=" O LEU D 47 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'D' and resid 10 through 14 Processing sheet with id=AC8, first strand: chain 'D' and resid 4 through 7 Processing sheet with id=AC9, first strand: chain 'E' and resid 494 through 499 removed outlier: 5.150A pdb=" N VAL E 608 " --> pdb=" O VAL E 36 " (cutoff:3.500A) removed outlier: 7.605A pdb=" N VAL E 38 " --> pdb=" O THR E 606 " (cutoff:3.500A) removed outlier: 7.244A pdb=" N THR E 606 " --> pdb=" O VAL E 38 " (cutoff:3.500A) removed outlier: 7.897A pdb=" N TYR E 40 " --> pdb=" O CYS E 604 " (cutoff:3.500A) removed outlier: 8.126A pdb=" N CYS E 604 " --> pdb=" O TYR E 40 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'E' and resid 45 through 47 removed outlier: 4.838A pdb=" N VAL E 242 " --> pdb=" O LEU E 86 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'E' and resid 53 through 55 Processing sheet with id=AD3, first strand: chain 'E' and resid 91 through 94 Processing sheet with id=AD4, first strand: chain 'E' and resid 169 through 177 Processing sheet with id=AD5, first strand: chain 'E' and resid 202 through 203 removed outlier: 6.571A pdb=" N THR E 202 " --> pdb=" O TYR E 435 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'E' and resid 259 through 261 removed outlier: 6.650A pdb=" N LEU E 260 " --> pdb=" O THR E 450 " (cutoff:3.500A) removed outlier: 10.303A pdb=" N THR E 444 " --> pdb=" O ILE E 294 " (cutoff:3.500A) removed outlier: 11.608A pdb=" N ILE E 294 " --> pdb=" O THR E 444 " (cutoff:3.500A) removed outlier: 9.863A pdb=" N LYS E 446 " --> pdb=" O VAL E 292 " (cutoff:3.500A) removed outlier: 10.635A pdb=" N VAL E 292 " --> pdb=" O LYS E 446 " (cutoff:3.500A) removed outlier: 9.192A pdb=" N ASN E 448 " --> pdb=" O GLU E 290 " (cutoff:3.500A) removed outlier: 9.790A pdb=" N GLU E 290 " --> pdb=" O ASN E 448 " (cutoff:3.500A) removed outlier: 6.895A pdb=" N THR E 450 " --> pdb=" O LEU E 288 " (cutoff:3.500A) removed outlier: 6.438A pdb=" N GLU E 293 " --> pdb=" O SER E 334 " (cutoff:3.500A) removed outlier: 4.123A pdb=" N ALA E 329 " --> pdb=" O CYS E 418 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'E' and resid 271 through 273 removed outlier: 6.895A pdb=" N THR E 450 " --> pdb=" O LEU E 288 " (cutoff:3.500A) removed outlier: 9.790A pdb=" N GLU E 290 " --> pdb=" O ASN E 448 " (cutoff:3.500A) removed outlier: 9.192A pdb=" N ASN E 448 " --> pdb=" O GLU E 290 " (cutoff:3.500A) removed outlier: 10.635A pdb=" N VAL E 292 " --> pdb=" O LYS E 446 " (cutoff:3.500A) removed outlier: 9.863A pdb=" N LYS E 446 " --> pdb=" O VAL E 292 " (cutoff:3.500A) removed outlier: 11.608A pdb=" N ILE E 294 " --> pdb=" O THR E 444 " (cutoff:3.500A) removed outlier: 10.303A pdb=" N THR E 444 " --> pdb=" O ILE E 294 " (cutoff:3.500A) removed outlier: 6.352A pdb=" N ILE E 357 " --> pdb=" O GLU E 466 " (cutoff:3.500A) removed outlier: 7.472A pdb=" N PHE E 468 " --> pdb=" O ILE E 357 " (cutoff:3.500A) removed outlier: 6.526A pdb=" N ASN E 359 " --> pdb=" O PHE E 468 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'E' and resid 303 through 312 removed outlier: 6.421A pdb=" N GLN E 315 " --> pdb=" O ILE E 309 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'F' and resid 3 through 7 Processing sheet with id=AE1, first strand: chain 'F' and resid 56 through 58 removed outlier: 6.615A pdb=" N TRP F 36 " --> pdb=" O ILE F 48 " (cutoff:3.500A) removed outlier: 4.332A pdb=" N CYS F 50 " --> pdb=" O MET F 35 " (cutoff:3.500A) removed outlier: 6.037A pdb=" N MET F 35 " --> pdb=" O CYS F 50 " (cutoff:3.500A) removed outlier: 6.934A pdb=" N CYS F 92 " --> pdb=" O LEU F 102 " (cutoff:3.500A) removed outlier: 7.046A pdb=" N LEU F 102 " --> pdb=" O CYS F 92 " (cutoff:3.500A) removed outlier: 6.420A pdb=" N ARG F 94 " --> pdb=" O PHE F 100J" (cutoff:3.500A) removed outlier: 4.354A pdb=" N PHE F 100J" --> pdb=" O ARG F 94 " (cutoff:3.500A) removed outlier: 6.418A pdb=" N ALA F 96 " --> pdb=" O LYS F 100H" (cutoff:3.500A) removed outlier: 5.715A pdb=" N GLY G 91 " --> pdb=" O LEU F 100G" (cutoff:3.500A) removed outlier: 9.227A pdb=" N HIS F 100I" --> pdb=" O LEU G 89 " (cutoff:3.500A) removed outlier: 11.165A pdb=" N LEU G 89 " --> pdb=" O HIS F 100I" (cutoff:3.500A) removed outlier: 13.391A pdb=" N ASN F 101 " --> pdb=" O TYR G 87 " (cutoff:3.500A) removed outlier: 15.550A pdb=" N TYR G 87 " --> pdb=" O ASN F 101 " (cutoff:3.500A) removed outlier: 15.427A pdb=" N TRP F 103 " --> pdb=" O THR G 85 " (cutoff:3.500A) removed outlier: 17.159A pdb=" N THR G 85 " --> pdb=" O TRP F 103 " (cutoff:3.500A) removed outlier: 6.545A pdb=" N LEU G 33 " --> pdb=" O TYR G 49 " (cutoff:3.500A) removed outlier: 5.053A pdb=" N TYR G 49 " --> pdb=" O LEU G 33 " (cutoff:3.500A) removed outlier: 6.409A pdb=" N TRP G 35 " --> pdb=" O LEU G 47 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'G' and resid 10 through 14 Processing sheet with id=AE3, first strand: chain 'G' and resid 4 through 7 791 hydrogen bonds defined for protein. 2112 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: 3.98 Time building geometry restraints manager: 3.21 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: 4117 1.32 - 1.44: 5694 1.44 - 1.57: 10692 1.57 - 1.70: 32 1.70 - 1.83: 168 Bond restraints: 20703 Sorted by residual: bond pdb=" CB PHE B 159 " pdb=" CG PHE B 159 " ideal model delta sigma weight residual 1.502 1.365 0.137 2.30e-02 1.89e+03 3.57e+01 bond pdb=" CB PHE E 159 " pdb=" CG PHE E 159 " ideal model delta sigma weight residual 1.502 1.365 0.137 2.30e-02 1.89e+03 3.53e+01 bond pdb=" CB PHE A 159 " pdb=" CG PHE A 159 " ideal model delta sigma weight residual 1.502 1.365 0.137 2.30e-02 1.89e+03 3.53e+01 bond pdb=" CB TYR D 49 " pdb=" CG TYR D 49 " ideal model delta sigma weight residual 1.512 1.397 0.115 2.20e-02 2.07e+03 2.75e+01 bond pdb=" CB TYR G 49 " pdb=" CG TYR G 49 " ideal model delta sigma weight residual 1.512 1.397 0.115 2.20e-02 2.07e+03 2.74e+01 ... (remaining 20698 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.08: 22437 2.08 - 4.16: 4485 4.16 - 6.23: 972 6.23 - 8.31: 164 8.31 - 10.39: 46 Bond angle restraints: 28104 Sorted by residual: angle pdb=" C LYS A 492 " pdb=" N PRO A 493 " pdb=" CA PRO A 493 " ideal model delta sigma weight residual 119.56 127.74 -8.18 1.02e+00 9.61e-01 6.43e+01 angle pdb=" C LYS E 492 " pdb=" N PRO E 493 " pdb=" CA PRO E 493 " ideal model delta sigma weight residual 119.56 127.71 -8.15 1.02e+00 9.61e-01 6.38e+01 angle pdb=" C LYS B 492 " pdb=" N PRO B 493 " pdb=" CA PRO B 493 " ideal model delta sigma weight residual 119.56 127.67 -8.11 1.02e+00 9.61e-01 6.33e+01 angle pdb=" CA PHE L 98 " pdb=" CB PHE L 98 " pdb=" CG PHE L 98 " ideal model delta sigma weight residual 113.80 121.74 -7.94 1.00e+00 1.00e+00 6.31e+01 angle pdb=" CA PHE G 98 " pdb=" CB PHE G 98 " pdb=" CG PHE G 98 " ideal model delta sigma weight residual 113.80 121.74 -7.94 1.00e+00 1.00e+00 6.30e+01 ... (remaining 28099 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.51: 10851 16.51 - 33.02: 309 33.02 - 49.52: 85 49.52 - 66.03: 47 66.03 - 82.54: 30 Dihedral angle restraints: 11322 sinusoidal: 4500 harmonic: 6822 Sorted by residual: dihedral pdb=" CB CYS B 119 " pdb=" SG CYS B 119 " pdb=" SG CYS B 205 " pdb=" CB CYS B 205 " ideal model delta sinusoidal sigma weight residual -86.00 -131.42 45.42 1 1.00e+01 1.00e-02 2.86e+01 dihedral pdb=" CB CYS A 119 " pdb=" SG CYS A 119 " pdb=" SG CYS A 205 " pdb=" CB CYS A 205 " ideal model delta sinusoidal sigma weight residual -86.00 -131.41 45.41 1 1.00e+01 1.00e-02 2.86e+01 dihedral pdb=" CB CYS E 119 " pdb=" SG CYS E 119 " pdb=" SG CYS E 205 " pdb=" CB CYS E 205 " ideal model delta sinusoidal sigma weight residual -86.00 -131.41 45.41 1 1.00e+01 1.00e-02 2.86e+01 ... (remaining 11319 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.114: 2669 0.114 - 0.227: 784 0.227 - 0.341: 93 0.341 - 0.455: 9 0.455 - 0.569: 9 Chirality restraints: 3564 Sorted by residual: chirality pdb=" C1 NAG i 2 " pdb=" O4 NAG i 1 " pdb=" C2 NAG i 2 " pdb=" O5 NAG i 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.58 0.18 2.00e-02 2.50e+03 8.07e+01 chirality pdb=" C1 NAG x 2 " pdb=" O4 NAG x 1 " pdb=" C2 NAG x 2 " pdb=" O5 NAG x 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.58 0.18 2.00e-02 2.50e+03 7.87e+01 chirality pdb=" C1 NAG T 2 " pdb=" O4 NAG T 1 " pdb=" C2 NAG T 2 " pdb=" O5 NAG T 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.58 0.18 2.00e-02 2.50e+03 7.78e+01 ... (remaining 3561 not shown) Planarity restraints: 3438 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C2 NAG i 1 " -0.098 2.00e-02 2.50e+03 8.10e-02 8.21e+01 pdb=" C7 NAG i 1 " 0.020 2.00e-02 2.50e+03 pdb=" C8 NAG i 1 " -0.072 2.00e-02 2.50e+03 pdb=" N2 NAG i 1 " 0.132 2.00e-02 2.50e+03 pdb=" O7 NAG i 1 " 0.017 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG T 1 " 0.098 2.00e-02 2.50e+03 8.10e-02 8.21e+01 pdb=" C7 NAG T 1 " -0.020 2.00e-02 2.50e+03 pdb=" C8 NAG T 1 " 0.072 2.00e-02 2.50e+03 pdb=" N2 NAG T 1 " -0.132 2.00e-02 2.50e+03 pdb=" O7 NAG T 1 " -0.017 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG x 1 " 0.098 2.00e-02 2.50e+03 8.10e-02 8.20e+01 pdb=" C7 NAG x 1 " -0.020 2.00e-02 2.50e+03 pdb=" C8 NAG x 1 " 0.072 2.00e-02 2.50e+03 pdb=" N2 NAG x 1 " -0.132 2.00e-02 2.50e+03 pdb=" O7 NAG x 1 " -0.017 2.00e-02 2.50e+03 ... (remaining 3435 not shown) Histogram of nonbonded interaction distances: 2.32 - 2.84: 6824 2.84 - 3.35: 17991 3.35 - 3.87: 34923 3.87 - 4.38: 39887 4.38 - 4.90: 64499 Nonbonded interactions: 164124 Sorted by model distance: nonbonded pdb=" N ASN E 398 " pdb=" OD1 ASN E 398 " model vdw 2.319 3.120 nonbonded pdb=" N ASN A 398 " pdb=" OD1 ASN A 398 " model vdw 2.319 3.120 nonbonded pdb=" N ASN B 398 " pdb=" OD1 ASN B 398 " model vdw 2.320 3.120 nonbonded pdb=" O4 NAG Z 2 " pdb=" O6 NAG Z 2 " model vdw 2.339 3.040 nonbonded pdb=" O4 NAG o 2 " pdb=" O6 NAG o 2 " model vdw 2.339 3.040 ... (remaining 164119 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: 0.04 Found NCS groups: ncs_group { reference = chain '0' selection = chain 'J' selection = chain 'K' selection = chain 'M' selection = chain 'N' selection = chain 'O' selection = chain 'P' selection = chain 'R' selection = chain 'T' selection = chain 'U' selection = chain 'V' selection = chain 'W' selection = chain 'Z' selection = chain 'a' selection = chain 'b' selection = chain 'c' selection = chain 'd' selection = chain 'e' selection = chain 'g' selection = chain 'i' selection = chain 'j' selection = chain 'k' selection = chain 'l' selection = chain 'o' selection = chain 'p' selection = chain 'q' selection = chain 'r' selection = chain 's' selection = chain 't' selection = chain 'v' selection = chain 'x' selection = chain 'y' selection = chain 'z' } ncs_group { reference = (chain '1' and resid 1 through 2) selection = (chain 'S' and resid 1 through 2) selection = (chain 'X' and resid 1 through 2) selection = (chain 'h' and resid 1 through 2) selection = (chain 'm' and resid 1 through 2) selection = (chain 'w' and resid 1 through 2) } ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'E' } ncs_group { reference = chain 'C' selection = chain 'F' selection = chain 'H' } ncs_group { reference = chain 'D' selection = chain 'G' selection = chain 'L' } ncs_group { reference = chain 'I' selection = chain 'Q' selection = chain 'Y' selection = chain 'f' selection = chain 'n' selection = chain 'u' } 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: 1.700 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: 0.030 Extract box with map and model: 0.350 Check model and map are aligned: 0.060 Set scattering table: 0.070 Process input model: 20.690 Find NCS groups from input model: 0.590 Set up NCS constraints: 0.080 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.240 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 24.810 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8097 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 0.137 20877 Z= 1.134 Angle : 1.873 10.392 28587 Z= 1.165 Chirality : 0.104 0.569 3564 Planarity : 0.010 0.081 3372 Dihedral : 10.542 82.539 6831 Min Nonbonded Distance : 2.319 Molprobity Statistics. All-atom Clashscore : 1.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.06 % Favored : 97.94 % Rotamer: Outliers : 0.44 % Allowed : 0.74 % Favored : 98.82 % Cbeta Deviations : 0.14 % Peptide Plane: Cis-proline : 3.03 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.08 (0.16), residues: 2325 helix: -0.98 (0.21), residues: 426 sheet: 0.69 (0.21), residues: 540 loop : 0.27 (0.16), residues: 1359 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 344 TYR 0.059 0.008 TYR D 87 PHE 0.045 0.007 PHE D 98 TRP 0.056 0.010 TRP E 35 HIS 0.015 0.003 HIS B 374 Details of bonding type rmsd/Z covalent geometry : bond 0.02113 / 1.13 (20703) covalent geometry : angle 1.85433 / 1.17 (28104) SS BOND : bond 0.02998 / 1.73 ( 39) SS BOND : angle 2.08999 / 1.49 ( 78) hydrogen bonds : bond 0.16470 / 11.10 ( 776) hydrogen bonds : angle 8.85667 / 6.16 ( 2112) link_ALPHA1-3 : bond 0.03712 / 2.00 ( 6) link_ALPHA1-3 : angle 3.39575 / 1.77 ( 18) link_ALPHA1-6 : bond 0.03152 / 1.66 ( 6) link_ALPHA1-6 : angle 3.35491 / 1.80 ( 18) link_BETA1-4 : bond 0.03509 / 2.17 ( 54) link_BETA1-4 : angle 3.26011 / 2.27 ( 162) link_BETA1-6 : bond 0.00215 / 0.11 ( 3) link_BETA1-6 : angle 2.88950 / 1.31 ( 9) link_NAG-ASN : bond 0.02670 / 1.68 ( 66) link_NAG-ASN : angle 2.37063 / 1.63 ( 198) *********************** 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 526 residues out of total 2040 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 517 time to evaluate : 0.758 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: A 84 MET cc_start: 0.8162 (ttp) cc_final: 0.7957 (ttm) REVERT: A 207 LYS cc_start: 0.8716 (mmtt) cc_final: 0.8129 (tptp) REVERT: A 387 THR cc_start: 0.8811 (p) cc_final: 0.8465 (t) REVERT: A 426 MET cc_start: 0.8776 (tpp) cc_final: 0.8452 (mmm) REVERT: A 536 THR cc_start: 0.8903 (m) cc_final: 0.8684 (p) REVERT: A 571 TRP cc_start: 0.7758 (m100) cc_final: 0.7360 (m100) REVERT: H 11 LEU cc_start: 0.6083 (tt) cc_final: 0.5835 (mp) REVERT: H 33 ASP cc_start: 0.8137 (m-30) cc_final: 0.7845 (t0) REVERT: H 108 LEU cc_start: 0.6739 (tp) cc_final: 0.6387 (tt) REVERT: L 74 THR cc_start: 0.8623 (m) cc_final: 0.8388 (p) REVERT: B 84 MET cc_start: 0.8164 (ttp) cc_final: 0.7930 (ttm) REVERT: B 207 LYS cc_start: 0.8696 (mmtt) cc_final: 0.8323 (tmtt) REVERT: B 358 ILE cc_start: 0.9043 (mt) cc_final: 0.8753 (mm) REVERT: B 387 THR cc_start: 0.8757 (p) cc_final: 0.8366 (t) REVERT: B 426 MET cc_start: 0.8867 (tpp) cc_final: 0.8580 (mmm) REVERT: B 500 ARG cc_start: 0.7694 (ptt90) cc_final: 0.7366 (tpm170) REVERT: B 536 THR cc_start: 0.8811 (m) cc_final: 0.8582 (p) REVERT: B 571 TRP cc_start: 0.7558 (m100) cc_final: 0.7161 (m100) REVERT: C 33 ASP cc_start: 0.8137 (m-30) cc_final: 0.7612 (t0) REVERT: C 108 LEU cc_start: 0.6949 (tp) cc_final: 0.6597 (tt) REVERT: D 74 THR cc_start: 0.8548 (m) cc_final: 0.8241 (p) REVERT: E 84 MET cc_start: 0.8162 (ttp) cc_final: 0.7931 (ttm) REVERT: E 207 LYS cc_start: 0.8619 (mmtt) cc_final: 0.8242 (tmtt) REVERT: E 387 THR cc_start: 0.8889 (p) cc_final: 0.8469 (t) REVERT: E 426 MET cc_start: 0.8787 (tpp) cc_final: 0.8258 (mmm) REVERT: E 530 MET cc_start: 0.8908 (mtm) cc_final: 0.8686 (mtm) REVERT: E 536 THR cc_start: 0.8875 (m) cc_final: 0.8658 (p) REVERT: E 571 TRP cc_start: 0.7778 (m100) cc_final: 0.7182 (m100) REVERT: F 33 ASP cc_start: 0.8150 (m-30) cc_final: 0.7648 (t0) REVERT: F 108 LEU cc_start: 0.6900 (tp) cc_final: 0.6563 (tt) REVERT: G 74 THR cc_start: 0.8542 (m) cc_final: 0.8228 (p) outliers start: 9 outliers final: 3 residues processed: 526 average time/residue: 0.1691 time to fit residues: 131.8801 Evaluate side-chains 279 residues out of total 2040 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 276 time to evaluate : 0.774 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 637 ASN Chi-restraints excluded: chain B residue 637 ASN Chi-restraints excluded: chain E residue 637 ASN Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 234 random chunks: chunk 216 optimal weight: 5.9990 chunk 98 optimal weight: 0.9990 chunk 194 optimal weight: 0.9980 chunk 227 optimal weight: 6.9990 chunk 107 optimal weight: 2.9990 chunk 10 optimal weight: 2.9990 chunk 66 optimal weight: 1.9990 chunk 130 optimal weight: 0.9980 chunk 124 optimal weight: 3.9990 chunk 103 optimal weight: 0.9980 chunk 200 optimal weight: 2.9990 overall best weight: 1.1984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 540 GLN ** A 591 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 651 ASN H 2 GLN B 540 GLN ** B 591 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 651 ASN C 2 GLN E 195 ASN E 352 HIS E 540 GLN ** E 591 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 651 ASN F 2 GLN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3648 r_free = 0.3648 target = 0.105360 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3238 r_free = 0.3238 target = 0.082230 restraints weight = 51249.845| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3261 r_free = 0.3261 target = 0.083913 restraints weight = 33350.540| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3275 r_free = 0.3275 target = 0.084606 restraints weight = 23525.405| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3302 r_free = 0.3302 target = 0.086039 restraints weight = 20334.091| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3306 r_free = 0.3306 target = 0.086163 restraints weight = 17105.387| |-----------------------------------------------------------------------------| r_work (final): 0.3300 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7958 moved from start: 0.2866 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 20877 Z= 0.174 Angle : 0.827 10.296 28587 Z= 0.406 Chirality : 0.050 0.344 3564 Planarity : 0.004 0.030 3372 Dihedral : 5.877 29.519 2559 Min Nonbonded Distance : 2.393 Molprobity Statistics. All-atom Clashscore : 9.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.32 % Favored : 97.68 % Rotamer: Outliers : 2.94 % Allowed : 8.24 % Favored : 88.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.11 (0.17), residues: 2325 helix: -0.07 (0.24), residues: 423 sheet: 0.57 (0.20), residues: 600 loop : -0.01 (0.17), residues: 1302 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG H 94 TYR 0.021 0.002 TYR D 92 PHE 0.017 0.002 PHE B 159 TRP 0.028 0.002 TRP A 479 HIS 0.016 0.002 HIS C 100I Details of bonding type rmsd/Z covalent geometry : bond 0.00380 / 0.17 (20703) covalent geometry : angle 0.78908 / 0.40 (28104) SS BOND : bond 0.00311 / 0.23 ( 39) SS BOND : angle 0.90582 / 0.66 ( 78) hydrogen bonds : bond 0.05111 / 3.49 ( 776) hydrogen bonds : angle 7.15370 / 4.95 ( 2112) link_ALPHA1-3 : bond 0.00374 / 0.20 ( 6) link_ALPHA1-3 : angle 1.94798 / 1.08 ( 18) link_ALPHA1-6 : bond 0.00477 / 0.26 ( 6) link_ALPHA1-6 : angle 1.76680 / 1.03 ( 18) link_BETA1-4 : bond 0.00489 / 0.32 ( 54) link_BETA1-4 : angle 1.97685 / 1.35 ( 162) link_BETA1-6 : bond 0.00022 / 0.01 ( 3) link_BETA1-6 : angle 1.61955 / 0.74 ( 9) link_NAG-ASN : bond 0.00537 / 0.34 ( 66) link_NAG-ASN : angle 2.47061 / 1.66 ( 198) *********************** 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 394 residues out of total 2040 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 334 time to evaluate : 0.766 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: A 104 MET cc_start: 0.8914 (ttp) cc_final: 0.8427 (tpt) REVERT: A 207 LYS cc_start: 0.8303 (mmtt) cc_final: 0.8006 (tmtt) REVERT: A 309 ILE cc_start: 0.9229 (pt) cc_final: 0.8989 (mm) REVERT: A 387 THR cc_start: 0.8592 (p) cc_final: 0.8148 (t) REVERT: A 426 MET cc_start: 0.7959 (tpp) cc_final: 0.7431 (mmm) REVERT: H 2 GLN cc_start: 0.7368 (OUTLIER) cc_final: 0.7149 (pm20) REVERT: H 31 TRP cc_start: 0.7458 (m-10) cc_final: 0.6937 (m-10) REVERT: H 100 HIS cc_start: 0.6384 (m-70) cc_final: 0.6180 (m-70) REVERT: H 108 LEU cc_start: 0.7216 (tp) cc_final: 0.6811 (tt) REVERT: L 49 TYR cc_start: 0.6994 (m-80) cc_final: 0.6579 (m-80) REVERT: L 70 GLN cc_start: 0.7354 (tp40) cc_final: 0.6589 (pp30) REVERT: L 87 TYR cc_start: 0.4683 (m-80) cc_final: 0.4465 (m-80) REVERT: L 95 ASP cc_start: 0.7255 (t0) cc_final: 0.6829 (t0) REVERT: L 96 PHE cc_start: 0.7707 (m-80) cc_final: 0.7265 (m-10) REVERT: B 207 LYS cc_start: 0.8254 (mmtt) cc_final: 0.7888 (tmtt) REVERT: B 387 THR cc_start: 0.8549 (p) cc_final: 0.8099 (t) REVERT: B 426 MET cc_start: 0.8069 (tpp) cc_final: 0.7793 (mmm) REVERT: B 651 ASN cc_start: 0.7958 (OUTLIER) cc_final: 0.7700 (t0) REVERT: C 67 LEU cc_start: 0.6967 (tp) cc_final: 0.6749 (mt) REVERT: C 100 LYS cc_start: 0.8451 (ttmt) cc_final: 0.8199 (ttpp) REVERT: C 102 LEU cc_start: 0.8181 (mm) cc_final: 0.7967 (mm) REVERT: C 108 LEU cc_start: 0.7081 (tp) cc_final: 0.6624 (tt) REVERT: D 27 GLU cc_start: 0.5490 (mt-10) cc_final: 0.5190 (mp0) REVERT: E 207 LYS cc_start: 0.8313 (mmtt) cc_final: 0.8075 (tmtt) REVERT: E 387 THR cc_start: 0.8598 (p) cc_final: 0.8198 (t) REVERT: E 426 MET cc_start: 0.8088 (tpp) cc_final: 0.7718 (mmm) REVERT: F 31 TRP cc_start: 0.7672 (m-10) cc_final: 0.7010 (m-10) REVERT: G 19 VAL cc_start: 0.7341 (t) cc_final: 0.6790 (t) REVERT: G 37 GLN cc_start: 0.7993 (tt0) cc_final: 0.7405 (tt0) REVERT: G 87 TYR cc_start: 0.4332 (m-80) cc_final: 0.3690 (m-80) outliers start: 60 outliers final: 16 residues processed: 377 average time/residue: 0.1506 time to fit residues: 86.9532 Evaluate side-chains 268 residues out of total 2040 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 250 time to evaluate : 0.750 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 163 THR Chi-restraints excluded: chain A residue 342 LEU Chi-restraints excluded: chain A residue 538 THR Chi-restraints excluded: chain A residue 576 LEU Chi-restraints excluded: chain H residue 2 GLN Chi-restraints excluded: chain H residue 45 LEU Chi-restraints excluded: chain H residue 68 THR Chi-restraints excluded: chain B residue 570 VAL Chi-restraints excluded: chain B residue 576 LEU Chi-restraints excluded: chain B residue 589 ASP Chi-restraints excluded: chain B residue 651 ASN Chi-restraints excluded: chain C residue 68 THR Chi-restraints excluded: chain D residue 47 LEU Chi-restraints excluded: chain E residue 538 THR Chi-restraints excluded: chain E residue 576 LEU Chi-restraints excluded: chain F residue 68 THR Chi-restraints excluded: chain G residue 46 LEU Chi-restraints excluded: chain G residue 47 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 234 random chunks: chunk 231 optimal weight: 0.9980 chunk 159 optimal weight: 0.0370 chunk 7 optimal weight: 0.6980 chunk 111 optimal weight: 4.9990 chunk 67 optimal weight: 0.4980 chunk 116 optimal weight: 6.9990 chunk 92 optimal weight: 0.9980 chunk 102 optimal weight: 1.9990 chunk 65 optimal weight: 9.9990 chunk 61 optimal weight: 0.0670 chunk 122 optimal weight: 8.9990 overall best weight: 0.4596 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 591 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 651 ASN A 652 GLN L 70 GLN ** B 300 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 591 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 651 ASN C 2 GLN C 80 GLN ** E 591 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 651 ASN E 652 GLN F 2 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3652 r_free = 0.3652 target = 0.105457 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3246 r_free = 0.3246 target = 0.082622 restraints weight = 51819.401| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3262 r_free = 0.3262 target = 0.083937 restraints weight = 30901.867| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3278 r_free = 0.3278 target = 0.084745 restraints weight = 22265.819| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3289 r_free = 0.3289 target = 0.085270 restraints weight = 21149.030| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3294 r_free = 0.3294 target = 0.085468 restraints weight = 19074.768| |-----------------------------------------------------------------------------| r_work (final): 0.3286 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7996 moved from start: 0.3584 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 20877 Z= 0.132 Angle : 0.713 8.895 28587 Z= 0.352 Chirality : 0.046 0.236 3564 Planarity : 0.004 0.032 3372 Dihedral : 5.329 24.681 2553 Min Nonbonded Distance : 2.389 Molprobity Statistics. All-atom Clashscore : 9.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.58 % Favored : 97.42 % Rotamer: Outliers : 2.94 % Allowed : 9.85 % Favored : 87.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.19 (0.17), residues: 2325 helix: 0.60 (0.26), residues: 405 sheet: 0.46 (0.20), residues: 666 loop : -0.13 (0.17), residues: 1254 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG D 24 TYR 0.019 0.002 TYR G 49 PHE 0.024 0.003 PHE B 376 TRP 0.017 0.002 TRP B 479 HIS 0.005 0.001 HIS E 105 Details of bonding type rmsd/Z covalent geometry : bond 0.00281 / 0.13 (20703) covalent geometry : angle 0.68338 / 0.35 (28104) SS BOND : bond 0.00230 / 0.17 ( 39) SS BOND : angle 1.09890 / 0.86 ( 78) hydrogen bonds : bond 0.04504 / 3.04 ( 776) hydrogen bonds : angle 6.72178 / 4.65 ( 2112) link_ALPHA1-3 : bond 0.00459 / 0.24 ( 6) link_ALPHA1-3 : angle 1.27775 / 0.73 ( 18) link_ALPHA1-6 : bond 0.00576 / 0.29 ( 6) link_ALPHA1-6 : angle 1.35600 / 0.75 ( 18) link_BETA1-4 : bond 0.00493 / 0.31 ( 54) link_BETA1-4 : angle 1.48622 / 1.03 ( 162) link_BETA1-6 : bond 0.00122 / 0.06 ( 3) link_BETA1-6 : angle 1.45978 / 0.68 ( 9) link_NAG-ASN : bond 0.00371 / 0.25 ( 66) link_NAG-ASN : angle 2.11957 / 1.41 ( 198) *********************** 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 346 residues out of total 2040 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 286 time to evaluate : 0.898 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 104 MET cc_start: 0.8897 (OUTLIER) cc_final: 0.8539 (tpp) REVERT: A 207 LYS cc_start: 0.8239 (mmtt) cc_final: 0.8006 (tmtt) REVERT: A 387 THR cc_start: 0.8668 (p) cc_final: 0.8190 (t) REVERT: A 426 MET cc_start: 0.7966 (tpp) cc_final: 0.7370 (mmm) REVERT: A 620 ASP cc_start: 0.6645 (OUTLIER) cc_final: 0.6345 (t0) REVERT: H 2 GLN cc_start: 0.7799 (pm20) cc_final: 0.7299 (pp30) REVERT: H 100 HIS cc_start: 0.5969 (m-70) cc_final: 0.5693 (m-70) REVERT: H 102 LEU cc_start: 0.8324 (mm) cc_final: 0.8034 (mm) REVERT: H 108 LEU cc_start: 0.7307 (tp) cc_final: 0.6931 (tt) REVERT: L 49 TYR cc_start: 0.7362 (m-80) cc_final: 0.6234 (m-80) REVERT: L 73 LEU cc_start: 0.6801 (tp) cc_final: 0.6513 (tt) REVERT: L 87 TYR cc_start: 0.4748 (m-80) cc_final: 0.4399 (m-80) REVERT: B 207 LYS cc_start: 0.8217 (mmtt) cc_final: 0.7722 (tptm) REVERT: B 387 THR cc_start: 0.8644 (p) cc_final: 0.8158 (t) REVERT: B 426 MET cc_start: 0.7940 (tpp) cc_final: 0.7616 (mmm) REVERT: C 66 ARG cc_start: 0.8029 (ttm110) cc_final: 0.7747 (ttm110) REVERT: C 67 LEU cc_start: 0.7244 (tp) cc_final: 0.6855 (mt) REVERT: C 79 LEU cc_start: 0.7284 (OUTLIER) cc_final: 0.6749 (tt) REVERT: C 100 LYS cc_start: 0.8372 (ttmt) cc_final: 0.8079 (ttpp) REVERT: D 24 ARG cc_start: 0.8613 (mmm-85) cc_final: 0.8297 (mmm-85) REVERT: D 70 GLN cc_start: 0.7747 (tp-100) cc_final: 0.6614 (pp30) REVERT: E 104 MET cc_start: 0.8902 (ttt) cc_final: 0.8676 (tpp) REVERT: E 207 LYS cc_start: 0.8245 (mmtt) cc_final: 0.7932 (tmtt) REVERT: E 387 THR cc_start: 0.8655 (p) cc_final: 0.8197 (t) REVERT: E 620 ASP cc_start: 0.6981 (OUTLIER) cc_final: 0.6637 (t0) REVERT: F 33 ASP cc_start: 0.8109 (m-30) cc_final: 0.7301 (m-30) REVERT: F 102 LEU cc_start: 0.8671 (OUTLIER) cc_final: 0.8307 (mm) REVERT: G 37 GLN cc_start: 0.7878 (OUTLIER) cc_final: 0.7671 (tt0) REVERT: G 87 TYR cc_start: 0.4435 (m-80) cc_final: 0.3794 (m-80) outliers start: 60 outliers final: 27 residues processed: 323 average time/residue: 0.1569 time to fit residues: 77.8727 Evaluate side-chains 283 residues out of total 2040 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 250 time to evaluate : 0.658 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 104 MET Chi-restraints excluded: chain A residue 163 THR Chi-restraints excluded: chain A residue 536 THR Chi-restraints excluded: chain A residue 538 THR Chi-restraints excluded: chain A residue 576 LEU Chi-restraints excluded: chain A residue 620 ASP Chi-restraints excluded: chain H residue 35 MET Chi-restraints excluded: chain H residue 51 ILE Chi-restraints excluded: chain H residue 68 THR Chi-restraints excluded: chain L residue 33 LEU Chi-restraints excluded: chain L residue 88 CYS Chi-restraints excluded: chain B residue 159 PHE Chi-restraints excluded: chain B residue 333 ILE Chi-restraints excluded: chain B residue 430 VAL Chi-restraints excluded: chain B residue 488 VAL Chi-restraints excluded: chain B residue 536 THR Chi-restraints excluded: chain B residue 576 LEU Chi-restraints excluded: chain B residue 589 ASP Chi-restraints excluded: chain C residue 61 ASN Chi-restraints excluded: chain C residue 68 THR Chi-restraints excluded: chain C residue 79 LEU Chi-restraints excluded: chain E residue 49 GLU Chi-restraints excluded: chain E residue 271 ILE Chi-restraints excluded: chain E residue 333 ILE Chi-restraints excluded: chain E residue 430 VAL Chi-restraints excluded: chain E residue 536 THR Chi-restraints excluded: chain E residue 538 THR Chi-restraints excluded: chain E residue 620 ASP Chi-restraints excluded: chain F residue 35 MET Chi-restraints excluded: chain F residue 68 THR Chi-restraints excluded: chain F residue 102 LEU Chi-restraints excluded: chain G residue 37 GLN Chi-restraints excluded: chain G residue 75 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 234 random chunks: chunk 61 optimal weight: 6.9990 chunk 132 optimal weight: 0.0470 chunk 192 optimal weight: 7.9990 chunk 66 optimal weight: 0.9980 chunk 170 optimal weight: 0.8980 chunk 70 optimal weight: 5.9990 chunk 39 optimal weight: 9.9990 chunk 219 optimal weight: 6.9990 chunk 16 optimal weight: 4.9990 chunk 44 optimal weight: 6.9990 chunk 218 optimal weight: 5.9990 overall best weight: 2.5882 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 651 ASN L 70 GLN B 300 ASN B 651 ASN C 2 GLN C 61 ASN ** E 591 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 651 ASN F 2 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3587 r_free = 0.3587 target = 0.101477 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3160 r_free = 0.3160 target = 0.078345 restraints weight = 52427.673| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3166 r_free = 0.3166 target = 0.079231 restraints weight = 35665.339| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3188 r_free = 0.3188 target = 0.080228 restraints weight = 25657.947| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3212 r_free = 0.3212 target = 0.081288 restraints weight = 22077.310| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3217 r_free = 0.3217 target = 0.081482 restraints weight = 19165.124| |-----------------------------------------------------------------------------| r_work (final): 0.3210 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8094 moved from start: 0.3971 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.067 20877 Z= 0.217 Angle : 0.748 8.107 28587 Z= 0.365 Chirality : 0.047 0.257 3564 Planarity : 0.004 0.042 3372 Dihedral : 5.356 25.499 2553 Min Nonbonded Distance : 2.377 Molprobity Statistics. All-atom Clashscore : 9.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.44 % Favored : 96.56 % Rotamer: Outliers : 3.14 % Allowed : 10.78 % Favored : 86.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.04 (0.17), residues: 2325 helix: 0.35 (0.26), residues: 417 sheet: 0.31 (0.19), residues: 693 loop : -0.27 (0.18), residues: 1215 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG H 66 TYR 0.018 0.002 TYR L 90 PHE 0.022 0.003 PHE A 376 TRP 0.024 0.002 TRP A 596 HIS 0.007 0.002 HIS B 105 Details of bonding type rmsd/Z covalent geometry : bond 0.00497 / 0.22 (20703) covalent geometry : angle 0.72066 / 0.36 (28104) SS BOND : bond 0.00316 / 0.22 ( 39) SS BOND : angle 1.25377 / 0.89 ( 78) hydrogen bonds : bond 0.04287 / 2.87 ( 776) hydrogen bonds : angle 6.44619 / 4.47 ( 2112) link_ALPHA1-3 : bond 0.00150 / 0.08 ( 6) link_ALPHA1-3 : angle 1.69016 / 0.94 ( 18) link_ALPHA1-6 : bond 0.00597 / 0.32 ( 6) link_ALPHA1-6 : angle 1.54843 / 0.88 ( 18) link_BETA1-4 : bond 0.00400 / 0.25 ( 54) link_BETA1-4 : angle 1.49257 / 1.05 ( 162) link_BETA1-6 : bond 0.00046 / 0.02 ( 3) link_BETA1-6 : angle 1.83985 / 0.84 ( 9) link_NAG-ASN : bond 0.00423 / 0.27 ( 66) link_NAG-ASN : angle 2.00514 / 1.35 ( 198) *********************** 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 310 residues out of total 2040 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 246 time to evaluate : 0.779 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 104 MET cc_start: 0.9061 (OUTLIER) cc_final: 0.8334 (tpt) REVERT: A 207 LYS cc_start: 0.8278 (mmtt) cc_final: 0.7793 (tptp) REVERT: A 387 THR cc_start: 0.8862 (p) cc_final: 0.8380 (t) REVERT: A 426 MET cc_start: 0.7878 (tpp) cc_final: 0.7632 (mmm) REVERT: A 620 ASP cc_start: 0.6766 (OUTLIER) cc_final: 0.6466 (t0) REVERT: A 629 MET cc_start: 0.8888 (mmm) cc_final: 0.8077 (mmm) REVERT: H 35 MET cc_start: 0.7593 (OUTLIER) cc_final: 0.7217 (mmp) REVERT: H 67 LEU cc_start: 0.7501 (tp) cc_final: 0.7076 (mt) REVERT: H 100 LYS cc_start: 0.8473 (mtpt) cc_final: 0.8233 (ttmt) REVERT: L 24 ARG cc_start: 0.8358 (mmm-85) cc_final: 0.8096 (mmm160) REVERT: L 49 TYR cc_start: 0.7471 (m-80) cc_final: 0.7090 (m-80) REVERT: L 70 GLN cc_start: 0.6859 (tp-100) cc_final: 0.6524 (mt0) REVERT: L 74 THR cc_start: 0.7973 (p) cc_final: 0.7696 (p) REVERT: L 87 TYR cc_start: 0.5020 (m-80) cc_final: 0.4533 (m-80) REVERT: B 84 MET cc_start: 0.7643 (tmm) cc_final: 0.6970 (tmm) REVERT: B 104 MET cc_start: 0.9078 (ttt) cc_final: 0.8606 (tpp) REVERT: B 207 LYS cc_start: 0.8277 (mmtt) cc_final: 0.7716 (tptm) REVERT: B 387 THR cc_start: 0.8746 (p) cc_final: 0.8362 (t) REVERT: B 426 MET cc_start: 0.7882 (tpp) cc_final: 0.7637 (mmm) REVERT: C 100 LYS cc_start: 0.8188 (ttmt) cc_final: 0.7943 (ttpp) REVERT: D 63 LYS cc_start: 0.7445 (tptp) cc_final: 0.7141 (mptt) REVERT: D 70 GLN cc_start: 0.7839 (tp-100) cc_final: 0.6724 (pp30) REVERT: D 73 LEU cc_start: 0.6838 (tp) cc_final: 0.6590 (tt) REVERT: E 104 MET cc_start: 0.9036 (ttt) cc_final: 0.8786 (tpp) REVERT: E 207 LYS cc_start: 0.8281 (mmtt) cc_final: 0.7882 (tmtt) REVERT: E 387 THR cc_start: 0.8749 (p) cc_final: 0.8350 (t) REVERT: E 500 ARG cc_start: 0.4918 (tpt170) cc_final: 0.4589 (tpm170) REVERT: E 629 MET cc_start: 0.8796 (mmm) cc_final: 0.8034 (mmm) REVERT: F 67 LEU cc_start: 0.7590 (OUTLIER) cc_final: 0.6950 (mt) REVERT: G 37 GLN cc_start: 0.8022 (OUTLIER) cc_final: 0.7455 (tt0) REVERT: G 63 LYS cc_start: 0.7338 (tptp) cc_final: 0.6961 (mptt) REVERT: G 87 TYR cc_start: 0.4799 (m-80) cc_final: 0.4279 (m-80) outliers start: 64 outliers final: 33 residues processed: 289 average time/residue: 0.1579 time to fit residues: 69.7257 Evaluate side-chains 269 residues out of total 2040 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 231 time to evaluate : 0.634 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 104 MET Chi-restraints excluded: chain A residue 163 THR Chi-restraints excluded: chain A residue 536 THR Chi-restraints excluded: chain A residue 538 THR Chi-restraints excluded: chain A residue 620 ASP Chi-restraints excluded: chain H residue 35 MET Chi-restraints excluded: chain H residue 68 THR Chi-restraints excluded: chain H residue 77 VAL Chi-restraints excluded: chain H residue 100 LEU Chi-restraints excluded: chain L residue 75 ILE Chi-restraints excluded: chain B residue 159 PHE Chi-restraints excluded: chain B residue 213 ILE Chi-restraints excluded: chain B residue 362 THR Chi-restraints excluded: chain B residue 488 VAL Chi-restraints excluded: chain B residue 536 THR Chi-restraints excluded: chain B residue 570 VAL Chi-restraints excluded: chain B residue 587 LEU Chi-restraints excluded: chain B residue 589 ASP Chi-restraints excluded: chain C residue 2 GLN Chi-restraints excluded: chain C residue 35 MET Chi-restraints excluded: chain C residue 68 THR Chi-restraints excluded: chain C residue 77 VAL Chi-restraints excluded: chain D residue 37 GLN Chi-restraints excluded: chain D residue 47 LEU Chi-restraints excluded: chain D residue 75 ILE Chi-restraints excluded: chain D residue 89 LEU Chi-restraints excluded: chain E residue 271 ILE Chi-restraints excluded: chain E residue 538 THR Chi-restraints excluded: chain E residue 570 VAL Chi-restraints excluded: chain E residue 589 ASP Chi-restraints excluded: chain F residue 2 GLN Chi-restraints excluded: chain F residue 35 MET Chi-restraints excluded: chain F residue 67 LEU Chi-restraints excluded: chain F residue 68 THR Chi-restraints excluded: chain F residue 77 VAL Chi-restraints excluded: chain G residue 37 GLN Chi-restraints excluded: chain G residue 47 LEU Chi-restraints excluded: chain G residue 75 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 234 random chunks: chunk 107 optimal weight: 5.9990 chunk 3 optimal weight: 0.0070 chunk 88 optimal weight: 2.9990 chunk 181 optimal weight: 7.9990 chunk 56 optimal weight: 0.0170 chunk 174 optimal weight: 4.9990 chunk 57 optimal weight: 10.0000 chunk 169 optimal weight: 5.9990 chunk 159 optimal weight: 8.9990 chunk 175 optimal weight: 3.9990 chunk 226 optimal weight: 10.0000 overall best weight: 2.4042 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 651 ASN E 287 HIS E 651 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3572 r_free = 0.3572 target = 0.100655 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3146 r_free = 0.3146 target = 0.077618 restraints weight = 52757.096| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3155 r_free = 0.3155 target = 0.078616 restraints weight = 36455.559| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3178 r_free = 0.3178 target = 0.079684 restraints weight = 25514.895| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3207 r_free = 0.3207 target = 0.080990 restraints weight = 21347.140| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3212 r_free = 0.3212 target = 0.081223 restraints weight = 18452.223| |-----------------------------------------------------------------------------| r_work (final): 0.3207 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8105 moved from start: 0.4299 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.084 20877 Z= 0.199 Angle : 0.735 9.987 28587 Z= 0.357 Chirality : 0.047 0.257 3564 Planarity : 0.004 0.053 3372 Dihedral : 5.323 23.596 2553 Min Nonbonded Distance : 2.384 Molprobity Statistics. All-atom Clashscore : 9.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.04 % Favored : 95.96 % Rotamer: Outliers : 2.89 % Allowed : 11.03 % Favored : 86.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.12 (0.17), residues: 2325 helix: 0.33 (0.26), residues: 417 sheet: 0.45 (0.20), residues: 663 loop : -0.46 (0.17), residues: 1245 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 66 TYR 0.015 0.002 TYR D 92 PHE 0.022 0.003 PHE L 71 TRP 0.024 0.002 TRP F 62 HIS 0.006 0.002 HIS B 105 Details of bonding type rmsd/Z covalent geometry : bond 0.00455 / 0.20 (20703) covalent geometry : angle 0.70222 / 0.35 (28104) SS BOND : bond 0.00416 / 0.30 ( 39) SS BOND : angle 1.33414 / 1.03 ( 78) hydrogen bonds : bond 0.04280 / 2.87 ( 776) hydrogen bonds : angle 6.31653 / 4.38 ( 2112) link_ALPHA1-3 : bond 0.00396 / 0.20 ( 6) link_ALPHA1-3 : angle 1.59633 / 0.88 ( 18) link_ALPHA1-6 : bond 0.00500 / 0.27 ( 6) link_ALPHA1-6 : angle 1.48828 / 0.86 ( 18) link_BETA1-4 : bond 0.00323 / 0.20 ( 54) link_BETA1-4 : angle 1.39628 / 0.98 ( 162) link_BETA1-6 : bond 0.00286 / 0.14 ( 3) link_BETA1-6 : angle 1.72463 / 0.78 ( 9) link_NAG-ASN : bond 0.00398 / 0.25 ( 66) link_NAG-ASN : angle 2.27020 / 1.52 ( 198) *********************** 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 314 residues out of total 2040 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 255 time to evaluate : 0.879 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 104 MET cc_start: 0.9059 (OUTLIER) cc_final: 0.8364 (tpt) REVERT: A 207 LYS cc_start: 0.8242 (mmtt) cc_final: 0.7666 (tptp) REVERT: A 387 THR cc_start: 0.8939 (p) cc_final: 0.8473 (t) REVERT: A 620 ASP cc_start: 0.6705 (OUTLIER) cc_final: 0.6417 (t0) REVERT: A 629 MET cc_start: 0.8901 (mmm) cc_final: 0.8305 (mmm) REVERT: H 5 GLU cc_start: 0.8432 (tm-30) cc_final: 0.8203 (tm-30) REVERT: H 35 MET cc_start: 0.7571 (OUTLIER) cc_final: 0.7179 (mmp) REVERT: H 67 LEU cc_start: 0.7506 (tp) cc_final: 0.7162 (mt) REVERT: H 102 LEU cc_start: 0.8366 (mm) cc_final: 0.8000 (mm) REVERT: H 108 LEU cc_start: 0.7076 (tp) cc_final: 0.6612 (tt) REVERT: L 4 MET cc_start: 0.6083 (OUTLIER) cc_final: 0.5550 (mtp) REVERT: L 27 GLU cc_start: 0.6043 (mp0) cc_final: 0.5602 (mp0) REVERT: L 49 TYR cc_start: 0.7419 (m-80) cc_final: 0.6863 (m-80) REVERT: L 74 THR cc_start: 0.8127 (p) cc_final: 0.7908 (p) REVERT: L 87 TYR cc_start: 0.5106 (m-80) cc_final: 0.4724 (m-80) REVERT: L 95 ASP cc_start: 0.7887 (t0) cc_final: 0.7648 (t70) REVERT: B 207 LYS cc_start: 0.8230 (mmtt) cc_final: 0.7790 (tmtt) REVERT: B 387 THR cc_start: 0.8804 (p) cc_final: 0.8378 (t) REVERT: B 629 MET cc_start: 0.8842 (mmm) cc_final: 0.8177 (mmm) REVERT: C 33 ASP cc_start: 0.8116 (m-30) cc_final: 0.7598 (m-30) REVERT: C 35 MET cc_start: 0.7967 (OUTLIER) cc_final: 0.7732 (mmp) REVERT: C 108 LEU cc_start: 0.7349 (tp) cc_final: 0.6888 (tt) REVERT: D 24 ARG cc_start: 0.8756 (mmm-85) cc_final: 0.8378 (mmm-85) REVERT: D 63 LYS cc_start: 0.7491 (tptp) cc_final: 0.7240 (mptt) REVERT: D 70 GLN cc_start: 0.7751 (tp-100) cc_final: 0.6866 (pp30) REVERT: D 73 LEU cc_start: 0.6801 (tp) cc_final: 0.6589 (tt) REVERT: E 104 MET cc_start: 0.9045 (ttt) cc_final: 0.8820 (tpp) REVERT: E 207 LYS cc_start: 0.8224 (mmtt) cc_final: 0.7738 (tmtt) REVERT: E 387 THR cc_start: 0.8748 (p) cc_final: 0.8354 (t) REVERT: E 620 ASP cc_start: 0.6965 (OUTLIER) cc_final: 0.6415 (t0) REVERT: E 629 MET cc_start: 0.8867 (mmm) cc_final: 0.8103 (mmm) REVERT: E 650 GLN cc_start: 0.7468 (OUTLIER) cc_final: 0.7186 (mp10) REVERT: F 67 LEU cc_start: 0.7590 (tp) cc_final: 0.6954 (mt) REVERT: F 81 MET cc_start: 0.7310 (tpp) cc_final: 0.7042 (tpp) REVERT: G 24 ARG cc_start: 0.8484 (mmm-85) cc_final: 0.8100 (mmm-85) REVERT: G 63 LYS cc_start: 0.7215 (tptp) cc_final: 0.6907 (mptt) REVERT: G 87 TYR cc_start: 0.5109 (m-80) cc_final: 0.4778 (m-80) outliers start: 59 outliers final: 34 residues processed: 294 average time/residue: 0.1557 time to fit residues: 70.5434 Evaluate side-chains 271 residues out of total 2040 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 230 time to evaluate : 0.765 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 56 SER Chi-restraints excluded: chain A residue 104 MET Chi-restraints excluded: chain A residue 125 LEU Chi-restraints excluded: chain A residue 213 ILE Chi-restraints excluded: chain A residue 536 THR Chi-restraints excluded: chain A residue 538 THR Chi-restraints excluded: chain A residue 620 ASP Chi-restraints excluded: chain H residue 35 MET Chi-restraints excluded: chain H residue 68 THR Chi-restraints excluded: chain H residue 77 VAL Chi-restraints excluded: chain H residue 100 LEU Chi-restraints excluded: chain L residue 4 MET Chi-restraints excluded: chain L residue 75 ILE Chi-restraints excluded: chain B residue 159 PHE Chi-restraints excluded: chain B residue 213 ILE Chi-restraints excluded: chain B residue 320 THR Chi-restraints excluded: chain B residue 362 THR Chi-restraints excluded: chain B residue 430 VAL Chi-restraints excluded: chain B residue 488 VAL Chi-restraints excluded: chain B residue 536 THR Chi-restraints excluded: chain B residue 570 VAL Chi-restraints excluded: chain C residue 35 MET Chi-restraints excluded: chain C residue 51 ILE Chi-restraints excluded: chain C residue 68 THR Chi-restraints excluded: chain C residue 77 VAL Chi-restraints excluded: chain D residue 47 LEU Chi-restraints excluded: chain D residue 75 ILE Chi-restraints excluded: chain D residue 89 LEU Chi-restraints excluded: chain E residue 271 ILE Chi-restraints excluded: chain E residue 430 VAL Chi-restraints excluded: chain E residue 536 THR Chi-restraints excluded: chain E residue 538 THR Chi-restraints excluded: chain E residue 620 ASP Chi-restraints excluded: chain E residue 650 GLN Chi-restraints excluded: chain F residue 35 MET Chi-restraints excluded: chain F residue 51 ILE Chi-restraints excluded: chain F residue 68 THR Chi-restraints excluded: chain F residue 77 VAL Chi-restraints excluded: chain F residue 80 GLN Chi-restraints excluded: chain G residue 47 LEU Chi-restraints excluded: chain G residue 75 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 234 random chunks: chunk 227 optimal weight: 8.9990 chunk 100 optimal weight: 10.0000 chunk 81 optimal weight: 5.9990 chunk 183 optimal weight: 1.9990 chunk 230 optimal weight: 3.9990 chunk 124 optimal weight: 4.9990 chunk 224 optimal weight: 9.9990 chunk 160 optimal weight: 4.9990 chunk 215 optimal weight: 0.0170 chunk 165 optimal weight: 7.9990 chunk 39 optimal weight: 9.9990 overall best weight: 3.2026 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 287 HIS A 651 ASN B 287 HIS ** E 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 540 GLN ** E 591 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 651 ASN F 2 GLN ** G 70 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3539 r_free = 0.3539 target = 0.098692 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3101 r_free = 0.3101 target = 0.075521 restraints weight = 53153.591| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3118 r_free = 0.3118 target = 0.076869 restraints weight = 35450.296| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3140 r_free = 0.3140 target = 0.077781 restraints weight = 24694.645| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3161 r_free = 0.3161 target = 0.078691 restraints weight = 21409.554| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3165 r_free = 0.3165 target = 0.078871 restraints weight = 18798.440| |-----------------------------------------------------------------------------| r_work (final): 0.3158 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8178 moved from start: 0.4705 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.084 20877 Z= 0.244 Angle : 0.789 10.990 28587 Z= 0.381 Chirality : 0.048 0.274 3564 Planarity : 0.004 0.056 3372 Dihedral : 5.541 24.507 2553 Min Nonbonded Distance : 2.298 Molprobity Statistics. All-atom Clashscore : 10.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.13 % Favored : 95.87 % Rotamer: Outliers : 3.24 % Allowed : 11.03 % Favored : 85.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.31 (0.17), residues: 2325 helix: 0.14 (0.26), residues: 420 sheet: 0.42 (0.20), residues: 648 loop : -0.61 (0.17), residues: 1257 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG C 66 TYR 0.017 0.002 TYR D 92 PHE 0.020 0.003 PHE B 383 TRP 0.029 0.002 TRP A 571 HIS 0.008 0.002 HIS B 105 Details of bonding type rmsd/Z covalent geometry : bond 0.00560 / 0.24 (20703) covalent geometry : angle 0.75444 / 0.37 (28104) SS BOND : bond 0.00494 / 0.33 ( 39) SS BOND : angle 1.69486 / 1.29 ( 78) hydrogen bonds : bond 0.04314 / 2.87 ( 776) hydrogen bonds : angle 6.30988 / 4.40 ( 2112) link_ALPHA1-3 : bond 0.00150 / 0.08 ( 6) link_ALPHA1-3 : angle 1.82793 / 1.02 ( 18) link_ALPHA1-6 : bond 0.00533 / 0.29 ( 6) link_ALPHA1-6 : angle 1.59052 / 0.92 ( 18) link_BETA1-4 : bond 0.00334 / 0.21 ( 54) link_BETA1-4 : angle 1.51994 / 1.07 ( 162) link_BETA1-6 : bond 0.00338 / 0.17 ( 3) link_BETA1-6 : angle 1.94238 / 0.87 ( 9) link_NAG-ASN : bond 0.00503 / 0.31 ( 66) link_NAG-ASN : angle 2.33646 / 1.55 ( 198) *********************** 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 312 residues out of total 2040 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 246 time to evaluate : 0.767 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 104 MET cc_start: 0.9007 (OUTLIER) cc_final: 0.8582 (tpt) REVERT: A 207 LYS cc_start: 0.8260 (mmtt) cc_final: 0.7666 (tptp) REVERT: A 387 THR cc_start: 0.8970 (p) cc_final: 0.8576 (t) REVERT: A 620 ASP cc_start: 0.6781 (OUTLIER) cc_final: 0.6475 (t0) REVERT: A 629 MET cc_start: 0.8947 (mmm) cc_final: 0.8501 (mmt) REVERT: H 35 MET cc_start: 0.7554 (OUTLIER) cc_final: 0.7164 (mmp) REVERT: H 67 LEU cc_start: 0.7551 (tp) cc_final: 0.7168 (mt) REVERT: H 71 LYS cc_start: 0.7165 (ttpt) cc_final: 0.6261 (ptpp) REVERT: H 80 GLN cc_start: 0.8313 (mp10) cc_final: 0.7981 (mp10) REVERT: H 108 LEU cc_start: 0.7187 (tp) cc_final: 0.6749 (tt) REVERT: L 4 MET cc_start: 0.6108 (OUTLIER) cc_final: 0.5725 (mtp) REVERT: L 27 GLU cc_start: 0.6178 (mp0) cc_final: 0.5750 (mp0) REVERT: L 49 TYR cc_start: 0.7455 (m-80) cc_final: 0.6925 (m-80) REVERT: L 74 THR cc_start: 0.8205 (p) cc_final: 0.7988 (p) REVERT: L 87 TYR cc_start: 0.5393 (m-80) cc_final: 0.4968 (m-80) REVERT: B 84 MET cc_start: 0.7615 (tmm) cc_final: 0.7216 (tmm) REVERT: B 207 LYS cc_start: 0.8269 (mmtt) cc_final: 0.7840 (tmtt) REVERT: B 387 THR cc_start: 0.8862 (p) cc_final: 0.8373 (t) REVERT: B 629 MET cc_start: 0.8860 (mmm) cc_final: 0.8504 (mmm) REVERT: C 35 MET cc_start: 0.8120 (OUTLIER) cc_final: 0.7829 (mmp) REVERT: C 71 LYS cc_start: 0.6905 (ttpt) cc_final: 0.5786 (pttm) REVERT: D 4 MET cc_start: 0.6213 (ttp) cc_final: 0.5977 (ttm) REVERT: D 24 ARG cc_start: 0.8819 (mmm-85) cc_final: 0.8606 (mmm-85) REVERT: D 70 GLN cc_start: 0.7803 (tp-100) cc_final: 0.6835 (pp30) REVERT: D 73 LEU cc_start: 0.6995 (tp) cc_final: 0.6789 (tt) REVERT: E 104 MET cc_start: 0.9033 (ttt) cc_final: 0.8794 (tpp) REVERT: E 207 LYS cc_start: 0.8356 (mmtt) cc_final: 0.7924 (tmtt) REVERT: E 387 THR cc_start: 0.8896 (p) cc_final: 0.8433 (t) REVERT: E 620 ASP cc_start: 0.6871 (OUTLIER) cc_final: 0.6507 (t0) REVERT: E 629 MET cc_start: 0.8954 (mmm) cc_final: 0.8375 (mmm) REVERT: E 650 GLN cc_start: 0.7518 (OUTLIER) cc_final: 0.7194 (mp10) REVERT: F 2 GLN cc_start: 0.7894 (OUTLIER) cc_final: 0.7626 (pm20) REVERT: F 62 TRP cc_start: 0.7859 (t60) cc_final: 0.7531 (t60) REVERT: F 67 LEU cc_start: 0.7551 (OUTLIER) cc_final: 0.6890 (mt) REVERT: F 81 MET cc_start: 0.7188 (tpp) cc_final: 0.6931 (tpp) REVERT: F 100 LYS cc_start: 0.8333 (OUTLIER) cc_final: 0.7840 (ttmt) REVERT: G 27 GLU cc_start: 0.5598 (mp0) cc_final: 0.5385 (pm20) REVERT: G 63 LYS cc_start: 0.7513 (tptp) cc_final: 0.7215 (mptt) REVERT: G 87 TYR cc_start: 0.5490 (m-80) cc_final: 0.5186 (m-80) outliers start: 66 outliers final: 44 residues processed: 288 average time/residue: 0.1508 time to fit residues: 66.2200 Evaluate side-chains 273 residues out of total 2040 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 219 time to evaluate : 0.504 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 104 MET Chi-restraints excluded: chain A residue 125 LEU Chi-restraints excluded: chain A residue 159 PHE Chi-restraints excluded: chain A residue 213 ILE Chi-restraints excluded: chain A residue 536 THR Chi-restraints excluded: chain A residue 538 THR Chi-restraints excluded: chain A residue 587 LEU Chi-restraints excluded: chain A residue 602 LEU Chi-restraints excluded: chain A residue 620 ASP Chi-restraints excluded: chain H residue 35 MET Chi-restraints excluded: chain H residue 68 THR Chi-restraints excluded: chain H residue 77 VAL Chi-restraints excluded: chain H residue 82 THR Chi-restraints excluded: chain H residue 100 LEU Chi-restraints excluded: chain L residue 4 MET Chi-restraints excluded: chain L residue 37 GLN Chi-restraints excluded: chain L residue 47 LEU Chi-restraints excluded: chain L residue 75 ILE Chi-restraints excluded: chain L residue 89 LEU Chi-restraints excluded: chain B residue 104 MET Chi-restraints excluded: chain B residue 159 PHE Chi-restraints excluded: chain B residue 213 ILE Chi-restraints excluded: chain B residue 320 THR Chi-restraints excluded: chain B residue 362 THR Chi-restraints excluded: chain B residue 430 VAL Chi-restraints excluded: chain B residue 488 VAL Chi-restraints excluded: chain B residue 536 THR Chi-restraints excluded: chain B residue 570 VAL Chi-restraints excluded: chain B residue 587 LEU Chi-restraints excluded: chain C residue 35 MET Chi-restraints excluded: chain C residue 51 ILE Chi-restraints excluded: chain C residue 68 THR Chi-restraints excluded: chain C residue 77 VAL Chi-restraints excluded: chain D residue 37 GLN Chi-restraints excluded: chain D residue 75 ILE Chi-restraints excluded: chain D residue 89 LEU Chi-restraints excluded: chain E residue 50 THR Chi-restraints excluded: chain E residue 159 PHE Chi-restraints excluded: chain E residue 271 ILE Chi-restraints excluded: chain E residue 342 LEU Chi-restraints excluded: chain E residue 430 VAL Chi-restraints excluded: chain E residue 536 THR Chi-restraints excluded: chain E residue 538 THR Chi-restraints excluded: chain E residue 620 ASP Chi-restraints excluded: chain E residue 650 GLN Chi-restraints excluded: chain F residue 2 GLN Chi-restraints excluded: chain F residue 51 ILE Chi-restraints excluded: chain F residue 67 LEU Chi-restraints excluded: chain F residue 68 THR Chi-restraints excluded: chain F residue 77 VAL Chi-restraints excluded: chain F residue 80 GLN Chi-restraints excluded: chain F residue 100 LYS Chi-restraints excluded: chain G residue 11 VAL Chi-restraints excluded: chain G residue 75 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 234 random chunks: chunk 135 optimal weight: 9.9990 chunk 142 optimal weight: 5.9990 chunk 21 optimal weight: 7.9990 chunk 217 optimal weight: 7.9990 chunk 146 optimal weight: 10.0000 chunk 69 optimal weight: 9.9990 chunk 66 optimal weight: 5.9990 chunk 11 optimal weight: 0.9980 chunk 159 optimal weight: 0.3980 chunk 156 optimal weight: 6.9990 chunk 139 optimal weight: 2.9990 overall best weight: 3.2786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 591 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 651 ASN ** B 591 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 651 ASN ** E 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 591 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 651 ASN ** G 70 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3527 r_free = 0.3527 target = 0.098010 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3090 r_free = 0.3090 target = 0.075041 restraints weight = 53451.569| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3105 r_free = 0.3105 target = 0.076199 restraints weight = 35358.167| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3127 r_free = 0.3127 target = 0.077150 restraints weight = 25011.300| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3154 r_free = 0.3154 target = 0.078415 restraints weight = 21368.699| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3159 r_free = 0.3159 target = 0.078597 restraints weight = 18626.864| |-----------------------------------------------------------------------------| r_work (final): 0.3152 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8190 moved from start: 0.5039 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.076 20877 Z= 0.243 Angle : 0.786 8.123 28587 Z= 0.380 Chirality : 0.048 0.282 3564 Planarity : 0.004 0.064 3372 Dihedral : 5.625 25.293 2553 Min Nonbonded Distance : 2.291 Molprobity Statistics. All-atom Clashscore : 10.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.69 % Favored : 95.31 % Rotamer: Outliers : 3.19 % Allowed : 11.86 % Favored : 84.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.49 (0.17), residues: 2325 helix: 0.12 (0.26), residues: 420 sheet: 0.22 (0.20), residues: 666 loop : -0.74 (0.17), residues: 1239 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG C 66 TYR 0.014 0.002 TYR D 92 PHE 0.021 0.003 PHE B 383 TRP 0.026 0.002 TRP A 571 HIS 0.008 0.002 HIS B 105 Details of bonding type rmsd/Z covalent geometry : bond 0.00559 / 0.24 (20703) covalent geometry : angle 0.75052 / 0.37 (28104) SS BOND : bond 0.00418 / 0.29 ( 39) SS BOND : angle 1.68693 / 1.31 ( 78) hydrogen bonds : bond 0.04239 / 2.84 ( 776) hydrogen bonds : angle 6.27381 / 4.37 ( 2112) link_ALPHA1-3 : bond 0.00086 / 0.05 ( 6) link_ALPHA1-3 : angle 1.76559 / 1.00 ( 18) link_ALPHA1-6 : bond 0.00503 / 0.27 ( 6) link_ALPHA1-6 : angle 1.62857 / 0.94 ( 18) link_BETA1-4 : bond 0.00335 / 0.21 ( 54) link_BETA1-4 : angle 1.47960 / 1.04 ( 162) link_BETA1-6 : bond 0.00409 / 0.21 ( 3) link_BETA1-6 : angle 1.99078 / 0.90 ( 9) link_NAG-ASN : bond 0.00450 / 0.28 ( 66) link_NAG-ASN : angle 2.37040 / 1.55 ( 198) *********************** 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 308 residues out of total 2040 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 243 time to evaluate : 0.797 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 104 MET cc_start: 0.9016 (OUTLIER) cc_final: 0.8578 (tpt) REVERT: A 207 LYS cc_start: 0.8220 (mmtt) cc_final: 0.7741 (tptp) REVERT: A 387 THR cc_start: 0.8999 (p) cc_final: 0.8605 (t) REVERT: A 629 MET cc_start: 0.8905 (mmm) cc_final: 0.8489 (mmt) REVERT: A 650 GLN cc_start: 0.7438 (OUTLIER) cc_final: 0.7136 (mp10) REVERT: H 35 MET cc_start: 0.7511 (OUTLIER) cc_final: 0.7058 (mmp) REVERT: H 67 LEU cc_start: 0.7590 (tp) cc_final: 0.7148 (mt) REVERT: H 71 LYS cc_start: 0.6746 (ttpt) cc_final: 0.5975 (ptpp) REVERT: H 80 GLN cc_start: 0.8278 (mp10) cc_final: 0.7991 (mp10) REVERT: L 27 GLU cc_start: 0.6125 (mp0) cc_final: 0.5853 (mp0) REVERT: L 49 TYR cc_start: 0.7518 (m-80) cc_final: 0.7010 (m-80) REVERT: L 74 THR cc_start: 0.8214 (p) cc_final: 0.8014 (p) REVERT: L 87 TYR cc_start: 0.5387 (m-80) cc_final: 0.4931 (m-80) REVERT: L 95 ASP cc_start: 0.7915 (t70) cc_final: 0.7547 (t0) REVERT: B 207 LYS cc_start: 0.8277 (mmtt) cc_final: 0.7863 (tmtt) REVERT: C 66 ARG cc_start: 0.7308 (ttp-110) cc_final: 0.7100 (ttp-110) REVERT: C 71 LYS cc_start: 0.6997 (ttpt) cc_final: 0.5897 (pttm) REVERT: D 4 MET cc_start: 0.6505 (ttp) cc_final: 0.6292 (ttm) REVERT: D 53 LYS cc_start: 0.8305 (pttp) cc_final: 0.8046 (pttp) REVERT: D 70 GLN cc_start: 0.7916 (tp-100) cc_final: 0.6940 (pp30) REVERT: D 73 LEU cc_start: 0.6971 (tp) cc_final: 0.6762 (tt) REVERT: E 104 MET cc_start: 0.9037 (ttt) cc_final: 0.8757 (tpp) REVERT: E 207 LYS cc_start: 0.8371 (mmtt) cc_final: 0.7847 (tmtt) REVERT: E 530 MET cc_start: 0.9049 (mtm) cc_final: 0.8618 (ttm) REVERT: E 536 THR cc_start: 0.9393 (OUTLIER) cc_final: 0.9169 (m) REVERT: E 629 MET cc_start: 0.8945 (mmm) cc_final: 0.8397 (mmm) REVERT: E 650 GLN cc_start: 0.7552 (OUTLIER) cc_final: 0.7207 (mp10) REVERT: F 62 TRP cc_start: 0.7911 (t60) cc_final: 0.7587 (t60) REVERT: F 67 LEU cc_start: 0.7546 (OUTLIER) cc_final: 0.6953 (mt) REVERT: F 81 MET cc_start: 0.7534 (tpp) cc_final: 0.7285 (tpp) REVERT: F 100 LYS cc_start: 0.8318 (OUTLIER) cc_final: 0.7715 (ttpp) REVERT: G 87 TYR cc_start: 0.5672 (m-80) cc_final: 0.5427 (m-80) outliers start: 65 outliers final: 38 residues processed: 285 average time/residue: 0.1540 time to fit residues: 67.3193 Evaluate side-chains 264 residues out of total 2040 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 219 time to evaluate : 0.766 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 104 MET Chi-restraints excluded: chain A residue 159 PHE Chi-restraints excluded: chain A residue 213 ILE Chi-restraints excluded: chain A residue 536 THR Chi-restraints excluded: chain A residue 587 LEU Chi-restraints excluded: chain A residue 650 GLN Chi-restraints excluded: chain H residue 35 MET Chi-restraints excluded: chain H residue 51 ILE Chi-restraints excluded: chain H residue 68 THR Chi-restraints excluded: chain H residue 77 VAL Chi-restraints excluded: chain H residue 82 THR Chi-restraints excluded: chain H residue 100 LEU Chi-restraints excluded: chain L residue 75 ILE Chi-restraints excluded: chain L residue 89 LEU Chi-restraints excluded: chain B residue 56 SER Chi-restraints excluded: chain B residue 159 PHE Chi-restraints excluded: chain B residue 213 ILE Chi-restraints excluded: chain B residue 320 THR Chi-restraints excluded: chain B residue 430 VAL Chi-restraints excluded: chain B residue 488 VAL Chi-restraints excluded: chain B residue 536 THR Chi-restraints excluded: chain B residue 538 THR Chi-restraints excluded: chain B residue 570 VAL Chi-restraints excluded: chain C residue 51 ILE Chi-restraints excluded: chain C residue 68 THR Chi-restraints excluded: chain C residue 77 VAL Chi-restraints excluded: chain D residue 37 GLN Chi-restraints excluded: chain D residue 75 ILE Chi-restraints excluded: chain D residue 89 LEU Chi-restraints excluded: chain E residue 50 THR Chi-restraints excluded: chain E residue 159 PHE Chi-restraints excluded: chain E residue 271 ILE Chi-restraints excluded: chain E residue 430 VAL Chi-restraints excluded: chain E residue 536 THR Chi-restraints excluded: chain E residue 538 THR Chi-restraints excluded: chain E residue 570 VAL Chi-restraints excluded: chain E residue 650 GLN Chi-restraints excluded: chain F residue 51 ILE Chi-restraints excluded: chain F residue 67 LEU Chi-restraints excluded: chain F residue 68 THR Chi-restraints excluded: chain F residue 77 VAL Chi-restraints excluded: chain F residue 80 GLN Chi-restraints excluded: chain F residue 100 LYS Chi-restraints excluded: chain G residue 75 ILE Chi-restraints excluded: chain G residue 89 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 234 random chunks: chunk 59 optimal weight: 0.1980 chunk 93 optimal weight: 3.9990 chunk 31 optimal weight: 7.9990 chunk 184 optimal weight: 1.9990 chunk 141 optimal weight: 0.0770 chunk 35 optimal weight: 0.0570 chunk 99 optimal weight: 0.3980 chunk 168 optimal weight: 0.0970 chunk 134 optimal weight: 6.9990 chunk 109 optimal weight: 7.9990 chunk 129 optimal weight: 0.5980 overall best weight: 0.1654 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 591 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 651 ASN B 652 GLN ** E 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 591 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 651 ASN F 2 GLN F 80 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3605 r_free = 0.3605 target = 0.102551 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3191 r_free = 0.3191 target = 0.080012 restraints weight = 52317.728| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3206 r_free = 0.3206 target = 0.081317 restraints weight = 34327.678| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3227 r_free = 0.3227 target = 0.082287 restraints weight = 24170.292| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3254 r_free = 0.3254 target = 0.083480 restraints weight = 20121.065| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3257 r_free = 0.3257 target = 0.083623 restraints weight = 17925.266| |-----------------------------------------------------------------------------| r_work (final): 0.3252 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8068 moved from start: 0.5238 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.059 20877 Z= 0.119 Angle : 0.690 10.067 28587 Z= 0.335 Chirality : 0.045 0.228 3564 Planarity : 0.004 0.071 3372 Dihedral : 5.129 24.549 2553 Min Nonbonded Distance : 2.404 Molprobity Statistics. All-atom Clashscore : 9.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.87 % Favored : 96.13 % Rotamer: Outliers : 2.21 % Allowed : 13.04 % Favored : 84.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.15 (0.17), residues: 2325 helix: 0.93 (0.27), residues: 384 sheet: 0.28 (0.20), residues: 702 loop : -0.61 (0.18), residues: 1239 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A 542 TYR 0.020 0.001 TYR D 92 PHE 0.017 0.002 PHE E 376 TRP 0.024 0.002 TRP H 47 HIS 0.004 0.001 HIS A 374 Details of bonding type rmsd/Z covalent geometry : bond 0.00250 / 0.12 (20703) covalent geometry : angle 0.66121 / 0.33 (28104) SS BOND : bond 0.00540 / 0.24 ( 39) SS BOND : angle 1.43066 / 1.11 ( 78) hydrogen bonds : bond 0.03726 / 2.54 ( 776) hydrogen bonds : angle 5.99535 / 4.16 ( 2112) link_ALPHA1-3 : bond 0.00251 / 0.13 ( 6) link_ALPHA1-3 : angle 1.41659 / 0.81 ( 18) link_ALPHA1-6 : bond 0.00590 / 0.31 ( 6) link_ALPHA1-6 : angle 1.46410 / 0.82 ( 18) link_BETA1-4 : bond 0.00453 / 0.29 ( 54) link_BETA1-4 : angle 1.25318 / 0.90 ( 162) link_BETA1-6 : bond 0.00083 / 0.04 ( 3) link_BETA1-6 : angle 1.49949 / 0.69 ( 9) link_NAG-ASN : bond 0.00455 / 0.31 ( 66) link_NAG-ASN : angle 2.01406 / 1.26 ( 198) *********************** 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 295 residues out of total 2040 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 250 time to evaluate : 0.764 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 104 MET cc_start: 0.8817 (OUTLIER) cc_final: 0.8456 (tpt) REVERT: A 207 LYS cc_start: 0.8181 (mmtt) cc_final: 0.7506 (tptp) REVERT: A 387 THR cc_start: 0.8980 (p) cc_final: 0.8556 (t) REVERT: A 620 ASP cc_start: 0.6585 (OUTLIER) cc_final: 0.6276 (t0) REVERT: A 650 GLN cc_start: 0.7352 (OUTLIER) cc_final: 0.7082 (mp10) REVERT: H 36 TRP cc_start: 0.6411 (m100) cc_final: 0.6044 (m100) REVERT: H 102 LEU cc_start: 0.8241 (mm) cc_final: 0.7885 (mm) REVERT: H 108 LEU cc_start: 0.7167 (tp) cc_final: 0.6696 (tt) REVERT: L 49 TYR cc_start: 0.7534 (m-80) cc_final: 0.7000 (m-80) REVERT: L 63 LYS cc_start: 0.7693 (tptp) cc_final: 0.7299 (mptt) REVERT: L 87 TYR cc_start: 0.5301 (m-80) cc_final: 0.4697 (m-80) REVERT: L 95 ASP cc_start: 0.8015 (t70) cc_final: 0.7673 (t0) REVERT: B 84 MET cc_start: 0.7388 (tmm) cc_final: 0.6933 (tmm) REVERT: B 207 LYS cc_start: 0.8277 (mmtt) cc_final: 0.7792 (tmtt) REVERT: B 530 MET cc_start: 0.8781 (mtm) cc_final: 0.8471 (mtm) REVERT: B 650 GLN cc_start: 0.7485 (OUTLIER) cc_final: 0.7246 (mp10) REVERT: C 47 TRP cc_start: 0.6535 (t-100) cc_final: 0.6100 (t-100) REVERT: D 4 MET cc_start: 0.6465 (ttp) cc_final: 0.6225 (ttm) REVERT: D 24 ARG cc_start: 0.8704 (mmm-85) cc_final: 0.8361 (mmm-85) REVERT: D 70 GLN cc_start: 0.7792 (tp-100) cc_final: 0.6984 (pp30) REVERT: E 207 LYS cc_start: 0.8282 (mmtt) cc_final: 0.7815 (tmtt) REVERT: E 387 THR cc_start: 0.8864 (p) cc_final: 0.8332 (t) REVERT: E 620 ASP cc_start: 0.6682 (OUTLIER) cc_final: 0.6247 (t0) REVERT: E 629 MET cc_start: 0.8701 (mmm) cc_final: 0.8340 (mmm) REVERT: E 650 GLN cc_start: 0.7238 (OUTLIER) cc_final: 0.6861 (mp10) REVERT: F 2 GLN cc_start: 0.8127 (OUTLIER) cc_final: 0.7128 (pp30) REVERT: F 36 TRP cc_start: 0.6490 (m100) cc_final: 0.6126 (m100) REVERT: F 67 LEU cc_start: 0.7278 (tp) cc_final: 0.6829 (mt) REVERT: F 100 LYS cc_start: 0.8197 (OUTLIER) cc_final: 0.7843 (ttmt) outliers start: 45 outliers final: 23 residues processed: 277 average time/residue: 0.1545 time to fit residues: 65.1953 Evaluate side-chains 255 residues out of total 2040 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 224 time to evaluate : 0.753 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 104 MET Chi-restraints excluded: chain A residue 620 ASP Chi-restraints excluded: chain A residue 650 GLN Chi-restraints excluded: chain H residue 68 THR Chi-restraints excluded: chain H residue 82 THR Chi-restraints excluded: chain L residue 75 ILE Chi-restraints excluded: chain L residue 89 LEU Chi-restraints excluded: chain B residue 159 PHE Chi-restraints excluded: chain B residue 430 VAL Chi-restraints excluded: chain B residue 488 VAL Chi-restraints excluded: chain B residue 650 GLN Chi-restraints excluded: chain C residue 51 ILE Chi-restraints excluded: chain C residue 68 THR Chi-restraints excluded: chain C residue 77 VAL Chi-restraints excluded: chain C residue 82 THR Chi-restraints excluded: chain D residue 37 GLN Chi-restraints excluded: chain D residue 47 LEU Chi-restraints excluded: chain D residue 75 ILE Chi-restraints excluded: chain D residue 89 LEU Chi-restraints excluded: chain E residue 159 PHE Chi-restraints excluded: chain E residue 271 ILE Chi-restraints excluded: chain E residue 430 VAL Chi-restraints excluded: chain E residue 536 THR Chi-restraints excluded: chain E residue 538 THR Chi-restraints excluded: chain E residue 620 ASP Chi-restraints excluded: chain E residue 650 GLN Chi-restraints excluded: chain E residue 651 ASN Chi-restraints excluded: chain F residue 2 GLN Chi-restraints excluded: chain F residue 68 THR Chi-restraints excluded: chain F residue 100 LYS Chi-restraints excluded: chain G residue 75 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 234 random chunks: chunk 203 optimal weight: 0.9980 chunk 197 optimal weight: 6.9990 chunk 51 optimal weight: 2.9990 chunk 87 optimal weight: 0.0270 chunk 77 optimal weight: 20.0000 chunk 100 optimal weight: 9.9990 chunk 33 optimal weight: 5.9990 chunk 84 optimal weight: 5.9990 chunk 17 optimal weight: 3.9990 chunk 105 optimal weight: 1.9990 chunk 61 optimal weight: 1.9990 overall best weight: 1.6044 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 591 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 651 ASN ** E 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 591 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 651 ASN F 2 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3570 r_free = 0.3570 target = 0.100546 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3151 r_free = 0.3151 target = 0.078036 restraints weight = 52577.353| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3164 r_free = 0.3164 target = 0.079178 restraints weight = 34513.943| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3186 r_free = 0.3186 target = 0.080200 restraints weight = 25154.142| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3197 r_free = 0.3197 target = 0.080613 restraints weight = 21623.415| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3202 r_free = 0.3202 target = 0.080829 restraints weight = 19685.350| |-----------------------------------------------------------------------------| r_work (final): 0.3194 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8131 moved from start: 0.5338 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.081 20877 Z= 0.157 Angle : 0.706 10.112 28587 Z= 0.343 Chirality : 0.046 0.356 3564 Planarity : 0.004 0.063 3372 Dihedral : 5.198 45.356 2553 Min Nonbonded Distance : 2.235 Molprobity Statistics. All-atom Clashscore : 9.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.13 % Favored : 95.87 % Rotamer: Outliers : 1.76 % Allowed : 13.63 % Favored : 84.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % 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: -0.16 (0.17), residues: 2325 helix: 0.99 (0.27), residues: 381 sheet: 0.28 (0.19), residues: 729 loop : -0.66 (0.18), residues: 1215 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG C 66 TYR 0.019 0.001 TYR D 92 PHE 0.028 0.002 PHE L 71 TRP 0.027 0.002 TRP A 571 HIS 0.006 0.001 HIS E 105 Details of bonding type rmsd/Z covalent geometry : bond 0.00367 / 0.16 (20703) covalent geometry : angle 0.67293 / 0.34 (28104) SS BOND : bond 0.00329 / 0.25 ( 39) SS BOND : angle 1.42128 / 1.08 ( 78) hydrogen bonds : bond 0.03752 / 2.53 ( 776) hydrogen bonds : angle 5.95080 / 4.14 ( 2112) link_ALPHA1-3 : bond 0.00151 / 0.08 ( 6) link_ALPHA1-3 : angle 1.54827 / 0.89 ( 18) link_ALPHA1-6 : bond 0.00490 / 0.26 ( 6) link_ALPHA1-6 : angle 1.47000 / 0.84 ( 18) link_BETA1-4 : bond 0.00377 / 0.24 ( 54) link_BETA1-4 : angle 1.32222 / 0.93 ( 162) link_BETA1-6 : bond 0.00083 / 0.04 ( 3) link_BETA1-6 : angle 1.66099 / 0.76 ( 9) link_NAG-ASN : bond 0.00355 / 0.25 ( 66) link_NAG-ASN : angle 2.22117 / 1.44 ( 198) *********************** 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 268 residues out of total 2040 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 232 time to evaluate : 0.756 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 104 MET cc_start: 0.8896 (OUTLIER) cc_final: 0.8443 (tpt) REVERT: A 111 LEU cc_start: 0.8743 (mt) cc_final: 0.8427 (tt) REVERT: A 207 LYS cc_start: 0.8221 (mmtt) cc_final: 0.7601 (tptp) REVERT: A 387 THR cc_start: 0.9012 (p) cc_final: 0.8589 (t) REVERT: A 650 GLN cc_start: 0.7518 (OUTLIER) cc_final: 0.7258 (mp10) REVERT: H 36 TRP cc_start: 0.6385 (m100) cc_final: 0.6053 (m100) REVERT: H 47 TRP cc_start: 0.6611 (t-100) cc_final: 0.6170 (t-100) REVERT: H 102 LEU cc_start: 0.8370 (mm) cc_final: 0.8002 (mm) REVERT: H 108 LEU cc_start: 0.7060 (tp) cc_final: 0.6618 (tt) REVERT: L 27 GLU cc_start: 0.6369 (mp0) cc_final: 0.6081 (mp0) REVERT: L 49 TYR cc_start: 0.7532 (m-80) cc_final: 0.7029 (m-80) REVERT: L 63 LYS cc_start: 0.7689 (tptp) cc_final: 0.7271 (mptt) REVERT: L 87 TYR cc_start: 0.5527 (m-80) cc_final: 0.4912 (m-80) REVERT: L 95 ASP cc_start: 0.8084 (t70) cc_final: 0.7745 (t0) REVERT: B 207 LYS cc_start: 0.8302 (mmtt) cc_final: 0.7824 (tmtt) REVERT: B 650 GLN cc_start: 0.7597 (OUTLIER) cc_final: 0.7349 (mp10) REVERT: C 47 TRP cc_start: 0.6480 (t-100) cc_final: 0.6025 (t-100) REVERT: D 4 MET cc_start: 0.6484 (ttp) cc_final: 0.6229 (ttm) REVERT: D 24 ARG cc_start: 0.8723 (mmm-85) cc_final: 0.8332 (mmm-85) REVERT: D 70 GLN cc_start: 0.7909 (tp-100) cc_final: 0.7096 (pp30) REVERT: E 104 MET cc_start: 0.8788 (tpp) cc_final: 0.8540 (tpt) REVERT: E 207 LYS cc_start: 0.8342 (mmtt) cc_final: 0.7852 (tmtt) REVERT: E 387 THR cc_start: 0.8889 (p) cc_final: 0.8385 (t) REVERT: E 629 MET cc_start: 0.8826 (mmm) cc_final: 0.8346 (mmm) REVERT: E 650 GLN cc_start: 0.7366 (OUTLIER) cc_final: 0.6936 (mp10) REVERT: F 2 GLN cc_start: 0.8016 (OUTLIER) cc_final: 0.7065 (pp30) REVERT: F 36 TRP cc_start: 0.6504 (m100) cc_final: 0.6082 (m100) REVERT: F 62 TRP cc_start: 0.7799 (t60) cc_final: 0.7515 (t60) REVERT: F 66 ARG cc_start: 0.7587 (ttp-110) cc_final: 0.7382 (ttp-110) REVERT: F 67 LEU cc_start: 0.7158 (OUTLIER) cc_final: 0.6732 (mt) REVERT: F 100 LYS cc_start: 0.8172 (OUTLIER) cc_final: 0.7639 (ttmt) REVERT: G 87 TYR cc_start: 0.5532 (m-80) cc_final: 0.5140 (m-80) outliers start: 36 outliers final: 21 residues processed: 253 average time/residue: 0.1477 time to fit residues: 57.3852 Evaluate side-chains 252 residues out of total 2040 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 224 time to evaluate : 0.735 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 104 MET Chi-restraints excluded: chain A residue 159 PHE Chi-restraints excluded: chain A residue 213 ILE Chi-restraints excluded: chain A residue 650 GLN Chi-restraints excluded: chain A residue 651 ASN Chi-restraints excluded: chain H residue 68 THR Chi-restraints excluded: chain L residue 75 ILE Chi-restraints excluded: chain B residue 159 PHE Chi-restraints excluded: chain B residue 187 ASN Chi-restraints excluded: chain B residue 430 VAL Chi-restraints excluded: chain B residue 488 VAL Chi-restraints excluded: chain B residue 650 GLN Chi-restraints excluded: chain C residue 51 ILE Chi-restraints excluded: chain C residue 68 THR Chi-restraints excluded: chain C residue 77 VAL Chi-restraints excluded: chain C residue 100 HIS Chi-restraints excluded: chain D residue 75 ILE Chi-restraints excluded: chain E residue 159 PHE Chi-restraints excluded: chain E residue 271 ILE Chi-restraints excluded: chain E residue 430 VAL Chi-restraints excluded: chain E residue 536 THR Chi-restraints excluded: chain E residue 538 THR Chi-restraints excluded: chain E residue 650 GLN Chi-restraints excluded: chain F residue 2 GLN Chi-restraints excluded: chain F residue 67 LEU Chi-restraints excluded: chain F residue 68 THR Chi-restraints excluded: chain F residue 100 LYS Chi-restraints excluded: chain G residue 75 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 234 random chunks: chunk 183 optimal weight: 6.9990 chunk 5 optimal weight: 7.9990 chunk 207 optimal weight: 3.9990 chunk 90 optimal weight: 0.9990 chunk 219 optimal weight: 9.9990 chunk 205 optimal weight: 4.9990 chunk 26 optimal weight: 6.9990 chunk 35 optimal weight: 5.9990 chunk 191 optimal weight: 0.6980 chunk 31 optimal weight: 7.9990 chunk 204 optimal weight: 0.9980 overall best weight: 2.3386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 591 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 651 ASN ** E 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 591 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 651 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3556 r_free = 0.3556 target = 0.099641 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3126 r_free = 0.3126 target = 0.076803 restraints weight = 53232.258| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3143 r_free = 0.3143 target = 0.078112 restraints weight = 34443.504| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3165 r_free = 0.3165 target = 0.079089 restraints weight = 24815.048| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3175 r_free = 0.3175 target = 0.079474 restraints weight = 21550.920| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3179 r_free = 0.3179 target = 0.079670 restraints weight = 19537.336| |-----------------------------------------------------------------------------| r_work (final): 0.3171 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8166 moved from start: 0.5441 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.083 20877 Z= 0.191 Angle : 0.745 13.412 28587 Z= 0.361 Chirality : 0.046 0.303 3564 Planarity : 0.004 0.062 3372 Dihedral : 5.300 37.981 2553 Min Nonbonded Distance : 2.269 Molprobity Statistics. All-atom Clashscore : 10.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.47 % Favored : 95.53 % Rotamer: Outliers : 1.67 % Allowed : 13.82 % Favored : 84.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % 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: -0.20 (0.17), residues: 2325 helix: 0.88 (0.26), residues: 381 sheet: 0.30 (0.19), residues: 711 loop : -0.69 (0.18), residues: 1233 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG C 66 TYR 0.018 0.002 TYR D 92 PHE 0.025 0.002 PHE L 71 TRP 0.037 0.002 TRP A 571 HIS 0.006 0.001 HIS A 105 Details of bonding type rmsd/Z covalent geometry : bond 0.00441 / 0.19 (20703) covalent geometry : angle 0.70621 / 0.35 (28104) SS BOND : bond 0.00426 / 0.31 ( 39) SS BOND : angle 2.22291 / 1.55 ( 78) hydrogen bonds : bond 0.03846 / 2.56 ( 776) hydrogen bonds : angle 6.00811 / 4.18 ( 2112) link_ALPHA1-3 : bond 0.00057 / 0.03 ( 6) link_ALPHA1-3 : angle 1.63003 / 0.93 ( 18) link_ALPHA1-6 : bond 0.00497 / 0.27 ( 6) link_ALPHA1-6 : angle 1.52845 / 0.88 ( 18) link_BETA1-4 : bond 0.00352 / 0.22 ( 54) link_BETA1-4 : angle 1.37141 / 0.97 ( 162) link_BETA1-6 : bond 0.00209 / 0.11 ( 3) link_BETA1-6 : angle 1.77862 / 0.81 ( 9) link_NAG-ASN : bond 0.00372 / 0.25 ( 66) link_NAG-ASN : angle 2.27624 / 1.48 ( 198) ********************** 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 254 residues out of total 2040 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 220 time to evaluate : 0.688 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 104 MET cc_start: 0.8860 (OUTLIER) cc_final: 0.8401 (tpt) REVERT: A 111 LEU cc_start: 0.8764 (mt) cc_final: 0.8398 (tt) REVERT: A 207 LYS cc_start: 0.8105 (mmtt) cc_final: 0.7625 (tptp) REVERT: A 387 THR cc_start: 0.9031 (p) cc_final: 0.8614 (t) REVERT: A 650 GLN cc_start: 0.7429 (OUTLIER) cc_final: 0.7228 (mp10) REVERT: H 36 TRP cc_start: 0.6328 (m100) cc_final: 0.6022 (m100) REVERT: H 47 TRP cc_start: 0.6469 (t-100) cc_final: 0.6085 (t-100) REVERT: H 108 LEU cc_start: 0.7053 (tp) cc_final: 0.6606 (tt) REVERT: L 27 GLU cc_start: 0.6433 (mp0) cc_final: 0.6107 (mp0) REVERT: L 49 TYR cc_start: 0.7547 (m-80) cc_final: 0.7031 (m-80) REVERT: L 63 LYS cc_start: 0.7742 (tptp) cc_final: 0.7297 (mptt) REVERT: L 87 TYR cc_start: 0.5477 (m-80) cc_final: 0.4979 (m-80) REVERT: L 95 ASP cc_start: 0.8094 (t70) cc_final: 0.7854 (t0) REVERT: B 207 LYS cc_start: 0.8340 (mmtt) cc_final: 0.7841 (tmtt) REVERT: B 650 GLN cc_start: 0.7611 (OUTLIER) cc_final: 0.7268 (mp10) REVERT: C 47 TRP cc_start: 0.6360 (t-100) cc_final: 0.5957 (t-100) REVERT: D 4 MET cc_start: 0.6477 (ttp) cc_final: 0.6256 (ttm) REVERT: D 24 ARG cc_start: 0.8735 (mmm-85) cc_final: 0.8339 (mmm-85) REVERT: D 70 GLN cc_start: 0.7934 (tp-100) cc_final: 0.7082 (pp30) REVERT: E 104 MET cc_start: 0.8769 (tpp) cc_final: 0.8518 (tpt) REVERT: E 207 LYS cc_start: 0.8329 (mmtt) cc_final: 0.7862 (tmtt) REVERT: E 629 MET cc_start: 0.8815 (mmm) cc_final: 0.8519 (mmm) REVERT: E 650 GLN cc_start: 0.7366 (OUTLIER) cc_final: 0.6896 (mp10) REVERT: F 36 TRP cc_start: 0.6505 (m100) cc_final: 0.6081 (m100) REVERT: F 62 TRP cc_start: 0.7862 (t60) cc_final: 0.7564 (t60) REVERT: F 67 LEU cc_start: 0.7308 (OUTLIER) cc_final: 0.6656 (mt) REVERT: F 100 LYS cc_start: 0.8075 (OUTLIER) cc_final: 0.7821 (ttmt) outliers start: 34 outliers final: 25 residues processed: 246 average time/residue: 0.1546 time to fit residues: 58.6037 Evaluate side-chains 246 residues out of total 2040 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 215 time to evaluate : 0.639 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 104 MET Chi-restraints excluded: chain A residue 159 PHE Chi-restraints excluded: chain A residue 213 ILE Chi-restraints excluded: chain A residue 650 GLN Chi-restraints excluded: chain H residue 51 ILE Chi-restraints excluded: chain H residue 68 THR Chi-restraints excluded: chain L residue 75 ILE Chi-restraints excluded: chain B residue 159 PHE Chi-restraints excluded: chain B residue 187 ASN Chi-restraints excluded: chain B residue 309 ILE Chi-restraints excluded: chain B residue 320 THR Chi-restraints excluded: chain B residue 430 VAL Chi-restraints excluded: chain B residue 488 VAL Chi-restraints excluded: chain B residue 608 VAL Chi-restraints excluded: chain B residue 650 GLN Chi-restraints excluded: chain C residue 10 ASP Chi-restraints excluded: chain C residue 51 ILE Chi-restraints excluded: chain C residue 68 THR Chi-restraints excluded: chain C residue 77 VAL Chi-restraints excluded: chain C residue 100 HIS Chi-restraints excluded: chain D residue 75 ILE Chi-restraints excluded: chain E residue 159 PHE Chi-restraints excluded: chain E residue 271 ILE Chi-restraints excluded: chain E residue 430 VAL Chi-restraints excluded: chain E residue 536 THR Chi-restraints excluded: chain E residue 538 THR Chi-restraints excluded: chain E residue 650 GLN Chi-restraints excluded: chain F residue 67 LEU Chi-restraints excluded: chain F residue 68 THR Chi-restraints excluded: chain F residue 100 LYS Chi-restraints excluded: chain G residue 75 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 234 random chunks: chunk 3 optimal weight: 0.0070 chunk 16 optimal weight: 0.6980 chunk 76 optimal weight: 6.9990 chunk 96 optimal weight: 4.9990 chunk 118 optimal weight: 5.9990 chunk 0 optimal weight: 7.9990 chunk 11 optimal weight: 4.9990 chunk 32 optimal weight: 3.9990 chunk 190 optimal weight: 10.0000 chunk 14 optimal weight: 0.4980 chunk 211 optimal weight: 40.0000 overall best weight: 2.0402 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 591 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 651 ASN ** H 80 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 591 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 651 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3555 r_free = 0.3555 target = 0.099537 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3132 r_free = 0.3132 target = 0.077041 restraints weight = 53214.045| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3144 r_free = 0.3144 target = 0.078075 restraints weight = 35519.430| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3165 r_free = 0.3165 target = 0.079051 restraints weight = 25803.586| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3179 r_free = 0.3179 target = 0.079649 restraints weight = 22499.089| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3184 r_free = 0.3184 target = 0.079835 restraints weight = 20064.129| |-----------------------------------------------------------------------------| r_work (final): 0.3177 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8157 moved from start: 0.5577 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.080 20877 Z= 0.173 Angle : 0.724 10.782 28587 Z= 0.350 Chirality : 0.046 0.256 3564 Planarity : 0.004 0.059 3372 Dihedral : 5.329 44.637 2553 Min Nonbonded Distance : 2.326 Molprobity Statistics. All-atom Clashscore : 10.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.65 % Favored : 95.35 % Rotamer: Outliers : 1.62 % Allowed : 14.02 % Favored : 84.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % 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: -0.19 (0.17), residues: 2325 helix: 0.92 (0.26), residues: 381 sheet: 0.30 (0.19), residues: 711 loop : -0.69 (0.18), residues: 1233 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG C 66 TYR 0.019 0.001 TYR D 92 PHE 0.021 0.002 PHE L 71 TRP 0.031 0.002 TRP A 571 HIS 0.006 0.001 HIS A 105 Details of bonding type rmsd/Z covalent geometry : bond 0.00403 / 0.17 (20703) covalent geometry : angle 0.68880 / 0.34 (28104) SS BOND : bond 0.00407 / 0.31 ( 39) SS BOND : angle 1.83177 / 1.26 ( 78) hydrogen bonds : bond 0.03766 / 2.52 ( 776) hydrogen bonds : angle 5.98555 / 4.16 ( 2112) link_ALPHA1-3 : bond 0.00071 / 0.04 ( 6) link_ALPHA1-3 : angle 1.61237 / 0.92 ( 18) link_ALPHA1-6 : bond 0.00506 / 0.27 ( 6) link_ALPHA1-6 : angle 1.52076 / 0.88 ( 18) link_BETA1-4 : bond 0.00349 / 0.22 ( 54) link_BETA1-4 : angle 1.34686 / 0.95 ( 162) link_BETA1-6 : bond 0.00212 / 0.11 ( 3) link_BETA1-6 : angle 1.77947 / 0.81 ( 9) link_NAG-ASN : bond 0.00354 / 0.24 ( 66) link_NAG-ASN : angle 2.24031 / 1.44 ( 198) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3012.37 seconds wall clock time: 53 minutes 23.24 seconds (3203.24 seconds total)