Starting phenix.real_space_refine on Thu Mar 5 23:58:37 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7mxe_24072/03_2026/7mxe_24072.cif Found real_map, /net/cci-nas-00/data/ceres_data/7mxe_24072/03_2026/7mxe_24072.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.7 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/7mxe_24072/03_2026/7mxe_24072.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7mxe_24072/03_2026/7mxe_24072.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7mxe_24072/03_2026/7mxe_24072.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7mxe_24072/03_2026/7mxe_24072.map" } resolution = 3.7 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= 0.004 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 5338 atoms to isotropic. 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 124 5.16 5 C 13833 2.51 5 N 3672 2.21 5 O 4520 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 109 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 22149 Number of models: 1 Model: "" Number of chains: 51 Chain: "A" Number of atoms: 1014 Number of conformers: 1 Conformer: "" Number of residues, atoms: 132, 1014 Classifications: {'peptide': 132} Link IDs: {'PTRANS': 4, 'TRANS': 127} Chain: "B" Number of atoms: 795 Number of conformers: 1 Conformer: "" Number of residues, atoms: 108, 795 Classifications: {'peptide': 108} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'PCIS': 2, 'PTRANS': 3, 'TRANS': 102} Unresolved non-hydrogen bonds: 28 Unresolved non-hydrogen angles: 31 Unresolved non-hydrogen dihedrals: 25 Planarities with less than four sites: {'ARG:plan': 2, 'GLN:plan1': 1} Unresolved non-hydrogen planarities: 14 Chain: "C" Number of atoms: 988 Number of conformers: 1 Conformer: "" Number of residues, atoms: 124, 988 Classifications: {'peptide': 124} Link IDs: {'PTRANS': 1, 'TRANS': 122} Chain breaks: 1 Chain: "D" Number of atoms: 975 Number of conformers: 1 Conformer: "" Number of residues, atoms: 122, 975 Classifications: {'peptide': 122} Link IDs: {'PTRANS': 1, 'TRANS': 120} Chain breaks: 1 Chain: "F" Number of atoms: 822 Number of conformers: 1 Conformer: "" Number of residues, atoms: 99, 822 Classifications: {'peptide': 99} Link IDs: {'PTRANS': 1, 'TRANS': 97} Chain: "G" Number of atoms: 3479 Number of conformers: 1 Conformer: "" Number of residues, atoms: 442, 3479 Classifications: {'peptide': 442} Link IDs: {'PTRANS': 22, 'TRANS': 419} Chain breaks: 3 Chain: "H" Number of atoms: 1014 Number of conformers: 1 Conformer: "" Number of residues, atoms: 132, 1014 Classifications: {'peptide': 132} Link IDs: {'PTRANS': 4, 'TRANS': 127} Chain: "J" Number of atoms: 3479 Number of conformers: 1 Conformer: "" Number of residues, atoms: 442, 3479 Classifications: {'peptide': 442} Link IDs: {'PTRANS': 22, 'TRANS': 419} Chain breaks: 3 Chain: "L" Number of atoms: 823 Number of conformers: 1 Conformer: "" Number of residues, atoms: 108, 823 Classifications: {'peptide': 108} Link IDs: {'PCIS': 2, 'PTRANS': 3, 'TRANS': 102} Chain: "M" Number of atoms: 1014 Number of conformers: 1 Conformer: "" Number of residues, atoms: 132, 1014 Classifications: {'peptide': 132} Link IDs: {'PTRANS': 4, 'TRANS': 127} Chain: "O" Number of atoms: 799 Number of conformers: 1 Conformer: "" Number of residues, atoms: 108, 799 Classifications: {'peptide': 108} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PCIS': 2, 'PTRANS': 3, 'TRANS': 102} Unresolved non-hydrogen bonds: 24 Unresolved non-hydrogen angles: 27 Unresolved non-hydrogen dihedrals: 21 Planarities with less than four sites: {'ARG:plan': 2, 'GLN:plan1': 1} Unresolved non-hydrogen planarities: 14 Chain: "P" Number of atoms: 3449 Number of conformers: 1 Conformer: "" Number of residues, atoms: 438, 3449 Classifications: {'peptide': 438} Link IDs: {'PTRANS': 20, 'TRANS': 417} Chain breaks: 4 Chain: "R" Number of atoms: 989 Number of conformers: 1 Conformer: "" Number of residues, atoms: 129, 989 Classifications: {'peptide': 129} Link IDs: {'PTRANS': 6, 'TRANS': 122} Chain: "W" Number of atoms: 840 Number of conformers: 1 Conformer: "" Number of residues, atoms: 116, 840 Classifications: {'peptide': 116} Link IDs: {'PTRANS': 4, 'TRANS': 111} Chain: "E" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "I" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "K" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "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 dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "Q" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "S" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "T" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "U" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "V" Number of atoms: 50 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 50 Unusual residues: {'BMA': 1, 'MAN': 1, 'NAG': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Chain: "X" Number of atoms: 72 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 72 Unusual residues: {'BMA': 1, 'MAN': 3, 'NAG': 2} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 18 Unresolved non-hydrogen chiralities: 6 Chain: "Y" Number of atoms: 127 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 127 Unusual residues: {'BMA': 1, 'MAN': 8, 'NAG': 2} Classifications: {'undetermined': 11} Link IDs: {None: 10} Unresolved non-hydrogen bonds: 11 Unresolved non-hydrogen angles: 22 Unresolved non-hydrogen dihedrals: 33 Unresolved non-hydrogen chiralities: 11 Chain: "Z" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "a" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "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 dihedrals: 6 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 dihedrals: 6 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 dihedrals: 6 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 dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "f" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "g" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "h" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Chain: "i" Number of atoms: 116 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 116 Unusual residues: {'BMA': 1, 'MAN': 7, 'NAG': 2} Classifications: {'undetermined': 10} Link IDs: {None: 9} Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 20 Unresolved non-hydrogen dihedrals: 30 Unresolved non-hydrogen chiralities: 10 Chain: "j" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "k" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "l" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "m" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "n" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "o" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "p" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "q" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "r" Number of atoms: 116 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 116 Unusual residues: {'BMA': 1, 'MAN': 7, 'NAG': 2} Classifications: {'undetermined': 10} Link IDs: {None: 9} Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 20 Unresolved non-hydrogen dihedrals: 30 Unresolved non-hydrogen chiralities: 10 Chain: "s" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Chain: "t" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "C" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "F" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "G" Number of atoms: 126 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 126 Unusual residues: {'NAG': 9} Classifications: {'undetermined': 9} Link IDs: {None: 8} Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 18 Unresolved non-hydrogen dihedrals: 27 Unresolved non-hydrogen chiralities: 9 Chain: "J" Number of atoms: 70 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 70 Unusual residues: {'NAG': 5} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Chain: "P" Number of atoms: 98 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 98 Unusual residues: {'NAG': 7} Classifications: {'undetermined': 7} Link IDs: {None: 6} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 21 Unresolved non-hydrogen chiralities: 7 Time building chain proxies: 4.58, per 1000 atoms: 0.21 Number of scatterers: 22149 At special positions: 0 Unit cell: (127.214, 156.637, 155.772, 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 124 16.00 O 4520 8.00 N 3672 7.00 C 13833 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=40, symmetry=0 Simple disulfide: pdb=" SG CYS A 22 " - pdb=" SG CYS A 92 " distance=2.03 Simple disulfide: pdb=" SG CYS B 23 " - pdb=" SG CYS B 88 " distance=2.03 Simple disulfide: pdb=" SG CYS C 598 " - pdb=" SG CYS C 604 " distance=2.03 Simple disulfide: pdb=" SG CYS D 598 " - pdb=" SG CYS D 604 " distance=2.03 Simple disulfide: pdb=" SG CYS D 605 " - pdb=" SG CYS G 501 " distance=2.03 Simple disulfide: pdb=" SG CYS F 598 " - pdb=" SG CYS F 604 " distance=2.03 Simple disulfide: pdb=" SG CYS F 605 " - pdb=" SG CYS J 501 " distance=2.03 Simple disulfide: pdb=" SG CYS G 54 " - pdb=" SG CYS G 74 " distance=2.03 Simple disulfide: pdb=" SG CYS G 119 " - pdb=" SG CYS G 205 " distance=2.04 Simple disulfide: pdb=" SG CYS G 126 " - pdb=" SG CYS G 196 " distance=2.03 Simple disulfide: pdb=" SG CYS G 131 " - pdb=" SG CYS G 157 " distance=2.03 Simple disulfide: pdb=" SG CYS G 218 " - pdb=" SG CYS G 247 " distance=2.04 Simple disulfide: pdb=" SG CYS G 228 " - pdb=" SG CYS G 239 " distance=2.03 Simple disulfide: pdb=" SG CYS G 296 " - pdb=" SG CYS G 331 " distance=2.03 Simple disulfide: pdb=" SG CYS G 378 " - pdb=" SG CYS G 445 " distance=2.03 Simple disulfide: pdb=" SG CYS G 385 " - pdb=" SG CYS G 418 " distance=2.03 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 92 " distance=2.03 Simple disulfide: pdb=" SG CYS J 54 " - pdb=" SG CYS J 74 " distance=2.03 Simple disulfide: pdb=" SG CYS J 119 " - pdb=" SG CYS J 205 " distance=2.03 Simple disulfide: pdb=" SG CYS J 126 " - pdb=" SG CYS J 196 " distance=2.03 Simple disulfide: pdb=" SG CYS J 131 " - pdb=" SG CYS J 157 " distance=2.03 Simple disulfide: pdb=" SG CYS J 218 " - pdb=" SG CYS J 247 " distance=2.03 Simple disulfide: pdb=" SG CYS J 228 " - pdb=" SG CYS J 239 " distance=2.03 Simple disulfide: pdb=" SG CYS J 296 " - pdb=" SG CYS J 331 " distance=2.03 Simple disulfide: pdb=" SG CYS J 378 " - pdb=" SG CYS J 445 " distance=2.03 Simple disulfide: pdb=" SG CYS J 385 " - pdb=" SG CYS J 418 " distance=2.03 Simple disulfide: pdb=" SG CYS L 23 " - pdb=" SG CYS L 88 " distance=2.03 Simple disulfide: pdb=" SG CYS M 22 " - pdb=" SG CYS M 92 " distance=2.03 Simple disulfide: pdb=" SG CYS O 23 " - pdb=" SG CYS O 88 " distance=2.03 Simple disulfide: pdb=" SG CYS P 54 " - pdb=" SG CYS P 74 " distance=2.03 Simple disulfide: pdb=" SG CYS P 119 " - pdb=" SG CYS P 205 " distance=2.04 Simple disulfide: pdb=" SG CYS P 126 " - pdb=" SG CYS P 196 " distance=2.03 Simple disulfide: pdb=" SG CYS P 131 " - pdb=" SG CYS P 157 " distance=2.03 Simple disulfide: pdb=" SG CYS P 218 " - pdb=" SG CYS P 247 " distance=2.04 Simple disulfide: pdb=" SG CYS P 228 " - pdb=" SG CYS P 239 " distance=2.03 Simple disulfide: pdb=" SG CYS P 296 " - pdb=" SG CYS P 331 " distance=2.03 Simple disulfide: pdb=" SG CYS P 378 " - pdb=" SG CYS P 445 " distance=2.03 Simple disulfide: pdb=" SG CYS P 385 " - pdb=" SG CYS P 418 " distance=2.03 Simple disulfide: pdb=" SG CYS R 22 " - pdb=" SG CYS R 92 " distance=2.03 Simple disulfide: pdb=" SG CYS W 23 " - pdb=" SG CYS W 88 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=2, symmetry=0 Links applied ALPHA1-2 " MAN X 4 " - " MAN X 5 " " MAN Y 4 " - " MAN Y 5 " " MAN Y 5 " - " MAN Y 6 " " MAN Y 8 " - " MAN Y 9 " " MAN Y 10 " - " MAN Y 11 " " MAN i 4 " - " MAN i 5 " " MAN i 5 " - " MAN i 6 " " MAN i 8 " - " MAN i 9 " " MAN r 4 " - " MAN r 5 " " MAN r 5 " - " MAN r 6 " " MAN r 8 " - " MAN r 9 " ALPHA1-3 " BMA V 3 " - " MAN V 4 " " BMA X 3 " - " MAN X 4 " " BMA Y 3 " - " MAN Y 4 " " MAN Y 7 " - " MAN Y 8 " " BMA h 3 " - " MAN h 4 " " BMA i 3 " - " MAN i 4 " " MAN i 7 " - " MAN i 10 " " BMA r 3 " - " MAN r 4 " " MAN r 7 " - " MAN r 10 " " BMA s 3 " - " MAN s 4 " ALPHA1-6 " BMA X 3 " - " MAN X 6 " " BMA Y 3 " - " MAN Y 7 " " MAN Y 7 " - " MAN Y 10 " " BMA h 3 " - " MAN h 5 " " BMA i 3 " - " MAN i 7 " " MAN i 7 " - " MAN i 8 " " BMA r 3 " - " MAN r 7 " " MAN r 7 " - " MAN r 8 " " BMA s 3 " - " MAN s 5 " BETA1-4 " NAG E 1 " - " NAG E 2 " " NAG I 1 " - " NAG I 2 " " NAG K 1 " - " NAG K 2 " " NAG N 1 " - " NAG N 2 " " NAG Q 1 " - " NAG Q 2 " " NAG S 1 " - " NAG S 2 " " NAG T 1 " - " NAG T 2 " " NAG U 1 " - " NAG U 2 " " NAG V 1 " - " NAG V 2 " " NAG V 2 " - " BMA V 3 " " NAG X 1 " - " NAG X 2 " " NAG X 2 " - " BMA X 3 " " NAG Y 1 " - " NAG Y 2 " " NAG Y 2 " - " BMA Y 3 " " NAG Z 1 " - " NAG Z 2 " " NAG 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 g 1 " - " NAG g 2 " " NAG h 1 " - " NAG h 2 " " NAG h 2 " - " BMA h 3 " " NAG i 1 " - " NAG i 2 " " NAG i 2 " - " BMA i 3 " " NAG j 1 " - " NAG j 2 " " NAG j 2 " - " BMA j 3 " " NAG k 1 " - " NAG k 2 " " NAG k 2 " - " BMA k 3 " " NAG l 1 " - " NAG l 2 " " NAG m 1 " - " NAG m 2 " " NAG n 1 " - " NAG n 2 " " NAG o 1 " - " NAG o 2 " " NAG p 1 " - " NAG p 2 " " NAG p 2 " - " BMA p 3 " " NAG q 1 " - " NAG q 2 " " NAG q 2 " - " BMA q 3 " " NAG r 1 " - " NAG r 2 " " NAG r 2 " - " BMA r 3 " " NAG s 1 " - " NAG s 2 " " NAG s 2 " - " BMA s 3 " " NAG t 1 " - " NAG t 2 " NAG-ASN " NAG C 701 " - " ASN C 611 " " NAG E 1 " - " ASN C 637 " " NAG F 701 " - " ASN F 611 " " NAG G 601 " - " ASN G 88 " " NAG G 602 " - " ASN G 295 " " NAG G 603 " - " ASN G 339 " " NAG G 604 " - " ASN G 355 " " NAG G 605 " - " ASN G 386 " " NAG G 606 " - " ASN G 392 " " NAG G 607 " - " ASN G 363 " " NAG G 608 " - " ASN G 448 " " NAG G 609 " - " ASN G 301 " " NAG I 1 " - " ASN D 637 " " NAG J 601 " - " ASN J 133 " " NAG J 602 " - " ASN J 301 " " NAG J 603 " - " ASN J 339 " " NAG J 604 " - " ASN J 355 " " NAG J 605 " - " ASN J 88 " " NAG K 1 " - " ASN F 637 " " NAG N 1 " - " ASN G 133 " " NAG P 601 " - " ASN P 88 " " NAG P 602 " - " ASN P 133 " " NAG P 603 " - " ASN P 197 " " NAG P 604 " - " ASN P 355 " " NAG P 605 " - " ASN P 392 " " NAG P 606 " - " ASN P 363 " " NAG P 607 " - " ASN P 301 " " NAG Q 1 " - " ASN G 156 " " NAG S 1 " - " ASN G 160 " " NAG T 1 " - " ASN G 197 " " NAG U 1 " - " ASN G 332 " " NAG V 1 " - " ASN G 262 " " NAG X 1 " - " ASN G 276 " " NAG Y 1 " - " ASN G 234 " " NAG Z 1 " - " ASN J 156 " " NAG a 1 " - " ASN J 160 " " NAG b 1 " - " ASN J 197 " " NAG c 1 " - " ASN J 295 " " NAG d 1 " - " ASN J 386 " " NAG e 1 " - " ASN J 392 " " NAG f 1 " - " ASN J 363 " " NAG g 1 " - " ASN J 332 " " NAG h 1 " - " ASN J 276 " " NAG i 1 " - " ASN J 234 " " NAG j 1 " - " ASN J 262 " " NAG k 1 " - " ASN J 448 " " NAG l 1 " - " ASN P 156 " " NAG m 1 " - " ASN P 160 " " NAG n 1 " - " ASN P 295 " " NAG o 1 " - " ASN P 448 " " NAG p 1 " - " ASN P 332 " " NAG q 1 " - " ASN P 262 " " NAG r 1 " - " ASN P 234 " " NAG s 1 " - " ASN P 276 " " NAG t 1 " - " ASN P 386 " Number of additional bonds: simple=2, symmetry=0 Coordination: Other bonds: Time building additional restraints: 1.73 Conformation dependent library (CDL) restraints added in 944.1 milliseconds 5160 Ramachandran restraints generated. 2580 Oldfield, 0 Emsley, 2580 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4842 Finding SS restraints... Secondary structure from input PDB file: 35 helices and 44 sheets defined 13.6% alpha, 30.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.80 Creating SS restraints... Processing helix chain 'B' and resid 79 through 83 removed outlier: 3.776A pdb=" N ASP B 82 " --> pdb=" O GLN B 79 " (cutoff:3.500A) removed outlier: 4.113A pdb=" N PHE B 83 " --> pdb=" O ALA B 80 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 79 through 83' Processing helix chain 'C' and resid 536 through 541 removed outlier: 4.324A pdb=" N GLN C 540 " --> pdb=" O THR C 536 " (cutoff:3.500A) Processing helix chain 'C' and resid 569 through 597 removed outlier: 3.749A pdb=" N ILE C 573 " --> pdb=" O THR C 569 " (cutoff:3.500A) removed outlier: 3.786A pdb=" N LYS C 574 " --> pdb=" O VAL C 570 " (cutoff:3.500A) removed outlier: 3.993A pdb=" N GLN C 575 " --> pdb=" O TRP C 571 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N ASP C 589 " --> pdb=" O ARG C 585 " (cutoff:3.500A) removed outlier: 3.910A pdb=" N LEU C 592 " --> pdb=" O ARG C 588 " (cutoff:3.500A) removed outlier: 3.820A pdb=" N TRP C 596 " --> pdb=" O LEU C 592 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N GLY C 597 " --> pdb=" O LEU C 593 " (cutoff:3.500A) Processing helix chain 'C' and resid 627 through 635 removed outlier: 3.651A pdb=" N ASP C 632 " --> pdb=" O TRP C 628 " (cutoff:3.500A) removed outlier: 4.366A pdb=" N LYS C 633 " --> pdb=" O LEU C 629 " (cutoff:3.500A) Processing helix chain 'C' and resid 638 through 658 removed outlier: 3.622A pdb=" N ILE C 642 " --> pdb=" O TYR C 638 " (cutoff:3.500A) removed outlier: 3.984A pdb=" N GLU C 647 " --> pdb=" O TYR C 643 " (cutoff:3.500A) removed outlier: 3.790A pdb=" N GLU C 648 " --> pdb=" O GLY C 644 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N SER C 649 " --> pdb=" O LEU C 645 " (cutoff:3.500A) removed outlier: 4.099A pdb=" N GLN C 650 " --> pdb=" O LEU C 646 " (cutoff:3.500A) removed outlier: 3.810A pdb=" N GLN C 658 " --> pdb=" O GLU C 654 " (cutoff:3.500A) Processing helix chain 'D' and resid 529 through 534 removed outlier: 3.553A pdb=" N SER D 534 " --> pdb=" O MET D 530 " (cutoff:3.500A) Processing helix chain 'D' and resid 536 through 541 removed outlier: 4.161A pdb=" N GLN D 540 " --> pdb=" O THR D 536 " (cutoff:3.500A) Processing helix chain 'D' and resid 571 through 595 removed outlier: 3.923A pdb=" N GLN D 575 " --> pdb=" O TRP D 571 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N LEU D 576 " --> pdb=" O GLY D 572 " (cutoff:3.500A) removed outlier: 4.271A pdb=" N ASP D 589 " --> pdb=" O ARG D 585 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N LEU D 592 " --> pdb=" O ARG D 588 " (cutoff:3.500A) removed outlier: 3.957A pdb=" N LEU D 593 " --> pdb=" O ASP D 589 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N GLY D 594 " --> pdb=" O GLN D 590 " (cutoff:3.500A) removed outlier: 3.686A pdb=" N ILE D 595 " --> pdb=" O GLN D 591 " (cutoff:3.500A) Processing helix chain 'D' and resid 627 through 635 removed outlier: 3.670A pdb=" N ASP D 632 " --> pdb=" O TRP D 628 " (cutoff:3.500A) removed outlier: 4.530A pdb=" N LYS D 633 " --> pdb=" O LEU D 629 " (cutoff:3.500A) removed outlier: 3.905A pdb=" N GLU D 634 " --> pdb=" O GLN D 630 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N ILE D 635 " --> pdb=" O TRP D 631 " (cutoff:3.500A) Processing helix chain 'D' and resid 638 through 650 removed outlier: 3.540A pdb=" N ILE D 642 " --> pdb=" O TYR D 638 " (cutoff:3.500A) removed outlier: 3.762A pdb=" N GLU D 647 " --> pdb=" O TYR D 643 " (cutoff:3.500A) removed outlier: 3.869A pdb=" N GLU D 648 " --> pdb=" O GLY D 644 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N SER D 649 " --> pdb=" O LEU D 645 " (cutoff:3.500A) removed outlier: 4.047A pdb=" N GLN D 650 " --> pdb=" O LEU D 646 " (cutoff:3.500A) Processing helix chain 'D' and resid 656 through 660 removed outlier: 3.563A pdb=" N ASP D 659 " --> pdb=" O ASN D 656 " (cutoff:3.500A) Processing helix chain 'F' and resid 574 through 595 removed outlier: 3.717A pdb=" N ALA F 578 " --> pdb=" O LYS F 574 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N ARG F 579 " --> pdb=" O GLN F 575 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N ASP F 589 " --> pdb=" O ARG F 585 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N ILE F 595 " --> pdb=" O GLN F 591 " (cutoff:3.500A) Processing helix chain 'F' and resid 618 through 626 removed outlier: 3.868A pdb=" N ILE F 622 " --> pdb=" O ASN F 618 " (cutoff:3.500A) removed outlier: 3.946A pdb=" N TRP F 623 " --> pdb=" O LEU F 619 " (cutoff:3.500A) removed outlier: 4.392A pdb=" N ASP F 624 " --> pdb=" O SER F 620 " (cutoff:3.500A) Processing helix chain 'F' and resid 627 through 635 removed outlier: 3.511A pdb=" N ILE F 635 " --> pdb=" O TRP F 631 " (cutoff:3.500A) Processing helix chain 'F' and resid 636 through 638 No H-bonds generated for 'chain 'F' and resid 636 through 638' Processing helix chain 'F' and resid 639 through 662 removed outlier: 3.552A pdb=" N TYR F 643 " --> pdb=" O THR F 639 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N ASN F 651 " --> pdb=" O GLU F 647 " (cutoff:3.500A) Processing helix chain 'G' and resid 99 through 113 removed outlier: 3.858A pdb=" N HIS G 105 " --> pdb=" O VAL G 101 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N THR G 106 " --> pdb=" O GLU G 102 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N ASP G 113 " --> pdb=" O ILE G 109 " (cutoff:3.500A) Processing helix chain 'G' and resid 122 through 126 removed outlier: 3.928A pdb=" N LEU G 125 " --> pdb=" O LEU G 122 " (cutoff:3.500A) removed outlier: 4.553A pdb=" N CYS G 126 " --> pdb=" O THR G 123 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 122 through 126' Processing helix chain 'G' and resid 335 through 350 removed outlier: 3.788A pdb=" N LYS G 344 " --> pdb=" O GLU G 340 " (cutoff:3.500A) Processing helix chain 'G' and resid 368 through 373 removed outlier: 3.910A pdb=" N THR G 372 " --> pdb=" O ASP G 368 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N THR G 373 " --> pdb=" O LEU G 369 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 368 through 373' Processing helix chain 'G' and resid 425 through 429 removed outlier: 4.153A pdb=" N GLN G 428 " --> pdb=" O ASN G 425 " (cutoff:3.500A) Processing helix chain 'G' and resid 475 through 480 removed outlier: 3.686A pdb=" N TRP G 479 " --> pdb=" O MET G 475 " (cutoff:3.500A) Processing helix chain 'J' and resid 96 through 98 No H-bonds generated for 'chain 'J' and resid 96 through 98' Processing helix chain 'J' and resid 99 through 113 removed outlier: 3.554A pdb=" N THR J 106 " --> pdb=" O GLU J 102 " (cutoff:3.500A) Processing helix chain 'J' and resid 177 through 179 No H-bonds generated for 'chain 'J' and resid 177 through 179' Processing helix chain 'J' and resid 335 through 350 removed outlier: 3.659A pdb=" N ASN J 339 " --> pdb=" O LYS J 335 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N GLU J 340 " --> pdb=" O ALA J 336 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N ARG J 350 " --> pdb=" O VAL J 346 " (cutoff:3.500A) Processing helix chain 'J' and resid 368 through 373 removed outlier: 3.546A pdb=" N THR J 372 " --> pdb=" O ASP J 368 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N THR J 373 " --> pdb=" O LEU J 369 " (cutoff:3.500A) No H-bonds generated for 'chain 'J' and resid 368 through 373' Processing helix chain 'J' and resid 425 through 429 removed outlier: 3.997A pdb=" N GLN J 428 " --> pdb=" O ASN J 425 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N ARG J 429 " --> pdb=" O MET J 426 " (cutoff:3.500A) No H-bonds generated for 'chain 'J' and resid 425 through 429' Processing helix chain 'P' and resid 96 through 98 No H-bonds generated for 'chain 'P' and resid 96 through 98' Processing helix chain 'P' and resid 99 through 113 Processing helix chain 'P' and resid 122 through 126 removed outlier: 3.894A pdb=" N LEU P 125 " --> pdb=" O LEU P 122 " (cutoff:3.500A) removed outlier: 4.288A pdb=" N CYS P 126 " --> pdb=" O THR P 123 " (cutoff:3.500A) No H-bonds generated for 'chain 'P' and resid 122 through 126' Processing helix chain 'P' and resid 335 through 350 removed outlier: 3.653A pdb=" N ASN P 339 " --> pdb=" O LYS P 335 " (cutoff:3.500A) removed outlier: 3.844A pdb=" N GLU P 340 " --> pdb=" O ALA P 336 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N GLN P 348 " --> pdb=" O LYS P 344 " (cutoff:3.500A) Processing helix chain 'P' and resid 368 through 373 removed outlier: 3.583A pdb=" N THR P 373 " --> pdb=" O LEU P 369 " (cutoff:3.500A) Processing helix chain 'P' and resid 475 through 481 removed outlier: 3.766A pdb=" N TRP P 479 " --> pdb=" O MET P 475 " (cutoff:3.500A) removed outlier: 3.925A pdb=" N SER P 481 " --> pdb=" O ASP P 477 " (cutoff:3.500A) Processing helix chain 'R' and resid 61 through 64 removed outlier: 3.996A pdb=" N GLU R 64 " --> pdb=" O PRO R 61 " (cutoff:3.500A) No H-bonds generated for 'chain 'R' and resid 61 through 64' Processing sheet with id=AA1, first strand: chain 'A' and resid 3 through 5 Processing sheet with id=AA2, first strand: chain 'A' and resid 10 through 12 removed outlier: 6.665A pdb=" N GLU A 10 " --> pdb=" O SER A 110 " (cutoff:3.500A) removed outlier: 6.380A pdb=" N ARG A 38 " --> pdb=" O TYR A 47 " (cutoff:3.500A) removed outlier: 5.321A pdb=" N TYR A 47 " --> pdb=" O ARG A 38 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 100E through 100F Processing sheet with id=AA4, first strand: chain 'B' and resid 5 through 7 Processing sheet with id=AA5, first strand: chain 'B' and resid 10 through 13 removed outlier: 3.541A pdb=" N GLU B 105 " --> pdb=" O LEU B 11 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 53 through 54 removed outlier: 6.676A pdb=" N TRP B 35 " --> pdb=" O LEU B 47 " (cutoff:3.500A) removed outlier: 5.276A pdb=" N TYR B 49 " --> pdb=" O VAL B 33 " (cutoff:3.500A) removed outlier: 7.327A pdb=" N VAL B 33 " --> pdb=" O TYR B 49 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'C' and resid 605 through 609 removed outlier: 7.580A pdb=" N THR C 606 " --> pdb=" O VAL P 38 " (cutoff:3.500A) removed outlier: 8.237A pdb=" N VAL P 38 " --> pdb=" O THR C 606 " (cutoff:3.500A) removed outlier: 5.780A pdb=" N VAL C 608 " --> pdb=" O VAL P 36 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N VAL P 36 " --> pdb=" O VAL C 608 " (cutoff:3.500A) removed outlier: 8.909A pdb=" N ILE P 491 " --> pdb=" O PRO P 43 " (cutoff:3.500A) removed outlier: 7.926A pdb=" N TRP P 45 " --> pdb=" O VAL P 489 " (cutoff:3.500A) removed outlier: 8.069A pdb=" N VAL P 489 " --> pdb=" O TRP P 45 " (cutoff:3.500A) removed outlier: 9.622A pdb=" N ASP P 47 " --> pdb=" O LYS P 487 " (cutoff:3.500A) removed outlier: 12.012A pdb=" N LYS P 487 " --> pdb=" O ASP P 47 " (cutoff:3.500A) removed outlier: 3.940A pdb=" N ILE P 225 " --> pdb=" O VAL P 245 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'D' and resid 604 through 609 removed outlier: 3.550A pdb=" N CYS D 604 " --> pdb=" O VAL G 38 " (cutoff:3.500A) removed outlier: 4.786A pdb=" N VAL G 36 " --> pdb=" O THR D 606 " (cutoff:3.500A) removed outlier: 8.941A pdb=" N VAL G 38 " --> pdb=" O PRO G 498 " (cutoff:3.500A) removed outlier: 9.745A pdb=" N TYR G 40 " --> pdb=" O VAL G 496 " (cutoff:3.500A) removed outlier: 10.045A pdb=" N VAL G 496 " --> pdb=" O TYR G 40 " (cutoff:3.500A) removed outlier: 6.152A pdb=" N VAL G 42 " --> pdb=" O LEU G 494 " (cutoff:3.500A) removed outlier: 5.635A pdb=" N LEU G 494 " --> pdb=" O VAL G 42 " (cutoff:3.500A) removed outlier: 4.100A pdb=" N VAL G 44 " --> pdb=" O GLU G 492 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'F' and resid 605 through 609 removed outlier: 7.723A pdb=" N THR F 606 " --> pdb=" O VAL J 38 " (cutoff:3.500A) removed outlier: 8.453A pdb=" N VAL J 38 " --> pdb=" O THR F 606 " (cutoff:3.500A) removed outlier: 5.716A pdb=" N VAL F 608 " --> pdb=" O VAL J 36 " (cutoff:3.500A) removed outlier: 8.869A pdb=" N ILE J 491 " --> pdb=" O PRO J 43 " (cutoff:3.500A) removed outlier: 8.082A pdb=" N TRP J 45 " --> pdb=" O VAL J 489 " (cutoff:3.500A) removed outlier: 8.344A pdb=" N VAL J 489 " --> pdb=" O TRP J 45 " (cutoff:3.500A) removed outlier: 8.781A pdb=" N ASP J 47 " --> pdb=" O LYS J 487 " (cutoff:3.500A) removed outlier: 11.861A pdb=" N LYS J 487 " --> pdb=" O ASP J 47 " (cutoff:3.500A) removed outlier: 3.925A pdb=" N VAL J 242 " --> pdb=" O LEU J 86 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'G' and resid 91 through 94 Processing sheet with id=AB2, first strand: chain 'G' and resid 169 through 177 removed outlier: 3.622A pdb=" N CYS G 131 " --> pdb=" O LYS G 189 " (cutoff:3.500A) removed outlier: 4.052A pdb=" N LYS G 189 " --> pdb=" O CYS G 131 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'G' and resid 259 through 261 removed outlier: 5.887A pdb=" N LEU G 260 " --> pdb=" O THR G 450 " (cutoff:3.500A) removed outlier: 3.808A pdb=" N ILE G 443 " --> pdb=" O ARG G 298 " (cutoff:3.500A) removed outlier: 3.815A pdb=" N VAL G 292 " --> pdb=" O ILE G 449 " (cutoff:3.500A) removed outlier: 7.056A pdb=" N GLN G 293 " --> pdb=" O SER G 334 " (cutoff:3.500A) removed outlier: 4.155A pdb=" N SER G 334 " --> pdb=" O GLN G 293 " (cutoff:3.500A) removed outlier: 4.417A pdb=" N ALA G 329 " --> pdb=" O CYS G 418 " (cutoff:3.500A) removed outlier: 4.129A pdb=" N PHE G 382 " --> pdb=" O LYS G 421 " (cutoff:3.500A) removed outlier: 3.816A pdb=" N GLU G 381 " --> pdb=" O CYS G 378 " (cutoff:3.500A) removed outlier: 4.014A pdb=" N CYS G 378 " --> pdb=" O GLU G 381 " (cutoff:3.500A) removed outlier: 3.819A pdb=" N PHE G 383 " --> pdb=" O PHE G 376 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N PHE G 376 " --> pdb=" O PHE G 383 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'G' and resid 271 through 273 removed outlier: 6.980A pdb=" N ARG G 360 " --> pdb=" O PHE G 468 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'G' and resid 304 through 312 removed outlier: 6.540A pdb=" N GLN G 315 " --> pdb=" O ILE G 309 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'H' and resid 3 through 6 Processing sheet with id=AB7, first strand: chain 'H' and resid 10 through 12 removed outlier: 3.763A pdb=" N GLU H 10 " --> pdb=" O LEU H 108 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N SER H 110 " --> pdb=" O GLU H 10 " (cutoff:3.500A) removed outlier: 6.509A pdb=" N ARG H 38 " --> pdb=" O TYR H 47 " (cutoff:3.500A) removed outlier: 5.337A pdb=" N TYR H 47 " --> pdb=" O ARG H 38 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'H' and resid 100E through 100F Processing sheet with id=AB9, first strand: chain 'J' and resid 75 through 76 removed outlier: 7.342A pdb=" N CYS J 54 " --> pdb=" O VAL J 75 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'J' and resid 66 through 67 removed outlier: 7.765A pdb=" N HIS J 66 " --> pdb=" O SER J 209 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC1 Processing sheet with id=AC2, first strand: chain 'J' and resid 91 through 94 Processing sheet with id=AC3, first strand: chain 'J' and resid 169 through 176 Processing sheet with id=AC4, first strand: chain 'J' and resid 271 through 274 removed outlier: 3.774A pdb=" N SER J 393 " --> pdb=" O PHE J 361 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'J' and resid 374 through 378 removed outlier: 3.608A pdb=" N CYS J 378 " --> pdb=" O GLU J 381 " (cutoff:3.500A) removed outlier: 3.851A pdb=" N GLU J 381 " --> pdb=" O CYS J 378 " (cutoff:3.500A) removed outlier: 3.912A pdb=" N PHE J 382 " --> pdb=" O LYS J 421 " (cutoff:3.500A) removed outlier: 4.356A pdb=" N ALA J 329 " --> pdb=" O CYS J 418 " (cutoff:3.500A) removed outlier: 4.312A pdb=" N SER J 334 " --> pdb=" O GLN J 293 " (cutoff:3.500A) removed outlier: 7.691A pdb=" N GLN J 293 " --> pdb=" O SER J 334 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N VAL J 292 " --> pdb=" O ILE J 449 " (cutoff:3.500A) removed outlier: 3.811A pdb=" N ILE J 443 " --> pdb=" O ARG J 298 " (cutoff:3.500A) removed outlier: 5.908A pdb=" N ASN J 300 " --> pdb=" O GLY J 441 " (cutoff:3.500A) removed outlier: 5.564A pdb=" N GLY J 441 " --> pdb=" O ASN J 300 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'J' and resid 304 through 307 Processing sheet with id=AC7, first strand: chain 'L' and resid 5 through 7 Processing sheet with id=AC8, first strand: chain 'L' and resid 10 through 13 Processing sheet with id=AC9, first strand: chain 'L' and resid 53 through 54 removed outlier: 6.817A pdb=" N TRP L 35 " --> pdb=" O LEU L 47 " (cutoff:3.500A) removed outlier: 4.883A pdb=" N TYR L 49 " --> pdb=" O VAL L 33 " (cutoff:3.500A) removed outlier: 6.838A pdb=" N VAL L 33 " --> pdb=" O TYR L 49 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'M' and resid 3 through 6 Processing sheet with id=AD2, first strand: chain 'M' and resid 10 through 12 removed outlier: 3.688A pdb=" N GLU M 10 " --> pdb=" O LEU M 108 " (cutoff:3.500A) removed outlier: 4.173A pdb=" N SER M 110 " --> pdb=" O GLU M 10 " (cutoff:3.500A) removed outlier: 4.098A pdb=" N LYS M 12 " --> pdb=" O SER M 110 " (cutoff:3.500A) removed outlier: 6.517A pdb=" N ARG M 38 " --> pdb=" O TYR M 47 " (cutoff:3.500A) removed outlier: 5.485A pdb=" N TYR M 47 " --> pdb=" O ARG M 38 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'M' and resid 10 through 12 removed outlier: 3.688A pdb=" N GLU M 10 " --> pdb=" O LEU M 108 " (cutoff:3.500A) removed outlier: 4.173A pdb=" N SER M 110 " --> pdb=" O GLU M 10 " (cutoff:3.500A) removed outlier: 4.098A pdb=" N LYS M 12 " --> pdb=" O SER M 110 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'M' and resid 100E through 100F removed outlier: 3.590A pdb=" N VAL M 100I" --> pdb=" O HIS M 100F" (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'O' and resid 5 through 7 Processing sheet with id=AD6, first strand: chain 'O' and resid 10 through 13 removed outlier: 7.373A pdb=" N LEU O 11 " --> pdb=" O GLU O 105 " (cutoff:3.500A) removed outlier: 7.136A pdb=" N VAL O 33 " --> pdb=" O TYR O 49 " (cutoff:3.500A) removed outlier: 5.240A pdb=" N TYR O 49 " --> pdb=" O VAL O 33 " (cutoff:3.500A) removed outlier: 6.684A pdb=" N TRP O 35 " --> pdb=" O LEU O 47 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'P' and resid 91 through 94 removed outlier: 3.522A pdb=" N GLU P 91 " --> pdb=" O CYS P 239 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'P' and resid 169 through 177 Processing sheet with id=AD9, first strand: chain 'P' and resid 271 through 274 Processing sheet with id=AE1, first strand: chain 'P' and resid 374 through 378 removed outlier: 4.290A pdb=" N ALA P 329 " --> pdb=" O CYS P 418 " (cutoff:3.500A) removed outlier: 3.747A pdb=" N ILE P 443 " --> pdb=" O ARG P 298 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'P' and resid 304 through 312 removed outlier: 6.660A pdb=" N GLN P 315 " --> pdb=" O ILE P 309 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'R' and resid 3 through 7 removed outlier: 3.629A pdb=" N SER R 7 " --> pdb=" O THR R 21 " (cutoff:3.500A) removed outlier: 3.954A pdb=" N THR R 21 " --> pdb=" O SER R 7 " (cutoff:3.500A) removed outlier: 3.860A pdb=" N CYS R 22 " --> pdb=" O PHE R 78 " (cutoff:3.500A) removed outlier: 4.422A pdb=" N PHE R 78 " --> pdb=" O CYS R 22 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'R' and resid 57 through 59 removed outlier: 6.684A pdb=" N TRP R 36 " --> pdb=" O VAL R 48 " (cutoff:3.500A) removed outlier: 4.362A pdb=" N ARG R 50 " --> pdb=" O TRP R 35 " (cutoff:3.500A) removed outlier: 6.606A pdb=" N TRP R 35 " --> pdb=" O ARG R 50 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'R' and resid 57 through 59 removed outlier: 6.684A pdb=" N TRP R 36 " --> pdb=" O VAL R 48 " (cutoff:3.500A) removed outlier: 4.362A pdb=" N ARG R 50 " --> pdb=" O TRP R 35 " (cutoff:3.500A) removed outlier: 6.606A pdb=" N TRP R 35 " --> pdb=" O ARG R 50 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'W' and resid 19 through 24 Processing sheet with id=AE7, first strand: chain 'W' and resid 45 through 50 removed outlier: 5.850A pdb=" N PHE W 46 " --> pdb=" O GLN W 37 " (cutoff:3.500A) removed outlier: 6.470A pdb=" N GLN W 37 " --> pdb=" O PHE W 46 " (cutoff:3.500A) removed outlier: 3.746A pdb=" N MET W 48 " --> pdb=" O TRP W 35 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'W' and resid 89 through 92 663 hydrogen bonds defined for protein. 1740 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: 3.87 Time building geometry restraints manager: 2.24 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 6833 1.34 - 1.47: 5867 1.47 - 1.59: 9723 1.59 - 1.72: 0 1.72 - 1.84: 166 Bond restraints: 22589 Sorted by residual: bond pdb=" C THR P 123 " pdb=" N PRO P 124 " ideal model delta sigma weight residual 1.331 1.395 -0.063 7.90e-03 1.60e+04 6.42e+01 bond pdb=" C PRO A 75 " pdb=" N PRO A 76 " ideal model delta sigma weight residual 1.332 1.389 -0.058 1.30e-02 5.92e+03 1.97e+01 bond pdb=" N PRO A 76 " pdb=" CD PRO A 76 " ideal model delta sigma weight residual 1.473 1.531 -0.058 1.40e-02 5.10e+03 1.73e+01 bond pdb=" N PRO J 313 " pdb=" CD PRO J 313 " ideal model delta sigma weight residual 1.473 1.528 -0.055 1.40e-02 5.10e+03 1.55e+01 bond pdb=" N ASN D 656 " pdb=" CA ASN D 656 " ideal model delta sigma weight residual 1.460 1.485 -0.024 8.20e-03 1.49e+04 8.78e+00 ... (remaining 22584 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.70: 30190 2.70 - 5.40: 406 5.40 - 8.10: 75 8.10 - 10.80: 10 10.80 - 13.50: 1 Bond angle restraints: 30682 Sorted by residual: angle pdb=" C PRO A 75 " pdb=" N PRO A 76 " pdb=" CA PRO A 76 " ideal model delta sigma weight residual 119.76 113.91 5.85 1.03e+00 9.43e-01 3.23e+01 angle pdb=" C ASP P 140 " pdb=" N ASP P 141 " pdb=" CA ASP P 141 " ideal model delta sigma weight residual 122.61 130.89 -8.28 1.56e+00 4.11e-01 2.82e+01 angle pdb=" C SER P 460 " pdb=" N THR P 461 " pdb=" CA THR P 461 " ideal model delta sigma weight residual 121.54 130.34 -8.80 1.91e+00 2.74e-01 2.12e+01 angle pdb=" CA PRO J 313 " pdb=" N PRO J 313 " pdb=" CD PRO J 313 " ideal model delta sigma weight residual 112.00 106.12 5.88 1.40e+00 5.10e-01 1.76e+01 angle pdb=" C ASN D 656 " pdb=" CA ASN D 656 " pdb=" CB ASN D 656 " ideal model delta sigma weight residual 116.53 110.50 6.03 1.47e+00 4.63e-01 1.68e+01 ... (remaining 30677 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 23.30: 14267 23.30 - 46.60: 580 46.60 - 69.89: 109 69.89 - 93.19: 75 93.19 - 116.49: 47 Dihedral angle restraints: 15078 sinusoidal: 7546 harmonic: 7532 Sorted by residual: dihedral pdb=" CB CYS G 126 " pdb=" SG CYS G 126 " pdb=" SG CYS G 196 " pdb=" CB CYS G 196 " ideal model delta sinusoidal sigma weight residual 93.00 169.55 -76.55 1 1.00e+01 1.00e-02 7.37e+01 dihedral pdb=" CB CYS P 119 " pdb=" SG CYS P 119 " pdb=" SG CYS P 205 " pdb=" CB CYS P 205 " ideal model delta sinusoidal sigma weight residual -86.00 -159.61 73.61 1 1.00e+01 1.00e-02 6.89e+01 dihedral pdb=" CB CYS J 119 " pdb=" SG CYS J 119 " pdb=" SG CYS J 205 " pdb=" CB CYS J 205 " ideal model delta sinusoidal sigma weight residual -86.00 -146.09 60.09 1 1.00e+01 1.00e-02 4.81e+01 ... (remaining 15075 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.075: 3288 0.075 - 0.150: 507 0.150 - 0.225: 23 0.225 - 0.300: 15 0.300 - 0.375: 2 Chirality restraints: 3835 Sorted by residual: chirality pdb=" C2 NAG I 2 " pdb=" C1 NAG I 2 " pdb=" C3 NAG I 2 " pdb=" N2 NAG I 2 " both_signs ideal model delta sigma weight residual False -2.49 -2.12 -0.38 2.00e-01 2.50e+01 3.52e+00 chirality pdb=" C5 BMA h 3 " pdb=" C4 BMA h 3 " pdb=" C6 BMA h 3 " pdb=" O5 BMA h 3 " both_signs ideal model delta sigma weight residual False -2.27 -2.58 0.30 2.00e-01 2.50e+01 2.26e+00 chirality pdb=" C5 BMA Y 3 " pdb=" C4 BMA Y 3 " pdb=" C6 BMA Y 3 " pdb=" O5 BMA Y 3 " both_signs ideal model delta sigma weight residual False -2.27 -2.57 0.30 2.00e-01 2.50e+01 2.20e+00 ... (remaining 3832 not shown) Planarity restraints: 3769 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C2 NAG F 701 " 0.075 2.00e-02 2.50e+03 6.15e-02 4.73e+01 pdb=" C7 NAG F 701 " -0.020 2.00e-02 2.50e+03 pdb=" C8 NAG F 701 " 0.057 2.00e-02 2.50e+03 pdb=" N2 NAG F 701 " -0.097 2.00e-02 2.50e+03 pdb=" O7 NAG F 701 " -0.014 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN F 611 " -0.033 2.00e-02 2.50e+03 3.65e-02 1.67e+01 pdb=" CG ASN F 611 " 0.012 2.00e-02 2.50e+03 pdb=" OD1 ASN F 611 " 0.006 2.00e-02 2.50e+03 pdb=" ND2 ASN F 611 " 0.058 2.00e-02 2.50e+03 pdb=" C1 NAG F 701 " -0.045 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG C 701 " -0.044 2.00e-02 2.50e+03 3.63e-02 1.64e+01 pdb=" C7 NAG C 701 " 0.012 2.00e-02 2.50e+03 pdb=" C8 NAG C 701 " -0.033 2.00e-02 2.50e+03 pdb=" N2 NAG C 701 " 0.058 2.00e-02 2.50e+03 pdb=" O7 NAG C 701 " 0.008 2.00e-02 2.50e+03 ... (remaining 3766 not shown) Histogram of nonbonded interaction distances: 2.12 - 2.67: 333 2.67 - 3.23: 17582 3.23 - 3.79: 30500 3.79 - 4.34: 41400 4.34 - 4.90: 70316 Nonbonded interactions: 160131 Sorted by model distance: nonbonded pdb=" O GLU D 657 " pdb=" N ASP D 659 " model vdw 2.116 3.120 nonbonded pdb=" CA GLY D 597 " pdb=" OE1 GLN D 650 " model vdw 2.211 3.440 nonbonded pdb=" O LEU W 4 " pdb=" OG1 THR W 24 " model vdw 2.266 3.040 nonbonded pdb=" O ILE A 2 " pdb=" ND1 HIS A 3 " model vdw 2.285 3.120 nonbonded pdb=" O ASN D 656 " pdb=" OD2 ASP D 659 " model vdw 2.313 3.040 ... (remaining 160126 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'H' selection = chain 'M' } ncs_group { reference = chain 'B' selection = (chain 'L' and (resid 1 through 19 or (resid 20 and (name N or name CA or name C \ or name O or name CB )) or resid 21 through 41 or (resid 42 through 43 and (nam \ e N or name CA or name C or name O or name CB )) or resid 44 through 62 or (resi \ d 63 and (name N or name CA or name C or name O or name CB )) or resid 64 throug \ h 99 or (resid 100 and (name N or name CA or name C or name O or name CB )) or r \ esid 101 through 102 or (resid 103 and (name N or name CA or name C or name O or \ name CB )) or resid 104 through 106 or (resid 107 and (name N or name CA or nam \ e C or name O or name CB )))) selection = (chain 'O' and (resid 1 through 106 or (resid 107 and (name N or name CA or name \ C or name O or name CB )))) } ncs_group { reference = (chain 'C' and resid 520 through 660) selection = (chain 'D' and (resid 520 through 546 or resid 567 through 660)) } ncs_group { reference = chain 'E' selection = chain 'I' selection = chain 'K' selection = chain 'N' selection = chain 'Q' selection = chain 'S' selection = chain 'T' selection = chain 'U' selection = chain 'Z' selection = chain 'a' selection = chain 'b' selection = chain 'c' selection = chain 'd' selection = chain 'e' selection = chain 'f' selection = chain 'g' selection = chain 'l' selection = chain 'm' selection = chain 'n' selection = chain 'o' selection = chain 't' } ncs_group { reference = (chain 'G' and (resid 33 through 77 or resid 82 through 605)) selection = (chain 'J' and (resid 33 through 77 or resid 82 through 605)) selection = (chain 'P' and resid 33 through 605) } ncs_group { reference = (chain 'Y' and (resid 2 or resid 5 through 11)) selection = (chain 'i' and (resid 1 or resid 4 through 10)) selection = (chain 'r' and (resid 1 or resid 4 through 10)) } ncs_group { reference = chain 'h' selection = chain 's' } ncs_group { reference = chain 'j' selection = chain 'k' selection = chain 'p' selection = chain 'q' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.900 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.060 Construct map_model_manager: 0.010 Extract box with map and model: 0.230 Check model and map are aligned: 0.060 Set scattering table: 0.060 Process input model: 17.900 Find NCS groups from input model: 0.520 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:1.210 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 23.030 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8297 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.268 22759 Z= 0.330 Angle : 0.790 13.501 31146 Z= 0.373 Chirality : 0.053 0.375 3835 Planarity : 0.004 0.062 3714 Dihedral : 14.971 116.490 10116 Min Nonbonded Distance : 2.116 Molprobity Statistics. All-atom Clashscore : 4.20 Ramachandran Plot: Outliers : 0.04 % Allowed : 3.37 % Favored : 96.59 % Rotamer: Outliers : 0.35 % Allowed : 4.37 % Favored : 95.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.77 % 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: -3.38 (0.14), residues: 2580 helix: -3.38 (0.18), residues: 307 sheet: -1.02 (0.17), residues: 868 loop : -2.87 (0.13), residues: 1405 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG L 63 TYR 0.010 0.001 TYR O 36 PHE 0.016 0.001 PHE R 78 TRP 0.008 0.000 TRP M 53 HIS 0.003 0.000 HIS P 105 Details of bonding type rmsd covalent geometry : bond 0.00533 (22589) covalent geometry : angle 0.77267 (30682) SS BOND : bond 0.00270 ( 40) SS BOND : angle 0.99255 ( 80) hydrogen bonds : bond 0.13478 ( 644) hydrogen bonds : angle 5.90524 ( 1740) Misc. bond : bond 0.18984 ( 2) link_ALPHA1-2 : bond 0.00389 ( 11) link_ALPHA1-2 : angle 1.47157 ( 33) link_ALPHA1-3 : bond 0.00589 ( 10) link_ALPHA1-3 : angle 1.42960 ( 30) link_ALPHA1-6 : bond 0.00518 ( 9) link_ALPHA1-6 : angle 1.18383 ( 27) link_BETA1-4 : bond 0.00875 ( 43) link_BETA1-4 : angle 1.98581 ( 129) link_NAG-ASN : bond 0.00426 ( 55) link_NAG-ASN : angle 1.51839 ( 165) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5160 Ramachandran restraints generated. 2580 Oldfield, 0 Emsley, 2580 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5160 Ramachandran restraints generated. 2580 Oldfield, 0 Emsley, 2580 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 471 residues out of total 2278 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 463 time to evaluate : 0.676 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 568 LEU cc_start: 0.7074 (mt) cc_final: 0.6721 (pp) REVERT: C 607 ASN cc_start: 0.9034 (t0) cc_final: 0.8786 (t0) REVERT: C 660 LEU cc_start: 0.8345 (tp) cc_final: 0.8108 (tt) REVERT: D 601 LYS cc_start: 0.8811 (mtpp) cc_final: 0.8572 (mtmm) REVERT: D 618 ASN cc_start: 0.7660 (m-40) cc_final: 0.7442 (m-40) REVERT: D 648 GLU cc_start: 0.7083 (pp20) cc_final: 0.6774 (pp20) REVERT: D 652 GLN cc_start: 0.8010 (OUTLIER) cc_final: 0.7507 (mp-120) REVERT: D 655 LYS cc_start: 0.7971 (OUTLIER) cc_final: 0.6877 (mptt) REVERT: G 78 ASP cc_start: 0.8474 (t0) cc_final: 0.7918 (t0) REVERT: G 478 ASN cc_start: 0.8758 (m110) cc_final: 0.8540 (t0) REVERT: J 326 ILE cc_start: 0.8981 (mm) cc_final: 0.8752 (mm) REVERT: L 63 ARG cc_start: 0.7212 (mmm-85) cc_final: 0.6582 (mmm-85) REVERT: L 77 ASN cc_start: 0.7723 (t0) cc_final: 0.7267 (t0) REVERT: L 88 CYS cc_start: 0.6802 (p) cc_final: 0.6197 (p) REVERT: P 161 MET cc_start: 0.8456 (tpp) cc_final: 0.8136 (tpt) REVERT: P 359 ILE cc_start: 0.9196 (mm) cc_final: 0.8891 (mm) REVERT: P 395 TRP cc_start: 0.7786 (m100) cc_final: 0.7560 (m100) REVERT: P 430 ILE cc_start: 0.8754 (mt) cc_final: 0.8491 (tp) REVERT: R 16 GLU cc_start: 0.7846 (mt-10) cc_final: 0.7606 (mt-10) REVERT: R 91 TYR cc_start: 0.8042 (m-80) cc_final: 0.7801 (m-80) outliers start: 8 outliers final: 1 residues processed: 470 average time/residue: 0.1523 time to fit residues: 108.8553 Evaluate side-chains 301 residues out of total 2278 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 298 time to evaluate : 0.687 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 652 GLN Chi-restraints excluded: chain D residue 655 LYS Chi-restraints excluded: chain P residue 247 CYS Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 256 random chunks: chunk 197 optimal weight: 3.9990 chunk 215 optimal weight: 6.9990 chunk 20 optimal weight: 10.0000 chunk 132 optimal weight: 4.9990 chunk 248 optimal weight: 10.0000 chunk 207 optimal weight: 3.9990 chunk 155 optimal weight: 4.9990 chunk 244 optimal weight: 1.9990 chunk 183 optimal weight: 7.9990 chunk 111 optimal weight: 7.9990 chunk 71 optimal weight: 5.9990 overall best weight: 3.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 6 GLN A 39 GLN ** C 540 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 575 GLN C 577 GLN C 650 GLN D 590 GLN F 575 GLN F 591 GLN F 607 ASN G 82 GLN G 302 ASN G 411 ASN ** J 103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 183 GLN J 203 GLN M 43 GLN O 3 GLN O 38 GLN P 33 ASN P 103 GLN P 356 ASN P 428 GLN Total number of N/Q/H flips: 21 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3175 r_free = 0.3175 target = 0.103051 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2849 r_free = 0.2849 target = 0.082510 restraints weight = 38205.301| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.2880 r_free = 0.2880 target = 0.084709 restraints weight = 26096.505| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.2900 r_free = 0.2900 target = 0.085932 restraints weight = 18897.204| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.2902 r_free = 0.2902 target = 0.086045 restraints weight = 17121.814| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.2904 r_free = 0.2904 target = 0.086124 restraints weight = 16007.505| |-----------------------------------------------------------------------------| r_work (final): 0.2854 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8693 moved from start: 0.2603 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.078 22759 Z= 0.264 Angle : 0.771 13.688 31146 Z= 0.368 Chirality : 0.050 0.288 3835 Planarity : 0.005 0.054 3714 Dihedral : 11.107 86.756 5423 Min Nonbonded Distance : 2.226 Molprobity Statistics. All-atom Clashscore : 3.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.31 % Favored : 94.69 % Rotamer: Outliers : 2.69 % Allowed : 12.00 % Favored : 85.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.77 % 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: -2.53 (0.15), residues: 2580 helix: -1.79 (0.26), residues: 348 sheet: -0.65 (0.18), residues: 862 loop : -2.40 (0.14), residues: 1370 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG R 50 TYR 0.023 0.002 TYR B 91 PHE 0.035 0.003 PHE R 78 TRP 0.022 0.002 TRP J 45 HIS 0.007 0.001 HIS J 374 Details of bonding type rmsd covalent geometry : bond 0.00636 (22589) covalent geometry : angle 0.73252 (30682) SS BOND : bond 0.00834 ( 40) SS BOND : angle 1.59715 ( 80) hydrogen bonds : bond 0.05320 ( 644) hydrogen bonds : angle 5.06144 ( 1740) Misc. bond : bond 0.00105 ( 2) link_ALPHA1-2 : bond 0.00251 ( 11) link_ALPHA1-2 : angle 2.20919 ( 33) link_ALPHA1-3 : bond 0.01027 ( 10) link_ALPHA1-3 : angle 2.38270 ( 30) link_ALPHA1-6 : bond 0.00376 ( 9) link_ALPHA1-6 : angle 2.21699 ( 27) link_BETA1-4 : bond 0.00588 ( 43) link_BETA1-4 : angle 2.18183 ( 129) link_NAG-ASN : bond 0.00352 ( 55) link_NAG-ASN : angle 2.12545 ( 165) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5160 Ramachandran restraints generated. 2580 Oldfield, 0 Emsley, 2580 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5160 Ramachandran restraints generated. 2580 Oldfield, 0 Emsley, 2580 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 355 residues out of total 2278 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 294 time to evaluate : 0.735 Fit side-chains revert: symmetry clash REVERT: F 607 ASN cc_start: 0.8641 (OUTLIER) cc_final: 0.8382 (t0) REVERT: G 368 ASP cc_start: 0.7022 (p0) cc_final: 0.6758 (p0) REVERT: J 104 MET cc_start: 0.8753 (ttt) cc_final: 0.8487 (ttt) REVERT: L 77 ASN cc_start: 0.8015 (t0) cc_final: 0.7619 (t0) REVERT: M 56 LYS cc_start: 0.8128 (mmtm) cc_final: 0.7916 (mttm) REVERT: P 205 CYS cc_start: 0.6210 (OUTLIER) cc_final: 0.5662 (m) REVERT: P 359 ILE cc_start: 0.9271 (mm) cc_final: 0.8970 (mm) outliers start: 61 outliers final: 36 residues processed: 340 average time/residue: 0.1416 time to fit residues: 75.4689 Evaluate side-chains 284 residues out of total 2278 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 246 time to evaluate : 0.703 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 94 THR Chi-restraints excluded: chain B residue 1 ASP Chi-restraints excluded: chain B residue 11 LEU Chi-restraints excluded: chain B residue 33 VAL Chi-restraints excluded: chain B residue 72 THR Chi-restraints excluded: chain C residue 569 THR Chi-restraints excluded: chain C residue 595 ILE Chi-restraints excluded: chain D residue 652 GLN Chi-restraints excluded: chain F residue 595 ILE Chi-restraints excluded: chain F residue 607 ASN Chi-restraints excluded: chain F residue 627 THR Chi-restraints excluded: chain G residue 49 GLU Chi-restraints excluded: chain G residue 188 ASN Chi-restraints excluded: chain G residue 196 CYS Chi-restraints excluded: chain G residue 198 THR Chi-restraints excluded: chain G residue 420 ILE Chi-restraints excluded: chain H residue 2 ILE Chi-restraints excluded: chain H residue 11 VAL Chi-restraints excluded: chain H residue 35 VAL Chi-restraints excluded: chain H residue 77 ILE Chi-restraints excluded: chain H residue 82 LEU Chi-restraints excluded: chain H residue 87 THR Chi-restraints excluded: chain H residue 111 VAL Chi-restraints excluded: chain J residue 120 VAL Chi-restraints excluded: chain J residue 198 THR Chi-restraints excluded: chain J residue 261 LEU Chi-restraints excluded: chain J residue 377 ASN Chi-restraints excluded: chain L residue 33 VAL Chi-restraints excluded: chain L residue 48 ILE Chi-restraints excluded: chain M residue 69 ILE Chi-restraints excluded: chain M residue 80 LEU Chi-restraints excluded: chain P residue 71 THR Chi-restraints excluded: chain P residue 205 CYS Chi-restraints excluded: chain P residue 242 VAL Chi-restraints excluded: chain P residue 247 CYS Chi-restraints excluded: chain P residue 257 THR Chi-restraints excluded: chain P residue 277 ILE Chi-restraints excluded: chain R residue 20 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 256 random chunks: chunk 195 optimal weight: 4.9990 chunk 21 optimal weight: 0.9980 chunk 128 optimal weight: 0.2980 chunk 71 optimal weight: 6.9990 chunk 54 optimal weight: 0.6980 chunk 53 optimal weight: 8.9990 chunk 176 optimal weight: 8.9990 chunk 147 optimal weight: 8.9990 chunk 243 optimal weight: 0.8980 chunk 196 optimal weight: 0.7980 chunk 130 optimal weight: 3.9990 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 39 GLN D 653 GLN G 103 GLN G 411 ASN J 103 GLN P 183 GLN W 1 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3219 r_free = 0.3219 target = 0.106121 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2915 r_free = 0.2915 target = 0.086552 restraints weight = 37604.004| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.2938 r_free = 0.2938 target = 0.088322 restraints weight = 26397.914| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.2943 r_free = 0.2943 target = 0.088669 restraints weight = 20389.392| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.2949 r_free = 0.2949 target = 0.089030 restraints weight = 19999.223| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.2951 r_free = 0.2951 target = 0.089173 restraints weight = 18012.324| |-----------------------------------------------------------------------------| r_work (final): 0.2898 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8628 moved from start: 0.2592 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 22759 Z= 0.104 Angle : 0.609 19.827 31146 Z= 0.288 Chirality : 0.044 0.256 3835 Planarity : 0.003 0.038 3714 Dihedral : 9.627 78.656 5419 Min Nonbonded Distance : 2.382 Molprobity Statistics. All-atom Clashscore : 2.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.83 % Favored : 97.17 % Rotamer: Outliers : 1.99 % Allowed : 14.64 % Favored : 83.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.77 % 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: -2.01 (0.16), residues: 2580 helix: -1.03 (0.29), residues: 344 sheet: -0.36 (0.18), residues: 830 loop : -2.08 (0.14), residues: 1406 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG G 429 TYR 0.016 0.001 TYR M 47 PHE 0.011 0.001 PHE R 78 TRP 0.008 0.001 TRP P 45 HIS 0.005 0.001 HIS H 61 Details of bonding type rmsd covalent geometry : bond 0.00223 (22589) covalent geometry : angle 0.56735 (30682) SS BOND : bond 0.00352 ( 40) SS BOND : angle 2.40946 ( 80) hydrogen bonds : bond 0.03502 ( 644) hydrogen bonds : angle 4.59235 ( 1740) Misc. bond : bond 0.00050 ( 2) link_ALPHA1-2 : bond 0.00434 ( 11) link_ALPHA1-2 : angle 1.51268 ( 33) link_ALPHA1-3 : bond 0.01299 ( 10) link_ALPHA1-3 : angle 1.87535 ( 30) link_ALPHA1-6 : bond 0.00655 ( 9) link_ALPHA1-6 : angle 1.64184 ( 27) link_BETA1-4 : bond 0.00510 ( 43) link_BETA1-4 : angle 1.80940 ( 129) link_NAG-ASN : bond 0.00331 ( 55) link_NAG-ASN : angle 1.79447 ( 165) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5160 Ramachandran restraints generated. 2580 Oldfield, 0 Emsley, 2580 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5160 Ramachandran restraints generated. 2580 Oldfield, 0 Emsley, 2580 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 313 residues out of total 2278 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 268 time to evaluate : 0.595 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 535 MET cc_start: 0.8585 (mpp) cc_final: 0.8142 (mtm) REVERT: D 655 LYS cc_start: 0.8191 (OUTLIER) cc_final: 0.7436 (mptt) REVERT: F 591 GLN cc_start: 0.8926 (OUTLIER) cc_final: 0.8565 (tt0) REVERT: F 659 ASP cc_start: 0.7119 (OUTLIER) cc_final: 0.6914 (t0) REVERT: G 84 ILE cc_start: 0.8953 (mm) cc_final: 0.8714 (mt) REVERT: L 65 SER cc_start: 0.8746 (m) cc_final: 0.8488 (p) REVERT: L 77 ASN cc_start: 0.7911 (t0) cc_final: 0.7561 (t0) REVERT: M 56 LYS cc_start: 0.7991 (mmtm) cc_final: 0.7775 (mttm) REVERT: P 205 CYS cc_start: 0.5991 (OUTLIER) cc_final: 0.5774 (m) REVERT: P 359 ILE cc_start: 0.9250 (mm) cc_final: 0.8947 (mm) REVERT: R 16 GLU cc_start: 0.7846 (mt-10) cc_final: 0.7624 (mt-10) outliers start: 45 outliers final: 23 residues processed: 298 average time/residue: 0.1401 time to fit residues: 65.6958 Evaluate side-chains 284 residues out of total 2278 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 257 time to evaluate : 0.735 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 92 CYS Chi-restraints excluded: chain B residue 1 ASP Chi-restraints excluded: chain B residue 10 THR Chi-restraints excluded: chain B residue 33 VAL Chi-restraints excluded: chain C residue 569 THR Chi-restraints excluded: chain C residue 595 ILE Chi-restraints excluded: chain D residue 615 SER Chi-restraints excluded: chain D residue 652 GLN Chi-restraints excluded: chain D residue 655 LYS Chi-restraints excluded: chain F residue 591 GLN Chi-restraints excluded: chain F residue 595 ILE Chi-restraints excluded: chain F residue 659 ASP Chi-restraints excluded: chain G residue 49 GLU Chi-restraints excluded: chain G residue 196 CYS Chi-restraints excluded: chain G residue 202 THR Chi-restraints excluded: chain G residue 218 CYS Chi-restraints excluded: chain G residue 247 CYS Chi-restraints excluded: chain G residue 420 ILE Chi-restraints excluded: chain H residue 2 ILE Chi-restraints excluded: chain H residue 87 THR Chi-restraints excluded: chain J residue 261 LEU Chi-restraints excluded: chain J residue 492 GLU Chi-restraints excluded: chain L residue 22 SER Chi-restraints excluded: chain L residue 33 VAL Chi-restraints excluded: chain M residue 111 VAL Chi-restraints excluded: chain P residue 205 CYS Chi-restraints excluded: chain R residue 100 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 256 random chunks: chunk 33 optimal weight: 5.9990 chunk 129 optimal weight: 4.9990 chunk 90 optimal weight: 0.8980 chunk 82 optimal weight: 4.9990 chunk 194 optimal weight: 2.9990 chunk 168 optimal weight: 30.0000 chunk 217 optimal weight: 9.9990 chunk 22 optimal weight: 2.9990 chunk 66 optimal weight: 6.9990 chunk 220 optimal weight: 7.9990 chunk 176 optimal weight: 9.9990 overall best weight: 3.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 540 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 590 GLN C 658 GLN D 653 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3133 r_free = 0.3133 target = 0.100292 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2813 r_free = 0.2813 target = 0.080341 restraints weight = 38336.418| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.2827 r_free = 0.2827 target = 0.081482 restraints weight = 27701.900| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.2841 r_free = 0.2841 target = 0.082358 restraints weight = 23063.444| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.2846 r_free = 0.2846 target = 0.082642 restraints weight = 20324.759| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.2848 r_free = 0.2848 target = 0.082756 restraints weight = 19136.160| |-----------------------------------------------------------------------------| r_work (final): 0.2801 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8738 moved from start: 0.3198 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.051 22759 Z= 0.213 Angle : 0.721 16.634 31146 Z= 0.341 Chirality : 0.047 0.312 3835 Planarity : 0.004 0.050 3714 Dihedral : 9.321 76.280 5418 Min Nonbonded Distance : 2.256 Molprobity Statistics. All-atom Clashscore : 3.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.66 % Favored : 94.34 % Rotamer: Outliers : 3.22 % Allowed : 15.39 % Favored : 81.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.77 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.08 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.88 (0.16), residues: 2580 helix: -0.98 (0.28), residues: 351 sheet: -0.37 (0.18), residues: 886 loop : -1.96 (0.15), residues: 1343 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG J 480 TYR 0.014 0.002 TYR B 91 PHE 0.026 0.002 PHE R 78 TRP 0.010 0.001 TRP R 47 HIS 0.005 0.001 HIS P 216 Details of bonding type rmsd covalent geometry : bond 0.00508 (22589) covalent geometry : angle 0.66997 (30682) SS BOND : bond 0.00527 ( 40) SS BOND : angle 2.85669 ( 80) hydrogen bonds : bond 0.04728 ( 644) hydrogen bonds : angle 4.87169 ( 1740) Misc. bond : bond 0.00046 ( 2) link_ALPHA1-2 : bond 0.00248 ( 11) link_ALPHA1-2 : angle 1.75356 ( 33) link_ALPHA1-3 : bond 0.01294 ( 10) link_ALPHA1-3 : angle 1.86418 ( 30) link_ALPHA1-6 : bond 0.00519 ( 9) link_ALPHA1-6 : angle 1.69344 ( 27) link_BETA1-4 : bond 0.00513 ( 43) link_BETA1-4 : angle 1.91735 ( 129) link_NAG-ASN : bond 0.00390 ( 55) link_NAG-ASN : angle 2.49737 ( 165) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5160 Ramachandran restraints generated. 2580 Oldfield, 0 Emsley, 2580 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5160 Ramachandran restraints generated. 2580 Oldfield, 0 Emsley, 2580 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 335 residues out of total 2278 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 73 poor density : 262 time to evaluate : 0.826 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 655 LYS cc_start: 0.8279 (OUTLIER) cc_final: 0.7733 (mptt) REVERT: J 95 MET cc_start: 0.9273 (ptm) cc_final: 0.9067 (ttp) REVERT: L 65 SER cc_start: 0.8741 (m) cc_final: 0.8444 (p) REVERT: L 77 ASN cc_start: 0.7924 (t0) cc_final: 0.7530 (t0) REVERT: P 116 LEU cc_start: 0.9141 (OUTLIER) cc_final: 0.8914 (mp) REVERT: P 199 SER cc_start: 0.8998 (t) cc_final: 0.8680 (m) REVERT: P 359 ILE cc_start: 0.9290 (mm) cc_final: 0.9001 (mm) REVERT: R 16 GLU cc_start: 0.7928 (mt-10) cc_final: 0.7538 (mt-10) REVERT: W 79 GLN cc_start: 0.8826 (mm-40) cc_final: 0.8471 (mm110) outliers start: 73 outliers final: 53 residues processed: 318 average time/residue: 0.1377 time to fit residues: 68.6658 Evaluate side-chains 301 residues out of total 2278 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 246 time to evaluate : 0.832 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 37 VAL Chi-restraints excluded: chain A residue 51 ILE Chi-restraints excluded: chain A residue 77 ILE Chi-restraints excluded: chain A residue 92 CYS Chi-restraints excluded: chain A residue 94 THR Chi-restraints excluded: chain B residue 1 ASP Chi-restraints excluded: chain B residue 10 THR Chi-restraints excluded: chain B residue 33 VAL Chi-restraints excluded: chain B residue 65 SER Chi-restraints excluded: chain B residue 72 THR Chi-restraints excluded: chain C residue 569 THR Chi-restraints excluded: chain C residue 595 ILE Chi-restraints excluded: chain D residue 652 GLN Chi-restraints excluded: chain D residue 655 LYS Chi-restraints excluded: chain F residue 595 ILE Chi-restraints excluded: chain F residue 627 THR Chi-restraints excluded: chain G residue 49 GLU Chi-restraints excluded: chain G residue 188 ASN Chi-restraints excluded: chain G residue 196 CYS Chi-restraints excluded: chain G residue 198 THR Chi-restraints excluded: chain G residue 202 THR Chi-restraints excluded: chain G residue 218 CYS Chi-restraints excluded: chain G residue 247 CYS Chi-restraints excluded: chain G residue 411 ASN Chi-restraints excluded: chain G residue 420 ILE Chi-restraints excluded: chain G residue 447 SER Chi-restraints excluded: chain G residue 501 CYS Chi-restraints excluded: chain H residue 2 ILE Chi-restraints excluded: chain H residue 11 VAL Chi-restraints excluded: chain H residue 35 VAL Chi-restraints excluded: chain H residue 77 ILE Chi-restraints excluded: chain H residue 87 THR Chi-restraints excluded: chain H residue 111 VAL Chi-restraints excluded: chain J residue 202 THR Chi-restraints excluded: chain J residue 257 THR Chi-restraints excluded: chain J residue 261 LEU Chi-restraints excluded: chain J residue 492 GLU Chi-restraints excluded: chain L residue 22 SER Chi-restraints excluded: chain L residue 33 VAL Chi-restraints excluded: chain M residue 80 LEU Chi-restraints excluded: chain M residue 107 THR Chi-restraints excluded: chain M residue 111 VAL Chi-restraints excluded: chain P residue 54 CYS Chi-restraints excluded: chain P residue 116 LEU Chi-restraints excluded: chain P residue 120 VAL Chi-restraints excluded: chain P residue 166 ARG Chi-restraints excluded: chain P residue 202 THR Chi-restraints excluded: chain P residue 205 CYS Chi-restraints excluded: chain P residue 242 VAL Chi-restraints excluded: chain P residue 247 CYS Chi-restraints excluded: chain P residue 277 ILE Chi-restraints excluded: chain R residue 20 LEU Chi-restraints excluded: chain R residue 29 ILE Chi-restraints excluded: chain R residue 87 THR Chi-restraints excluded: chain W residue 78 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 256 random chunks: chunk 50 optimal weight: 0.3980 chunk 25 optimal weight: 3.9990 chunk 23 optimal weight: 7.9990 chunk 146 optimal weight: 7.9990 chunk 220 optimal weight: 9.9990 chunk 90 optimal weight: 2.9990 chunk 155 optimal weight: 3.9990 chunk 183 optimal weight: 10.0000 chunk 16 optimal weight: 30.0000 chunk 41 optimal weight: 7.9990 chunk 83 optimal weight: 6.9990 overall best weight: 3.6788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 540 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 658 GLN D 653 GLN F 616 ASN ** J 195 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 35AASN W 70 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3108 r_free = 0.3108 target = 0.098769 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2779 r_free = 0.2779 target = 0.078388 restraints weight = 38269.087| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.2808 r_free = 0.2808 target = 0.080412 restraints weight = 28884.824| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.2817 r_free = 0.2817 target = 0.080981 restraints weight = 21781.040| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.2826 r_free = 0.2826 target = 0.081496 restraints weight = 19620.070| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.2827 r_free = 0.2827 target = 0.081564 restraints weight = 18651.876| |-----------------------------------------------------------------------------| r_work (final): 0.2822 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8767 moved from start: 0.3660 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.056 22759 Z= 0.229 Angle : 0.724 15.536 31146 Z= 0.344 Chirality : 0.048 0.350 3835 Planarity : 0.004 0.050 3714 Dihedral : 9.154 73.590 5418 Min Nonbonded Distance : 2.275 Molprobity Statistics. All-atom Clashscore : 3.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.19 % Favored : 94.81 % Rotamer: Outliers : 3.75 % Allowed : 16.14 % Favored : 80.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.77 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.08 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.80 (0.16), residues: 2580 helix: -0.90 (0.29), residues: 351 sheet: -0.37 (0.18), residues: 897 loop : -1.88 (0.16), residues: 1332 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG J 327 TYR 0.014 0.002 TYR B 87 PHE 0.022 0.002 PHE R 78 TRP 0.012 0.001 TRP F 571 HIS 0.005 0.001 HIS P 105 Details of bonding type rmsd covalent geometry : bond 0.00552 (22589) covalent geometry : angle 0.67690 (30682) SS BOND : bond 0.00525 ( 40) SS BOND : angle 2.80006 ( 80) hydrogen bonds : bond 0.04812 ( 644) hydrogen bonds : angle 4.99593 ( 1740) Misc. bond : bond 0.00069 ( 2) link_ALPHA1-2 : bond 0.00244 ( 11) link_ALPHA1-2 : angle 1.68578 ( 33) link_ALPHA1-3 : bond 0.01363 ( 10) link_ALPHA1-3 : angle 1.79748 ( 30) link_ALPHA1-6 : bond 0.00534 ( 9) link_ALPHA1-6 : angle 1.66278 ( 27) link_BETA1-4 : bond 0.00506 ( 43) link_BETA1-4 : angle 1.92238 ( 129) link_NAG-ASN : bond 0.00282 ( 55) link_NAG-ASN : angle 2.33205 ( 165) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5160 Ramachandran restraints generated. 2580 Oldfield, 0 Emsley, 2580 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5160 Ramachandran restraints generated. 2580 Oldfield, 0 Emsley, 2580 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 331 residues out of total 2278 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 85 poor density : 246 time to evaluate : 0.772 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 23 LYS cc_start: 0.9052 (mttt) cc_final: 0.8610 (mtmm) REVERT: B 3 GLN cc_start: 0.8525 (mp10) cc_final: 0.8172 (mt0) REVERT: B 27 SER cc_start: 0.8966 (t) cc_final: 0.8505 (p) REVERT: D 655 LYS cc_start: 0.8284 (OUTLIER) cc_final: 0.7937 (mptt) REVERT: G 84 ILE cc_start: 0.9078 (mm) cc_final: 0.8834 (mt) REVERT: J 207 LYS cc_start: 0.8134 (tptp) cc_final: 0.7900 (tptp) REVERT: L 65 SER cc_start: 0.8712 (m) cc_final: 0.8492 (p) REVERT: L 77 ASN cc_start: 0.7833 (t0) cc_final: 0.7492 (t0) REVERT: P 199 SER cc_start: 0.9115 (t) cc_final: 0.8772 (m) REVERT: P 359 ILE cc_start: 0.9317 (mm) cc_final: 0.9009 (mm) REVERT: W 79 GLN cc_start: 0.8748 (mm-40) cc_final: 0.8477 (mm110) outliers start: 85 outliers final: 60 residues processed: 314 average time/residue: 0.1412 time to fit residues: 69.7372 Evaluate side-chains 301 residues out of total 2278 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 240 time to evaluate : 0.719 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 51 ILE Chi-restraints excluded: chain A residue 77 ILE Chi-restraints excluded: chain A residue 92 CYS Chi-restraints excluded: chain A residue 94 THR Chi-restraints excluded: chain B residue 1 ASP Chi-restraints excluded: chain B residue 10 THR Chi-restraints excluded: chain B residue 11 LEU Chi-restraints excluded: chain B residue 33 VAL Chi-restraints excluded: chain B residue 58 VAL Chi-restraints excluded: chain B residue 65 SER Chi-restraints excluded: chain B residue 72 THR Chi-restraints excluded: chain B residue 81 GLU Chi-restraints excluded: chain C residue 569 THR Chi-restraints excluded: chain C residue 595 ILE Chi-restraints excluded: chain D residue 615 SER Chi-restraints excluded: chain D residue 652 GLN Chi-restraints excluded: chain D residue 655 LYS Chi-restraints excluded: chain F residue 595 ILE Chi-restraints excluded: chain F residue 627 THR Chi-restraints excluded: chain G residue 49 GLU Chi-restraints excluded: chain G residue 188 ASN Chi-restraints excluded: chain G residue 196 CYS Chi-restraints excluded: chain G residue 198 THR Chi-restraints excluded: chain G residue 202 THR Chi-restraints excluded: chain G residue 218 CYS Chi-restraints excluded: chain G residue 247 CYS Chi-restraints excluded: chain G residue 411 ASN Chi-restraints excluded: chain G residue 420 ILE Chi-restraints excluded: chain G residue 501 CYS Chi-restraints excluded: chain H residue 2 ILE Chi-restraints excluded: chain H residue 11 VAL Chi-restraints excluded: chain H residue 35 VAL Chi-restraints excluded: chain H residue 71 VAL Chi-restraints excluded: chain H residue 77 ILE Chi-restraints excluded: chain H residue 87 THR Chi-restraints excluded: chain H residue 111 VAL Chi-restraints excluded: chain J residue 54 CYS Chi-restraints excluded: chain J residue 202 THR Chi-restraints excluded: chain J residue 257 THR Chi-restraints excluded: chain J residue 261 LEU Chi-restraints excluded: chain J residue 294 ILE Chi-restraints excluded: chain J residue 377 ASN Chi-restraints excluded: chain J residue 492 GLU Chi-restraints excluded: chain L residue 1 ASP Chi-restraints excluded: chain L residue 22 SER Chi-restraints excluded: chain L residue 33 VAL Chi-restraints excluded: chain M residue 69 ILE Chi-restraints excluded: chain M residue 107 THR Chi-restraints excluded: chain M residue 111 VAL Chi-restraints excluded: chain P residue 54 CYS Chi-restraints excluded: chain P residue 120 VAL Chi-restraints excluded: chain P residue 123 THR Chi-restraints excluded: chain P residue 166 ARG Chi-restraints excluded: chain P residue 202 THR Chi-restraints excluded: chain P residue 242 VAL Chi-restraints excluded: chain P residue 247 CYS Chi-restraints excluded: chain P residue 257 THR Chi-restraints excluded: chain P residue 277 ILE Chi-restraints excluded: chain R residue 20 LEU Chi-restraints excluded: chain R residue 29 ILE Chi-restraints excluded: chain R residue 87 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 256 random chunks: chunk 96 optimal weight: 5.9990 chunk 26 optimal weight: 0.9990 chunk 153 optimal weight: 5.9990 chunk 107 optimal weight: 1.9990 chunk 148 optimal weight: 6.9990 chunk 200 optimal weight: 7.9990 chunk 95 optimal weight: 0.8980 chunk 126 optimal weight: 5.9990 chunk 119 optimal weight: 0.4980 chunk 185 optimal weight: 2.9990 chunk 154 optimal weight: 3.9990 overall best weight: 1.4786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 658 GLN D 616 ASN ** J 195 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** W 6 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3152 r_free = 0.3152 target = 0.101574 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.2822 r_free = 0.2822 target = 0.081013 restraints weight = 38326.864| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.2860 r_free = 0.2860 target = 0.083615 restraints weight = 26259.369| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.2867 r_free = 0.2867 target = 0.084005 restraints weight = 18807.939| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.2871 r_free = 0.2871 target = 0.084248 restraints weight = 17779.239| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.2874 r_free = 0.2874 target = 0.084467 restraints weight = 16802.191| |-----------------------------------------------------------------------------| r_work (final): 0.2813 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8725 moved from start: 0.3605 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 22759 Z= 0.123 Angle : 0.622 14.433 31146 Z= 0.296 Chirality : 0.044 0.259 3835 Planarity : 0.003 0.038 3714 Dihedral : 8.575 71.956 5418 Min Nonbonded Distance : 2.348 Molprobity Statistics. All-atom Clashscore : 3.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.65 % Favored : 95.35 % Rotamer: Outliers : 2.65 % Allowed : 17.47 % Favored : 79.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.77 % 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: -1.51 (0.16), residues: 2580 helix: -0.47 (0.30), residues: 338 sheet: -0.20 (0.18), residues: 864 loop : -1.69 (0.16), residues: 1378 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG J 327 TYR 0.014 0.001 TYR M 47 PHE 0.014 0.001 PHE J 383 TRP 0.010 0.001 TRP L 32 HIS 0.003 0.001 HIS R 77 Details of bonding type rmsd covalent geometry : bond 0.00281 (22589) covalent geometry : angle 0.58045 (30682) SS BOND : bond 0.00547 ( 40) SS BOND : angle 2.43579 ( 80) hydrogen bonds : bond 0.03839 ( 644) hydrogen bonds : angle 4.72408 ( 1740) Misc. bond : bond 0.00068 ( 2) link_ALPHA1-2 : bond 0.00277 ( 11) link_ALPHA1-2 : angle 1.58146 ( 33) link_ALPHA1-3 : bond 0.01366 ( 10) link_ALPHA1-3 : angle 1.87367 ( 30) link_ALPHA1-6 : bond 0.00559 ( 9) link_ALPHA1-6 : angle 1.58306 ( 27) link_BETA1-4 : bond 0.00504 ( 43) link_BETA1-4 : angle 1.76899 ( 129) link_NAG-ASN : bond 0.00238 ( 55) link_NAG-ASN : angle 1.86904 ( 165) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5160 Ramachandran restraints generated. 2580 Oldfield, 0 Emsley, 2580 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5160 Ramachandran restraints generated. 2580 Oldfield, 0 Emsley, 2580 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 308 residues out of total 2278 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 248 time to evaluate : 0.746 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: D 655 LYS cc_start: 0.8200 (OUTLIER) cc_final: 0.7987 (mptt) REVERT: F 603 ILE cc_start: 0.8730 (OUTLIER) cc_final: 0.8511 (mm) REVERT: F 656 ASN cc_start: 0.8073 (m-40) cc_final: 0.7840 (m-40) REVERT: J 207 LYS cc_start: 0.8103 (tptp) cc_final: 0.7849 (tptp) REVERT: L 77 ASN cc_start: 0.7773 (t0) cc_final: 0.7376 (t0) REVERT: P 199 SER cc_start: 0.9080 (t) cc_final: 0.8768 (m) REVERT: P 359 ILE cc_start: 0.9267 (mm) cc_final: 0.8960 (mm) REVERT: R 16 GLU cc_start: 0.7820 (mt-10) cc_final: 0.7424 (mt-10) REVERT: W 79 GLN cc_start: 0.8791 (mm-40) cc_final: 0.8547 (mm110) outliers start: 60 outliers final: 47 residues processed: 293 average time/residue: 0.1380 time to fit residues: 64.1636 Evaluate side-chains 290 residues out of total 2278 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 241 time to evaluate : 0.742 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 92 CYS Chi-restraints excluded: chain B residue 1 ASP Chi-restraints excluded: chain B residue 10 THR Chi-restraints excluded: chain B residue 33 VAL Chi-restraints excluded: chain B residue 65 SER Chi-restraints excluded: chain B residue 69 THR Chi-restraints excluded: chain B residue 72 THR Chi-restraints excluded: chain B residue 81 GLU Chi-restraints excluded: chain C residue 569 THR Chi-restraints excluded: chain C residue 595 ILE Chi-restraints excluded: chain C residue 615 SER Chi-restraints excluded: chain D residue 601 LYS Chi-restraints excluded: chain D residue 652 GLN Chi-restraints excluded: chain D residue 655 LYS Chi-restraints excluded: chain F residue 595 ILE Chi-restraints excluded: chain F residue 603 ILE Chi-restraints excluded: chain F residue 627 THR Chi-restraints excluded: chain G residue 49 GLU Chi-restraints excluded: chain G residue 188 ASN Chi-restraints excluded: chain G residue 196 CYS Chi-restraints excluded: chain G residue 198 THR Chi-restraints excluded: chain G residue 202 THR Chi-restraints excluded: chain G residue 218 CYS Chi-restraints excluded: chain G residue 247 CYS Chi-restraints excluded: chain G residue 411 ASN Chi-restraints excluded: chain G residue 420 ILE Chi-restraints excluded: chain G residue 501 CYS Chi-restraints excluded: chain H residue 2 ILE Chi-restraints excluded: chain H residue 11 VAL Chi-restraints excluded: chain H residue 35 VAL Chi-restraints excluded: chain H residue 77 ILE Chi-restraints excluded: chain H residue 87 THR Chi-restraints excluded: chain H residue 111 VAL Chi-restraints excluded: chain J residue 54 CYS Chi-restraints excluded: chain J residue 202 THR Chi-restraints excluded: chain J residue 261 LEU Chi-restraints excluded: chain J residue 294 ILE Chi-restraints excluded: chain J residue 492 GLU Chi-restraints excluded: chain L residue 1 ASP Chi-restraints excluded: chain L residue 33 VAL Chi-restraints excluded: chain M residue 111 VAL Chi-restraints excluded: chain P residue 54 CYS Chi-restraints excluded: chain P residue 123 THR Chi-restraints excluded: chain P residue 166 ARG Chi-restraints excluded: chain P residue 247 CYS Chi-restraints excluded: chain P residue 467 THR Chi-restraints excluded: chain R residue 29 ILE Chi-restraints excluded: chain R residue 87 THR Chi-restraints excluded: chain R residue 100 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 256 random chunks: chunk 220 optimal weight: 10.0000 chunk 113 optimal weight: 3.9990 chunk 67 optimal weight: 10.0000 chunk 159 optimal weight: 0.9990 chunk 171 optimal weight: 3.9990 chunk 158 optimal weight: 20.0000 chunk 145 optimal weight: 0.0070 chunk 218 optimal weight: 0.0670 chunk 16 optimal weight: 10.0000 chunk 170 optimal weight: 3.9990 chunk 193 optimal weight: 8.9990 overall best weight: 1.8142 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 540 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 616 ASN D 653 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3148 r_free = 0.3148 target = 0.101303 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2819 r_free = 0.2819 target = 0.080848 restraints weight = 38141.330| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.2852 r_free = 0.2852 target = 0.083133 restraints weight = 25941.430| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.2861 r_free = 0.2861 target = 0.083619 restraints weight = 20018.714| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.2865 r_free = 0.2865 target = 0.083882 restraints weight = 17706.793| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.2871 r_free = 0.2871 target = 0.084200 restraints weight = 17285.231| |-----------------------------------------------------------------------------| r_work (final): 0.2814 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8727 moved from start: 0.3660 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 22759 Z= 0.135 Angle : 0.623 13.908 31146 Z= 0.296 Chirality : 0.044 0.259 3835 Planarity : 0.003 0.036 3714 Dihedral : 8.321 72.311 5418 Min Nonbonded Distance : 2.323 Molprobity Statistics. All-atom Clashscore : 3.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.77 % Favored : 95.23 % Rotamer: Outliers : 2.82 % Allowed : 17.87 % Favored : 79.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.77 % 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: -1.38 (0.16), residues: 2580 helix: -0.34 (0.30), residues: 339 sheet: -0.14 (0.18), residues: 864 loop : -1.61 (0.16), residues: 1377 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG J 327 TYR 0.013 0.001 TYR M 47 PHE 0.015 0.001 PHE R 78 TRP 0.009 0.001 TRP F 571 HIS 0.003 0.001 HIS P 105 Details of bonding type rmsd covalent geometry : bond 0.00315 (22589) covalent geometry : angle 0.58104 (30682) SS BOND : bond 0.00406 ( 40) SS BOND : angle 2.46306 ( 80) hydrogen bonds : bond 0.03844 ( 644) hydrogen bonds : angle 4.64238 ( 1740) Misc. bond : bond 0.00070 ( 2) link_ALPHA1-2 : bond 0.00238 ( 11) link_ALPHA1-2 : angle 1.59711 ( 33) link_ALPHA1-3 : bond 0.01376 ( 10) link_ALPHA1-3 : angle 1.83703 ( 30) link_ALPHA1-6 : bond 0.00551 ( 9) link_ALPHA1-6 : angle 1.56721 ( 27) link_BETA1-4 : bond 0.00510 ( 43) link_BETA1-4 : angle 1.76617 ( 129) link_NAG-ASN : bond 0.00406 ( 55) link_NAG-ASN : angle 1.88272 ( 165) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5160 Ramachandran restraints generated. 2580 Oldfield, 0 Emsley, 2580 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5160 Ramachandran restraints generated. 2580 Oldfield, 0 Emsley, 2580 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 305 residues out of total 2278 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 241 time to evaluate : 0.803 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: F 591 GLN cc_start: 0.9023 (OUTLIER) cc_final: 0.8678 (tt0) REVERT: G 95 MET cc_start: 0.9038 (ptm) cc_final: 0.8803 (ttp) REVERT: J 207 LYS cc_start: 0.8133 (tptp) cc_final: 0.7905 (tptp) REVERT: L 77 ASN cc_start: 0.7837 (t0) cc_final: 0.7328 (t0) REVERT: L 79 GLN cc_start: 0.8398 (mm-40) cc_final: 0.7751 (mt0) REVERT: P 116 LEU cc_start: 0.9092 (OUTLIER) cc_final: 0.8858 (mp) REVERT: P 199 SER cc_start: 0.9109 (t) cc_final: 0.8806 (m) REVERT: P 308 ARG cc_start: 0.8366 (OUTLIER) cc_final: 0.7701 (mtm110) REVERT: P 359 ILE cc_start: 0.9271 (mm) cc_final: 0.8971 (mm) REVERT: R 16 GLU cc_start: 0.7836 (mt-10) cc_final: 0.7443 (mt-10) REVERT: W 79 GLN cc_start: 0.8758 (mm-40) cc_final: 0.8524 (mm110) outliers start: 64 outliers final: 51 residues processed: 289 average time/residue: 0.1407 time to fit residues: 63.9620 Evaluate side-chains 291 residues out of total 2278 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 237 time to evaluate : 0.548 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 92 CYS Chi-restraints excluded: chain B residue 1 ASP Chi-restraints excluded: chain B residue 10 THR Chi-restraints excluded: chain B residue 33 VAL Chi-restraints excluded: chain B residue 65 SER Chi-restraints excluded: chain B residue 69 THR Chi-restraints excluded: chain B residue 72 THR Chi-restraints excluded: chain B residue 81 GLU Chi-restraints excluded: chain C residue 569 THR Chi-restraints excluded: chain C residue 595 ILE Chi-restraints excluded: chain D residue 601 LYS Chi-restraints excluded: chain D residue 615 SER Chi-restraints excluded: chain D residue 652 GLN Chi-restraints excluded: chain F residue 591 GLN Chi-restraints excluded: chain F residue 595 ILE Chi-restraints excluded: chain F residue 627 THR Chi-restraints excluded: chain G residue 54 CYS Chi-restraints excluded: chain G residue 188 ASN Chi-restraints excluded: chain G residue 196 CYS Chi-restraints excluded: chain G residue 198 THR Chi-restraints excluded: chain G residue 202 THR Chi-restraints excluded: chain G residue 205 CYS Chi-restraints excluded: chain G residue 218 CYS Chi-restraints excluded: chain G residue 247 CYS Chi-restraints excluded: chain G residue 411 ASN Chi-restraints excluded: chain G residue 420 ILE Chi-restraints excluded: chain G residue 501 CYS Chi-restraints excluded: chain H residue 2 ILE Chi-restraints excluded: chain H residue 11 VAL Chi-restraints excluded: chain H residue 35 VAL Chi-restraints excluded: chain H residue 71 VAL Chi-restraints excluded: chain H residue 77 ILE Chi-restraints excluded: chain H residue 87 THR Chi-restraints excluded: chain H residue 111 VAL Chi-restraints excluded: chain J residue 54 CYS Chi-restraints excluded: chain J residue 202 THR Chi-restraints excluded: chain J residue 261 LEU Chi-restraints excluded: chain J residue 294 ILE Chi-restraints excluded: chain J residue 492 GLU Chi-restraints excluded: chain L residue 14 SER Chi-restraints excluded: chain L residue 33 VAL Chi-restraints excluded: chain L residue 54 LEU Chi-restraints excluded: chain M residue 80 LEU Chi-restraints excluded: chain M residue 111 VAL Chi-restraints excluded: chain P residue 54 CYS Chi-restraints excluded: chain P residue 116 LEU Chi-restraints excluded: chain P residue 123 THR Chi-restraints excluded: chain P residue 166 ARG Chi-restraints excluded: chain P residue 247 CYS Chi-restraints excluded: chain P residue 308 ARG Chi-restraints excluded: chain P residue 430 ILE Chi-restraints excluded: chain P residue 467 THR Chi-restraints excluded: chain R residue 29 ILE Chi-restraints excluded: chain R residue 87 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 256 random chunks: chunk 215 optimal weight: 10.0000 chunk 233 optimal weight: 6.9990 chunk 182 optimal weight: 2.9990 chunk 239 optimal weight: 0.2980 chunk 116 optimal weight: 6.9990 chunk 232 optimal weight: 2.9990 chunk 130 optimal weight: 6.9990 chunk 225 optimal weight: 6.9990 chunk 230 optimal weight: 9.9990 chunk 22 optimal weight: 0.8980 chunk 209 optimal weight: 6.9990 overall best weight: 2.8386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 540 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 616 ASN D 653 GLN F 656 ASN P 195 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3125 r_free = 0.3125 target = 0.099782 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2791 r_free = 0.2791 target = 0.079060 restraints weight = 38182.339| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.2821 r_free = 0.2821 target = 0.081167 restraints weight = 27093.233| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.2832 r_free = 0.2832 target = 0.081850 restraints weight = 20375.868| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.2840 r_free = 0.2840 target = 0.082325 restraints weight = 18196.065| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.2842 r_free = 0.2842 target = 0.082448 restraints weight = 17440.544| |-----------------------------------------------------------------------------| r_work (final): 0.2790 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8758 moved from start: 0.3828 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 22759 Z= 0.184 Angle : 0.667 14.183 31146 Z= 0.319 Chirality : 0.046 0.265 3835 Planarity : 0.004 0.038 3714 Dihedral : 8.383 73.453 5418 Min Nonbonded Distance : 2.292 Molprobity Statistics. All-atom Clashscore : 3.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.85 % Favored : 94.15 % Rotamer: Outliers : 3.22 % Allowed : 17.82 % Favored : 78.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.77 % 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: -1.43 (0.16), residues: 2580 helix: -0.40 (0.29), residues: 344 sheet: -0.15 (0.18), residues: 870 loop : -1.65 (0.16), residues: 1366 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG J 327 TYR 0.014 0.001 TYR B 91 PHE 0.020 0.002 PHE R 78 TRP 0.010 0.001 TRP R 47 HIS 0.004 0.001 HIS P 105 Details of bonding type rmsd covalent geometry : bond 0.00442 (22589) covalent geometry : angle 0.62661 (30682) SS BOND : bond 0.00454 ( 40) SS BOND : angle 2.50764 ( 80) hydrogen bonds : bond 0.04376 ( 644) hydrogen bonds : angle 4.75894 ( 1740) Misc. bond : bond 0.00077 ( 2) link_ALPHA1-2 : bond 0.00211 ( 11) link_ALPHA1-2 : angle 1.65850 ( 33) link_ALPHA1-3 : bond 0.01372 ( 10) link_ALPHA1-3 : angle 1.80961 ( 30) link_ALPHA1-6 : bond 0.00527 ( 9) link_ALPHA1-6 : angle 1.61345 ( 27) link_BETA1-4 : bond 0.00517 ( 43) link_BETA1-4 : angle 1.86095 ( 129) link_NAG-ASN : bond 0.00230 ( 55) link_NAG-ASN : angle 1.93592 ( 165) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5160 Ramachandran restraints generated. 2580 Oldfield, 0 Emsley, 2580 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5160 Ramachandran restraints generated. 2580 Oldfield, 0 Emsley, 2580 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 308 residues out of total 2278 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 73 poor density : 235 time to evaluate : 0.845 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 23 LYS cc_start: 0.9047 (mttt) cc_final: 0.8611 (mtmm) REVERT: B 27 SER cc_start: 0.9044 (t) cc_final: 0.8591 (p) REVERT: D 655 LYS cc_start: 0.8503 (OUTLIER) cc_final: 0.8094 (mptt) REVERT: J 207 LYS cc_start: 0.8254 (tptp) cc_final: 0.8020 (tptp) REVERT: L 77 ASN cc_start: 0.7810 (t0) cc_final: 0.7328 (t0) REVERT: L 79 GLN cc_start: 0.8381 (mm-40) cc_final: 0.7761 (mt0) REVERT: P 116 LEU cc_start: 0.9152 (OUTLIER) cc_final: 0.8904 (mp) REVERT: P 199 SER cc_start: 0.9131 (t) cc_final: 0.8797 (m) REVERT: P 308 ARG cc_start: 0.8379 (OUTLIER) cc_final: 0.7711 (mtm110) REVERT: P 359 ILE cc_start: 0.9299 (mm) cc_final: 0.8998 (mm) REVERT: R 16 GLU cc_start: 0.7845 (mt-10) cc_final: 0.7383 (mt-10) REVERT: W 79 GLN cc_start: 0.8734 (mm-40) cc_final: 0.8478 (mm110) outliers start: 73 outliers final: 61 residues processed: 290 average time/residue: 0.1444 time to fit residues: 65.7235 Evaluate side-chains 295 residues out of total 2278 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 231 time to evaluate : 0.766 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 18 VAL Chi-restraints excluded: chain A residue 92 CYS Chi-restraints excluded: chain B residue 1 ASP Chi-restraints excluded: chain B residue 10 THR Chi-restraints excluded: chain B residue 33 VAL Chi-restraints excluded: chain B residue 65 SER Chi-restraints excluded: chain B residue 69 THR Chi-restraints excluded: chain B residue 72 THR Chi-restraints excluded: chain B residue 81 GLU Chi-restraints excluded: chain C residue 569 THR Chi-restraints excluded: chain C residue 595 ILE Chi-restraints excluded: chain C residue 615 SER Chi-restraints excluded: chain D residue 615 SER Chi-restraints excluded: chain D residue 652 GLN Chi-restraints excluded: chain D residue 655 LYS Chi-restraints excluded: chain F residue 595 ILE Chi-restraints excluded: chain F residue 627 THR Chi-restraints excluded: chain G residue 38 VAL Chi-restraints excluded: chain G residue 54 CYS Chi-restraints excluded: chain G residue 188 ASN Chi-restraints excluded: chain G residue 196 CYS Chi-restraints excluded: chain G residue 198 THR Chi-restraints excluded: chain G residue 199 SER Chi-restraints excluded: chain G residue 202 THR Chi-restraints excluded: chain G residue 205 CYS Chi-restraints excluded: chain G residue 218 CYS Chi-restraints excluded: chain G residue 247 CYS Chi-restraints excluded: chain G residue 420 ILE Chi-restraints excluded: chain G residue 501 CYS Chi-restraints excluded: chain H residue 2 ILE Chi-restraints excluded: chain H residue 11 VAL Chi-restraints excluded: chain H residue 35 VAL Chi-restraints excluded: chain H residue 71 VAL Chi-restraints excluded: chain H residue 77 ILE Chi-restraints excluded: chain H residue 87 THR Chi-restraints excluded: chain H residue 92 CYS Chi-restraints excluded: chain H residue 100 VAL Chi-restraints excluded: chain H residue 111 VAL Chi-restraints excluded: chain J residue 54 CYS Chi-restraints excluded: chain J residue 202 THR Chi-restraints excluded: chain J residue 261 LEU Chi-restraints excluded: chain J residue 294 ILE Chi-restraints excluded: chain J residue 492 GLU Chi-restraints excluded: chain L residue 14 SER Chi-restraints excluded: chain L residue 33 VAL Chi-restraints excluded: chain L residue 46 LEU Chi-restraints excluded: chain L residue 54 LEU Chi-restraints excluded: chain M residue 69 ILE Chi-restraints excluded: chain M residue 107 THR Chi-restraints excluded: chain M residue 111 VAL Chi-restraints excluded: chain O residue 33 VAL Chi-restraints excluded: chain P residue 54 CYS Chi-restraints excluded: chain P residue 116 LEU Chi-restraints excluded: chain P residue 123 THR Chi-restraints excluded: chain P residue 166 ARG Chi-restraints excluded: chain P residue 195 ASN Chi-restraints excluded: chain P residue 202 THR Chi-restraints excluded: chain P residue 247 CYS Chi-restraints excluded: chain P residue 308 ARG Chi-restraints excluded: chain P residue 430 ILE Chi-restraints excluded: chain P residue 467 THR Chi-restraints excluded: chain R residue 24 VAL Chi-restraints excluded: chain R residue 29 ILE Chi-restraints excluded: chain R residue 87 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 256 random chunks: chunk 189 optimal weight: 1.9990 chunk 92 optimal weight: 0.9980 chunk 243 optimal weight: 2.9990 chunk 251 optimal weight: 2.9990 chunk 43 optimal weight: 8.9990 chunk 164 optimal weight: 10.0000 chunk 20 optimal weight: 6.9990 chunk 111 optimal weight: 7.9990 chunk 232 optimal weight: 0.9990 chunk 223 optimal weight: 4.9990 chunk 226 optimal weight: 3.9990 overall best weight: 1.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 540 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 653 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3134 r_free = 0.3134 target = 0.100388 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2807 r_free = 0.2807 target = 0.080046 restraints weight = 38400.927| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.2839 r_free = 0.2839 target = 0.082306 restraints weight = 28735.704| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.2858 r_free = 0.2858 target = 0.083379 restraints weight = 21813.839| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.2857 r_free = 0.2857 target = 0.083369 restraints weight = 18069.336| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.2859 r_free = 0.2859 target = 0.083458 restraints weight = 18356.671| |-----------------------------------------------------------------------------| r_work (final): 0.2803 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8734 moved from start: 0.3843 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 22759 Z= 0.144 Angle : 0.634 13.811 31146 Z= 0.303 Chirality : 0.045 0.261 3835 Planarity : 0.003 0.035 3714 Dihedral : 8.178 72.855 5418 Min Nonbonded Distance : 2.334 Molprobity Statistics. All-atom Clashscore : 3.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.84 % Favored : 95.16 % Rotamer: Outliers : 3.00 % Allowed : 18.22 % Favored : 78.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.77 % 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: -1.30 (0.16), residues: 2580 helix: -0.26 (0.30), residues: 344 sheet: 0.01 (0.18), residues: 872 loop : -1.65 (0.16), residues: 1364 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG J 327 TYR 0.013 0.001 TYR M 47 PHE 0.015 0.001 PHE R 78 TRP 0.011 0.001 TRP F 571 HIS 0.003 0.001 HIS P 105 Details of bonding type rmsd covalent geometry : bond 0.00338 (22589) covalent geometry : angle 0.59348 (30682) SS BOND : bond 0.00420 ( 40) SS BOND : angle 2.43220 ( 80) hydrogen bonds : bond 0.03974 ( 644) hydrogen bonds : angle 4.68236 ( 1740) Misc. bond : bond 0.00139 ( 2) link_ALPHA1-2 : bond 0.00240 ( 11) link_ALPHA1-2 : angle 1.59198 ( 33) link_ALPHA1-3 : bond 0.01381 ( 10) link_ALPHA1-3 : angle 1.81557 ( 30) link_ALPHA1-6 : bond 0.00535 ( 9) link_ALPHA1-6 : angle 1.56476 ( 27) link_BETA1-4 : bond 0.00515 ( 43) link_BETA1-4 : angle 1.79627 ( 129) link_NAG-ASN : bond 0.00218 ( 55) link_NAG-ASN : angle 1.87304 ( 165) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5160 Ramachandran restraints generated. 2580 Oldfield, 0 Emsley, 2580 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5160 Ramachandran restraints generated. 2580 Oldfield, 0 Emsley, 2580 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 306 residues out of total 2278 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 238 time to evaluate : 0.766 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 23 LYS cc_start: 0.9034 (mttt) cc_final: 0.8597 (mtmm) REVERT: B 27 SER cc_start: 0.9025 (t) cc_final: 0.8584 (p) REVERT: D 655 LYS cc_start: 0.8550 (OUTLIER) cc_final: 0.8103 (mptt) REVERT: G 95 MET cc_start: 0.9046 (ptm) cc_final: 0.8841 (ttp) REVERT: J 207 LYS cc_start: 0.8276 (tptp) cc_final: 0.8022 (tptp) REVERT: L 77 ASN cc_start: 0.7785 (t0) cc_final: 0.7310 (t0) REVERT: L 79 GLN cc_start: 0.8380 (mm-40) cc_final: 0.7783 (mt0) REVERT: P 116 LEU cc_start: 0.9117 (OUTLIER) cc_final: 0.8877 (mp) REVERT: P 199 SER cc_start: 0.9075 (t) cc_final: 0.8770 (m) REVERT: P 308 ARG cc_start: 0.8359 (OUTLIER) cc_final: 0.7695 (mtm110) REVERT: P 359 ILE cc_start: 0.9294 (mm) cc_final: 0.8995 (mm) REVERT: R 16 GLU cc_start: 0.7850 (mt-10) cc_final: 0.7425 (mt-10) outliers start: 68 outliers final: 58 residues processed: 289 average time/residue: 0.1423 time to fit residues: 64.6708 Evaluate side-chains 296 residues out of total 2278 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 235 time to evaluate : 0.599 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 92 CYS Chi-restraints excluded: chain B residue 1 ASP Chi-restraints excluded: chain B residue 10 THR Chi-restraints excluded: chain B residue 33 VAL Chi-restraints excluded: chain B residue 65 SER Chi-restraints excluded: chain B residue 69 THR Chi-restraints excluded: chain B residue 72 THR Chi-restraints excluded: chain B residue 81 GLU Chi-restraints excluded: chain C residue 569 THR Chi-restraints excluded: chain C residue 595 ILE Chi-restraints excluded: chain C residue 615 SER Chi-restraints excluded: chain D residue 615 SER Chi-restraints excluded: chain D residue 652 GLN Chi-restraints excluded: chain D residue 655 LYS Chi-restraints excluded: chain F residue 595 ILE Chi-restraints excluded: chain F residue 627 THR Chi-restraints excluded: chain G residue 38 VAL Chi-restraints excluded: chain G residue 54 CYS Chi-restraints excluded: chain G residue 188 ASN Chi-restraints excluded: chain G residue 196 CYS Chi-restraints excluded: chain G residue 198 THR Chi-restraints excluded: chain G residue 202 THR Chi-restraints excluded: chain G residue 205 CYS Chi-restraints excluded: chain G residue 218 CYS Chi-restraints excluded: chain G residue 247 CYS Chi-restraints excluded: chain G residue 420 ILE Chi-restraints excluded: chain G residue 501 CYS Chi-restraints excluded: chain H residue 2 ILE Chi-restraints excluded: chain H residue 35 VAL Chi-restraints excluded: chain H residue 71 VAL Chi-restraints excluded: chain H residue 77 ILE Chi-restraints excluded: chain H residue 87 THR Chi-restraints excluded: chain H residue 92 CYS Chi-restraints excluded: chain H residue 100 VAL Chi-restraints excluded: chain H residue 111 VAL Chi-restraints excluded: chain J residue 54 CYS Chi-restraints excluded: chain J residue 202 THR Chi-restraints excluded: chain J residue 261 LEU Chi-restraints excluded: chain J residue 294 ILE Chi-restraints excluded: chain J residue 492 GLU Chi-restraints excluded: chain L residue 14 SER Chi-restraints excluded: chain L residue 33 VAL Chi-restraints excluded: chain L residue 46 LEU Chi-restraints excluded: chain M residue 80 LEU Chi-restraints excluded: chain M residue 107 THR Chi-restraints excluded: chain M residue 111 VAL Chi-restraints excluded: chain O residue 27 SER Chi-restraints excluded: chain O residue 33 VAL Chi-restraints excluded: chain P residue 54 CYS Chi-restraints excluded: chain P residue 116 LEU Chi-restraints excluded: chain P residue 123 THR Chi-restraints excluded: chain P residue 166 ARG Chi-restraints excluded: chain P residue 202 THR Chi-restraints excluded: chain P residue 205 CYS Chi-restraints excluded: chain P residue 247 CYS Chi-restraints excluded: chain P residue 308 ARG Chi-restraints excluded: chain P residue 467 THR Chi-restraints excluded: chain R residue 24 VAL Chi-restraints excluded: chain R residue 29 ILE Chi-restraints excluded: chain R residue 87 THR Chi-restraints excluded: chain W residue 69 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 256 random chunks: chunk 254 optimal weight: 5.9990 chunk 187 optimal weight: 10.0000 chunk 188 optimal weight: 4.9990 chunk 137 optimal weight: 4.9990 chunk 163 optimal weight: 7.9990 chunk 253 optimal weight: 10.0000 chunk 215 optimal weight: 9.9990 chunk 52 optimal weight: 4.9990 chunk 139 optimal weight: 5.9990 chunk 223 optimal weight: 5.9990 chunk 1 optimal weight: 5.9990 overall best weight: 5.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 540 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 658 GLN ** D 540 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 653 GLN O 38 GLN P 195 ASN W 70 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3066 r_free = 0.3066 target = 0.096046 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2723 r_free = 0.2723 target = 0.075359 restraints weight = 39090.168| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.2755 r_free = 0.2755 target = 0.077429 restraints weight = 26884.021| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.2779 r_free = 0.2779 target = 0.078842 restraints weight = 19685.444| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.2780 r_free = 0.2780 target = 0.078882 restraints weight = 17588.184| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.2782 r_free = 0.2782 target = 0.078977 restraints weight = 16517.418| |-----------------------------------------------------------------------------| r_work (final): 0.2718 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8812 moved from start: 0.4206 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.065 22759 Z= 0.333 Angle : 0.831 15.864 31146 Z= 0.398 Chirality : 0.051 0.284 3835 Planarity : 0.005 0.058 3714 Dihedral : 9.151 72.680 5418 Min Nonbonded Distance : 2.228 Molprobity Statistics. All-atom Clashscore : 3.74 Ramachandran Plot: Outliers : 0.04 % Allowed : 7.56 % Favored : 92.40 % Rotamer: Outliers : 3.04 % Allowed : 18.22 % Favored : 78.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.77 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.08 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.68 (0.16), residues: 2580 helix: -0.69 (0.29), residues: 345 sheet: -0.29 (0.18), residues: 867 loop : -1.81 (0.16), residues: 1368 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG O 24 TYR 0.020 0.002 TYR L 91 PHE 0.025 0.002 PHE R 78 TRP 0.016 0.002 TRP J 45 HIS 0.006 0.001 HIS P 105 Details of bonding type rmsd covalent geometry : bond 0.00809 (22589) covalent geometry : angle 0.78699 (30682) SS BOND : bond 0.00564 ( 40) SS BOND : angle 2.96792 ( 80) hydrogen bonds : bond 0.05680 ( 644) hydrogen bonds : angle 5.22986 ( 1740) Misc. bond : bond 0.00101 ( 2) link_ALPHA1-2 : bond 0.00267 ( 11) link_ALPHA1-2 : angle 1.87396 ( 33) link_ALPHA1-3 : bond 0.01413 ( 10) link_ALPHA1-3 : angle 1.88844 ( 30) link_ALPHA1-6 : bond 0.00509 ( 9) link_ALPHA1-6 : angle 1.77310 ( 27) link_BETA1-4 : bond 0.00582 ( 43) link_BETA1-4 : angle 2.24377 ( 129) link_NAG-ASN : bond 0.00397 ( 55) link_NAG-ASN : angle 2.29427 ( 165) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5160 Ramachandran restraints generated. 2580 Oldfield, 0 Emsley, 2580 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5160 Ramachandran restraints generated. 2580 Oldfield, 0 Emsley, 2580 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 303 residues out of total 2278 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 234 time to evaluate : 0.766 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 23 LYS cc_start: 0.9122 (mttt) cc_final: 0.8661 (mtmm) REVERT: B 27 SER cc_start: 0.9104 (t) cc_final: 0.8651 (p) REVERT: D 655 LYS cc_start: 0.8660 (OUTLIER) cc_final: 0.8192 (mptt) REVERT: J 207 LYS cc_start: 0.8517 (tptp) cc_final: 0.8180 (tptp) REVERT: L 77 ASN cc_start: 0.7799 (t0) cc_final: 0.7320 (t0) REVERT: L 79 GLN cc_start: 0.8500 (mm-40) cc_final: 0.7861 (mt0) REVERT: M 64 ARG cc_start: 0.7313 (mtt180) cc_final: 0.7106 (mtm180) REVERT: P 116 LEU cc_start: 0.9241 (OUTLIER) cc_final: 0.8931 (mp) REVERT: P 308 ARG cc_start: 0.8393 (OUTLIER) cc_final: 0.7695 (mtm110) REVERT: P 359 ILE cc_start: 0.9327 (mm) cc_final: 0.9024 (mm) REVERT: R 16 GLU cc_start: 0.7851 (mt-10) cc_final: 0.7357 (mt-10) REVERT: W 81 GLU cc_start: 0.7167 (pm20) cc_final: 0.6953 (pm20) outliers start: 69 outliers final: 61 residues processed: 291 average time/residue: 0.1395 time to fit residues: 64.1570 Evaluate side-chains 290 residues out of total 2278 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 226 time to evaluate : 0.836 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 18 VAL Chi-restraints excluded: chain A residue 92 CYS Chi-restraints excluded: chain B residue 1 ASP Chi-restraints excluded: chain B residue 10 THR Chi-restraints excluded: chain B residue 33 VAL Chi-restraints excluded: chain B residue 65 SER Chi-restraints excluded: chain B residue 72 THR Chi-restraints excluded: chain B residue 81 GLU Chi-restraints excluded: chain C residue 569 THR Chi-restraints excluded: chain C residue 595 ILE Chi-restraints excluded: chain D residue 652 GLN Chi-restraints excluded: chain D residue 655 LYS Chi-restraints excluded: chain F residue 595 ILE Chi-restraints excluded: chain G residue 38 VAL Chi-restraints excluded: chain G residue 54 CYS Chi-restraints excluded: chain G residue 188 ASN Chi-restraints excluded: chain G residue 196 CYS Chi-restraints excluded: chain G residue 198 THR Chi-restraints excluded: chain G residue 202 THR Chi-restraints excluded: chain G residue 205 CYS Chi-restraints excluded: chain G residue 218 CYS Chi-restraints excluded: chain G residue 247 CYS Chi-restraints excluded: chain G residue 420 ILE Chi-restraints excluded: chain G residue 501 CYS Chi-restraints excluded: chain H residue 2 ILE Chi-restraints excluded: chain H residue 11 VAL Chi-restraints excluded: chain H residue 35 VAL Chi-restraints excluded: chain H residue 71 VAL Chi-restraints excluded: chain H residue 77 ILE Chi-restraints excluded: chain H residue 87 THR Chi-restraints excluded: chain H residue 100 VAL Chi-restraints excluded: chain H residue 111 VAL Chi-restraints excluded: chain J residue 54 CYS Chi-restraints excluded: chain J residue 132 THR Chi-restraints excluded: chain J residue 202 THR Chi-restraints excluded: chain J residue 261 LEU Chi-restraints excluded: chain J residue 346 VAL Chi-restraints excluded: chain J residue 492 GLU Chi-restraints excluded: chain L residue 14 SER Chi-restraints excluded: chain L residue 33 VAL Chi-restraints excluded: chain L residue 46 LEU Chi-restraints excluded: chain L residue 54 LEU Chi-restraints excluded: chain M residue 69 ILE Chi-restraints excluded: chain M residue 80 LEU Chi-restraints excluded: chain M residue 107 THR Chi-restraints excluded: chain M residue 111 VAL Chi-restraints excluded: chain O residue 27 SER Chi-restraints excluded: chain O residue 33 VAL Chi-restraints excluded: chain O residue 74 THR Chi-restraints excluded: chain P residue 54 CYS Chi-restraints excluded: chain P residue 116 LEU Chi-restraints excluded: chain P residue 123 THR Chi-restraints excluded: chain P residue 166 ARG Chi-restraints excluded: chain P residue 195 ASN Chi-restraints excluded: chain P residue 202 THR Chi-restraints excluded: chain P residue 205 CYS Chi-restraints excluded: chain P residue 242 VAL Chi-restraints excluded: chain P residue 247 CYS Chi-restraints excluded: chain P residue 308 ARG Chi-restraints excluded: chain P residue 467 THR Chi-restraints excluded: chain R residue 24 VAL Chi-restraints excluded: chain R residue 29 ILE Chi-restraints excluded: chain R residue 87 THR Chi-restraints excluded: chain W residue 5 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 256 random chunks: chunk 31 optimal weight: 1.9990 chunk 153 optimal weight: 4.9990 chunk 103 optimal weight: 3.9990 chunk 157 optimal weight: 4.9990 chunk 192 optimal weight: 0.9990 chunk 248 optimal weight: 5.9990 chunk 3 optimal weight: 0.9990 chunk 210 optimal weight: 0.9990 chunk 219 optimal weight: 5.9990 chunk 106 optimal weight: 7.9990 chunk 62 optimal weight: 0.9980 overall best weight: 1.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 77 ASN ** C 540 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 540 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 653 GLN P 293 GLN W 70 ASN W 92 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3057 r_free = 0.3057 target = 0.095432 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.2714 r_free = 0.2714 target = 0.074895 restraints weight = 38935.209| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.2740 r_free = 0.2740 target = 0.076533 restraints weight = 29626.491| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.2746 r_free = 0.2746 target = 0.076894 restraints weight = 23963.006| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.2749 r_free = 0.2749 target = 0.077041 restraints weight = 21093.553| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.2761 r_free = 0.2761 target = 0.077798 restraints weight = 20628.865| |-----------------------------------------------------------------------------| r_work (final): 0.2717 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8814 moved from start: 0.4220 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.148 22759 Z= 0.264 Angle : 0.924 59.200 31146 Z= 0.480 Chirality : 0.050 0.640 3835 Planarity : 0.005 0.059 3714 Dihedral : 9.142 72.868 5418 Min Nonbonded Distance : 2.183 Molprobity Statistics. All-atom Clashscore : 4.24 Ramachandran Plot: Outliers : 0.04 % Allowed : 7.56 % Favored : 92.40 % Rotamer: Outliers : 3.18 % Allowed : 18.17 % Favored : 78.65 % Cbeta Deviations : 0.04 % Peptide Plane: Cis-proline : 5.77 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.08 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.69 (0.16), residues: 2580 helix: -0.67 (0.29), residues: 345 sheet: -0.31 (0.18), residues: 867 loop : -1.81 (0.16), residues: 1368 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG F 617 TYR 0.020 0.002 TYR L 91 PHE 0.023 0.002 PHE R 78 TRP 0.015 0.001 TRP R 47 HIS 0.005 0.001 HIS P 105 Details of bonding type rmsd covalent geometry : bond 0.00627 (22589) covalent geometry : angle 0.88620 (30682) SS BOND : bond 0.00600 ( 40) SS BOND : angle 2.91339 ( 80) hydrogen bonds : bond 0.05419 ( 644) hydrogen bonds : angle 5.22397 ( 1740) Misc. bond : bond 0.00088 ( 2) link_ALPHA1-2 : bond 0.00294 ( 11) link_ALPHA1-2 : angle 1.92078 ( 33) link_ALPHA1-3 : bond 0.01253 ( 10) link_ALPHA1-3 : angle 1.93253 ( 30) link_ALPHA1-6 : bond 0.00459 ( 9) link_ALPHA1-6 : angle 1.75434 ( 27) link_BETA1-4 : bond 0.00557 ( 43) link_BETA1-4 : angle 2.21784 ( 129) link_NAG-ASN : bond 0.00402 ( 55) link_NAG-ASN : angle 2.30633 ( 165) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2976.52 seconds wall clock time: 52 minutes 28.91 seconds (3148.91 seconds total)